Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017745.1 Corchorus olitorius cultivar O-4 contig17778, 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: 31740
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Found at i:876 original size:28 final size:28
Alignment explanation
Indices: 844--919 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 28
834 TTAAGATGTC
* * *
844 AAAATTACTATTTTGCCCTTGGTCGGCT
1 AAAATTACAATTTTGCCCTTAGTCGACT
* * * *
872 AAAATTACCATTTTACCCATAGTTGACT
1 AAAATTACAATTTTGCCCTTAGTCGACT
900 -AAATTACAATTTTGCCCTTA
1 AAAATTACAATTTTGCCCTTA
920 AATGCCGTTA
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
27 17 0.44
28 22 0.56
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (28 bp):
AAAATTACAATTTTGCCCTTAGTCGACT
Found at i:1346 original size:12 final size:12
Alignment explanation
Indices: 1329--1371 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
1319 AGTTCATTAC
*
1329 TGTTTATTAAAT
1 TGTTTAATAAAT
1341 TGTTTAATAAAT
1 TGTTTAATAAAT
*
1353 GGTTTTAAATAAAT
1 TG-TTT-AATAAAT
1367 TGTTT
1 TGTTT
1372 TGGGTGCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 12 0.46
13 6 0.23
14 8 0.31
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (12 bp):
TGTTTAATAAAT
Found at i:6506 original size:27 final size:26
Alignment explanation
Indices: 6469--6580 Score: 103
Period size: 27 Copynumber: 4.5 Consensus size: 26
6459 ACCAAAAAGA
*
6469 TTTTTA-TTATTTATTTACTATTTATC
1 TTTTTATTTATTAATTTACTA-TTATC
6495 TTTTTATTTATTAATTTA--ATTAT-
1 TTTTTATTTATTAATTTACTATTATC
* * *
6518 TATCTATTTATTAA-CTA-T-TTATC
1 TTTTTATTTATTAATTTACTATTATC
*
6541 TTTATATTTATTAATTTAGCTATTATC
1 TTTTTATTTATTAATTTA-CTATTATC
*
6568 TATTTATTTATTA
1 TTTTTATTTATTA
6581 TTATTATCTT
Statistics
Matches: 70, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
22 6 0.09
23 24 0.34
24 6 0.09
25 1 0.01
26 7 0.10
27 26 0.37
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (26 bp):
TTTTTATTTATTAATTTACTATTATC
Found at i:6535 original size:46 final size:46
Alignment explanation
Indices: 6472--6575 Score: 165
Period size: 46 Copynumber: 2.3 Consensus size: 46
6462 AAAAAGATTT
* * *
6472 TTAT-TATTTATTTACTATTTATCTTTTTATTTATTAATTTAATTA
1 TTATCTATTTATTAACTATTTATCTTTATATTTATTAATTTAACTA
*
6517 TTATCTATTTATTAACTATTTATCTTTATATTTATTAATTTAGCTA
1 TTATCTATTTATTAACTATTTATCTTTATATTTATTAATTTAACTA
6563 TTATCTATTTATT
1 TTATCTATTTATT
6576 TATTATTATT
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
45 4 0.07
46 50 0.93
ACGTcount: A:0.29, C:0.07, G:0.01, T:0.63
Consensus pattern (46 bp):
TTATCTATTTATTAACTATTTATCTTTATATTTATTAATTTAACTA
Found at i:7880 original size:28 final size:27
Alignment explanation
Indices: 7831--7892 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 27
7821 TAAGATTTCC
* * * *
7831 AAATTACTACTTTGCCCTTGGTTGGCT
1 AAATTACCACTTTACCCCTGGTTGACT
*
7858 AAAATTACCATTTTACCCCTGGTTGACT
1 -AAATTACCACTTTACCCCTGGTTGACT
7886 AAATTAC
1 AAATTAC
7893 AGTTTTGCCC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 7 0.24
28 22 0.76
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (27 bp):
AAATTACCACTTTACCCCTGGTTGACT
Found at i:11290 original size:25 final size:25
Alignment explanation
Indices: 11261--11310 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
11251 TAGTATTTTG
11261 CATTCATGTAGCTCAAAGCTAATTT
1 CATTCATGTAGCTCAAAGCTAATTT
*
11286 CATTCATGTAGCTCAAATCTAATTT
1 CATTCATGTAGCTCAAAGCTAATTT
11311 AATCAACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (25 bp):
CATTCATGTAGCTCAAAGCTAATTT
Found at i:11491 original size:12 final size:12
Alignment explanation
