Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018007.1 Corchorus olitorius cultivar O-4 contig18040, 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: 47997
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Found at i:1240 original size:49 final size:48
Alignment explanation
Indices: 1175--1303 Score: 172
Period size: 49 Copynumber: 2.7 Consensus size: 48
1165 TTACATTTCC
** *
1175 TGCACTTTTTCTCAATTTTTACTACAAAATTGAACTTTT-ATTTTTACT
1 TGCACTTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAATTTTCA-T
*
1223 TGCACCTTTTTCTCAATTTTTAAGACAAAATTGATCTTTTAATTTTCAT
1 TGCA-CTTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAATTTTCAT
* *
1272 TGCACTTTTTATCAATTTTT-GGACAAAATTGA
1 TGCACTTTTTCTCAATTTTTAAGACAAAATTGA
1304 TTGGCACGAT
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
47 11 0.15
48 19 0.26
49 37 0.51
50 6 0.08
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.49
Consensus pattern (48 bp):
TGCACTTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAATTTTCAT
Found at i:2024 original size:18 final size:18
Alignment explanation
Indices: 2001--2045 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
1991 GCAAATGGCG
2001 CCACACCAAGTGGTCGCA
1 CCACACCAAGTGGTCGCA
2019 CCACACCAAGTGGTCGCA
1 CCACACCAAGTGGTCGCA
*
2037 CCGCACCAA
1 CCACACCAA
2046 ATTGCCACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.29, C:0.42, G:0.20, T:0.09
Consensus pattern (18 bp):
CCACACCAAGTGGTCGCA
Found at i:3315 original size:15 final size:15
Alignment explanation
Indices: 3276--3323 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
3266 TGCCATGGAG
*
3276 GAAGATGATGGCACC
1 GAAGATGACGGCACC
*
3291 -AAAATCGACGGCACC
1 GAAGAT-GACGGCACC
*
3306 GAAGATGACGACACC
1 GAAGATGACGGCACC
3321 GAA
1 GAA
3324 AGTGTTTACT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
14 4 0.15
15 19 0.70
16 4 0.15
ACGTcount: A:0.40, C:0.25, G:0.27, T:0.08
Consensus pattern (15 bp):
GAAGATGACGGCACC
Found at i:6005 original size:49 final size:48
Alignment explanation
Indices: 5940--6068 Score: 154
Period size: 49 Copynumber: 2.7 Consensus size: 48
5930 TACTTTCTAC
* ** *
5940 TGCACTTTTTCTCAATTTTTACTACAAAATTGAACTTTT-ATTTTTACT
1 TGCAATTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAATTTTCA-T
*
5988 TGCATATTTTTCTCAATTTTTAAGACAAAATTGATCTTTTAATTTTCAT
1 TGCA-ATTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAATTTTCAT
* * *
6037 TGCACTTTTTATCAATTTTT-GGACAAAATTGA
1 TGCAATTTTTCTCAATTTTTAAGACAAAATTGA
6069 TTGGCACGCT
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
47 11 0.15
48 18 0.25
49 36 0.51
50 6 0.08
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (48 bp):
TGCAATTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAATTTTCAT
Found at i:7393 original size:159 final size:160
Alignment explanation
Indices: 7103--7412 Score: 453
Period size: 159 Copynumber: 1.9 Consensus size: 160
