Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021046.1 Corchorus olitorius cultivar O-4 contig21079, 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: 48624
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:813 original size:17 final size:18
Alignment explanation
Indices: 783--817 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
773 TAAAAAGGTT
783 TTCAAAAATCCAAAAAAA
1 TTCAAAAATCCAAAAAAA
*
801 TTCAAAACT-CAAAAAAA
1 TTCAAAAATCCAAAAAAA
818 AAGAAAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (18 bp):
TTCAAAAATCCAAAAAAA
Found at i:818 original size:18 final size:18
Alignment explanation
Indices: 783--818 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
773 TAAAAAGGTT
*
783 TTCAAAAATCCAAAAAAA
1 TTCAAAAATCAAAAAAAA
*
801 TTCAAAACTCAAAAAAAA
1 TTCAAAAATCAAAAAAAA
819 AGAAAAGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (18 bp):
TTCAAAAATCAAAAAAAA
Found at i:877 original size:43 final size:43
Alignment explanation
Indices: 829--914 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
819 AGAAAAGAAG
829 AAGTATTCAATTTAAAATTTTCAAATTGGGAAAGTTCCCATCA
1 AAGTATTCAATTTAAAATTTTCAAATTGGGAAAGTTCCCATCA
**
872 AAGTATTCAATTTAAGTTTTTCAAATTGGGAAAGTTCCCATCA
1 AAGTATTCAATTTAAAATTTTCAAATTGGGAAAGTTCCCATCA
915 GTTTTCAAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (43 bp):
AAGTATTCAATTTAAAATTTTCAAATTGGGAAAGTTCCCATCA
Found at i:931 original size:50 final size:51
Alignment explanation
Indices: 869--965 Score: 135
Period size: 52 Copynumber: 1.9 Consensus size: 51
859 AAAGTTCCCA
869 TCAAAGTATTCAATTTAAG-T-TTTTCAAATTGGGAAAGTTCCCATCAGTTT
1 TCAAAGTATTCAATTT-AGCTGTTTTCAAATTGGGAAAGTTCCCATCAGTTT
* * *
919 TCAAAGTGTTCAATTTAGCTGGTTTTTAAATTGGGAGAGTTCCCATC
1 TCAAAGTATTCAATTTAGCT-GTTTTCAAATTGGGAAAGTTCCCATC
966 GGGTTTTAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
49 2 0.05
50 16 0.39
52 23 0.56
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (51 bp):
TCAAAGTATTCAATTTAGCTGTTTTCAAATTGGGAAAGTTCCCATCAGTTT
Found at i:1026 original size:40 final size:40
Alignment explanation
Indices: 968--1080 Score: 165
Period size: 40 Copynumber: 2.9 Consensus size: 40
958 TTCCCATCGG
*
968 GTTTTAGTTTTCACTTTAGGGAAAGTTCGCATCATTTTCA
1 GTTTTAGTTTTCACTTTAGGGAAAGTTCCCATCATTTTCA
*
1008 GTTTTAGTTTTCATTTTAGGGAAAGTTCCCATCATTTTCA
1 GTTTTAGTTTTCACTTTAGGGAAAGTTCCCATCATTTTCA
* ***
1048 GCTTTAGTTTTCAAAGT-GGGAAAGTTCCCATCA
1 GTTTTAGTTTTCACTTTAGGGAAAGTTCCCATCA
1081 AAAAGCATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 16 0.24
40 51 0.76
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (40 bp):
GTTTTAGTTTTCACTTTAGGGAAAGTTCCCATCATTTTCA
Found at i:12493 original size:15 final size:14
Alignment explanation
Indices: 12473--12624 Score: 82
Period size: 15 Copynumber: 10.7 Consensus size: 14
12463 ATCCTTATCT
12473 TCTTCAGCTTCATGA
1 TCTTCA-CTTCATGA
*
12488 TCTTCAACTTCATAA
1 TCTTC-ACTTCATGA
* **
12503 TCATC-C-TCATCT
1 TCTTCACTTCATGA
12515 TCTTCATCTTCATGA
1 TCTTCA-CTTCATGA
*
12530 TCTTCAACTTCATAA
1 TCTTC-ACTTCATGA
* **
12545 TCATC-C-TCATCT
1 TCTTCACTTCATGA
12557 TCTTCTACTTCATGA
1 TCTTC-ACTTCATGA
*
12572 TCTTCAACTTCATAA
1 TCTTC-ACTTCATGA
