Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018246.1 Corchorus olitorius cultivar O-4 contig18279, 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: 47931
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:7268 original size:29 final size:29
Alignment explanation
Indices: 7236--7324 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 29
7226 TATAGTAGAT
7236 TTTTAAGGAAGGACTAATATTTTACTCTG
1 TTTTAAGGAAGGACTAATATTTTACTCTG
* * * *
7265 TTTTAAGG-A--ACTATTAATTATAGT-AG
1 TTTTAAGGAAGGACTAAT-ATTTTACTCTG
*
7291 ACTTTAAGGAAGGACTAATATTTTACTCTG
1 -TTTTAAGGAAGGACTAATATTTTACTCTG
7321 TTTT
1 TTTT
7325 TTGAGGAACT
Statistics
Matches: 44, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
26 6 0.14
27 13 0.30
28 2 0.05
29 17 0.39
30 6 0.14
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.43
Consensus pattern (29 bp):
TTTTAAGGAAGGACTAATATTTTACTCTG
Found at i:10013 original size:9 final size:9
Alignment explanation
Indices: 9999--10023 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
9989 CATATGTGTA
9999 TATCTATAC
1 TATCTATAC
10008 TATCTATAC
1 TATCTATAC
10017 TATCTAT
1 TATCTAT
10024 CTAATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (9 bp):
TATCTATAC
Found at i:11634 original size:178 final size:177
Alignment explanation
Indices: 11269--11651 Score: 493
Period size: 178 Copynumber: 2.1 Consensus size: 177
11259 CCATAAGCGC
* * * ** * *
11269 AAATTATGTAATATTAAGTAGACCGTTTATTTTCGTTAACCGAAACAACTAATTCTTTGGAAGCA
1 AAATTATATAATATTAAGTAGACCGTCTATTCTCGTTAACCGAAACAAAAAATTCTTCGGAAACA
* **
11334 TTTTTTATACCTTGAACAATAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATAGAAC
66 TTTTTGATACCTTGAACAATAAATTTAGTTTTCGAGTCCCGCATGAAAGTTGTAGATCATAGAAC
*
11399 AACCTTTCAAGAGACACTTAAATCATCTCAATTAGACAACTGAAGCA
131 AACCTTTCAAGAGACACTTAAATCATCTCAATCAGACAACTGAAGCA
*
11446 AAAGTTATATAATATTAAGTGGACCGTCTATTCTCGTTAACCGAAACAAAAAAATT-TTCGGAAA
1 AAA-TTATATAATATTAAGTAGACCGTCTATTCTCGTTAACCGAAAC-AAAAAATTCTTCGGAAA
* *
11510 CATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCCGCATGAAAGTTGTAGATCATGG
64 CATTTTTGATACCTTG-AACAATAAATTTAGTTTTCGAGTCCCGCATGAAAGTTGTAGATCATAG
* * * * * *
11574 AACAATCTTTTAATAGACACTTAAATCATCTTAATCGGATAACTGGAGAG-A
128 AACAACCTTTCAAGAGACACTTAAATCATCTCAATCAGACAACT-GA-AGCA
* *
11625 AAATTATATAATGTTAAAATAGACCGT
1 AAATTATATAATATT-AAGTAGACCGT
11652 TTAACCAAAC
Statistics
Matches: 177, Mismatches: 23, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
177 7 0.04
178 147 0.83
179 21 0.12
180 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (177 bp):
AAATTATATAATATTAAGTAGACCGTCTATTCTCGTTAACCGAAACAAAAAATTCTTCGGAAACA
TTTTTGATACCTTGAACAATAAATTTAGTTTTCGAGTCCCGCATGAAAGTTGTAGATCATAGAAC
AACCTTTCAAGAGACACTTAAATCATCTCAATCAGACAACTGAAGCA
Found at i:12179 original size:56 final size:56
Alignment explanation
Indices: 12093--12203 Score: 195
Period size: 56 Copynumber: 2.0 Consensus size: 56
12083 TTCGAGTCAA
*
12093 ACATAGTATTAAATTCATTTAATAAGAAGAATGCAAACGGATAATGAAGAAAATTG
1 ACATAGTATTAAATCCATTTAATAAGAAGAATGCAAACGGATAATGAAGAAAATTG
* *
12149 ACATAGTATTAAATCCATTTAATAAGAAGAATGCAAATGGGTAATGAAGAAAATT
1 ACATAGTATTAAATCCATTTAATAAGAAGAATGCAAACGGATAATGAAGAAAATT
12204 TACTCAATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.27
