Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010066.1 Corchorus capsularis cultivar CVL-1 contig10087, 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: 23346
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6013 original size:18 final size:18
Alignment explanation
Indices: 5986--6027 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
5976 ATCGAAATTT
*
5986 GTTAACTCTTTTTGTT-CC
1 GTTAATTCTTTTT-TTGCC
6004 GTTAATTCTTTTTTTGCC
1 GTTAATTCTTTTTTTGCC
6022 GTTAAT
1 GTTAAT
6028 ATCGTTAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.14, C:0.17, G:0.12, T:0.57
Consensus pattern (18 bp):
GTTAATTCTTTTTTTGCC
Found at i:10906 original size:12 final size:12
Alignment explanation
Indices: 10889--10932 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
10879 AACATTTTAT
10889 ATGAACATGTTC
1 ATGAACATGTTC
* *
10901 ATGAACAT-CTA
1 ATGAACATGTTC
10912 ATCGAACATGTTC
1 AT-GAACATGTTC
10925 ATGAACAT
1 ATGAACAT
10933 AAACGAACCG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 3 0.12
12 20 0.77
13 3 0.12
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (12 bp):
ATGAACATGTTC
Found at i:11359 original size:4 final size:4
Alignment explanation
Indices: 11350--11384 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
11340 ATTTTGACCT
*
11350 TTTA TTTA TTTA TTTA TTTA TTTA ATTA CTTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TT
11385 AAATTAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.89
5 3 0.11
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:11384 original size:13 final size:12
Alignment explanation
Indices: 11351--11390 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
11341 TTTTGACCTT
*
11351 TTATTTATTTAT
1 TTATTTATTTAA
11363 TTATTTATTTAA
1 TTATTTATTTAA
*
11375 TTACTTTATTAAA
1 TTA-TTTATTTAA
11388 TTA
1 TTA
11391 ATTTTTATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (12 bp):
TTATTTATTTAA
Found at i:13027 original size:61 final size:61
Alignment explanation
Indices: 12951--13073 Score: 219
Period size: 61 Copynumber: 2.0 Consensus size: 61
12941 CATTCGACCC
* *
12951 TGGTGTATAATTCATGCAGCATGCACTCAAAAATACCAAAAATAGAGCATGTAGATAGCAT
1 TGGTGCATAATTCATGAAGCATGCACTCAAAAATACCAAAAATAGAGCATGTAGATAGCAT
*
13012 TGGTGCATAATTCATGAAGCATGCACTCAAAATTACCAAAAATAGAGCATGTAGATAGCAT
1 TGGTGCATAATTCATGAAGCATGCACTCAAAAATACCAAAAATAGAGCATGTAGATAGCAT
13073 T
1 T
13074 TTCAATCACA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (61 bp):
TGGTGCATAATTCATGAAGCATGCACTCAAAAATACCAAAAATAGAGCATGTAGATAGCAT
Found at i:14316 original size:12 final size:12
Alignment explanation
Indices: 14299--14337 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
14289 TAGCAACCAA
*
14299 AAATACAGAAAG
1 AAATACAAAAAG
*
14311 AAATACAAAAAA
1 AAATACAAAAAG
14323 AAATACAAAAAG
1 AAATACAAAAAG
14335 AAA
1 AAA
14338 AAAAGAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.77, C:0.08, G:0.08, T:0.08
Consensus pattern (12 bp):
AAATACAAAAAG
Found at i:14346 original size:24 final size:24
Alignment explanation
Indices: 14297--14347 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
14287 CTTAGCAACC
* *
14297 AAAAATACAGAAAGAAATACAAAA
1 AAAAATACAAAAAGAAATAAAAAA
*
14321 AAAAATACAAAAAGAAA-AAAAGA
1 AAAAATACAAAAAGAAATAAAAAA
14344 AAAA
1 AAAA
14348 GCAAAAACAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.80, C:0.06, G:0.08, T:0.06
Consensus pattern (24 bp):
AAAAATACAAAAAGAAATAAAAAA
Found at i:15774 original size:63 final size:62
Alignment explanation
Indices: 15670--16031 Score: 300
Period size: 63 Copynumber: 5.7 Consensus size: 62
15660 TTTATTGTTT
* * * * * *
15670 TTTCCATTTCCCAAAATCCCCTTTCGGACAAAGGGTTAGTTTTGTCACATTTCTAGCATCTAG