* **
12587 TCATC-C-TCATCT
1 TCTTCACTTCATGA
12599 TCTTCTACTTCATGA
1 TCTTC-ACTTCATGA
12614 TCTTCAACTTC
1 TCTTC-ACTTC
12625 CTCTTCCTCA
Statistics
Matches: 103, Mismatches: 23, Indels: 22
0.70 0.16 0.15
Matches are distributed among these distances:
12 24 0.23
13 3 0.03
14 3 0.03
15 71 0.69
16 2 0.02
ACGTcount: A:0.23, C:0.31, G:0.03, T:0.43
Consensus pattern (14 bp):
TCTTCACTTCATGA
Found at i:12512 original size:27 final size:27
Alignment explanation
Indices: 12482--12611 Score: 71
Period size: 27 Copynumber: 4.7 Consensus size: 27
12472 TTCTTCAGCT
*
12482 TCATGATCTTCAACTTCATAATCATCC
1 TCATCATCTTCAACTTCATAATCATCC
* * * * *
12509 TCATCTTCTTCATCTTCATGATCTTCA
1 TCATCATCTTCAACTTCATAATCATCC
* * ** * * ** *
12536 ACTTCATAATCATCCTCATCTTCTTCTAC
1 TCATCATCTTCAACTTCATAATCATC--C
*
12565 TTCATGATCTTCAACTTCATAATCATCC
1 -TCATCATCTTCAACTTCATAATCATCC
* *
12593 TCATCTTCTTCTACTTCAT
1 TCATCATCTTCAACTTCAT
12612 GATCTTCAAC
Statistics
Matches: 72, Mismatches: 28, Indels: 6
0.68 0.26 0.06
Matches are distributed among these distances:
27 55 0.76
28 1 0.01
30 16 0.22
ACGTcount: A:0.24, C:0.31, G:0.02, T:0.43
Consensus pattern (27 bp):
TCATCATCTTCAACTTCATAATCATCC
Found at i:12515 original size:42 final size:42
Alignment explanation
Indices: 12454--12624 Score: 292
Period size: 42 Copynumber: 4.1 Consensus size: 42
12444 TAGTGACATG
* *
12454 TTCATCATCATCCTTATCTTCTTC-AGCTTCATGATCTTCAAC
1 TTCATAATCATCCTCATCTTCTTCTA-CTTCATGATCTTCAAC
12496 TTCATAATCATCCTCATCTTCTTC-ATCTTCATGATCTTCAAC
1 TTCATAATCATCCTCATCTTCTTCTA-CTTCATGATCTTCAAC
12538 TTCATAATCATCCTCATCTTCTTCTACTTCATGATCTTCAAC
1 TTCATAATCATCCTCATCTTCTTCTACTTCATGATCTTCAAC
12580 TTCATAATCATCCTCATCTTCTTCTACTTCATGATCTTCAAC
1 TTCATAATCATCCTCATCTTCTTCTACTTCATGATCTTCAAC
12622 TTC
1 TTC
12625 CTCTTCCTCA
Statistics
Matches: 125, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
42 124 0.99
43 1 0.01
ACGTcount: A:0.23, C:0.31, G:0.03, T:0.43
Consensus pattern (42 bp):
TTCATAATCATCCTCATCTTCTTCTACTTCATGATCTTCAAC
Found at i:14545 original size:3 final size:3
Alignment explanation
Indices: 14537--14580 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
14527 TTTTCTCCGG
*
14537 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TCC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
14581 TCTGTTGGCC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:15478 original size:217 final size:216
Alignment explanation
Indices: 15045--15478 Score: 823
Period size: 217 Copynumber: 2.0 Consensus size: 216
15035 TTTTGATCTA
15045 TCAAAACTAACGATTTTAAGTTGCTTGCTTGCATTATCTGTTATTGCTTTAATCTGTTGACTTTT
1 TCAAAACTAACGATTTTAAGTTGCTTGCTTGCATTATCTGTTATTGCTTTAATCTGTTGACTTTT
*
15110 TCTAACTCAGCTTTGTTGCCTAAATGATTGGATTTTTATCCTTTTTTTAACTTGGTACGGGCTTT
66 TCTAACTCAACTTTGTTGCCTAAATGATTGGATTTTTATCCTTTTTTTAACTTGGTACGGGCTTT
*
15175 TTTCAATTCTTAGTTTAGTTTAGAGTGAAGCAAATTATAATGAGATTATACATGTTTTTTATCTA
131 TTTCAATTCTTAGTTTAGTTTAGAGTGAAGCAAATTATAATGAGATTATACATGTTTTCTATCTA
15240 ATCTTCAAATTTCTTTTTGTG
196 ATCTTCAAATTTCTTTTTGTG
15261 TCAAAACTAACGATTTTAAGTTGCTTGCTTGCATTATCTGTTATTGCTTTAATCTGTTGACTTTT
