Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022992.1 Corchorus olitorius cultivar O-4 contig23025, 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: 54010
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:4630 original size:111 final size:111
Alignment explanation
Indices: 4444--4651 Score: 247
Period size: 111 Copynumber: 1.9 Consensus size: 111
4434 GTGATATTGA
* * * **
4444 GAGAGAAGCCTCTGCATCCAGAAGATCTACGAAGAGATCAAGTCAGGCAAAAGTTACAACAGAAT
1 GAGAGAAGCCTCTGCATCCAGAAGATCTACCAAGAGATCAAGCCAAGCAAAAGCCACAACAGAAT
4509 CAGAGCAGAATCTCACACCAAGCAAGAATGACGGGATTGGCAAGGG
66 CAGAGCAGAATCTCACACCAAGCAAGAATGACGGGATTGGCAAGGG
* * ** ** *
4555 GAGAGTAGCGTCTGCATTTAGAAGATCTACC-AGAGGATCAAGCCAAGCAAAAGCCACAATTGAT
1 GAGAGAAGCCTCTGCATCCAGAAGATCTACCAAGA-GATCAAGCCAAGCAAAAGCCACAACAGAA
* * * * *
4619 TCTGAGGAGAATCTCTCTCCAAGGAAGAATGAC
65 TCAGAGCAGAATCTCACACCAAGCAAGAATGAC
4652 AAATGTGACA
Statistics
Matches: 79, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
110 3 0.04
111 76 0.96
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.16
Consensus pattern (111 bp):
GAGAGAAGCCTCTGCATCCAGAAGATCTACCAAGAGATCAAGCCAAGCAAAAGCCACAACAGAAT
CAGAGCAGAATCTCACACCAAGCAAGAATGACGGGATTGGCAAGGG
Found at i:4879 original size:54 final size:54
Alignment explanation
Indices: 4805--4908 Score: 181
Period size: 54 Copynumber: 1.9 Consensus size: 54
4795 GCCAAAAGAT
*
4805 GGTGCTACTTCAGGTGACACAAGTGATCAAAGGACTAACACACCAAAAAACAAA
1 GGTGCTACTTCAGGTAACACAAGTGATCAAAGGACTAACACACCAAAAAACAAA
* *
4859 GGTGGTACTTCAGGTAACACAGGTGATCAAAGGACTAACACACCAAAAAA
1 GGTGCTACTTCAGGTAACACAAGTGATCAAAGGACTAACACACCAAAAAA
4909 GGCTAAGAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.43, C:0.21, G:0.20, T:0.15
Consensus pattern (54 bp):
GGTGCTACTTCAGGTAACACAAGTGATCAAAGGACTAACACACCAAAAAACAAA
Found at i:13538 original size:15 final size:15
Alignment explanation
Indices: 13514--13547 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
13504 CTAACTCAAT
*
13514 AAACTCAACTAACTC
1 AAACTAAACTAACTC
*
13529 AAACTAAACTGACTC
1 AAACTAAACTAACTC
13544 AAAC
1 AAAC
13548 ATCCAAGATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.29, G:0.03, T:0.18
Consensus pattern (15 bp):
AAACTAAACTAACTC
Found at i:16203 original size:30 final size:30
Alignment explanation
Indices: 16143--16199 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
16133 CAAATCTGAG
*
16143 GTGAAAGAAAGTTGTTTCTTCTCGAATTCT
1 GTGAAAGAAAGTTCTTTCTTCTCGAATTCT
*
16173 GTGAAAGAGAGTTCTTTCTTCTC-AATT
1 GTGAAAGAAAGTTCTTTCTTCTCGAATT
16200 TCTGGTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.40
Consensus pattern (30 bp):
GTGAAAGAAAGTTCTTTCTTCTCGAATTCT
Found at i:17429 original size:18 final size:18
Alignment explanation
Indices: 17395--17429 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17385 GTCCAATTAA
**
17395 AATATTTTGATTGAATTG
1 AATATTTTGATCAAATTG
17413 AATATTTTGATCAAATT
1 AATATTTTGATCAAATT
17430 AAAATATTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (18 bp):
AATATTTTGATCAAATTG
Found at i:19066 original size:21 final size:21
Alignment explanation
