Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017580.1 Corchorus olitorius cultivar O-4 contig17613, 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: 42420
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:627 original size:325 final size:323
Alignment explanation
Indices: 6--1251 Score: 1665
Period size: 325 Copynumber: 3.9 Consensus size: 323
1 GTCTC
* * *
6 AGTTTTGCATGATTTTTGGCAAAAAGACTCCTTGAAATATCTATTTTCATATAACCAAATCTTAA
1 AGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTTAG
* * *
71 CCAATTTGGATTTACGGATTTCTTTTTACGAGCATCTTAATTTTGTTTCGATTTAATTAGTAATA
66 CCAATTTGGATTTAAGGATTTCTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATA
* * *
136 AATTCGGAAAAGAATT-AGAAAAACAATATTCGAAGCGT-AAACAACCCTTAAATTTTTTTGGCG
131 AATTCGGAAAAAAATTGA-AAAAACGATATTCGAAGCGTGAAA-ACCCCTTAAATTTTTTTGGCG
* * * * *
199 TTCAATAATATATTATTTTAGAGTTTTGTGG-GAAAAAATGAGGAAAAAAAGTTTTCGGGTCAAT
194 TTGAATTATATATTTTTTTAGAGTTGTGTGGCAAAAAAATGA-G-AAAAAAGTTTTCGGGTCAAT
* *
263 TTTTAGCCGAAATCATATACAAACCATCAAGGTTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGG
257 TTTTAGCCGAAATCATGTACAAACCATCACGG-TTTTTTGCTAAAAACGCGTTTCGGGGCCCCGG
*
328 TTT
321 CTT
* * * * *
331 AGTTCTGCATTATTGTTGGCAGAAAGACTCCTTGAAATATCAATATTCATATAACCAATTCTTAG
1 AGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTTAG
*
396 CCAATTTGGATTTAAGGATTTCTTTTTACGAGAATCTGAATTTTGTTTCGATTTAATTAGAAATA
66 CCAATTTGGATTTAAGGATTTCTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATA
461 AATTCGGAAAAAAAATTGAAAAAACGATATTCGAAGCGTGAAAACCCCTTAAATTTTTTTTGGCG
131 AATTCGG-AAAAAAATTGAAAAAACGATATTCGAAGCGTGAAAACCCCTTAAA-TTTTTTTGGCG
* * *
526 TTGAATCATATATTTTTTTAGAATTGTGTGGCAAAAAAATGAGAAAAAAGATTTCGGGTCAATTT
194 TTGAATTATATATTTTTTTAGAGTTGTGTGGCAAAAAAATGAGAAAAAAGTTTTCGGGTCAATTT
* * * *
591 TTAGCCAAAATCGTGTACAAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTC
259 TTAGCCGAAATCATGTACAAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGGCTT
* *
656 AGTTTTGCAAT-ATTTTTAGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCA
1 AGTTTTGC-ATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTTA
* * *
720 GTCAATTTGGATTTAAGGATTTCTTTTTAAGAGCATCTGAATTTTGTTTCGATTTTATTAGAAAT
65 GCCAATTTGGATTTAAGGATTTCTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAAT
* * * * *
785 AAATGCGG-AAAAAATGGAAAAAACGATATTGGAAGCGTAAAAAACCCCTTCAATTTTCTTTGGC
130 AAATTCGGAAAAAAATTGAAAAAACGATATTCGAAGCGT-GAAAACCCCTTAAATTTT-TTTGGC
849 GTTGAATTATAT-TTTTTTTAGAGTTGTGTGGCAAAAAAATGAGAAAAAAGTTTTCGGGTCAATT
193 GTTGAATTATATATTTTTTTAGAGTTGTGTGGCAAAAAAATGAGAAAAAAGTTTTCGGGTCAATT
* * * * *
913 TTTATCCGAAATCGTGT----ACTATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCTGGCT
258 TTTAGCCGAAATCATGTACAAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGGCT
974 T
323 T
* * *
975 AGTTTTGCATGATTTTTTGGCAGAAAGGCTCCTTGAAATATCTATATTTATATAACAAAATCTTA
1 AGTTTTGCATGA-TTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTTA
* *
1040 GCCACA-TTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA
65 GCCA-ATTTGGATTTAAGGATTTCTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAA
* * ** ** * * * *
