Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013730.1 Corchorus olitorius cultivar O-4 contig13763, 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: 23022
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:979 original size:15 final size:15
Alignment explanation
Indices: 959--1000 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
949 ACAGAGATTG
959 ACAGAAAGCAATTAA
1 ACAGAAAGCAATTAA
*
974 ACAGAAAACAATTAA
1 ACAGAAAGCAATTAA
*
989 ATTAGAAAGCAA
1 A-CAGAAAGCAA
1001 AGCAAAGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.62, C:0.12, G:0.12, T:0.14
Consensus pattern (15 bp):
ACAGAAAGCAATTAA
Found at i:4863 original size:39 final size:39
Alignment explanation
Indices: 4818--4900 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 39
4808 AATAAGACTT
* * *
4818 TGAAATTCACTAAGAAAACATTGACCCTGAACAGGATTC
1 TGAAATTAACTAAGAAAACAATGACCCTAAACAGGATTC
* * * *
4857 TGAAATTAACTGATAAAACAATGATCCTAAATAGGATTC
1 TGAAATTAACTAAGAAAACAATGACCCTAAACAGGATTC
*
4896 AGAAA
1 TGAAA
4901 ACAATGATCC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.24
Consensus pattern (39 bp):
TGAAATTAACTAAGAAAACAATGACCCTAAACAGGATTC
Found at i:4902 original size:27 final size:27
Alignment explanation
Indices: 4871--4950 Score: 115
Period size: 28 Copynumber: 2.9 Consensus size: 27
4861 ATTAACTGAT
*
4871 AAAACAATGATCCTAAATAGGATTCAG
1 AAAACAATGATCCTGAATAGGATTCAG
* *
4898 AAAACAATGATCCTGAATAGCATCTGAG
1 AAAACAATGATCCTGAATAGGAT-TCAG
*
4926 AAAGCAATGATCCTGAATAGGATTC
1 AAAACAATGATCCTGAATAGGATTC
4951 TAAAATTCAC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 22 0.48
28 24 0.52
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (27 bp):
AAAACAATGATCCTGAATAGGATTCAG
Found at i:4936 original size:28 final size:28
Alignment explanation
Indices: 4866--4945 Score: 108
Period size: 27 Copynumber: 2.9 Consensus size: 28
4856 CTGAAATTAA
* * *
4866 CTGATAAAACAATGATCCTAAATAGGAT
1 CTGAGAAAACAATGATCCTGAATAGCAT
*
4894 -TCAGAAAACAATGATCCTGAATAGCAT
1 CTGAGAAAACAATGATCCTGAATAGCAT
*
4921 CTGAGAAAGCAATGATCCTGAATAG
1 CTGAGAAAACAATGATCCTGAATAG
4946 GATTCTAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 23 0.51
28 22 0.49
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (28 bp):
CTGAGAAAACAATGATCCTGAATAGCAT
Found at i:4987 original size:40 final size:39
Alignment explanation
Indices: 4926--5209 Score: 292
Period size: 40 Copynumber: 7.3 Consensus size: 39
4916 AGCATCTGAG
* * *
4926 AAAGCAATGATCCTGAATAGGATTCTAAAATTCACTTGAT
1 AAAGCAATGATCCTGAGTAGGATTCTGAAATT-AATTGAT
* *
4966 AAAGCAATGATCATGAGTAGGATTCTGAAATTAATCTAAT
1 AAAGCAATGATCCTGAGTAGGATTCTGAAATTAAT-TGAT
* * *
5006 AAAGCAATGATCCCT-AATAGGCTTGTG--ATTAATTTGAT
1 AAAGCAATGAT-CCTGAGTAGGATTCTGAAATTAA-TTGAT
5044 AAAGCAATGATCCTGAGTAGGATTCTGAAATTAATTTGAT
1 AAAGCAATGATCCTGAGTAGGATTCTGAAATTAA-TTGAT
* *
5084 AAAGCAATGATCTTGAGTAGGATTCTGAAATTAATCTAAT
