Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019160.1 Corchorus olitorius cultivar O-4 contig19193, 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: 56553
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1188 original size:13 final size:13
Alignment explanation
Indices: 1170--1196 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1160 TATGAGACTG
1170 AGGGAGTACTAAA
1 AGGGAGTACTAAA
1183 AGGGAGTACTAAA
1 AGGGAGTACTAAA
1196 A
1 A
1197 TGTACTATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.30, T:0.15
Consensus pattern (13 bp):
AGGGAGTACTAAA
Found at i:4314 original size:19 final size:21
Alignment explanation
Indices: 4267--4314 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
4257 GAAACGTATT
4267 TTAAAAATAATATTTTAAAAA
1 TTAAAAATAATATTTTAAAAA
*
4288 TTGTAAAAT-AT-TTTTAAAAA
1 TT-AAAAATAATATTTTAAAAA
4308 TTAAAAA
1 TTAAAAA
4315 GAAAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 4 0.17
20 11 0.46
21 4 0.17
22 5 0.21
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TTAAAAATAATATTTTAAAAA
Found at i:6734 original size:2 final size:2
Alignment explanation
Indices: 6727--6755 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6717 TGTGGATAAG
6727 TA TA 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 TA TA T
6756 CTTATCTTAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13896 original size:20 final size:20
Alignment explanation
Indices: 13867--13905 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
13857 AAAAAGATCA
13867 ATGAAAAAGGTTTGAGACTT
1 ATGAAAAAGGTTTGAGACTT
*
13887 ATGAAGAAGGTTTGAGACT
1 ATGAAAAAGGTTTGAGACT
13906 CCAAATCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.28, T:0.28
Consensus pattern (20 bp):
ATGAAAAAGGTTTGAGACTT
Found at i:15472 original size:25 final size:24
Alignment explanation
Indices: 15436--15482 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
15426 AATACTTACA
15436 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGGTATTTTT
15460 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
15483 GTGCAAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (24 bp):
TTAATTAAATTCTTAGGTATTTTT
Found at i:16322 original size:36 final size:36
Alignment explanation
Indices: 16275--16344 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
16265 GAGATTTTGG
* *
16275 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
16311 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
16345 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:19591 original size:20 final size:20
Alignment explanation
Indices: 19566--19608 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
19556 ATTTTTGATA
19566 TAATCTTAAATAGTTTTAAG
1 TAATCTTAAATAGTTTTAAG
19586 TAATCTTAAATAGTTTTAAG
1 TAATCTTAAATAGTTTTAAG
19606 TAA
1 TAA
19609 GAAGATTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (20 bp):
TAATCTTAAATAGTTTTAAG
Found at i:23829 original size:99 final size:99
Alignment explanation
Indices: 23658--23839 Score: 310
Period size: 99 Copynumber: 1.8 Consensus size: 99
23648 TCAGAGGTGT
* * * *
23658 GCGATTGTGGAGTGTTGTGCTTGCATTCCACGGGTTAAGTCTTAGATGGCCGGTAATTGGCTTAA
1 GCGATTGTGGAGTGTTGTGCTTGCACTCCACGGGTTAAGTCTTAGATGACCGATAATTGACTTAA
*
23723 GACTTGACGATTTGGGCCACACGGGGGAGAGATG
66 GACTTGACGAGTTGGGCCACACGGGGGAGAGATG
*
23757 GCGATTGTGGAGTGTTGTGCTTGCACTCCACGGGTTAAGTCTTGGATGACCGATAATTGACTTAA