1 TTTCAATTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTTGTCACA-CTCTTGCATTTAG
*
15733 TTTCAATTTCCCAAAATACCCTTTCGGACAAAGGGTTAGTTTTGTCACACTCTTGCATTTAG
1 TTTCAATTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTTGTCACACTCTTGCATTTAG
* * * * ** ** * *
15795 TCTCAATTTCCCAGAATACCCTTTCGGATAAAGGGTCAATTCAGTCACACTCCCGTATTTAA
1 TTTCAATTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTTGTCACACTCTTGCATTTAG
* * * * * * * **
15857 TTTCTGATTTCGCTAAATGCCCTTTCAGACAAAGGGTCAATTTTCTCACAACTC-TGCATACAAG
1 TTTC-AATTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTTGTCAC-ACTCTTGCAT-TTAG
* * * *
15921 TTT-AATCTTGGTTTCCTAGAATACCCTTTCGGACAAAGGGTCAACTTTT-TCACTCTTCTTGCA
1 TTTCAA------TTTCCCAAAATACCCTTTCGGACAAAGGGTC-AGTTTTGTCACAC-TCTTGCA
15984 TTTAG
58 TTTAG
*
15989 ATTT-TATTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTT
1 -TTTCAATTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTT
16032 ATCATGTTTC
Statistics
Matches: 239, Mismatches: 47, Indels: 27
0.76 0.15 0.09
Matches are distributed among these distances:
62 70 0.29
63 113 0.47
64 8 0.03
67 1 0.00
68 33 0.14
69 14 0.06
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (62 bp):
TTTCAATTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTTGTCACACTCTTGCATTTAG
Found at i:15829 original size:62 final size:63
Alignment explanation
Indices: 15675--15830 Score: 242
Period size: 62 Copynumber: 2.5 Consensus size: 63
15665 TGTTTTTTCC
* * *
15675 ATTTCCCAAAATCCCCTTTCGGACAAAGGGTTAGTTTTGTCACATTTCTAGCATCTAGTTTCA
1 ATTTCCCAAAATACCCTTTCGGACAAAGGGTTAGTTTTGTCACATCTCTAGCATCTAGTCTCA
* *
15738 ATTTCCCAAAATACCCTTTCGGACAAAGGGTTAGTTTTGTCACA-CTCTTGCATTTAGTCTCA
1 ATTTCCCAAAATACCCTTTCGGACAAAGGGTTAGTTTTGTCACATCTCTAGCATCTAGTCTCA
* *
15800 ATTTCCCAGAATACCCTTTCGGATAAAGGGT
1 ATTTCCCAAAATACCCTTTCGGACAAAGGGT
15831 CAATTCAGTC
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
62 43 0.50
63 43 0.50
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (63 bp):
ATTTCCCAAAATACCCTTTCGGACAAAGGGTTAGTTTTGTCACATCTCTAGCATCTAGTCTCA
Found at i:20687 original size:28 final size:29
Alignment explanation
Indices: 20652--20706 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
20642 TGCCAAGCTT
*
20652 ATGAGAAA-TTTTAAGAATATAAAAAGCA
1 ATGAGAAAGTTTGAAGAATATAAAAAGCA
* *
20680 ATGAGAAAGTTTGGAGGATATAAAAAG
1 ATGAGAAAGTTTGAAGAATATAAAAAG
20707 ATAAACCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.53, C:0.02, G:0.22, T:0.24
Consensus pattern (29 bp):
ATGAGAAAGTTTGAAGAATATAAAAAGCA
Found at i:22165 original size:23 final size:23
Alignment explanation
Indices: 22139--22185 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
22129 GCTCTTGGTT
22139 ATATCCATCTATGTGATGTAATC
1 ATATCCATCTATGTGATGTAATC
22162 ATATCCATCTATGTGATGTAATC
1 ATATCCATCTATGTGATGTAATC
22185 A
1 A
22186 AAAAGCCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (23 bp):
ATATCCATCTATGTGATGTAATC
Found at i:22380 original size:59 final size:59
Alignment explanation
Indices: 22261--22380 Score: 134
Period size: 59 Copynumber: 2.0 Consensus size: 59
22251 AGATATTTCG
*** **** * **
22261 TAAATTACGGTAATTTTATCTTTTATAATAATATGCTTTTTTTTTTGGTATATTTATAA
1 TAAATTACGGTAATTTTATCTTTTATAATAATATGCTTTTGAATTAAAAAAAAATATAA
22320 TAAATTACGGTAATTTTATCTTTTATAATAATATGCTTATTGAATTAAAAAAAAAT-TAA
1 TAAATTACGGTAATTTTATCTTTTATAATAATATGCTT-TTGAATTAAAAAAAAATATAA
22379 TA
1 TA
22381 TGCTTATTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
59 43 0.86
60 7 0.14
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.49
Consensus pattern (59 bp):
TAAATTACGGTAATTTTATCTTTTATAATAATATGCTTTTGAATTAAAAAAAAATATAA
Done.