Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011572.1 Corchorus capsularis cultivar CVL-1 contig11593, 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: 53979
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:703 original size:16 final size:15
Alignment explanation
Indices: 665--704 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
655 TTGTCTGATT
*
665 TTAATTTGATTAATTA
1 TTAA-TTGATCAATTA
681 TTAATTGATCAATCTA
1 TTAATTGATCAAT-TA
697 TTAATTGA
1 TTAATTGA
705 AATTGACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (15 bp):
TTAATTGATCAATTA
Found at i:837 original size:19 final size:18
Alignment explanation
Indices: 822--856 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
812 AACTAATTTG
822 ATTACCTATAATTAATTAT
1 ATTA-CTATAATTAATTAT
841 ATTACT-TAATTAATTA
1 ATTACTATAATTAATTA
857 ATTTTGATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 2 0.12
19 4 0.25
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTACTATAATTAATTAT
Found at i:1092 original size:26 final size:25
Alignment explanation
Indices: 1063--1119 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 25
1053 ATTTCTACAT
*
1063 AAATTTAGTAAC-CTCACATTCTTAGA
1 AAATTTAGAAACACT-ACATTCTTA-A
1089 AAATTTAGAAACACTACATTCTTAA
1 AAATTTAGAAACACTACATTCTTAA
1114 AAATTT
1 AAATTT
1120 CAGGTTTCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 7 0.24
26 20 0.69
27 2 0.07
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (25 bp):
AAATTTAGAAACACTACATTCTTAA
Found at i:2540 original size:30 final size:30
Alignment explanation
Indices: 2506--2564 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
2496 TCAACTAATT
*
2506 AATCAATCAAAAGTAATTAATATATTTCTC
1 AATCAACCAAAAGTAATTAATATATTTCTC
* *
2536 AATCAACCTAAAGTAATTAATTTATTTCT
1 AATCAACCAAAAGTAATTAATATATTTCT
2565 TTTTGTCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.39
Consensus pattern (30 bp):
AATCAACCAAAAGTAATTAATATATTTCTC
Found at i:2596 original size:2 final size:2
Alignment explanation
Indices: 2589--2623 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
2579 CTCAGTTTTA
2589 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
2624 GATTATCTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6722 original size:168 final size:165
Alignment explanation
Indices: 6351--6795 Score: 530
Period size: 168 Copynumber: 2.7 Consensus size: 165
6341 TGAGTCATTT
*
6351 GTCAATTGAGAAATGACCAAAAAATTTAGTTATTTAATCCACTCAAGAATCAAAAGTTAGGATAT
1 GTCAATTGAGAAATGACC-AAAAAGTTAGTTATTTAATCCACTCAAGAATCAAAAGTTAGGATAT
* * * * ** * * ** * **
6416 TTAAGTAATCTGCCAAGAAGGTAAAGACGAAAAATATTAGTTCTCTATTTCATCATCAATTCTTG
65 TTAAGTAATCTGCCAAGTAGGAAAAGACAAAAAAAAAAAGTTCTCTACTCCAAAAGCAAGCCTTG
* * *
6481 ATGGGGATCTTTTATTAATTCCACTACTCTATTCAA
130 ATAGGGATCTTTTAATAATTCCACTACTCTATTAAA
* * * * * *
6517 TTCCATTAAGAAATGACCAGAAAGATTACTTATTTAATCCTCTCAAGAATCAAAAGTTAGGATAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCACTCAAGAATCAAAAGTTAGGATAT
*
6582 TTAAGTAATATGCCAAGTAGGAAAAGACAAAAAAAAAAAAGTTCTCTAACTCCAAAAGCAAGCCT
65 TTAAGTAATCTGCCAAGTAGGAAAAGAC-AAAAAAAAAAAGTTCTCT-ACTCCAAAAGCAAGCCT
* *
6647 TGGTAGGGATCTTTTAATAATTCCATTACTCTATTAAA
128 TGATAGGGATCTTTTAATAATTCCACTACTCTATTAAA
* * * *
6685 GTCAATTGAGAAATGACTAAAAAGTCTAGTTATTTAATCCCCTCAAGAATAAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAGT-TAGTTATTTAATCCACTCAAGAATCAAAAGTTAGGATAT
