Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015176.1 Corchorus olitorius cultivar O-4 contig15209, 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: 49587
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:820 original size:30 final size:29
Alignment explanation
Indices: 745--821 Score: 86
Period size: 27 Copynumber: 2.7 Consensus size: 29
735 TTGACCCAAA
* *
745 CTTATAAGTAGATGGACTAAATTGATATT
1 CTTATAAGTAGAAGGACCAAATTGATATT
* *
774 -TT-TAAGTAGAAAGACCAAATTGACTTTT
1 CTTATAAGTAGAAGGACCAAATTGA-TATT
*
802 CTTATAAGTATAAGGACCAA
1 CTTATAAGTAGAAGGACCAA
822 CCACGTATTC
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
27 18 0.46
28 5 0.13
29 2 0.05
30 14 0.36
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (29 bp):
CTTATAAGTAGAAGGACCAAATTGATATT
Found at i:2630 original size:21 final size:21
Alignment explanation
Indices: 2606--2645 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2596 TCCTCTCCAC
*
2606 AACCCT-TTCCTCAATTTCCGA
1 AACCCTCTTCC-CAAATTCCGA
2627 AACCCTCTTCCCAAATTCC
1 AACCCTCTTCCCAAATTCC
2646 TCAAAAGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.25, C:0.42, G:0.03, T:0.30
Consensus pattern (21 bp):
AACCCTCTTCCCAAATTCCGA
Found at i:16077 original size:2 final size:2
Alignment explanation
Indices: 16070--16108 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
16060 TGATCAAAGG
16070 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16109 CTTATTACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17849 original size:2 final size:2
Alignment explanation
Indices: 17842--17866 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17832 TGACTAATCG
17842 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
17867 TGCATATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23365 original size:7 final size:7
Alignment explanation
Indices: 23350--23379 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
23340 CCGTTCAGGG
*
23350 TGCCCAT
1 TGCCTAT
23357 TGCCTAT
1 TGCCTAT
23364 TGCCTAT
1 TGCCTAT
23371 TGCCTAT
1 TGCCTAT
23378 TG
1 TG
23380 GCAGGACCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.13, C:0.30, G:0.17, T:0.40
Consensus pattern (7 bp):
TGCCTAT
Found at i:27281 original size:21 final size:21
Alignment explanation
Indices: 27257--27323 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
27247 AATTCTCTGT
27257 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
27278 AAATAATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
27299 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
27320 AAAT
1 AAAT
27324 CCTAATCCTT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:27303 original size:42 final size:42
Alignment explanation
Indices: 27244--27323 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
27234 GCTAAGTCTT
27244 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATAATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATAATA
*
27286 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAAT
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAAT
27324 CCTAATCCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.30
