Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga10g01421.F4
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: 4093
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Found at i:983 original size:342 final size:342
Alignment explanation
Indices: 345--1029 Score: 1129
Period size: 342 Copynumber: 2.0 Consensus size: 342
335 GGCCATTGTC
* * * * *
345 AGAATGAAACATTATGCGCTTGTTGTTTTTCTGGGTAGCCAGATGGAATTACGGGGAGTTTCACA
1 AGAATGAAACATTATGCGCTTGCTGTTTCTCTGGGCAGCCAGATGAAACTACGGGGAGTTTCACA
* * *
410 TAATGCTTATTCTTTCACCATCTTGATTAATTGCTTTTGTCATTTAGGTAAAGTTGATTTTGGGT
66 TAATGCTCATTCTTTCAACATCTTGATTAATTGCTTTTGTCAGTTAGGTAAAGTTGATTTTGGGT
475 TTTCTGTTTTGGGGAAAATGCTCAAGTTAGGTTTTGAACCTAATGTTGTAACTTTGTCCACCTTG
131 TTTCTGTTTTGGGGAAAATGCTCAAGTTAGGTTTTGAACCTAATGTTGTAACTTTGTCCACCTTG
* * * * *
540 ATTAATGGACTTTGTAATCAAAGCAGGGTTTCTCAGGCTGTGAAATTGTTTTATGAAATGATCGA
196 ATTAATGGACTTTGTAATCAAAACAAGGTTTCTCAGGCTGTCAAATTGTTTGATGAAATGATCAA
* * * *
605 AAAAGGGTATCGACCTGATTCATTTGCTTGCAATACAGTACTTAATGGGTTGTGCAAGTCTGGTA
261 AAAAGGGTATCGACCTGATTCAGTTGCTTACAATACAGTACTTAATGGGTTGTGCAAGACTGGGA
670 ACACTGGTCGAGCTGTT
326 ACACTGGTCGAGCTGTT
*
687 AGAATGAAACATTATGCGCTTGCTGTTTCTCTGGGCAGCCAGATGAAACTATGGGGAGTTTCACA
1 AGAATGAAACATTATGCGCTTGCTGTTTCTCTGGGCAGCCAGATGAAACTACGGGGAGTTTCACA
* *
752 TGATGCTCATTCTTTCAACATTTTGATTAATTGCTTTTGTCAGTTAGGTAAAGTTGATTTTGGGT
66 TAATGCTCATTCTTTCAACATCTTGATTAATTGCTTTTGTCAGTTAGGTAAAGTTGATTTTGGGT
* *
817 TTTCTGTTTTGGGGAAAATGCTCAAGTTAGGTTTTGAACCTGATGTTGTAACTTTGTCCACTTTG
131 TTTCTGTTTTGGGGAAAATGCTCAAGTTAGGTTTTGAACCTAATGTTGTAACTTTGTCCACCTTG
*
882 ATTAATGGACTTTGTAATCAAAACAAGGTTTCTCAGGCTG-CAAGTTTGTTTGATGAAATGATCA
196 ATTAATGGACTTTGTAATCAAAACAAGGTTTCTCAGGCTGTCAA-ATTGTTTGATGAAATGATCA
* *
946 AAAAAGGGTGTCGACCTGATTCAGTTGCTTACAATACAGTACTTAATGGGTTGTGTAAGACTGGG
260 AAAAAGGGTATCGACCTGATTCAGTTGCTTACAATACAGTACTTAATGGGTTGTGCAAGACTGGG
1011 AACACTGGTCGAGCTGTT
325 AACACTGGTCGAGCTGTT
1029 A
1 A
1030 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:1468 original size:105 final size:102
Alignment explanation
Indices: 1359--1813 Score: 389
Period size: 105 Copynumber: 4.3 Consensus size: 102
1349 CTTTAATGCG
**
1359 ATGAGAAAGCAAGGCATCAAGCCTGATGTTGTCACCTATAATATATTGGTTGATGCATGGTGCAA
1 ATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCACCTATAATATATTGGTTGATGCAT--TGCAA
* * * * *
1424 GGAGAGGCTAATTTCTGAATCTTTGGATGTAGTTCACACA
64 GGAGAGGAT-ATTTCTGAAGCTGTAGATATAGTTCACACA
* * * *
1464 ATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCACGTATAGTACATTAGTTGATGCGCATTGCAA