* * * **
6750 TTAAATAATCTGCCAAGTGGGAAAAGACGAAAAAAATTAGTTCTCT
65 TTAAGTAATCTGCCAAGTAGGAAAAGACAAAAAAAAAAAGTTCTCT
6796 CGCTCCTCAT
Statistics
Matches: 234, Mismatches: 41, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
165 4 0.02
166 78 0.33
167 30 0.13
168 122 0.52
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (165 bp):
GTCAATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCACTCAAGAATCAAAAGTTAGGATATT
TAAGTAATCTGCCAAGTAGGAAAAGACAAAAAAAAAAAGTTCTCTACTCCAAAAGCAAGCCTTGA
TAGGGATCTTTTAATAATTCCACTACTCTATTAAA
Found at i:6874 original size:2 final size:2
Alignment explanation
Indices: 6867--6899 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6857 ATGTAGTATG
6867 TA 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 TA T
6900 TAATGGCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10703 original size:54 final size:53
Alignment explanation
Indices: 10640--10741 Score: 143
Period size: 54 Copynumber: 1.9 Consensus size: 53
10630 CAACAAGACT
* * *
10640 AAAAATTGCAATACCAGTTTC-AACAAAATTATAACACCAGATTCAACCAAGAA
1 AAAAATTGCAACACCAGATTCAAACAAAATT-CAACACCAGATTCAACCAAGAA
*
10693 AAAAATTTGCAACACCAGATTCAAACAAAATTCAGCACCAGATTCAACC
1 AAAAA-TTGCAACACCAGATTCAAACAAAATTCAACACCAGATTCAACC
10742 CATAGTACTT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
53 5 0.12
54 29 0.67
55 9 0.21
ACGTcount: A:0.49, C:0.24, G:0.08, T:0.20
Consensus pattern (53 bp):
AAAAATTGCAACACCAGATTCAAACAAAATTCAACACCAGATTCAACCAAGAA
Found at i:17055 original size:156 final size:153
Alignment explanation
Indices: 16560--17107 Score: 647
Period size: 155 Copynumber: 3.5 Consensus size: 153
16550 TCAAACGGGT
* * *
16560 TTAAGATGAAAAACTTATGCACGTTTTTCAGTTAAGGACAATTTGGGGTGAGAAACC-AGTTCAC
1 TTAAAATGAAAAACTTATGCATGTTTTTCAGTTAAGGACAGTTTGGGGTGAGAAACCTAGTTCAC
* * * * * *
16624 CATGAAGGAGAGCTCGATTTTACTTAAAAAATTTTCCATAGTTTTATGGAGATAATATAAGTCTC
66 CATCAAGGAGAGCTCGATTTTACTT-AGAATTTTTCCATAGTCTTATGGAGATAATCTAAGTCAC
*
16689 TTGGCCAAATTTCATCTCAATCAGAC
130 TTGG--AAATTTCATCTCAATCGGAC
* * * *
16715 TTAAGATGAAAAACTTATACATGTTTTTCAGTTAAGGACAGTTTGGGGTGAGAAAACAAGTTCAC
1 TTAAAATGAAAAACTTATGCATGTTTTTCAGTTAAGGACAGTTTGGGGTGAGAAACCTAGTTCAC
* * * * *
16780 TATCAAGGAGAGTTCTG-TTTTACTTAGAATTTTTCCATAGCCTTATGGCGATAATCTAAGCTTA
66 CATCAAGGAGAGCTC-GATTTTACTTAGAATTTTTCCATAGTCTTATGGAGATAATCTAAG-TCA
* * * *
16844 CTGGTGGAAA-TTCAGC-CTTATTGGAA
129 CT--TGGAAATTTCATCTC-AATCGGAC
* * * **
16870 ATAGAATGAAAAACTTATGCATGTTTTTCATTTAAGGACAGTTTGGGAAGAGAAACCTAGTT-AG
1 TTAAAATGAAAAACTTATGCATGTTTTTCAGTTAAGGACAGTTTGGGGTGAGAAACCTAGTTCA-
*
16934 CCATCAAGGAGAGCTCGATTTTACTTAGAATTTTTTCCATAGTCTTATGGAGATAATCTAAGTCC
65 CCATCAAGGAGAGCTCGATTTTACTTAGAA-TTTTTCCATAGTCTTATGGAGATAATCTAAGTCA
16999 CTTGGAAAAATTTCATCTCAATCGGAC
129 CTTGG--AAATTTCATCTCAATCGGAC
* * *
17026 TTAAAATGAAAAACTTATGCATGTTTTTCATTTAAGGACAGTTTGAGGTGTGAAACCTAGTTCAC
1 TTAAAATGAAAAACTTATGCATGTTTTTCAGTTAAGGACAGTTTGGGGTGAGAAACCTAGTTCAC
* *
17091 CATGAAGGAGGGCTCGA
66 CATCAAGGAGAGCTCGA
17108 ACCTAGCCAA
Statistics
Matches: 332, Mismatches: 47, Indels: 27
0.82 0.12 0.07
Matches are distributed among these distances:
153 3 0.01
154 3 0.01
155 176 0.53
156 144 0.43
157 3 0.01
158 3 0.01
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (153 bp):
