rcm-1

Ncra_rcm-1      MANHHPSPTMQMQMHHGPPGPPGPPPASIPSWNQQR-----QAFMSLTENVWIGIGSVSELMGNHNEALEAYERALAANPNSVTAMNAASLVLRTREDFPKASEYLQRILKIEPANGEAWGSLGHCFLMM  125    TPR_15  TPR_8  TPR_9 
Asub_rcm-1      MMASQTSPTASMHPHHVVQQGRGQPNGHVALQPPHQAKPASQFLQQANEGIWLQLGSVSEMMGEYDSATQAYERALSFNHHSVQAMLAISCILRSKDQFPAAVEYLKQILRIEVANGEVWSALGHCYLMM  130    TPR_19  TPR_8  TPR_9 
Anam_rcm-1      -MASQTSPTAAMHPHHVVQQGRGQPNGHVALQPPHQPKPASHFLQQANEGIWLQLGSVSEMMGEYDSATQAYERALSFNNHSVQAMLAISCILRSKDQFPAAVEYLKQILRIEVANGEVWSALGHCYLMM  129    TPR_15  TPR_19  TPR_9 
Apul_rcm-1      MMASQTSPTAAMHPHHVVQQGRGQPNGLVALQPPQQAKPASHFLQQANEGIWLQLGSVSELMGELDSATQAYERALSFNHHSVQAMLAISCILRSKDQFPAAVEYLKQILRIENANGEVWSSLGHCYLMM  130    TPR_15  TPR_19  TPR_9 
Amel_rcm-1      -MASQTSPTTAMHPHHVVQQGRGQPNGHVALQPPHPAKPASHYLQQANEGIWLQLGTVSEMMGEYDSATQAYERALSFNNHSVQAMLAISCILRSKDQFPAAVEYLKQILRIEVANGEVWSALGHCYLMM  129    TPR_15  TPR_19  TPR_9 
                     :.***  *: **      * * . :.    :      : : . .*.:*: :*:** :**: :.* :******: * :** ** * * :**::::** * ***::**:** ****. .:****:**

Ncra_rcm-1      EDLQQAYAAYQAALVNLPNPK---EPRLWYGIGILYDRYGSLDHAEEAFSQVMAMDPNFDKAHEIYFRLGIIYKQQHKYQQSLDCFRYIVNSPPTPLTEEDIWFQIGHVHEQQKDYDGAKQAYERVLQRD  252    TPR_9 
Asub_rcm-1      DDLQQAYSAYQQALYHLPDPK---EPKLWYGIGILYDRYGSLEHAEEAFSQVMRMDPRFEKANEIYFRLGIIYKQQQKFQQSLECFKYIVTDPPRPLSEEDIWFQIGHVYEQQKEYDSAKSAYMRVLDRD  257    TPR_9 
Anam_rcm-1      DDLQQAYSAYQQALYHLPDPK---EPKLWYGIGILYDRYGSLEHAEEAFSQVMRMDPRFEKANEIYFRLGIIYKQQQKFQQSLECFKYIVTDPPRPLSEEDIWFQIGHVYEQQKEYDSAKSAYMRVLDRD  256    TPR_9 
Apul_rcm-1      DDLQQAYSAYQQALYHLPDPKTRQEPKLWYGIGILYDRYGSLEHAEEAFSQVMRMDPRFEKANEIYFRLGIIYKQQQKFQQSLECFKYIVNDPPRPLSEEDIWFQIGHVYEQQKEYDSAKSAYMRVLDRD  260    TPR_9 
Amel_rcm-1      DDLQQAYSAYQQALYHLPDPK---EPKLWYGIGILYDRYGSLEHAEEAFSQVMRMDPRFEKANEIYFRLGIIYKQQQKFQQSLECFKYIVTDPPRPLSEEDIWFQIGHVYEQQKEYDSAKSAYMRVLDRD  256    TPR_9 
                *:******:*** ** :**:**   **:***************:****** *** ***.*:**:*************:*:****:**:***..** **:*********** ****:**.**.** ***:*

