Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga01g02400.M1
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: 5268
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Found at i:3104 original size:131 final size:131
Alignment explanation
Indices: 2870--3128 Score: 464
Period size: 131 Copynumber: 2.0 Consensus size: 131
2860 AATTGAGAAC
2870 TGCAAGAAATTGGGAGTTCTTCCGATAATCGGAGGATGTTCATCTCTTGAAAAGCTTAGAATATC
1 TGCAAGAAATTGGGAGTTCTTCCGATAATCGGAGGATGTTCATCTCTTGAAAAGCTTAGAATATC
2935 CGGTTGCGAAAAATTAAGCAAGATCGGAGACGGGCTGTCAACCTCCACTTGTCTCAAAGAATTAG
66 CGGTTGCGAAAAATTAAGCAAGATCGGAGACGGGCTGTCAACCTCCACTTGTCTCAAAGAATTAG
3000 G
131 G
* * * *
3001 TGCAAGGAATTGGGAGTTCTTCCGATAATCGGAGGATGTTCGTCTCTTGAAAAGCTTAGGATTTC
1 TGCAAGAAATTGGGAGTTCTTCCGATAATCGGAGGATGTTCATCTCTTGAAAAGCTTAGAATATC
* *
3066 CGGTTGCGAAAAATTAAGCAAGATTGGATACGGGCTGTCAACCTCCACTTGTCTCAAAGAATT
66 CGGTTGCGAAAAATTAAGCAAGATCGGAGACGGGCTGTCAACCTCCACTTGTCTCAAAGAATT
3129 CGGTCTATCG
Statistics
Matches: 122, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
131 122 1.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (131 bp):
TGCAAGAAATTGGGAGTTCTTCCGATAATCGGAGGATGTTCATCTCTTGAAAAGCTTAGAATATC
CGGTTGCGAAAAATTAAGCAAGATCGGAGACGGGCTGTCAACCTCCACTTGTCTCAAAGAATTAG
G
Found at i:3325 original size:341 final size:341
Alignment explanation
Indices: 2702--3340 Score: 915
Period size: 341 Copynumber: 1.9 Consensus size: 341
2692 ACAATGCTCT
** * * * *
2702 TCTCTTGAAAAGCTTAGCATTTCATTTTGTGAAAAATTAAGTAAGATTGGAAACGGATTATCTAC
1 TCTCTTGAAAAGCTTAGCATTTCAGGTTGCGAAAAATTAAGCAAGATTGGAAACGGACTATCAAC
* * *
2767 CTCCACTTGTCTCAAAGAATTAGACCTACATGCTTGTCCTAATTTAAGTTCAATTCCAAATTTAG
66 CTCCACTTGTCTCAAAGAATTAGACCTACAGGATTGTCCTAATGTAAGTTCAATTCCAAATTTAG
* * *
2832 AAGGATTTTCCTCTCTTCAAAATTTGTCAATTGAGAACTGCAAGAAATTGGGAGTTCTTCCGATA
131 AAGGATTTTCCTCTCTTCAAAATCTGTCAATTGAGAACTGCAAAAAATTGGGAGTTCTTCCAATA
* *
2897 ATCGGAGGATGTTCATCTCTTGAAAAGCTTAGAATATCCGGTTGCGAAAAATTAAGCAAGATCGG
196 ACCGGAGGATGTTCATCTCTTCAAAAGCTTAGAATATCCGGTTGCGAAAAATTAAGCAAGATCGG
* *
2962 AGACGGGCTGTCAACCTCCACTTGTCTCA-AAGAATTAGGTGCAAGGAATTGGGAGTTCTTCCGA