1 TCAAAACTAACGATTTTAAGTTGCTTGCTTGCATTATCTGTTATTGCTTTAATCTGTTGACTTTT
* *
15326 TCTAACTCAACTTTGTTGCTTAAATGATTGGATTTTTATTCTTTTTTTTAACTTGGTACGGGCTT
66 TCTAACTCAACTTTGTTGCCTAAATGATTGGATTTTTA-TCCTTTTTTTAACTTGGTACGGGCTT
15391 TTTTCAATTCTTAGTTTAGTTTAGAGTGAAGCAAATTATAATGAGATTATACATGTTTTCTATCT
130 TTTTCAATTCTTAGTTTAGTTTAGAGTGAAGCAAATTATAATGAGATTATACATGTTTTCTATCT
15456 AATCTTCAAATTTCTTTTTGTG
195 AATCTTCAAATTTCTTTTTGTG
15478 T
1 T
15479 ATGTTTTTTT
Statistics
Matches: 213, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
216 101 0.47
217 112 0.53
ACGTcount: A:0.24, C:0.13, G:0.14, T:0.49
Consensus pattern (216 bp):
TCAAAACTAACGATTTTAAGTTGCTTGCTTGCATTATCTGTTATTGCTTTAATCTGTTGACTTTT
TCTAACTCAACTTTGTTGCCTAAATGATTGGATTTTTATCCTTTTTTTAACTTGGTACGGGCTTT
TTTCAATTCTTAGTTTAGTTTAGAGTGAAGCAAATTATAATGAGATTATACATGTTTTCTATCTA
ATCTTCAAATTTCTTTTTGTG
Found at i:22504 original size:5 final size:5
Alignment explanation
Indices: 22494--22541 Score: 96
Period size: 5 Copynumber: 9.6 Consensus size: 5
22484 CATAAATAAT
22494 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAA
22542 CCCCAAACAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:23733 original size:37 final size:36
Alignment explanation
Indices: 23691--23760 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
23681 AGTACATGGT
23691 CTAAACACATCAAAAAC-AAGGATTTAAACATAAAATC
1 CTAAACACA-CAAAAACTAAGGATTTAAAC-TAAAATC
* * *
23728 CTAAACATAGAAAACCTAAGGATTTAAACTAAA
1 CTAAACACACAAAAACTAAGGATTTAAACTAAA
23761 TTACAGTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 9 0.31
37 20 0.69
ACGTcount: A:0.56, C:0.17, G:0.07, T:0.20
Consensus pattern (36 bp):
CTAAACACACAAAAACTAAGGATTTAAACTAAAATC
Found at i:26879 original size:25 final size:25
Alignment explanation
Indices: 26851--26900 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
26841 ATTATGAAAA
*
26851 TTTCCAAATTTATAAGCTAAAGGTT
1 TTTCCAAATTTATAAACTAAAGGTT
26876 TTTCCAAATTTATAAACTAAAGGTT
1 TTTCCAAATTTATAAACTAAAGGTT
26901 ATAAACTCAA
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:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (25 bp):
TTTCCAAATTTATAAACTAAAGGTT
Found at i:30216 original size:84 final size:84
Alignment explanation
Indices: 30109--30279 Score: 324
Period size: 84 Copynumber: 2.0 Consensus size: 84
30099 CTAAAATTGT
*
30109 AATATGCAAAGAAATGAAATGCATTTTCTTTTCTTTTCTATTACTTTTTCAAAGTTTCAAATTCC
1 AATATGCAAAGAAATGAAATGCATTTTCTTTTCTATTCTATTACTTTTTCAAAGTTTCAAATTCC
*
30174 AAGCAAGGCTGTACTTAGC
66 AAGCAAGACTGTACTTAGC
30193 AATATGCAAAGAAATGAAATGCATTTTCTTTTCTATTCTATTACTTTTTCAAAGTTTCAAATTCC
1 AATATGCAAAGAAATGAAATGCATTTTCTTTTCTATTCTATTACTTTTTCAAAGTTTCAAATTCC
30258 AAGCAAGACTGTACTTAGC
66 AAGCAAGACTGTACTTAGC
30277 AAT
1 AAT
30280 CCTCGAAAGC
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (84 bp):
AATATGCAAAGAAATGAAATGCATTTTCTTTTCTATTCTATTACTTTTTCAAAGTTTCAAATTCC
AAGCAAGACTGTACTTAGC
Found at i:33438 original size:27 final size:28
Alignment explanation
Indices: 33377--33439 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
33367 CAACATGTTA
*
33377 AAGGAG-AAGAAGGAAGAAAAGAAGAAG
1 AAGGAGAAAGAAGGAAGAAAACAAGAAG
** *
33404 AAAAAGAAAG-AGGAAGAAAACAAGAGG