1 GCGATTGTGGAGTGTTGTGCTTGCACTCCACGGGTTAAGTCTTAGATGACCGATAATTGACTTAA
23822 GACTTGACGAGTTGGGCC
66 GACTTGACGAGTTGGGCC
23840 GGGGGCACTC
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 77 1.00
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (99 bp):
GCGATTGTGGAGTGTTGTGCTTGCACTCCACGGGTTAAGTCTTAGATGACCGATAATTGACTTAA
GACTTGACGAGTTGGGCCACACGGGGGAGAGATG
Found at i:23887 original size:65 final size:65
Alignment explanation
Indices: 23779--23900 Score: 226
Period size: 65 Copynumber: 1.9 Consensus size: 65
23769 TGTTGTGCTT
23779 GCACTCCACGGGTTAAGTCTTGGATGACCGATAATTGACTTAAGACTTGACGAGTTGGGCCGGGG
1 GCACTCCACGGGTTAAGTCTTGGATGACCGATAATTGACTTAAGACTTGACGAGTTGGGCCGGGG
* *
23844 GCACTCCACGGGTTAAGTCTTGGATGGCCGATAATTGATTTAAGACTTGACGAGTTG
1 GCACTCCACGGGTTAAGTCTTGGATGACCGATAATTGACTTAAGACTTGACGAGTTG
23901 AACCGCATGG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 55 1.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (65 bp):
GCACTCCACGGGTTAAGTCTTGGATGACCGATAATTGACTTAAGACTTGACGAGTTGGGCCGGGG
Found at i:24045 original size:83 final size:85
Alignment explanation
Indices: 23845--24101 Score: 401
Period size: 83 Copynumber: 3.0 Consensus size: 85
23835 GGGCCGGGGG
** **
23845 CACTCCACGGGTTAAGTCTTGGATGGCCGATAATTGATTTAAGACTTGACGAGTTGAACCGCATG
1 CACTCCACGGGTTAAGTCTTGGATGGCCGATAATTGGCTTAAGACTTGACGAGTTG-GGCGCA-G
*
23910 GGGGAGAGATGATGATTCACAA
64 GGGGAGAGATGAGGATTCACAA
*
23932 CACTCCACGGGTTAAGTCTTGGATGACCGATAATTGGCTTAAGACTTGACGAGTTGGGC-CA-GG
1 CACTCCACGGGTTAAGTCTTGGATGGCCGATAATTGGCTTAAGACTTGACGAGTTGGGCGCAGGG
23995 GGAGAGATGAGGATTCACAA
66 GGAGAGATGAGGATTCACAA
*
24015 CACTCCACGGGTTAAGTCTTGGATGGCCGATAATTGGCTCAAGACTTGACGAGTTGGGCCGCACG
1 CACTCCACGGGTTAAGTCTTGGATGGCCGATAATTGGCTTAAGACTTGACGAGTTGGG-CGCA-G
24080 GGGGAGAGATGAGGATTCACAA
64 GGGGAGAGATGAGGATTCACAA
24102 GTGAATCGGG
Statistics
Matches: 158, Mismatches: 8, Indels: 8
0.91 0.05 0.05
Matches are distributed among these distances:
83 77 0.49
84 1 0.01
85 4 0.03
86 1 0.01
87 75 0.47
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (85 bp):
CACTCCACGGGTTAAGTCTTGGATGGCCGATAATTGGCTTAAGACTTGACGAGTTGGGCGCAGGG
GGAGAGATGAGGATTCACAA
Found at i:30382 original size:17 final size:19
Alignment explanation
Indices: 30348--30383 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
30338 TTTTGTTTGG
30348 TAGGAATGAAATACAGAAA
1 TAGGAATGAAATACAGAAA
30367 TAGGAA-GAAA-ACAGAAA
1 TAGGAATGAAATACAGAAA
30384 AGAAATGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 4 0.24
19 6 0.35
ACGTcount: A:0.61, C:0.06, G:0.22, T:0.11
Consensus pattern (19 bp):
TAGGAATGAAATACAGAAA
Found at i:46460 original size:25 final size:25
Alignment explanation
Indices: 46426--46474 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
46416 CCAAACAATC
46426 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
46451 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
46475 CAAACCAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.12, C:0.33, G:0.20, T:0.35
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:46500 original size:21 final size:21
Alignment explanation
Indices: 46471--46512 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
46461 TCGCTCGGTC
*
46471 TCTACAAACCAATC-ATCACA
1 TCTACAAACCAAACAATCACA
46491 TCTACCAAACCAAACAATCACA
1 TCTA-CAAACCAAACAATCACA
46513 CACACCCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.17
Consensus pattern (21 bp):
TCTACAAACCAAACAATCACA
Done.