1 ATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCACCTATAATATATTGGTTGAT--GCATTGCAA
* ** * * * *
1529 GGAGGGGAGGGTTTCTGAAGCCGAAGATATTGTTGACACA
64 GGAGAGGA-TATTTCTGAAGCTGTAGATATAGTTCACACA
* * * *
1569 ATGAGAAAGGAAGGCATTGAGCCCGATGTTGTGACGTATAATATATTGGTTGATGCGTATTGCAA
1 ATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCACCTATAATATATTGGTTGATGC--ATTGCAA
*
1634 GGAGAGGAGTATTTCTAAAGCTGTAGATACTA-TTGC-CACA
64 GGAGAGGA-TATTTCTGAAGCTGTAGATA-TAGTT-CACACA
** * ** *
1674 ATGAGAAAGCAAGGTGTGGAGCCTGATGTTGTCACCTATAATATATTTATCGATGCACTTTGCAA
1 ATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCACCTATAATATATTGGTTGATGCA--TTGCAA
* * * *
1739 GAATG-GGATGGTTTCTGAAGCTG-A-ATGTATTGTCGACACA
64 GGA-GAGGAT-ATTTCTGAAGCTGTAGATATAGT-TC-ACACA
* * * *
1779 ATGAGAAAACAATGCATTGAGCCTAATTTTGTCAC
1 ATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCAC
1814 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:1676 original size:210 final size:210
Alignment explanation
Indices: 1359--1801 Score: 527
Period size: 210 Copynumber: 2.1 Consensus size: 210
1349 CTTTAATGCG
** * *
1359 ATGAGAAAGCAAGGCATCAAGCCTGATGTTGTCACCTATAATATATTGGTTGATGCATGGTGCAA
1 ATGAGAAAGCAAGGCATTGAGCCCGATGTTGTCACCTATAATATATTGGTTGATGCATAGTGCAA
* * * * * *
1424 GGAGAGGCTAATTTCTGAATCTTTGGATGTAGTTCACACAATGAGAAAGCAAGGCATTGAGCCTG
66 GGAGAGGCTAATTTCTAAAGCTGTAGATCTAGTTCACACAATGAGAAAGCAAGGCATGGAGCCTG
* * * * *
1489 ATGTTGTCACGTATAGTACA-TTAGTTGATGCGCATTGCAAGGAGGGGAGGGTTTCTGAAGCCGA
131 ATGTTGTCACCTATAATACATTTA-TCGATGCACATTGCAAGAAGGGGAGGGTTTCTGAAGCCGA
*
1553 A-GATATTGTTGACACA
195 ATG-TATTGTCGACACA
* * * * *
1569 ATGAGAAAGGAAGGCATTGAGCCCGATGTTGTGACGTATAATATATTGGTTGATGCGTATTGCAA
1 ATGAGAAAGCAAGGCATTGAGCCCGATGTTGTCACCTATAATATATTGGTTGATGCATAGTGCAA
* **
1634 GGAGAGGAGT-ATTTCTAAAGCTGTAGATACTA-TTGC-CACAATGAGAAAGCAAGGTGTGGAGC
66 GGAGAGG-CTAATTTCTAAAGCTGTAGAT-CTAGTT-CACACAATGAGAAAGCAAGGCATGGAGC
* * * * *
1696 CTGATGTTGTCACCTATAATATATTTATCGATGCACTTTGCAAGAATGGGATGGTTTCTGAAGCT
128 CTGATGTTGTCACCTATAATACATTTATCGATGCACATTGCAAGAAGGGGAGGGTTTCTGAAGCC
1761 GAATGTATTGTCGACACA
193 GAATGTATTGTCGACACA
* *
1779 ATGAGAAAACAATGCATTGAGCC
1 ATGAGAAAGCAAGGCATTGAGCC
1802 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:2759 original size:22 final size:21
Alignment explanation
Indices: 2717--2760 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
2707 ATCCTCAACA
2717 CTTCATTGCAAAAGCTCGAAG
1 CTTCATTGCAAAAGCTCGAAG
2738 CTTCACTTGCTAAAAGCT-GAAG
1 CTTCA-TTGC-AAAAGCTCGAAG
2760 C
1 C
2761 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
Done.