Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019286.1 Corchorus olitorius cultivar O-4 contig19319, 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: 52999
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:3438 original size:18 final size:19
Alignment explanation
Indices: 3415--3454 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
3405 AGGGTTCTTG
*
3415 ATTTGTGGAATT-GACCTA
1 ATTTGTGCAATTAGACCTA
*
3433 ATTTGTGCAATTAGCCCTA
1 ATTTGTGCAATTAGACCTA
3452 ATT
1 ATT
3455 GGAGAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (19 bp):
ATTTGTGCAATTAGACCTA
Found at i:7417 original size:17 final size:17
Alignment explanation
Indices: 7369--7428 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
7359 CAATGGAGAT
*
7369 CATGGAAATG-ATG-AG
1 CATGGAGATGCATGAAG
*
7384 CATGGAG-TGCTAGGAAG
1 CATGGAGATGC-ATGAAG
7401 CATGGAGATGCATGAAG
1 CATGGAGATGCATGAAG
7418 AACATGGAGAT
1 --CATGGAGAT
7429 ATCGTTGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 2 0.06
15 6 0.17
16 2 0.06
17 14 0.39
18 3 0.08
19 9 0.25
ACGTcount: A:0.37, C:0.10, G:0.35, T:0.18
Consensus pattern (17 bp):
CATGGAGATGCATGAAG
Found at i:9607 original size:21 final size:21
Alignment explanation
Indices: 9583--9653 Score: 133
Period size: 21 Copynumber: 3.4 Consensus size: 21
9573 TGCTAGGAGA
9583 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
9604 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
9625 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
9646 TCATTGGA
1 TCATTGGA
9654 ATTGCCTAAG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:10721 original size:15 final size:15
Alignment explanation
Indices: 10701--10735 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
10691 GTTCTTAAAA
10701 TTCATTTAGGATGGG
1 TTCATTTAGGATGGG
*
10716 TTCATTTTGGATGGG
1 TTCATTTAGGATGGG
10731 TTCAT
1 TTCAT
10736 AAATCGATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.09, G:0.29, T:0.46
Consensus pattern (15 bp):
TTCATTTAGGATGGG
Found at i:24556 original size:393 final size:393
Alignment explanation
Indices: 23830--24607 Score: 1461
Period size: 393 Copynumber: 2.0 Consensus size: 393
23820 CTCTCAGGGA
23830 ATTTCAATGCTTTCAACAAAATTTTGGTCAAGTTAGAAAATAAAAAGAAGCAAAATGAAACATAT
1 ATTTCAATGCTTTCAACAAAATTTTGGTCAAGTTAGAAAATAAAAAGAAGCAAAATGAAACATAT
*
23895 ACAAAAAAATGTTGCATATAAAAAAAATTGTACTTTCATAGACGCGGGTACGTTTCAAGAATTGG
66 ACAAAAAAATGTTGCATATAAAAAAAATTCTACTTTCATAGACGCGGGTACGTTTCAAGAATTGG
*
23960 ATGCTTTGACTTATACTTAAATTGATATATATTTAATATTTAATTTAAAATTTATTTCAATTTAA
131 ATGCTTTGACTTATACTTAAATTGATATATATTTAATATTTAATTTAAAAGTTATTTCAATTTAA
*
24025 TTATGTTTTTTTTACACTTGAACATTTGGCTCAATGTTAAGGTGCATGATCTCTGAACCGCTAGC
196 TTATGTTTTTTTTACACTTGAACATTTGGCTCAATGCTAAGGTGCATGATCTCTGAACCGCTAGC
*
24090 TCTCAGGGTCAAGTCCCATCGTATTCAATGTGTGTGGTTTGTGCAGCTTTATGTTGGCTTTGTTA
261 TCTCAGGGTCAAGTCCCATCGTATTCAATGTGTGTGCTTTGTGCAGCTTTATGTTGGCTTTGTTA
24155 TATTTATTATAGTTTGTTTATTTGGCCATTTATCATTGGATGTTCGGGTATATAAGGATTGTTTG
326 TATTTATTATAGTTTGTTTATTTGGCCATTTATCATTGGATGTTCGGGTATATAAGGATTGTTTG
24220 GCC
391 GCC
24223 ATTTCAATGCTTTCAACAAAATTTTGGTCAAGTTAGAAAATAAAAAGAAGCAAAATGAAACATAT
1 ATTTCAATGCTTTCAACAAAATTTTGGTCAAGTTAGAAAATAAAAAGAAGCAAAATGAAACATAT
24288 ACAAAAAAAATGTTGCATA-AAAAAAAATTCTACTTTCATAGA-GACGGGTACGTTTCAAGAATT
66 AC-AAAAAAATGTTGCATATAAAAAAAATTCTACTTTCATAGACG-CGGGTACGTTTCAAGAATT
24351 GGATGCTTTGACTTATACTTAAATTGATATATATTTAATATTTAATTTAAAAGTTATTTCAATTT
129 GGATGCTTTGACTTATACTTAAATTGATATATATTTAATATTTAATTTAAAAGTTATTTCAATTT
*
24416 AATTATGTTTTTTTTACACTTGAACATTTGGCTCAATGCTAAGGTGCATGCTCTCTGAACCGCTA
194 AATTATGTTTTTTTTACACTTGAACATTTGGCTCAATGCTAAGGTGCATGATCTCTGAACCGCTA
24481 GCTCTCAGGGTCAAGTCCCATCGTATTCAATGTGTGTGCTTTGTGCAGCTTTATGTTGGCTTTGT