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATAATA
Found at i:27460 original size:55 final size:57
Alignment explanation
Indices: 27390--27503 Score: 187
Period size: 57 Copynumber: 2.0 Consensus size: 57
27380 TTTATTCTGT
27390 AGAATAACTAAGTAGAGATA-GGG-GATAAGATTTATTATAACATTTATTATGTGAA
1 AGAATAACTAAGTAGAGATAGGGGCGATAAGATTTATTATAACATTTATTATGTGAA
* * *
27445 AGAATAATTAAGTAGAGATAGGGGCGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAACTAAGTAGAGATAGGGGCGATAAGATTTATTATAACATTTATTATGTGAA
27502 AG
1 AG
27504 GAAACAGATA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
55 19 0.35
56 3 0.06
57 32 0.59
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.32
Consensus pattern (57 bp):
AGAATAACTAAGTAGAGATAGGGGCGATAAGATTTATTATAACATTTATTATGTGAA
Found at i:27701 original size:13 final size:13
Alignment explanation
Indices: 27678--27715 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
27668 TGGGTGTTTC
27678 AAATA-ATATATA
1 AAATATATATATA
27690 AAATATATATATA
1 AAATATATATATA
*
27703 ATATATATATATA
1 AAATATATATATA
27716 TATGGCCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 5 0.21
13 19 0.79
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AAATATATATATA
Found at i:27712 original size:11 final size:11
Alignment explanation
Indices: 27680--27718 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
27670 GGTGTTTCAA
27680 ATAATATATA-
1 ATAATATATAT
27690 A-AATATATAT
1 ATAATATATAT
27700 ATAATATATAT
1 ATAATATATAT
27711 AT-ATATAT
1 ATAATATAT
27719 GGCCATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 8 0.30
10 8 0.30
11 11 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATAATATATAT
Found at i:33207 original size:6 final size:6
Alignment explanation
Indices: 33196--33256 Score: 68
Period size: 6 Copynumber: 10.2 Consensus size: 6
33186 TATATACCTG
* ** ** *
33196 TCGAGC TCGAGC TCGAGC TCGAAC TCGATA TCGAAT TCGAGC TCGAAC
1 TCGAGC TCGAGC TCGAGC TCGAGC TCGAGC TCGAGC TCGAGC TCGAGC
33244 TCGAGC TCGAGC T
1 TCGAGC TCGAGC T
33257 TGAATTTTAG
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.23, C:0.30, G:0.26, T:0.21
Consensus pattern (6 bp):
TCGAGC
Found at i:33213 original size:12 final size:12
Alignment explanation
Indices: 33196--33253 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
33186 TATATACCTG
*
33196 TCGAGCTCGAGC
1 TCGAGCTCGAAC
33208 TCGAGCTCGAAC
1 TCGAGCTCGAAC
** *
33220 TCGATATCGAAT
1 TCGAGCTCGAAC
33232 TCGAGCTCGAAC
1 TCGAGCTCGAAC
33244 TCGAGCTCGA
1 TCGAGCTCGA
33254 GCTTGAATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.24, C:0.29, G:0.26, T:0.21
Consensus pattern (12 bp):
TCGAGCTCGAAC
Found at i:33337 original size:23 final size:22
Alignment explanation
Indices: 33311--33355 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 22
33301 ATCGAACTTG
33311 TCGAGCCGAGCTCGATACTCGAT
1 TCGAGCCGAGCTCGA-ACTCGAT
33334 TCGAGCCGAGCTCGAACTCGAT
1 TCGAGCCGAGCTCGAACTCGAT
33356 GGTCAAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.22, C:0.31, G:0.27, T:0.20
Consensus pattern (22 bp):
TCGAGCCGAGCTCGAACTCGAT
Found at i:33875 original size:13 final size:13
Alignment explanation