1 AAGGAGAAAGAAGGAAGAAAACAAGAAG
33431 AAGGAGAAA
1 AAGGAGAAA
33440 TAAGAGGAGG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
27 26 0.90
28 3 0.10
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (28 bp):
AAGGAGAAAGAAGGAAGAAAACAAGAAG
Found at i:33469 original size:30 final size:31
Alignment explanation
Indices: 33394--33472 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 31
33384 AGAAGGAAGA
33394 AAAGAAGAAGAAAAAGAAAGAGGAAGAAAAC
1 AAAGAAGAAGAAAAAGAAAGAGGAAGAAAAC
* *
33425 AAGAGGAAGGAGAAATAAG-AGGAGGAAG-AAAC
1 AA-A-GAAGAAGAAA-AAGAAAGAGGAAGAAAAC
*
33457 TAAGAAGAAGAAAAAG
1 AAAGAAGAAGAAAAAG
33473 GGCTTCCTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
29 3 0.07
30 9 0.22
31 3 0.07
32 6 0.15
33 17 0.41
34 3 0.07
ACGTcount: A:0.65, C:0.03, G:0.30, T:0.03
Consensus pattern (31 bp):
AAAGAAGAAGAAAAAGAAAGAGGAAGAAAAC
Found at i:33914 original size:5 final size:6
Alignment explanation
Indices: 33900--33939 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
33890 GCAAGGTTTA
*
33900 TTTTGT TTTTGT TTTTGT TTTTAT TTTTGT TTTTGT TTTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTT
33940 TCGCTACGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.03, C:0.00, G:0.12, T:0.85
Consensus pattern (6 bp):
TTTTGT
Found at i:35251 original size:16 final size:16
Alignment explanation
Indices: 35232--35271 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
35222 CAAACCCGAT
35232 TGACCCAAAACCTGAA
1 TGACCCAAAACCTGAA
** *
35248 TGACCTGAAACCTGAG
1 TGACCCAAAACCTGAA
35264 TGACCCAA
1 TGACCCAA
35272 GACCCAATTA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.30, G:0.17, T:0.15
Consensus pattern (16 bp):
TGACCCAAAACCTGAA
Found at i:36148 original size:19 final size:19
Alignment explanation
Indices: 36124--36161 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
36114 TAGGTTCAAA
36124 AGCAGGTGTTGAAAGATTT
1 AGCAGGTGTTGAAAGATTT
36143 AGCAGGTGTTGAAAGATTT
1 AGCAGGTGTTGAAAGATTT
36162 TAATTGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.32
Consensus pattern (19 bp):
AGCAGGTGTTGAAAGATTT
Found at i:37016 original size:12 final size:12
Alignment explanation
Indices: 36999--37028 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
36989 TGAGGAGAAA
36999 AAGAAGAAAAAG
1 AAGAAGAAAAAG
*
37011 AAGAAGAAAAAT
1 AAGAAGAAAAAG
37023 AAGAAG
1 AAGAAG
37029 GTTAAGAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.03
Consensus pattern (12 bp):
AAGAAGAAAAAG
Found at i:46543 original size:61 final size:60
Alignment explanation
Indices: 46448--46570 Score: 174
Period size: 61 Copynumber: 2.0 Consensus size: 60
46438 TACTTCACTC
* *
46448 CATTTTTTTAACGGAAAATAATCAGGATTTGAATTATAATCATCGGAAACATTCTATCTTG
1 CATTTCTTTAACGGAAAATAATCAGGATTTGAATTATAATCATCGGAAACATTCGAT-TTG
* * * * *
46509 CATTTCTTTGACGGAAAATTATTATGATTTGAATTATGATCATCGGAAACATTCGATTTG
1 CATTTCTTTAACGGAAAATAATCAGGATTTGAATTATAATCATCGGAAACATTCGATTTG
46569 CA
1 CA
46571 ATTGATGGCA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
60 5 0.09
61 50 0.91
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (60 bp):
CATTTCTTTAACGGAAAATAATCAGGATTTGAATTATAATCATCGGAAACATTCGATTTG
Done.