7093 GGAAACTTGA
* *
7103 ATCACCTTAATCGGACATATGGCGCAAAAATTATGTAATATTAAGTGAACTGTCCATTCCCGATA
1 ATCACCTTAATCAGACATATGGAGCAAAAATTATGTAATATTAAGTGAACTGTCCATTCCCGATA
* * * *
7168 ACCGAAACAACTAATTTTTTGGAAGCATTTTTTATACTTGAAACATTAAATTTAGCTTTCGGGTC
66 ACCGAAACAACTAATTTTTCGAAAGCATTTTTTATACTTGAAACATTAAATTTAACTTTCGAGTC
*
7233 C-TCTATAAAAGTTGTAGATCAGACACTTAG
131 CTTC-ATAAAAGTTGCAGATCAGACACTTAG
* * * * *
7263 ATCACCTTAATTAGACATTTGGAGCAAAAGTTATGTAATATTAAGTGGACTGTCCATTCCCGTTA
1 ATCACCTTAATCAGACATATGGAGCAAAAATTATGTAATATTAAGTGAACTGTCCATTCCCGATA
* * *
7328 ACC-AAATAACTAATTTTTCGAAATCATTTTTTATACTTGAAACATTAAATTTAATTTTCGAGTC
66 ACCGAAACAACTAATTTTTCGAAAGCATTTTTTATACTTGAAACATTAAATTTAACTTTCGAGTC
*
7392 CTTCATGAAAGTTGCAGATCA
131 CTTCATAAAAGTTGCAGATCA
7413 TGAAACAATC
Statistics
Matches: 133, Mismatches: 16, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
159 70 0.53
160 63 0.47
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (160 bp):
ATCACCTTAATCAGACATATGGAGCAAAAATTATGTAATATTAAGTGAACTGTCCATTCCCGATA
ACCGAAACAACTAATTTTTCGAAAGCATTTTTTATACTTGAAACATTAAATTTAACTTTCGAGTC
CTTCATAAAAGTTGCAGATCAGACACTTAG
Found at i:9289 original size:2 final size:2
Alignment explanation
Indices: 9284--9322 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
9274 GTGGCCAAAC
9284 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
9323 TAATCTTTTA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11570 original size:26 final size:26
Alignment explanation
Indices: 11534--11586 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
11524 GATGGTACTG
11534 AGCTGCTGGATTCCTCAAACTAATTA
1 AGCTGCTGGATTCCTCAAACTAATTA
11560 AGCTGCTGGATTCCTCAAACTAATTA
1 AGCTGCTGGATTCCTCAAACTAATTA
11586 A
1 A
11587 TGTAATTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (26 bp):
AGCTGCTGGATTCCTCAAACTAATTA
Found at i:16023 original size:25 final size:24
Alignment explanation
Indices: 15989--16037 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 24
15979 AAGGGCGGGG
15989 CTAGTTTACATAAATTAGTTTACAT
1 CTAGTTTACATAAATTA-TTTACAT
16014 CTAGTTTACATAAATTATTTACAT
1 CTAGTTTACATAAATTATTTACAT
16038 AAATTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (24 bp):
CTAGTTTACATAAATTATTTACAT
Found at i:16036 original size:13 final size:14
Alignment explanation
Indices: 15990--16048 Score: 72
Period size: 14 Copynumber: 4.5 Consensus size: 14
15980 AGGGCGGGGC
15990 TAGTTTACATAAAT
1 TAGTTTACATAAAT
*
16004 TAGTTTACAT---C
1 TAGTTTACATAAAT
16015 TAGTTTACATAAAT
1 TAGTTTACATAAAT
16029 TA-TTTACATAAAT
1 TAGTTTACATAAAT
*
16042 TATTTTA
1 TAGTTTA
16049 TGTATATATG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
11 10 0.26
13 13 0.33
14 16 0.41
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.47
Consensus pattern (14 bp):
TAGTTTACATAAAT
Found at i:22462 original size:46 final size:46
Alignment explanation
Indices: 22405--22523 Score: 202