Indices: 33857--33882 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33847 ACTTGTTGGT
33857 AAATGATTATAAA
1 AAATGATTATAAA
33870 AAATGATTATAAA
1 AAATGATTATAAA
33883 TGAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (13 bp):
AAATGATTATAAA
Found at i:35717 original size:10 final size:11
Alignment explanation
Indices: 35677--35720 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
35667 CTCAATTAAT
35677 GTTCGTTTAATA
1 GTTCGTTT-ATA
*
35689 GATCGTTTATA
1 GTTCGTTTATA
*
35700 GCTCGTTTAT-
1 GTTCGTTTATA
35710 GTTCGTTTATA
1 GTTCGTTTATA
35721 TTATATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 9 0.32
11 12 0.43
12 7 0.25
ACGTcount: A:0.20, C:0.11, G:0.18, T:0.50
Consensus pattern (11 bp):
GTTCGTTTATA
Found at i:35747 original size:27 final size:24
Alignment explanation
Indices: 35716--35765 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
35706 TTATGTTCGT
35716 TTATATTATATATTTTATATATAATAA
1 TTATATT-TATA-TTTATATA-AATAA
*
35743 TTATATTTTTATTTATATAAATA
1 TTATATTTATATTTATATAAATA
35766 TTAAAATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 8 0.36
26 3 0.14
27 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTATATTTATATTTATATAAATAA
Found at i:39135 original size:19 final size:19
Alignment explanation
Indices: 39111--39149 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
39101 TTTTCCTGAA
39111 ACTTATTGCAGGCCATAAG
1 ACTTATTGCAGGCCATAAG
39130 ACTTATTGCAGGCCATAAG
1 ACTTATTGCAGGCCATAAG
39149 A
1 A
39150 AGGATGAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (19 bp):
ACTTATTGCAGGCCATAAG
Found at i:40284 original size:12 final size:12
Alignment explanation
Indices: 40243--40277 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
40233 GCTGCGTGAG
*
40243 CATGATCATGAC
1 CATGGTCATGAC
*
40255 CGTGGTCATGAC
1 CATGGTCATGAC
40267 CATGGTCATGA
1 CATGGTCATGA
40278 TGATGGTGGT
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:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (12 bp):
CATGGTCATGAC
Found at i:41232 original size:25 final size:25
Alignment explanation
Indices: 41211--41519 Score: 363
Period size: 25 Copynumber: 12.4 Consensus size: 25
41201 TGTGTTTTCT
*
41211 AAACGCAAGCACAGGCTCGTTTGCT
1 AAACGCAAGCACAGGCTCGTTTGCC
* *
41236 AAATGCAAGCACAGGCTCGTTTGCT
1 AAACGCAAGCACAGGCTCGTTTGCC
*
41261 AAACGCAAGCTA-AGGCTCGCTTGCC
1 AAACGCAAGC-ACAGGCTCGTTTGCC
* * *
41286 AAACGCAAGCACAGGTTCGTTTTCT
1 AAACGCAAGCACAGGCTCGTTTGCC
* *
41311 AAACACAAGCACAGGCTCGTTTGCT
1 AAACGCAAGCACAGGCTCGTTTGCC
* *
41336 AAATGCAAGCACAGGCTCGTTTGCT
1 AAACGCAAGCACAGGCTCGTTTGCC
*
41361 AAACGCAAGCTA-AGGCTCGCTTGCC
1 AAACGCAAGC-ACAGGCTCGTTTGCC
* * *
41386 AAACGCAAGCACAGGTTCGTTTTCA
1 AAACGCAAGCACAGGCTCGTTTGCC
*
41411 AAACGCAAGCTA-AGGCTCGCTTGCC
1 AAACGCAAGC-ACAGGCTCGTTTGCC
* *
41436 AAACGCAAGCACAGGTTCGTTTTCC
1 AAACGCAAGCACAGGCTCGTTTGCC
* *
41461 AAACGCAAGCACAGGTTCGTTTTCC
1 AAACGCAAGCACAGGCTCGTTTGCC
* *
41486 AAGCGCAAGCACAGGCTCGTTTTCC
1 AAACGCAAGCACAGGCTCGTTTGCC
*
41511 AAACACAAG
1 AAACGCAAG
41520 AACATGAGCG
Statistics
Matches: 247, Mismatches: 31, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
24 3 0.01
25 241 0.98
26 3 0.01