Ncra_rcm-1      PKHAKVLQQLGWLHHQQSNSVASQEKAIEYLNQSVAADQTDAQSWYLLGRCYMQLQKYPKAYEAYQQAVYRDGRNPTFWCSIGVLYYQINQYRDALDAYSRAIRLNPFISEVWYDLGTLYESCNNQISDA  382    TPR_9 
Asub_rcm-1      PNHAKVLQQLGWLHHQQSTSFSSQEQAIEYLEKSVNSDQTDAQSWYLLGRCYMSQQKYPKAYEAYQQAVYRDGRNPTFWCSIGVLYYQINQYRDALDAYSRAIRLNPNISEVWYDLGTLYESCNNQTNDA  387    TPR_9 
Anam_rcm-1      PNHAKVLQQLGWLHHQQSTSFSSQEQAIEYLEKSVNSDQTDAQSWYLLGRCYMSQQKYPKAYEAYQQAVYRDGRNPTFWCSIGVLYYQINQYRDALDAYSRAIRLNPNISEVWYDLGTLYESCNNQTNDA  386    TPR_9 
Apul_rcm-1      PNHAKVLQQLGWLHHQQSTSFNSQEQAIEYLEKSVNSDQTDAQSWYLLGRCYMSQQKYPKAYEAYQQAVYRDGRNPTFWCSIGVLYYQINQYRDALDAYSRAIRLNPNISEVWYDLGTLYESCNNQTNDA  390    TPR_9 
Amel_rcm-1      PNHAKVLQQLGWLHHQQSTSFSSQEQAIEYLEKSVNSDQTDAQSWYLLGRCYMSQQKYPKAYEAYQQAVYRDGRNPTFWCSIGVLYYQINQYRDALDAYSRAIRLNPNISEVWYDLGTLYESCNNQTNDA  386    TPR_9 
                **:****************.*. ***:*****::** :** *************. ******************************************** ******* ****************** .*

Ncra_rcm-1      LDAYQRAAELDPNNPHIKTRLQLLRSGQANGGAPPGSVPMPTDIHPQTYN-ASGAVGPPGPQWAGSGSGQPPHQPPQPMHNGGPGPGQGANSWGGRISDINPPPQPP---NPYASGQDREPFRGPAPPLP  508    TPR_9 
Asub_rcm-1      LDAYSRAAELDPTNVHIKARLALLKGQPTNGLPNQAGAPLPQDVPPQAYQPGALGAGPPAPQWGAPPPGQAQAAQQPP---GADWSR--TNRLADLQNPQNPGAQPQ-MLNPYDSRDRLAQHVPPRQPTP  511    TPR_9  TPR_20  TPR_17 
Anam_rcm-1      LDAYSRAAELDPTNVHIKARLALLKGQPTNGLPNQAGAPLPQDVPPQAYQPGALGAGPPAPQWGAPLPGQAQAAQQPPP--GANWSR--DNRLADLQNPQNPGAQPQQMLNPYDSRDRLAQHVPPRQPTP  512    TPR_9  TPR_20  TPR_17 
Apul_rcm-1      LDAYSRAAELDPTNVHIKARLALLKGQPTNGLPNQAGAPLPQDVPPQAYQPGALGAGPPAPQWGAPPPGQAQGAQQPPLPAGGDWSR--ANRLADLQNPQNPGAQPQ-MLNPYDSRDRLAQHVPPRQPTP  517    TPR_9  TPR_20  TPR_17 
Amel_rcm-1      LDAYSRAAELDPTNVHIKARLALLKGQPTNGLPNQAGAPLPQDVPPQAYQPGALGAGPPAPQWGAPPPGQAQAAQQPPP--GADWSR--NNRLADLQNPQNPGSQPQ-MLNPYDSRDRLAQHVPPRQPTP  511    TPR_9  TPR_20  TPR_17 
                *****.*******.* ***:** **:.  : * .  ...*:* *: **:*: .: ..***.***... .**.      *   *.  .    *  ..  .  ** .**    *** * :    .  *  * 