Consensus pattern (56 bp):
ACATAGTATTAAATCCATTTAATAAGAAGAATGCAAACGGATAATGAAGAAAATTG
Found at i:25992 original size:16 final size:16
Alignment explanation
Indices: 25971--26015 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
25961 AACATCCCGA
*
25971 ACCCGAACCCGAAACT
1 ACCCGAACCCGAAAAT
*
25987 ACCCGAGCCCGAAAAT
1 ACCCGAACCCGAAAAT
26003 ACCCGAACCCGAA
1 ACCCGAACCCGAA
26016 GCAGCCCGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.38, C:0.42, G:0.16, T:0.04
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:26580 original size:31 final size:31
Alignment explanation
Indices: 26509--26580 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
26499 GTCTATCAGA
*
26509 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
*
26540 TAATT-ATTTGTTTAATTTAATG-C-TTAATTT
1 T-TTTAATTTGTTTAATTTAA-GACTTTAATTT
26570 GTTTTAATTTG
1 -TTTTAATTTG
26581 CAATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 8 0.24
31 23 0.68
32 3 0.09
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:27061 original size:16 final size:16
Alignment explanation
Indices: 27037--27143 Score: 94
Period size: 16 Copynumber: 6.7 Consensus size: 16
27027 CTACCCGAGA
*
27037 CCGAGCCCGAAAATAC
1 CCGAACCCGAAAATAC
*
27053 CCGAACCCG-ACATAAC
1 CCGAACCCGAAAAT-AC
27069 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
**
27085 CCGAACCCG-ACTTAAC
1 CCGAACCCGAAAAT-AC
27101 CCGATA-CCGAAAATAC
1 CCGA-ACCCGAAAATAC
* * * *
27117 CCAAACCTGAAAAAAT
1 CCGAACCCGAAAATAC
27133 CCGAACCCGAA
1 CCGAACCCGAA
27144 CCCACCCGAG
Statistics
Matches: 72, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
15 6 0.08
16 60 0.83
17 6 0.08
ACGTcount: A:0.41, C:0.37, G:0.13, T:0.08
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:27083 original size:32 final size:32
Alignment explanation
Indices: 27037--27143 Score: 135
Period size: 32 Copynumber: 3.3 Consensus size: 32
27027 CTACCCGAGA
*
27037 CCGAGCCCGAAAATACCCGAACCCGACATAAC
1 CCGAACCCGAAAATACCCGAACCCGACATAAC
*
27069 CCGAACCCGAAAATACCCGAACCCGACTTAAC
1 CCGAACCCGAAAATACCCGAACCCGACATAAC
* * * * *
27101 CCGATA-CCGAAAATACCCAAACCTGAAAAAAT
1 CCGA-ACCCGAAAATACCCGAACCCGACATAAC
27133 CCGAACCCGAA
1 CCGAACCCGAA
27144 CCCACCCGAG
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
31 1 0.02
32 63 0.97
33 1 0.02
ACGTcount: A:0.41, C:0.37, G:0.13, T:0.08
Consensus pattern (32 bp):
CCGAACCCGAAAATACCCGAACCCGACATAAC
Found at i:27802 original size:2 final size:2
Alignment explanation
Indices: 27795--27836 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
27785 TAACATGTTC
27795 AT AT AT 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 AT AT AT
27837 CCCACTAAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32787 original size:18 final size:19
Alignment explanation
Indices: 32758--32794 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
32748 TGGAGGCCTT
32758 GCGGATGGCGGAAGAGACG
1 GCGGATGGCGGAAGAGACG
*
32777 GCGGA-GGCGGAGGAGACG
1 GCGGATGGCGGAAGAGACG
32795 AAGGAGGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.24, C:0.16, G:0.57, T:0.03
Consensus pattern (19 bp):
GCGGATGGCGGAAGAGACG
Found at i:38825 original size:26 final size:26
Alignment explanation
