Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014565.1 Corchorus olitorius cultivar O-4 contig14598, 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: 68569
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:3137 original size:33 final size:33
Alignment explanation
Indices: 3081--3150 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
3071 AATTCCTTCA
* ** * *
3081 GCTGGCTTGGATTGATCATCTCACTGACATTTT
1 GCTGCCTTGGATCAATCAACTCACTAACATTTT
*
3114 GCTGCCTTGGATCAATCAACTCACTAACCTTTT
1 GCTGCCTTGGATCAATCAACTCACTAACATTTT
3147 GCTG
1 GCTG
3151 ATTGGATGCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.36
Consensus pattern (33 bp):
GCTGCCTTGGATCAATCAACTCACTAACATTTT
Found at i:4212 original size:18 final size:17
Alignment explanation
Indices: 4169--4223 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 17
4159 GATCTTGATT
*
4169 TTTCAGGGCTTTTCTGC
1 TTTCAGAGCTTTTCTGC
4186 -TTCAGAGCTTTTCTGC
1 TTTCAGAGCTTTTCTGC
*
4202 TTTGTAGAGCTTCTT-TGC
1 TTT-CAGAGCTT-TTCTGC
4220 TTTC
1 TTTC
4224 TTGAATTGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
16 15 0.47
17 2 0.06
18 13 0.41
19 2 0.06
ACGTcount: A:0.09, C:0.22, G:0.20, T:0.49
Consensus pattern (17 bp):
TTTCAGAGCTTTTCTGC
Found at i:4661 original size:28 final size:29
Alignment explanation
Indices: 4629--4684 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
4619 GTACAATTCC
4629 CTCC-TTTAACATGTCAAACAATCTAACT
1 CTCCTTTTAACATGTCAAACAATCTAACT
**
4657 CTCCTTTTAATTTGTCAAACAATCTAAC
1 CTCCTTTTAACATGTCAAACAATCTAAC
4685 GGTCATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.36
Consensus pattern (29 bp):
CTCCTTTTAACATGTCAAACAATCTAACT
Found at i:14755 original size:26 final size:26
Alignment explanation
Indices: 14719--14771 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 26
14709 ACAAGGTAAG
14719 AGCTACTATATTTGTAT-GGAGTACTT
1 AGCTACTATATTTGT-TCGGAGTACTT
14745 AGCTACTATATTTGTTCGGAGTACTT
1 AGCTACTATATTTGTTCGGAGTACTT
14771 A
1 A
14772 AAATTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (26 bp):
AGCTACTATATTTGTTCGGAGTACTT
Found at i:18012 original size:24 final size:26
Alignment explanation
Indices: 17980--18027 Score: 82
Period size: 24 Copynumber: 1.9 Consensus size: 26
17970 TTGCTTTGAA
17980 GTTCCTTTTTCAA-A-TTTCCTCATG
1 GTTCCTTTTTCAATATTTTCCTCATG
18004 GTTCCTTTTTCAATATTTTCCTCA
1 GTTCCTTTTTCAATATTTTCCTCA
18028 ATCAAGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 13 0.59
25 1 0.05
26 8 0.36
ACGTcount: A:0.17, C:0.25, G:0.06, T:0.52
Consensus pattern (26 bp):
GTTCCTTTTTCAATATTTTCCTCATG
Found at i:21907 original size:12 final size:12
Alignment explanation
Indices: 21890--21914 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21880 AATCTGAACC
21890 TGAATATATTTA
1 TGAATATATTTA
21902 TGAATATATTTA
1 TGAATATATTTA
21914 T
1 T
21915 AACATCGTTG
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:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TGAATATATTTA
Found at i:23730 original size:23 final size:23
Alignment explanation
Indices: 23704--23747 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
23694 TTTAAGTTTT
*
23704 AAATTTTCCAAAATT-TATTTTAA
1 AAATTTT-AAAAATTATATTTTAA
23727 AAATTTTAAAAATTATATTTT
1 AAATTTTAAAAATTATATTTT
23748 TGTAATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (23 bp):
