Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007403.1 Corchorus capsularis cultivar CVL-1 contig07424, 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: 37600
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--60 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
43 TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC
61 CCTCCTTTTC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:10955 original size:22 final size:22
Alignment explanation
Indices: 10930--11133 Score: 143
Period size: 22 Copynumber: 9.3 Consensus size: 22
10920 TACCCCTAAA
* * *
10930 AAAAATTCATAGCGAGCTTATC
1 AAAATTTCATAGAGAGGTTATC
10952 AAAATTTCATA-AGATGGTTATC
1 AAAATTTCATAGAGA-GGTTATC
* *
10974 AAAATTTCATAGTGTGGTTATC
1 AAAATTTCATAGAGAGGTTATC
* *
10996 AAAATTTCATAG-GAAGATTACC
1 AAAATTTCATAGAG-AGGTTATC
** *
11018 GTAATTTCATA-ATGTGGTTATC
1 AAAATTTCATAGA-GAGGTTATC
* *
11040 AAAATTTCATA-ATAAGGTAATC
1 AAAATTTCATAGA-GAGGTTATC
* *
11062 GAAATTTCATAGGGAGGTTATC
1 AAAATTTCATAGAGAGGTTATC
* *
11084 GAAATTTCATA-AGGAGATTATC
1 AAAATTTCATAGA-GAGGTTATC
*
11106 GAAATTTCATA-ATGTA-GTTATC
1 AAAATTTCATAGA-G-AGGTTATC
11128 AAAATT
1 AAAATT
11134 GTATGGCATA
Statistics
Matches: 147, Mismatches: 27, Indels: 16
0.77 0.14 0.08
Matches are distributed among these distances:
21 3 0.02
22 141 0.96
23 3 0.02
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
AAAATTTCATAGAGAGGTTATC
Found at i:10984 original size:44 final size:44
Alignment explanation
Indices: 10935--11133 Score: 220
Period size: 44 Copynumber: 4.5 Consensus size: 44
10925 CTAAAAAAAA
* * * * *
10935 TTCATAGCGAGCTTATCAAAATTTCATAAGATGGTTATCAAAAT
1 TTCATAGTGAGGTTATCAAAATTTCATAAGAAGATTATCGAAAT
* * * *
10979 TTCATAGTGTGGTTATCAAAATTTCATAGGAAGATTACCGTAAT
1 TTCATAGTGAGGTTATCAAAATTTCATAAGAAGATTATCGAAAT
* * * * *
11023 TTCATAATGTGGTTATCAAAATTTCATAATAAGGTAATCGAAAT
1 TTCATAGTGAGGTTATCAAAATTTCATAAGAAGATTATCGAAAT
* * *
11067 TTCATAGGGAGGTTATCGAAATTTCATAAGGAGATTATCGAAAT
1 TTCATAGTGAGGTTATCAAAATTTCATAAGAAGATTATCGAAAT
*
11111 TTCATAATGTA-GTTATCAAAATT
1 TTCATAGTG-AGGTTATCAAAATT
11134 GTATGGCATA
Statistics
Matches: 127, Mismatches: 27, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
44 126 0.99
45 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (44 bp):
TTCATAGTGAGGTTATCAAAATTTCATAAGAAGATTATCGAAAT
Found at i:11005 original size:66 final size:66
Alignment explanation
Indices: 10930--11133 Score: 225
Period size: 66 Copynumber: 3.1 Consensus size: 66
10920 TACCCCTAAA
* * * *
10930 AAAAATTCATAGCGAGCTTATCAAAATTTCATAA-GATGGTTATCAAAATTTCATAGTGTGGTTA
1 AAAATTTCATAG-GAGATTATCGAAATTTCATAAGGATGGTTATCAAAATTTCATAATGTGGTTA
10994 TC
65 TC
* * * ** *
10996 AAAATTTCATAGGAAGATTACCGTAATTTCATAATG-TGGTTATCAAAATTTCATAATAAGGTAA
1 AAAATTTCATAGG-AGATTATCGAAATTTCATAAGGATGGTTATCAAAATTTCATAATGTGGTTA
11060 TC
65 TC
* * * * *
11062 GAAATTTCATAGGGAGGTTATCGAAATTTCATAAGGA-GATTATCGAAATTTCATAATGTAGTTA
1 AAAATTTCATA-GGAGATTATCGAAATTTCATAAGGATGGTTATCAAAATTTCATAATGTGGTTA
