Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015148.1 Corchorus capsularis cultivar CVL-1 contig15169, 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: 65815
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Found at i:5395 original size:15 final size:15
Alignment explanation
Indices: 5375--5412 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
5365 TCGTGGCTCC
5375 TCTTCCGGGGCTGGG
1 TCTTCCGGGGCTGGG
*
5390 TCTTCCGGGGTTGGG
1 TCTTCCGGGGCTGGG
5405 TCTTCCGG
1 TCTTCCGG
5413 TGGTGATGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.00, C:0.26, G:0.42, T:0.32
Consensus pattern (15 bp):
TCTTCCGGGGCTGGG
Found at i:6103 original size:27 final size:27
Alignment explanation
Indices: 6065--6118 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
6055 CTTAGAGTCG
*
6065 GGTGCAGGTGAAAATGAAGAAGAATCA
1 GGTGCAGGTGAAAAAGAAGAAGAATCA
6092 GGTGCAGGTGAAAAAGAAGAAGAATCA
1 GGTGCAGGTGAAAAAGAAGAAGAATCA
6119 AGGGAAGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.46, C:0.07, G:0.33, T:0.13
Consensus pattern (27 bp):
GGTGCAGGTGAAAAAGAAGAAGAATCA
Found at i:15698 original size:2 final size:2
Alignment explanation
Indices: 15652--15685 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
15642 ATTAGTAAAT
*
15652 TA TA TT 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
15686 GTAAAAGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:16884 original size:9 final size:9
Alignment explanation
Indices: 16853--16905 Score: 63
Period size: 9 Copynumber: 5.9 Consensus size: 9
16843 AGGGTTTTCG
*
16853 GCGTTAGCC
1 GCGTTGGCC
*
16862 GCGTT-GTC
1 GCGTTGGCC
16870 GCCGTTGGCC
1 G-CGTTGGCC
16880 GCGTTGGCC
1 GCGTTGGCC
*
16889 GCGTTGGCA
1 GCGTTGGCC
16898 GCGTTGGC
1 GCGTTGGC
16906 GTTATTGGCG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
8 3 0.08
9 33 0.85
10 3 0.08
ACGTcount: A:0.04, C:0.30, G:0.42, T:0.25
Consensus pattern (9 bp):
GCGTTGGCC
Found at i:16902 original size:27 final size:27
Alignment explanation
Indices: 16853--16905 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
16843 AGGGTTTTCG
*
16853 GCGTTAGCCGCGTTGTCGCCGTTGGCC
1 GCGTTAGCCGCGTTGGCGCCGTTGGCC
*
16880 GCGTTGGCCGCGTTGGCAG-CGTTGGC
1 GCGTTAGCCGCGTTGGC-GCCGTTGGC
16906 GTTATTGGCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.04, C:0.30, G:0.42, T:0.25
Consensus pattern (27 bp):
GCGTTAGCCGCGTTGGCGCCGTTGGCC
Found at i:16922 original size:9 final size:9
Alignment explanation
Indices: 16851--16922 Score: 54
Period size: 9 Copynumber: 8.0 Consensus size: 9
16841 CTAGGGTTTT
*
16851 CGGCGTTAG
1 CGGCGTTGG
* *
16860 CCGCGTTGT
1 CGGCGTTGG
*
16869 CGCCGTTGG
1 CGGCGTTGG
*
16878 CCGCGTTGG
1 CGGCGTTGG
*
16887 CCGCGTTGG
1 CGGCGTTGG
*
16896 CAGCGTTGG
1 CGGCGTTGG
***
16905 CGTTATTGG
1 CGGCGTTGG
16914 CGGCGTTGG
1 CGGCGTTGG
16923 GCTTGAAAGT
Statistics
Matches: 47, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
9 47 1.00
ACGTcount: A:0.04, C:0.26, G:0.43, T:0.26
Consensus pattern (9 bp):
CGGCGTTGG
Found at i:17611 original size:69 final size:69
Alignment explanation
Indices: 17499--17630 Score: 246
