Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g01334.P2
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4340
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Found at i:3507 original size:282 final size:282
Alignment explanation
Indices: 3003--4340 Score: 1772
Period size: 282 Copynumber: 4.8 Consensus size: 282
2993 CATTGTTTAC
* * * * ** * * * *
3003 ACCTGAAGAATGCGGCAGCTTAGCTGGATCAGATTCCCGG-CCTTGTTGGACAGCATTATGTA-A
1 ACCTGAAGAATGTGGCAGCTCAGCTGGATTAGATT-TCGGAAGTTGTCGAACAGCTTTATCTATA
* * * *** *
3066 TTCCTTCAGAGATCTTGCCTCCACAACAGGTAATTTTGATTTGTTACCTGTGTCATCCTGTG--G
65 -TCCTCCAGAGATCTTGCCTCGACAACAGGTAATTTTGATTTGTTATCTCCATGAT-CTG-GCAG
* * * * * *
3129 TTCCACAATCATACTTGGAACAATTACTTCCTCAACATCAGCTCCTTCATGCAGTTGCTTAAAAG
127 TTTCTCAATCATACTCGGAACAATTACTTCCTCAACGTCAACTCCTTCATGAAGTTGCTTAAAAG
*
3194 CCAAATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTAATCTCAGTCTTC
192 CCAAATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTAGTCTCAGTCTTC
* *
3259 ATATCTTTTGATGGTTCATTCCTTGA
257 GTATCTTTTGATGATTCATTCCTTGA
* * * *
3285 ACCTGAAGAATGTGGCAGCTCAGCTGGATTAGATTTCGGAAGTTGTTGAATAGCTTTGTCTATGT
1 ACCTGAAGAATGTGGCAGCTCAGCTGGATTAGATTTCGGAAGTTGTCGAACAGCTTTATCTATAT
*
3350 CCTCCAGAGATCTTGCCTCGACAACAGGTAATTTTGATTTGTTATCTCCATGGTCTGGCAGTTTC
66 CCTCCAGAGATCTTGCCTCGACAACAGGTAATTTTGATTTGTTATCTCCATGATCTGGCAGTTTC
*
3415 TCAATCATACTCGGAACAATTACTTCCTCAATGTCAACTCCTTCATGAAGTTGCTTAAAAGCCAA
131 TCAATCATACTCGGAACAATTACTTCCTCAACGTCAACTCCTTCATGAAGTTGCTTAAAAGCCAA
* * * ** *
3480 ATCAATATCTTCGGCTGGTCTTGCTTCAAAAACTGGCAGCACCACATTAGTCTTGGTCTTCGCAT
196 ATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTAGTCTCAGTCTTCGTAT
*
3545 CTTTTGATGATTCAATCCTTGA
261 CTTTTGATGATTCATTCCTTGA
* ** * * * *
3567 GCCTGAAGAA--T---A--T--GCTGGATTAGATTTCACAAGTTGTTGAATAGCTTTGTCTAAAT
1 ACCTGAAGAATGTGGCAGCTCAGCTGGATTAGATTTCGGAAGTTGTCGAACAGCTTTATCTATAT
* *
3623 CCTCCAGAGATCTTGCCTCAACAACAGGTAATTTTGATTTGTTATCTCCAAGATCTGGCAGTTTC
66 CCTCCAGAGATCTTGCCTCGACAACAGGTAATTTTGATTTGTTATCTCCATGATCTGGCAGTTTC
* * **
3688 TCAATCATACTCGGAACAATTACTTCCTCGACATTGACTCCTTCATGAAGTTGCTTAAAAGCCAA
131 TCAATCATACTCGGAACAATTACTTCCTCAACGTCAACTCCTTCATGAAGTTGCTTAAAAGCCAA
* * * * * *
3753 ATCAATATCTTCTGCTGACCTTGTTTCAAGAACTGGAAGCACCACATTAGTCTCAGTATCCTTAT
196 ATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTAGTCTCAGTCTTCGTAT
* *
3818 CTGTTAATGATTCATTCCTT-A
261 CTTTTGATGATTCATTCCTTGA
* *
3839 AGCCTGAAGAATGTGGCGGCTCAGCTGGATTAGA-TTCTGGAAGTTGTCGAACAGCTTTATGTAT
1 A-CCTGAAGAATGTGGCAGCTCAGCTGGATTAGATTTC-GGAAGTTGTCGAACAGCTTTATCTAT
*
3903 ATCCTCCAGAGATCTTGCCTCGACAATAGGTAATTTTGATTTGTTATCTCCATGATCTGGCAGTT
64 ATCCTCCAGAGATCTTGCCTCGACAACAGGTAATTTTGATTTGTTATCTCCATGATCTGGCAGTT
* *
3968 TCTCGATCATACTTGGAACAATTACTTCCTCAACGTCAACTCCTTCATGAAGTTGCTTAAAAGCC
