Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008237.1 Corchorus capsularis cultivar CVL-1 contig08258, 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: 39380
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:1278 original size:2 final size:2
Alignment explanation
Indices: 1271--1304 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1261 TCTCATAAAC
1271 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1305 GTCATTCTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4586 original size:97 final size:97
Alignment explanation
Indices: 4420--4602 Score: 330
Period size: 97 Copynumber: 1.9 Consensus size: 97
4410 TCCGTATCTT
* **
4420 ATTTTATTTACAATTGGGCCAAGTTGCAATGTACGATGAGAATCAAGAGTCTAGGATGTTATGGC
1 ATTTTATTTACAATTGGGCCAAGTTGCAATGTACGATCAGAATCAAGAGTCTAGGATGTTACAGC
*
4485 AGAAATCTAAACCTAGTAGAGGTGGCAAAATG
66 AGAAATCAAAACCTAGTAGAGGTGGCAAAATG
4517 ATTTTATTTACAATTGGGCCAAGTTGCAATGTACGATCAGAATCAAGAGTCTAGGATGTTACAGC
1 ATTTTATTTACAATTGGGCCAAGTTGCAATGTACGATCAGAATCAAGAGTCTAGGATGTTACAGC
4582 AGAAATCAAAACCTAGTAGAG
66 AGAAATCAAAACCTAGTAGAG
4603 TCGCCAAAAT
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
97 82 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (97 bp):
ATTTTATTTACAATTGGGCCAAGTTGCAATGTACGATCAGAATCAAGAGTCTAGGATGTTACAGC
AGAAATCAAAACCTAGTAGAGGTGGCAAAATG
Found at i:5852 original size:13 final size:13
Alignment explanation
Indices: 5834--5864 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5824 ATATATGTCT
5834 AATTTTAGACTCA
1 AATTTTAGACTCA
*
5847 AATTTTAGAGTCA
1 AATTTTAGACTCA
5860 AATTT
1 AATTT
5865 CCTAATCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.42
Consensus pattern (13 bp):
AATTTTAGACTCA
Found at i:25924 original size:19 final size:19
Alignment explanation
Indices: 25900--25945 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
25890 TGGAAACCGG
*
25900 AAAGTGAATGTTGTATTTT
1 AAAGTGAAAGTTGTATTTT
25919 AAAGTGAAAGTTGTATTTT
1 AAAGTGAAAGTTGTATTTT
*
25938 AAATTGAA
1 AAAGTGAA
25946 GAATATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (19 bp):
AAAGTGAAAGTTGTATTTT
Found at i:26713 original size:32 final size:33
Alignment explanation
Indices: 26677--26745 Score: 113
Period size: 35 Copynumber: 2.1 Consensus size: 33
26667 TCCTTCTAGA
26677 AAGTCCTGCAATTTTC-TTCTTCTTCCTTGAGG
1 AAGTCCTGCAATTTTCTTTCTTCTTCCTTGAGG
26709 AAGTCCTGCAATTTTCTTATTCTTCTTCCTTGAGG
1 AAGTCCTGCAATTTTC-T-TTCTTCTTCCTTGAGG
26744 AA
1 AA
26746 ATCAAAACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 16 0.47
35 18 0.53
