Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013354.1 Corchorus capsularis cultivar CVL-1 contig13375, 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: 50417
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4098 original size:43 final size:43
Alignment explanation
Indices: 4033--4135 Score: 199
Period size: 43 Copynumber: 2.4 Consensus size: 43
4023 AACAGCAAAA
4033 CACTACTCTGCTTTGTCTTTTTTTTC-TTTTTTTTTTGGCATT
1 CACTACTCTGCTTTGTCTTTTTTTTCTTTTTTTTTTTGGCATT
4075 CACTACTCTGCTTTGTCTTTTTTTTCTTTTTTTTTTTGGCATT
1 CACTACTCTGCTTTGTCTTTTTTTTCTTTTTTTTTTTGGCATT
4118 CACTACTCTGCTTTGTCT
1 CACTACTCTGCTTTGTCT
4136 GAATGAACAT
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 26 0.43
43 34 0.57
ACGTcount: A:0.08, C:0.21, G:0.10, T:0.61
Consensus pattern (43 bp):
CACTACTCTGCTTTGTCTTTTTTTTCTTTTTTTTTTTGGCATT
Found at i:12726 original size:13 final size:13
Alignment explanation
Indices: 12708--12740 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
12698 AATTTTCTAT
12708 TTTTTTTTCTTCC
1 TTTTTTTTCTTCC
*
12721 -TTTTTTTCTTTC
1 TTTTTTTTCTTCC
12733 TTTTTTTT
1 TTTTTTTT
12741 ATCGATAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTTCTTCC
Found at i:13513 original size:42 final size:42
Alignment explanation
Indices: 13463--13543 Score: 162
Period size: 42 Copynumber: 1.9 Consensus size: 42
13453 ACATGTGAAA
13463 TTATAATTGTAGCTTTAAAAACTTAATCAGTGATGAAAACAT
1 TTATAATTGTAGCTTTAAAAACTTAATCAGTGATGAAAACAT
13505 TTATAATTGTAGCTTTAAAAACTTAATCAGTGATGAAAA
1 TTATAATTGTAGCTTTAAAAACTTAATCAGTGATGAAAA
13544 AATATATGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (42 bp):
TTATAATTGTAGCTTTAAAAACTTAATCAGTGATGAAAACAT
Found at i:27544 original size:31 final size:31
Alignment explanation
Indices: 27502--27582 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
27492 GCTTAATACC
*
27502 CAAATTAGCCCCTTAACTATCCATTTT-GGGA
1 CAAATTGGCCCCTTAACT-TCCATTTTGGGGA
* ***
27533 CAAATTGGCCCCTTAGCTTTTTTTTTGGGGA
1 CAAATTGGCCCCTTAACTTCCATTTTGGGGA
*
27564 CAAATTGGCCCATTAACTT
1 CAAATTGGCCCCTTAACTT
27583 TTAAAAACGA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 5 0.12
31 37 0.88
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
CAAATTGGCCCCTTAACTTCCATTTTGGGGA
Found at i:27561 original size:30 final size:31
Alignment explanation
Indices: 27525--27584 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
27515 TAACTATCCA
* *
27525 TTTT-GGGACAAATTGGCCCCTTAGCTTTTT
1 TTTTGGGGACAAATTGGCCCATTAACTTTTT
27555 TTTTGGGGACAAATTGGCCCATTAACTTTT
1 TTTTGGGGACAAATTGGCCCATTAACTTTT
27585 AAAAACGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (31 bp):
TTTTGGGGACAAATTGGCCCATTAACTTTTT
Found at i:28331 original size:29 final size:30
Alignment explanation
Indices: 28275--28333 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
28265 TCTCGTTTTT
*
28275 AAAAGTTAATGGGCCAATTTGTCCCCAAAA
1 AAAAGTTAAAGGGCCAATTTGTCCCCAAAA
28305 AAAAGTTAAAGGGCCAATTTGT-CCCAAAA
1 AAAAGTTAAAGGGCCAATTTGTCCCCAAAA
28334 TGGATAGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (30 bp):
AAAAGTTAAAGGGCCAATTTGTCCCCAAAA