261 AGACGGACTATCAACCTCCACTTGTCTCAGAA-AATTAGGTGCAAGGAATTGGGAGTTCTTCCGA
3026 TAATCGGAGGATGTTCG
325 TAATCGGAGGATGTTCG
* * * * *
3043 TCTCTTGAAAAGCTTAGGATTTCCGGTTGCGAAAAATTAAGCAAGATTGGATACGGGCTGTCAAC
1 TCTCTTGAAAAGCTTAGCATTTCAGGTTGCGAAAAATTAAGCAAGATTGGAAACGGACTATCAAC
* ** * *
3108 CTCCACTTGTCTCAAAGAATTCGGTCTATC-GGATTGTCCTAATGTAAGTTCCATTCCAAATTTG
66 CTCCACTTGTCTCAAAGAATTAGACCTA-CAGGATTGTCCTAATGTAAGTTCAATTCCAAATTTA
* * *
3172 GAAGGCTTTTCCTCTCTTCAATATCTGTCAATTGAGAGCTGCAAAAAATTGGGAGTTCTTCCAAT
130 GAAGGATTTTCCTCTCTTCAAAATCTGTCAATTGAGAACTGCAAAAAATTGGGAGTTCTTCCAAT
* * *
3237 AACCGGAGGATGTTCATCTCTTCAAAAGCTTA-AGATTTCTGGTTGCGAAAAATTAAGCAAGATT
195 AACCGGAGGATGTTCATCTCTTCAAAAGCTTAGA-ATATCCGGTTGCGAAAAATTAAGCAAGATC
* * *
3301 GGAGATGGATTATCTACCTCCACTTGTCTCAGAAAATTAG
259 GGAGACGGACTATCAACCTCCACTTGTCTCAGAAAATTAG
3341 ATCTAAAATA
Statistics
Matches: 260, Mismatches: 35, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
340 1 0.00
341 256 0.98
342 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Consensus pattern (341 bp):
TCTCTTGAAAAGCTTAGCATTTCAGGTTGCGAAAAATTAAGCAAGATTGGAAACGGACTATCAAC
CTCCACTTGTCTCAAAGAATTAGACCTACAGGATTGTCCTAATGTAAGTTCAATTCCAAATTTAG
AAGGATTTTCCTCTCTTCAAAATCTGTCAATTGAGAACTGCAAAAAATTGGGAGTTCTTCCAATA
ACCGGAGGATGTTCATCTCTTCAAAAGCTTAGAATATCCGGTTGCGAAAAATTAAGCAAGATCGG
AGACGGACTATCAACCTCCACTTGTCTCAGAAAATTAGGTGCAAGGAATTGGGAGTTCTTCCGAT
AATCGGAGGATGTTCG
Found at i:3370 original size:210 final size:210
Alignment explanation
Indices: 2998--3825 Score: 999
Period size: 210 Copynumber: 3.9 Consensus size: 210
2988 TCAAAGAATT
** * * * *
2998 AGGTGCAAGGAATTGGGAGTTCTTCCGATAATCGGAGGATGTTCGTCTCTTGAAAAGCTTAGGAT
1 AGGTGCAAAAAATTGGAAGTTCTTCCGATAACCGGAGGATGTTCATCTCTTGAAAAGCTTAGCAT
* * * *
3063 TTCCGGTTGCGAAAAATTAAGCAAGATTGGATACGGGCTGTCAACCTCCACTTGTCTCAAAGAAT
66 TTCTGGTTGCGAAAAATTAAGCAAGATTGGAGACGGACTATCAACCTCCACTTGTCTCAAAGAAT
* * **** * *
3128 TCGGTCTATCGGATTGTCCTAATGTAAGTTCCATTCCAAATTTGGAAGGCTTTTCCTCTCTTCAA
131 TAGATCTAAAATATTGTCCTAATTTAAGTTCCATTCCAAATTTGGAAGGATTTTCCTCTCTTCAA
*
3193 TATCTGTCAATTGAG
