Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024262.1 Corchorus olitorius cultivar O-4 contig24295, 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: 39906
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:402 original size:15 final size:15
Alignment explanation
Indices: 372--413 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
362 TTATTTTGTT
372 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
*
388 TTGTTCTCTGTTTAA
1 TTGTTTTCTGTTTAA
403 TTGTTTTCTGT
1 TTGTTTTCTGT
414 CAACCTCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:4269 original size:38 final size:38
Alignment explanation
Indices: 4172--4502 Score: 280
Period size: 39 Copynumber: 8.6 Consensus size: 38
4162 GCTTAGGGTT
* * * * **
4172 TTCATCTAAATGAACCTACTTAGGTC-CTCGTTTAGAAT
1 TTCATTTAAGTGAACCTGCTTAGGTCTCT-GCTTAGAGC
* *
4210 TTCCATTTAAGTAAATCTGCTTAGGTCTCTGCTTAGAGC
1 TT-CATTTAAGTGAACCTGCTTAGGTCTCTGCTTAGAGC
* * *
4249 TTCATTTAAGTGAACTTGCTTAGGTC-CTTGTTTAGAAC
1 TTCATTTAAGTGAACCTGCTTAGGTCTC-TGCTTAGAGC
* * *
4287 TTTCGTTTAAGTGAACCTGCTTAGGTC-CTTGTTTAGAAC
1 -TTCATTTAAGTGAACCTGCTTAGGTCTC-TGCTTAGAGC
* *
4326 TTCCGTTTAAGTGAACCTGCTTAGGTCTCTGCTTAGAGT
1 TT-CATTTAAGTGAACCTGCTTAGGTCTCTGCTTAGAGC
* * * *
4365 TTCGTTTAA-TCAAACATGCTTAGGTCTCTGCTTAGAGT
1 TTCATTTAAGT-GAACCTGCTTAGGTCTCTGCTTAGAGC
* * * *
4403 TTCATTTAA-TCAAACCTACTTAGGTC-CTTGTTTAGAAC
1 TTCATTTAAGT-GAACCTGCTTAGGTCTC-TGCTTAGAGC
*
4441 TTCCATTTAAGTGAACCTGCTTAGGTCTCTACTTAGAGC
1 TT-CATTTAAGTGAACCTGCTTAGGTCTCTGCTTAGAGC
*
4480 TTCATTTAA-TCAAACCTGCTTAG
1 TTCATTTAAGT-GAACCTGCTTAG
4503 AGCTTCGTTT
Statistics
Matches: 249, Mismatches: 32, Indels: 24
0.82 0.10 0.08
Matches are distributed among these distances:
37 4 0.02
38 115 0.46
39 125 0.50
40 5 0.02
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (38 bp):
TTCATTTAAGTGAACCTGCTTAGGTCTCTGCTTAGAGC
Found at i:4489 original size:77 final size:77
Alignment explanation
Indices: 4184--4502 Score: 344
Period size: 77 Copynumber: 4.1 Consensus size: 77
4174 CATCTAAATG
* * * *
4184 AACCTACTTAGGTCCTCGTTTAGAATTTCCATTTAAGTAAATCTGCTTAGGTCTCTGCTTAGAGC
1 AACCTGCTTAGGTCCTTGTTTAGAACTTCCATTTAAGTAAACCTGCTTAGGTCTCTGCTTAGAGC
*
4249 TTCATTTAAGTG
66 TTCATTTAAGTA
* * * * * *
4261 AACTTGCTTAGGTCCTTGTTTAGAACTTTCGTTTAAGTGAACCTGCTTAGGTC-CTTGTTTAGAA
1 AACCTGCTTAGGTCCTTGTTTAGAACTTCCATTTAAGTAAACCTGCTTAGGTCTC-TGCTTAGAG
* *
4325 CTTCCGTTTAAGTG
65 CTT-CATTTAAGTA
* * * * *
4339 AACCTGCTTAGGT-CTCTGCTTAG-AGTTTCGTTTAA-TCAAACATGCTTAGGTCTCTGCTTAGA
1 AACCTGCTTAGGTCCT-TGTTTAGAACTTCCATTTAAGT-AAACCTGCTTAGGTCTCTGCTTAGA
*
4401 GTTTCATTTAA-TCA
64 GCTTCATTTAAGT-A
* * *
4415 AACCTACTTAGGTCCTTGTTTAGAACTTCCATTTAAGTGAACCTGCTTAGGTCTCTACTTAGAGC
1 AACCTGCTTAGGTCCTTGTTTAGAACTTCCATTTAAGTAAACCTGCTTAGGTCTCTGCTTAGAGC
4480 TTCATTTAA-TCA
66 TTCATTTAAGT-A
4492 AACCTGCTTAG
1 AACCTGCTTAG
4503 AGCTTCGTTT
Statistics
Matches: 202, Mismatches: 31, Indels: 18
0.80 0.12 0.07
Matches are distributed among these distances:
75 1 0.00
76 26 0.13
77 146 0.72
78 29 0.14
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (77 bp):
