Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012221.1 Corchorus capsularis cultivar CVL-1 contig12242, 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: 37330
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:15127 original size:12 final size:13
Alignment explanation
Indices: 15110--15138 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
15100 GATCGATCAG
15110 ATTTATTTATT-T
1 ATTTATTTATTAT
15122 ATTTATTTATTAT
1 ATTTATTTATTAT
15135 ATTT
1 ATTT
15139 GTTCGATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTATTTATTAT
Found at i:15880 original size:12 final size:12
Alignment explanation
Indices: 15863--15887 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15853 GGGGTCAAAG
15863 TCTTCTTCTTTT
1 TCTTCTTCTTTT
15875 TCTTCTTCTTTT
1 TCTTCTTCTTTT
15887 T
1 T
15888 TTTTTCAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TCTTCTTCTTTT
Found at i:17051 original size:33 final size:32
Alignment explanation
Indices: 17014--17085 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
17004 CCGCCCTAGT
17014 GGGGCGGCACAGCCGTGGCAAAGCCGCCCCACC
1 GGGGCGGC-CAGCCGTGGCAAAGCCGCCCCACC
* * * *
17047 GGGGCAGCCTGCCGTGGCAAAGCCGCCCCTCT
1 GGGGCGGCCAGCCGTGGCAAAGCCGCCCCACC
17079 GGGGCGG
1 GGGGCGG
17086 TTTGAGCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 27 0.79
33 7 0.21
ACGTcount: A:0.14, C:0.39, G:0.40, T:0.07
Consensus pattern (32 bp):
GGGGCGGCCAGCCGTGGCAAAGCCGCCCCACC
Found at i:17492 original size:23 final size:23
Alignment explanation
Indices: 17462--17511 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
17452 CTTGTACCTA
*
17462 TTCTAGAGCAATGTGGCAAAGGG
1 TTCTAGAGCAATGCGGCAAAGGG
*
17485 TTCTAGAGCAGTGCGGCAAAGGG
1 TTCTAGAGCAATGCGGCAAAGGG
17508 TTCT
1 TTCT
17512 CTCAACTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.26, C:0.16, G:0.34, T:0.24
Consensus pattern (23 bp):
TTCTAGAGCAATGCGGCAAAGGG
Found at i:18211 original size:22 final size:22
Alignment explanation
Indices: 18186--18398 Score: 71
Period size: 22 Copynumber: 9.8 Consensus size: 22
18176 ATAATCCCAT
18186 TATGAAATTTTGATAACATTCC
1 TATGAAATTTTGATAACATTCC
* * *
18208 TATGAAATTTTAATAATGA-TAC
1 TATGAAATTTTGATAA-CATTCC
* * * **
18230 TATGGAATTTTGAGAACCTTTT
1 TATGAAATTTTGATAACATTCC
* ** * *
18252 TAT-AATTTTTTTTAACCTTCT
1 TATGAAATTTTGATAACATTCC
* * *
18273 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACATTCC
* * *
18295 TAAGGAATTTTGA-AGAC---CAG
1 TATGAAATTTTGATA-ACATTC-C
*
18315 TATGAAATTTTGATAACTTTCC
1 TATGAAATTTTGATAACATTCC
* * * *
18337 AATGAAATTTTGCTAACCAATAC
1 TATGAAATTTTGATAA-CATTCC
* * *
18360 TATGAGATGTTGATAAC-CTCC
1 TATGAAATTTTGATAACATTCC
* *
18381 ATATGATATATTGATAAC
1 -TATGAAATTTTGATAAC
18399 CACGTTTTTT
Statistics
Matches: 140, Mismatches: 40, Indels: 22
0.69 0.20 0.11
Matches are distributed among these distances:
19 1 0.01
20 13 0.09
21 19 0.14
22 90 0.64
23 17 0.12
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACATTCC
Found at i:18399 original size:45 final size:45
