Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009599.1 Corchorus capsularis cultivar CVL-1 contig09620, 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: 39358
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:4620 original size:21 final size:21
Alignment explanation
Indices: 4594--4644 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
4584 AGGGGGTTGT
4594 TGATGGTGCTGCTGCTGGTGC
1 TGATGGTGCTGCTGCTGGTGC
*
4615 TGATGGTGCTGCTGCTGTTGC
1 TGATGGTGCTGCTGCTGGTGC
*
4636 TGCTGGTGC
1 TGATGGTGC
4645 ATCCTAGCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.04, C:0.20, G:0.41, T:0.35
Consensus pattern (21 bp):
TGATGGTGCTGCTGCTGGTGC
Found at i:10288 original size:58 final size:58
Alignment explanation
Indices: 10198--10320 Score: 219
Period size: 58 Copynumber: 2.1 Consensus size: 58
10188 GGTGCATTCA
*
10198 ATATAATATTCTAAATTTTTAGGGTCTGTATGCTCAACTCCAAATTAATTGGAACCCG
1 ATATAATATTCTAAACTTTTAGGGTCTGTATGCTCAACTCCAAATTAATTGGAACCCG
* *
10256 ATATAATATTCTAAACTTTTAGGGTCTTTATGCTCAACTCCGAATTAATTGGAACCCG
1 ATATAATATTCTAAACTTTTAGGGTCTGTATGCTCAACTCCAAATTAATTGGAACCCG
10314 ATATAAT
1 ATATAAT
10321 TATAAAATAT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (58 bp):
ATATAATATTCTAAACTTTTAGGGTCTGTATGCTCAACTCCAAATTAATTGGAACCCG
Found at i:10732 original size:59 final size:59
Alignment explanation
Indices: 10625--10747 Score: 162
Period size: 59 Copynumber: 2.1 Consensus size: 59
10615 CTGCTCAAAT
*
10625 ATAGGTTCTTAACATATGCAAAAATCTCAATTTAGGGCTCATAATTTTAATTTGGTTAA
1 ATAGGTTCTTAACATATGCAAAAATCTCAATTAAGGGCTCATAATTTTAATTTGGTTAA
* * *
10684 ATAGG-TCTTAAACATATGC-GAAATACTCAATTGAAGGTC-CATACTTTTAATTTGGTTAA
1 ATAGGTTCTT-AACATATGCAAAAAT-CTCAATT-AAGGGCTCATAATTTTAATTTGGTTAA
10743 ATAGG
1 ATAGG
10748 ACCCCTAATG
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
58 8 0.14
59 45 0.79
60 4 0.07
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (59 bp):
ATAGGTTCTTAACATATGCAAAAATCTCAATTAAGGGCTCATAATTTTAATTTGGTTAA
Found at i:10943 original size:57 final size:57
Alignment explanation
Indices: 10842--10949 Score: 155
Period size: 57 Copynumber: 1.9 Consensus size: 57
10832 GCATTTTCGG
* *
10842 ATACGTTAAGTCCCTATTTAACCAAATTAAAAACATGGACCCTAAATTGAGTTTCCC
1 ATACGTTAAGACCCTATTTAACCAAATTAAAAACATAGACCCTAAATTGAGTTTCCC
* * *
10899 ATACGTTAGGACCCTATTTAACCAAATTAAAAATATA-AGTCCTAAATTGAG
1 ATACGTTAAGACCCTATTTAACCAAATTAAAAACATAGA-CCCTAAATTGAG
10950 CATTTTCGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
56 1 0.02
57 44 0.98
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (57 bp):
ATACGTTAAGACCCTATTTAACCAAATTAAAAACATAGACCCTAAATTGAGTTTCCC
Found at i:13674 original size:150 final size:150
Alignment explanation
Indices: 13398--13679 Score: 420
Period size: 150 Copynumber: 1.9 Consensus size: 150
13388 CAACTCACAA
* * * * *
13398 AAGGCCCGAAGTACATGCAGATGGGTTGATCGATCTTGAAGATCGAGAGAATGGCTGTTGGTATT
1 AAGGCCCGAAGTACATGCAGATGGGTGGATCGATCCTAAAGATCGAGAGAATAGCTGATGGTATT
** * * * **
13463 GTTTAAATTCCATCTCCACAAATTAAACCTGAAGCAACTGCCCCTGTGTAATCATCAGCATCCTT
66 GTCCAAATACCATCACCACAAATTAAACCTGAAGCAACTGCCCCAGCATAATCATCAGCATCCTT
13528 CCCTGATCAACTACTTGCAG
131 CCCTGATCAACTACTTGCAG
*
13548 AAGGCCCGAAGTACATGCAGATGGGTGGATCGATCCTAAAGATCGAGAGTATAGCTGATGGTATT
1 AAGGCCCGAAGTACATGCAGATGGGTGGATCGATCCTAAAGATCGAGAGAATAGCTGATGGTATT
* * *
13613 GTCCAAATACCGTCACCACAAATTAAACCTGAAGCAACTGCCCCAGCATAATCCTCTGCATCCTT
66 GTCCAAATACCATCACCACAAATTAAACCTGAAGCAACTGCCCCAGCATAATCATCAGCATCCTT
13678 CC
131 CC
13680 GGTTCAATTG
Statistics
Matches: 116, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