TTAAAATGAAAAACTTATGCATGTTTTTCAGTTAAGGACAGTTTGGGGTGAGAAACCTAGTTCAC
CATCAAGGAGAGCTCGATTTTACTTAGAATTTTTCCATAGTCTTATGGAGATAATCTAAGTCACT
TGGAAATTTCATCTCAATCGGAC
Found at i:17452 original size:26 final size:27
Alignment explanation
Indices: 17423--17483 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
17413 GTGACATATT
*
17423 AGAGGGAAGATTTTCCGCCTG-ATACC
1 AGAGGGAAGATTTTCCACCTGAATACC
*
17449 AGAGGGAAGATTTTCCACTTGATATACC
1 AGAGGGAAGATTTTCCACCTGA-ATACC
17477 AGAGGGA
1 AGAGGGA
17484 GATGTCCTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 19 0.61
28 12 0.39
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.23
Consensus pattern (27 bp):
AGAGGGAAGATTTTCCACCTGAATACC
Found at i:27413 original size:160 final size:158
Alignment explanation
Indices: 27021--27445 Score: 570
Period size: 160 Copynumber: 2.7 Consensus size: 158
27011 GCAACGTATG
* * *
27021 AAGTAGAAGAACTAATTCATCGTACC-GGGAAAGCTAACTAGAATAAACGTAAATGTTCAGCAAG
1 AAGTAGAAGAACTAATTCATCGTACCAGCG-AAGCTAACTAGAATAAACGTAAATGTACAGCAAA
* * * * **
27085 AGCGACCTCTGACCAGAAACTATCTAATTTA-GTACATTTGTCCATCTCAAGTCTGAATTTGAAA
65 AGTGACCTCTGATCAGAAACTATCTAATTTACG-ACATTAGTCCATCACAAGTCTGAATCGGAAA
* *
27149 ATTAATATTTCAACCCATATTATCTACCAT
129 ATTAATACTTCAACCCATATTATCTACAAT
* * *
27179 AA--AGAAGAACTAATTCATCGTACCATCAAAGCTAACTACAATAAACGTAAATGTACAGCAAAA
1 AAGTAGAAGAACTAATTCATCGTACCAGCGAAGCTAACTAGAATAAACGTAAATGTACAGCAAAA
* ** * *
27242 GTGCCCTCTGATCAGAAAAAATCTAATTTACGACATTAGTCCATCACGGAGTCTGGATCGGAAAA
66 GTGACCTCTGATCAGAAACTATCTAATTTACGACATTAGTCCATCAC-AAGTCTGAATCGGAAAA
27307 TTAATACTTCAACCCATATTATCTACAAT
130 TTAATACTTCAACCCATATTATCTACAAT
* *
27336 AAAGTAGAAGAACTAATTCATCGTACCAGCGAAGGTAACTAGAATAAAAGTAAATGTACAGCAAA
1 -AAGTAGAAGAACTAATTCATCGTACCAGCGAAGCTAACTAGAATAAACGTAAATGTACAGCAAA
* * *
27401 AATGAGCTCTGATCAGAAACTATTTAATTTACGACATTAGTCCAT
65 AGTGACCTCTGATCAGAAACTATCTAATTTACGACATTAGTCCAT
27446 TGCCGAGCTA
Statistics
Matches: 231, Mismatches: 30, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
156 92 0.40
157 41 0.18
158 4 0.02
160 94 0.41
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (158 bp):
AAGTAGAAGAACTAATTCATCGTACCAGCGAAGCTAACTAGAATAAACGTAAATGTACAGCAAAA
GTGACCTCTGATCAGAAACTATCTAATTTACGACATTAGTCCATCACAAGTCTGAATCGGAAAAT
TAATACTTCAACCCATATTATCTACAAT
Found at i:28830 original size:2 final size:2
Alignment explanation
Indices: 28823--28857 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
28813 GCAATTGATA
28823 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
28858 AGAGAGAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:31492 original size:2 final size:2
Alignment explanation
Indices: 31479--31515 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
31469 GAAAATTTGT
*
31479 TA TA TA TT 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 TA TA TA T
31516 TTACAAGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:32270 original size:19 final size:19
Alignment explanation
Indices: 32248--32289 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
32238 ATGTGAGTAT
*
32248 TATTATCCAATTAACAGCA
1 TATTATCCAATTAAAAGCA
32267 TATTATCCAATTAAAAGCA
1 TATTATCCAATTAAAAGCA
32286 TATT
1 TATT
32290 TCATTACCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.36
Consensus pattern (19 bp):
TATTATCCAATTAAAAGCA
