Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga10g01421.F2
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: 4802
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Found at i:848 original size:342 final size:342
Alignment explanation
Indices: 210--894 Score: 1129
Period size: 342 Copynumber: 2.0 Consensus size: 342
200 GGCCATTGTC
* * * * *
210 AGAATGAAACATTATGCGCTTGTTGTTTTTCTGGGTAGCCAGATGGAATTACGGGGAGTTTCACA
1 AGAATGAAACATTATGCGCTTGCTGTTTCTCTGGGCAGCCAGATGAAACTACGGGGAGTTTCACA
* * *
275 TAATGCTTATTCTTTCACCATCTTGATTAATTGCTTTTGTCATTTAGGTAAAGTTGATTTTGGGT
66 TAATGCTCATTCTTTCAACATCTTGATTAATTGCTTTTGTCAGTTAGGTAAAGTTGATTTTGGGT
340 TTTCTGTTTTGGGGAAAATGCTCAAGTTAGGTTTTGAACCTAATGTTGTAACTTTGTCCACCTTG
131 TTTCTGTTTTGGGGAAAATGCTCAAGTTAGGTTTTGAACCTAATGTTGTAACTTTGTCCACCTTG
* * * * *
405 ATTAATGGACTTTGTAATCAAAGCAGGGTTTCTCAGGCTGTGAAATTGTTTTATGAAATGATCGA
196 ATTAATGGACTTTGTAATCAAAACAAGGTTTCTCAGGCTGTCAAATTGTTTGATGAAATGATCAA
* * * *
470 AAAAGGGTATCGACCTGATTCATTTGCTTGCAATACAGTACTTAATGGGTTGTGCAAGTCTGGTA
261 AAAAGGGTATCGACCTGATTCAGTTGCTTACAATACAGTACTTAATGGGTTGTGCAAGACTGGGA
535 ACACTGGTCGAGCTGTT
326 ACACTGGTCGAGCTGTT
*
552 AGAATGAAACATTATGCGCTTGCTGTTTCTCTGGGCAGCCAGATGAAACTATGGGGAGTTTCACA
1 AGAATGAAACATTATGCGCTTGCTGTTTCTCTGGGCAGCCAGATGAAACTACGGGGAGTTTCACA
* *
617 TGATGCTCATTCTTTCAACATTTTGATTAATTGCTTTTGTCAGTTAGGTAAAGTTGATTTTGGGT
66 TAATGCTCATTCTTTCAACATCTTGATTAATTGCTTTTGTCAGTTAGGTAAAGTTGATTTTGGGT
* *
682 TTTCTGTTTTGGGGAAAATGCTCAAGTTAGGTTTTGAACCTGATGTTGTAACTTTGTCCACTTTG
131 TTTCTGTTTTGGGGAAAATGCTCAAGTTAGGTTTTGAACCTAATGTTGTAACTTTGTCCACCTTG
*
747 ATTAATGGACTTTGTAATCAAAACAAGGTTTCTCAGGCTG-CAAGTTTGTTTGATGAAATGATCA
196 ATTAATGGACTTTGTAATCAAAACAAGGTTTCTCAGGCTGTCAA-ATTGTTTGATGAAATGATCA
* *
811 AAAAAGGGTGTCGACCTGATTCAGTTGCTTACAATACAGTACTTAATGGGTTGTGTAAGACTGGG
260 AAAAAGGGTATCGACCTGATTCAGTTGCTTACAATACAGTACTTAATGGGTTGTGCAAGACTGGG
876 AACACTGGTCGAGCTGTT
325 AACACTGGTCGAGCTGTT
894 A
1 A
895 AGTTTCTAAG
Statistics
Matches: 317, Mismatches: 25, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
341 2 0.01
342 315 0.99
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (342 bp):
AGAATGAAACATTATGCGCTTGCTGTTTCTCTGGGCAGCCAGATGAAACTACGGGGAGTTTCACA
TAATGCTCATTCTTTCAACATCTTGATTAATTGCTTTTGTCAGTTAGGTAAAGTTGATTTTGGGT
TTTCTGTTTTGGGGAAAATGCTCAAGTTAGGTTTTGAACCTAATGTTGTAACTTTGTCCACCTTG
ATTAATGGACTTTGTAATCAAAACAAGGTTTCTCAGGCTGTCAAATTGTTTGATGAAATGATCAA