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.43
Consensus pattern (33 bp):
AAGTCCTGCAATTTTCTTTCTTCTTCCTTGAGG
Found at i:27326 original size:25 final size:25
Alignment explanation
Indices: 27298--27346 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
27288 TTCTCATTAG
*
27298 GTATGGGATTGTTCTTCTTACCTTC
1 GTATGGGATTGTTCTTCTCACCTTC
27323 GTATGGGATTGTTCTTCTCACCTT
1 GTATGGGATTGTTCTTCTCACCTT
27347 ATGTAGATTT
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:0.20, G:0.20, T:0.47
Consensus pattern (25 bp):
GTATGGGATTGTTCTTCTCACCTTC
Found at i:27561 original size:22 final size:22
Alignment explanation
Indices: 27515--27562 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
27505 GGAGTGTTGG
* * *
27515 TGGTGGCTGGTGGGGCGGAGTA
1 TGGTGGCAGGTGCGGCGGAGAA
*
27537 TGGTGGCAGGTGCGGCGGTGAA
1 TGGTGGCAGGTGCGGCGGAGAA
27559 TGGT
1 TGGT
27563 TTTTCATGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.10, C:0.10, G:0.56, T:0.23
Consensus pattern (22 bp):
TGGTGGCAGGTGCGGCGGAGAA
Found at i:31742 original size:440 final size:439
Alignment explanation
Indices: 30920--31810 Score: 1236
Period size: 440 Copynumber: 2.0 Consensus size: 439
30910 TCTCGTTAAA
* *
30920 AAAATTATATGATATTAAATAGACCATCAATCGAAACCACAAAATTTCGGAAACATCTTTTAGAA
1 AAAATTATATGATATTAAATAGACCAGCAATCAAAACCACAAAATTTCGGAAACATCTTTTAGAA
* * * *
30985 TTGAAACATAAAAATTAGCTTTTGAGTCTTTAATGAAAGCTGTAGCTAGATCATGAAATTACCTT
66 TTAAAACATAAAAATTAGCTTTTCAGTCCTTAATGAAA-C-GTAGCTAGATCATCAAATTACCTT
* * * * ** * *
31050 TTAATAGACAACTGAATTACTTTAATTGGACAAAAAGAACAACGAAAAAAAAAGCAGAAGCGTTA
129 TTAATAAACAACTGAATCACCTTAATCGGACAAAAAGAACAAAAAAAAAAAAAACAGAAGCATTA
* * * * *
31115 AATCGAATAAGATAGAATTTGTAAAGGACTAAAATAGTATTAAGTAGAAAAGTATGATAGTCATT
194 AATCGAATAAGATAGAATTAGTAAAGGACTAAAATAGTATAAAATAGAAAAATATGAGAGTCATT
* * *
31180 TGATAAATAATCCAAATAAGAAAATGCTTGTTGATGGAGATCTTGAGACATCAAATTTCCTTTTG
259 TGATAAATAATCCAAATAAGAAAATGCTTGTTGATGGAGATCTTGAAACATAAAAATTCCTTTTG
* * * *
31245 GACCCTTCACGAAACTCATAGATCTAATTTAGCTTTCCGGTCCTTCATGAAAGTCGTAGATCATG
324 AACCCTTCACGAAACTCATAGATCAAATTTAGCTTTCAGGTCATTCATGAAAGTCGTAGATCATG
* *
31310 CAATAACCTTTTAACCGACACTTGAATAACTTTAATCGGATATGTGGATCG
389 CAATAACCTTTTAACCGACACTTAAATAACTTTAATCGGACATGTGGATCG
* * * *
31361 AAAATTATATGATATTAAATAGACCGGCAATCAAAACCACCAAATTTTGGAAGTAC-T-TTTTTG
1 AAAATTATATGATATTAAATAGACCAGCAATCAAAACCACAAAATTTCGGAA--ACATCTTTTAG
* *
31424 AATTAAAACATAAAAATT-GACTTTTCAGTCCTTCATGAAA-GTCG-TAGATCATCAAATTACCT
64 AATTAAAACATAAAAATTAG-CTTTTCAGTCCTTAATGAAACGTAGCTAGATCATCAAATTACCT
* * * **