Indices: 11474--11498 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11464 AAATCACATC
11474 TTCATTTAGTAT
1 TTCATTTAGTAT
11486 TTCATTTAGTAT
1 TTCATTTAGTAT
11498 T
1 T
11499 ATAGTCAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (12 bp):
TTCATTTAGTAT
Found at i:14308 original size:39 final size:39
Alignment explanation
Indices: 14259--14374 Score: 171
Period size: 39 Copynumber: 2.9 Consensus size: 39
14249 CCAAGTCAAC
14259 CTGCCACGTCATCTGCCACGTCACCAGTTGACCATTGCA
1 CTGCCACGTCATCTGCCACGTCACCAGTTGACCATTGCA
* *
14298 CTGCCACGTCATCTGCCACGTCACTAGTTGACCAGTGCA
1 CTGCCACGTCATCTGCCACGTCACCAGTTGACCATTGCA
* *
14337 CTGCCACATCATCCTGCCACGTCATTC-GTTGACCATTG
1 CTGCCACGTCAT-CTGCCACGTCA-CCAGTTGACCATTG
14375 ACCAGTAAAC
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
39 48 0.70
40 21 0.30
ACGTcount: A:0.20, C:0.37, G:0.18, T:0.25
Consensus pattern (39 bp):
CTGCCACGTCATCTGCCACGTCACCAGTTGACCATTGCA
Found at i:14418 original size:13 final size:13
Alignment explanation
Indices: 14400--14475 Score: 55
Period size: 13 Copynumber: 5.7 Consensus size: 13
14390 ACGTCATCAA
14400 GTTGACTTTGATC
1 GTTGACTTTGATC
** *
14413 GTTGACTTTTCTGT
1 GTTGACTTTGAT-C
*
14427 GTTGACTTTGACC
1 GTTGACTTTGATC
*
14440 GTTGACTTTTCGGT-
1 GTTGAC-TTT-GATC
*
14454 GTTGACTTTGACC
1 GTTGACTTTGATC
*
14467 ATTGACTTT
1 GTTGACTTT
14476 TTGGTTGACC
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
12 1 0.02
13 27 0.57
14 18 0.38
15 1 0.02
ACGTcount: A:0.13, C:0.17, G:0.22, T:0.47
Consensus pattern (13 bp):
GTTGACTTTGATC
Found at i:14431 original size:27 final size:27
Alignment explanation
Indices: 14400--14484 Score: 129
Period size: 27 Copynumber: 3.2 Consensus size: 27
14390 ACGTCATCAA
*
14400 GTTGACTTTGATCGTTGACTTTTCTGT
1 GTTGACTTTGACCGTTGACTTTTCTGT
*
14427 GTTGACTTTGACCGTTGACTTTTCGGT
1 GTTGACTTTGACCGTTGACTTTTCTGT
*
14454 GTTGACTTTGACCATTGACTTTT-TG-
1 GTTGACTTTGACCGTTGACTTTTCTGT
14479 GTTGAC
1 GTTGAC
14485 CAGTTTTTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
25 6 0.11
26 1 0.02
27 47 0.87
ACGTcount: A:0.13, C:0.16, G:0.24, T:0.47
Consensus pattern (27 bp):
GTTGACTTTGACCGTTGACTTTTCTGT
Found at i:20253 original size:40 final size:40
Alignment explanation
Indices: 20194--20470 Score: 317
Period size: 40 Copynumber: 7.0 Consensus size: 40
20184 TGTCTAGTCC
* * *
20194 AAATACCCAGTTTGTCCTTCCCCACCGGAAGGTGCTGTTT
1 AAATAACCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTT
*
20234 AAATAACCAGTTTGCCCTTCCCCACCGGAAGATGTTGTTT
1 AAATAACCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTT
* *
20274 AAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCT
1 AAATAACCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTT
* * * * *
20314 AAATACCCAATTTGCCCTTCCCAACCTGAAGGTGTTATTT
1 AAATAACCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTT
20354 AAAT-ACCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTT
1 AAATAACCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTT
* * * * ** *
20393 AAAT-ACAAGTTTGCCTTTCCCTACCAGAAAATGTTGTCT
1 AAATAACCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTT
* * * * *
20432 AAAT-TCTTAGTTTGCCCTTCCTCATCGGGAGGTGTTGTT
1 AAATAAC-CAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT
20471 CCTATTCCCT
Statistics
Matches: 201, Mismatches: 35, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 67 0.33
40 134 0.67
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (40 bp):
AAATAACCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTT
Found at i:22595 original size:15 final size:16
Alignment explanation
Indices: 22562--22601 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
22552 TTGCTTTGTT