1104 TTAATTCGGAAAAAAA-TGGAAAAACGATATTATAAGCAAGAAAATCCCGTCAATCTTTTTGGCG
129 TAAATTCGGAAAAAAATTGAAAAAACGATATTCGAAGCGTGAAAACCCCTTAAATTTTTTTGGCG
* * * * * *
1168 TTGAATTATATACTTTTTCT-GAGTAT-CGTGGCAAAAAATTGAGAAAAAACTTTTCGTGTCAGT
194 TTGAATTATATA-TTTTTTTAGAGT-TGTGTGGCAAAAAAATGAGAAAAAAGTTTTCGGGTCAAT
*
1231 TTTTAGCTGAAATCATGTACA
257 TTTTAGCCGAAATCATGTACA
1252 TGGACGTATC
Statistics
Matches: 818, Mismatches: 85, Indels: 39
0.87 0.09 0.04
Matches are distributed among these distances:
318 20 0.02
319 114 0.14
320 135 0.17
321 7 0.01
323 97 0.12
324 29 0.04
325 280 0.34
326 85 0.10
327 42 0.05
328 9 0.01
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (323 bp):
AGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTTAG
CCAATTTGGATTTAAGGATTTCTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATA
AATTCGGAAAAAAATTGAAAAAACGATATTCGAAGCGTGAAAACCCCTTAAATTTTTTTGGCGTT
GAATTATATATTTTTTTAGAGTTGTGTGGCAAAAAAATGAGAAAAAAGTTTTCGGGTCAATTTTT
AGCCGAAATCATGTACAAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGGCTT
Found at i:2111 original size:19 final size:19
Alignment explanation
Indices: 2087--2127 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
2077 GTTCTGCATG
2087 ATTTTTGGCGTCGAGACTC
1 ATTTTTGGCGTCGAGACTC
2106 ATTTTTGGCGTCGAGACTC
1 ATTTTTGGCGTCGAGACTC
2125 ATT
1 ATT
2128 GAAATATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (19 bp):
ATTTTTGGCGTCGAGACTC
Found at i:3485 original size:16 final size:17
Alignment explanation
Indices: 3452--3485 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3442 AGGTGCTTTG
*
3452 ATGAAACCTTCAAGAAA
1 ATGAAACCATCAAGAAA
3469 ATGAAACCATC-AGAAA
1 ATGAAACCATCAAGAAA
3485 A
1 A
3486 GATTGAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.56, C:0.18, G:0.12, T:0.15
Consensus pattern (17 bp):
ATGAAACCATCAAGAAA
Found at i:11160 original size:3 final size:3
Alignment explanation
Indices: 11145--11176 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
11135 AACTCCAATC
*
11145 TCT TCT TCG TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
11177 ACTTACACTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.34, G:0.03, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:15056 original size:18 final size:17
Alignment explanation
Indices: 15035--15080 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
15025 TGGACAGTAC
*
15035 AACAAAAACAAAACGAAA
1 AACAAAAA-AAAACAAAA
15053 AACAAACAAAAAACAAAA
1 AACAAA-AAAAAACAAAA
15071 AACAGAAAAA
1 AACA-AAAAA
15081 TGAAATCGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.80, C:0.15, G:0.04, T:0.00
Consensus pattern (17 bp):
AACAAAAAAAAACAAAA
Found at i:21635 original size:2 final size:2
Alignment explanation
Indices: 21628--21667 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
21618 GTGTCACAGG
21628 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
21668 ATGCAATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:30566 original size:7 final size:7
Alignment explanation
Indices: 30554--30590 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
30544 TAGTCATAGT
30554 CCTTACG
1 CCTTACG
30561 CCTTACG