Period size: 46 Copynumber: 2.6 Consensus size: 46
22395 CATGAAATGG
* *
22405 TAAGTGTTTTATGAAGTTTTTGAATTAGGAATTTACAATTCATAAC
1 TAAGTGCTTTATGAAGTTTTTGAATTAGGAATTTACAATACATAAC
22451 TAAGTGCTTTATGAAGTTTTTGAATTAGGAATTTACAATACATAAC
1 TAAGTGCTTTATGAAGTTTTTGAATTAGGAATTTACAATACATAAC
*
22497 TAAGTGCTTTATGAATGGTTTTGAATT
1 TAAGTGCTTTATGAA-GTTTTTGAATT
22524 TATGCAGAGC
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
46 59 0.86
47 10 0.14
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.43
Consensus pattern (46 bp):
TAAGTGCTTTATGAAGTTTTTGAATTAGGAATTTACAATACATAAC
Found at i:22847 original size:14 final size:14
Alignment explanation
Indices: 22828--22854 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22818 CTGCAGAAAA
22828 TTATAGGCTCACTG
1 TTATAGGCTCACTG
22842 TTATAGGCTCACT
1 TTATAGGCTCACT
22855 TTTGCTTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (14 bp):
TTATAGGCTCACTG
Found at i:23427 original size:384 final size:389
Alignment explanation
Indices: 22704--23467 Score: 1342
Period size: 384 Copynumber: 2.0 Consensus size: 389
22694 CTACTAATCG
*
22704 TATGATTGTTGAGTTTTAGGAGTAAGTTGACTTTATATATCTGGTTTAAAGTTTCATATTGATGC
1 TATGATTGTTGAGTTTTAGGAGTAAGTTGACTTTATATATCTGGTTGAAAGTTTCATATTGATGC
22769 CAAGAATTAAAAGAATAAAAAAAATGAGAGTGAATATTGGTTACTAACACTGCAGAAAATTATAG
66 CAAGAATTAAAAGAATAAAAAAAATGAGAGTGAATATTGGTTACTAACACTGCAG--AA-TATA-
22834 GCTCACTGTTATAGGCTCACTTTTGCTTATCTAAATTTTTATTAGAGTTTTATCTTAGAAATATA
127 ---CAC--TTATAGGCTCACTTTTGCTTATCTAAATTTTTATTAGAGTTTTATCTTAGAAATATA
*
22899 AGAATCTATCACGAAAGAGAGCTGCTGATGTTTATTCTTACTTACTATGCCTTAAGTACGTATAG
187 AGAATCTATCACGAAAGAGAGCTGCAGATGTTTATTCTTACTTACTATGCCTTAAGTACGTATAG
22964 CTTTGAGTATTTAGACTTTGGCATAGTTGCACCTTGAGTATGCTATTGAGTGGTTTCTTCATTGC
252 CTTTGAGTATTTAGACTTTGGCATAGTTGCACCTTGAGTATGCTATTGAGTGGTTTCTTCATTGC
* *
23029 CTAAATGTTCATGTATGATGTAATATTGTTGTAATTGTTGCTGGTTTCCTTGGTAATTGCAATAG
317 CTAAAGGTTCATGTATGATGTAATATTGTTGTAATTGTTGCTGGTATCCTTGGTAATTGCAATAG
23094 GGTTCACA
382 GGTTCACA
23102 TATGATTGTTGAGTTTTAGGAGTAAGTTGACTTTATATATCTGGTTGAAAGTTTCATATTGATGC
1 TATGATTGTTGAGTTTTAGGAGTAAGTTGACTTTATATATCTGGTTGAAAGTTTCATATTGATGC
23167 CAAGAATTAAAAGAATAAAAAAAATGAGAGTGAATATTGGTTACTAACACTGCAG-A-A-A-A-T
66 CAAGAATTAAAAGAATAAAAAAAATGAGAGTGAATATTGGTTACTAACACTGCAGAATATACACT
23227 TATAGGCTCACTTTTGCTTATCTAAATTTTTATTAGAGTTTTATCTTAGAAATATAAGAATCTAT
131 TATAGGCTCACTTTTGCTTATCTAAATTTTTATTAGAGTTTTATCTTAGAAATATAAGAATCTAT
23292 CACGAAAGAGAGCTGCAGATGTTTATTCTTACTTACTATGCCTTAAGTACGTATAGCTTTGAGTA
196 CACGAAAGAGAGCTGCAGATGTTTATTCTTACTTACTATGCCTTAAGTACGTATAGCTTTGAGTA
* *
23357 TTTAGACTTTGGCATAGTTGCACCTTGAGTATGCTATTGAGTGGTTTCTTCATTGCAGT-AGGGT
261 TTTAGACTTTGGCATAGTTGCACCTTGAGTATGCTATTGAGTGGTTTCTTCATTGC-CTAAAGGT
23421 TCATGTATGATGTAATATTGTTGTAATTGTTGCTGGTATCCTTGGTA
325 TCATGTATGATGTAATATTGTTGTAATTGTTGCTGGTATCCTTGGTA
23468 CCAATCTTTA
Statistics
Matches: 359, Mismatches: 6, Indels: 16