22562 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
22578 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
22593 TTGCTTTCT
1 TTGTTTTCT
22602 TTCATCCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:23032 original size:24 final size:24
Alignment explanation
Indices: 22968--23032 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
22958 TTTTTGGGTC
*
22968 ATAAAAAAAGGATTTTGCGTTTTTA
1 ATAAAAAAAGG-TTTTCCGTTTTTA
**
22993 ATTAAAAAAA-AATTTCCGTTTTTGA
1 A-TAAAAAAAGGTTTTCCGTTTTT-A
23018 A-AAAAAAAGGTTTTC
1 ATAAAAAAAGGTTTTC
23033 TACGTCATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
23 7 0.22
24 14 0.44
25 3 0.09
26 8 0.25
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (24 bp):
ATAAAAAAAGGTTTTCCGTTTTTA
Found at i:25143 original size:21 final size:21
Alignment explanation
Indices: 25122--25163 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
25112 GCCCACATGG
*
25122 TTGCTTTGAGCACCCATGTGGT
1 TTGC-TTGAGCACCCAGGTGGT
*
25144 TTGCTTGAGGACCCAGGTGG
1 TTGCTTGAGCACCCAGGTGG
25164 GCAGTGTCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.14, C:0.21, G:0.33, T:0.31
Consensus pattern (21 bp):
TTGCTTGAGCACCCAGGTGGT
Found at i:26205 original size:26 final size:25
Alignment explanation
Indices: 26163--26211 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
26153 ATGATTTAGG
*
26163 GGTTACTAACTCCCTTTTTCTTTTGA
1 GGTTACTAACACCCTTTTT-TTTTGA
*
26189 GGTTACTAACACTCTTTTTTTTT
1 GGTTACTAACACCCTTTTTTTTT
26212 CAGAGGGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.16, C:0.20, G:0.10, T:0.53
Consensus pattern (25 bp):
GGTTACTAACACCCTTTTTTTTTGA
Found at i:28774 original size:15 final size:15
Alignment explanation
Indices: 28754--28842 Score: 85
Period size: 15 Copynumber: 5.9 Consensus size: 15
28744 AACACTTTCA
28754 GTGCCATCATCTTCG
1 GTGCCATCATCTTCG
*
28769 GTGCCATCAGT-TTTG
1 GTGCCATCA-TCTTCG
* *
28784 GTGCCATTAGT-TTTG
1 GTGCCATCA-TCTTCG
28799 GTGCCATCATCTTCG
1 GTGCCATCATCTTCG
* *
28814 GTGCCGTCGATGTT-G
1 GTGCCATC-ATCTTCG
28829 GTGCCATCATCTTC
1 GTGCCATCATCTTC
28843 TTCCATGACA
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
14 5 0.08
15 52 0.84
16 5 0.08
ACGTcount: A:0.12, C:0.26, G:0.25, T:0.37
Consensus pattern (15 bp):
GTGCCATCATCTTCG
Found at i:30085 original size:18 final size:18
Alignment explanation
Indices: 30058--30145 Score: 131
Period size: 18 Copynumber: 4.9 Consensus size: 18
30048 AAGTGTGGCA
30058 ACTTGGTGCGGTGCGACC
1 ACTTGGTGCGGTGCGACC
*
30076 ACTGGGTGCGGTGCGACC
1 ACTTGGTGCGGTGCGACC
*
30094 ACTTGGTGTGGTGCGACC
1 ACTTGGTGCGGTGCGACC
* **
30112 ATTTGGTGCGGTGCGAAT
1 ACTTGGTGCGGTGCGACC
30130 ACTTGGTGCGGTGCGA
1 ACTTGGTGCGGTGCGA
30146 TTTGTTGTTG
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.12, C:0.22, G:0.41, T:0.25
Consensus pattern (18 bp):
ACTTGGTGCGGTGCGACC
Found at i:30753 original size:48 final size:47
Alignment explanation
Indices: 30678--30819 Score: 164
Period size: 49 Copynumber: 3.0 Consensus size: 47
30668 GAGCGTGCCA
* * *
30678 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCGA-TGAAAATTAAAAG
1 ATCAATTTTGTCAAAAAATTGAGAAAAAGTGCAAGT-AAAAATAAAAG
*
30725 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG
1 ATCAATTTTGTC-AAAAAATTGAGAAAAAG-TGCAAGTAAAAATAAAAG
*
30774 TTCAATTTTGT-AGCAAAAATTGAGAAAAAGTGC-AGTAAAAAGTAAA
1 ATCAATTTTGTCA--AAAAATTGAGAAAAAGTGCAAGTAAAAA-TAAA
30820 TGATTGCTTT
Statistics
Matches: 83, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
47 20 0.24
48 22 0.27
49 40 0.48
50 1 0.01
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.27
Consensus pattern (47 bp):
ATCAATTTTGTCAAAAAATTGAGAAAAAGTGCAAGTAAAAATAAAAG
Done.