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (25 bp):
AAACGCAAGCACAGGCTCGTTTGCC
Found at i:41267 original size:50 final size:50
Alignment explanation
Indices: 41204--41519 Score: 404
Period size: 50 Copynumber: 6.3 Consensus size: 50
41194 TAGCCTATGT
* * *
41204 GTTTTCTAAACGCAAGC-ACAGGCTCGTTTGCTAAATGCAAGCACAGGCTC
1 GTTTTCTAAACGCAAGCTA-AGGCTCGCTTGCCAAACGCAAGCACAGGCTC
* *
41254 GTTTGCTAAACGCAAGCTAAGGCTCGCTTGCCAAACGCAAGCACAGGTTC
1 GTTTTCTAAACGCAAGCTAAGGCTCGCTTGCCAAACGCAAGCACAGGCTC
* * * *
41304 GTTTTCTAAACACAAGC-ACAGGCTCGTTTGCTAAATGCAAGCACAGGCTC
1 GTTTTCTAAACGCAAGCTA-AGGCTCGCTTGCCAAACGCAAGCACAGGCTC
* *
41354 GTTTGCTAAACGCAAGCTAAGGCTCGCTTGCCAAACGCAAGCACAGGTTC
1 GTTTTCTAAACGCAAGCTAAGGCTCGCTTGCCAAACGCAAGCACAGGCTC
* *
41404 GTTTTCAAAACGCAAGCTAAGGCTCGCTTGCCAAACGCAAGCACAGGTTC
1 GTTTTCTAAACGCAAGCTAAGGCTCGCTTGCCAAACGCAAGCACAGGCTC
* * * * *
41454 GTTTTCCAAACGCAAGC-ACAGGTTCGTTTTCCAAGCGCAAGCACAGGCTC
1 GTTTTCTAAACGCAAGCTA-AGGCTCGCTTGCCAAACGCAAGCACAGGCTC
* *
41504 GTTTTCCAAACACAAG
1 GTTTTCTAAACGCAAG
41520 AACATGAGCG
Statistics
Matches: 236, Mismatches: 26, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
49 2 0.01
50 232 0.98
51 2 0.01
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.22
Consensus pattern (50 bp):
GTTTTCTAAACGCAAGCTAAGGCTCGCTTGCCAAACGCAAGCACAGGCTC
Found at i:41377 original size:100 final size:100
Alignment explanation
Indices: 41204--41519 Score: 465
Period size: 100 Copynumber: 3.2 Consensus size: 100
41194 TAGCCTATGT
*
41204 GTTTTCTAAACGCAAGCACAGGCTCGTTTGCTAAATGCAAGCACAGGCTCGTTTGCTAAACGCAA
1 GTTTTCTAAACACAAGCACAGGCTCGTTTGCTAAATGCAAGCACAGGCTCGTTTGCTAAACGCAA
41269 GCTAAGGCTCGCTTGCCAAACGCAAGCACAGGTTC
66 GCTAAGGCTCGCTTGCCAAACGCAAGCACAGGTTC
41304 GTTTTCTAAACACAAGCACAGGCTCGTTTGCTAAATGCAAGCACAGGCTCGTTTGCTAAACGCAA
1 GTTTTCTAAACACAAGCACAGGCTCGTTTGCTAAATGCAAGCACAGGCTCGTTTGCTAAACGCAA
41369 GCTAAGGCTCGCTTGCCAAACGCAAGCACAGGTTC
66 GCTAAGGCTCGCTTGCCAAACGCAAGCACAGGTTC
* * * * * * * *
41404 GTTTTCAAAACGCAAGCTA-AGGCTCGCTTGCCAAACGCAAGCACAGGTTCGTTTTCCAAACGCA
1 GTTTTCTAAACACAAGC-ACAGGCTCGTTTGCTAAATGCAAGCACAGGCTCGTTTGCTAAACGCA
* * * * *
41468 AGC-ACAGGTTCGTTTTCCAAGCGCAAGCACAGGCTC
65 AGCTA-AGGCTCGCTTGCCAAACGCAAGCACAGGTTC
*
41504 GTTTTCCAAACACAAG
1 GTTTTCTAAACACAAG
41520 AACATGAGCG
Statistics
Matches: 198, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
99 1 0.01
100 196 0.99
101 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.22
Consensus pattern (100 bp):
GTTTTCTAAACACAAGCACAGGCTCGTTTGCTAAATGCAAGCACAGGCTCGTTTGCTAAACGCAA
GCTAAGGCTCGCTTGCCAAACGCAAGCACAGGTTC
Found at i:46169 original size:2 final size:2
Alignment explanation
Indices: 46162--46190 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
46152 CATTGCATAA
46162 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
46191 ATAGAGAGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:49550 original size:2 final size:2
Alignment explanation
Indices: 49543--49587 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
49533 AGAGCATCCA
49543 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
49585 AT A
1 AT A
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.