Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013295.1 Corchorus olitorius cultivar O-4 contig13328, whole genome shotgun sequence
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: 28723
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:1493 original size:67 final size:66
Alignment explanation
Indices: 1415--1549 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 66
1405 TTGTTTTTGT
1415 TCTTGTTGAGTGAGTTCTTTCAATTTAAAATAAAAGTTTATGTGTTTTGGTATTTTTCTCCTCTC
1 TCTTGTTGAGTGAGTTCTTTCAATTTAAAATAAAA-TTTATGTGTTTTGGTATTTTTCTCCTCTC
1480 AA
65 AA
*
1482 TCTTGTTGAGTGAGTTTTTTCAATTTAAAATAAAATTTATGTGTTTTGGTATTTTTCTCCTCTCA
1 TCTTGTTGAGTGAGTTCTTTCAATTTAAAATAAAATTTATGTGTTTTGGTATTTTTCTCCTCTCA
1547 A
66 A
1548 TC
1 TC
1550 AATTTAAAAG
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
66 33 0.49
67 34 0.51
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.50
Consensus pattern (66 bp):
TCTTGTTGAGTGAGTTCTTTCAATTTAAAATAAAATTTATGTGTTTTGGTATTTTTCTCCTCTCA
A
Found at i:1699 original size:43 final size:44
Alignment explanation
Indices: 1638--1767 Score: 192
Period size: 43 Copynumber: 3.0 Consensus size: 44
1628 AGGAGAATAG
1638 AAAAGAAAAGAAGAGATGCAGTTTGTGCAGGGAATCTCCAT-AA
1 AAAAGAAAAGAAGAGATGCAGTTTGTGCAGGGAATCTCCATCAA
1681 AAAAGAAAAGAAGAGATGCAGTTTGTGCAGGGAATCTCCATCAA
1 AAAAGAAAAGAAGAGATGCAGTTTGTGCAGGGAATCTCCATCAA
**** * *
1725 CTTTG-ATAGAAGAGATGCAGTTTATGCAGGGAATCTCCATCAA
1 AAAAGAAAAGAAGAGATGCAGTTTGTGCAGGGAATCTCCATCAA
1768 CTTTGATGAG
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
43 77 0.96
44 3 0.04
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.22
Consensus pattern (44 bp):
AAAAGAAAAGAAGAGATGCAGTTTGTGCAGGGAATCTCCATCAA
Found at i:2244 original size:72 final size:72
Alignment explanation
Indices: 2138--2288 Score: 189
Period size: 72 Copynumber: 2.1 Consensus size: 72
2128 TGAAGATCAT
* * *
2138 GGTTTGTGGGATAATAGTTTTGATGCAAAGTTTTCTGCTGAAGTCTTGAGATTGTAAAAAATTGA
1 GGTTTGTGGGATAATAGTTTGGATGCAAAGTTTTCTACTGAAATCTTGAGATTGTAAAAAATTGA
2203 -CTTTGAA
66 TC-TTGAA
** * * *
2210 GGTTTGTGGGATTCTAGTTTGGATGCGAAA-TTTTCTACTGAAATTTTTAGATTGTCAAAAATTG
1 GGTTTGTGGGATAATAGTTTGGATGC-AAAGTTTTCTACTGAAATCTTGAGATTGTAAAAAATTG
*
2274 ATCTTGAT
65 ATCTTGAA
2282 GGTTTGT
1 GGTTTGT
2289 TTGCAAAAGC
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
72 64 0.94
73 4 0.06
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.42
Consensus pattern (72 bp):
GGTTTGTGGGATAATAGTTTGGATGCAAAGTTTTCTACTGAAATCTTGAGATTGTAAAAAATTGA
TCTTGAA
Found at i:7518 original size:23 final size:23
Alignment explanation
Indices: 7485--7534 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
7475 GAGTTGTGTG
* *
7485 TTCATGTATCTAGTAAAACGGTC
1 TTCATGCATCTAGTAAAACGGTA
*
7508 TTCATGCATCTAGTAAAATGGTA
1 TTCATGCATCTAGTAAAACGGTA
7531 TTCA
1 TTCA
7535 CGTATTAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (23 bp):
TTCATGCATCTAGTAAAACGGTA
Found at i:11879 original size:23 final size:23
Alignment explanation
Indices: 11853--11911 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
11843 AGGGAGTTGT
