Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012863.1 Corchorus capsularis cultivar CVL-1 contig12884, 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: 86419
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:140 original size:21 final size:20
Alignment explanation
Indices: 98--141 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
88 TCTTGTAATC
*
98 TAAAATTACTAAAAAAGTTA
1 TAAAATTACTAAAAAAGCTA
* *
118 TAAAAGTTATTAAAATAGCTA
1 TAAAA-TTACTAAAAAAGCTA
139 TAA
1 TAA
142 TGCTTTTCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
TAAAATTACTAAAAAAGCTA
Found at i:1457 original size:343 final size:331
Alignment explanation
Indices: 817--1468 Score: 801
Period size: 343 Copynumber: 1.9 Consensus size: 331
807 TGGTTATTGA
* *
817 TTTTCTTATCTAAGATTACTTAAAGTTATAAAGGTTATGGAAAACATTATAGTTCTATCTACATT
1 TTTTCTTACCTAAGATTACTTAAAGTTATAAAGGTTATGGAAAACATTATAGTACTATCTACATT
* * * **
882 CAAGTAATCTTACATCCTTATTAATTTTAGTAACTTTTAATCAATAATGGAAGTTACCAATTTTA
66 CAAATAACCTTACATCCTTATTAAGTTTAGTAACTTTTAATCAATAATAAAAGTTACCAATTTTA
* * * *
947 TTACTTAAGTGATCTACTGAGACACCTATAAAAGTTATTAAAATTGTATTACCAATCCTTAATAA
131 TTACTTAAGT-ATCTACTAAAAAACCTATAAAAGTAATTAAAATTGTATTACCAATCCTTAATAA
* * *
1012 CATTAGTAAACTTTCATCAATGGTAATGATTTACCTTTTTTCTCTCAAAAGTTACTGAAAAACCT
195 CATGAGTAAACTTTCATCAATGGTAATGATTTACCTTGTTTCTCTCAAAAGTTACTAAAAAACCT
** * * ** *
1077 ATAATTTTTATAAAAAATGTATGGTACCATCAACTAATTCAATGACCTTATATTATAAAGGTAAA
260 ATAATGATCATAAAAAATGTATAGTACCAAAAACTAATTCAATAACCTTATATTATAAAGGTAAA
1142 GTACTGC
325 GTACTGC
* *
1149 TTTTCTTACCTAAGATTACTTAAAAGGTTATAAAGGTTAT-GAAAAGCTTTATAGTACTATCTAG
1 TTTTCTTACCTAAGATTACTT-AAA-GTTATAAAGGTTATGGAAAA-CATTATAGTACTATCTAC
* * * *
1213 ATTGAAATAACCTTACACGTTCTTATTAAGTTTAGTAACTTTTCATCATTAATAAAAGTTACCAA
63 ATTCAAATAACCTTACA--TCCTTATTAAGTTTAGTAACTTTTAATCAATAATAAAAGTTACCAA
*
1278 TTTTATTACTTAAGT-T-TACTAAAAAAGCTATAAAAGTAAATTAAAATTGTATTTACTAATCCT
126 TTTTATTACTTAAGTATCTACTAAAAAACCTATAAAAGT-AATTAAAATTGTA--T--T-A-CC-
* *
1341 TACATTCTTAATAACATGATTAAACTTTCATCAATGGTGAAT-ATTTACCCTTGTTT-TCTCAAA
183 -A-ATCCTTAATAACATGAGTAAACTTTCATCAATGGT-AATGATTTA-CCTTGTTTCTCTCAAA
* * * *
1404 AGTTATTAAAAAATCTATAATGATCATAAAAGATGTATAGTACTAAAAACTAATTCAATAACCTT
244 AGTTACTAAAAAACCTATAATGATCATAAAAAATGTATAGTACCAAAAACTAATTCAATAACCTT
1469 TCATTTTTTG
Statistics
Matches: 269, Mismatches: 34, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
332 20 0.07
333 25 0.09
334 56 0.21
336 56 0.21
338 1 0.00
339 1 0.00
340 2 0.01
342 1 0.00
343 97 0.36
344 10 0.04
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.38
Consensus pattern (331 bp):
TTTTCTTACCTAAGATTACTTAAAGTTATAAAGGTTATGGAAAACATTATAGTACTATCTACATT
CAAATAACCTTACATCCTTATTAAGTTTAGTAACTTTTAATCAATAATAAAAGTTACCAATTTTA
TTACTTAAGTATCTACTAAAAAACCTATAAAAGTAATTAAAATTGTATTACCAATCCTTAATAAC