AACCTGCTTAGGTCCTTGTTTAGAACTTCCATTTAAGTAAACCTGCTTAGGTCTCTGCTTAGAGC
TTCATTTAAGTA
Found at i:4508 original size:26 final size:26
Alignment explanation
Indices: 4472--4528 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
4462 TAGGTCTCTA
4472 CTTAGAGCTTCATTTAATCAAACCTG
1 CTTAGAGCTTCATTTAATCAAACCTG
*
4498 CTTAGAGCTTCGTTTAATCAAACCTG
1 CTTAGAGCTTCATTTAATCAAACCTG
4524 CTTAG
1 CTTAG
4529 GACCTTCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (26 bp):
CTTAGAGCTTCATTTAATCAAACCTG
Found at i:4539 original size:26 final size:26
Alignment explanation
Indices: 4472--4539 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
4462 TAGGTCTCTA
*
4472 CTTAGAGCTTCATTTAATCAAACCTG
1 CTTAGACCTTCATTTAATCAAACCTG
* *
4498 CTTAGAGCTTCGTTTAATCAAACCTG
1 CTTAGACCTTCATTTAATCAAACCTG
4524 CTTAGGACCTTC-TTTA
1 CTTA-GACCTTCATTTA
4540 GAGTCTATCT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
26 33 0.85
27 6 0.15
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (26 bp):
CTTAGACCTTCATTTAATCAAACCTG
Found at i:9033 original size:140 final size:140
Alignment explanation
Indices: 8857--9136 Score: 535
Period size: 140 Copynumber: 2.0 Consensus size: 140
8847 TAAACTGGGA
8857 TAAGAGATTGATCGAAGGGTCCGGTCATTTCTTTTACAACCCAACAATTTTTCTAAAAAACTCAA
1 TAAGAGATTGATCGAAGGGTCCGGTCATTTCTTTTACAACCCAACAATTTTTCTAAAAAACTCAA
8922 AACTCATTTGTGCTTGTGTAACTTTGTTTTCAAAATCAAATAAAGGATTTACTTTCA-TTAAATT
66 AACTCATTTGTGCTTGTGTAACTTTGTTTTCAAAATCAAATAAAGGATTTACTTT-ATTTAAATT
8986 ATTTAAAATTT
130 ATTTAAAATTT
*
8997 TAAGAGATTGATCGAAGGGTTCGGTCATTTCTTTTACAACCCAACAATTTTTCTAAAAAACTCAA
1 TAAGAGATTGATCGAAGGGTCCGGTCATTTCTTTTACAACCCAACAATTTTTCTAAAAAACTCAA
9062 AACTCATTTGTGCTTGTGTAACTTTGTTTTCAAAATCAAATAAAGGATTTACTTTATTTAAATTA
66 AACTCATTTGTGCTTGTGTAACTTTGTTTTCAAAATCAAATAAAGGATTTACTTTATTTAAATTA
9127 TTTAAAATTT
131 TTTAAAATTT
9137 AGAAATAATC
Statistics
Matches: 138, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
139 1 0.01
140 137 0.99
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.39
Consensus pattern (140 bp):
TAAGAGATTGATCGAAGGGTCCGGTCATTTCTTTTACAACCCAACAATTTTTCTAAAAAACTCAA
AACTCATTTGTGCTTGTGTAACTTTGTTTTCAAAATCAAATAAAGGATTTACTTTATTTAAATTA
TTTAAAATTT
Found at i:14747 original size:9 final size:9
Alignment explanation
Indices: 14735--14759 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
14725 GTAAAACACC
14735 AAACAAACA
1 AAACAAACA
14744 AAACAAACA
1 AAACAAACA
14753 AAACAAA
1 AAACAAA
14760 GCAACCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (9 bp):
AAACAAACA
Found at i:17471 original size:18 final size:19
Alignment explanation
Indices: 17457--17525 Score: 70
Period size: 23 Copynumber: 3.4 Consensus size: 19
17447 CAATTATTTT
17457 TTAATT-TTTAATTA-TAA
1 TTAATTATTTAATTATTAA
17474 TTAATTATTTAATTATTAA
1 TTAATTATTTAATTATTAA
17493 TTATTATTAATTTAAATTATTATTA
1 TTA--ATT-ATTT-AATTATTA--A
17518 TTAATTAT
1 TTAATTAT
17526 AATTTATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.14
18 8 0.18
19 6 0.14
21 3 0.07
22 6 0.14
23 11 0.25
25 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTAATTATTTAATTATTAA
Found at i:17479 original size:10 final size:10
Alignment explanation
Indices: 17464--17529 Score: 56
Period size: 10 Copynumber: 7.2 Consensus size: 10
17454 TTTTTAATTT
17464 TTAATTATAA
1 TTAATTATAA
17474 TTAATTAT--
1 TTAATTATAA
17482 TTAA-T-T-A
1 TTAATTATAA
*
17489 TTAATTATTA
1 TTAATTATAA
17499 TTAATT-TAAA
1 TTAATTAT-AA
*
17509 TT-ATTATTA
1 TTAATTATAA
17518 TTAATTATAA
1 TTAATTATAA
17528 TT
1 TT
17530 TATAATTAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
6 1 0.02
7 5 0.11
8 5 0.11
9 8 0.17
10 27 0.59
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TTAATTATAA
Found at i:17492 original size:25 final size:25
Alignment explanation
Indices: 17448--17529 Score: 85
Period size: 25 Copynumber: 3.2 Consensus size: 25
17438 TGCCGCCACC
* *
17448 AATT-ATTTTTTAATTTTTAATTAT
1 AATTAATTATTTAATTATTAATTAT
17472 AATTAATTATTTAATTATTAATTAT
1 AATTAATTATTTAATTATTAATTAT
* *
17497 TATTAATTTAAATTATTATTATTAATTAT
1 AATTAA-TT--ATT-TAATTATTAATTAT
17526 AATT
1 AATT
17530 TATAATTAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
24 4 0.08
25 23 0.48
26 2 0.04
28 3 0.06
29 16 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
AATTAATTATTTAATTATTAATTAT
Found at i:17495 original size:7 final size:7
Alignment explanation
Indices: 17473--17544 Score: 62
Period size: 7 Copynumber: 10.1 Consensus size: 7
17463 TTTAATTATA
17473 ATTAATT
1 ATTAATT
17480 ATTTAATT
1 A-TTAATT
17488 ATTAATT
1 ATTAATT
17495 ATT-ATT
1 ATTAATT
17501 AATTTAAATT
1 -A-TT-AATT
17511 ATT-ATT
1 ATTAATT
17517 ATTAATT
1 ATTAATT
17524 A-TAATT
1 ATTAATT
17530 -TATAATT
1 AT-TAATT
*
17537 AATAATT
1 ATTAATT
17544 A
1 A
17545 AAAAAATAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 18
0.74 0.01 0.24
Matches are distributed among these distances:
6 14 0.25
7 26 0.47
8 11 0.20
9 1 0.02
10 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATTAATT
Found at i:17545 original size:7 final size:7
Alignment explanation
Indices: 17465--17545 Score: 53
Period size: 7 Copynumber: 12.0 Consensus size: 7
17455 TTTTAATTTT
17465 TAATT-A
1 TAATTAA
17471 TAATTAA
1 TAATTAA
*
17478 TTATTTAA
1 -TAATTAA
*
17486 TTATTAA
1 TAATTAA
* *
17493 TTATTAT
1 TAATTAA
*
17500 TAATTTA
1 TAATTAA
17507 -AATT-A
1 TAATTAA
* *
17512 TTATTAT
1 TAATTAA
17519 TAATT-A
1 TAATTAA
*
17525 TAATTTA
1 TAATTAA
17532 TAATTAA
1 TAATTAA
17539 TAATTAA
1 TAATTAA
17546 AAAAATAAAA
Statistics
Matches: 58, Mismatches: 12, Indels: 9
0.73 0.15 0.11
Matches are distributed among these distances:
5 1 0.02
6 17 0.29
7 34 0.59
8 6 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
TAATTAA
Found at i:20219 original size:21 final size:21
Alignment explanation
Indices: 20193--20233 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20183 GGCTATTTAG
20193 CCTATGAAATTTTG-TAACCTT
1 CCTATG-AATTTTGATAACCTT
*
20214 CCTATGATTTTTGATAACCT
1 CCTATGAATTTTGATAACCT
20234 CACTGTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.44
Consensus pattern (21 bp):
CCTATGAATTTTGATAACCTT
Found at i:23053 original size:21 final size:22
Alignment explanation
