Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012609.1 Corchorus olitorius cultivar O-4 contig12642, 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: 63002
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:182 original size:41 final size:42
Alignment explanation
Indices: 137--221 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 42
127 TTATCTAAAT
* *
137 TCTACT-CT-ATCTCTAGGTAATTCATCAAAATAAAGCTGATA
1 TCTACTCCTCATCTCTAGATAATTCATC-AAATAAAGCTAATA
178 TCTACTCCTCCATCTCTAGATAATTCATCAAATAAAGCTAATA
1 TCTACTCCT-CATCTCTAGATAATTCATCAAATAAAGCTAATA
221 T
1 T
222 TAATGTTGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
41 6 0.15
42 2 0.05
43 14 0.36
44 17 0.44
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.34
Consensus pattern (42 bp):
TCTACTCCTCATCTCTAGATAATTCATCAAATAAAGCTAATA
Found at i:2453 original size:9 final size:9
Alignment explanation
Indices: 2439--2473 Score: 70
Period size: 9 Copynumber: 3.9 Consensus size: 9
2429 CGATTCCCGA
2439 TTGAACCGG
1 TTGAACCGG
2448 TTGAACCGG
1 TTGAACCGG
2457 TTGAACCGG
1 TTGAACCGG
2466 TTGAACCG
1 TTGAACCG
2474 ACCGGTCCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (9 bp):
TTGAACCGG
Found at i:3569 original size:111 final size:115
Alignment explanation
Indices: 3355--3573 Score: 365
Period size: 111 Copynumber: 1.9 Consensus size: 115
3345 CTTAGATATA
* * *
3355 AATAAATTGAGACTCTTGAAGGTTTGTCAAAAAAATGTGATAAAAGCAAAAAACTTCAATTTTTA
1 AATAAATTGAGACTCTTGAACGTTTGTCAAAAAAATGTGACAAAAACAAAAAACTTCAATTTTTA
3420 TTGTAACACATTAAATATTACCTCAATCTTATTATACTATTATTATAAAT
66 TTGTAACACATTAAATATTACCTCAATCTTATTATACTATTATTATAAAT
* *
3470 AATAAATTGAGACTCTTGAACGTTTGT-AAAAAAATGTGACAAAAAC-AAAGACTTCATTTTTTA
1 AATAAATTGAGACTCTTGAACGTTTGTCAAAAAAATGTGACAAAAACAAAAAACTTCAATTTTTA
3533 TTGT-A-ACATTAAATATTACCTCAATCTTATTATACTATTAT
66 TTGTAACACATTAAATATTACCTCAATCTTATTATACTATTAT
3574 CATATTTAGT
Statistics
Matches: 99, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
111 36 0.36
112 1 0.01
113 19 0.19
114 17 0.17
115 26 0.26
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (115 bp):
AATAAATTGAGACTCTTGAACGTTTGTCAAAAAAATGTGACAAAAACAAAAAACTTCAATTTTTA
TTGTAACACATTAAATATTACCTCAATCTTATTATACTATTATTATAAAT
Found at i:4649 original size:17 final size:17
Alignment explanation
Indices: 4627--4660 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4617 TAAACTTCAT
*
4627 TATATGAATAATTATTA
1 TATATGAATAAATATTA
4644 TATATGAATAAATATTA
1 TATATGAATAAATATTA
4661 AATAAGATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
TATATGAATAAATATTA
Found at i:4942 original size:25 final size:24
Alignment explanation
Indices: 4914--4971 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
4904 GTGGATTGTA
*
4914 AAATAAATTGAATAATAAAGACATT
1 AAATAAATTGAAGAATAAA-ACATT
* *
4939 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATAAAACATT
*
4963 AAAAAAATT
1 AAATAAATT
4972 CAAGGCCGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 13 0.45
25 16 0.55
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.29
Consensus pattern (24 bp):
AAATAAATTGAAGAATAAAACATT
Found at i:5949 original size:107 final size:108
Alignment explanation
Indices: 5728--5921 Score: 277
Period size: 107 Copynumber: 1.8 Consensus size: 108
5718 TAAAATGGTA
* *
5728 AAAAATTAAAAATAGGTATAAGGATATTAGATTGAATTAAATAAAAAATAGAGTTTTTTATTTGA
1 AAAAATT-AAAATAGGTATAAGGATATTAGATTGAATTAAATAAAAAATACAGTTTTTTAGTTGA
*** *
5793 GTAAAACTATAAAAGTATATTTAAAAATTATAATATATAAAAGT
65 GTAAAACTATAAAAGTATAAACAAAAATTATAAAATATAAAAGT
* *