11126 TC
65 TC
11128 AAAATT
1 AAAATT
11134 GTATGGCATA
Statistics
Matches: 113, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
65 1 0.01
66 109 0.96
67 3 0.03
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (66 bp):
AAAATTTCATAGGAGATTATCGAAATTTCATAAGGATGGTTATCAAAATTTCATAATGTGGTTAT
C
Found at i:11190 original size:31 final size:31
Alignment explanation
Indices: 11152--11228 Score: 154
Period size: 31 Copynumber: 2.5 Consensus size: 31
11142 TAAGTCCAAT
11152 TTTGCCCCCTGAACTTATACCAGTTAGACGC
1 TTTGCCCCCTGAACTTATACCAGTTAGACGC
11183 TTTGCCCCCTGAACTTATACCAGTTAGACGC
1 TTTGCCCCCTGAACTTATACCAGTTAGACGC
11214 TTTGCCCCCTGAACT
1 TTTGCCCCCTGAACT
11229 ATCGGTTTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.21, C:0.34, G:0.16, T:0.30
Consensus pattern (31 bp):
TTTGCCCCCTGAACTTATACCAGTTAGACGC
Found at i:11596 original size:22 final size:22
Alignment explanation
Indices: 11567--11711 Score: 150
Period size: 22 Copynumber: 6.6 Consensus size: 22
11557 CTTTAGGATT
* *
11567 TCAAAATTTCATTGTGTGGTTA
1 TCAAAATTTCATAGTGAGGTTA
* *
11589 CCAAAATTTCATTG-GAAGGTTA
1 TCAAAATTTCATAGTG-AGGTTA
* * *
11611 TCAAAATTTGATGGT-AGGGTA
1 TCAAAATTTCATAGTGAGGTTA
*
11632 TTCAAAATTTCATAGTAAGGTTA
1 -TCAAAATTTCATAGTGAGGTTA
* *
11655 TCAAAATTTCACAGTAAGGTTA
1 TCAAAATTTCATAGTGAGGTTA
* *
11677 TCAAAATTCCATAGTGTGGTTA
1 TCAAAATTTCATAGTGAGGTTA
11699 TCAAAATTTCATA
1 TCAAAATTTCATA
11712 AAGGGTTATC
Statistics
Matches: 104, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
21 6 0.06
22 93 0.89
23 5 0.05
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.37
Consensus pattern (22 bp):
TCAAAATTTCATAGTGAGGTTA
Found at i:11703 original size:66 final size:66
Alignment explanation
Indices: 11566--11723 Score: 171
Period size: 66 Copynumber: 2.4 Consensus size: 66
11556 TCTTTAGGAT
* ** * ** **
11566 TTCAAAATTTCATTGTGTGGTTACCAAAATTTCATTGGAAGGTTATCAAAATTTGATGGTAGGGT
1 TTCAAAATTTCATAGTAAGGTTATCAAAATTTCACAGGAAGGTTATCAAAATTCCATGGTAGGGT
11631 A
66 A
* *
11632 TTCAAAATTTCATAGTAAGGTTATCAAAATTTCACAGTAAGGTTATCAAAATTCCATAGT-GTGG
1 TTCAAAATTTCATAGTAAGGTTATCAAAATTTCACAGGAAGGTTATCAAAATTCCATGGTAG-GG
11696 T-
65 TA
11697 TATCAAAATTTCATA--AAGGGTTATCAA
1 T-TCAAAATTTCATAGTAA-GGTTATCAA
11724 TACCAACATT
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
64 2 0.03
65 11 0.14
66 66 0.84
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (66 bp):
TTCAAAATTTCATAGTAAGGTTATCAAAATTTCACAGGAAGGTTATCAAAATTCCATGGTAGGGT
A
Found at i:11876 original size:22 final size:23
Alignment explanation
Indices: 11851--11907 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
11841 ATGAGGTTTT
11851 CAAAATTTCATAGGG-AGACTAA
1 CAAAATTTCATAGGGAAGACTAA
* **
11873 CAAAATTTCAAAGGGAAGTTTAA
1 CAAAATTTCATAGGGAAGACTAA
11896 CAAAATTTCATA
1 CAAAATTTCATA
11908 TGTGAATTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 14 0.47
23 16 0.53
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.26
