Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011929.1 Corchorus capsularis cultivar CVL-1 contig11950, 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: 33472
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Found at i:5430 original size:30 final size:30
Alignment explanation
Indices: 5385--5459 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
5375 AGCAAAATCA
* *
5385 AGCAACCAAAAGTCCTGCACAA-GCCACTAC
1 AGCAAGCAAAGGTCCTGCA-AACGCCACTAC
* *
5415 AGCAAGCAAAGGTCCTGCAAACTCCACTGC
1 AGCAAGCAAAGGTCCTGCAAACGCCACTAC
5445 AGCAAGCAAAGGTCC
1 AGCAAGCAAAGGTCC
5460 ACCAAAGAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 2 0.05
30 38 0.95
ACGTcount: A:0.37, C:0.33, G:0.19, T:0.11
Consensus pattern (30 bp):
AGCAAGCAAAGGTCCTGCAAACGCCACTAC
Found at i:6891 original size:18 final size:18
Alignment explanation
Indices: 6868--6903 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6858 CAGTAACAAA
* *
6868 GAACCTCTTCGGTCGATT
1 GAACCTCTCCAGTCGATT
6886 GAACCTCTCCAGTCGATT
1 GAACCTCTCCAGTCGATT
6904 TACACCTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.31, G:0.19, T:0.31
Consensus pattern (18 bp):
GAACCTCTCCAGTCGATT
Found at i:10211 original size:20 final size:21
Alignment explanation
Indices: 10188--10231 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
10178 AAATAAAATA
* *
10188 AAAAACTACTCATTTTA-GAT
1 AAAAACTACCCATTATAGGAT
*
10208 AAAAATTACCCATTATAGGAT
1 AAAAACTACCCATTATAGGAT
10229 AAA
1 AAA
10232 TATAATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.30
Consensus pattern (21 bp):
AAAAACTACCCATTATAGGAT
Found at i:10417 original size:20 final size:20
Alignment explanation
Indices: 10392--10429 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
10382 ATTCAAAATA
10392 AAATAAAAACTACACATTTT
1 AAATAAAAACTACACATTTT
*
10412 AAATAAAAACTACCCATT
1 AAATAAAAACTACACATT
10430 ATACCAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.26
Consensus pattern (20 bp):
AAATAAAAACTACACATTTT
Found at i:11556 original size:9 final size:9
Alignment explanation
Indices: 11542--11573 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
11532 CGATCATAAT
11542 ATTATTATG
1 ATTATTATG
11551 ATTATTATG
1 ATTATTATG
11560 ATTATTATG
1 ATTATTATG
11569 ATTAT
1 ATTAT
11574 ATATTTCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.56
Consensus pattern (9 bp):
ATTATTATG
Found at i:15891 original size:16 final size:16
Alignment explanation
Indices: 15870--15902 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
15860 AATCCTACAT
15870 GAACAAGCAGACAAAA
1 GAACAAGCAGACAAAA
15886 GAACAAGCAGACAAAA
1 GAACAAGCAGACAAAA
15902 G
1 G
15903 GAGAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.61, C:0.18, G:0.21, T:0.00
Consensus pattern (16 bp):
GAACAAGCAGACAAAA
Found at i:20539 original size:4 final size:4
Alignment explanation
Indices: 20532--20557 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
20522 AGAAAAAAAA
20532 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
20558 TTTTTCAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:22360 original size:11 final size:10
Alignment explanation
Indices: 22342--22375 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
22332 AATTGTCTTC
22342 AAATCTTCAA
1 AAATCTTCAA
22352 AATATCTTCAA
1 AA-ATCTTCAA
22363 GAAATCTTCAA
1 -AAATCTTCAA
22374 AA
1 AA
22376 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:23949 original size:38 final size:38
Alignment explanation
Indices: 23905--24094 Score: 154
Period size: 38 Copynumber: 4.8 Consensus size: 38
23895 CTTGTATTCG
23905 GAGTTTATGGTATTATTCAGCAGTGGGTGGTATTTTCA
1 GAGTTTATGGTATTATTCAGCAGTGGGTGGTATTTTCA
* * *
23943 GAGTTTATGGTATTAGTCAGCAGTGGATGGAATTTTCA
1 GAGTTTATGGTATTATTCAGCAGTGGGTGGTATTTTCA
* * ** * *
23981 GACTATGTGTTTAATTATGGATATCATT-ATTCAGT-ACTTGTA--TTCG
1 G---A---G--T--TTATGG-TATTATTCA-GCAGTGGGTGGTATTTTCA