1 AAAGCAATGATCCTGAGTAGGATTCTGAAATTAAT-TGAT
* * *
5124 AAAGCAATGATCCAGAGTAGGA-TCGTG--ATTGATTGGT
1 AAAGCAATGATCCTGAGTAGGATTC-TGAAATTAATTGAT
* * ** * *
5161 AAAGAAATGATCCTGAGCAGGATTCTGAAATCGACTAAT
1 AAAGCAATGATCCTGAGTAGGATTCTGAAATTAATTGAT
5200 AAAGCAATGA
1 AAAGCAATGA
5210 CCATGAACAA
Statistics
Matches: 205, Mismatches: 28, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
37 26 0.13
38 35 0.17
39 21 0.10
40 121 0.59
41 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (39 bp):
AAAGCAATGATCCTGAGTAGGATTCTGAAATTAATTGAT
Found at i:5063 original size:78 final size:79
Alignment explanation
Indices: 4926--5146 Score: 284
Period size: 78 Copynumber: 2.8 Consensus size: 79
4916 AGCATCTGAG
* * * *
4926 AAAGCAATGATCCTGAATAGGATTCTAAAATTCACTTGATAAAGCAATGATCATGAGTAGGATTC
1 AAAGCAATGATCCTGAATAGGATTCT-GAATTAATTTGATAAAGCAATGATCCTGAGTAGGATTC
4991 TGAAATTAATCTAAT
65 TGAAATTAATCTAAT
* *
5006 AAAGCAATGATCCCT-AATAGGCTTGTG-ATTAATTTGATAAAGCAATGATCCTGAGTAGGATTC
1 AAAGCAATGAT-CCTGAATAGGATTCTGAATTAATTTGATAAAGCAATGATCCTGAGTAGGATTC
* *
5069 TGAAATTAATTTGAT
65 TGAAATTAATCTAAT
* * * * *
5084 AAAGCAATGATCTTGAGTAGGATTCTGAAATTAATCTAATAAAGCAATGATCCAGAGTAGGAT
1 AAAGCAATGATCCTGAATAGGATTCTG-AATTAATTTGATAAAGCAATGATCCTGAGTAGGAT
5147 CGTGATTGAT
Statistics
Matches: 122, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
77 2 0.02
78 66 0.54
80 51 0.42
81 3 0.02
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (79 bp):
AAAGCAATGATCCTGAATAGGATTCTGAATTAATTTGATAAAGCAATGATCCTGAGTAGGATTCT
GAAATTAATCTAAT
Found at i:5134 original size:118 final size:117
Alignment explanation
Indices: 4926--5215 Score: 402
Period size: 118 Copynumber: 2.5 Consensus size: 117
4916 AGCATCTGAG
* * *
4926 AAAGCAATGATCCTGAATAGGATTCTAAAATTCACTTGATAAAGCAATGATCATGAGTAGGATTC
1 AAAGCAATGATCCTGAGTAGGATTCTGAAATTAACTTGATAAAGCAATGATCATGAGTAGGATTC
** * *
4991 TGAAATTAATCTAATAAAGCAATGATCCCTAATAGGCTTGTGATTAATTTGAT
66 TGAAATTAATCTAATAAAGCAATGATCCAGAATAGGATCGTGATTAA-TTGAT
* *
5044 AAAGCAATGATCCTGAGTAGGATTCTGAAATTAATTTGATAAAGCAATGATCTTGAGTAGGATTC
1 AAAGCAATGATCCTGAGTAGGATTCTGAAATTAACTTGATAAAGCAATGATCATGAGTAGGATTC
* * *
5109 TGAAATTAATCTAATAAAGCAATGATCCAGAGTAGGATCGTGATTGATTGGT
66 TGAAATTAATCTAATAAAGCAATGATCCAGAATAGGATCGTGATTAATTGAT
* * ** * *
5161 AAAGAAATGATCCTGAGCAGGATTCTGAAATCGAC-TAATAAAGCAATGACCATGA
1 AAAGCAATGATCCTGAGTAGGATTCTGAAATTAACTTGATAAAGCAATGATCATGA
5216 ACAAGATTAA
Statistics
Matches: 152, Mismatches: 20, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
116 17 0.11
117 34 0.22
118 101 0.66
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (117 bp):
AAAGCAATGATCCTGAGTAGGATTCTGAAATTAACTTGATAAAGCAATGATCATGAGTAGGATTC
TGAAATTAATCTAATAAAGCAATGATCCAGAATAGGATCGTGATTAATTGAT
Found at i:5237 original size:76 final size:77
Alignment explanation
Indices: 5083--5259 Score: 189
Period size: 76 Copynumber: 2.3 Consensus size: 77
5073 ATTAATTTGA
* * * * ** *
