Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011809.1 Corchorus capsularis cultivar CVL-1 contig11830, 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: 35123
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2366 original size:332 final size:332
Alignment explanation
Indices: 731--3295 Score: 3253
Period size: 332 Copynumber: 7.8 Consensus size: 332
721 AATATGGTTT
* * *
731 ATTTCTGATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGTGGT
1 ATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
** *
796 TGAGATTTGATTGGATGAATATAGATATTTCCTGGAGTGTCGGCGCCAAAAATCATGTAAAACTG
66 TGAGATTTGATTGGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGTAAAACTG
* *
861 AGTC-GAGGCCCTGGAACGCGTTTTCAACCAGAAACCGTGATGGTTTCTACACGATTTCGACCAA
131 AGTCGGA-GCCCTGGAACGCGTTTTCAACCAGAAACCGTGATGGTTTGTACACGATTTCGGCCAA
*
925 AATTTTGCAAGAAATTGACCCGAAATGTTTTTCCTCAATTTTTGACTAAAATGCTCAT-AAAAAT
195 AATTTTGCAAAAAATTGACCCGAAATGTTTTTCCTCAATTTTTGACTAAAATGCTCATAAAAAAT
* * * *
989 ATAGAGTTCAACATCATAAATATTTATGGGCATTTCATACTTCAAATATGGTTTATCCTCCTTTT
260 ATAGAGTTCAACGTCATAAAGATTTAT-GGCTTTTCATGCTTCAAATATGGTTTATCCTCCTTTT
*
1054 TTCGAATTA
324 TTCAAATTA
* * * *
1063 ATTTCCGATTAAATCGAAACATGATTAAGATGCTCGTAACAACAAATCCTTAAATCCAAAGTGGC
1 ATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* * * * * *
1128 TGAGAATTGATTGGATGAATATAGATGTTTCAAGGAGTCTTGGC-ACAATAAACCATGCAAAA-T
66 TGAGATTTGATTGGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAA-AAATCATGTAAAACT
* * ** * *
1191 GAGT-TG-GCGCTGCAGAACGCGTTTTCAGTCAGAAACCGTGA-----TATACACGATTTCAGCC
130 GAGTCGGAGCCCTG--GAACGCGTTTTCAACCAGAAACCGTGATGGTTTGTACACGATTTCGGCC
* * * * * *
1249 AAAATTTTGC-AAAAATTAACTCGAAATATATTTCCTCAATTTTTGACCAAAATGATCATAAAAA
193 AAAATTTTGCAAAAAATTGACCCGAAATGTTTTTCCTCAATTTTTGACTAAAATGCTCATAAAAA
* * *
1313 ATATAGAATTCAACGTCATAATGATTTATTGGCTTTTCAGGCTTCAAATATGGTTTAATACCT--
258 ATATAGAGTTCAACGTCATAAAGATTTA-TGGCTTTTCATGCTTCAAATATGGTTT-AT-CCTCC
1376 TTTTTTCAAATTA
320 TTTTTTCAAATTA
* *
1389 ATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAAAACATATCCTTAAATCCAAAGTGGC
1 ATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* * * * * *
1454 TGAGATTTGGTTGGATGAATATAGATATTTCAAGGAGTCTTGACACAAAAAATCATG-CAAACTG
66 TGAGATTTGATTGGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGTAAAACTG
* * * ** * *
1518 AGCCGGTGCTGC-GGAACGCGTTTTCAGTCAGAAACAGTGA-----TGTACACGATTTCAGCCAA
131 AGTCGGAGC-CCTGGAACGCGTTTTCAACCAGAAACCGTGATGGTTTGTACACGATTTCGGCCAA
* * * ** * *
1577 AATTTTGC-AAAAATTAACCCGAAATATATTTCCTCAATTTTTGAAAAAAATGATTATAAAAAAT
195 AATTTTGCAAAAAATTGACCCGAAATGTTTTTCCTCAATTTTTGACTAAAATGCTCATAAAAAAT
* ** * * * * *
1641 ATAGAATTCAACGTCATAATCATTTATTTGCTTTTTAGGCTTCAAATATGGTTTA-ACACCTTTT
260 ATAGAGTTCAACGTCATAAAGATTTA-TGGCTTTTCATGCTTCAAATATGGTTTATCCTCCTTTT
1705 TATCAAATTA