196 AATCTGTCAATTGAG
* * * *
3208 AGCTGCAAAAAATTGGGAGTTCTTCCAATAACCGGAGGATGTTCATCTCTTCAAAAGCTTAAG-A
1 AGGTGCAAAAAATTGGAAGTTCTTCCGATAACCGGAGGATGTTCATCTCTTGAAAAGCTT-AGCA
* * *
3272 TTTCTGGTTGCGAAAAATTAAGCAAGATTGGAGATGGATTATCTACCTCCACTTGTCTCAGAA-A
65 TTTCTGGTTGCGAAAAATTAAGCAAGATTGGAGACGGACTATCAACCTCCACTTGTCTCA-AAGA
* *
3336 ATTAGATCTAAAATATTGTCCTAATTTAAGTTCCATTCCGAATTTGGAAAGATTTTCCTCTCTTC
129 ATTAGATCTAAAATATTGTCCTAATTTAAGTTCCATTCCAAATTTGGAAGGATTTTCCTCTCTTC
3401 AAAATCTGTCAATTGAG
194 AAAATCTGTCAATTGAG
* * * * *
3418 AGGTGCAAGACATTGGAAGTTCTTCCGATAACGGGAGAATGTTCATCTCTTGAAGAGCTTAGCAT
1 AGGTGCAAAAAATTGGAAGTTCTTCCGATAACCGGAGGATGTTCATCTCTTGAAAAGCTTAGCAT
* * * * *
3483 TATC-GTTTGCGAAAAACTAAGCAAGATTGGAGACGGGCTGTCAACCTCCACTTGTCTCAAAAAA
66 T-TCTGGTTGCGAAAAATTAAGCAAGATTGGAGACGGACTATCAACCTCCACTTGTCTCAAAGAA
** * * * * *
3547 TTACGA-CT-ATGTAGTTGTCCTAACTTAATTTCAATTCCGGAA-TTGGAAGGATTTTCTTCTCT
130 TTA-GATCTAAAATA-TTGTCCTAATTTAAGTTCCATTCC-AAATTTGGAAGGATTTTCCTCTCT
3609 TCAAAATCTGTCAATT-AG
192 TCAAAATCTGTCAATTGAG
*** *
3627 ATGGTGCAGCGAATTGGAAGTTCTTCCGATAACCGGAGGATGTTCATCTCTTGAAAAACTTAGCA
1 A-GGTGCAAAAAATTGGAAGTTCTTCCGATAACCGGAGGATGTTCATCTCTTGAAAAGCTTAGCA
* * * * *
3692 TTT-TCGATTGC-AAAAAGTTAAGTAAGATTGGAGACGGATTATCTACCTCCACTTGTCTTAAAG
65 TTTCT-GGTTGCGAAAAA-TTAAGCAAGATTGGAGACGGACTATCAACCTCCACTTGTCTCAAAG
* * *
3755 AATTAGATCTAAAATGTTGTCCTAATTTAAGTTCGATTCCAAATTTGGAAGGATTTTCGTCTCTT
128 AATTAGATCTAAAATATTGTCCTAATTTAAGTTCCATTCCAAATTTGGAAGGATTTTCCTCTCTT
3820 CAAAAT
193 CAAAAT
3826 GTATCCGTTG
Statistics
Matches: 530, Mismatches: 73, Indels: 30
0.84 0.12 0.05
Matches are distributed among these distances:
209 20 0.04
210 497 0.94
211 13 0.02
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (210 bp):
AGGTGCAAAAAATTGGAAGTTCTTCCGATAACCGGAGGATGTTCATCTCTTGAAAAGCTTAGCAT
TTCTGGTTGCGAAAAATTAAGCAAGATTGGAGACGGACTATCAACCTCCACTTGTCTCAAAGAAT
TAGATCTAAAATATTGTCCTAATTTAAGTTCCATTCCAAATTTGGAAGGATTTTCCTCTCTTCAA
AATCTGTCAATTGAG
Found at i:3777 original size:420 final size:420
Alignment explanation
Indices: 2998--3825 Score: 1158
