Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018003.1 Corchorus olitorius cultivar O-4 contig18036, 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: 66341
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4926 original size:13 final size:13
Alignment explanation
Indices: 4908--4932 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4898 ATTTTACCAC
4908 CTTAAAATTATTG
1 CTTAAAATTATTG
4921 CTTAAAATTATT
1 CTTAAAATTATT
4933 TTTTGGCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
CTTAAAATTATTG
Found at i:9006 original size:16 final size:15
Alignment explanation
Indices: 8985--9026 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
8975 TTACTTTGTT
8985 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
*
9001 TTGTTTTCTTTTTAA
1 TTGTTTTCTGTTTAA
9016 TTGTTTTCTGT
1 TTGTTTTCTGT
9027 CAACCTCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.12, C:0.07, G:0.12, T:0.69
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:12833 original size:23 final size:23
Alignment explanation
Indices: 12805--12857 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
12795 CCGTGCCTTG
*
12805 GCCTGGCTATTGCGTGGTATAGT
1 GCCTGGCTATTGCGCGGTATAGT
12828 GCCTGGCTATTGCGCGGTATAGT
1 GCCTGGCTATTGCGCGGTATAGT
12851 GCCTGGC
1 GCCTGGC
12858 CTTGGCCTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.11, C:0.23, G:0.36, T:0.30
Consensus pattern (23 bp):
GCCTGGCTATTGCGCGGTATAGT
Found at i:20377 original size:178 final size:178
Alignment explanation
Indices: 20078--20426 Score: 680
Period size: 178 Copynumber: 2.0 Consensus size: 178
20068 ATATTTCCAA
20078 GAGAATAATATTACCACATTCATAATCGACTCCCTAAGATGTTTATTTGACTCTCTTAAAAGCGT
1 GAGAATAATATTACCACATTCATAATCGACTCCCTAAGATGTTTATTTGACTCTCTTAAAAGCGT
*
20143 GTAAGGGAAATGCCCTCTTATAAGAAGTTTCATAATTAATGTTATTAAAAAGTTTGAAAAGATTT
66 GTAAGGGAAATGCCCTCTTATAAGAAGTTTCATAATTAATGTAATTAAAAAGTTTGAAAAGATTT
20208 CTAGAAAATTAAAGTCACTAAAAAACTTTTTAAGTTTATTATAGCGTT
131 CTAGAAAATTAAAGTCACTAAAAAACTTTTTAAGTTTATTATAGCGTT
*
20256 GAGAATAATATTACCACATTCATAATCGACTCTCTAAGATGTTTATTTGACTCTCTTAAAAGCGT
1 GAGAATAATATTACCACATTCATAATCGACTCCCTAAGATGTTTATTTGACTCTCTTAAAAGCGT
20321 GTAAGGGAAATGCCCTCTTATAAGAAGTTTCATAATTAATGTAATTAAAAAGTTTGAAAAGATTT
66 GTAAGGGAAATGCCCTCTTATAAGAAGTTTCATAATTAATGTAATTAAAAAGTTTGAAAAGATTT
20386 CTAGAAAATTAAAGTCACTAAAAAACTTTTTAAGTTTATTA
131 CTAGAAAATTAAAGTCACTAAAAAACTTTTTAAGTTTATTA
20427 CAAAGCTTAC
Statistics
Matches: 169, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
178 169 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (178 bp):
GAGAATAATATTACCACATTCATAATCGACTCCCTAAGATGTTTATTTGACTCTCTTAAAAGCGT
GTAAGGGAAATGCCCTCTTATAAGAAGTTTCATAATTAATGTAATTAAAAAGTTTGAAAAGATTT
CTAGAAAATTAAAGTCACTAAAAAACTTTTTAAGTTTATTATAGCGTT
Found at i:20619 original size:26 final size:25
Alignment explanation
Indices: 20563--20625 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
20553 GTATATTAGT
*
20563 ATACCAAAATTTCTAAGAATACTAGG
1 ATACTAAAA-TTCTAAGAATACTAGG
*
20589 ATACTGAAAATTCTAAGAAT-GTGAGG
1 ATACT-AAAATTCTAAGAATACT-AGG
*
20615 TTACTAAAATT
1 ATACTAAAATT
20626 ATACAATACA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 7 0.22
26 21 0.66
27 4 0.12
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.30
Consensus pattern (25 bp):
ATACTAAAATTCTAAGAATACTAGG
Found at i:21892 original size:19 final size:18
Alignment explanation
Indices: 21868--21903 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21858 TGAAGATTTA