AAAAGGGTATCGACCTGATTCAGTTGCTTACAATACAGTACTTAATGGGTTGTGCAAGACTGGGA
ACACTGGTCGAGCTGTT
Found at i:1333 original size:105 final size:102
Alignment explanation
Indices: 1224--1678 Score: 389
Period size: 105 Copynumber: 4.3 Consensus size: 102
1214 CTTTAATGCG
**
1224 ATGAGAAAGCAAGGCATCAAGCCTGATGTTGTCACCTATAATATATTGGTTGATGCATGGTGCAA
1 ATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCACCTATAATATATTGGTTGATGCAT--TGCAA
* * * * *
1289 GGAGAGGCTAATTTCTGAATCTTTGGATGTAGTTCACACA
64 GGAGAGGAT-ATTTCTGAAGCTGTAGATATAGTTCACACA
* * * *
1329 ATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCACGTATAGTACATTAGTTGATGCGCATTGCAA
1 ATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCACCTATAATATATTGGTTGAT--GCATTGCAA
* ** * * * *
1394 GGAGGGGAGGGTTTCTGAAGCCGAAGATATTGTTGACACA
64 GGAGAGGA-TATTTCTGAAGCTGTAGATATAGTTCACACA
* * * *
1434 ATGAGAAAGGAAGGCATTGAGCCCGATGTTGTGACGTATAATATATTGGTTGATGCGTATTGCAA
1 ATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCACCTATAATATATTGGTTGATGC--ATTGCAA
*
1499 GGAGAGGAGTATTTCTAAAGCTGTAGATACTA-TTGC-CACA
64 GGAGAGGA-TATTTCTGAAGCTGTAGATA-TAGTT-CACACA
** * ** *
1539 ATGAGAAAGCAAGGTGTGGAGCCTGATGTTGTCACCTATAATATATTTATCGATGCACTTTGCAA
1 ATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCACCTATAATATATTGGTTGATGCA--TTGCAA
* * * *
1604 GAATG-GGATGGTTTCTGAAGCTG-A-ATGTATTGTCGACACA
64 GGA-GAGGAT-ATTTCTGAAGCTGTAGATATAGT-TC-ACACA
* * * *
1644 ATGAGAAAACAATGCATTGAGCCTAATTTTGTCAC
1 ATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCAC
1679 ATACAGAACT
Statistics
Matches: 282, Mismatches: 53, Indels: 30
0.77 0.15 0.08
Matches are distributed among these distances:
102 2 0.01
103 7 0.02
104 3 0.01
105 264 0.94
106 2 0.01
107 4 0.01
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (102 bp):
ATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCACCTATAATATATTGGTTGATGCATTGCAAGG
AGAGGATATTTCTGAAGCTGTAGATATAGTTCACACA
Found at i:1541 original size:210 final size:210
Alignment explanation
Indices: 1224--1666 Score: 527
Period size: 210 Copynumber: 2.1 Consensus size: 210
1214 CTTTAATGCG
** * *
1224 ATGAGAAAGCAAGGCATCAAGCCTGATGTTGTCACCTATAATATATTGGTTGATGCATGGTGCAA
1 ATGAGAAAGCAAGGCATTGAGCCCGATGTTGTCACCTATAATATATTGGTTGATGCATAGTGCAA
* * * * * *
1289 GGAGAGGCTAATTTCTGAATCTTTGGATGTAGTTCACACAATGAGAAAGCAAGGCATTGAGCCTG
66 GGAGAGGCTAATTTCTAAAGCTGTAGATCTAGTTCACACAATGAGAAAGCAAGGCATGGAGCCTG
* * * * *
1354 ATGTTGTCACGTATAGTACA-TTAGTTGATGCGCATTGCAAGGAGGGGAGGGTTTCTGAAGCCGA