Found at i:32678 original size:107 final size:105
Alignment explanation
Indices: 32451--32713 Score: 341
Period size: 107 Copynumber: 2.5 Consensus size: 105
32441 AATTTTTCTA
* * **
32451 ACCCTTAAAATTAAATTTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTAATTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
* **
32514 TTTCTAAAACCCTATAGCAATATTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATATTATTAATTATAAAATTT
* * * *
32554 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGTTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
* *
32619 TTTCTAAAACCCTATAATAATAAATTATTAATTTTAAAATTT
66 TTTCTAAAACCCTATAACAAT--ATTATTAATTATAAAATTT
* * * *
32661 ACCCTTAAAATACAAATAAAATTTTAATTTGAGGCTAAATTTAATGAAATTAA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAA
32714 GGCTAAACTT
Statistics
Matches: 137, Mismatches: 19, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
103 26 0.19
104 14 0.10
105 34 0.25
107 63 0.46
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.42
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
TTTCTAAAACCCTATAACAATATTATTAATTATAAAATTT
Found at i:49538 original size:29 final size:28
Alignment explanation
Indices: 49503--49598 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 28
49493 CGTTAGGACT
49503 TTATTTGGCTAAATTAAAAGATCAGACCC
1 TTATTTGG-TAAATTAAAAGATCAGACCC
** * *
49532 TTATTTGAGTATTTTGGCAAACG-TTAGACCC
1 TTATTTG-GTAAATT---AAAAGATCAGACCC
*
49563 TTATTTGGTCAAGTTAAAAGATCAGACCC
1 TTATTTGGT-AAATTAAAAGATCAGACCC
49592 TTATTTG
1 TTATTTG
49599 ATCATTCTGA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
28 4 0.08
29 25 0.47
30 3 0.06
31 17 0.32
32 4 0.08
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (28 bp):
TTATTTGGTAAATTAAAAGATCAGACCC
Found at i:49613 original size:60 final size:60
Alignment explanation
Indices: 49465--49629 Score: 194
Period size: 60 Copynumber: 2.8 Consensus size: 60
49455 AAACTGACGC
* * *
49465 CAGACCCTTATTTGAGCATTTTCA-ATAACGTTAGGA-CTTTATTTGGCTAAATTAAAAGAT
1 CAGACCCTTATTTGATCATTTTGACA-AACGTTA-GACCCTTATTTGGCTAAATTAAAAGAT
* *
49525 CAGACCCTTATTTGAGT-ATTTTGGCAAACGTTAGACCCTTATTTGG-TCAAGTTAAAAGAT
1 CAGACCCTTATTTGA-TCATTTTGACAAACGTTAGACCCTTATTTGGCT-AAATTAAAAGAT
* * *
49585 CAGACCCTTATTTGATCATTCTGACAAACATTAGCCCCTTATTTG
1 CAGACCCTTATTTGATCATTTTGACAAACGTTAGACCCTTATTTG
49630 AGCAATTAGC
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
59 4 0.04
60 86 0.95
61 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (60 bp):
CAGACCCTTATTTGATCATTTTGACAAACGTTAGACCCTTATTTGGCTAAATTAAAAGAT
Found at i:51937 original size:1 final size:1
Alignment explanation
Indices: 51926--51955 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
51916 ATGGGTAAAG
*
51926 TTTTCTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
51956 CTCTTTAGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:53257 original size:37 final size:37
Alignment explanation
Indices: 53216--53290 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
53206 CATTTCTTAA
53216 CTGAATTTTCTTAAAAGAATTTATAAAATAAAACAGC
1 CTGAATTTTCTTAAAAGAATTTATAAAATAAAACAGC
53253 CTGAATTTTCTTAAAAGAATTTATAAAATAAAACAGC
1 CTGAATTTTCTTAAAAGAATTTATAAAATAAAACAGC
53290 C
1 C
53291 GCACGCGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (37 bp):
CTGAATTTTCTTAAAAGAATTTATAAAATAAAACAGC
Done.