Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022747.1 Corchorus olitorius cultivar O-4 contig22780, 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: 87288
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Found at i:31 original size:17 final size:17
Alignment explanation
Indices: 9--41 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1 GTATATGT
*
9 GCATCTATATATATATA
1 GCATCTATACATATATA
26 GCATCTATACATATAT
1 GCATCTATACATATAT
42 TTATATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.39
Consensus pattern (17 bp):
GCATCTATACATATATA
Found at i:54 original size:18 final size:19
Alignment explanation
Indices: 31--73 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
21 ATATAGCATC
*
31 TATACA-TATATTTATATA
1 TATACACTATATATATATA
*
49 TATACACGTATATATGTATA
1 TATACAC-TATATATATATA
69 TATAC
1 TATAC
74 GTACATATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (19 bp):
TATACACTATATATATATA
Found at i:75 original size:18 final size:18
Alignment explanation
Indices: 47--82 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
37 TATATTTATA
*
47 TATATACACGTATATATG
1 TATATACACGTACATATG
*
65 TATATATACGTACATATG
1 TATATACACGTACATATG
83 GAAAATGATC
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:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (18 bp):
TATATACACGTACATATG
Found at i:10580 original size:19 final size:18
Alignment explanation
Indices: 10556--10591 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
10546 TGAAGACTTA
10556 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
10575 TTGAAGACAATTGAAGA
1 TTGAAGACAATTGAAGA
10592 ATTAATTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:18926 original size:30 final size:29
Alignment explanation
Indices: 18883--18939 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
18873 TTAGGATTAG
18883 TTATTTATGCTTTAATTTTCAA-TTTCTT
1 TTATTTATGCTTTAATTTTCAAGTTTCTT
18911 TTATCTTATGTCTTTAATTTTCAAGTTTC
1 TTAT-TTATG-CTTTAATTTTCAAGTTTC
18940 ATTAATAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 4 0.15
29 5 0.19
30 13 0.50
31 4 0.15
ACGTcount: A:0.21, C:0.12, G:0.05, T:0.61
Consensus pattern (29 bp):
TTATTTATGCTTTAATTTTCAAGTTTCTT
Found at i:19966 original size:16 final size:18
Alignment explanation
Indices: 19931--19970 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
19921 TGAGTAATGG
19931 AGAAAGAGAGGAGCTTAT
1 AGAAAGAGAGGAGCTTAT
*
19949 AGAAAGA-AGTAG-TTAT
1 AGAAAGAGAGGAGCTTAT
19965 AGAAAG
1 AGAAAG
19971 TGAAGAATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.48
17 4 0.19
18 7 0.33
ACGTcount: A:0.50, C:0.03, G:0.30, T:0.17
Consensus pattern (18 bp):
AGAAAGAGAGGAGCTTAT
Found at i:21789 original size:22 final size:22
Alignment explanation
Indices: 21747--21789 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
21737 TTTTCTGCTA
**
21747 ATTGTTTTCTTTAATTTTCTTG
1 ATTGTTTTCTTTAATAGTCTTG
21769 ATTGTTTTC-TTAGATAGTCTT
1 ATTGTTTTCTTTA-ATAGTCTT
21790 AATTACTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63
Consensus pattern (22 bp):
ATTGTTTTCTTTAATAGTCTTG
Found at i:28837 original size:39 final size:39
Alignment explanation
Indices: 28794--28991 Score: 145
Period size: 39 Copynumber: 5.1 Consensus size: 39
28784 TCCCGTTTAC
*
28794 AATTTCCATCTAAGTAAACATGCTTAGGTCTCTGCTTAG
1 AATTTCCATCTAAGTAAACCTGCTTAGGTCTCTGCTTAG
* * * *
28833 AATTTTCATTTAAGAAAACCTGTTTAGGATCTCTGCTTAG
1 AATTTCCATCTAAGTAAACCTGCTTAGG-TCTCTGCTTAG
* ** * * *
28873 AGTTTTGATC-AAGTAAGCCTGCTTAGGTCCCT-ATATAG
1 AATTTCCATCTAAGTAAACCTGCTTAGGTCTCTGCT-TAG
* * * *
28911 AGTTGCCATTTAAGTAAACCTGCTTAGGTCTATG-TTCAG
1 AATTTCCATCTAAGTAAACCTGCTTAGGTCTCTGCTT-AG
* * * * *
28950 AA-TTCCGTTTAAGAAAACCTGCTTGGGT-TCTCGTTTAG
1 AATTTCCATCTAAGTAAACCTGCTTAGGTCTCT-GCTTAG
28988 AATT
1 AATT
28992 CTTGTTTAAT
Statistics
Matches: 125, Mismatches: 26, Indels: 16
0.75 0.16 0.10
Matches are distributed among these distances:
37 3 0.02
38 41 0.33
39 63 0.50
40 18 0.14
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (39 bp):
AATTTCCATCTAAGTAAACCTGCTTAGGTCTCTGCTTAG
Found at i:28969 original size:38 final size:38
Alignment explanation