*
21868 TTGAAGACACTTTGAAGAT
1 TTGAAGAC-CATTGAAGAT
21887 TTGAAGACCATTGAAGA
1 TTGAAGACCATTGAAGA
21904 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACCATTGAAGAT
Found at i:30531 original size:30 final size:29
Alignment explanation
Indices: 30488--30544 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
30478 TTAGCATTAG
*
30488 TTATTTATGCTTTAATTTTCAA-TTTCCT
1 TTATTTATGCTTTAATATTCAAGTTTCCT
30516 TTATCTTATGTCTTTAATATTCAAGTTTC
1 TTAT-TTATG-CTTTAATATTCAAGTTTC
30545 ATTAATAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 4 0.16
29 5 0.20
30 12 0.48
31 4 0.16
ACGTcount: A:0.23, C:0.14, G:0.05, T:0.58
Consensus pattern (29 bp):
TTATTTATGCTTTAATATTCAAGTTTCCT
Found at i:32091 original size:19 final size:18
Alignment explanation
Indices: 32067--32102 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
32057 TAAAGATTTA
32067 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
32086 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
32103 ATAATTTCAA
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
Found at i:38339 original size:29 final size:29
Alignment explanation
Indices: 38306--38463 Score: 169
Period size: 28 Copynumber: 5.5 Consensus size: 29
38296 AATAAACTTG
* *
38306 AAATGACTAAAATGCCCCCTGAACATGAA
1 AAATGACCAAAATGCCCCCTGGACATGAA
38335 AAATGACCAAAATG-CCCCTGGACATGAA
1 AAATGACCAAAATGCCCCCTGGACATGAA
*
38363 AAATGACCAAAATACCCCC-GGACATGAA
1 AAATGACCAAAATGCCCCCTGGACATGAA
* * * * *
38391 TAATGATCACAATTCCCCTCTGGACCTAGAA
1 AAATGACCAAAATGCCCC-CTGGACAT-GAA
* * * *
38422 GAATGACCAGAATG-CCCCTGAACATGTA
1 AAATGACCAAAATGCCCCCTGGACATGAA
38450 AAATGACCAAAATG
1 AAATGACCAAAATG
38464 AGAAGCAAAG
Statistics
Matches: 108, Mismatches: 17, Indels: 9
0.81 0.13 0.07
Matches are distributed among these distances:
28 63 0.58
29 24 0.22
30 8 0.07
31 13 0.12
ACGTcount: A:0.42, C:0.25, G:0.16, T:0.17
Consensus pattern (29 bp):
AAATGACCAAAATGCCCCCTGGACATGAA
Found at i:41774 original size:22 final size:21
Alignment explanation
Indices: 41728--41800 Score: 69
Period size: 22 Copynumber: 3.5 Consensus size: 21
41718 TTACACAAGA
41728 TTACT-AAAATTTAATAAAGG
1 TTACTAAAAATTTAATAAAGG
* *
41748 CTACTAAAAATTGTAATAAGGG
1 TTACTAAAAATT-TAATAAAGG
* *
41770 TTACTAAAACGTTTAGT-AAGG
1 TTACTAAAA-ATTTAATAAAGG
*
41791 TTACTTAAAA
1 TTACTAAAAA
41801 GCTTATAAAC
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
20 4 0.10
21 17 0.40
22 19 0.45
23 2 0.05
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (21 bp):
TTACTAAAAATTTAATAAAGG
Found at i:43481 original size:22 final size:22
Alignment explanation
Indices: 43455--43497 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
43445 AATTTGTTCT
*
43455 ATCTTTTCTTTTATTTCGTTTG
1 ATCTTCTCTTTTATTTCGTTTG
* *
43477 ATCTTCTCTTTTCTTTGGTTT
1 ATCTTCTCTTTTATTTCGTTT
43498 TAGGTAGTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.07, C:0.16, G:0.09, T:0.67
Consensus pattern (22 bp):
ATCTTCTCTTTTATTTCGTTTG
Found at i:44657 original size:15 final size:15
Alignment explanation
Indices: 44637--44669 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
44627 AACAGTTTCA
44637 ACAACCTCTGCAGCC
1 ACAACCTCTGCAGCC
44652 ACAACCTCTGCAGCC
1 ACAACCTCTGCAGCC
44667 ACA
1 ACA
44670 TCAAGCACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.30, C:0.45, G:0.12, T:0.12
Consensus pattern (15 bp):
ACAACCTCTGCAGCC
Found at i:49359 original size:32 final size:32
Alignment explanation
Indices: 49310--49371 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
