Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022832.1 Corchorus olitorius cultivar O-4 contig22865, 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: 52648
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Found at i:6814 original size:28 final size:28
Alignment explanation
Indices: 6743--6815 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
6733 CCTGGGTGCA
* *
6743 CAAAATGACTAAAATACCCCTAGACATG
1 CAAAATGACCAAAATGCCCCTAGACATG
*
6771 CAAAATGACCAAAATGCCCCTGGACATG
1 CAAAATGACCAAAATGCCCCTAGACATG
*
6799 CAAAATGCCCAAAATGC
1 CAAAATGACCAAAATGC
6816 AAAATGACTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.44, C:0.27, G:0.14, T:0.15
Consensus pattern (28 bp):
CAAAATGACCAAAATGCCCCTAGACATG
Found at i:6828 original size:16 final size:16
Alignment explanation
Indices: 6796--6829 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6786 GCCCCTGGAC
*
6796 ATGCAAAATGCCCAAA
1 ATGCAAAATGACCAAA
*
6812 ATGCAAAATGACTAAA
1 ATGCAAAATGACCAAA
6828 AT
1 AT
6830 AAGAAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.18, G:0.12, T:0.18
Consensus pattern (16 bp):
ATGCAAAATGACCAAA
Found at i:7155 original size:50 final size:50
Alignment explanation
Indices: 7052--7236 Score: 262
Period size: 50 Copynumber: 3.7 Consensus size: 50
7042 CAATCAACTT
* * * * * *
7052 CTTTGAATTGTCTTCCAATTCAAATATAAAAAGGACCGTCGTCTGCTCATC
1 CTTTGAACTGTCTTCCAATTC-AATCTTAAAAGGACCGTCTTCCGCTTATC
* *
7103 CTTTGAACTGTCTCCCAATTCAATCTGAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
*
7153 CTTTGAACTGTCTTCCAATTCACTCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* *
7203 CTTTGAATTGTCTTCCAATTCACTCTTAAAAGGA
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGA
7237 TATCTAAATC
Statistics
Matches: 123, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 104 0.85
51 19 0.15
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (50 bp):
CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
Found at i:15996 original size:12 final size:12
Alignment explanation
Indices: 15960--15999 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
15950 GTGCGTGAAT
*
15960 ATGCAATGATGA
1 ATGCTATGATGA
15972 ATG-TATGATGA
1 ATGCTATGATGA
*
15983 ATGCTATGAAGA
1 ATGCTATGATGA
15995 ATGCT
1 ATGCT
16000 TATAAACTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (12 bp):
ATGCTATGATGA
Found at i:17011 original size:16 final size:16
Alignment explanation
Indices: 16990--17020 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
16980 TCTTGCTGCT
16990 TTAAGGCAACTTGGCC
1 TTAAGGCAACTTGGCC
17006 TTAAGGCAACTTGGC
1 TTAAGGCAACTTGGC
17021 TTTCAGCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (16 bp):
TTAAGGCAACTTGGCC
Found at i:23153 original size:28 final size:28
Alignment explanation
Indices: 23122--23192 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
23112 CCCTGGGTGC
*
23122 GCAAAATGACTAAAA-TACCCCTGGACAT
1 GCAAAATGACCAAAACT-CCCCTGGACAT
*
23150 GCAAAATGACCAAAACTCCCTTGGACAT
1 GCAAAATGACCAAAACTCCCCTGGACAT
*
23178 GCAAAATGCCCAAAA
1 GCAAAATGACCAAAA