Indices: 28919--29017 Score: 110
Period size: 38 Copynumber: 2.6 Consensus size: 38
28909 AGAGTTGCCA
* *
28919 TTTAAGTAAACCTGCTTAGGTCTATGTTCAGAATTC-CG
1 TTTAAGAAAACCTGCTTAGGTCT-CGTTCAGAATTCTCG
* * *
28957 TTTAAGAAAACCTGCTTGGGTTCTCGTTTAGAATTCTTG
1 TTTAAGAAAACCTGCTTAGG-TCTCGTTCAGAATTCTCG
**
28996 TTTAATCAAACCTGCTTAGGTC
1 TTTAAGAAAACCTGCTTAGGTC
29018 CCCCCCCCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
38 30 0.59
39 21 0.41
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (38 bp):
TTTAAGAAAACCTGCTTAGGTCTCGTTCAGAATTCTCG
Found at i:29975 original size:2 final size:2
Alignment explanation
Indices: 29968--29992 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29958 TCACTTTTAC
29968 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 A
29993 CGTACATATG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41639 original size:20 final size:20
Alignment explanation
Indices: 41594--41639 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
41584 TCTCTTTAAT
41594 TTTTATTGGGTTTAGAAACA
1 TTTTATTGGGTTTAGAAACA
41614 -TTTATT-GGTTTGAGAAACA
1 TTTTATTGGGTTT-AGAAACA
41633 TTTTATT
1 TTTTATT
41640 TTTGCTAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.21
19 13 0.54
20 6 0.25
ACGTcount: A:0.28, C:0.04, G:0.17, T:0.50
Consensus pattern (20 bp):
TTTTATTGGGTTTAGAAACA
Found at i:42459 original size:141 final size:142
Alignment explanation
Indices: 42193--42463 Score: 391
Period size: 141 Copynumber: 1.9 Consensus size: 142
42183 ATTCCTTTCG
* * *
42193 TCACTATTATCAATAATTATAGTGTCAAAAAATGCCGTCACACAAGAGTAAGTATAATGATAACT
1 TCACTATTATCAATAATTATAGTGTCAAAAAATGCCATCACAAAAGAGTAAGTATAATGACAACT
* *
42258 TATATAGTCACTATTAGGGTTTCTTGTGTCGACATAATCACCATTAATAGGTACAGTTATTGTGT
66 TATATAGTCACTATTAGGGTTTCTTGTGTCGACATAATCACCATTAATAGATACAATTATTGTGT
42323 CGATCCCTTGCA
131 CGATCCCTTGCA
* * * *
42335 TCACTATTATCAATAATTATAGTGTC-AAAACTGTCATCACAAAAGATTCAGTATAATGACAACT
1 TCACTATTATCAATAATTATAGTGTCAAAAAATGCCATCACAAAAGAGTAAGTATAATGACAACT
* * * *** *
42399 TATATTGTCACTCTTAGTGTTTCTTGTGTCGACATAATTGTCATTATTAGATACAATTATTGTGT
66 TATATAGTCACTATTAGGGTTTCTTGTGTCGACATAATCACCATTAATAGATACAATTATTGTGT
42464 TGATGATGTC
Statistics
Matches: 113, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
141 87 0.77
142 26 0.23
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.37
Consensus pattern (142 bp):
TCACTATTATCAATAATTATAGTGTCAAAAAATGCCATCACAAAAGAGTAAGTATAATGACAACT
TATATAGTCACTATTAGGGTTTCTTGTGTCGACATAATCACCATTAATAGATACAATTATTGTGT
CGATCCCTTGCA
Found at i:50436 original size:27 final size:27
Alignment explanation
Indices: 50405--50476 Score: 126
Period size: 27 Copynumber: 2.7 Consensus size: 27
50395 ATGTGAACTT
*
50405 AAAATGACCAAAATGCCCCTGAATGTG
1 AAAATGACCAAAATGCCCCTGAATGTA
*
50432 CAAATGACCAAAATGCCCCTGAATGTA
1 AAAATGACCAAAATGCCCCTGAATGTA
50459 AAAATGACCAAAATGCCC
1 AAAATGACCAAAATGCCC
50477 TAGGTGATCC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.43, C:0.25, G:0.15, T:0.17
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATGTA
Found at i:51478 original size:36 final size:36
Alignment explanation
Indices: 51431--51501 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
51421 CTGGATATTA
*
51431 TCATGTAGAATATTTGAATAAATTTGAAGAAATACT
1 TCATGTAGAATATTTGAATAAATTCGAAGAAATACT
* *
51467 TCATGTAGAATATTTGAATAGATTCGAAGAGATAC
1 TCATGTAGAATATTTGAATAAATTCGAAGAAATAC
51502 ATAGAAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.34
Consensus pattern (36 bp):
TCATGTAGAATATTTGAATAAATTCGAAGAAATACT
Found at i:52434 original size:18 final size:18
Alignment explanation
Indices: 52413--52448 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
52403 TTTATACCTT
*
52413 TTATATGTGATATAGATA
1 TTATATATGATATAGATA
*
52431 TTATATATGGTATAGATA
1 TTATATATGATATAGATA
52449 AATAGTGGTA
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:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (18 bp):
TTATATATGATATAGATA
Found at i:52506 original size:35 final size:35
Alignment explanation
Indices: 52432--52506 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 35
52422 ATATAGATAT
* *