150 116 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (150 bp):
AAGGCCCGAAGTACATGCAGATGGGTGGATCGATCCTAAAGATCGAGAGAATAGCTGATGGTATT
GTCCAAATACCATCACCACAAATTAAACCTGAAGCAACTGCCCCAGCATAATCATCAGCATCCTT
CCCTGATCAACTACTTGCAG
Found at i:17972 original size:148 final size:148
Alignment explanation
Indices: 17704--18000 Score: 594
Period size: 148 Copynumber: 2.0 Consensus size: 148
17694 TAATTTCTTA
17704 TAGCTAAAAGTTTATTACTTCTGCCAAATTTTACAGGTTGATTACCCCTAAAGCTAAGCTTCTAA
1 TAGCTAAAAGTTTATTACTTCTGCCAAATTTTACAGGTTGATTACCCCTAAAGCTAAGCTTCTAA
17769 TGCTTTAAAACCAAATTCAAAGAAGGTTTGAATTTCAATTATAATATGATCACGGAATGAAATTA
66 TGCTTTAAAACCAAATTCAAAGAAGGTTTGAATTTCAATTATAATATGATCACGGAATGAAATTA
17834 GCCAAAAATTGATAAAAT
131 GCCAAAAATTGATAAAAT
17852 TAGCTAAAAGTTTATTACTTCTGCCAAATTTTACAGGTTGATTACCCCTAAAGCTAAGCTTCTAA
1 TAGCTAAAAGTTTATTACTTCTGCCAAATTTTACAGGTTGATTACCCCTAAAGCTAAGCTTCTAA
17917 TGCTTTAAAACCAAATTCAAAGAAGGTTTGAATTTCAATTATAATATGATCACGGAATGAAATTA
66 TGCTTTAAAACCAAATTCAAAGAAGGTTTGAATTTCAATTATAATATGATCACGGAATGAAATTA
17982 GCCAAAAATTGATAAAAT
131 GCCAAAAATTGATAAAAT
18000 T
1 T
18001 TGGTAACAAT
Statistics
Matches: 149, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
148 149 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.33
Consensus pattern (148 bp):
TAGCTAAAAGTTTATTACTTCTGCCAAATTTTACAGGTTGATTACCCCTAAAGCTAAGCTTCTAA
TGCTTTAAAACCAAATTCAAAGAAGGTTTGAATTTCAATTATAATATGATCACGGAATGAAATTA
GCCAAAAATTGATAAAAT
Found at i:19138 original size:21 final size:21
Alignment explanation
Indices: 19114--19153 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19104 TAGTATTTTA
19114 TTAAATATTT-CAACTTTTTGG
1 TTAAAT-TTTACAACTTTTTGG
*
19135 TTAAATTTTACAATTTTTT
1 TTAAATTTTACAACTTTTT
19154 TTCATAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.57
Consensus pattern (21 bp):
TTAAATTTTACAACTTTTTGG
Found at i:19814 original size:2 final size:2
Alignment explanation
Indices: 19807--19885 Score: 70
Period size: 2 Copynumber: 44.5 Consensus size: 2
19797 CCGTTTAGTA
*
19807 AT AT AT AT A- AT -T AA AT AT AT AT -T AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
19845 A- AT AT -T AA AT AT AT AT A- AT -T AT AT AT AT A- AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19881 AT AT A
1 AT AT A
19886 ATTATTAAAC
Statistics
Matches: 63, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
1 10 0.16
2 53 0.84
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:19832 original size:21 final size:22
Alignment explanation
Indices: 19805--19890 Score: 95
Period size: 24 Copynumber: 3.7 Consensus size: 22
19795 AACCGTTTAG
19805 TAATATATATAATTA-AATATA
1 TAATATATATAATTATAATATA
*
19826 TATTATATAT-ATATATAATAATA
1 TAATATATATAAT-TATAAT-ATA
19849 TTAAATATATATAATTATATATATAA
1 -T-AATATATATAATTATA-ATAT-A
19875 TAATATATATAATTAT
1 TAATATATATAATTAT
19891 TAAACGGTTC
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
20 2 0.04
21 11 0.20
22 3 0.05
23 3 0.05
24 16 0.29
25 15 0.27
26 5 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATATATATAATTATAATATA
Found at i:19868 original size:31 final size:32
Alignment explanation
Indices: 19816--19880 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 32
19806 AATATATATA
*
19816 ATTAAATATATATTATATATATATATAATAAT
1 ATTAAATATATATAATATATATATATAATAAT
19848 ATTAAATATATATAAT-TATATATATAATAAT
1 ATTAAATATATATAATATATATATATAATAAT
19879 AT
1 AT
19881 ATATAATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 17 0.53
32 15 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
ATTAAATATATATAATATATATATATAATAAT
Found at i:20262 original size:37 final size:35