AAATTTTAAAAATTATATTTTAA
Found at i:28688 original size:27 final size:28
Alignment explanation
Indices: 28658--28716 Score: 111
Period size: 27 Copynumber: 2.1 Consensus size: 28
28648 TTTTATATTA
28658 TGTTCGTTGAAAAACCTTTAATCA-CCT
1 TGTTCGTTGAAAAACCTTTAATCACCCT
28685 TGTTCGTTGAAAAACCTTTAATCACCCT
1 TGTTCGTTGAAAAACCTTTAATCACCCT
28713 TGTT
1 TGTT
28717 TACAAGTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 24 0.77
28 7 0.23
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (28 bp):
TGTTCGTTGAAAAACCTTTAATCACCCT
Found at i:30229 original size:31 final size:31
Alignment explanation
Indices: 30151--30280 Score: 145
Period size: 31 Copynumber: 4.2 Consensus size: 31
30141 CGTGGCATAC
** *
30151 CACGTGTCACTTTTTGAAACACATGGCATGT
1 CACGTGTCACTTTTTGGTACACATGGCGTGT
*
30182 CATGTGTCACTTTTTGGTACACATGGCGTGAT
1 CACGTGTCACTTTTTGGTACACATGGCGTG-T
*
30214 -ACGTGTCACTTTTTGGTACACGTGGCGTGT
1 CACGTGTCACTTTTTGGTACACATGGCGTGT
* ** * *
30244 CACATGTCGGTTTTTTGGTACACGTGGCATGT
1 CACGTGTC-ACTTTTTGGTACACATGGCGTGT
30276 CACGT
1 CACGT
30281 CGGACACCGT
Statistics
Matches: 85, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
30 1 0.01
31 59 0.69
32 25 0.29
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.35
Consensus pattern (31 bp):
CACGTGTCACTTTTTGGTACACATGGCGTGT
Found at i:40237 original size:22 final size:22
Alignment explanation
Indices: 40142--40625 Score: 97
Period size: 22 Copynumber: 21.6 Consensus size: 22
40132 AATCTTTTTT
*
40142 TGAAATTTTGATAA-TTTCAGTA
1 TGAAATTTTGATAACCTTCA-TA
* * * * *
40164 TCAAAGTTTGATAATCTTTTAAA
1 TGAAATTTTGATAA-CCTTCATA
* *
40187 T-AAATTTTGAAAACCATCTAATTA
1 TGAAATTTTGATAACC-T-TCA-TA
40211 TGAAATTTTGATAACCTTCATA
1 TGAAATTTTGATAACCTTCATA
* *
40233 TGAAAATTTGACAA--TTCCACTA
1 TGAAATTTTGATAACCTT-CA-TA
* * **
40255 AGAAATTTT-AAAATTTTC-TCGA
1 TGAAATTTTGATAACCTTCAT--A
* * *
40277 TGATATTTTGATATCCTCCATA
1 TGAAATTTTGATAACCTTCATA
* * *
40299 TGAAATCTTGATCATAACC-ACACAA
1 TGAAAT-TT--TGATAACCTTCA-TA
* * *
40324 TAAAATTTTGGTAACCATGC-TA
1 TGAAATTTTGATAACC-TTCATA
*
40346 TGAAATTTTGATAACC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
* * * * *
40368 TTAAATTTTGATAAAGACTCCCTG
1 TGAAATTTTGAT-AA-CCTTCATA
* * * *
40392 TAAAACTTTGATAACCTCCGTA
1 TGAAATTTTGATAACCTTCATA
* * *
40414 TGGAATTTTGATAAAC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
* *
40436 TGAATTTTTGAT-ACC-TCACAA
1 TGAAATTTTGATAACCTTCA-TA
* * *
40457 TTAAATATTGATAACCCCTC-TA
1 TGAAATTTTGATAA-CCTTCATA
* *
40479 TAAAATTTTGATAATCTCTGCATA
1 TGAAATTTTGATAA-C-CTTCATA
*
40503 --AAATTTTTGATAA-CTTCCTTA
1 TGAAA-TTTTGATAACCTT-CATA
*
40524 TGAAATTTTGATAAGCAC-ACA-A
1 TGAAATTTTGATAA-C-CTTCATA
* ** *
40546 TGAAAATTTGATAAGTTTCTTA
1 TGAAATTTTGATAACCTTCATA
* * *
40568 TGAAATTTCGATAACCTCCATT
1 TGAAATTTTGATAACCTTCATA
**
40590 TGAAATTTTGATAATTTTCCA-A
1 TGAAATTTTGATAACCTT-CATA
*
40612 AGAAATTTTGATAA
1 TGAAATTTTGATAA
40626 GCACACAATG
Statistics
Matches: 333, Mismatches: 88, Indels: 82
0.66 0.17 0.16
Matches are distributed among these distances:
20 6 0.02
21 26 0.08
22 208 0.62
23 37 0.11
24 29 0.09
25 27 0.08
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCATA
Found at i:40568 original size:44 final size:44
Alignment explanation
Indices: 40508--40648 Score: 167
Period size: 44 Copynumber: 3.2 Consensus size: 44
40498 GCATAAAATT
* *