52432 TATATATGGTATAGATAAATAGTGGTATACCTTTT
1 TATATATGGTATAAATAAATAGTGGTATACCTTTA
*
52467 TATATATGGTATAAATAGATAGTGGTATA-CTTGTA
1 TATATATGGTATAAATAAATAGTGGTATACCTT-TA
52502 TATAT
1 TATAT
52507 CGTATTATAG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 3 0.08
35 33 0.92
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.43
Consensus pattern (35 bp):
TATATATGGTATAAATAAATAGTGGTATACCTTTA
Found at i:54617 original size:131 final size:133
Alignment explanation
Indices: 54480--54733 Score: 397
Period size: 132 Copynumber: 1.9 Consensus size: 133
54470 CGTTGTTTAA
*
54480 ACTTTTATAATTTTACTCAACTAAAAACTCTA-TTTTTATGTACTTAAATCTAATA-CCTTTATA
1 ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTTATGTAATTAAATCTAATATCC-TTATA
* * * *
54543 ACTATTTTATTTTTACCATTTTACTATTTTAATT-AAAAACTTATATATATTAGAATTTTTTTGA
65 ACTAATTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAAAATTTTTTTGA
54607 TTAT
130 TTAT
* * *
54611 ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTTATATCCTTATAC
1 ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTTATGTAATTAAATCTAATATCCTTATAA
*
54676 CTAATTTATTTTTATCATTTTACTAATTTAATTAAAAAACTTAGATATATTAAAATTT
66 CTAATTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAAAATTT
54734 GGATAAATGA
Statistics
Matches: 111, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
131 32 0.29
132 55 0.50
133 24 0.22
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (133 bp):
ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTTATGTAATTAAATCTAATATCCTTATAA
CTAATTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAAAATTTTTTTGAT
TAT
Found at i:54801 original size:17 final size:17
Alignment explanation
Indices: 54760--54793 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
54750 TCCTAGTTAA
54760 AAAATTATAACAATATG
1 AAAATTATAACAATATG
54777 AAAATTATAACAATATG
1 AAAATTATAACAATATG
54794 GATTTTATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (17 bp):
AAAATTATAACAATATG
Found at i:54971 original size:18 final size:18
Alignment explanation
Indices: 54950--54987 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
54940 GGATTGAGCA
54950 AGTTATCGAGTTTGAATT
1 AGTTATCGAGTTTGAATT
*
54968 AGTTATCGAGTTTGGATT
1 AGTTATCGAGTTTGAATT
54986 AG
1 AG
54988 ATTCTGACGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.42
Consensus pattern (18 bp):
AGTTATCGAGTTTGAATT
Found at i:60390 original size:2 final size:2
Alignment explanation
Indices: 60374--60406 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
60364 GTCACAACTC
60374 AT AT -T AT AT -T 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 A
60407 CATAATTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:68320 original size:2 final size:2
Alignment explanation
Indices: 68313--68339 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
68303 CTACAAACTG
68313 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 A
68340 GACACGCACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:70584 original size:17 final size:17
Alignment explanation
Indices: 70564--70598 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
70554 TGAATCCGCC
* *
70564 TGAACCCTGAACCTGAA
1 TGAACCCAGAACCCGAA
70581 TGAACCCAGAACCCGAA
1 TGAACCCAGAACCCGAA
70598 T
1 T
70599 AAGACCCGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.31, G:0.17, T:0.14
Consensus pattern (17 bp):
TGAACCCAGAACCCGAA
Found at i:84430 original size:17 final size:17
Alignment explanation
Indices: 84391--84433 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
84381 ATTTATTGAG
*
84391 ATAATTATAATTATAAA
1 ATAATTATTATTATAAA
* **
84408 AGAATTATTATTATTCA
1 ATAATTATTATTATAAA
84425 ATAATTATT
1 ATAATTATT
84434 CCTAATTTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
ATAATTATTATTATAAA
Found at i:85874 original size:19 final size:18
Alignment explanation
Indices: 85850--85885 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
85840 TGATGATTTA
85850 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
85869 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
85886 ATTATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Done.