324 T-TCAAATTA
* * *
1715 ATTTCTGATTAAATCGAAACATGATTCTGATGCTCGTAAAAACAAATCCGTAAATCCAAAGTGGC
1 ATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* ** *
1780 TGAGATTTGATTGGATGAATATAGATATTTCAAGGAGTCTTGATGCCAAAAATCATTTAAAACTG
66 TGAGATTTGATTGGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGTAAAACTG
* * * * ** *
1845 AGTCGG-GGCCTCGGAACCCGTTTTCAGCTAGAAACCGTGAAACG--T-T-CACGATTTCGCCCA
131 AGTCGGAGCCCT-GGAACGCGTTTTCAACCAGAAACCGTG-ATGGTTTGTACACGATTTCGGCCA
* * * * * *
1905 AAATTTTGCAAAAAATAGACTCGAAATTTTTTTCCTCAATTTTTGGCAAAAATGGTCATAAAAAA
194 AAATTTTGCAAAAAATTGACCCGAAATGTTTTTCCTCAATTTTTGACTAAAATGCTCATAAAAAA
*
1970 TATAGAGTTCAACGTCATAAAGATTTATAGGCTTTTCATGCTTCAAATATGGTTTATGCTCCTTT
259 TATAGAGTTCAACGTCATAAAGATTTAT-GGCTTTTCATGCTTCAAATATGGTTTATCCTCCTTT
*
2035 TTTCTAATTA
323 TTTCAAATTA
* * * * * *
2045 ATTTCCGGTTTAATCGAAACATGATTCAGATGCTCGAAAAAACAGATTAC-TAAATCCAATGTGG
1 ATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAAAACA-AATCCTTAAATCCAATGTGG
* *
2109 GTGAGATTTGATTGGATGAATATAGATATTTC-TGGAGTCTCGGCGCCAAAAATCATGTAAAACT
65 CTGAGATTTGATTGGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGTAAAACT
* **
2173 GTGTCGGAGCCCTGGAACGCGTTTTCAACCAGAAACCGTGATGGTTTGTACAAAATTTCGGCCAA
130 GAGTCGGAGCCCTGGAACGCGTTTTCAACCAGAAACCGTGATGGTTTGTACACGATTTCGGCCAA
2238 AATTTTGCAAAAAATTGACCCGAAATG-TTTTCC-CAAGATTTTTGACTAAAATGCTCATAAAAA
195 AATTTTGCAAAAAATTGACCCGAAATGTTTTTCCTC-A-ATTTTTGACTAAAATGCTCATAAAAA
*
2301 ATATAGAGTTCAACGTCATAAAGATTTATGGCCTTTTCATGCTTCAAATATTGTTTATCCTCCTT
258 ATATAGAGTTCAACGTCATAAAGATTTATGG-CTTTTCATGCTTCAAATATGGTTTATCCTCCTT
*
2366 TTTTCGAATTA
322 TTTTCAAATTA
2377 ATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
1 ATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* * * * *
2442 TGAGATTTGATTGGATGAATATAGATATATCCAGGACTCTCGGCGCCAAAAATCAGGTAAAATTG
66 TGAGATTTGATTGGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGTAAAACTG
* * * * *
2507 AGCCGGGGCCCTGGAACGCGTTTTCGACCAGAAACCGTGATGGTTTGTACACAATTTCGGTCAAA
131 AGTCGGAGCCCTGGAACGCGTTTTCAACCAGAAACCGTGATGGTTTGTACACGATTTCGGCCAAA
2572 ATTTTGCAAAAAATTGACCCGAAATGTTTTTCCTCAATTTTTGACTAAAATGCTCATAAAAAATA
196 ATTTTGCAAAAAATTGACCCGAAATGTTTTTCCTCAATTTTTGACTAAAATGCTCATAAAAAATA
* *
2637 TAGAGTTCAACATCATAAATATTTATGGGCTTTTCATGCTTCAAATATGG-TTATCCTCCTTTTT
261 TAGAGTTCAACGTCATAAAGATTTAT-GGCTTTTCATGCTTCAAATATGGTTTATCCTCCTTTTT
*
2701 TCGAATTA
325 TCAAATTA
*
2709 ATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
1 ATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* *
2774 TGAGATTTGATTGGATAAATATAGATATTTCCAA-GAGTCTC-GCGCCAAAAATCAGGTAAAACT
66 TGAGATTTGATTGGATGAATATAGATATTT-CAAGGAGTCTCGGCGCCAAAAATCATGTAAAACT
* * ** * * *
2837 GAGCCGGGGCCCTGGAACGCGTTTTCGTCTC-GAAACCGTGATGGTTTGTAGA-GAAATTCGCCC
130 GAGTCGGAGCCCTGGAACGCGTTTTCAAC-CAGAAACCGTGATGGTTTGTACACG-ATTTCGGCC