259 GCTCTCAGGGTCAAGTCCCATCGTATTCAATGTGTGTGCTTTGTGCAGCTTTATGTTGGCTTTGT
* *
24546 TATGTTTATTATAGTTTGTTTATTTGGCCATTTATCATTGGATGTTTGGGTATATAAGGATT
324 TATATTTATTATAGTTTGTTTATTTGGCCATTTATCATTGGATGTTCGGGTATATAAGGATT
24608 TTTTTTATAA
Statistics
Matches: 376, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
392 1 0.00
393 359 0.95
394 16 0.04
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (393 bp):
ATTTCAATGCTTTCAACAAAATTTTGGTCAAGTTAGAAAATAAAAAGAAGCAAAATGAAACATAT
ACAAAAAAATGTTGCATATAAAAAAAATTCTACTTTCATAGACGCGGGTACGTTTCAAGAATTGG
ATGCTTTGACTTATACTTAAATTGATATATATTTAATATTTAATTTAAAAGTTATTTCAATTTAA
TTATGTTTTTTTTACACTTGAACATTTGGCTCAATGCTAAGGTGCATGATCTCTGAACCGCTAGC
TCTCAGGGTCAAGTCCCATCGTATTCAATGTGTGTGCTTTGTGCAGCTTTATGTTGGCTTTGTTA
TATTTATTATAGTTTGTTTATTTGGCCATTTATCATTGGATGTTCGGGTATATAAGGATTGTTTG
GCC
Found at i:29514 original size:16 final size:16
Alignment explanation
Indices: 29493--29523 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29483 AGGAATAGGC
*
29493 AATCAATCTAAGCAAT
1 AATCAATCAAAGCAAT
29509 AATCAATCAAAGCAA
1 AATCAATCAAAGCAA
29524 AGTAAAGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.19, G:0.06, T:0.19
Consensus pattern (16 bp):
AATCAATCAAAGCAAT
Found at i:33559 original size:31 final size:29
Alignment explanation
Indices: 33517--33581 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 29
33507 GCTTAATACC
33517 CAAATTAGCCCCTTAACTATCCATTTTGGGA
1 CAAATTAGCCCCTTAACT-T-CATTTTGGGA
* **
33548 CAAATTGGCCCCTTAACTTTTTTTTGGGA
1 CAAATTAGCCCCTTAACTTCATTTTGGGA
33577 CAAAT
1 CAAAT
33582 AAATCCCATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 13 0.42
30 1 0.03
31 17 0.55
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (29 bp):
CAAATTAGCCCCTTAACTTCATTTTGGGA
Found at i:35228 original size:45 final size:44
Alignment explanation
Indices: 35158--35243 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 44
35148 AACTTCCTAG
* *
35158 AAAAACAAAAACTTAAAAGAAAAAATTAGTAGTAAAAGTTCTTAAAC
1 AAAAACAAAAACTTAAAACAAAAAATAAG-AG-AAAA-TTCTTAAAC
*
35205 AAAAA-AAAAAC-TAAAACAGAAAATAAGAGAAAATTCTTA
1 AAAAACAAAAACTTAAAACAAAAAATAAGAGAAAATTCTTA
35244 GAGTTGATTG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
42 6 0.17
43 4 0.11
44 2 0.06
45 13 0.36
46 6 0.17
47 5 0.14
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.19
Consensus pattern (44 bp):
AAAAACAAAAACTTAAAACAAAAAATAAGAGAAAATTCTTAAAC
Found at i:37029 original size:65 final size:65
Alignment explanation
Indices: 36920--37049 Score: 215
Period size: 65 Copynumber: 2.0 Consensus size: 65
36910 GGAAAAATTG
* * *
36920 GTCCTACCCATGCATGGAGTACCCTTGGCCTACCCACGCCTGGGCTAGTGTAGAAAGTTTGAATC
1 GTCCAACCCATGCATGGAGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTGGAATC
* *
36985 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCATGCCTGGGCTAGTGCAGAAAGTTGGAATC
1 GTCCAACCCATGCATGGAGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTGGAATC
37050 AATAGCAAGC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.22, C:0.29, G:0.26, T:0.23
Consensus pattern (65 bp):
GTCCAACCCATGCATGGAGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTGGAATC
Found at i:37267 original size:21 final size:21
Alignment explanation
Indices: 37243--37334 Score: 141
Period size: 21 Copynumber: 4.4 Consensus size: 21
37233 CTTAGGCAAT
*
37243 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
* *
37264 TCCAATTAGCTTGGAACCTTT
1 TCCAATGAGCTTGGAACCTTC
37285 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
37306 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
37327 TCCAATGA
1 TCCAATGA
37335 ACTCCTAGCA
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
20 3 0.05
21 62 0.95
