Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011855.1 Corchorus capsularis cultivar CVL-1 contig11876, 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: 59945
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:9549 original size:21 final size:23
Alignment explanation
Indices: 9525--9568 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
9515 ACATATCAAT
9525 CTCA-CCAAGATC-AAC-CAACCA
1 CTCAGCCAA-ATCTAACACAACCA
9546 CTCAGCCAAATCTAACACAACCA
1 CTCAGCCAAATCTAACACAACCA
9569 TGCCACCAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 7 0.35
22 7 0.35
23 6 0.30
ACGTcount: A:0.43, C:0.41, G:0.05, T:0.11
Consensus pattern (23 bp):
CTCAGCCAAATCTAACACAACCA
Found at i:16059 original size:19 final size:20
Alignment explanation
Indices: 16021--16063 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
16011 AGTTGATTAC
16021 TTTATTTAGTTTGCTTTTAA
1 TTTATTTAGTTTGCTTTTAA
* *
16041 TTTATTTTG-TTGGTTTTAA
1 TTTATTTAGTTTGCTTTTAA
16060 TTTA
1 TTTA
16064 GAATGACCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.19, C:0.02, G:0.12, T:0.67
Consensus pattern (20 bp):
TTTATTTAGTTTGCTTTTAA
Found at i:21427 original size:27 final size:26
Alignment explanation
Indices: 21395--21472 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 26
21385 AAGTAGACTT
21395 AAAATGACCAAAATGCCCCTGAATGTG-C
1 AAAATGACCAAAATGCCCCTG---GTGCC
*
21423 -AAATGACCAGAATGCCCCTGGTGCC
1 AAAATGACCAAAATGCCCCTGGTGCC
21448 AAAATGACCAAAATGCCCCTAGGTG
1 AAAATGACCAAAATGCCCCT-GGTG
21473 ACCCTAATGC
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
24 3 0.07
25 1 0.02
26 18 0.40
27 23 0.51
ACGTcount: A:0.36, C:0.27, G:0.21, T:0.17
Consensus pattern (26 bp):
AAAATGACCAAAATGCCCCTGGTGCC
Found at i:25845 original size:12 final size:13
Alignment explanation
Indices: 25820--25853 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
25810 ATAATTATTG
25820 TTTGCTTTATTAA
1 TTTGCTTTATTAA
25833 TTTGCTTTA-TAA
1 TTTGCTTTATTAA
*
25845 TCTGCTTTA
1 TTTGCTTTA
25854 GATTTAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:25879 original size:28 final size:24
Alignment explanation
Indices: 25847--25905 Score: 64
Period size: 28 Copynumber: 2.3 Consensus size: 24
25837 CTTTATAATC
25847 TGCTTTAGATTTAGATTTAGATTTGTTT
1 TGCTTTAGATTTAG-TTTA-A-TTG-TT
**
25875 TGCTTTATTTTTAGTTTAATTGTT
1 TGCTTTAGATTTAGTTTAATTGTT
25899 TGCTTTA
1 TGCTTTA
25906 TAATTGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 9 0.31
25 3 0.10
26 1 0.03
27 4 0.14
28 12 0.41
ACGTcount: A:0.19, C:0.05, G:0.15, T:0.61
Consensus pattern (24 bp):
TGCTTTAGATTTAGTTTAATTGTT
Found at i:26231 original size:39 final size:40
Alignment explanation
Indices: 26158--26239 Score: 130
Period size: 40 Copynumber: 2.1 Consensus size: 40
26148 TAGTTTTTGA
* *
26158 TTTTCCGTTTTTTCTAAAAAAAAAAAAAAGTTTTTCCGTT
1 TTTTCCGATTTTTCTAAAAAAAAAAAAAAGTTTTTCCGAT
*
26198 TTTTCCGATTTTTCTAAAAAAAAAAAATA-TTTTTCCGAT
1 TTTTCCGATTTTTCTAAAAAAAAAAAAAAGTTTTTCCGAT
26237 TTT
1 TTT
26240 AATTTATGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 12 0.31
40 27 0.69
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.46
Consensus pattern (40 bp):
TTTTCCGATTTTTCTAAAAAAAAAAAAAAGTTTTTCCGAT
Found at i:32873 original size:12 final size:13
Alignment explanation
Indices: 32848--32881 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
32838 ATAATTATTG
32848 TTTGCTTTATTAA
1 TTTGCTTTATTAA
32861 TTTGCTTTA-TAA
1 TTTGCTTTATTAA
*
32873 TCTGCTTTA
1 TTTGCTTTA
32882 GATTTAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:32907 original size:28 final size:24
Alignment explanation
Indices: 32875--32933 Score: 64
Period size: 28 Copynumber: 2.3 Consensus size: 24
32865 CTTTATAATC
32875 TGCTTTAGATTTAGATTTAGATTTGCTT
1 TGCTTTAGATTTAG-TTTA-A-TTG-TT
**
32903 TGCTTTATTTTTAGTTTAATTGTT
1 TGCTTTAGATTTAGTTTAATTGTT