Ncra_rcm-1      RQPSPRQEQQMRPYQEARAPEPLRRGPTPPQAHYAPPPPPPPQQPHQPHPQQQLQQGPQPTREGGSGTRVRNPNYANPQNVVPSNSGPGPNGPPPPNAMMHFNNSPRTDGRPPHMHENRMPSPKSAYPQH  638   
Asub_rcm-1      PKQEPRQYQDQP--QRPPPPAHRGLSPSPKVLYNAPGPGAYPPAPQAQTPSQLPQPLPQQQGPAPP-NRIANPNYGPQSSSVPPPAASMGAPPPAPGQAPGYPNRMASPPEIRPIIESQNTSPNGKFGRQ  638   
Anam_rcm-1      PKQEPRQYQDQP--QRPPPPAHRGLSPSPKVLYNAPGPGAYPSAPQAQTPSQLPQPLPQQQGPAPP-NRIANPNYGPQSSSVPPPAASMGAPPPAQGQAPGYPNRMASPPEIRPIIESQNTSPNGKFGRQ  639   
Apul_rcm-1      PKQEPRQFQDQP--QRPPPPAHRGLSPSPKVLYNAPGPGAYPPAPQAQTPSQLPQPLPQQQGPAPP-NRIANPNYGPQSSSVPPPAVSMGAPPPAQGQASGYPNRMGSPPEIRPIMENQNTSPNGKFGRQ  644   
Amel_rcm-1      PKQEPRQYQEQPQPQRPPPPAHRGLSPSPKVLYNAPGPGAYPPAPQAQTPSQLPQPLPQQ-GSAPP-NRIANPNYGPQSSSVPPPAASMGAPPPAQGQAPGYPNRMASPPEIRPIIENQNTSPNGKFGRQ  639   
                * : .*** *:    *.. .      .*:*   : ** * . *  *:   *.*  *  **    . . .*: ****.  .  **. : .    **. .    : *   :  .   : *.: .**:. : :

Ncra_rcm-1      QPPYPPHGEQGGPGGPEPGPPHPPQSGMAGEPPHQREHDPRPPSVGPKRMREWEDDRE----VKKPATEETRVRMDDHRHRRPSMTPPRMEPPYARRNSSEARRFDERRMEDSRRVEEQRRAEEQRRMED  764    TPR_7 
Asub_rcm-1      --PFEHHPTSGTP--SIAGGAPPPNAALQAAESAAREREDRPSTAPPKRHREWEDEASNMSSQKKPANEESRSRLEDPSSRR-ASPPDRMD-----------------RIPNS----------PYRSPSE  736    TPR_14  TPR_16 
Anam_rcm-1      --PFEHHPTSGTP--SIAGGAPPPSAALQAAEAAAREREDRPSTAPPKRHREWEDDASSMSSQKKPANEESRSRLDDPSSRR-ASPPDRMD-----------------RIPKS----------PYRSPSE  737    TPR_16  TPR_14 
Apul_rcm-1      --PFEHHPTSGTP--SIAGGAPPPSAAMHAAEAAAREREDRPSTAPPKRHREWEDDASSMSSQKKPANEESRSRLEDPSSRR-ASPPDRMD-----------------RIPNS----------PYRSPSE  742   
Amel_rcm-1      --PFEHHPTSGTP--SIAGGAPPPNAALQAAEAAAREREDRPSTAPPKRHREWEDDASSMSSQKKPANEESRSRLEDPSSRR-ASPPDRMD-----------------RLPKS----------PYRSPSE  737    TPR_16 
                :  *:  *   * *  . .* . **.:.: .  .  **:: **.:. *** *****: .     ****.* :* *::*   ** : .* **:                 *: .*            *  .