129 TCTCAATCATACTCGGAACAATTACTTCCTCAACGTCAACTCCTTCATGAAGTTGCTTAAAAGCC
* * *
4033 AAATCAATATCTTCAGCTGATCTTGGTTCAAGAA-TAGGCAGCACCACATTAGTCTCAGTTTTCG
194 AAATCAATATCTTCTGCTGATCTTGCTTCAAGAACT-GGCAGCACCACATTAGTCTCAGTCTTCG
4097 TATCTTTTGATGATTCATTCCTTGA
258 TATCTTTTGATGATTCATTCCTTGA
* * * *
4122 GCCTGAAGAATGTGGCGGCTCAGCTGGATTAGATTCCGGAAGTTGTCGAACAGCTTTATGTATAT
1 ACCTGAAGAATGTGGCAGCTCAGCTGGATTAGATTTCGGAAGTTGTCGAACAGCTTTATCTATAT
* * *
4187 CCTCCAGAGACCTTGCCTCGAAAACAGGTAATTTTGATTTGTTACCTCCATGATCTGGCAGTTTC
66 CCTCCAGAGATCTTGCCTCGACAACAGGTAATTTTGATTTGTTATCTCCATGATCTGGCAGTTTC
** * * *
4252 TTGATCATACTCGGAACAGTTACTTCCTCAACGTCGACTCCTTCATGAAGTTGCTTAAAAGTCAA
131 TCAATCATACTCGGAACAATTACTTCCTCAACGTCAACTCCTTCATGAAGTTGCTTAAAAGCCAA
*
4317 ATAAATATCTTCTGCTGATCTTGC
196 ATCAATATCTTCTGCTGATCTTGC
Statistics
Matches: 932, Mismatches: 106, Indels: 36
0.87 0.10 0.03
Matches are distributed among these distances:
272 1 0.00
273 240 0.26
275 2 0.00
277 1 0.00
280 3 0.00
281 10 0.01
282 672 0.72
283 3 0.00
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (282 bp):
ACCTGAAGAATGTGGCAGCTCAGCTGGATTAGATTTCGGAAGTTGTCGAACAGCTTTATCTATAT
CCTCCAGAGATCTTGCCTCGACAACAGGTAATTTTGATTTGTTATCTCCATGATCTGGCAGTTTC
TCAATCATACTCGGAACAATTACTTCCTCAACGTCAACTCCTTCATGAAGTTGCTTAAAAGCCAA
ATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACATTAGTCTCAGTCTTCGTAT
CTTTTGATGATTCATTCCTTGA
Found at i:4075 original size:555 final size:558
Alignment explanation
Indices: 3052--4340 Score: 1815
Period size: 555 Copynumber: 2.3 Consensus size: 558
3042 GCCTTGTTGG
* * * * * **
3052 ACAGCATTATGTAATTCCTTCAGAGATCTTGCCTCCACAACAGGTAATTTTGATTTGTTACCTGT
1 ACAGCTTTATCTAAATCCTCCAGAGATCTTGCCTCAACAACAGGTAATTTTGATTTGTTACCTCC
* * * * * *
3117 GTCATCCTGTG--GTTCCACAATCATACTTGGAACAATTACTTCCTCAACA-TCAGCTCCTTCAT
66 ATGAT-CTG-GCAGTTTCTCAATCATACTCGGAACAATTACTTCCTCAACATTGA-CTCCTTCAT
* *
3179 GCAGTTGCTTAAAAGCCAAATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGCAGCACCACA
128 GAAGTTGCTTAAAAGCCAAATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGAAGCACCACA
* * * * *
3244 TTAATCTCAGTCTTCATATCTTTTGATGGTTCATTCCTTGAACCTGAAGAATGTGGCAGCTCAGC
193 TTAATCTCAGTATCCATATCTGTTAATGATTCATTCCTTGAACCTGAAGAATGTGGCAGCTCAGC
* * * *
3309 TGGATTAGATTTCGGAAGTTGTTGAATAGCTTTGTCTATGTCCTCCAGAGATCTTGCCTCGACAA
258 TGGATTAGATTTCGGAAGTTGTCGAACAGCTTTATCTATATCCTCCAGAGATCTTGCCTCGACAA
*
3374 CAGGTAATTTTGATTTGTTATCTCCATGGTCTGGCAGTTTCTCAATCATACTCGGAACAATTACT
323 CAGGTAATTTTGATTTGTTATCTCCATGATCTGGCAGTTTCTCAATCATACTCGGAACAATTACT
* * *
3439 TCCTCAATGTCAACTCCTTCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCGGCTGGTCTTGC
388 TCCTCAACGTCAACTCCTTCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCAGCTGATCTTGC
**
3504 TTCAAAAACTGGCAGCACCACATTAGTCTTGGTCTTCGCATCTTTTGATGATTCAATCCTTGAGC
453 TTCAAAAACTGGCAGCACCACATTAGTCTCAGTCTTCGCATCTTTTGATGATTCAATCCTTGAGC