ATGAGTAAACTTTCATCAATGGTAATGATTTACCTTGTTTCTCTCAAAAGTTACTAAAAAACCTA
TAATGATCATAAAAAATGTATAGTACCAAAAACTAATTCAATAACCTTATATTATAAAGGTAAAG
TACTGC
Found at i:1987 original size:3 final size:3
Alignment explanation
Indices: 1979--2018 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1969 TCAACAAATT
1979 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2019 ATTTTGATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:6787 original size:93 final size:93
Alignment explanation
Indices: 6628--6808 Score: 272
Period size: 93 Copynumber: 1.9 Consensus size: 93
6618 ATTCAAAGAT
6628 ATTTTGACAAGTTAATCAATTGAGGGTGAACATCTAGGACCAAATAAGGGTGAACACCATGTAAA
1 ATTTTGACAAGTTAATCAATTGAGGGTGAACATCTAGGACCAAATAAGGGTGAACACCATGTAAA
6693 ATTACATACAAAATATTAAGAAATAGGC
66 ATTACATACAAAATATTAAGAAATAGGC
* * ** ** *
6721 ATTTTGACGAGTTAATTAATTGAGGGTGGGCATCTAGGACCATGTAAGGGTGGACACCATGTAAA
1 ATTTTGACAAGTTAATCAATTGAGGGTGAACATCTAGGACCAAATAAGGGTGAACACCATGTAAA
** *
6786 ATTACATGGAAAATGTTAAGAAA
66 ATTACATACAAAATATTAAGAAA
6809 GTTGAAGGCT
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 78 1.00
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (93 bp):
ATTTTGACAAGTTAATCAATTGAGGGTGAACATCTAGGACCAAATAAGGGTGAACACCATGTAAA
ATTACATACAAAATATTAAGAAATAGGC
Found at i:13421 original size:6 final size:6
Alignment explanation
Indices: 13410--13443 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
13400 AAAACAAGAT
* *
13410 AAAAAG AAAAAG AAAATG AGAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
13444 TGAGCATTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:13435 original size:18 final size:18
Alignment explanation
Indices: 13412--13447 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
13402 AACAAGATAA
13412 AAAGAAAAAGAAAATGAG
1 AAAGAAAAAGAAAATGAG
13430 AAAGAAAAAGAAAATGAG
1 AAAGAAAAAGAAAATGAG
13448 CATTACATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (18 bp):
AAAGAAAAAGAAAATGAG
Found at i:25044 original size:2 final size:2
Alignment explanation
Indices: 25039--25069 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25029 CGAGAGAGAG
25039 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
25070 GGAAAATGGG
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:34488 original size:2 final size:2
Alignment explanation
Indices: 34481--34512 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
34471 TGATATAGCC
34481 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
34513 GTTGAAAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36034 original size:22 final size:23
Alignment explanation
Indices: 35999--36045 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
35989 GTAGTTAATC
*
35999 ATAAATTAACTAATTAAA-ACTA
1 ATAAACTAACTAATTAAATACTA
*
36021 ATAAACTAAGTAATTAAATACTA
1 ATAAACTAACTAATTAAATACTA
36044 AT
1 AT