31486 TTTAATAAACACCTGAATCACCTTAATCGGACAAATATAACAAAAATAATAAAAATAACTTAAGC
128 TTTAATAAACAACTGAATCACCTTAATCGGACAAAAAGAACAAAAA-AA-AAAAA-AACAGAAGC
* * *
31551 ATTAAATCGATTAAGATAGAATTAGTAAAGGACT-AAGTAGTATAAAATAGAAAAATATGAGGGT
190 ATTAAATCGAATAAGATAGAATTAGTAAAGGACTAAAATAGTATAAAATAGAAAAATATGAGAGT
*
31615 CATTTGATAAATAATCCAAATAAGAAAATGTTTGTTGATGGAGATCTTGAAACATAAAAATTCCT
255 CATTTGATAAATAATCCAAATAAGAAAATGCTTGTTGATGGAGATCTTGAAACATAAAAATTCC-
*
31680 TTTTGAACCCTTCACGAAACTCGTAGATCAAATTTAGCTTTCAGGTCATTCATGAAAGTCGTAGA
319 TTTTGAACCCTTCACGAAACTCATAGATCAAATTTAGCTTTCAGGTCATTCATGAAAGTCGTAGA
* * *
31745 TCATGCAATAGCCTTTTAACCGACACTTAAATAACTTTAATCGGACATTTGGATTG
384 TCATGCAATAACCTTTTAACCGACACTTAAATAACTTTAATCGGACATGTGGATCG
31801 AAAATTATAT
1 AAAATTATAT
31811 ATACTATATG
Statistics
Matches: 396, Mismatches: 47, Indels: 15
0.86 0.10 0.03
Matches are distributed among these distances:
437 54 0.14
438 5 0.01
439 89 0.22
440 159 0.40
441 86 0.22
442 1 0.00
443 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (439 bp):
AAAATTATATGATATTAAATAGACCAGCAATCAAAACCACAAAATTTCGGAAACATCTTTTAGAA
TTAAAACATAAAAATTAGCTTTTCAGTCCTTAATGAAACGTAGCTAGATCATCAAATTACCTTTT
AATAAACAACTGAATCACCTTAATCGGACAAAAAGAACAAAAAAAAAAAAAACAGAAGCATTAAA
TCGAATAAGATAGAATTAGTAAAGGACTAAAATAGTATAAAATAGAAAAATATGAGAGTCATTTG
ATAAATAATCCAAATAAGAAAATGCTTGTTGATGGAGATCTTGAAACATAAAAATTCCTTTTGAA
CCCTTCACGAAACTCATAGATCAAATTTAGCTTTCAGGTCATTCATGAAAGTCGTAGATCATGCA
ATAACCTTTTAACCGACACTTAAATAACTTTAATCGGACATGTGGATCG
Found at i:32283 original size:27 final size:27
Alignment explanation
Indices: 32247--32310 Score: 103
Period size: 27 Copynumber: 2.3 Consensus size: 27
32237 ATTTCTGGAA
32247 AACAAGGGAAATG-GACAATTAAAAAGG
1 AACAAGGGAAA-GAGACAATTAAAAAGG
32274 AACAAGGGAAAGAGACAATTAAAAAGG
1 AACAAGGGAAAGAGACAATTAAAAAGG
32301 AACAGAGGGA
1 AACA-AGGGA
32311 GTATTATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
26 1 0.03
27 29 0.83
28 5 0.14
ACGTcount: A:0.56, C:0.08, G:0.28, T:0.08
Consensus pattern (27 bp):
AACAAGGGAAAGAGACAATTAAAAAGG
Found at i:36651 original size:29 final size:29
Alignment explanation
Indices: 36619--36680 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
36609 CTTCGCTTGT
*
36619 TCCATAAACACCA-CCGCTGCTTCACCTTC
1 TCCACAAACA-CAGCCGCTGCTTCACCTTC
** *
36648 TCCACAAACACAGCCTTTGCTTCGCCTTC
1 TCCACAAACACAGCCGCTGCTTCACCTTC
36677 TCCA
1 TCCA
36681 AAAAATCGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 2 0.07
29 26 0.93
ACGTcount: A:0.23, C:0.44, G:0.08, T:0.26
Consensus pattern (29 bp):
TCCACAAACACAGCCGCTGCTTCACCTTC
Done.