24027 GAGTTTATGGTATTATTCAGCAGTGGGTGGTATTTTCA
1 GAGTTTATGGTATTATTCAGCAGTGGGTGGTATTTTCA
*
24065 GAGTTTATGGTATTATTCAGCAGTTGGTGG
1 GAGTTTATGGTATTATTCAGCAGTGGGTGG
24095 AGTGTATTCT
Statistics
Matches: 118, Mismatches: 18, Indels: 32
0.70 0.11 0.19
Matches are distributed among these distances:
35 10 0.08
36 11 0.09
38 69 0.58
40 1 0.01
41 1 0.01
43 1 0.01
44 1 0.01
46 5 0.04
48 10 0.08
49 9 0.08
ACGTcount: A:0.23, C:0.08, G:0.27, T:0.42
Consensus pattern (38 bp):
GAGTTTATGGTATTATTCAGCAGTGGGTGGTATTTTCA
Found at i:23955 original size:18 final size:19
Alignment explanation
Indices: 23899--23962 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
23889 TCAGTACTTG
*
23899 TATTCGGAGTTTATGGTAT
1 TATTCAGAGTTTATGGTAT
***
23918 TATTCAGCAGTGGGTGGTAT
1 TATTCAG-AGTTTATGGTAT
23938 T-TTCAGAGTTTATGGTAT
1 TATTCAGAGTTTATGGTAT
*
23956 TAGTCAG
1 TATTCAG
23963 CAGTGGATGG
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
18 10 0.29
19 15 0.43
20 10 0.29
ACGTcount: A:0.22, C:0.08, G:0.28, T:0.42
Consensus pattern (19 bp):
TATTCAGAGTTTATGGTAT
Found at i:23981 original size:19 final size:19
Alignment explanation
Indices: 23911--23981 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
23901 TTCGGAGTTT
23911 ATGGTATTATTCAGCAGTGG
1 ATGGTATT-TTCAGCAGTGG
* **
23931 GTGGTATTTTCAG-AGTTT
1 ATGGTATTTTCAGCAGTGG
*
23949 ATGGTATTAGTCAGCAGTGG
1 ATGGTATT-TTCAGCAGTGG
*
23969 ATGGAATTTTCAG
1 ATGGTATTTTCAG
23982 ACTATGTGTT
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
18 10 0.25
19 13 0.32
20 17 0.43
ACGTcount: A:0.24, C:0.08, G:0.30, T:0.38
Consensus pattern (19 bp):
ATGGTATTTTCAGCAGTGG
Found at i:24035 original size:122 final size:117
Alignment explanation
Indices: 23828--24095 Score: 410
Period size: 122 Copynumber: 2.2 Consensus size: 117
23818 ATTAGTCAGT
* * *
23828 TTTATGGTATCATTCAGTAGTTGGTGGTATTTTCAAACAATGTGTGTAATTATATTATTATTCAG
1 TTTATGGTATTATTCAGCAG-TGGTGGAATTTTCAAACAATGTGTGTAATTATATTATTATTCAG
23893 TACTTGTATTCGGAGTTTATGGTATTATTCAGCAGTGGGTGGTATTTTCAGAG
65 TACTTGTATTCGGAGTTTATGGTATTATTCAGCAGTGGGTGGTATTTTCAGAG
* * * *
23946 TTTATGGTATTAGTCAGCAGTGGATGGAATTTTCAGACTATGTGTTTAATTATGGATATCATTAT
1 TTTATGGTATTATTCAGCAGTGG-TGGAATTTTCAAACAATGTGTGTAATTAT--AT-T-ATTAT
24011 TCAGTACTTGTATTCGGAGTTTATGGTATTATTCAGCAGTGGGTGGTATTTTCAGAG
61 TCAGTACTTGTATTCGGAGTTTATGGTATTATTCAGCAGTGGGTGGTATTTTCAGAG
24068 TTTATGGTATTATTCAGCAGTTGGTGGA
1 TTTATGGTATTATTCAGCAG-TGGTGGA
24096 GTGTATTCTT
Statistics
Matches: 136, Mismatches: 8, Indels: 8
0.89 0.05 0.05
Matches are distributed among these distances:
117 3 0.02
118 42 0.31
120 2 0.01
121 1 0.01
122 85 0.62
123 3 0.02
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.43
Consensus pattern (117 bp):
TTTATGGTATTATTCAGCAGTGGTGGAATTTTCAAACAATGTGTGTAATTATATTATTATTCAGT
ACTTGTATTCGGAGTTTATGGTATTATTCAGCAGTGGGTGGTATTTTCAGAG
Found at i:24083 original size:19 final size:20
Alignment explanation
Indices: 24028--24089 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
24018 TTGTATTCGG
24028 AGTTTATGGTATTATTCAGC
1 AGTTTATGGTATTATTCAGC
***
24048 AGTGGGTGGTATT-TTCAG-
1 AGTTTATGGTATTATTCAGC
24066 AGTTTATGGTATTATTCAGC
1 AGTTTATGGTATTATTCAGC
24086 AGTT
1 AGTT
24090 GGTGGAGTGT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 10 0.29
19 10 0.29
20 14 0.41
ACGTcount: A:0.23, C:0.08, G:0.26, T:0.44
Consensus pattern (20 bp):
AGTTTATGGTATTATTCAGC
Found at i:33098 original size:20 final size:21
Alignment explanation
Indices: 33073--33113 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
33063 TATTTTTATA
33073 GCTATTCTTATATG-ATTTTT
1 GCTATTCTTATATGTATTTTT
* *
33093 GCTATTTTTATGTGTATTTTT
1 GCTATTCTTATATGTATTTTT
33114 ACCCTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.17, C:0.07, G:0.12, T:0.63
Consensus pattern (21 bp):
GCTATTCTTATATGTATTTTT
Done.