36046 TAATTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (23 bp):
ATAAACTAACTAATTAAATACTA
Found at i:36057 original size:22 final size:22
Alignment explanation
Indices: 36010--36059 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
36000 TAAATTAACT
*
36010 AATTAAAACTAATAAACTAAGT
1 AATTAAAACTAATAAACTAAGA
* *
36032 AATTAAATACTAATTAATTAA-A
1 AATTAAA-ACTAATAAACTAAGA
36054 AATTAA
1 AATTAA
36060 TTTAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (22 bp):
AATTAAAACTAATAAACTAAGA
Found at i:36060 original size:15 final size:15
Alignment explanation
Indices: 36023--36061 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
36013 TAAAACTAAT
*
36023 AAACTAAGTAATTAA
1 AAACTAATTAATTAA
*
36038 ATACTAATTAATTAA
1 AAACTAATTAATTAA
*
36053 AAATTAATT
1 AAACTAATT
36062 TAAAAAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (15 bp):
AAACTAATTAATTAA
Found at i:39656 original size:14 final size:15
Alignment explanation
Indices: 39637--39665 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39627 ACAAATGCTA
39637 GATTTTGGAT-TTTG
1 GATTTTGGATATTTG
39651 GATTTTGGATATTTG
1 GATTTTGGATATTTG
39666 AGGGATTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.17, C:0.00, G:0.28, T:0.55
Consensus pattern (15 bp):
GATTTTGGATATTTG
Found at i:41145 original size:91 final size:91
Alignment explanation
Indices: 40983--41158 Score: 253
Period size: 91 Copynumber: 1.9 Consensus size: 91
40973 ATTTTAAAAC
* * *
40983 TTAAATAATTCAAAAAATGGACATGTGTCAACTCTACAACCCGCTTGTGGAGTCCAAAATTTACA
1 TTAAATAATTCAAAAAATGAACATGTGTCAACTCCACAACCCGCTTGTAGAGTCCAAAATTTACA
*
41048 CCGCCAATATATCATATAATCACCCT
66 CCGCCAATATATCAAATAATCACCCT
* * * * **
41074 TTAATTAATTCAGAAAATGAACATGTGTTAACTCCATAACCCGCTTGTAGAGTTTAAAATTTACA
1 TTAAATAATTCAAAAAATGAACATGTGTCAACTCCACAACCCGCTTGTAGAGTCCAAAATTTACA
*
41139 CGGCCAATATATCAAATAAT
66 CCGCCAATATATCAAATAAT
41159 TACCTTACAA
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
91 74 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (91 bp):
TTAAATAATTCAAAAAATGAACATGTGTCAACTCCACAACCCGCTTGTAGAGTCCAAAATTTACA
CCGCCAATATATCAAATAATCACCCT
Found at i:46660 original size:18 final size:18
Alignment explanation
Indices: 46622--46660 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
46612 CGCTTCCGCC
*
46622 GATGATTACAGTAAATTT
1 GATGATTACAGTAAATAT
* *
46640 GATGATTATAGTAAGTAT
1 GATGATTACAGTAAATAT
46658 GAT
1 GAT
46661 TCAAAGTATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (18 bp):
GATGATTACAGTAAATAT
Found at i:47071 original size:39 final size:39
Alignment explanation
Indices: 47028--47103 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
47018 AAACCAGACA
* * * *
47028 ACTACAAGCCAAAGCCTGAGGGAGAGAACAAGCCAAATT
1 ACTACAAACCAAAGCCAGAAGGAGAAAACAAGCCAAATT
* *
47067 ACTACAAACCCAAGCCAGAAGGAGAAAAGAAGCCAAA
1 ACTACAAACCAAAGCCAGAAGGAGAAAACAAGCCAAA