Found at i:29945 original size:51 final size:51
Alignment explanation
Indices: 29855--29958 Score: 154
Period size: 51 Copynumber: 2.0 Consensus size: 51
29845 ACAGGTAATC
* *
29855 TCTCTATGATTTCCATGCAAATTTCATCAGGCAAGTGACTATGATGAGTTG
1 TCTCTAAGATTTCCATGCAAATTTCATCAGACAAGTGACTATGATGAGTTG
* * * *
29906 TCTCTAAGATTTCCTTGCAAATTTCCTCCGACAATTGACTATGATGAGTTG
1 TCTCTAAGATTTCCATGCAAATTTCATCAGACAAGTGACTATGATGAGTTG
29957 TC
1 TC
29959 ATATTTTTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (51 bp):
TCTCTAAGATTTCCATGCAAATTTCATCAGACAAGTGACTATGATGAGTTG
Found at i:30109 original size:14 final size:15
Alignment explanation
Indices: 30090--30122 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
30080 TTAAAGATTC
30090 TAAAAATT-AAAAAG
1 TAAAAATTGAAAAAG
*
30104 TAAAAATTGATAAAG
1 TAAAAATTGAAAAAG
30119 TAAA
1 TAAA
30123 GAATCGAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (15 bp):
TAAAAATTGAAAAAG
Found at i:31056 original size:26 final size:26
Alignment explanation
Indices: 31022--31072 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
31012 TTTTTAAAAA
31022 AAAACACCTCAAACTCTTGG-GAAAC
1 AAAACACCTCAAACTCTTGGAGAAAC
31047 AAAACAACCTCAAACTCTTGGAGAAA
1 AAAAC-ACCTCAAACTCTTGGAGAAA
31073 AACACACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 5 0.21
26 15 0.62
27 4 0.17
ACGTcount: A:0.47, C:0.25, G:0.12, T:0.16
Consensus pattern (26 bp):
AAAACACCTCAAACTCTTGGAGAAAC
Found at i:31762 original size:2 final size:2
Alignment explanation
Indices: 31750--31789 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
31740 CGGTAAGATT
*
31750 TA TA GA TA TA TA 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 TA TA TA TA TA TA
31790 AAGACTAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:41731 original size:31 final size:31
Alignment explanation
Indices: 41696--41774 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
41686 AGTTTTTGTT
*
41696 TTTAGACTCAAATTGGTCACCTTTTGAAAGA
1 TTTAGACTCAAATTGGTCAACTTTTGAAAGA
** * * * *
41727 TTTAGGTTCAACTTGGGCAACTTTTGAATGG
1 TTTAGACTCAAATTGGTCAACTTTTGAAAGA
41758 TTTAGACTCAAATTGGT
1 TTTAGACTCAAATTGGT
41775 GGTTAAAAAT
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (31 bp):
TTTAGACTCAAATTGGTCAACTTTTGAAAGA
Found at i:41916 original size:104 final size:104
Alignment explanation
Indices: 41736--41924 Score: 326
Period size: 104 Copynumber: 1.8 Consensus size: 104
41726 ATTTAGGTTC
* *
41736 AACTTGGGCAACTTTTGAATGGTTTAGACTCAAATTGGTGGTTAAAAATTCGAAGTGGATGCGTA
1 AACTTGGGCAACTTTTGAATGGTTTAAACTCAAATTGGTGGCTAAAAATTCGAAGTGGATGCGTA
*
41801 TTTTCTTTCACTAATGCGTGCTAACAGCGCGTAGACTTT
66 TTTTCTTTCACTAACGCGTGCTAACAGCGCGTAGACTTT
*
41840 AACTTGGGCAACTTTTGAATGGTTTAAACTCAAATTGGTGGCTAAAAATTTC-AGGTGGATGCGT
1 AACTTGGGCAACTTTTGAATGGTTTAAACTCAAATTGGTGGCTAAAAA-TTCGAAGTGGATGCGT
41904 ATTTTCTTTCACTAACGCGTG
65 ATTTTCTTTCACTAACGCGTG
41925 TTAATTTCTG
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 77 0.96
105 3 0.04
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (104 bp):
AACTTGGGCAACTTTTGAATGGTTTAAACTCAAATTGGTGGCTAAAAATTCGAAGTGGATGCGTA
TTTTCTTTCACTAACGCGTGCTAACAGCGCGTAGACTTT
Done.