Alignment explanation
Indices: 20206--20274 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
20196 ACGAACTTGA
*
20206 ACTCATAATCGAGCACTCTATCAACAAACCACACG
1 ACTCATAATCGAGCACTCTACCAACAAACCACACG
*
20241 ACTCATAATCAAGAGCACTCTACCAACCAACCAC
1 ACTCATAATC--GAGCACTCTACCAACAAACCAC
20275 GTTATTATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 10 0.33
37 20 0.67
ACGTcount: A:0.41, C:0.36, G:0.07, T:0.16
Consensus pattern (35 bp):
ACTCATAATCGAGCACTCTACCAACAAACCACACG
Found at i:30661 original size:80 final size:78
Alignment explanation
Indices: 30520--30676 Score: 192
Period size: 80 Copynumber: 2.0 Consensus size: 78
30510 AATAAACATC
* * *
30520 CTTAACCTTCAAATGACAAAGATTACAGCATTTCAGCAAATTCCAATGCTTCCTAGCTTACCATA
1 CTTAACCTTCAAATGACAAAAATTACAGCATTTCAGCAAATTCCAATACTTCCAAGCTTACC--A
*
30585 TTCAACTAAAACAAT
64 TTCAACCAAAACAAT
* * * *
30600 CTTAACCTTGAAATGACAAAAATTACAGCGTTTCAGCAGATTCC-ATCACTTTCAATG-TTACCA
1 CTTAACCTTCAAATGACAAAAATTACAGCATTTCAGCAAATTCCAAT-ACTTCCAA-GCTTACCA
30663 TTCAACCAAAACAA
64 TTCAACCAAAACAA
30677 ATAATCCCAA
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 14 0.21
79 2 0.03
80 50 0.75
81 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.08, T:0.28
Consensus pattern (78 bp):
CTTAACCTTCAAATGACAAAAATTACAGCATTTCAGCAAATTCCAATACTTCCAAGCTTACCATT
CAACCAAAACAAT
Found at i:31941 original size:21 final size:21
Alignment explanation
Indices: 31879--31945 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 21
31869 GTTCAATTTG
31879 TAAAATTAAATTTTGGATCAT
1 TAAAATTAAATTTTGGATCAT
* ** *
31900 TAATATCTATTTTGTTAGGATTAT
1 TAAAAT-TAAATT-TT-GGATCAT
31924 TAAAATTAAATTTTGGATCAT
1 TAAAATTAAATTTTGGATCAT
31945 T
1 T
31946 TTAAAGTGTT
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
21 12 0.34
22 6 0.17
23 6 0.17
24 11 0.31
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.48
Consensus pattern (21 bp):
TAAAATTAAATTTTGGATCAT
Found at i:35985 original size:13 final size:14
Alignment explanation
Indices: 35967--35996 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
35957 GGGCAATTTG
35967 TATA-TTATGCACA
1 TATATTTATGCACA
35980 TATATTTATGCACA
1 TATATTTATGCACA
35994 TAT
1 TAT
35997 CTTTGTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (14 bp):
TATATTTATGCACA
Found at i:36980 original size:29 final size:29
Alignment explanation
Indices: 36913--37015 Score: 107
Period size: 30 Copynumber: 3.4 Consensus size: 29
36903 ACTTAATACC
**
36913 CATTTTGCCCCCTGAACTTGTATCGTTTGGA
1 CATTTTGCCCCCTGAACTTCAAT--TTTGGA
* * *
36944 CGTTTTGCCCCTTGAACTTCAATTTTGGG
1 CATTTTGCCCCCTGAACTTCAATTTTGGA
**
36973 CATTTTGCCCCCAAAACTCTCAATTTTGGA
1 CATTTTGCCCCCTGAACT-TCAATTTTGGA
*
37003 CATTTTACCCCCT
1 CATTTTGCCCCCT
37016 CTCAAACGAT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
29 19 0.32
30 21 0.36
31 19 0.32
ACGTcount: A:0.18, C:0.29, G:0.15, T:0.38
Consensus pattern (29 bp):
CATTTTGCCCCCTGAACTTCAATTTTGGA
Found at i:37716 original size:1 final size:1
Alignment explanation
Indices: 37710--37747 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
37700 ATATTCTTTG
37710 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
37748 ATCTTAATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:38336 original size:7 final size:7
Alignment explanation
Indices: 38324--38348 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
38314 AGGTGTCGAT
38324 GGCAGTC
1 GGCAGTC
38331 GGCAGTC
1 GGCAGTC
38338 GGCAGTC
1 GGCAGTC
38345 GGCA
1 GGCA
38349 AATAACATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.28, G:0.44, T:0.12
Consensus pattern (7 bp):
GGCAGTC
Done.