0.94 0.02 0.04
Matches are distributed among these distances:
384 235 0.65
385 1 0.00
387 1 0.00
392 1 0.00
393 1 0.00
395 1 0.00
398 119 0.33
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (389 bp):
TATGATTGTTGAGTTTTAGGAGTAAGTTGACTTTATATATCTGGTTGAAAGTTTCATATTGATGC
CAAGAATTAAAAGAATAAAAAAAATGAGAGTGAATATTGGTTACTAACACTGCAGAATATACACT
TATAGGCTCACTTTTGCTTATCTAAATTTTTATTAGAGTTTTATCTTAGAAATATAAGAATCTAT
CACGAAAGAGAGCTGCAGATGTTTATTCTTACTTACTATGCCTTAAGTACGTATAGCTTTGAGTA
TTTAGACTTTGGCATAGTTGCACCTTGAGTATGCTATTGAGTGGTTTCTTCATTGCCTAAAGGTT
CATGTATGATGTAATATTGTTGTAATTGTTGCTGGTATCCTTGGTAATTGCAATAGGGTTCACA
Found at i:34594 original size:3 final size:3
Alignment explanation
Indices: 34586--34618 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
34576 ATTTCAGAAA
*
34586 AAT AAT AAT AAT AAT AAT AAT TAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
34619 TTTGGATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:36330 original size:3 final size:3
Alignment explanation
Indices: 36322--36369 Score: 60
Period size: 3 Copynumber: 14.7 Consensus size: 3
36312 AAACAATGGG
36322 ATT ATT ATT ATT ATT ATT ATT ATT ATAT ATAT ATAT ATAT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T AT-T AT-T AT-T ATT ATT AT
36370 ATACCAGTGG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 29 0.66
4 15 0.34
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:40144 original size:34 final size:36
Alignment explanation
Indices: 40079--40156 Score: 115
Period size: 34 Copynumber: 2.2 Consensus size: 36
40069 CTTATTATAT
40079 ATATGGAACTATAATCTTACTTACTTACTTGATTGAGA
1 ATATGGAACTATAA--TTACTTACTTACTTGATTGAGA
*
40117 ATATGGAACTATAA-T-CTTACTTGCTTGATTGAGA
1 ATATGGAACTATAATTACTTACTTACTTGATTGAGA
40151 ATATGG
1 ATATGG
40157 GAGTAGGGTC
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
34 24 0.62
35 1 0.03
38 14 0.36
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (36 bp):
ATATGGAACTATAATTACTTACTTACTTGATTGAGA
Found at i:45414 original size:2 final size:2
Alignment explanation
Indices: 45407--45447 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
45397 TATGTTTTAT
45407 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
45448 TATATATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:47543 original size:2 final size:2
Alignment explanation
Indices: 47536--47563 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
47526 ACTAGTATTT
47536 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47564 GTCAAAGCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47811 original size:5 final size:5
Alignment explanation
Indices: 47801--47834 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
47791 CTAGCTAAAC
*
47801 TTTCT TTTCT TTTCT TTTCTT TTTTT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTC-T TTTCT TTTCT TTT
47835 TTAAATAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTCT
Done.