Indices: 19042--19108 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
19032 AACTTTCTGT
19042 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * **
19063 AAATCATAGAAAATTCTTTA-T-
1 AAATTA-AG-AAATACTCAACTC
19084 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
19105 AAAT
1 AAAT
19109 CCTAATCCTT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
19 7 0.21
20 3 0.09
21 14 0.41
22 3 0.09
23 7 0.21
ACGTcount: A:0.52, C:0.15, G:0.04, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:19252 original size:56 final size:57
Alignment explanation
Indices: 19175--19289 Score: 205
Period size: 57 Copynumber: 2.0 Consensus size: 57
19165 TTTGTTTTAT
*
19175 AGAATAATTAAGTAGAGATA-GGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAAATAGGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
*
19231 AGAATAATTAAGTAGAAATAGGGGGGATATGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAAATAGGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
19288 AG
1 AG
19290 GAAACAGATA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
56 19 0.34
57 37 0.66
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34
Consensus pattern (57 bp):
AGAATAATTAAGTAGAAATAGGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
Found at i:20987 original size:60 final size:63
Alignment explanation
Indices: 20783--21056 Score: 455
Period size: 64 Copynumber: 4.3 Consensus size: 63
20773 TAATTTTGCC
* *
20783 ATAAATAAATGAATCAATTAGTAATTTTATGTTGGTAAAAAAATAAATTGATTGAACATGAAAA
1 ATAAATAAATGAATCAATTAGTAATTTTATGTTAGT-AAAAAATAAATTGATTGAACATGCAAA
20847 ATAAATAAATGAATCAATTAGTAATTTTATGTTAGTAAAAAATAAATTGATTGAACATGCAAA
1 ATAAATAAATGAATCAATTAGTAATTTTATGTTAGTAAAAAATAAATTGATTGAACATGCAAA
*
20910 ATAAATAAATGAATCAATTAGTAATTTTATGTTAGT-AAAAA-AAA-TGATTGAACATGCTAA
1 ATAAATAAATGAATCAATTAGTAATTTTATGTTAGTAAAAAATAAATTGATTGAACATGCAAA
* *
20970 ATAAATAAATGAATCAATTAGTAATTTTATGTTAGTAAAAAAATAAATTGATTGAACATACTAA
1 ATAAATAAATGAATCAATTAGTAATTTTATGTTAGT-AAAAAATAAATTGATTGAACATGCAAA
21034 ATAAATAAATGAATCAAGTTAGT
1 ATAAATAAATGAATCAA-TTAGT
21057 CGTTAGTTAA
Statistics
Matches: 201, Mismatches: 4, Indels: 9
0.94 0.02 0.04
Matches are distributed among these distances:
60 51 0.25
61 3 0.01
62 10 0.05
63 65 0.32
64 67 0.33
65 5 0.02
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.33
Consensus pattern (63 bp):
ATAAATAAATGAATCAATTAGTAATTTTATGTTAGTAAAAAATAAATTGATTGAACATGCAAA
Found at i:33659 original size:31 final size:31
Alignment explanation
Indices: 33617--33748 Score: 115
Period size: 31 Copynumber: 4.3 Consensus size: 31
33607 ACGGTGTCTA
* * *
33617 ACGTGGTACGCCACGTGTACCAAAAAGCGAC
1 ACGTGGCACGCCACATGTACCAAAAAGTGAC
33648 ACGTGGCACGCCACATGTACCAAAAAGTGAC
1 ACGTGGCACGCCACATGTACCAAAAAGTGAC
* ** ** **
33679 ACATATCACGTTATGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACATGTACCAAAAAGTGAC
* * * *
33710 ATGTGGCATGCCTCATGCA-CAAAAAG-GAC
1 ACGTGGCACGCCACATGTACCAAAAAGTGAC
*
33739 ACGTGCCACG
1 ACGTGGCACG
33749 TGTCATTTTT
Statistics
Matches: 77, Mismatches: 24, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
29 10 0.13