11853 GTGTTCATGTATCTAGTAAAATG
1 GTGTTCATGTATCTAGTAAAATG
11876 GTGTTCATGTATCTAGTAAAATG
1 GTGTTCATGTATCTAGTAAAATG
*
11899 GTATTCATGTATC
1 GTGTTCATGTATC
11912 AGAATTAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (23 bp):
GTGTTCATGTATCTAGTAAAATG
Found at i:24389 original size:314 final size:315
Alignment explanation
Indices: 23796--24424 Score: 1064
Period size: 314 Copynumber: 2.0 Consensus size: 315
23786 ATGTCAATAG
*
23796 TTTACCCATGAATCAACCATTATTGCAGATACATTTATAGCACCAATCCTTTGGAATTCCGGCAG
1 TTTACCCATGAATCAACCATTATTGCAAATACATTTATAGCACCAATCCTTTGGAA-T-CGGCAG
*
23861 ACGAGTTGAACCGGTAAATCCTAATATCCACACACAATTAATATGTAATTAAAACACACTTAATC
64 ACGAGTTGAACCGATAAATCCTAATATCCACACACAATTAATATGTAATTAAAACACACTTAATC
* * * *
23926 ATAAATATAAAAATAGTAAATTACAGAAAAGGGCAGTAGGAAAGTAAGGGAGGAAATTCATCGAG
129 ATAAATATAAAAATAGTAAATTACAAAAAAGGACAGCAGGAAAGTAAGGAAGGAAATTCATCGAG
**
23991 GGACTTTTTAGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAAAACAAAAGGAGGCACCACATTA
194 GGACTTTTTAGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAAAACAAAAGGAAACACCACATTA
*
24056 ATCCTCAATTGGGCCTTTAAGTAATTTTCATAGTCACTAAAAATAATATATAGTATA
259 ATCCTCAATTGGGCCTTTAAGTAATTTCCATAGTCACTAAAAATAATATATAGTATA
* *
24113 TTTACCCATGAATCAACCATTATTGCAAATACATTTATAGCACCAAT-CTTTTGAA-CGGCAGAG
1 TTTACCCATGAATCAACCATTATTGCAAATACATTTATAGCACCAATCCTTTGGAATCGGCAGAC
*
24176 GAGTTGAACTGATAAATCCTAATATCCACACACAATTAATATGTAATTAAAACACACTTAATCAT
66 GAGTTGAACCGATAAATCCTAATATCCACACACAATTAATATGTAATTAAAACACACTTAATCAT
*
24241 AAATATAAAAATAGTAAATTACAAAAAAGGACAGCAGGAAAAGTAAGGAAGGAAATTCATCGAGT
131 AAATATAAAAATAGTAAATTACAAAAAAGGACAGCAGG-AAAGTAAGGAAGGAAATTCATCGAGG
* **
24306 GTCTTTTTAGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAAGCCAAAAGGAAACACCACATTAA
195 GACTTTTTAGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAAAACAAAAGGAAACACCACATTAA
*
24371 TCCTCAATTTGGCCTTTAAGTAATTTCCATAGTCACTAAAAATAATATATAGTA
260 TCCTCAATTGGGCCTTTAAGTAATTTCCATAGTCACTAAAAATAATATATAGTA
24425 AGTATATATA
Statistics
Matches: 294, Mismatches: 17, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
313 105 0.36
314 136 0.46
316 7 0.02
317 46 0.16
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (315 bp):
TTTACCCATGAATCAACCATTATTGCAAATACATTTATAGCACCAATCCTTTGGAATCGGCAGAC
GAGTTGAACCGATAAATCCTAATATCCACACACAATTAATATGTAATTAAAACACACTTAATCAT
AAATATAAAAATAGTAAATTACAAAAAAGGACAGCAGGAAAGTAAGGAAGGAAATTCATCGAGGG
ACTTTTTAGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAAAACAAAAGGAAACACCACATTAAT
CCTCAATTGGGCCTTTAAGTAATTTCCATAGTCACTAAAAATAATATATAGTATA
Found at i:26141 original size:29 final size:29
Alignment explanation
Indices: 26109--26164 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
26099 ACCTATATAA
26109 AAAC-AATCAAAATCATCCCATCTATTCAC
1 AAACTAATCAAAA-CATCCCATCTATTCAC
* * *
26138 AAACTACTCTAGACATCCCATCTATTC
1 AAACTAATCAAAACATCCCATCTATTC
26165 TAGAAACATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 18 0.78
30 5 0.22
ACGTcount: A:0.39, C:0.32, G:0.02, T:0.27
Consensus pattern (29 bp):
AAACTAATCAAAACATCCCATCTATTCAC
Done.