Ncra_rcm-1      MRRAEEQRHQNEGYHPSEAAHHPQSHSAPAHLPPMQQGSAPMQNLIHEQGHGPQQPVPGPQQQGPGPAHQPAPEDRRMDHPPAQHPPIVN--------EPERAARKMDVDEDYDDSGEEDKKGGIIPGPS  886    TPR_7 
Asub_rcm-1      TRRADDQRRATENYHPSEAAHHPPALGPP-QVKPQP--SPRIG--ATEERREQHTPAPPAQQLAPPPQPQPQPPTQAPTPVQSQAAPQP-------QPHLEPAARKMDMDEDYDDSGDEEKRP--VKPQS  852   
Anam_rcm-1      VRRADDQRRATENYHPSEAAHHPPALGPP-QVNPQP--SPRIP--TTEERREQPTPAPPTQQLPPP-QPQPQPPTQAPTPVQSQAPPQP----QPQQPHLEPAARKMDMDEDYDDSGDEEKRP--IKAQS  855   
Apul_rcm-1      VRRAEDQRRATDNYHPSEAAHHPPALGPP-QVKPQPQPSPRIG--ANEERREQHTPAPPAQQLPPPPQPQPQPPTQAPTPVQSQPPPQP----QPQQPHLEPAARKMEMDEDYDDSGDEDKRP--VKPQS  863   
Amel_rcm-1      VRRADDQRRATENYHPSEAAHHSPALGPPSQVNPQP--SPRIG--ATEERKEQPTPVPSAQQLPPPPQPQTQPPTQAPTPVQSQAPPQPPPQPQPQQPHLEPAARKMDMDEDYDDSGDEEKRP--VKPQS  861   
                  ***::**: .:.*********. : ..* :: *    *. :     *: :    *.*  **  *    *. *  :      :* .*           . * *****::********:* *:   :   

Ncra_rcm-1      SGSGPAANESKNGASTSGSFNGIMGQKSESN  917   
Asub_rcm-1      ERNSPKAS---NGTNHD--------------  866   
Anam_rcm-1      ARNSPKPS---NGAGHD--------------  869   
Apul_rcm-1      ERNSPKAS---NGVNHD--------------  877   
Amel_rcm-1      ERNSPKAS---NGAGHD--------------  875   
                *  ..* ..   **.. .             

Input files: MFA/Ncra.CLOCK.v02.Aure.rcm-1.aln (alignment), ALN//Ncra.CLOCK.v02.Aure.rcm-1.dom.rgns (regions: exons, domains, low-complexity, etc)

5 sequences, alignment length = 1040
sequence lengths:
  917  Ncra_rcm-1
  866  Asub_rcm-1
  869  Anam_rcm-1
  877  Apul_rcm-1
  875  Amel_rcm-1