32927 TGCTTTA
1 TGCTTTA
32934 TAATTGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 9 0.31
25 3 0.10
26 1 0.03
27 4 0.14
28 12 0.41
ACGTcount: A:0.19, C:0.07, G:0.15, T:0.59
Consensus pattern (24 bp):
TGCTTTAGATTTAGTTTAATTGTT
Found at i:37883 original size:67 final size:64
Alignment explanation
Indices: 37767--37895 Score: 206
Period size: 67 Copynumber: 2.0 Consensus size: 64
37757 CTTTTTTACA
*
37767 TTTTTTTCTTTTTTTTCCTTTTTTCCCTTTTTTCCTCCCTCCCTGACTTCTTTCTTCACGACTT
1 TTTTTTTCTTTTTTTTCCTTTTTTCCCTTTCTTCCTCCCTCCCTGACTTCTTTCTTCACGACTT
37831 TTTTTTTACTTTTTTTT-CTTTTTTCTCTTCTTTCTTCCTCCCTCCCTGACTTCTTTCTTCACGA
1 TTTTTTT-CTTTTTTTTCCTTTTTTC-C--CTTTCTTCCTCCCTCCCTGACTTCTTTCTTCACGA
37895 C
62 C
37896 CAGGACCCAA
Statistics
Matches: 60, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
64 15 0.25
65 10 0.17
67 35 0.58
ACGTcount: A:0.05, C:0.31, G:0.03, T:0.60
Consensus pattern (64 bp):
TTTTTTTCTTTTTTTTCCTTTTTTCCCTTTCTTCCTCCCTCCCTGACTTCTTTCTTCACGACTT
Found at i:39086 original size:13 final size:13
Alignment explanation
Indices: 39044--39089 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
39034 ACTTTTTATA
39044 TTTATTTTTCTTT
1 TTTATTTTTCTTT
*
39057 TTTCTTTTCTCTTT
1 TTTATTTT-TCTTT
39071 TTTATTTTT-TTAT
1 TTTATTTTTCTT-T
39084 TTTATT
1 TTTATT
39090 GAAAAGTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 2 0.07
13 15 0.52
14 12 0.41
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTATTTTTCTTT
Found at i:45691 original size:17 final size:17
Alignment explanation
Indices: 45669--45702 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
45659 GTTTGGTTGA
*
45669 AGGGGTTGCAAGGGGTG
1 AGGGGTAGCAAGGGGTG
*
45686 AGGGGTAGGAAGGGGTG
1 AGGGGTAGCAAGGGGTG
45703 GTCATCATCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.03, G:0.62, T:0.15
Consensus pattern (17 bp):
AGGGGTAGCAAGGGGTG
Found at i:45983 original size:16 final size:16
Alignment explanation
Indices: 45944--45976 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
45934 AAAGTACATA
*
45944 TAATAA-TTATTTTTT
1 TAATAATTTATATTTT
45959 TAATAATTTATATTTT
1 TAATAATTTATATTTT
45975 TA
1 TA
45977 TTTATTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TAATAATTTATATTTT
Found at i:46341 original size:15 final size:15
Alignment explanation
Indices: 46320--46358 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
46310 CCAACTCCTC
*
46320 CCCCTCCCTACCCCA
1 CCCCTCCCCACCCCA
* *
46335 CCTCTCCCCACCCTA
1 CCCCTCCCCACCCCA
46350 CCCCTCCCC
1 CCCCTCCCC
46359 CATTTGAACC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.10, C:0.74, G:0.00, T:0.15
Consensus pattern (15 bp):
CCCCTCCCCACCCCA
Found at i:46343 original size:20 final size:19
Alignment explanation
Indices: 46316--46353 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
46306 CCTCCCAACT
*
46316 CCTCCCCCTCCCTACCCCA
1 CCTCCCCCACCCTACCCCA
46335 CCTCTCCCCACCCTACCCC
1 CCTC-CCCCACCCTACCCC
46354 TCCCCCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.11, C:0.74, G:0.00, T:0.16
Consensus pattern (19 bp):
CCTCCCCCACCCTACCCCA
Found at i:47827 original size:2 final size:2
Alignment explanation
Indices: 47820--47844 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47810 TACTTTTGTT
47820 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
47845 TAACTTTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48455 original size:12 final size:11
Alignment explanation
Indices: 48414--48455 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
48404 TTTCCCAGAA
*
48414 TTTAATTTGCT
1 TTTAATTTACT
*
48425 TTTCATTTACT
1 TTTAATTTACT
48436 TTTAATTTACT
1 TTTAATTTACT
48447 TTCTAATTT
1 TT-TAATTT
48456 GTTTTTTAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 21 0.78
12 6 0.22
ACGTcount: A:0.21, C:0.12, G:0.02, T:0.64
Consensus pattern (11 bp):
TTTAATTTACT
Done.