5083 TAAAGCAATGATCTTGAGTAGGATTCTGAAATTAATCTAATAAAGCAATGATCCAGAGTAGGATC
1 TAAAGAAATGATCCTGAGCAGGATTCTGAAATCAATCTAATAAAGCAATGATCCAGAACAAGATC
*** *
5148 GTGATTGATTGG
66 AAAATTGACTGG
*
5160 TAAAGAAATGATCCTGAGCAGGATTCTGAAATCGA-CTAATAAAGCAATGA-CCATGAACAAGAT
1 TAAAGAAATGATCCTGAGCAGGATTCTGAAATCAATCTAATAAAGCAATGATCCA-GAACAAGAT
*
5223 TAAAATTGACTGG
65 CAAAATTGACTGG
* *
5236 TAAA-AACTGATCCTAAGCAGGATT
1 TAAAGAAATGATCCTGAGCAGGATT
5260 AAAACACATA
Statistics
Matches: 84, Mismatches: 15, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
75 21 0.25
76 33 0.39
77 30 0.36
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (77 bp):
TAAAGAAATGATCCTGAGCAGGATTCTGAAATCAATCTAATAAAGCAATGATCCAGAACAAGATC
AAAATTGACTGG
Found at i:5629 original size:140 final size:138
Alignment explanation
Indices: 5309--5660 Score: 453
Period size: 139 Copynumber: 2.5 Consensus size: 138
5299 ATATAGAATT
* * *
5309 CCCGGAGGACTTGTCAGAATTAATACCCGGAGGTTTCTGAAATCGTAG-CCGAAGGTCTTACAAA
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATCGT-GCCCGGAGGTCTTACAAA
* * *
5373 TGCAAACTCGACCTTGAGCAAGGTTTTTAAAAAATAAAGCAACTTTGATTAACAACTTTATGAAA
65 TGCAAACTCAACCTTGAGCAAGGTTTTTAAAAAATAAAGAAACTTTGATTAAAAAC-TTATGAAA
5438 AGAAGTGATA
129 AGAAGTGATA
* * *
5448 CCCGGAGAATTTATCAGAATTAACACCCGGAGGTTTCTGAAATGGTGCCCGGAGGTCTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATCGTGCCCGGAGGTCTTACAAAT
* **
5513 GCAAACTCAACCTTGAGCAAGGTTTTTTTTTTGAAATTTAAACGAAACTTTGATTAAAAAC-T-T
66 GCAAACTCAACCTTGAGCAAGG-----TTTTTAAAAAATAAA-GAAACTTTGATTAAAAACTTAT
*
5576 GATAAG-A-TGATA
125 GAAAAGAAGTGATA
* * *
5588 CCCGGAGGATTTATCAGAATTAATACCCTGAGGTTTCTGAAATTGTGCCTGGAGGTCTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATCGTGCCCGGAGGTCTTACAAAT
5653 GCAAACTC
66 GCAAACTC
5661 TGAGTAGAGA
Statistics
Matches: 188, Mismatches: 18, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
138 1 0.01
139 78 0.41
140 73 0.39
141 1 0.01
142 6 0.03
143 1 0.01
144 12 0.06
145 16 0.09
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (138 bp):
CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATCGTGCCCGGAGGTCTTACAAAT
GCAAACTCAACCTTGAGCAAGGTTTTTAAAAAATAAAGAAACTTTGATTAAAAACTTATGAAAAG
AAGTGATA
Found at i:18966 original size:48 final size:48
Alignment explanation
Indices: 18846--18972 Score: 139
Period size: 48 Copynumber: 2.6 Consensus size: 48
18836 GTGGTGTCTG
* ** *
18846 CCCGACCAAGGCCATGATCAACTTCTCTTTCCCTATCTCTGATGTCCA
1 CCCGAACAAGGCCAACATCAACTTCTCTTTCCCTATCTCTGACGTCCA
* * *
18894 CCTGAACAAGGCCAGCATCAACTTCTCTTTCCCTATCTCTGACGT-TA
1 CCCGAACAAGGCCAACATCAACTTCTCTTTCCCTATCTCTGACGTCCA
* * * *
18941 GCCCGACCAAGTCCAACGTCGACTTCTCTTTC
1 -CCCGAACAAGGCCAACATCAACTTCTCTTTC
18973 TTCAACTTCT
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
47 1 0.02
48 65 0.98
ACGTcount: A:0.21, C:0.37, G:0.13, T:0.28
Consensus pattern (48 bp):
CCCGAACAAGGCCAACATCAACTTCTCTTTCCCTATCTCTGACGTCCA
Done.