23193 TGCAAAATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
28 38 0.97
29 1 0.03
ACGTcount: A:0.44, C:0.27, G:0.14, T:0.15
Consensus pattern (28 bp):
GCAAAATGACCAAAACTCCCCTGGACAT
Found at i:23208 original size:16 final size:16
Alignment explanation
Indices: 23176--23209 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
23166 TCCCTTGGAC
*
23176 ATGCAAAATGCCCAAA
1 ATGCAAAATGACCAAA
*
23192 ATGCAAAATGACTAAA
1 ATGCAAAATGACCAAA
23208 AT
1 AT
23210 AAGAAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.18, G:0.12, T:0.18
Consensus pattern (16 bp):
ATGCAAAATGACCAAA
Found at i:34496 original size:219 final size:214
Alignment explanation
Indices: 34104--34534 Score: 702
Period size: 213 Copynumber: 2.0 Consensus size: 214
34094 TCGGGCGTTC
34104 TGTAATGTTAGTAAAGTATTGTTTTTACATAAAGGTGATTAACAATTGAACTTATGCAAGATTTA
1 TGTAATGTTAGTAAAGTATTGTTTTTACATAAAGGTGATTAACAATTGAACTTATGCAAGATTTA
* *
34169 GAATAAGAAATGGAAAGCAATCGGATAAGATACACAGATAGAGGGCATTGGTATTTGTCAATGAA
66 GAATAAGAAATGGAAAACAATCAGATAAGATACACAGATAGAGGGCATTGGTATTTGTCAATGAA
* * *
34234 AGAGAACGAATTACACTTCTTTGATTCCTCCTTTGTGATTGAAGA-TTAAATAGCATAACCACTG
131 AGAGAACAAATTACACTTCTTTGATTCCTCCTCTGTAATTGAAGAGTTAAATAGCATAACCACTG
34298 CAATTGAAAACAATTATTT
196 CAATTGAAAACAATTATTT
* * * * *
34317 TGTAATTTTGGTAAAGTATTGTTTTTACATGAGGGTGTTTAACAATTGAACTTATGCAAGATTTA
1 TGTAATGTTAGTAAAGTATTGTTTTTACATAAAGGTGATTAACAATTGAACTTATGCAAGATTTA
*
34382 GAATAAGGAATGGAAAACAATCAGATAAGATGCACATGCACAGATAGAGGGCATTGGTATTTGTC
66 GAATAAGAAATGGAAAACAATCAGATAAGAT----A--CACAGATAGAGGGCATTGGTATTTGTC
34447 AATGAAAGAGAACAAATTACACTTCTTTGATTCCTCCTCTGTAATTGAAGAGTTAAATAGCATAA
125 AATGAAAGAGAACAAATTACACTTCTTTGATTCCTCCTCTGTAATTGAAGAGTTAAATAGCATAA
34512 CCACTGCAATTGAAAACAATTAT
190 CCACTGCAATTGAAAACAATTAT
34535 ACAAAATCTC
Statistics
Matches: 200, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
213 88 0.44
217 1 0.00
219 75 0.38
220 36 0.18
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.32
Consensus pattern (214 bp):
TGTAATGTTAGTAAAGTATTGTTTTTACATAAAGGTGATTAACAATTGAACTTATGCAAGATTTA
GAATAAGAAATGGAAAACAATCAGATAAGATACACAGATAGAGGGCATTGGTATTTGTCAATGAA
AGAGAACAAATTACACTTCTTTGATTCCTCCTCTGTAATTGAAGAGTTAAATAGCATAACCACTG
CAATTGAAAACAATTATTT
Found at i:40025 original size:38 final size:39
Alignment explanation
Indices: 39967--40148 Score: 238
Period size: 37 Copynumber: 4.9 Consensus size: 39
39957 GGCTGTGCAT
*
39967 AGTGGACTCGTGCCTC-AGGGGTTAAACTGATTGGTAAG
1 AGTGGACCCGTGCCTCAAGGGGTTAAACTGATTGGTAAG
40005 AGTGGACCCGTG-CTCAAGGGGTTAAACTG-TTGGTAAG
1 AGTGGACCCGTGCCTCAAGGGGTTAAACTGATTGGTAAG
* * *
40042 AGTGAACCCGTG-CTCATGGGGTTAATCTG-TTGGTAAG
1 AGTGGACCCGTGCCTCAAGGGGTTAAACTGATTGGTAAG
* *
40079 AGTGGA-CCGTGCCTCAGGGGGTTAAACTTATTGGTAAG
1 AGTGGACCCGTGCCTCAAGGGGTTAAACTGATTGGTAAG
*
40117 AGTGGACCCATGCCTC-AGGGGTT-AACT-ATTGG
1 AGTGGACCCGTGCCTCAAGGGGTTAAACTGATTGG
40149 CTAGACTCGA
Statistics
Matches: 130, Mismatches: 10, Indels: 10
0.87 0.07 0.07
Matches are distributed among these distances:
36 10 0.08
37 68 0.52
38 44 0.34
39 8 0.06