Period size: 420 Copynumber: 2.0 Consensus size: 420
2988 TCAAAGAATT
* * * *
2998 AGGTGCAAGGAATTGGGAGTTCTTCCGATAATCGGAGGATGTTCGTCTCTTGAAAAGCTTAGGAT
1 AGGTGCAAGGAATTGGAAGTTCTTCCGATAATCGGAGAATGTTCATCTCTTGAAAAGCTTAGCAT
* * *
3063 TTCCGGTTGCGAAAAATTAAGCAAGATTGGATACGGGCTGTCAACCTCCACTTGTCTCAAAGAAT
66 TTCCGGTTGCGAAAAACTAAGCAAGATTGGAGACGGGCTGTCAACCTCCACTTGTCTCAAAAAAT
* * *
3128 TCGGTCTATCGGATTGTCCTAATGTAAGTTCCATTCCAAATTTGGAAGGCTTTTCCTCTCTTCAA
131 TCGGACTATCGGATTGTCCTAATGTAAGTTCAATTCCAAATTTGGAAGGATTTTCCTCTCTTCAA
* *
3193 TATCTGTCAATTGAGAGCTGCAAAAAATTGGGAGTTCTTCCAATAACCGGAGGATGTTCATCTCT
196 AATCTGTCAATTGAGAGCTGCAAAAAATTGGAAGTTCTTCCAATAACCGGAGGATGTTCATCTCT
* * *
3258 TCAAAAGCTTAAGATTTCTGGTTGCGAAAAATTAAGCAAGATTGGAGATGGATTATCTACCTCCA
261 TCAAAAACTTAAGATTTCTGATTGCGAAAAATTAAGCAAGATTGGAGACGGATTATCTACCTCCA
*
3323 CTTGTCTCAGAAAATTAGATCTAAAATATTGTCCTAATTTAAGTTCCATTCCGAATTTGGAAAGA
326 CTTGTCTCAGAAAATTAGATCTAAAATATTGTCCTAATTTAAGTTCCATTCCAAATTTGGAAAGA
3388 TTTTCCTCTCTTCAAAATCTGTCAATTGAG
391 TTTTCCTCTCTTCAAAATCTGTCAATTGAG
*
3418 AGGTGCAA-GACATTGGAAGTTCTTCCGATAA-CGGGAGAATGTTCATCTCTTGAAGAGCTTAGC
1 AGGTGCAAGGA-ATTGGAAGTTCTTCCGATAATC-GGAGAATGTTCATCTCTTGAAAAGCTTAGC
*
3481 ATTAT-CGTTTGCGAAAAACTAAGCAAGATTGGAGACGGGCTGTCAACCTCCACTTGTCTCAAAA
64 ATT-TCCGGTTGCGAAAAACTAAGCAAGATTGGAGACGGGCTGTCAACCTCCACTTGTCTCAAAA
* * * *
3545 AATTAC-GACTAT-GTAGTTGTCCTAACT-TAATTTCAATTCCGGAA-TTGGAAGGATTTTCTTC
128 AATT-CGGACTATCGGA-TTGTCCTAA-TGTAAGTTCAATTCC-AAATTTGGAAGGATTTTCCTC
* *** *
3606 TCTTCAAAATCTGTCAATT-AGATGGTGCAGCGAATTGGAAGTTCTTCCGATAACCGGAGGATGT
189 TCTTCAAAATCTGTCAATTGAGA-GCTGCAAAAAATTGGAAGTTCTTCCAATAACCGGAGGATGT
* *
3670 TCATCTCTTGAAAAACTT-AGCATTT-TCGATTGC-AAAAAGTTAAGTAAGATTGGAGACGGATT
253 TCATCTCTTCAAAAACTTAAG-ATTTCT-GATTGCGAAAAA-TTAAGCAAGATTGGAGACGGATT
* * *
3732 ATCTACCTCCACTTGTCTTA-AAGAATTAGATCTAAAATGTTGTCCTAATTTAAGTTCGATTCCA
315 ATCTACCTCCACTTGTCTCAGAA-AATTAGATCTAAAATATTGTCCTAATTTAAGTTCCATTCCA
* *
3796 AATTTGGAAGGATTTTCGTCTCTTCAAAAT
379 AATTTGGAAAGATTTTCCTCTCTTCAAAAT
3826 GTATCCGTTG
Statistics
Matches: 362, Mismatches: 34, Indels: 24
0.86 0.08 0.06