Indices: 23029--23070 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
23019 AAGTTTTCGG
23029 TTTTGCG-ATAAAAAAAAAAGT
1 TTTTGCGCATAAAAAAAAAAGT
23050 TTTTGCGTCATAAAAAAAAAA
1 TTTTGCG-CATAAAAAAAAAA
23071 TTTCTCTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
23 12 0.63
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.29
Consensus pattern (22 bp):
TTTTGCGCATAAAAAAAAAAGT
Found at i:29594 original size:15 final size:15
Alignment explanation
Indices: 29576--29604 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29566 GTTTCTAATA
29576 TAATTGTTTTCTTTT
1 TAATTGTTTTCTTTT
29591 TAATTGTTTTCTTT
1 TAATTGTTTTCTTT
29605 CAACCTCTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (15 bp):
TAATTGTTTTCTTTT
Found at i:31064 original size:16 final size:18
Alignment explanation
Indices: 31037--31075 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
31027 ATAATAATAT
31037 AATAATATATATAGTAGA
1 AATAATATATATAGTAGA
31055 AATAATATATATAGTAGA
1 AATAATATATATAGTAGA
31073 AAT
1 AAT
31076 TGGGTTGGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.33
Consensus pattern (18 bp):
AATAATATATATAGTAGA
Found at i:39217 original size:20 final size:20
Alignment explanation
Indices: 39192--39244 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
39182 CTGTAAAATT
39192 AACAAAAACAGAAAAAC-AAA
1 AACAAAAACA-AAAAACGAAA
*
39212 AACAAAAACAAAATACGAAA
1 AACAAAAACAAAAAACGAAA
*
39232 AATAAAAACAAAA
1 AACAAAAACAAAA
39245 CTAAAGGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 5 0.17
20 25 0.83
ACGTcount: A:0.79, C:0.13, G:0.04, T:0.04
Consensus pattern (20 bp):
AACAAAAACAAAAAACGAAA
Found at i:39218 original size:5 final size:6
Alignment explanation
Indices: 39192--39244 Score: 61
Period size: 6 Copynumber: 8.2 Consensus size: 6
39182 CTGTAAAATT
*
39192 AACAAA AACAGAAA AACAAA AACAAA AACAAA ATACGAAA AATAAA AACAAA
1 AACAAA AAC--AAA AACAAA AACAAA AACAAA A-AC-AAA AACAAA AACAAA
39244 A
1 A
39245 CTAAAGGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 28 0.68
7 3 0.07
8 10 0.24
ACGTcount: A:0.79, C:0.13, G:0.04, T:0.04
Consensus pattern (6 bp):
AACAAA
Found at i:39221 original size:26 final size:26
Alignment explanation
Indices: 39192--39244 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
39182 CTGTAAAATT
39192 AACAAAA-ACAGAAAAACAAAAACAAA
1 AACAAAATAC-GAAAAACAAAAACAAA
*
39218 AACAAAATACGAAAAATAAAAACAAA
1 AACAAAATACGAAAAACAAAAACAAA
39244 A
1 A
39245 CTAAAGGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.79, C:0.13, G:0.04, T:0.04
Consensus pattern (26 bp):
AACAAAATACGAAAAACAAAAACAAA
Found at i:39249 original size:12 final size:12
Alignment explanation
Indices: 39192--39244 Score: 61
Period size: 14 Copynumber: 4.1 Consensus size: 12
39182 CTGTAAAATT
39192 AACAAAAACAGAAA
1 AACAAAAAC--AAA
39206 AACAAAAACAAA
1 AACAAAAACAAA
39218 AACAAAATACGAAA
1 AACAAAA-AC-AAA
*
39232 AATAAAAACAAA
1 AACAAAAACAAA
39244 A
1 A
39245 CTAAAGGAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
12 14 0.39
13 4 0.11
14 18 0.50
ACGTcount: A:0.79, C:0.13, G:0.04, T:0.04
Consensus pattern (12 bp):
AACAAAAACAAA
Done.