#domain Ncra_rcm-1Asub_rcm-1Anam_rcm-1Apul_rcm-1Amel_rcm-1
1Apc31  55..137
2  159..257
3  271..353
4  374..406
1  60..142
2  164..252
3  278..358
4  379..416
1  59..141
2  163..251
3  277..357
4  378..415
1  60..142
2  167..255
3  281..361
4  378..420
1  59..141
2  163..251
3  277..357
4  378..415
2DUF22251  56..189
2  179..261
3  235..363
1  63..193
2  184..266
3  231..372
1  62..192
2  183..293
3  239..371
1  118..198
2  188..270
3  244..371
1  55..194
2  180..266
3  239..391
3Fis1_TPR_C1  55..85
2  90..114
3  154..185
4  221..261
5  295..320
6  325..363
0000
4TPR_11  44..76
2  85..110
3  111..144
4  147..180
5  184..209
6  221..254
7  255..271
8  275..292
9  293..326
10  327..359
11  361..395
1  50..81
2  90..112
3  116..149
4  152..185
5  190..215
6  226..259
7  260..273
8  280..297
9  298..331
10  332..365
11  366..400
1  49..80
2  89..111
3  115..148
4  151..184
5  189..214
6  225..258
7  259..272
8  279..296
9  297..330
10  331..364
11  365..399
1  50..81
2  90..114
3  116..149
4  155..188
5  193..217
6  229..262
7  263..276
8  283..300
9  301..334
10  335..368
11  369..403
1  49..80
2  89..111
3  115..148
4  151..184
5  189..214
6  225..258
7  259..272
8  279..296
9  297..330
10  331..364
11  365..399
5TPR_111  44..108
2  79..143
3  145..215
4  220..290
5  274..327
6  290..358
7  325..393
8  360..405
1  44..112
2  90..149
3  112..183
4  150..220
5  224..295
6  276..329
7  330..398
1  43..111
2  89..146
3  111..182
4  147..219
5  223..294
6  275..328
7  329..397
1  46..112
2  90..147
3  153..223
4  227..298
5  277..335
6  297..366
7  333..401
1  43..111
2  90..146
3  111..182
4  149..219
5  223..294
6  275..328
7  329..397
6TPR_121  40..109
2  107..179
3  179..211
4  217..291
5  274..324
6  289..359
7  326..394
1  44..114
2  112..184
3  186..216
4  222..296
5  278..328
6  294..364
7  329..399
1  43..113
2  111..183
3  185..215
4  221..295
5  277..327
6  293..363
7  328..398
1  46..114
2  113..187
3  189..219
4  225..299
5  283..331
6  297..367
7  332..402
1  43..113
2  111..183
3  185..215
4  221..295
5  277..327
6  293..363
7  328..398
7TPR_141  43..85
2  77..120
3  111..152
4  147..193
5  184..214
6  221..264
7  271..302
8  293..334
9  327..370
10  361..406
1  48..89
2  80..125
3  116..151
4  152..198
5  189..222
6  226..269
7  280..307
8  297..341
9  335..375
10  366..410
11  657..675
1  47..88
2  79..124
3  115..150
4  151..197
5  188..221
6  225..268
7  279..306
8  296..340
9  334..374
10  365..409
11  658..679
1  48..89
2  80..125
3  116..152
4  155..199
5  192..224
6  229..272
7  280..310
8  301..344
9  338..378
10  369..413
1  47..88
2  79..124
3  115..150
4  151..197
5  188..221
6  225..268
7  279..306
8  296..340
9  334..374
10  365..409
11  658..679
8TPR_151  28..151
2  179..327
3  318..393
4  361..405
1  34..157
2  186..332
3  322..399
4  366..410
1  33..156
2  185..330
3  326..398
4  365..408
1  27..151
2  143..224
3  198..335
4  330..375
5  368..413
1  33..156
2  165..331
3  327..397
4  365..409
9TPR_161  53..96
2  81..147
3  124..181
4  151..217
5  225..275
6  272..328
7  331..396
1  39..81
2  92..152
3  156..222
4  230..297
5  278..333
6  336..401
7  658..675
1  38..81
2  91..151
3  155..221
4  229..296
5  277..332
6  335..400
7  658..678
1  39..82
2  92..152
3  162..224
4  233..300
5  281..336
6  339..404
1  38..81
2  91..151
3  155..221
4  229..296
5  277..332
6  335..400
7  658..679
10TPR_171  65..98
2  99..132
3  133..168
4  169..205
5  221..242
6  243..279
7  281..314
8  315..348
9  349..383
10  384..398
1  50..68
2  70..103
3  104..137
4  138..173
5  175..210
6  226..247
7  248..284
8  286..319
9  320..353
10  354..388
11  389..417
1  49..67
2  69..102
3  103..136
4  137..172
5  174..209
6  225..246
7  247..283
8  285..318
9  319..352
10  353..387
11  388..416
1  70..103
2  104..137
3  138..176
4  178..213
5  225..250
6  251..288
7  289..322
8  323..356
9  357..391
10  392..420