131 ATGTTGTCACCTATAATACATTTA-TCGATGCACATTGCAAGAAGGGGAGGGTTTCTGAAGCCGA
*
1418 A-GATATTGTTGACACA
195 ATG-TATTGTCGACACA
* * * * *
1434 ATGAGAAAGGAAGGCATTGAGCCCGATGTTGTGACGTATAATATATTGGTTGATGCGTATTGCAA
1 ATGAGAAAGCAAGGCATTGAGCCCGATGTTGTCACCTATAATATATTGGTTGATGCATAGTGCAA
* **
1499 GGAGAGGAGT-ATTTCTAAAGCTGTAGATACTA-TTGC-CACAATGAGAAAGCAAGGTGTGGAGC
66 GGAGAGG-CTAATTTCTAAAGCTGTAGAT-CTAGTT-CACACAATGAGAAAGCAAGGCATGGAGC
* * * * *
1561 CTGATGTTGTCACCTATAATATATTTATCGATGCACTTTGCAAGAATGGGATGGTTTCTGAAGCT
128 CTGATGTTGTCACCTATAATACATTTATCGATGCACATTGCAAGAAGGGGAGGGTTTCTGAAGCC
1626 GAATGTATTGTCGACACA
193 GAATGTATTGTCGACACA
* *
1644 ATGAGAAAACAATGCATTGAGCC
1 ATGAGAAAGCAAGGCATTGAGCC
1667 TAATTTTGTC
Statistics
Matches: 196, Mismatches: 32, Indels: 10
0.82 0.13 0.04
Matches are distributed among these distances:
210 188 0.96
211 8 0.04
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (210 bp):
ATGAGAAAGCAAGGCATTGAGCCCGATGTTGTCACCTATAATATATTGGTTGATGCATAGTGCAA
GGAGAGGCTAATTTCTAAAGCTGTAGATCTAGTTCACACAATGAGAAAGCAAGGCATGGAGCCTG
ATGTTGTCACCTATAATACATTTATCGATGCACATTGCAAGAAGGGGAGGGTTTCTGAAGCCGAA
TGTATTGTCGACACA
Found at i:2624 original size:22 final size:21
Alignment explanation
Indices: 2582--2625 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
2572 ATCCTCAACA
2582 CTTCATTGCAAAAGCTCGAAG
1 CTTCATTGCAAAAGCTCGAAG
2603 CTTCACTTGCTAAAAGCT-GAAG
1 CTTCA-TTGC-AAAAGCTCGAAG
2625 C
1 C
2626 AATTGGCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 9 0.43
23 7 0.33
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (21 bp):
CTTCATTGCAAAAGCTCGAAG
Found at i:3665 original size:33 final size:32
Alignment explanation
Indices: 3613--3781 Score: 169
Period size: 33 Copynumber: 5.2 Consensus size: 32
3603 GTCCGTACAG
* *
3613 AACCTGCACGACCAAATGCTAATCCATATGACC
1 AACCTGCAC-AGCAAATGCTAATCCATATGGCC
3646 AACCTGCACAGCAACATGCTAATCCATA-GGCTC
1 AACCTGCACAGCAA-ATGCTAATCCATATGGC-C
* * *
3679 AAACTGCACAGCCAAATGCTAATCCACACGGCC
1 AACCTGCACAG-CAAATGCTAATCCATATGGCC
* * * * *
3712 AAACTTCTCAGCCAATGCTAATGCATATGGCC
1 AACCTGCACAGCAAATGCTAATCCATATGGCC
* * *
3744 AACCTGTACAGCTAAGTGCTAATCCATATGCCC
1 AACCTGCACAGC-AAATGCTAATCCATATGGCC
3777 AACCT
1 AACCT
3782 ACATAGTCAA
Statistics
Matches: 113, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
32 31 0.27
33 76 0.67
34 6 0.05
ACGTcount: A:0.34, C:0.33, G:0.14, T:0.20
Consensus pattern (32 bp):
AACCTGCACAGCAAATGCTAATCCATATGGCC
Done.