47104 CTATGGTGCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.49, C:0.24, G:0.21, T:0.07
Consensus pattern (39 bp):
ACTACAAACCAAAGCCAGAAGGAGAAAACAAGCCAAATT
Found at i:52209 original size:51 final size:51
Alignment explanation
Indices: 52115--52381 Score: 275
Period size: 54 Copynumber: 5.2 Consensus size: 51
52105 TCCCCAAAGC
*
52115 AAGAAGAAGAAGAAGAAGGATATTCACTCT-T-CGAATCATCATTTTCAACAG
1 AAGAAGAAGAAGAAGAAGAATATTCAC-CTATGCG-ATCATCATTTTCAACAG
* * * *
52166 AAGAAGAAGATGAAGAAGAATTTTCGCCTATGCGATCAACATTTTCAACAG
1 AAGAAGAAGAAGAAGAAGAATATTCACCTATGCGATCATCATTTTCAACAG
52217 -AG--GAAG--G-AGAAGAATATTCACCTATGCGATCATC-TTTTCCAACAGAGG
1 AAGAAGAAGAAGAAGAAGAATATTCACCTATGCGATCATCATTTT-CAAC--A-G
* *
52265 AAGAAGACGAAGAAGAAGAATATTCACCTATGCCATCATCATTTTCAACAG
1 AAGAAGAAGAAGAAGAAGAATATTCACCTATGCGATCATCATTTTCAACAG
* * * *
52316 AAGAAGATGAGGAAGAAGAAGGATATTCGCCAACTG-AATCATCATTTTCAACAG
1 AAGAAGA--A-GAAGAAGAAGAATATTCACCTA-TGCGATCATCATTTTCAACAG
52370 AAGAAGAAGAAG
1 AAGAAGAAGAAG
52382 GATTTTCGCC
Statistics
Matches: 184, Mismatches: 15, Indels: 34
0.79 0.06 0.15
Matches are distributed among these distances:
44 4 0.02
45 28 0.15
46 1 0.01
47 1 0.01
48 5 0.03
49 2 0.01
50 4 0.02
51 55 0.30
52 4 0.02
53 1 0.01
54 73 0.40
55 6 0.03
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.21
Consensus pattern (51 bp):
AAGAAGAAGAAGAAGAAGAATATTCACCTATGCGATCATCATTTTCAACAG
Found at i:52229 original size:45 final size:45
Alignment explanation
Indices: 52179--52267 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 45
52169 AAGAAGATGA
* *
52179 AGAAGAATTTTCGCCTATGCGATCAACATTTT-CAACAGAGGAAGG
1 AGAAGAATATTCACCTATGCGATCAAC-TTTTCCAACAGAGGAAGG
*
52224 AGAAGAATATTCACCTATGCGATCATCTTTTCCAACAGAGGAAG
1 AGAAGAATATTCACCTATGCGATCAACTTTTCCAACAGAGGAAG
52268 AAGACGAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 4 0.10
45 36 0.90
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (45 bp):
AGAAGAATATTCACCTATGCGATCAACTTTTCCAACAGAGGAAGG
Found at i:52390 original size:45 final size:45
Alignment explanation
Indices: 52327--52421 Score: 172
Period size: 45 Copynumber: 2.1 Consensus size: 45
52317 AGAAGATGAG
52327 GAAGAAGAAGGATATTCGCCAACTGAATCATCATTTTCAACAGAA
1 GAAGAAGAAGGATATTCGCCAACTGAATCATCATTTTCAACAGAA
* *
52372 GAAGAAGAAGGATTTTCGCCAATTGAATCATCATTTTCAACAGAA
1 GAAGAAGAAGGATATTCGCCAACTGAATCATCATTTTCAACAGAA
52417 GAAGA
1 GAAGA
52422 GAGCTCAGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (45 bp):
GAAGAAGAAGGATATTCGCCAACTGAATCATCATTTTCAACAGAA
Found at i:57016 original size:2 final size:2
Alignment explanation
Indices: 57009--57033 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56999 TCTATATGCA
57009 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
57034 TTTGTGTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Done.