1  48..68
2  69..102
3  103..136
4  137..172
5  174..209
6  225..246
7  247..283
8  285..318
9  319..352
10  353..387
11  388..416
11TPR_191  55..117
2  87..151
3  121..190
4  159..217
5  232..272
6  275..330
7  337..405
1  34..89
2  92..155
3  164..225
4  236..273
5  280..335
6  342..410
1  35..88
2  59..121
3  91..155
4  125..188
5  163..225
6  235..272
7  279..334
8  341..409
1  34..89
2  92..154
3  167..229
4  203..269
5  239..277
6  281..338
7  345..413
1  38..88
2  57..109
3  91..157
4  126..191
5  163..224
6  235..272
7  279..334
8  341..409
12TPR_21  43..76
2  77..110
3  111..144
4  147..180
5  184..211
6  221..254
7  255..270
8  275..292
9  293..326
10  327..359
11  361..395
1  49..81
2  82..112
3  116..149
4  152..185
5  189..216
6  226..259
7  260..273
8  280..297
9  298..331
10  332..365
11  366..400
1  48..80
2  81..111
3  115..148
4  151..184
5  188..215
6  225..258
7  259..272
8  279..296
9  297..330
10  331..364
11  365..399
1  49..81
2  82..115
3  116..149
4  155..188
5  192..219
6  229..262
7  263..276
8  282..300
9  301..334
10  335..368
11  369..403
1  48..80
2  81..111
3  115..148
4  151..184
5  188..215
6  225..258
7  259..272
8  279..296
9  297..330
10  331..364
11  365..399
13TPR_201  56..141
2  165..213
3  222..257
4  272..326
5  313..357
6  379..406
1  62..146
2  224..263
3  278..331
4  318..367
5  380..414
1  62..145
2  223..262
3  277..330
4  317..366
5  379..413
1  63..146
2  226..266
3  281..334
4  321..370
5  383..417
1  61..145
2  223..262
3  277..330
4  317..366
5  379..413
14TPR_61  46..76
2  82..110
3  116..144
4  149..179
5  185..214
6  222..254
7  256..287
8  294..323
9  332..359
10  362..395
1  50..76
2  83..111
3  117..148
4  153..184
5  190..219
6  227..259
7  261..293
8  299..328
9  337..364
10  367..400
1  49..75
2  82..110
3  116..147
4  152..183
5  189..218
6  226..258
7  260..292
8  298..327
9  336..363
10  366..399
1  50..76
2  83..111
3  117..148
4  156..187
5  193..222
6  230..262
7  264..296
8  302..331
9  340..367
10  370..403
1  49..75
2  82..110
3  116..147
4  152..183
5  189..218
6  226..258
7  260..292
8  298..327
9  336..363
10  366..399
15TPR_71  45..78
2  80..113
3  113..147
4  186..214
5  223..256
6  257..294
7  295..328
8  330..362
9  363..398
10  755..773
1  50..78
2  84..118
3  118..153
4  191..223
5  228..261
6  262..299
7  300..333
8  335..367
9  368..401
1  49..78
2  83..117
3  117..152
4  190..222
5  227..260
6  261..298
7  299..332
8  334..366
9  367..400
1  50..79
2  84..118
3  118..153
4  194..224
5  231..264
6  265..302
7  303..336
8  338..370
9  371..404
1  49..78
2  83..117
3  117..152
4  190..222
5  227..260
6  261..298
7  299..332
8  334..366
9  367..400
16TPR_81  43..76
2  78..110
3  111..138
4  147..180
5  184..215
6  221..254
7  255..292
8  293..327
9  327..361
10  361..396
1  46..79
2  82..112
3  116..149
4  152..185
5  188..216
6  226..259
7  276..297
8  298..332
9  332..366
10  365..401
1  45..81
2  81..111
3  115..148
4  151..184
5  187..215
6  225..258
7  275..296
8  297..331
9  331..365
10  364..400
1  46..79
2  82..115
3  116..149
4  155..188
5  191..218
6  229..262
7  278..300
8  301..335
9  335..369
10  368..404
1  45..81
2  81..111
3  115..148
4  151..184
5  187..215
6  225..258
7  275..296
8  297..331
9  331..365
10  364..400
17TPR_91  49..87
2  83..146
3  136..190
4  181..228
5  227..273
6  271..329
7  325..363
8  333..406
1  48..89
2  59..111
3  88..154
4  139..195
5  195..270
6  232..304
7  279..335
8  304..368
9  340..411
1  44..86
2  87..153
3  138..194
4  160..232
5  194..269
6  231..302
7  270..333
8  303..367
9  337..410
1  43..89
2  88..157
3  153..195
4  168..235
5  198..273
6  235..309
7  280..337
8  307..371
9  341..414
1  42..86
2  87..153
3  142..192
4  160..232
5  194..269
6  231..303
7  270..333
8  303..367
9  337..410

ARC.colors file was not found, using default colors.

Alignment Regions Colorize, ARC v061