Period size: 69 Copynumber: 1.9 Consensus size: 69
17489 AGTGGCCGGA
*
17499 GTTTGATTAACCAACTTTTGGCGACAGCTCCAGTGAAGTAGCCATCGACTCAAAGACAGGTGCGC
1 GTTTGATTAACCAACTTTTGGCGACAGCTCCAGTGAAGCAGCCATCGACTCAAAGACAGGTGCGC
17564 CGTT
66 CGTT
*
17568 GTTTGATTAACCAACTTTTGGCGGCAGCTCCAGTGAAGCAGCCATCGACTCAAAGACAGGTGC
1 GTTTGATTAACCAACTTTTGGCGACAGCTCCAGTGAAGCAGCCATCGACTCAAAGACAGGTGC
17631 AATGGAAGCC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (69 bp):
GTTTGATTAACCAACTTTTGGCGACAGCTCCAGTGAAGCAGCCATCGACTCAAAGACAGGTGCGC
CGTT
Found at i:19809 original size:17 final size:16
Alignment explanation
Indices: 19787--19818 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
19777 TGCAAATGTA
19787 ACTCATTTCATAGCAGC
1 ACTCATTTCAT-GCAGC
19804 ACTCATTTCATGCAG
1 ACTCATTTCATGCAG
19819 ATTCGAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.31
Consensus pattern (16 bp):
ACTCATTTCATGCAGC
Found at i:34139 original size:3 final size:3
Alignment explanation
Indices: 34131--34174 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
34121 CTTCTGTTTG
* * *
34131 TTC TTC TTC TTC TTC TCC TTC TTC TTC TTG TTT TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
34175 ATCTTTCTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:34181 original size:15 final size:15
Alignment explanation
Indices: 34134--34183 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
34124 CTGTTTGTTC
* *
34134 TTCTTCTTCTTCTCC
1 TTCTTCTTCTTATCT
* *
34149 TTCTTCTTCTTGTTT
1 TTCTTCTTCTTATCT
34164 TTCTTCTTCTTATCT
1 TTCTTCTTCTTATCT
34179 TTCTT
1 TTCTT
34184 GGGTTCAGGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.02, C:0.28, G:0.02, T:0.68
Consensus pattern (15 bp):
TTCTTCTTCTTATCT
Found at i:34820 original size:2 final size:2
Alignment explanation
Indices: 34813--34841 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
34803 GCCATTCTGT
34813 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
34842 TTTCCACGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:41708 original size:8 final size:8
Alignment explanation
Indices: 41695--41723 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
41685 TTATTACACC
41695 TTTTTTCT
1 TTTTTTCT
41703 TTTTTTCT
1 TTTTTTCT
41711 TTTTTTCT
1 TTTTTTCT
41719 TTTTT
1 TTTTT
41724 GGCATGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTCT
Found at i:42666 original size:19 final size:19
Alignment explanation
Indices: 42642--42679 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
42632 GAATCCTAAG
*
42642 AAAGATTAGATAGAAAGAA
1 AAAGATCAGATAGAAAGAA
42661 AAAGATCAGATAGAAAGAA
1 AAAGATCAGATAGAAAGAA
42680 GACGGGAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.63, C:0.03, G:0.21, T:0.13
Consensus pattern (19 bp):
AAAGATCAGATAGAAAGAA
Found at i:63109 original size:8 final size:8
Alignment explanation
Indices: 63092--63121 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
63082 AGAAGACCTA
*
63092 ATCTATAT
1 ATCTAAAT
63100 ATCTAAAT
1 ATCTAAAT
63108 ATCTAAAT
1 ATCTAAAT
63116 ATCTAA
1 ATCTAA
63122 TTTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (8 bp):
ATCTAAAT
Done.