Alignment explanation
Indices: 18315--18400 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
18305 TGAAGACCAG
* * * *
18315 TATGAAATTTTGATAACTTTCCAATGAAATTTTGCTAACCAATAC
1 TATGAAATGTTGATAACTCTCCAATGAAATATTGATAACCAATAC
* *
18360 TATGAGATGTTGATAAC-CTCCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACTCTCCA-ATGAAATATTGATAACCA
18401 CGTTTTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 4 0.12
45 30 0.88
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (45 bp):
TATGAAATGTTGATAACTCTCCAATGAAATATTGATAACCAATAC
Found at i:18539 original size:22 final size:22
Alignment explanation
Indices: 18510--18718 Score: 112
Period size: 22 Copynumber: 9.7 Consensus size: 22
18500 TGATGACTAC
18510 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
** **
18532 ATTTTTTGATAACCTCATTATG
1 AAATTTTGATAACCTCCCTATG
* *
18554 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
** * *
18576 AAATTTTGATCTGCAT-ACTATG
1 AAATTTTGAT-AACCTCCCTATG
*
18598 AAATTTTGATAACC-CTCTTATG
1 AAATTTTGATAACCTC-CCTATG
* ** *
18620 AAATTTTGA-AAACTAAACTATA
1 AAATTTTGATAACCT-CCCTATG
* * *
18642 AAATTTTGATATCCTCCATAATA
1 AAATTTTGATAACCTCCCT-ATG
* * *
18665 AAAGTTTAATAACCTGCC--T-
1 AAATTTTGATAACCTCCCTATG
*
18684 -AATTTTG-TAACCAT-ACTATG
1 AAATTTTGATAACC-TCCCTATG
18704 AAATTTTGATAACCT
1 AAATTTTGATAACCT
18719 TCCCAGAAAT
Statistics
Matches: 135, Mismatches: 39, Indels: 27
0.67 0.19 0.13
Matches are distributed among these distances:
17 6 0.04
18 6 0.04
19 1 0.01
20 1 0.01
21 12 0.09
22 89 0.66
23 20 0.15
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCTATG
Found at i:18923 original size:25 final size:22
Alignment explanation
Indices: 18869--19264 Score: 104
Period size: 22 Copynumber: 17.7 Consensus size: 22
18859 ATAACAACAT
18869 TATGAAATTTTGATAATCTTCC
1 TATGAAATTTTGATAATCTTCC
18891 TAT-AAATTTTGATAATCTGATCTC
1 TATGAAATTTTGATAATCT--TC-C
* * *
18915 TATGGAATTTCGATAATC-ACTC
1 TATGAAATTTTGATAATCTTC-C
* *
18937 TATGAGA-TTTGATAACCTT-C
1 TATGAAATTTTGATAATCTTCC
* *
18957 TATCAAATTTTGGT-A-C-TCC
1 TATGAAATTTTGATAATCTTCC
* * *
18976 TTATGAAATTGATACTTTTATAACCTTCA
1 -TATG-AA---AT--TTTGATAATCTTCC
** *
19005 TATGAAATTTTGATAA-CCACGA
1 TATGAAATTTTGATAATCTTC-C
*
19027 TAT-ATAATTTTGATAATCTCCC
1 TATGA-AATTTTGATAATCTTCC
* * *
19049 AATGAAATATT-AGTAA-CCTCC
1 TATGAAATTTTGA-TAATCTTCC
* * **
19070 TAATGAAATTTTGTTAACCACCC
1 T-ATGAAATTTTGATAATCTTCC
** *
19093 TATGAAATTTCAATAA-CTAACC
1 TATGAAATTTTGATAATCT-TCC
* * *
19115 TAAGAAATTTTAATAACCTGATCC
1 TATGAAATTTTGATAATCT--TCC
* * **
19139 TATGAAATTTCGGTAA-CCACAC
1 TATGAAATTTTGATAATCTTC-C
19161 TATGAAATTTTGATAA-CTTCC
1 TATGAAATTTTGATAATCTTCC
* **
19182 ATATGAAATTTTGGTAA-CCACGC
1 -TATGAAATTTTGATAATCTTC-C
* *
19205 TATGGAATTTTGATAA-CCTCC
1 TATGAAATTTTGATAATCTTCC
* * ** * *
19226 TCATGAAATTATAATAGCCATCT
1 T-ATGAAATTTTGATAATCTTCC
19249 TATGAAATTTTGATAA
1 TATGAAATTTTGATAA
19265 CCACATAGAG
Statistics
Matches: 278, Mismatches: 63, Indels: 66
0.68 0.15 0.16
Matches are distributed among these distances:
18 1 0.00
19 2 0.01
20 10 0.04
21 42 0.15
22 157 0.56
23 17 0.06
24 23 0.08
25 12 0.04
26 4 0.01
27 3 0.01
28 5 0.02
29 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAATCTTCC
Found at i:19020 original size:22 final size:22
Alignment explanation
Indices: 18991--19266 Score: 149
Period size: 22 Copynumber: 12.5 Consensus size: 22
18981 AAATTGATAC
*
18991 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACCTTCCTATGAAA
* *
19012 TTTTGATAACC-ACGATAT-ATAA
1 TTTTGATAACCTTC-CTATGA-AA
* * *
19034 TTTTGATAATCTCCCAATGAAA
1 TTTTGATAACCTTCCTATGAAA
*
19056 TATT-AGTAACC-TCCTAATGAAA
1 TTTTGA-TAACCTTCCT-ATGAAA
* **
19078 TTTTGTTAACCACCCTATGAAA
1 TTTTGATAACCTTCCTATGAAA
** * *
19100 TTTCAATAA-CTAACCTAAGAAA
1 TTTTGATAACCT-TCCTATGAAA
*
19122 TTTTAATAACCTGATCCTATGAAA
1 TTTTGATAACCT--TCCTATGAAA
* * *
19146 TTTCGGTAACC-ACACTATGAAA
1 TTTTGATAACCTTC-CTATGAAA
19168 TTTTGATAA-CTTCCATATGAAA
1 TTTTGATAACCTTCC-TATGAAA
* * *
19190 TTTTGGTAACC-ACGCTATGGAA
1 TTTTGATAACCTTC-CTATGAAA
19212 TTTTGATAACC-TCCTCATGAAA
1 TTTTGATAACCTTCCT-ATGAAA
* * * * *
19234 TTATAATAGCCATCTTATGAAA
1 TTTTGATAACCTTCCTATGAAA
19256 TTTTGATAACC
1 TTTTGATAACC
19267 ACATAGAGAC
Statistics
Matches: 195, Mismatches: 41, Indels: 37
0.71 0.15 0.14
Matches are distributed among these distances:
21 15 0.08
22 151 0.77
23 12 0.06
24 17 0.09
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.36
Consensus pattern (22 bp):
TTTTGATAACCTTCCTATGAAA
Found at i:19168 original size:46 final size:44
Alignment explanation
Indices: 18991--19235 Score: 182
Period size: 44 Copynumber: 5.5 Consensus size: 44
18981 AAATTGATAC
* * *
18991 TTTT-ATAACCTTCATATGAAATTTTGATAACCACGA-TAT-ATAA
1 TTTTGATAACCTTCCTATGAAATTTCGGTAACCAC-ACTATGA-AA
* * * * *
19034 TTTTGATAATCTCCCAATGAAATATT-AGTAACCTC-CTAATGAAA
1 TTTTGATAACCTTCCTATGAAAT-TTCGGTAACCACACT-ATGAAA
* ** ** * *
19078 TTTTGTTAACCACCCTATGAAATTTCAATAACTA-ACCTAAGAAA
1 TTTTGATAACCTTCCTATGAAATTTCGGTAACCACA-CTATGAAA
*
19122 TTTTAATAACCTGATCCTATGAAATTTCGGTAACCACACTATGAAA
1 TTTTGATAACCT--TCCTATGAAATTTCGGTAACCACACTATGAAA
* * *
19168 TTTTGATAA-CTTCCATATGAAATTTTGGTAACCACGCTATGGAA
1 TTTTGATAACCTTCC-TATGAAATTTCGGTAACCACACTATGAAA
19212 TTTTGATAACC-TCCTCATGAAATT
1 TTTTGATAACCTTCCT-ATGAAATT
19236 ATAATAGCCA
Statistics
Matches: 161, Mismatches: 27, Indels: 27
0.75 0.13 0.13
Matches are distributed among these distances:
43 11 0.07
44 108 0.67
45 8 0.05
46 33 0.20
47 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.36
Consensus pattern (44 bp):
TTTTGATAACCTTCCTATGAAATTTCGGTAACCACACTATGAAA
Found at i:19256 original size:134 final size:134
Alignment explanation
Indices: 19005--19266 Score: 293
Period size: 134 Copynumber: 2.0 Consensus size: 134
18995 ATAACCTTCA
* *
19005 TATGAAATTTTGATAACCACGATATATAATTTTGATAATCTCCCAATGAAATATTAGTAACCTCC
1 TATGAAATTTCGATAACCACGATATATAATTTTGATAATCTCCCAATGAAATATTAGTAACCACC
* *
19070 TAATGAAATTTTGTTAACCACCCTATGAAATTTCAATAACTAACCTAAGAAATTTTAATAACCTG