5837 AAAAATT-AAATAGTTATAAGGATATTAGATTTAATTAAAT-AAAAATACAG-TTTTTAGTTGAG
1 AAAAATTAAAATAGGTATAAGGATATTAGATTGAATTAAATAAAAAATACAGTTTTTTAGTTGAG
*
5899 TAAAACTATAAAAGTTTAAACAA
66 TAAAACTATAAAAGTATAAACAA
5922 TGACATTTAA
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
105 30 0.39
106 9 0.12
107 31 0.40
109 7 0.09
ACGTcount: A:0.53, C:0.02, G:0.11, T:0.35
Consensus pattern (108 bp):
AAAAATTAAAATAGGTATAAGGATATTAGATTGAATTAAATAAAAAATACAGTTTTTTAGTTGAG
TAAAACTATAAAAGTATAAACAAAAATTATAAAATATAAAAGT
Found at i:17568 original size:93 final size:93
Alignment explanation
Indices: 17471--17651 Score: 283
Period size: 93 Copynumber: 1.9 Consensus size: 93
17461 ATAATTAAAT
* *
17471 TAGTAATATCGTAAAAATAAAATA-TGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTT
1 TAGTAAAATCGTAAAAATAAAATAGT-TATAAGGATATTAGATTCAATTAAATAAAAATAGAGTT
*
17535 TTTAGTTGAGTAAAACTATAAAAACAAAA
65 TTTAGTTGACTAAAACTATAAAAACAAAA
* *
17564 TAGTAAAATGGTGAAAATAAAATAGTTATAAGGATATTAGATTCAATTAAATAAAAATAGAGTTT
1 TAGTAAAATCGTAAAAATAAAATAGTTATAAGGATATTAGATTCAATTAAATAAAAATAGAGTTT
* *
17629 TTAGTTGACTAGAATTATAAAAA
66 TTAGTTGACTAAAACTATAAAAA
17652 TTTAAACAAT
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
93 79 0.99
94 1 0.01
ACGTcount: A:0.51, C:0.03, G:0.13, T:0.33
Consensus pattern (93 bp):
TAGTAAAATCGTAAAAATAAAATAGTTATAAGGATATTAGATTCAATTAAATAAAAATAGAGTTT
TTAGTTGACTAAAACTATAAAAACAAAA
Found at i:27516 original size:8 final size:8
Alignment explanation
Indices: 27503--27527 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
27493 CAAATAATGT
27503 TACAATAC
1 TACAATAC
27511 TACAATAC
1 TACAATAC
27519 TACAATAC
1 TACAATAC
27527 T
1 T
27528 TAGTTCTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (8 bp):
TACAATAC
Found at i:37254 original size:24 final size:24
Alignment explanation
Indices: 37201--37255 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
37191 CCAACAACTT
**
37201 CCCCAACAACAACATTACATCCAA
1 CCCCAACAACAACAAAACATCCAA
**
37225 AACCAACAACAACAAAACA-CTCAA
1 CCCCAACAACAACAAAACATC-CAA
37249 CCCCAAC
1 CCCCAAC
37256 CTCAAGTTCA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.51, C:0.42, G:0.00, T:0.07
Consensus pattern (24 bp):
CCCCAACAACAACAAAACATCCAA
Found at i:39349 original size:109 final size:109
Alignment explanation
Indices: 39201--39408 Score: 380
Period size: 109 Copynumber: 1.9 Consensus size: 109
39191 AAGAGGAAAT
*
39201 TTAATAAACTACTCCGCTGTTTTTGGGAAGTGGAGCACACGGGGTTCGGTATCACAAATATCAAC
1 TTAATAAACTACTCCACTGTTTTTGGGAAGTGGAGCACACGGGGTTCGGTATCACAAATATCAAC
*
39266 CTTCGCGTCAGTCACGAACCAAAATTATGAGTATGCAAAACATC
66 CTTCGCATCAGTCACGAACCAAAATTATGAGTATGCAAAACATC
*
39310 TTAATAAATTACTCCACTGTTTTTGGGAAGTGGAGCACACGGGGTTCGGTATCACAAATATCAAC
1 TTAATAAACTACTCCACTGTTTTTGGGAAGTGGAGCACACGGGGTTCGGTATCACAAATATCAAC
*
39375 CTTCGCATCAGTCATGAACCAAAATTATGAGTAT
66 CTTCGCATCAGTCACGAACCAAAATTATGAGTAT
39409 TCAAGGCACC
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
109 95 1.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (109 bp):
TTAATAAACTACTCCACTGTTTTTGGGAAGTGGAGCACACGGGGTTCGGTATCACAAATATCAAC
CTTCGCATCAGTCACGAACCAAAATTATGAGTATGCAAAACATC
Found at i:51084 original size:22 final size:22
Alignment explanation
Indices: 51059--51104 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
51049 GTAAACATTA
* *
51059 AAAGCAATTGCAAGTTGTCTTC
1 AAAGCAATTGCAAGATGTCATC
51081 AAAGCAATTGCAAGATGTCATC
1 AAAGCAATTGCAAGATGTCATC
51103 AA
1 AA
51105 GTCTGTAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.26
Consensus pattern (22 bp):
AAAGCAATTGCAAGATGTCATC