1 CCTTACG
30568 CCTTACG
1 CCTTACG
30575 CCTTACG
1 CCTTACG
30582 CCTTACG
1 CCTTACG
30589 CC
1 CC
30591 GCTTGGGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.14, C:0.46, G:0.14, T:0.27
Consensus pattern (7 bp):
CCTTACG
Found at i:31332 original size:26 final size:27
Alignment explanation
Indices: 31278--31332 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
31268 CTGACTCAAA
* *
31278 AAAAAACTGAACTAACTCAACTGACTC
1 AAAAAACTGAACTAACCCAACAGACTC
31305 AAAAAACTG-ACTAAACCCAACAGA-TC
1 AAAAAACTGAACT-AACCCAACAGACTC
31331 AA
1 AA
31333 TAGATCTGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.53, C:0.25, G:0.07, T:0.15
Consensus pattern (27 bp):
AAAAAACTGAACTAACCCAACAGACTC
Found at i:34353 original size:294 final size:280
Alignment explanation
Indices: 33820--34657 Score: 1071
Period size: 294 Copynumber: 3.0 Consensus size: 280
33810 TTCTCAGACC
* *
33820 CATTAACTGCAGATTCACAAAGAGCTTTTCCCCATCTTTTAAACAACTCTGTGGGGAGGATTTCT
1 CATTAACTGCAGATTCACAAAGGGCTTTTCCCCATC-TTTAAACAAATCTGTGGGGAGGATTTCT
* *
33885 TGGCAGAAGTCAGGGTCCAAAAGCCCTTGACAGTTTGCTTCTGGACAAGTGATGCGGGTTTCGTT
65 CGGCAGAAGTCAGGGTCCAAAAGCCCTTGACAGTTTGCTTCTGGACAAGTGATGTGGGTTTCGTT
*
33950 ATTATCAAGTTTGGATGTGATGTACTTGACAGTGCAATCAATGCAGTAAAAGTGGGAGCAACCAT
130 ATTATCAAGTTTGGATGTGATGTACTTGACAGTGCAATCAATGCAGTAAAAGTGGGAGCAACCTT
* * * * *
34015 TGACGCCAAAAGAGTCATCCAGGGGTCTTGACTCAACACAGATTTCACACACATAATCATCATCA
195 TGACGCCAAAAGAGTCATCCAGGGGCCTTGACTCAACGCAGATTTCACAGACATAATTATCATCG
34080 ATTTCATATGTAGCAAAAAAATCAT-CATCGATTT
260 ATTTCATAT-T--------AA-C-TGCA--GA-TT
* * *
34114 CATTAACTGCAGATTCACAAAGGGCATTCCCCCATCTTTCAAACAAATCTACT-GGGAGGATTTC
1 CATTAACTGCAGATTCACAAAGGGCTTTTCCCCATCTTT-AAACAAATCT-GTGGGGAGGATTTC
*
34178 TCGGCAGAAGTCAGGGTCCAAAAGCCCTTGACAGTTTGCCTCTGGACAAGTGATGTGGGTTTCGT
64 TCGGCAGAAGTCAGGGTCCAAAAGCCCTTGACAGTTTGCTTCTGGACAAGTGATGTGGGTTTCGT
* * * * * *
34243 TATTATGAAGTTTGTATGTGATGTAGTTAACAGTGCAATCGATGCAGTAAAAGTGAGAGCAACCT
129 TATTATCAAGTTTGGATGTGATGTACTTGACAGTGCAATCAATGCAGTAAAAGTGGGAGCAACCT
* *
34308 TTGACGCCAAAAGAGTCATCCAGGGGCCTTGATTTAACGCAGATTTCACAGACATAATTATCATC
194 TTGACGCCAAAAGAGTCATCCAGGGGCCTTGACTCAACGCAGATTTCACAGACATAATTATCATC
34373 GATTTC--ATTAACTGCAGATT
259 GATTTCATATTAACTGCAGATT
* ** ** *** * * *
34393 CA-CAA--GGGGATTTTCCCTGGGCTTTTTCCCATCTGTTGAACAAACCTGTGGGGAGGATTTCT
1 CATTAACTGCAGATTCACAAAGGGCTTTTCCCCATCT-TTAAACAAATCTGTGGGGAGGATTTCT
* * *
34455 CGGCAGAATTGAGGGTCCAAAAGCCCTCGACAGTTTGCTTCTGGACAAGTGATGTGGGTTTCGTT
65 CGGCAGAAGTCAGGGTCCAAAAGCCCTTGACAGTTTGCTTCTGGACAAGTGATGTGGGTTTCGTT
* * **
34520 TTTATCAAGTTTGGATCTGATGTACTTGACAGTGCAATCAATGCAGT-AAAGATGGGAGCAATTT
130 ATTATCAAGTTTGGATGTGATGTACTTGACAGTGCAATCAATGCAGTAAAAG-TGGGAGCAACCT
* *
34584 TTGACGCCAAAAGAGTTATCCAGGGGCCTTGACTCAAAGCAGATTTCACAGACATAATTATCATC
194 TTGACGCCAAAAGAGTCATCCAGGGGCCTTGACTCAACGCAGATTTCACAGACATAATTATCATC
34649 GATTTCATA
259 GATTTCATA
34658 ATTATTCAAT
Statistics
Matches: 482, Mismatches: 54, Indels: 32
0.85 0.10 0.06
Matches are distributed among these distances:
275 5 0.01
276 216 0.45
277 2 0.00
278 3 0.01
279 4 0.01
280 2 0.00
281 1 0.00
282 3 0.01
283 2 0.00