30 7 0.09
31 60 0.78
ACGTcount: A:0.34, C:0.27, G:0.23, T:0.17
Consensus pattern (31 bp):
ACGTGGCACGCCACATGTACCAAAAAGTGAC
Found at i:35657 original size:28 final size:28
Alignment explanation
Indices: 35617--35674 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
35607 TTCTTTATGA
*
35617 AATAGTTTTTAATATCAAATACAAAATT
1 AATAATTTTTAATATCAAATACAAAATT
* *
35645 AATAATTTTTAATATTAAATATAAAATT
1 AATAATTTTTAATATCAAATACAAAATT
35673 AA
1 AA
35675 CTAAAAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (28 bp):
AATAATTTTTAATATCAAATACAAAATT
Found at i:45299 original size:51 final size:50
Alignment explanation
Indices: 45243--45398 Score: 115
Period size: 51 Copynumber: 3.1 Consensus size: 50
45233 TTCTCACGGG
45243 GAGTCCGGATCGAAATCTAAGGTCAATTACGAACTTAGCCGTTCTCACAAA
1 GAGTCCGGATCGAAATCTAAGG-CAATTACGAACTTAGCCGTTCTCACAAA
* ** * ** * * ** ***
45294 GAGTCCAGG-GC-TTATGTTCGGCCAACTTA-G--TTTCGATGTTCTCACGGG
1 GAGTCC-GGATCGAAATCTAAGG-CAA-TTACGAACTTAGCCGTTCTCACAAA
45342 GAGTCCGGATCGAAATCTAAGGCTAATTACGAACTTAGCCGTTCTCACAAA
1 GAGTCCGGATCGAAATCTAAGGC-AATTACGAACTTAGCCGTTCTCACAAA
45393 GAGTCC
1 GAGTCC
45399 AGCGCTTACG
Statistics
Matches: 70, Mismatches: 27, Indels: 16
0.62 0.24 0.14
Matches are distributed among these distances:
47 2 0.03
48 22 0.31
49 8 0.11
50 9 0.13
51 27 0.39
52 2 0.03
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.26
Consensus pattern (50 bp):
GAGTCCGGATCGAAATCTAAGGCAATTACGAACTTAGCCGTTCTCACAAA
Found at i:45354 original size:99 final size:99
Alignment explanation
Indices: 45181--45859 Score: 1062
Period size: 99 Copynumber: 6.8 Consensus size: 99
45171 AGGAACATGT
* * *
45181 CGTTCTCATAAAGAGTCGAGGGCTCACGTTCGGCCACAACTTAGTTTCGATGTTCTCACGGGGAG
1 CGTTCTCACAAAGAGTCCAGGGCTTACGTTCGG-C-CAACTTAGTTTCGATGTTCTCACGGGGAG
45246 TCCGGATCGAAATCTAAGGTCAATTACGAACTTAGC
64 TCCGGATCGAAATCTAAGGTCAATTACGAACTTAGC
*
45282 CGTTCTCACAAAGAGTCCAGGGCTTATGTTCGGCCAACTTAGTTTCGATGTTCTCACGGGGAGTC
1 CGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCCAACTTAGTTTCGATGTTCTCACGGGGAGTC
45347 CGGATCGAAATCTAAGG-CTAATTACGAACTTAGC
66 CGGATCGAAATCTAAGGTC-AATTACGAACTTAGC
*
45381 CGTTCTCACAAAGAGTCCAGCGCTTACGTTCGGCCACAACTTAGTTTCGATGTTCTCAC-GGGAG
1 CGTTCTCACAAAGAGTCCAGGGCTTACGTTCGG-C-CAACTTAGTTTCGATGTTCTCACGGGGAG
45445 TCCGGATCGAAATCTAAGGTCAATTACGAACGTT-GC
64 TCCGGATCGAAATCTAAGGTCAATTACGAAC-TTAGC
** *
45481 CGTTCTCACAAAGAGTCCAGGGCTTACGTTCTCCCAACTTAGTTTCGATGTTCTCACAGGGAGTC
1 CGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCCAACTTAGTTTCGATGTTCTCACGGGGAGTC
*
45546 CGGATCGAAATCTAAGGTCAAATACGAACTTAGC
66 CGGATCGAAATCTAAGGTCAATTACGAACTTAGC
* * *
45580 CGTTCTCACAAAGAGTCAAGGGCTTATGTTTGGCCAACTTAGTTTCGATGTTCTCACGGGGAGTC
1 CGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCCAACTTAGTTTCGATGTTCTCACGGGGAGTC
45645 CGGATCGAAATCTAAGG-CTAATTACGAACTTAGC
66 CGGATCGAAATCTAAGGTC-AATTACGAACTTAGC
* * *
45679 GGTTCTCACAAAGAGTCCAGCGCTTATGTTCGGCCACAACTTAGTTTCGATGTTCTCACGGGGAG
1 CGTTCTCACAAAGAGTCCAGGGCTTACGTTCGG-C-CAACTTAGTTTCGATGTTCTCACGGGGAG
45744 TCCGGATCGAAATCTAAGGTCAATTACGAACGTT-GC
64 TCCGGATCGAAATCTAAGGTCAATTACGAAC-TTAGC