Indices: 38796--38848 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
38786 TACAGTACAT
38796 TCCTGCATTTATTTATCCTTTGTTGG
1 TCCTGCATTTATTTATCCTTTGTTGG
38822 TCCTGCATTTATTTATCCTTTGTTGG
1 TCCTGCATTTATTTATCCTTTGTTGG
38848 T
1 T
38849 TCCTTTTGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.11, C:0.19, G:0.15, T:0.55
Consensus pattern (26 bp):
TCCTGCATTTATTTATCCTTTGTTGG
Found at i:39877 original size:261 final size:264
Alignment explanation
Indices: 39405--39929 Score: 896
Period size: 261 Copynumber: 2.0 Consensus size: 264
39395 GGAAAAAACC
* *
39405 GGTTGCCACTGGAGTTTTTAGTAAAGAGAATGAAAATGATTCTGGCTGTGTGAACATAAGTCCTT
1 GGTTGCCACTGGAGTTATTACTAAAGAGAATGAAAATGATTCTGGCTGTGTGAACATAAGTCCTT
39470 CGTCAAAGATAAGGAGAGTTTCACTAGTTAAGCAACAGAAAGAGACAAGTCAGTCACCAAGACAC
66 CGTCAAAGATAAGGAGAGTTTCACTAGTTAAGCAACAGAAAGAGACAAGTCAGTCACCAAGACAC
*
39535 AACAAGAACATTGATAGTGAAGATGACTATGCTTGTGAAAATGGAAGTCCACCATCAAAGTTACG
131 AACAAGAACATTGATAGTGAAGATGACCATGCTTGTGAAAATGGAAGTCCACCATCAAAGTTACG
39600 AAGAATTTCCCTGGTCAAGCGGATAAGCATGAAGCCCGATTCTCCTAATCAAGAAAACAACACCA
196 AAGAATTTCCCTGGTCAAGCGGATAAGCATGAAGCCCGATTCTCCTAATCAAGAAAACAACACCA
39665 AGTT
261 AGTT
* ** **
39669 GGTTGCCCCTGGAGTTATTACTAAAGAGAATGAGGATGATTAC-GGCTGTGTGAATGTAAGTCCT
1 GGTTGCCACTGGAGTTATTACTAAAGAGAATGAAAATGATT-CTGGCTGTGTGAACATAAGTCCT
* * *
39733 TCGTCAAAGATAAGGAGAGTTTCATTAGTTAAGCAACAGAAAGAGAC-A-T-GGTCACCAAGGCA
65 TCGTCAAAGATAAGGAGAGTTTCACTAGTTAAGCAACAGAAAGAGACAAGTCAGTCACCAAGACA
39795 CAACAAGAACATTGATAGTGAAGATGACCATGCTTGTGAAAATGGAAGTCCACCATCAAAGTTAC
130 CAACAAGAACATTGATAGTGAAGATGACCATGCTTGTGAAAATGGAAGTCCACCATCAAAGTTAC
* *
39860 GAAGAATTTCCCTGGTCAAGCGGATAAGCTTGAAGCCCGATTCTCCTAGTCAAGAAAACAACACC
195 GAAGAATTTCCCTGGTCAAGCGGATAAGCATGAAGCCCGATTCTCCTAATCAAGAAAACAACACC
39925 AAGTT
260 AAGTT
39930 TATGAAGAGG
Statistics
Matches: 247, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
261 143 0.58
262 1 0.00
263 1 0.00
264 101 0.41
265 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.23
Consensus pattern (264 bp):
GGTTGCCACTGGAGTTATTACTAAAGAGAATGAAAATGATTCTGGCTGTGTGAACATAAGTCCTT
CGTCAAAGATAAGGAGAGTTTCACTAGTTAAGCAACAGAAAGAGACAAGTCAGTCACCAAGACAC
AACAAGAACATTGATAGTGAAGATGACCATGCTTGTGAAAATGGAAGTCCACCATCAAAGTTACG
AAGAATTTCCCTGGTCAAGCGGATAAGCATGAAGCCCGATTCTCCTAATCAAGAAAACAACACCA
AGTT
Found at i:42721 original size:21 final size:24
Alignment explanation
Indices: 42671--42724 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 24
42661 TTAATCCAAT
42671 TCCATCATCATCTATTATATCACCA
1 TCCATCATCATCTA-TATATCACCA
*
42696 T-CATCATCATC-A-ATATCAGC-
1 TCCATCATCATCTATATATCACCA
42716 TCCATCATC
1 TCCATCATC
42725 CCCTCCATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 1 0.04
21 14 0.52
23 1 0.04
24 10 0.37
25 1 0.04
ACGTcount: A:0.31, C:0.33, G:0.02, T:0.33
Consensus pattern (24 bp):
TCCATCATCATCTATATATCACCA
Found at i:42936 original size:15 final size:15
Alignment explanation
Indices: 42909--42946 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
42899 GATATTTTAC
42909 ATCATCATCATCATG
1 ATCATCATCATCATG
* *
42924 ATGATCATGATCATG
1 ATCATCATCATCATG
42939 ATCATCAT
1 ATCATCAT
42947 TTCTTGTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (15 bp):
ATCATCATCATCATG
Done.