* *
3569 CTGAAGAA-T-AT-GCTGGATTAGATTTCACAAGTTGTTGA
518 CTGAAGAAGTGATAGCTGGATTAGATTCCACAAGTTGTCGA
* * *
3607 ATAGCTTTGTCTAAATCCTCCAGAGATCTTGCCTCAACAACAGGTAATTTTGATTTGTTATCTCC
1 ACAGCTTTATCTAAATCCTCCAGAGATCTTGCCTCAACAACAGGTAATTTTGATTTGTTACCTCC
* *
3672 AAGATCTGGCAGTTTCTCAATCATACTCGGAACAATTACTTCCTCGACATTGACTCCTTCATGAA
66 ATGATCTGGCAGTTTCTCAATCATACTCGGAACAATTACTTCCTCAACATTGACTCCTTCATGAA
* *
3737 GTTGCTTAAAAGCCAAATCAATATCTTCTGCTGACCTTGTTTCAAGAACTGGAAGCACCACATTA
131 GTTGCTTAAAAGCCAAATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGAAGCACCACATTA
* * *
3802 GTCTCAGTATCCTTATCTGTTAATGATTCATTCCTT-AAGCCTGAAGAATGTGGCGGCTCAGCTG
196 ATCTCAGTATCCATATCTGTTAATGATTCATTCCTTGAA-CCTGAAGAATGTGGCAGCTCAGCTG
* *
3866 GATTAGA-TTCTGGAAGTTGTCGAACAGCTTTATGTATATCCTCCAGAGATCTTGCCTCGACAAT
260 GATTAGATTTC-GGAAGTTGTCGAACAGCTTTATCTATATCCTCCAGAGATCTTGCCTCGACAAC
* *
3930 AGGTAATTTTGATTTGTTATCTCCATGATCTGGCAGTTTCTCGATCATACTTGGAACAATTACTT
324 AGGTAATTTTGATTTGTTATCTCCATGATCTGGCAGTTTCTCAATCATACTCGGAACAATTACTT
*
3995 CCTCAACGTCAACTCCTTCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCAGCTGATCTTGGT
389 CCTCAACGTCAACTCCTTCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCAGCTGATCTTGCT
* * * *
4060 TCAAGAA-TAGGCAGCACCACATTAGTCTCAGTTTTCGTATCTTTTGATGATTCATTCCTTGAGC
454 TCAAAAACT-GGCAGCACCACATTAGTCTCAGTCTTCGCATCTTTTGATGATTCAATCCTTGAGC
* **
4124 CTGAAGAATGTGGCGGCTCAGCTGGATTAGATTCCGGAAGTTGTCGA
518 CTGAAGAA-GT----GAT-AGCTGGATTAGATTCCACAAGTTGTCGA
* * *
4171 ACAGCTTTATGTATATCCTCCAGAGACCTTGCCTCGAA-AACAGGTAATTTTGATTTGTTACCTC
1 ACAGCTTTATCTAAATCCTCCAGAGATCTTGCCTC-AACAACAGGTAATTTTGATTTGTTACCTC
** * * *
4235 CATGATCTGGCAGTTTCTTGATCATACTCGGAACAGTTACTTCCTCAACGTCGACTCCTTCATGA
65 CATGATCTGGCAGTTTCTCAATCATACTCGGAACAATTACTTCCTCAACATTGACTCCTTCATGA
* *
4300 AGTTGCTTAAAAGTCAAATAAATATCTTCTGCTGATCTTGC
130 AGTTGCTTAAAAGCCAAATCAATATCTTCTGCTGATCTTGC
Statistics
Matches: 647, Mismatches: 71, Indels: 23
0.87 0.10 0.03
Matches are distributed among these distances:
553 1 0.00
554 9 0.01
555 458 0.71
556 2 0.00
557 1 0.00
562 1 0.00
564 173 0.27
565 2 0.00
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.34
Consensus pattern (558 bp):
ACAGCTTTATCTAAATCCTCCAGAGATCTTGCCTCAACAACAGGTAATTTTGATTTGTTACCTCC
ATGATCTGGCAGTTTCTCAATCATACTCGGAACAATTACTTCCTCAACATTGACTCCTTCATGAA
GTTGCTTAAAAGCCAAATCAATATCTTCTGCTGATCTTGCTTCAAGAACTGGAAGCACCACATTA
ATCTCAGTATCCATATCTGTTAATGATTCATTCCTTGAACCTGAAGAATGTGGCAGCTCAGCTGG
ATTAGATTTCGGAAGTTGTCGAACAGCTTTATCTATATCCTCCAGAGATCTTGCCTCGACAACAG
GTAATTTTGATTTGTTATCTCCATGATCTGGCAGTTTCTCAATCATACTCGGAACAATTACTTCC
TCAACGTCAACTCCTTCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCAGCTGATCTTGCTTC
AAAAACTGGCAGCACCACATTAGTCTCAGTCTTCGCATCTTTTGATGATTCAATCCTTGAGCCTG
AAGAAGTGATAGCTGGATTAGATTCCACAAGTTGTCGA
Done.