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:39210 original size:33 final size:33
Alignment explanation
Indices: 39173--39277 Score: 122
Period size: 33 Copynumber: 3.2 Consensus size: 33
39163 ATTAGCATCC
39173 AAAACAGAATTT-GTTTCATCACAAACAACACCT
1 AAAACAG-ATTTAGTTTCATCACAAACAACACCT
* *
39206 AAAACAGATTTAGTGTCATCACAAACAACACTT
1 AAAACAGATTTAGTTTCATCACAAACAACACCT
** * * * *
39239 AAATTAGGTTTAGTATCATCACTAACAACATCT
1 AAAACAGATTTAGTTTCATCACAAACAACACCT
39272 AAAACA
1 AAAACA
39278 CTCTTTGCAA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
32 4 0.07
33 56 0.93
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTTTCATCACAAACAACACCT
Found at i:39878 original size:15 final size:15
Alignment explanation
Indices: 39855--39886 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39845 AAACTAAGTG
*
39855 GAGCTTGTTGATTTT
1 GAGCATGTTGATTTT
39870 GAGCATGTTGATTTT
1 GAGCATGTTGATTTT
39885 GA
1 GA
39887 ACCCCCAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.28, T:0.47
Consensus pattern (15 bp):
GAGCATGTTGATTTT
Found at i:41664 original size:65 final size:65
Alignment explanation
Indices: 41555--41684 Score: 224
Period size: 65 Copynumber: 2.0 Consensus size: 65
41545 GGAAAAACTA
* *
41555 GTCCTACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCAAGTGCAGAAAGTTTGAATC
1 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCAAGTGCAGAAAGTTGGAATC
* *
41620 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACTCCTGGGCTAGTGCAGAAAGTTGGAATC
1 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCAAGTGCAGAAAGTTGGAATC
41685 AATAGCAAGC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.22, C:0.31, G:0.26, T:0.22
Consensus pattern (65 bp):
GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCAAGTGCAGAAAGTTGGAATC
Found at i:41904 original size:21 final size:21
Alignment explanation
Indices: 41880--42011 Score: 221
Period size: 21 Copynumber: 6.3 Consensus size: 21
41870 TAGGCAATTT
*
41880 CAATGAGCTTGAAACCTTCTC
1 CAATGAGCTTGGAACCTTCTC
41901 CAATGAGCTTGGAACCTTCTC
1 CAATGAGCTTGGAACCTTCTC
* *
41922 CATTGAGCTTGGAACTTTCTC
1 CAATGAGCTTGGAACCTTCTC
41943 CAATGAGCTTGGAACCTTCTC
1 CAATGAGCTTGGAACCTTCTC
41964 CAATGAGCTTGGAACCTTCTC
1 CAATGAGCTTGGAACCTTCTC
41985 CAATGAGCTTGGAA-CTTGCTC
1 CAATGAGCTTGGAACCTT-CTC
42006 CAATGA
1 CAATGA
42012 AGTCCTAGCA
Statistics
Matches: 105, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
20 3 0.03
21 102 0.97
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (21 bp):
CAATGAGCTTGGAACCTTCTC
Found at i:43197 original size:31 final size:32
Alignment explanation
Indices: 43150--43213 Score: 112
Period size: 31 Copynumber: 2.0 Consensus size: 32
43140 TCATTATGAC
43150 AAAAGAAATTTTGCTTATGATCCTCCTTGAAA
1 AAAAGAAATTTTGCTTATGATCCTCCTTGAAA
*
43182 AAAAGAAA-TTTGCTTATGATCCTCTTTGAAA
1 AAAAGAAATTTTGCTTATGATCCTCCTTGAAA
43213 A
1 A
43214 GAATTGATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 23 0.74
32 8 0.26
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.34
Consensus pattern (32 bp):
AAAAGAAATTTTGCTTATGATCCTCCTTGAAA
Found at i:48559 original size:2 final size:2
Alignment explanation
Indices: 48547--48585 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
48537 TAGTAATGGT
48547 TA TA TA T- TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48586 TTTGTTCCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:48567 original size:15 final size:15
Alignment explanation
Indices: 48547--48583 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
48537 TAGTAATGGT
48547 TATATATTATATATA
1 TATATATTATATATA
*
48562 TATATAATATATATA
1 TATATATTATATATA
48577 TATATAT
1 TATATAT
48584 ATTTTGTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATATATTATATATA
Done.