Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001400.1 Corchorus capsularis cultivar CVL-1 contig01400, 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: 6321
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Found at i:84 original size:49 final size:48
Alignment explanation
Indices: 3--170 Score: 218
Period size: 49 Copynumber: 3.5 Consensus size: 48
1 TA
* * *
3 TTATTCCGAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTTTTCTTCTC
1 TTATTCCAAAAATGCCCCTTCCCGGTCAGAAGGTCA-AGTCTTCTTCTC
* * *
52 TTATTCCAAAAATGCCCCTTCCTGGTCAGAAGGTCATG-GTT-TTCTC
1 TTATTCCAAAAATGCCCCTTCCCGGTCAGAAGGTCAAGTCTTCTTCTC
98 TTATTCCAAAAATGCCCCTTCCCGGTCAGAAGGTCAAGGTCTTCTTCAT-
1 TTATTCCAAAAATGCCCCTTCCCGGTCAGAAGGTCAA-GTCTTCTTC-TC
*
147 TTATTCC-AAAACGCCCCTTCCCGG
1 TTATTCCAAAAATGCCCCTTCCCGG
171 AGCTATAGGT
Statistics
Matches: 106, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
46 40 0.38
47 3 0.03
48 19 0.18
49 43 0.41
50 1 0.01
ACGTcount: A:0.21, C:0.30, G:0.17, T:0.32
Consensus pattern (48 bp):
TTATTCCAAAAATGCCCCTTCCCGGTCAGAAGGTCAAGTCTTCTTCTC
Found at i:114 original size:46 final size:46
Alignment explanation
Indices: 3--170 Score: 212
Period size: 46 Copynumber: 3.5 Consensus size: 46
1 TA
* * *
3 TTATTCCGAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTTTTCTTCTC
1 TTATTCCAAAAATGCCCCTTCCCGGTCAGAAGGTCA-AG-GTT-TTCTC
* *
52 TTATTCCAAAAATGCCCCTTCCTGGTCAGAAGGTCATGGTTTTCTC
1 TTATTCCAAAAATGCCCCTTCCCGGTCAGAAGGTCAAGGTTTTCTC
*
98 TTATTCCAAAAATGCCCCTTCCCGGTCAGAAGGTCAAGGTCTTCTTC
1 TTATTCCAAAAATGCCCCTTCCCGGTCAGAAGGTCAAGGTTTTC-TC
*
145 ATTTATTCC-AAAACGCCCCTTCCCGG
1 --TTATTCCAAAAATGCCCCTTCCCGG
171 AGCTATAGGT
Statistics
Matches: 107, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
46 46 0.43
47 4 0.04
48 17 0.16
49 40 0.37
ACGTcount: A:0.21, C:0.30, G:0.17, T:0.32
Consensus pattern (46 bp):
TTATTCCAAAAATGCCCCTTCCCGGTCAGAAGGTCAAGGTTTTCTC
Found at i:2289 original size:12 final size:12
Alignment explanation
Indices: 2252--2291 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
2242 GAATTTGGAT
2252 GATGGAGGTGAA
1 GATGGAGGTGAA
* *
2264 CATGGAGGTCAA
1 GATGGAGGTGAA
2276 GATGGAGGTGAA
1 GATGGAGGTGAA
2288 GATG
1 GATG
2292 ATGGTGGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.33, C:0.05, G:0.45, T:0.17
Consensus pattern (12 bp):
GATGGAGGTGAA
Found at i:4611 original size:26 final size:26
Alignment explanation
Indices: 4564--4613 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
4554 AAACACTTGG
*
4564 AGTGTTCTAGTTCCTGAGTTGATGGT
1 AGTGTTCTAGTTCCTGAATTGATGGT
*
4590 AGTGTTCTGGTTCCT-ACATTGATG
1 AGTGTTCTAGTTCCTGA-ATTGATG
4614 ATCAGCGTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 20 0.95
ACGTcount: A:0.16, C:0.14, G:0.28, T:0.42
Consensus pattern (26 bp):
AGTGTTCTAGTTCCTGAATTGATGGT