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.26
Consensus pattern (39 bp):
AGTGGACCCGTGCCTCAAGGGGTTAAACTGATTGGTAAG
Found at i:46326 original size:32 final size:32
Alignment explanation
Indices: 46290--46393 Score: 199
Period size: 32 Copynumber: 3.2 Consensus size: 32
46280 GTAGCCAGGC
*
46290 CATGGCCGGCCTAGCATATTTTGCGGCTCGGG
1 CATGGCCGACCTAGCATATTTTGCGGCTCGGG
46322 CATGGCCGACCTAGCATATTTTGCGGCTCGGG
1 CATGGCCGACCTAGCATATTTTGCGGCTCGGG
46354 CATGGCCGACCTAGCATATTTTGCGGCTCGGG
1 CATGGCCGACCTAGCATATTTTGCGGCTCGGG
46386 CATGGCCG
1 CATGGCCG
46394 GTCCTGGCCA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 71 1.00
ACGTcount: A:0.14, C:0.29, G:0.33, T:0.24
Consensus pattern (32 bp):
CATGGCCGACCTAGCATATTTTGCGGCTCGGG
Found at i:46621 original size:12 final size:12
Alignment explanation
Indices: 46604--46638 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
46594 TTTGAAATCC
46604 TAAAAAGAAAAA
1 TAAAAAGAAAAA
* *
46616 TAAAAACAAAAC
1 TAAAAAGAAAAA
46628 TAAAAAGAAAA
1 TAAAAAGAAAA
46639 TTAACATGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.80, C:0.06, G:0.06, T:0.09
Consensus pattern (12 bp):
TAAAAAGAAAAA
Found at i:48010 original size:26 final size:25
Alignment explanation
Indices: 47981--48052 Score: 99
Period size: 25 Copynumber: 2.8 Consensus size: 25
47971 CATAATTTTT
*
47981 TTTTTATTTTAGAAAACGCAAAAACAT
1 TTTTT-TTTTA-AAAACGCAAAAACAA
*
48008 TTTTTTTTTCAAAACGCAAAAACAA
1 TTTTTTTTTAAAAACGCAAAAACAA
48033 TTTTTTTTTCAAAAACGCAA
1 TTTTTTTTT-AAAAACGCAA
48053 TTTTTTTTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
25 23 0.56
26 13 0.32
27 5 0.12
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.39
Consensus pattern (25 bp):
TTTTTTTTTAAAAACGCAAAAACAA
Found at i:48021 original size:25 final size:26
Alignment explanation
Indices: 47993--48052 Score: 104
Period size: 25 Copynumber: 2.3 Consensus size: 26
47983 TTTATTTTAG
*
47993 AAAACGCAAAAACATTTTTTTTTTC-
1 AAAACGCAAAAACAATTTTTTTTTCA
48018 AAAACGCAAAAACAATTTTTTTTTCA
1 AAAACGCAAAAACAATTTTTTTTTCA
48044 AAAACGCAA
1 AAAACGCAA
48053 TTTTTTTTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 24 0.73
26 9 0.27
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.32
Consensus pattern (26 bp):
AAAACGCAAAAACAATTTTTTTTTCA
Found at i:48047 original size:18 final size:19
Alignment explanation
Indices: 48024--48063 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
48014 TTTCAAAACG
48024 CAAAAA-CAATTTTTTTTT
1 CAAAAACCAATTTTTTTTT
48042 CAAAAACGCAATTTTTTTTT
1 CAAAAAC-CAATTTTTTTTT
48062 CA
1 CA
48064 TTTTAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.30
20 14 0.70
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.45
Consensus pattern (19 bp):
CAAAAACCAATTTTTTTTT
Found at i:50527 original size:2 final size:2
Alignment explanation
Indices: 50522--50547 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
50512 ATAAGTCCAA
50522 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
50548 GCATACATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.