Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016421.1 Corchorus olitorius cultivar O-4 contig16454, 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: 33855
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:511 original size:19 final size:19
Alignment explanation
Indices: 491--527 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
481 AATTAATTAT
491 TTTA-ATATTATATTTTTA
1 TTTATATATTATATTTTTA
509 TTTATATATTATATTTTTA
1 TTTATATATTATATTTTTA
528 CTTAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATATATTATATTTTTA
Found at i:538 original size:19 final size:19
Alignment explanation
Indices: 497--538 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
487 TTATTTTAAT
* * *
497 ATTATATTTTTATTTATAT
1 ATTATATTTTTACTTAAAA
516 ATTATATTTTTACTTAAAA
1 ATTATATTTTTACTTAAAA
535 ATTA
1 ATTA
539 CTCCTAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTATATTTTTACTTAAAA
Found at i:1588 original size:323 final size:320
Alignment explanation
Indices: 863--1984 Score: 1461
Period size: 323 Copynumber: 3.5 Consensus size: 320
853 ATCCCTAGTG
* * * * * *
863 AAAACCCTTCAATCTTTTTGGTGTTGAATTATTTAATTTTTAAGAGTATTGTCGCAAAAAATTGA
1 AAAACCCTTCAATCTTTTTGGCGTTAAATTATATATTTTTTCAGAGTATTGTGGCAAAAAATTGA
* *
928 GAAAGAAATTTTCGGGTCAGTTTTTAGCTGAAATCATATACTAACCATCACGGTTTTTGGCTTAA
66 GAAAGAAATTTTCGGGTCAATTTTTAGCCGAAATCATATACTAACCATCACGGTTTTTGGCTTAA
993 AATTCGTTTCGGGGTCCCGGCTCAGTTTTGCATGATTTTTGGTATAAATACTCCTTGAAATATCT
131 AATTCGTTTCGGGGTCCCGGCTCAGTTTTGCATGATTTTTGGTATAAATACTCCTTGAAATATCT
* *
1058 ATATTCATCTAACCAAATTTCAGCCACATTGGAATTAAAGTTTTTTTTTACGAGCATCTAAATCT
196 ATATTCATCTAACCAAATTTCAGCCACATTGGAATTAAAATTTATTTTTACGAGCATCT-AATCT
*
1123 TGTTTCGATTTAATCAAAAATAAACTCGGAAAAAGATAGGGAAAACGATATCAAAAGCGTGA
260 TGTTTCGATTTAATCAAAAATAAACTCGGAAAAA-ATAGGGAAAACGATATCAGAAGCGTGA
* * *
1185 AAAACTCTTCAATTTTTTTGGCGTTAAATTATATATTTTTTCTGAGTATTGTGGCAAAAAAATTG
1 AAAACCCTTCAATCTTTTTGGCGTTAAATTATATATTTTTTCAGAGTATTGTGGC-AAAAAATTG
1250 AGAAAGAAATTTTCGGGTCAATTTTTAGCCGAAATCATATACTAACCATCACGGTTTTTGGCTTA
65 AGAAAGAAATTTTCGGGTCAATTTTTAGCCGAAATCATATACTAACCATCACGGTTTTTGGCTTA
*
1315 AAATTCGTTTCGGGGTCCCGGCTCAGTTTTGCATGATTTTCGGTATAAATACTCCTTGAAATATC
130 AAATTCGTTTCGGGGTCCCGGCTCAGTTTTGCATGATTTTTGGTATAAATACTCCTTGAAATATC
*
1380 TATATTCATCTAACCAAATTTCAGCCACATTGGAATTAAAATTTGTTTTTACGAGCATCT-ATCT
195 TATATTCATCTAACCAAATTTCAGCCACATTGGAATTAAAATTTATTTTTACGAGCATCTAATCT
1444 TGTTTCGATTTAATCAAAAATAAACTCGGCAAATAAATAGGGAAAACGATATCAGAAGCGTGA
260 TGTTTCGATTTAATCAAAAATAAACTCGG-AAA-AAATAGGGAAAACGATATCAGAAGCGTGA
* * *
1507 AAAACTCTTCAATTTTTTTGGCGTTAAATTATATATTTTTTCTGAGTATTGTGGCAAAAAAATTG
1 AAAACCCTTCAATCTTTTTGGCGTTAAATTATATATTTTTTCAGAGTATTGTGGC-AAAAAATTG
* * * *
1572 AGGAAA-AACTTTTTCGGGTCAGTTTTTGCGAAATTTTAGCCGAAATCATGTATTAACCATCACG
65 A-GAAAGAA-ATTTTC-GG---G----T-C-AATTTTTAGCCGAAATCATATACTAACCATCACG
* * ** * *
1636 GTTTTTGGC-TAAAA-TCGCATTCCGGGG-CCCGGCTCAGTTCTGCATGATTTTTGGCGTATAGA
118 GTTTTTGGCTTAAAATTCG--TTTCGGGGTCCCGGCTCAGTTTTGCATGATTTTTGGTATAAATA
* * * * *
1698 CTCCTTGAAATATCTATATTCATCGT-GCCAAA-TCCTAGCCACACTCGAATTAAGGATTTATTT
181 CTCCTTGAAATATCTATATTCATC-TAACCAAATTTC-AGCCACATTGGAATTAA-AATTTATTT
* * * * * * *
1761 TTACGAACATCTGAATCTTGTTTCGATTTAATTAGAATTTAATTCGGGAAAAAA-ATGGAAAAAC