Found at i:4827 original size:53 final size:53
Alignment explanation
Indices: 4767--4883 Score: 189
Period size: 53 Copynumber: 2.2 Consensus size: 53
4757 ATGGAGACCA
*
4767 TCGTTCTTCATGTAGGAAATCAGCGGTGTTTATGAATTTATCACGTGGGACTC
1 TCGTTCTTCATGGAGGAAATCAGCGGTGTTTATGAATTTATCACGTGGGACTC
* ** *
4820 TCGTTCTTCATGGAGGAGATTGGCGGTGTTTATGAATTTATCATGTGGGACTC
1 TCGTTCTTCATGGAGGAAATCAGCGGTGTTTATGAATTTATCACGTGGGACTC
4873 TCGTTCTTCAT
1 TCGTTCTTCAT
4884 ATGTGAGACC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 59 1.00
ACGTcount: A:0.20, C:0.16, G:0.26, T:0.38
Consensus pattern (53 bp):
TCGTTCTTCATGGAGGAAATCAGCGGTGTTTATGAATTTATCACGTGGGACTC
Found at i:5352 original size:77 final size:77
Alignment explanation
Indices: 5225--5519 Score: 358
Period size: 77 Copynumber: 3.7 Consensus size: 77
5215 ACGAATGTCG
**
5225 ACTCTTGGCGCTCTTCCGTCCAAACGAGATAGTCTCTTGGTGAG-CTGAACGTCCTCGTGCAACT
1 ACTCTTGGCGCTCTTCCGTCCAAACGAGGGAGTCTCTTGGTGAGAC-GAACGTCCTCGTGCAACT
5289 TAAACAGGGAGCC
65 TAAACAGGGAGCC
*
5302 ACTCTTGGCGCTCTTCCGTCCAAATGAGGGAGTCTCTTGGTGAGACGAACGTCCTCGTGCAACAT
1 ACTCTTGGCGCTCTTCCGTCCAAACGAGGGAGTCTCTTGGTGAGACGAACGTCCTCGTGCAAC-T
*
5367 AAACAGGGAGCCAAACAGGGAGCC
65 -----------TAAACAGGGAGCC
* * * *
5391 ACTCTTGGCGCTCTTCCGTCCAAACGAGGGATTCTCTTGGTGAGACGAACGTCCTCCTACAGCTT
1 ACTCTTGGCGCTCTTCCGTCCAAACGAGGGAGTCTCTTGGTGAGACGAACGTCCTCGTGCAACTT
5456 AAACAGGGAGCC
66 AAACAGGGAGCC
* * * *
5468 ACTTTTGTCGCTCTTCCGTCCTAACGAGGGAGTCTCTTGGCGAGACGAACGT
1 ACTCTTGGCGCTCTTCCGTCCAAACGAGGGAGTCTCTTGGTGAGACGAACGT
5520 ACACTCTTAG
Statistics
Matches: 190, Mismatches: 15, Indels: 26
0.82 0.06 0.11
Matches are distributed among these distances:
77 117 0.62
78 2 0.01
88 1 0.01
89 70 0.37
ACGTcount: A:0.22, C:0.28, G:0.26, T:0.23
Consensus pattern (77 bp):
ACTCTTGGCGCTCTTCCGTCCAAACGAGGGAGTCTCTTGGTGAGACGAACGTCCTCGTGCAACTT
AAACAGGGAGCC
Found at i:5384 original size:12 final size:12
Alignment explanation
Indices: 5367--5391 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5357 CGTGCAACAT
5367 AAACAGGGAGCC
1 AAACAGGGAGCC
5379 AAACAGGGAGCC
1 AAACAGGGAGCC
5391 A
1 A
5392 CTCTTGGCGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.24, G:0.32, T:0.00
Consensus pattern (12 bp):
AAACAGGGAGCC
Found at i:5441 original size:89 final size:89
Alignment explanation
Indices: 5290--5468 Score: 304
Period size: 89 Copynumber: 2.0 Consensus size: 89
5280 CGTGCAACTT
*
5290 AAACAGGGAGCCACTCTTGGCGCTCTTCCGTCCAAATGAGGGAGTCTCTTGGTGAGACGAACGTC
1 AAACAGGGAGCCACTCTTGGCGCTCTTCCGTCCAAACGAGGGAGTCTCTTGGTGAGACGAACGTC
* *
5355 CTCGTGCAACATAAACAGGGAGCC
66 CTCCTACAACATAAACAGGGAGCC
*
5379 AAACAGGGAGCCACTCTTGGCGCTCTTCCGTCCAAACGAGGGATTCTCTTGGTGAGACGAACGTC
1 AAACAGGGAGCCACTCTTGGCGCTCTTCCGTCCAAACGAGGGAGTCTCTTGGTGAGACGAACGTC
* *
5444 CTCCTACAGCTTAAACAGGGAGCC