* *
45780 CGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCCAACTTAGTTTTGATCTTCTCACGGGGAGTC
1 CGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCCAACTTAGTTTCGATGTTCTCACGGGGAGTC
* *
45845 TGGATCGAAAGCTAA
66 CGGATCGAAATCTAA
45860 TGTCTCTCTG
Statistics
Matches: 538, Mismatches: 28, Indels: 26
0.91 0.05 0.04
Matches are distributed among these distances:
98 27 0.05
99 293 0.54
100 70 0.13
101 145 0.27
102 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (99 bp):
CGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCCAACTTAGTTTCGATGTTCTCACGGGGAGTC
CGGATCGAAATCTAAGGTCAATTACGAACTTAGC
Found at i:45774 original size:200 final size:201
Alignment explanation
Indices: 45181--45859 Score: 1083
Period size: 200 Copynumber: 3.4 Consensus size: 201
45171 AGGAACATGT
* * *
45181 CGTTCTCATAAAGAGTCGAGGGCTCACGTTCGGCCACAACTTAGTTTCGATGTTCTCACGGGGAG
1 CGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCCACAACTTAGTTTCGATGTTCTCACGGGGAG
45246 TCCGGATCGAAATCTAAGGTCAATTACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCTTATGT
66 TCCGGATCGAAATCTAAGGTCAATTACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCTTATGT
45311 TCGG-CCAACTTAGTTTCGATGTTCTCACGGGGAGTCCGGATCGAAATCTAAGG-CTAATTACGA
131 TCGGCCCAACTTAGTTTCGATGTTCTCACGGGGAGTCCGGATCGAAATCTAAGGTC-AATTACGA
45374 ACTTAGC
195 ACTTAGC
*
45381 CGTTCTCACAAAGAGTCCAGCGCTTACGTTCGGCCACAACTTAGTTTCGATGTTCTCAC-GGGAG
1 CGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCCACAACTTAGTTTCGATGTTCTCACGGGGAG
*
45445 TCCGGATCGAAATCTAAGGTCAATTACGAACGTT-GCCGTTCTCACAAAGAGTCCAGGGCTTACG
66 TCCGGATCGAAATCTAAGGTCAATTACGAAC-TTAGCCGTTCTCACAAAGAGTCCAGGGCTTATG
* * *
45509 TTC-TCCCAACTTAGTTTCGATGTTCTCACAGGGAGTCCGGATCGAAATCTAAGGTCAAATACGA
130 TTCGGCCCAACTTAGTTTCGATGTTCTCACGGGGAGTCCGGATCGAAATCTAAGGTCAATTACGA
45573 ACTTAGC
195 ACTTAGC
* * *
45580 CGTTCTCACAAAGAGTCAAGGGCTTATGTTTGG-C-CAACTTAGTTTCGATGTTCTCACGGGGAG
1 CGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCCACAACTTAGTTTCGATGTTCTCACGGGGAG
* *
45643 TCCGGATCGAAATCTAAGG-CTAATTACGAACTTAGCGGTTCTCACAAAGAGTCCAGCGCTTATG
66 TCCGGATCGAAATCTAAGGTC-AATTACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCTTATG
45707 TTCGGCCACAACTTAGTTTCGATGTTCTCACGGGGAGTCCGGATCGAAATCTAAGGTCAATTACG
130 TTCGGCC-CAACTTAGTTTCGATGTTCTCACGGGGAGTCCGGATCGAAATCTAAGGTCAATTACG
45772 AACGTT-GC
194 AAC-TTAGC
* *
45780 CGTTCTCACAAAGAGTCCAGGGCTTACGTTCGG-C-CAACTTAGTTTTGATCTTCTCACGGGGAG
1 CGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCCACAACTTAGTTTCGATGTTCTCACGGGGAG
* *
45843 TCTGGATCGAAAGCTAA
66 TCCGGATCGAAATCTAA
45860 TGTCTCTCTG
Statistics
Matches: 445, Mismatches: 25, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
197 26 0.06
198 65 0.15
199 161 0.36
200 191 0.43
201 2 0.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (201 bp):
CGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCCACAACTTAGTTTCGATGTTCTCACGGGGAG
TCCGGATCGAAATCTAAGGTCAATTACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCTTATGT
TCGGCCCAACTTAGTTTCGATGTTCTCACGGGGAGTCCGGATCGAAATCTAAGGTCAATTACGAA
CTTAGC
Done.