* *
2900 AAAATATTGCAAAAAATTGACCGGAAATGTTTTTCCTCAATTTTTGACTAAAATGCTCATAAAAA
193 AAAATTTTGCAAAAAATTGACCCGAAATGTTTTTCCTCAATTTTTGACTAAAATGCTCATAAAAA
* * * * **
2965 ATATAGTGTTCAACGTCATAAAGATTTATGGGCTTTTCATGTTTCAATTATGGTTTTTCCTATTT
258 ATATAGAGTTCAACGTCATAAAGATTTAT-GGCTTTTCATGCTTCAAATATGGTTTATCCTCCTT
3030 TTTTCAAATTA
322 TTTTCAAATTA
* * * *
3041 ATTTCTGATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTAGT
1 ATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* * ** *
3106 TGTGATTTGATTGGATTAATATAGATATTTCAATAAGTCTCGGCGCCAAAAATTATGTAAAACTG
66 TGAGATTTGATTGGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGTAAAACTG
* * * * * * *
3171 AG-CTGAGACCCCGGAACGCGTTTTTAAACAGAAACCGTGATGGTTTGTATACGATTTCAGCTAA
131 AGTCGGAG-CCCTGGAACGCGTTTTCAACCAGAAACCGTGATGGTTTGTACACGATTTCGGCCAA
* * * *
3235 AATTTTACAAAAAATTGACCCGAAATGTTTTTCCTTAATTTTTGATTAAAATACTCATAAA
195 AATTTTGCAAAAAATTGACCCGAAATGTTTTTCCTCAATTTTTGACTAAAATGCTCATAAA
3296 TTTTTTATTT
Statistics
Matches: 1981, Mismatches: 203, Indels: 97
0.87 0.09 0.04
Matches are distributed among these distances:
323 1 0.00
325 52 0.03
326 477 0.24
327 40 0.02
328 9 0.00
329 86 0.04
330 191 0.10
331 248 0.13
332 557 0.28
333 309 0.16
334 10 0.01
335 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (332 bp):
ATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
TGAGATTTGATTGGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGTAAAACTG
AGTCGGAGCCCTGGAACGCGTTTTCAACCAGAAACCGTGATGGTTTGTACACGATTTCGGCCAAA
ATTTTGCAAAAAATTGACCCGAAATGTTTTTCCTCAATTTTTGACTAAAATGCTCATAAAAAATA
TAGAGTTCAACGTCATAAAGATTTATGGCTTTTCATGCTTCAAATATGGTTTATCCTCCTTTTTT
CAAATTA
Found at i:6282 original size:22 final size:22
Alignment explanation
Indices: 6247--6292 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
6237 TTAACAATTG
* *
6247 TTGAAGAATAAAATTCCACTAC
1 TTGAAAAATAAAATACCACTAC
* *
6269 TTGAAAAATGAAATACTACTAC
1 TTGAAAAATAAAATACCACTAC
6291 TT
1 TT
6293 AGATTTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.30
Consensus pattern (22 bp):
TTGAAAAATAAAATACCACTAC
Found at i:11707 original size:34 final size:34
Alignment explanation
Indices: 11664--11731 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
11654 TACTAGTATC
11664 ATTTCCATTCACTACATTAAGTCAAATTTGAAAT
1 ATTTCCATTCACTACATTAAGTCAAATTTGAAAT
11698 ATTTCCATTCACTACATTAAGTCAAATTTGAAAT
1 ATTTCCATTCACTACATTAAGTCAAATTTGAAAT
11732 TAAAATGCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (34 bp):
ATTTCCATTCACTACATTAAGTCAAATTTGAAAT
Found at i:20904 original size:2 final size:2
Alignment explanation
Indices: 20897--20927 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20887 TAATATCTTT
20897 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20928 TCATATAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25233 original size:37 final size:39