66 CTCCTACAACATAAACAGGGAGCC
5468 A
1 A
5469 CTTTTGTCGC
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 84 1.00
ACGTcount: A:0.26, C:0.28, G:0.27, T:0.20
Consensus pattern (89 bp):
AAACAGGGAGCCACTCTTGGCGCTCTTCCGTCCAAACGAGGGAGTCTCTTGGTGAGACGAACGTC
CTCCTACAACATAAACAGGGAGCC
Found at i:5661 original size:83 final size:83
Alignment explanation
Indices: 5561--5720 Score: 232
Period size: 83 Copynumber: 1.9 Consensus size: 83
5551 TAGTCTATTC
* * **
5561 TGAGACGAACGTCCTCGTGCTTCGTTATACGGGGGTGCTC-CTCTTGGCGCTCAGCCGTCCAAAT
1 TGAGACGAACGTCCTCGTGCTTCATTATACGAGGGAAC-CACTCTTGGCGCTCAGCCGTCCAAAT
5625 TAAACAGGGGGGCTCTTGG
65 TAAACAGGGGGGCTCTTGG
* * *
5644 TGAGACGAACGTCCTCGTGCTTCATTATACGAGGGAACCACTCTTGGCGGTCAGCTGTCTAAATT
1 TGAGACGAACGTCCTCGTGCTTCATTATACGAGGGAACCACTCTTGGCGCTCAGCCGTCCAAATT
*
5709 AAACTGGGGGGC
66 AAACAGGGGGGC
5721 ACTTTTGGCC
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
82 1 0.01
83 67 0.99
ACGTcount: A:0.20, C:0.25, G:0.30, T:0.25
Consensus pattern (83 bp):
TGAGACGAACGTCCTCGTGCTTCATTATACGAGGGAACCACTCTTGGCGCTCAGCCGTCCAAATT
AAACAGGGGGGCTCTTGG
Found at i:5879 original size:115 final size:116
Alignment explanation
Indices: 5641--5886 Score: 275
Period size: 115 Copynumber: 2.1 Consensus size: 116
5631 GGGGGGCTCT
* * * * *
5641 TGGTGAGACGAACGTCCTCGTGCTTCATTATACGAGGGAACCACTCTTGGCGGTCAGCTGTCTAA
1 TGGTGAGACGAACGTCCTCGTGCTTCATTATACGAGGGAACCACTCTTGCCGCTCAGCCGACCAA
* * *
5706 ATTAAACTGGGGGGCACTTTTGGCCCTCAATCGTCAAAACAAGGGAGTCTC
66 ATTAAACTAGGGGGCACTGTTAGCCCTCAATCGTCAAAACAAGGGAGTCTC
** * ** *
5757 TTCTGAGACGAACGTCTTCGTGCTTCATTATACG-GGGTGCCACTCTTGCCTCTCAGCCGACCAA
1 TGGTGAGACGAACGTCCTCGTGCTTCATTATACGAGGGAACCACTCTTGCCGCTCAGCCGACCAA
* * *
5821 ATTAAA-TAGGGGGCACTGTTAGCCCTTAGTCGTTC-AAACGAGAGG-GTCTC
66 ATTAAACTAGGGGGCACTGTTAGCCCTCAATCG-TCAAAACAAG-GGAGTCTC
*
5871 GTGGTGAGATGAACGT
1 -TGGTGAGACGAACGT
5887 GACATCCCAA
Statistics
Matches: 107, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
114 32 0.30
115 44 0.41
116 31 0.29
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (116 bp):
TGGTGAGACGAACGTCCTCGTGCTTCATTATACGAGGGAACCACTCTTGCCGCTCAGCCGACCAA
ATTAAACTAGGGGGCACTGTTAGCCCTCAATCGTCAAAACAAGGGAGTCTC
Found at i:5914 original size:38 final size:38
Alignment explanation
Indices: 5860--5959 Score: 137
Period size: 38 Copynumber: 2.6 Consensus size: 38
5850 TCGTTCAAAC
* * * *
5860 GAGAGGGTCTCGTGGTGAGATGAACGTGACATCCCAAT
1 GAGAGAGTCTCTTGGTGAGACGAACGTGACACCCCAAT
* *
5898 GAGGGAGTCTCTTGGTGAGACGAACGTGCCACCCCAAT
1 GAGAGAGTCTCTTGGTGAGACGAACGTGACACCCCAAT
*
5936 GAGAGAGTCTCTTGGCGAGACGAA
1 GAGAGAGTCTCTTGGTGAGACGAA
5960 TATCCTCGAG
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.26, C:0.21, G:0.34, T:0.19
Consensus pattern (38 bp):
GAGAGAGTCTCTTGGTGAGACGAACGTGACACCCCAAT
Done.