40508 TTTGATAACTTCCTTATGAAATTTTGATAAGCACACAATGAAAA
1 TTTGATAAGTTTCTTATGAAATTTTGATAAGCACACAATGAAAA
* * * * *
40552 TTTGATAAGTTTCTTATGAAATTTCGATAACCTC-CATTTGAAAT
1 TTTGATAAGTTTCTTATGAAATTTTGATAAGCACACA-ATGAAAA
* ** *
40596 TTTGATAATTTTCCAAAGAAATTTTGATAAGCACACAATGAAAA
1 TTTGATAAGTTTCTTATGAAATTTTGATAAGCACACAATGAAAA
40640 TTTGATAAG
1 TTTGATAAG
40649 CAAACATATA
Statistics
Matches: 78, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
43 2 0.03
44 74 0.95
45 2 0.03
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (44 bp):
TTTGATAAGTTTCTTATGAAATTTTGATAAGCACACAATGAAAA
Found at i:49420 original size:66 final size:66
Alignment explanation
Indices: 49342--49476 Score: 236
Period size: 66 Copynumber: 2.0 Consensus size: 66
49332 ACTTATCCAC
*
49342 TTTCAATTTCGTATACTTACTTCAAATGAATATAGGATAATTATATGATATACTTA-TGGTGTAA
1 TTTCAATCTCGTATACTTACTTCAAATGAATATAGGATAATTATATGATATACTTACT-GTGTAA
49406 AT
65 AT
*
49408 TTTCAATCTCGTATACTTACTTCAAATGAATATAGGATAATTATCTGATATACTTACTGTGTAAA
1 TTTCAATCTCGTATACTTACTTCAAATGAATATAGGATAATTATATGATATACTTACTGTGTAAA
49473 T
66 T
49474 TTT
1 TTT
49477 GGACTCCACA
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
66 65 0.98
67 1 0.02
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (66 bp):
TTTCAATCTCGTATACTTACTTCAAATGAATATAGGATAATTATATGATATACTTACTGTGTAAA
T
Found at i:50433 original size:35 final size:35
Alignment explanation
Indices: 50387--50454 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
50377 TCATTTCACA
50387 ATTCACATTTTTGATCACCCCCATCCATCAGGGCG
1 ATTCACATTTTTGATCACCCCCATCCATCAGGGCG
*
50422 ATTCACATTTTTGATCACCCCCATCCATTAGGG
1 ATTCACATTTTTGATCACCCCCATCCATCAGGG
50455 AAAAAAGAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.24, C:0.32, G:0.13, T:0.31
Consensus pattern (35 bp):
ATTCACATTTTTGATCACCCCCATCCATCAGGGCG
Found at i:59180 original size:2 final size:2
Alignment explanation
Indices: 59173--59205 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
59163 TCTTTCCCTC
59173 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 A
59206 ATCATTTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59348 original size:32 final size:32
Alignment explanation
Indices: 59307--59371 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
59297 GTGAACAGAA
*
59307 GTGTTAAATAATTAAATTTGAAGCACTCAAAG
1 GTGTTAAATAACTAAATTTGAAGCACTCAAAG
* *
59339 GTGTTAAATAACTAGATTTGAAGCAGTCAAAG
1 GTGTTAAATAACTAAATTTGAAGCACTCAAAG
59371 G
1 G
59372 GCATGGCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.29
Consensus pattern (32 bp):
GTGTTAAATAACTAAATTTGAAGCACTCAAAG
Found at i:60682 original size:25 final size:24
Alignment explanation
Indices: 60644--60699 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 24
60634 TTTAATACAG
* * *
60644 ATATCCATGGATATATCGAACGGAT
1 ATATCGATGAATATATCG-ACGAAT
60669 ATATCGATGAATATATCGACGAAT
1 ATATCGATGAATATATCGACGAAT
60693 ATATCGA
1 ATATCGA
60700 GGTATCAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 12 0.43
25 16 0.57
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (24 bp):
ATATCGATGAATATATCGACGAAT
Found at i:60696 original size:14 final size:12
Alignment explanation
Indices: 60654--60699 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
60644 ATATCCATGG
*
60654 ATATATCGAACGG
1 ATATATCG-ACGA
*
60667 ATATATCGATGA
1 ATATATCGACGA