Consensus pattern (23 bp):
CAAAATTTCATAGGGAAGACTAA
Found at i:20210 original size:35 final size:35
Alignment explanation
Indices: 20171--20250 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
20161 GGACGGCCTC
* * *
20171 AATAATGCTCTTCAAAGTTATCAAAAGTTGAAGGA
1 AATAATGCTCTGCAAAGTTATCAAAAATTGAAGAA
20206 AATAATGCTCTGCAAAGTTATCAAAAATTGAAGAA
1 AATAATGCTCTGCAAAGTTATCAAAAATTGAAGAA
*
20241 AATAGTGCTC
1 AATAATGCTC
20251 AAAAGTTGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (35 bp):
AATAATGCTCTGCAAAGTTATCAAAAATTGAAGAA
Found at i:20252 original size:23 final size:23
Alignment explanation
Indices: 20226--20273 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
20216 TGCAAAGTTA
20226 TCAAAAATTGAAGAAAATAGTGC
1 TCAAAAATTGAAGAAAATAGTGC
*
20249 TCAAAAGTTGAAGAAAATAGTGC
1 TCAAAAATTGAAGAAAATAGTGC
20272 TC
1 TC
20274 TGCAAAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.23
Consensus pattern (23 bp):
TCAAAAATTGAAGAAAATAGTGC
Found at i:20286 original size:26 final size:26
Alignment explanation
Indices: 20227--20305 Score: 110
Period size: 26 Copynumber: 3.2 Consensus size: 26
20217 GCAAAGTTAT
*
20227 CAAAAATTGAAGAAAATAGTG--CT-
1 CAAAAGTTGAAGAAAATAGTGCTCTG
20250 CAAAAGTTGAAGAAAATAGTGCTCTG
1 CAAAAGTTGAAGAAAATAGTGCTCTG
* *
20276 CAAAAGTTGAAGGAAATAATGCTCTG
1 CAAAAGTTGAAGAAAATAGTGCTCTG
20302 CAAA
1 CAAA
20306 GGAATCTCTG
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
23 20 0.40
25 2 0.04
26 28 0.56
ACGTcount: A:0.47, C:0.11, G:0.20, T:0.22
Consensus pattern (26 bp):
CAAAAGTTGAAGAAAATAGTGCTCTG
Found at i:20567 original size:12 final size:12
Alignment explanation
Indices: 20558--20607 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
20548 AGAAGTTTTC
20558 TCCAAAGTTTAT
1 TCCAAAGTTTAT
*
20570 TCCAAAGCTTAT
1 TCCAAAGTTTAT
20582 TCCAAA-TCTTAT
1 TCCAAAGT-TTAT
* *
20594 TTCAAATTTTAT
1 TCCAAAGTTTAT
20606 TC
1 TC
20608 TCTTATTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 31 0.97
13 1 0.03
ACGTcount: A:0.32, C:0.20, G:0.04, T:0.44
Consensus pattern (12 bp):
TCCAAAGTTTAT
Found at i:21550 original size:27 final size:25
Alignment explanation
Indices: 21496--21556 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 25
21486 CTAAATTTTC
21496 AATAT-TTTAATAATGAAATAATTAA
1 AATATATTTAATAATGAAAT-ATTAA
21521 AATATTATTTAATAATGATAAT-TTAGA
1 AATA-TATTTAATAATGA-AATATTA-A
21548 AATATATTT
1 AATATATTT
21557 GAAAAATTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
25 4 0.12
26 9 0.28
27 16 0.50
28 3 0.09
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (25 bp):
AATATATTTAATAATGAAATATTAA
Found at i:23013 original size:2 final size:2
Alignment explanation
Indices: 23006--23041 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
22996 ACCCATATGA
23006 AT 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 AT
23042 TCTCAATGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23540 original size:19 final size:19
Alignment explanation