Alignment explanation
Indices: 25157--25236 Score: 103
Period size: 37 Copynumber: 2.1 Consensus size: 39
25147 ACACACACAT
25157 ATATATATAATATATTATATATTAAAATAAAATTCTTAC
1 ATATATATAATATATTATATATTAAAATAAAATTCTTAC
* * *
25196 ATATATAT-ATATATTCT-TATT-TAATAAAATATTTTAC
1 ATATATATAATATATTATATATTAAAATAAAAT-TCTTAC
25233 ATAT
1 ATAT
25237 TCAAATAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 8 0.22
37 13 0.35
38 8 0.22
39 8 0.22
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (39 bp):
ATATATATAATATATTATATATTAAAATAAAATTCTTAC
Found at i:25440 original size:18 final size:18
Alignment explanation
Indices: 25417--25451 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25407 CCGACTTCCT
*
25417 AAACCGAATCACCCGACA
1 AAACCGAATCAACCGACA
*
25435 AAACCGACTCAACCGAC
1 AAACCGAATCAACCGAC
25452 TCATTTCACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.40, G:0.11, T:0.06
Consensus pattern (18 bp):
AAACCGAATCAACCGACA
Found at i:26759 original size:34 final size:34
Alignment explanation
Indices: 26716--26781 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
26706 GAAAGCTATT
26716 TGTAATGCCCAATATGATAACTACCATACTTTTA
1 TGTAATGCCCAATATGATAACTACCATACTTTTA
*
26750 TGTAATGCCCAATATGATAAGTACCATACTTT
1 TGTAATGCCCAATATGATAACTACCATACTTT
26782 ATCAATACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.35
Consensus pattern (34 bp):
TGTAATGCCCAATATGATAACTACCATACTTTTA
Found at i:27267 original size:23 final size:23
Alignment explanation
Indices: 27212--27284 Score: 94
Period size: 23 Copynumber: 3.1 Consensus size: 23
27202 GTACATTCCA
*
27212 AACCCTAATAGCTACCTC-CTCACT
1 AACCCTAATAGTTACCTCAC-C-CT
27236 GAACCCTAATAGTTACCTCACCCT
1 -AACCCTAATAGTTACCTCACCCT
*
27260 AACCCTAATAGTTAACTCACCCT
1 AACCCTAATAGTTACCTCACCCT
27283 AA
1 AA
27285 TAGTTGACTC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
23 24 0.53
24 2 0.04
25 18 0.40
26 1 0.02
ACGTcount: A:0.33, C:0.37, G:0.05, T:0.25
Consensus pattern (23 bp):
AACCCTAATAGTTACCTCACCCT
Found at i:27294 original size:17 final size:17
Alignment explanation
Indices: 27261--27296 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
27251 CCTCACCCTA
27261 ACCCTAATAGTTAACTC
1 ACCCTAATAGTTAACTC
*
27278 ACCCTAATAGTTGACTC
1 ACCCTAATAGTTAACTC
27295 AC
1 AC
27297 TGAAATGGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.31, G:0.08, T:0.28
Consensus pattern (17 bp):
ACCCTAATAGTTAACTC
Found at i:27763 original size:23 final size:23
Alignment explanation
Indices: 27720--27764 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
27710 GTTCGATAAA
* *
27720 TGTTCATTTATTAGCTTGTTTAT
1 TGTTCATTTAATAGCTCGTTTAT
27743 TGTTCATTTAAATA-CTCGTTTA
1 TGTTCATTT-AATAGCTCGTTTA
27765 AAATTCGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (23 bp):
TGTTCATTTAATAGCTCGTTTAT
Done.