60679 ATATATCGACGA
1 ATATATCGACGA
60691 ATATATCGA
1 ATATATCGA
60700 GGTATCAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 22 0.73
13 8 0.27
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.28
Consensus pattern (12 bp):
ATATATCGACGA
Found at i:61802 original size:10 final size:10
Alignment explanation
Indices: 61787--61832 Score: 74
Period size: 10 Copynumber: 4.6 Consensus size: 10
61777 AATTTAATAT
*
61787 GGATATATAC
1 GGATATTTAC
61797 GGATATTTAC
1 GGATATTTAC
*
61807 GGATATTTAT
1 GGATATTTAC
61817 GGATATTTAC
1 GGATATTTAC
61827 GGATAT
1 GGATAT
61833 ATCTAGGTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.39
Consensus pattern (10 bp):
GGATATTTAC
Found at i:65552 original size:44 final size:44
Alignment explanation
Indices: 65489--65588 Score: 112
Period size: 44 Copynumber: 2.3 Consensus size: 44
65479 TGACAATAAA
* * *
65489 ACCAAAATTACATAGGAAGGCTATCTAAA-TTTAATAGTGTTGTC
1 ACCAAAATTTCATAGGAAGGCTATCAAAACTTT-ATAGTGTAGTC
* * * *
65533 ACCAAAATTTCGTATGAAGGTTATCAAAACTTTATAGTGTAGTT
1 ACCAAAATTTCATAGGAAGGCTATCAAAACTTTATAGTGTAGTC
*
65577 ATCAAAATTTCA
1 ACCAAAATTTCA
65589 CATAGAGGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
44 43 0.93
45 3 0.07
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (44 bp):
ACCAAAATTTCATAGGAAGGCTATCAAAACTTTATAGTGTAGTC
Found at i:65560 original size:22 final size:22
Alignment explanation
Indices: 65535--65722 Score: 132
Period size: 22 Copynumber: 8.5 Consensus size: 22
65525 GTGTTGTCAC
*
65535 CAAAATTTCGTATGAAGGTTAT
1 CAAAATTTCATATGAAGGTTAT
*
65557 CAAAACTTT-ATAGTGTA-GTTAT
1 CAAAA-TTTCATA-TGAAGGTTAT
* *
65579 CAAAATTTCACAT-AGAGGTTAC
1 CAAAATTTCATATGA-AGGTTAT
* ** *
65601 CAAGATTTCATAAAAAGATTAT
1 CAAAATTTCATATGAAGGTTAT
* * * *
65623 CAAAATTTCTTAGGGAGGTTAA
1 CAAAATTTCATATGAAGGTTAT
* * *
65645 CAAAATTTCATACGAAAGATAT
1 CAAAATTTCATATGAAGGTTAT
* * *
65667 CAAAATTTTACAGTG-TGGTTAT
1 CAAAATTTCATA-TGAAGGTTAT
* *
65689 CAAAATTTCATAAGAAGGTTAA
1 CAAAATTTCATATGAAGGTTAT
65711 CAAAATTTCATA
1 CAAAATTTCATA
65723 GGGAGGAAAT
Statistics
Matches: 124, Mismatches: 34, Indels: 16
0.71 0.20 0.09
Matches are distributed among these distances:
21 6 0.05
22 110 0.89
23 8 0.06
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (22 bp):
CAAAATTTCATATGAAGGTTAT
Found at i:66056 original size:22 final size:22
Alignment explanation
Indices: 65992--66069 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
65982 CATAGGGAGA
* **
65992 TTATCAAAATTTCACACTAAGG
1 TTATCAAAATTTCACAATGTGG
****
66014 TTATCAAAATTTCTTTGTGTGG
1 TTATCAAAATTTCACAATGTGG
66036 TTATCAAAATTTCACAATGTGG
1 TTATCAAAATTTCACAATGTGG
*
66058 TTATCCAAATTT
1 TTATCAAAATTT
66070 TTATGTTGGA
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (22 bp):
TTATCAAAATTTCACAATGTGG
Found at i:66990 original size:37 final size:38
Alignment explanation
Indices: 66940--67015 Score: 127
Period size: 37 Copynumber: 2.0 Consensus size: 38
66930 TTGACAAATG
* *
66940 ATATAATGAATGGTTTTAAA-TTTTTGGTAAATATATA
1 ATATAATAAATGGTTTTAAATTTTTTGATAAATATATA
66977 ATATAATAAATGGTTTTAAATTTTTTGATAAATATATA
1 ATATAATAAATGGTTTTAAATTTTTTGATAAATATATA
67015 A
1 A
67016 CTTTTTTCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 19 0.53
38 17 0.47
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (38 bp):
ATATAATAAATGGTTTTAAATTTTTTGATAAATATATA
Done.