Indices: 23516--23555 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
23506 AGGCACTGTA
23516 CAGATGAGATTATACAGAT
1 CAGATGAGATTATACAGAT
23535 CAGATGAGATTATACAGAT
1 CAGATGAGATTATACAGAT
23554 CA
1 CA
23556 AATTCGCCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.25
Consensus pattern (19 bp):
CAGATGAGATTATACAGAT
Found at i:25604 original size:120 final size:120
Alignment explanation
Indices: 25386--25632 Score: 476
Period size: 120 Copynumber: 2.1 Consensus size: 120
25376 TTCCACCAGA
*
25386 TCTTGTCTCCTCCCTGGTTCCTTGTGCATCCAACTTCCTATCATCACTTCTCTTGTTCTTTTCCT
1 TCTTTTCTCCTCCCTGGTTCCTTGTGCATCCAACTTCCTATCATCACTTCTCTTGTTCTTTTCCT
25451 TCTCTTCAGCCAATACATTGGCATTCTTCGCCACCAATCTGACCATTCCCTCATC
66 TCTCTTCAGCCAATACATTGGCATTCTTCGCCACCAATCTGACCATTCCCTCATC
25506 TCTTTTCTCCTCCCTGGTTCCTTGTGCATCCAACTTCCTATCATCACTTCTCTTGTTCTTTTCCT
1 TCTTTTCTCCTCCCTGGTTCCTTGTGCATCCAACTTCCTATCATCACTTCTCTTGTTCTTTTCCT
*
25571 TCTCTTCAGCCAATACATTGGCATTCTTTGCCACCAATCTGACCATTCCCTCATC
66 TCTCTTCAGCCAATACATTGGCATTCTTCGCCACCAATCTGACCATTCCCTCATC
25626 TCTTTTC
1 TCTTTTC
25633 CGGTCAGTGC
Statistics
Matches: 125, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 125 1.00
ACGTcount: A:0.15, C:0.36, G:0.09, T:0.41
Consensus pattern (120 bp):
TCTTTTCTCCTCCCTGGTTCCTTGTGCATCCAACTTCCTATCATCACTTCTCTTGTTCTTTTCCT
TCTCTTCAGCCAATACATTGGCATTCTTCGCCACCAATCTGACCATTCCCTCATC
Found at i:29878 original size:129 final size:132
Alignment explanation
Indices: 29622--29878 Score: 360
Period size: 129 Copynumber: 2.0 Consensus size: 132
29612 GTTGTTACAG
* * *
29622 ACTCATTGAGTGTAACTGAACAAAATTCATAGCCTAAAAATTCGTCCTTGCTTCCTAACTACCGA
1 ACTCATTGACTGTAACTGAACAAAATTCATAGCCTAAAAATTCATCCTTGCTTCCTAACTACCAA
* ** * *
29687 ATTTAGTCTAACCAAGTAAAAGCTGTAACTTTAAACAGCATATCCTTTGCATTGAGATAGAAGAA
66 ATTTAGTCTAACCAAGTAAAAGCTGTAACTTTAAACAGCACATCCTTCACATTAAGAAAGAAGAA
29752 TA
131 TA
** * *
29754 ACTCATT-ACTGTAACTGAATGAAATTCATAGCCTAGAAATTCAT-CTTGCTTCCTAGCT-CCAA
1 ACTCATTGACTGTAACTGAACAAAATTCATAGCCTAAAAATTCATCCTTGCTTCCTAACTACCAA
*
29816 ATTTAGTCTAA-CAGAGTAAAAGCTGTAATTTTAAACAGCACATCCTTCACATTAAGAAAGAAG
66 ATTTAGTCTAACCA-AGTAAAAGCTGTAACTTTAAACAGCACATCCTTCACATTAAGAAAGAAG
29879 TATGACCAAA
Statistics
Matches: 111, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
128 2 0.02
129 57 0.51
130 13 0.12
131 32 0.29
132 7 0.06
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (132 bp):
ACTCATTGACTGTAACTGAACAAAATTCATAGCCTAAAAATTCATCCTTGCTTCCTAACTACCAA
ATTTAGTCTAACCAAGTAAAAGCTGTAACTTTAAACAGCACATCCTTCACATTAAGAAAGAAGAA
TA
Found at i:31979 original size:22 final size:22
Alignment explanation
Indices: 31949--32001 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
31939 CTGGGTATTT
* * *
31949 GAGAGAGAGAAAGGAGAAAGGA
1 GAGAAAGAGAAAGAAGAAAGAA
*
31971 GAGAAAGAGAGAGAAGAAAGAA
1 GAGAAAGAGAAAGAAGAAAGAA
*
31993 AAGAAAGAG
1 GAGAAAGAG
32002 CTTTCTTTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (22 bp):
GAGAAAGAGAAAGAAGAAAGAA
Done.