243 TTACGAGCATCT-AATCTTGTTTCGATTTAATCAAAAATAAACTC-GGAAAAAATA-GGGAAAAC
* *
1825 AATATTAGAAGCGTGA
305 GATATCAGAAGCGTGA
* * * *
1841 AAAACCCTTCAATCTTTTTGGTGTTGAATTATTTAATGTTTT-AGAGTATTGTGGCAAAAAATTG
1 AAAACCCTTCAATCTTTTTGGCGTTAAATTATAT-ATTTTTTCAGAGTATTGTGGCAAAAAATTG
* * * **
1905 AGAAAGAAATTTTCGGGTCAGTTTTTAGCCTAAGTCACGTACTAACCATCACGGTTTTTGGCTTA
65 AGAAAGAAATTTTCGGGTCAATTTTTAGCCGAAATCATATACTAACCATCACGGTTTTTGGCTTA
*
1970 AAATTCGGTTCGGGG
130 AAATTCGTTTCGGGG
1985 CCCTGGTTTA
Statistics
Matches: 715, Mismatches: 57, Indels: 56
0.86 0.07 0.07
Matches are distributed among these distances:
321 33 0.05
322 186 0.26
323 211 0.30
324 6 0.01
327 1 0.00
328 1 0.00
331 8 0.01
332 88 0.12
333 79 0.11
334 65 0.09
335 35 0.05
336 2 0.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (320 bp):
AAAACCCTTCAATCTTTTTGGCGTTAAATTATATATTTTTTCAGAGTATTGTGGCAAAAAATTGA
GAAAGAAATTTTCGGGTCAATTTTTAGCCGAAATCATATACTAACCATCACGGTTTTTGGCTTAA
AATTCGTTTCGGGGTCCCGGCTCAGTTTTGCATGATTTTTGGTATAAATACTCCTTGAAATATCT
ATATTCATCTAACCAAATTTCAGCCACATTGGAATTAAAATTTATTTTTACGAGCATCTAATCTT
GTTTCGATTTAATCAAAAATAAACTCGGAAAAAATAGGGAAAACGATATCAGAAGCGTGA
Found at i:2319 original size:25 final size:25
Alignment explanation
Indices: 2285--2333 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
2275 TTAAACAATC
2285 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
*
2310 TTGAGTACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
2334 CAAACCAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.12, C:0.31, G:0.20, T:0.37
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:2359 original size:21 final size:21
Alignment explanation
Indices: 2330--2371 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2320 TCGCTCGGTC
*
2330 TCTACAAACCAATC-ATCACA
1 TCTACAAACCAAACAATCACA
2350 TCTACCAAACCAAACAATCACA
1 TCTA-CAAACCAAACAATCACA
2372 CACACACACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.17
Consensus pattern (21 bp):
TCTACAAACCAAACAATCACA
Found at i:3249 original size:25 final size:25
Alignment explanation
Indices: 3215--3263 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
3205 TTAAACAATC
3215 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
3240 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
3264 CAAACCAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.12, C:0.33, G:0.20, T:0.35
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:3289 original size:21 final size:21
Alignment explanation
Indices: 3260--3301 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3250 TCGCTCGGTC
*
3260 TCTACAAACC-AATCATCACA
1 TCTACAAACCAAATAATCACA
3280 TCTACCAAACCAAATAATCACA
1 TCTA-CAAACCAAATAATCACA
3302 CACACACACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 6 0.32
22 9 0.47
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (21 bp):
TCTACAAACCAAATAATCACA
Found at i:12025 original size:39 final size:39
Alignment explanation
Indices: 11914--12016 Score: 136
Period size: 39 Copynumber: 2.6 Consensus size: 39
11904 TAACAGGTGG
* * *
11914 AAAGAACAAAAAATTGAATAAAGCAAAAGGCACAGGTAA
1 AAAGAACAATAAATTGGATAAAACAAAAGGCACAGGTAA
* * *
11953 AAAGAACAATAACTT-GATAAAAACAAAATGCACAGGTTA