49300 TATTCCCTTT
*
49310 TCCCATTTTGAAACCTAACCCCCCAATTCCTA
1 TCCCATTTTGAAACCTAACCCCCAAATTCCTA
*
49342 TCCC-TTTTCGAACCCTAACCCCCAAATTCC
1 TCCCATTTT-GAAACCTAACCCCCAAATTCC
49372 AAACTCATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 4 0.15
32 23 0.85
ACGTcount: A:0.26, C:0.44, G:0.03, T:0.27
Consensus pattern (32 bp):
TCCCATTTTGAAACCTAACCCCCAAATTCCTA
Found at i:51307 original size:10 final size:11
Alignment explanation
Indices: 51290--51321 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
51280 CTTTAGTTTG
51290 CATTTTCTTTT
1 CATTTTCTTTT
51301 C-TTTTC-TTT
1 CATTTTCTTTT
51310 CATTTTCTTTT
1 CATTTTCTTTT
51321 C
1 C
51322 CTTCCTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.21
10 10 0.53
11 5 0.26
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (11 bp):
CATTTTCTTTT
Found at i:53590 original size:50 final size:48
Alignment explanation
Indices: 53532--53649 Score: 164
Period size: 50 Copynumber: 2.4 Consensus size: 48
53522 TTACATTTCC
** * *
53532 TGCACTTTTTCTCAATTTTTACTACAAAATTGAACTTTTATTTTTTACT
1 TGCACTTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAATTTTCA-T
*
53581 TGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCTTTTAATTTTCAT
1 TGCA-CTTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAATTTTCAT
*
53630 TGCACTTTTTATCAATTTTT
1 TGCACTTTTTCTCAATTTTT
53650 GAATAAAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
48 15 0.24
49 9 0.15
50 38 0.61
ACGTcount: A:0.26, C:0.15, G:0.05, T:0.53
Consensus pattern (48 bp):
TGCACTTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAATTTTCAT
Found at i:54294 original size:24 final size:27
Alignment explanation
Indices: 54236--54299 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
54226 CCTCTCCATC
54236 ATGGTGTGAATAATGCAAATCAAGTGA
1 ATGGTGTGAATAATGCAAATCAAGTGA
*
54263 ATGGTGTGAATAATGC-CATCAA-T-A
1 ATGGTGTGAATAATGCAAATCAAGTGA
*
54287 ATGGTGTGGATAA
1 ATGGTGTGAATAA
54300 CCAAAATCGT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
24 13 0.37
25 1 0.03
26 5 0.14
27 16 0.46
ACGTcount: A:0.38, C:0.08, G:0.27, T:0.28
Consensus pattern (27 bp):
ATGGTGTGAATAATGCAAATCAAGTGA
Found at i:54498 original size:15 final size:15
Alignment explanation
Indices: 54478--54514 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
54468 TGCTAGGGTG
54478 AATGGTGCAAACAAC
1 AATGGTGCAAACAAC
54493 AATGGTGCAAACAAC
1 AATGGTGCAAACAAC
54508 AATGGTG
1 AATGGTG
54515 TGAACGATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.43, C:0.16, G:0.24, T:0.16
Consensus pattern (15 bp):
AATGGTGCAAACAAC
Found at i:60847 original size:21 final size:21
Alignment explanation
Indices: 60800--60848 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
60790 TTGGAATGGC
*
60800 GATGGCACAGGCATAGCCGGG
1 GATGGCACAGGCATAACCGGG
* * * *
60821 GGTGGCACGGGCTTAACCGGT
1 GATGGCACAGGCATAACCGGG
60842 GATGGCA
1 GATGGCA
60849 TGGTGAATGG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.22, G:0.43, T:0.14
Consensus pattern (21 bp):
GATGGCACAGGCATAACCGGG
Found at i:63712 original size:15 final size:16
Alignment explanation
Indices: 63688--63727 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
63678 AGAGGTTGAA
*
63688 AGAAATCAATTAAAC-
1 AGAAAACAATTAAACT
*
63703 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
63719 AGAAAACAA
1 AGAAAACAA
63728 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.07, T:0.17
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Done.