291 1 0.00
292 2 0.00
293 3 0.01
294 237 0.49
295 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (280 bp):
CATTAACTGCAGATTCACAAAGGGCTTTTCCCCATCTTTAAACAAATCTGTGGGGAGGATTTCTC
GGCAGAAGTCAGGGTCCAAAAGCCCTTGACAGTTTGCTTCTGGACAAGTGATGTGGGTTTCGTTA
TTATCAAGTTTGGATGTGATGTACTTGACAGTGCAATCAATGCAGTAAAAGTGGGAGCAACCTTT
GACGCCAAAAGAGTCATCCAGGGGCCTTGACTCAACGCAGATTTCACAGACATAATTATCATCGA
TTTCATATTAACTGCAGATT
Found at i:34709 original size:3 final size:3
Alignment explanation
Indices: 34701--34727 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
34691 CCAGTAATTC
34701 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
34728 ATATGCGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:34811 original size:15 final size:15
Alignment explanation
Indices: 34791--34822 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
34781 TTGATGATGT
34791 TCAGAAGCTTACCCA
1 TCAGAAGCTTACCCA
34806 TCAGAAGCTTACCCA
1 TCAGAAGCTTACCCA
34821 TC
1 TC
34823 TTCTTCTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.34, G:0.12, T:0.22
Consensus pattern (15 bp):
TCAGAAGCTTACCCA
Found at i:34856 original size:21 final size:21
Alignment explanation
Indices: 34832--34875 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
34822 CTTCTTCTTG
34832 AATTTGTTGGAAGAAATATGA
1 AATTTGTTGGAAGAAATATGA
34853 AATTTGTTGGAAGAAATATGA
1 AATTTGTTGGAAGAAATATGA
34874 AA
1 AA
34876 AGCTGCGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (21 bp):
AATTTGTTGGAAGAAATATGA
Found at i:35232 original size:53 final size:53
Alignment explanation
Indices: 35168--35273 Score: 153
Period size: 53 Copynumber: 2.0 Consensus size: 53
35158 ATAGTAGTTT
*
35168 TTATTTTAGTTTTA-TTTGTGAAAACCGTGAGATAAACTCT-GGTTCACATTATA
1 TTATTTTAGTTTTATTTTATGAAAACCGTGAGA-AAACT-TAGGTTCACATTATA
**
35221 TTATTTTAGTTTTATTTTATGAAAGTCGTGAGAAAACTTAGGTTCACATTATA
1 TTATTTTAGTTTTATTTTATGAAAACCGTGAGAAAACTTAGGTTCACATTATA
35274 ATTAGTATAG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
52 1 0.02
53 32 0.67
54 15 0.31
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.44
Consensus pattern (53 bp):
TTATTTTAGTTTTATTTTATGAAAACCGTGAGAAAACTTAGGTTCACATTATA
Found at i:35370 original size:17 final size:17
Alignment explanation
Indices: 35321--35370 Score: 75
Period size: 18 Copynumber: 2.9 Consensus size: 17
35311 AATGGATAGC
35321 AAAAACAA-TTGATTGT
1 AAAAACAACTTGATTGT
*
35337 AAAAACAACTTCAATTGT
1 AAAAACAACTT-GATTGT
35355 AAAAACAACTTGATTG
1 AAAAACAACTTGATTG
35371 AATAAGGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 8 0.27
17 6 0.20
18 16 0.53
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (17 bp):
AAAAACAACTTGATTGT
Found at i:35660 original size:29 final size:29
Alignment explanation
Indices: 35618--35676 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
35608 TTCAACATAA
35618 GGTTTAATATAAAGACTAATTTGATTTTT
1 GGTTTAATATAAAGACTAATTTGATTTTT
35647 GGTTTAATATAAAGACTAATTTGATTTTT
1 GGTTTAATATAAAGACTAATTTGATTTTT
35676 G
1 G
35677 TGATAACAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.03, G:0.15, T:0.47
Consensus pattern (29 bp):
GGTTTAATATAAAGACTAATTTGATTTTT
Done.