1 AAAGAACAATAAATTGGAT-AAAACAAAAGGCACAGGTAA
11992 AAAGAACAATAAATTGGATAAAACA
1 AAAGAACAATAAATTGGATAAAACA
12017 GAGAGCACAT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
38 2 0.04
39 50 0.91
40 3 0.05
ACGTcount: A:0.60, C:0.11, G:0.15, T:0.15
Consensus pattern (39 bp):
AAAGAACAATAAATTGGATAAAACAAAAGGCACAGGTAA
Found at i:14494 original size:19 final size:19
Alignment explanation
Indices: 14470--14506 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
14460 CTGTTTAGTA
14470 ACTGTACAGATAAGATTAC
1 ACTGTACAGATAAGATTAC
*
14489 ACTGTACAGATTAGATTA
1 ACTGTACAGATAAGATTA
14507 GGTACTGTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
ACTGTACAGATAAGATTAC
Found at i:18393 original size:81 final size:81
Alignment explanation
Indices: 18261--18581 Score: 489
Period size: 81 Copynumber: 4.0 Consensus size: 81
18251 TCCACATGAT
* * ** * *
18261 GTTCCTCTTCATTATATATGACTTCCGTTTGTTTTGAAGAAGAAATATCATCTCTCACATGTATT
1 GTTCCTCTTCATTATTTATGACTTCCATTTGTTTCAAAGTAGAAATATCATCTCTCACATGTCTT
*
18326 TTGGGTTCTGCACGAT
66 TTGGGTTCTGCACGAA
* * * * *
18342 GTTCATCTTCCTTATTTATGACTTCCATTTGATTCGATGTAGAAATATCATCTCTCACATGTCTT
1 GTTCCTCTTCATTATTTATGACTTCCATTTGTTTCAAAGTAGAAATATCATCTCTCACATGTCTT
*
18407 TTGGGTTCTGCATGAA
66 TTGGGTTCTGCACGAA
*
18423 GTTCCTCTTCATTATTTATGACTTCCATTTCTTTCAAAGTAGAAATATCATCTCTCACATGTCTT
1 GTTCCTCTTCATTATTTATGACTTCCATTTGTTTCAAAGTAGAAATATCATCTCTCACATGTCTT
*
18488 TTGGGTTCTGCATGAA
66 TTGGGTTCTGCACGAA
*
18504 GTTCCTCTTCATTATTTATGACTTCCGTTTGTTTCAAAGTAGAAATATCATCTCTCACATGTCTT
1 GTTCCTCTTCATTATTTATGACTTCCATTTGTTTCAAAGTAGAAATATCATCTCTCACATGTCTT
*
18569 TTAGGTTCTGCAC
66 TTGGGTTCTGCAC
18582 CACATATTAT
Statistics
Matches: 219, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 219 1.00
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (81 bp):
GTTCCTCTTCATTATTTATGACTTCCATTTGTTTCAAAGTAGAAATATCATCTCTCACATGTCTT
TTGGGTTCTGCACGAA
Found at i:31708 original size:71 final size:71
Alignment explanation
Indices: 31556--31754 Score: 240
Period size: 71 Copynumber: 2.8 Consensus size: 71
31546 ATTTCTGTTA
* * * * *
31556 GTAGATTCATCCACCATATCCAAATTCGTGAAATCAGAG-CAAAAT-TGAGCAAAACTCTAGACA
1 GTAGATTCATCCACCATATCCAGATTCGTG--ACCCGAGTC-GAATCAGAGCAAAACTCTAGACA
*
31619 TCTATGTTG
63 TCTACGTTG
*
31628 GTAGATTCATCCACCATATCCAGATTCGTGACCCGAGTCGAATCAGAGCAAAACTCTAGACGTCT
1 GTAGATTCATCCACCATATCCAGATTCGTGACCCGAGTCGAATCAGAGCAAAACTCTAGACATCT
*
31693 CCGTTG
66 ACGTTG
* * * * *
31699 GTAGATTCATCCATCATATCCAGATTCGTGACCCAAGTTGAATCAAAACAAAACTC
1 GTAGATTCATCCACCATATCCAGATTCGTGACCCGAGTCGAATCAGAGCAAAACTC
31755 CGGATACCAG
Statistics
Matches: 112, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
70 8 0.07
71 75 0.67
72 29 0.26
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (71 bp):
GTAGATTCATCCACCATATCCAGATTCGTGACCCGAGTCGAATCAGAGCAAAACTCTAGACATCT
ACGTTG
Found at i:31954 original size:24 final size:24
Alignment explanation
Indices: 31910--31955 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
31900 GATTTATATT
* *
31910 CCATGCACTGTCAGTGTATAGAGG
1 CCATACACTGTCAGTGCATAGAGG
31934 CCATACACTGTCAG-GCCATAGA
1 CCATACACTGTCAGTG-CATAGA
31956 ATTATGCCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (24 bp):
CCATACACTGTCAGTGCATAGAGG
Done.