66 TAATGAAATTTTGATAACCACCCTATGAAATTTCAATAACCAACCTAAGAAATTTTAATAACCTG
19135 ATCC
131 ATCC
* * * *
19139 TATGAAATTTCGGTAACCAC-ACTATGA-AATTTTGATAA-CTTCCATATGAAATTTTGGTAACC
1 TATGAAATTTCGATAACCACGA-TAT-ATAATTTTGATAATCTCCCA-ATGAAATATTAGTAACC
* * * * * * *
19201 ACGCT-ATGGAATTTTGATAACC-TCCTCATGAAATTAT-AATAGCCATCTTATGAAATTTTGAT
63 AC-CTAATGAAATTTTGATAACCACCCT-ATGAAATT-TCAATAACCAACCTAAGAAATTTTAAT
19263 AACC
125 AACC
19267 ACATAGAGAC
Statistics
Matches: 107, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
133 9 0.08
134 94 0.88
135 4 0.04
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (134 bp):
TATGAAATTTCGATAACCACGATATATAATTTTGATAATCTCCCAATGAAATATTAGTAACCACC
TAATGAAATTTTGATAACCACCCTATGAAATTTCAATAACCAACCTAAGAAATTTTAATAACCTG
ATCC
Found at i:19464 original size:19 final size:20
Alignment explanation
Indices: 19433--19470 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
19423 TATTGACATT
19433 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
19452 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
19471 ACTAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:19697 original size:30 final size:32
Alignment explanation
Indices: 19652--19717 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 32
19642 TGGCAATTTA
* * *
19652 GAAATATGTTTTTAAAAA-AGGGGTATAATTG
1 GAAATATGTTTTTAAAAATAAGGGTACAATCG
19683 GAAATATG-TTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTTAAAAATAAGGGTACAATCG
19714 GAAA
1 GAAA
19718 ATACAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 9 0.29
31 22 0.71
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.30
Consensus pattern (32 bp):
GAAATATGTTTTTAAAAATAAGGGTACAATCG
Found at i:23801 original size:19 final size:17
Alignment explanation
Indices: 23768--23802 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
23758 AGGAAGACTT
23768 AATTATTGGGAGAAATA
1 AATTATTGGGAGAAATA
23785 AATTGATTGGTGAGAAAT
1 AATT-ATTGG-GAGAAAT
23803 GTTTAAGGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 5 0.31
19 7 0.44
ACGTcount: A:0.43, C:0.00, G:0.26, T:0.31
Consensus pattern (17 bp):
AATTATTGGGAGAAATA
Found at i:31134 original size:3 final size:3
Alignment explanation
Indices: 31128--31153 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
31118 TGCCGAATTG
31128 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
31154 GTACTTGAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:36591 original size:2 final size:2
Alignment explanation
Indices: 36584--36625 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
36574 AAGAAAAGAA
* *
36584 AT AT AT AT AT AT AT AT AT CT TT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36625 A
1 A
36626 AGTCTAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:36850 original size:3 final size:3
Alignment explanation
Indices: 36844--36876 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
36834 ACTTCTTATT
36844 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
36877 TATTAGTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Done.