Found at i:51350 original size:19 final size:18
Alignment explanation
Indices: 51306--51376 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 18
51296 GTTCAGGGGT
*
51306 TATTA-TTATTTATTAGTCG
1 TATTATTTA-TTATTAAT-G
*
51325 TAATATTTATTATTAATG
1 TATTATTTATTATTAATG
51343 TTATTA-TTATTTATTAATG
1 -TATTATTTA-TTATTAATG
51362 TATTCATTTATTATT
1 TATT-ATTTATTATT
51377 TCCGCAGGTG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
18 8 0.18
19 30 0.68
20 6 0.14
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.61
Consensus pattern (18 bp):
TATTATTTATTATTAATG
Found at i:51355 original size:38 final size:38
Alignment explanation
Indices: 51304--51376 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
51294 GGGTTCAGGG
*
51304 GTTATTATTATTTATTAGTCGTAAT-ATTTATTATTAAT
1 GTTATTATTATTTATTAAT-GTAATCATTTATTATTAAT
*
51342 GTTATTATTATTTATTAATGTATTCATTTATTATT
1 GTTATTATTATTTATTAATGTAATCATTTATTATT
51377 TCCGCAGGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 4 0.12
38 28 0.88
ACGTcount: A:0.30, C:0.03, G:0.07, T:0.60
Consensus pattern (38 bp):
GTTATTATTATTTATTAATGTAATCATTTATTATTAAT
Found at i:55928 original size:26 final size:26
Alignment explanation
Indices: 55864--55930 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 26
55854 CCTTCCACCC
* *
55864 TAAATAAAAAATAATAATTAATTCTAG
1 TAAAT-AAAAATTATAATTAATTCTAA
55891 TAAATAAAAATTATAATTAATTAC-AA
1 TAAATAAAAATTATAATTAATT-CTAA
55917 T-AATAAATAATTAT
1 TAAATAAA-AATTAT
55931 TGTAAATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
25 6 0.17
26 24 0.67
27 6 0.17
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (26 bp):
TAAATAAAAATTATAATTAATTCTAA
Found at i:55938 original size:20 final size:20
Alignment explanation
Indices: 55872--55961 Score: 71
Period size: 20 Copynumber: 4.5 Consensus size: 20
55862 CCTAAATAAA
* *
55872 AAATAATAATTAATTCTAGT
1 AAATAATAAATAATTATAGT
* *
55892 AAATAAAAATTATAATTA-ATT
1 AAATAATAA--ATAATTATAGT
*
55913 ACAATAATAAATAATTATTGT
1 A-AATAATAAATAATTATAGT
55934 AAATAAT---TAATTATAGT
1 AAATAATAAATAATTATAGT
55951 CAAATAATAAA
1 -AAATAATAAA
55962 ATAACTAAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 15
0.70 0.10 0.19
Matches are distributed among these distances:
17 9 0.17
18 7 0.13
20 21 0.39
21 5 0.09
22 12 0.22
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (20 bp):
AAATAATAAATAATTATAGT
Found at i:55944 original size:17 final size:18
Alignment explanation
Indices: 55918--55958 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
55908 TAATTACAAT
* *
55918 AATAAATAATTATTGT-A
1 AATAATTAATTATAGTCA
55935 AATAATTAATTATAGTCA
1 AATAATTAATTATAGTCA
55953 AATAAT
1 AATAAT
55959 AAAATAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (18 bp):
AATAATTAATTATAGTCA
Found at i:60477 original size:19 final size:20
Alignment explanation
Indices: 60453--60490 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
60443 CGGAGGAAGA
60453 AAAAGAAGAA-AAAAAAAAG
1 AAAAGAAGAAGAAAAAAAAG
60472 AAAAGAAGAAGAAAAAAAA
1 AAAAGAAGAAGAAAAAAAA
60491 AACGGGGGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAAGAAGAAGAAAAAAAAG
Found at i:60818 original size:27 final size:26
Alignment explanation
Indices: 60764--60824 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
60754 GACCATTTTG
* *
60764 CCCTTAGATGTTAAATCACTAAATTA
1 CCCTTAGATGTTAAATCACGAAACTA
* *
60790 CCCTTAAGTTGTTAAATTACGAAACTA
1 CCCTT-AGATGTTAAATCACGAAACTA
*
60817 CCCATAGA
1 CCCTTAGA
60825 AGAGAAATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (26 bp):
CCCTTAGATGTTAAATCACGAAACTA
Done.