Matches are distributed among these distances:
419 18 0.05
420 339 0.94
421 5 0.01
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (420 bp):
AGGTGCAAGGAATTGGAAGTTCTTCCGATAATCGGAGAATGTTCATCTCTTGAAAAGCTTAGCAT
TTCCGGTTGCGAAAAACTAAGCAAGATTGGAGACGGGCTGTCAACCTCCACTTGTCTCAAAAAAT
TCGGACTATCGGATTGTCCTAATGTAAGTTCAATTCCAAATTTGGAAGGATTTTCCTCTCTTCAA
AATCTGTCAATTGAGAGCTGCAAAAAATTGGAAGTTCTTCCAATAACCGGAGGATGTTCATCTCT
TCAAAAACTTAAGATTTCTGATTGCGAAAAATTAAGCAAGATTGGAGACGGATTATCTACCTCCA
CTTGTCTCAGAAAATTAGATCTAAAATATTGTCCTAATTTAAGTTCCATTCCAAATTTGGAAAGA
TTTTCCTCTCTTCAAAATCTGTCAATTGAG
Found at i:4472 original size:144 final size:145
Alignment explanation
Indices: 4221--4629 Score: 484
Period size: 144 Copynumber: 2.8 Consensus size: 145
4211 TTGGTTGGGA
* * * *
4221 AAAGCTTAAGAGTCTCCCTCACCAATTTCAACTCCTAACCACCCTTGAAGATTTGACGATTGAAA
1 AAAGCTAAAGAGTCTTCCTCACCAACTTCAACTCCTAACTACCCTTGAAGATTTGACGATTGAAA
** * * * *
4286 GGTTTGGTGGAATAGAAGCCTTGCCAGACTGGTTGGGAAATCTCTCTTCTCTACGGCGTCTATAT
66 GGTTTCATGAAATAGAAGCCTTGCCAGAATGGTTGGGAAATCTCTCTTCTCTAAGGCATCTATAT
4351 TTGAGTGGTTTT-GG
131 TTGAGTGGTTTTCGG
* * * * *
4365 AAAGCTAAAGAGTCTTCCTCACCAGCTTCAACTCCTCACTGCCCTTGAAGATTTGACTA-TGCAG
1 AAAGCTAAAGAGTCTTCCTCACCAACTTCAACTCCTAACTACCCTTGAAGATTTGACGATTG-AA
*
4429 GGGTTTCATGAAATAGAAGCCTTGCCAGAATGGTTGGGAAATCTCTCTTCTCTAAGGCATCTATA
65 AGGTTTCATGAAATAGAAGCCTTGCCAGAATGGTTGGGAAATCTCTCTTCTCTAAGGCATCTATA
4494 TTTGAGTGGTTTTCGG
130 TTTGAGTGGTTTTCGG
* * ** * * *
4510 -AAGCTAAAGAGTTTTACTCACCAACTTCAACTCCTTTCTACCCTTGAATATTTAACGATAG-AA
1 AAAGCTAAAGAGTCTTCCTCACCAACTTCAACTCCTAACTACCCTTGAAGATTTGACGATTGAAA
* * * * * ** **
4573 GAGTTTCAAGGAATAGGAGCCTTGCCACAGTCATTCAGAAATCTCTCTTCTCTAAGG
66 G-GTTTCATGAAATAGAAGCCTTGCCAGAATGGTTGGGAAATCTCTCTTCTCTAAGG
4630 AGGCTGTGTA
Statistics
Matches: 224, Mismatches: 37, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
143 3 0.01
144 218 0.97
145 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (145 bp):
AAAGCTAAAGAGTCTTCCTCACCAACTTCAACTCCTAACTACCCTTGAAGATTTGACGATTGAAA
GGTTTCATGAAATAGAAGCCTTGCCAGAATGGTTGGGAAATCTCTCTTCTCTAAGGCATCTATAT
TTGAGTGGTTTTCGG
Done.