Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012011.1 Corchorus capsularis cultivar CVL-1 contig12032, 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: 55257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:759 original size:18 final size:20
Alignment explanation
Indices: 731--776 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
721 ATCAAACACC
731 TTTTCAT-TTCTTTCATT-T
1 TTTTCATATTCTTTCATTCT
*
749 TTTT-ATATTCTTTCTTTCT
1 TTTTCATATTCTTTCATTCT
768 TTTTCATAT
1 TTTTCATAT
777 GTAACGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 2 0.08
18 13 0.54
19 5 0.21
20 4 0.17
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTCATATTCTTTCATTCT
Found at i:1774 original size:25 final size:25
Alignment explanation
Indices: 1740--1793 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
1730 ATAATAATAC
1740 TAAACCATCAACTGCT-GTTTGGTGG
1 TAAACCATCAACT-CTGGTTTGGTGG
1765 TAAACCATCAACTCTGGTTTGGTGG
1 TAAACCATCAACTCTGGTTTGGTGG
1790 TAAA
1 TAAA
1794 ATGTTTGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 2 0.07
25 26 0.93
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (25 bp):
TAAACCATCAACTCTGGTTTGGTGG
Found at i:11257 original size:20 final size:20
Alignment explanation
Indices: 11232--11271 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
11222 CAATAAATTT
11232 TATTTGGGT-CAAATGAAATC
1 TATTTGGGTAC-AATGAAATC
11252 TATTTGGGTACAATGAAATC
1 TATTTGGGTACAATGAAATC
11272 GTGTTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (20 bp):
TATTTGGGTACAATGAAATC
Found at i:12276 original size:15 final size:15
Alignment explanation
Indices: 12256--12285 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12246 AAAATTGACT
12256 CCCAAATTCCAGCCA
1 CCCAAATTCCAGCCA
12271 CCCAAATTCCAGCCA
1 CCCAAATTCCAGCCA
12286 ATAAGGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.47, G:0.07, T:0.13
Consensus pattern (15 bp):
CCCAAATTCCAGCCA
Found at i:12676 original size:2 final size:2
Alignment explanation
Indices: 12669--12699 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12659 GGAGCTTTTC
12669 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12700 AATACTATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17856 original size:14 final size:14
Alignment explanation
Indices: 17814--17857 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
17804 ATAAATTATG
17814 TTATTTTTCACATA
1 TTATTTTTCACATA
**
17828 TT-TTTTTGGCGATA
1 TTATTTTTCAC-ATA
17842 TTATTTTTCACATA
1 TTATTTTTCACATA
17856 TT
1 TT
17858 TATATTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 6 0.25
14 12 0.50
15 6 0.25
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.59
Consensus pattern (14 bp):
TTATTTTTCACATA
Found at i:18680 original size:20 final size:21
Alignment explanation
Indices: 18639--18681 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
18629 GTAGTGAATG
18639 AATAATAATTTTTGGATTATA
1 AATAATAATTTTTGGATTATA
18660 AATAA-AATTTTTGG-TTAATA
1 AATAATAATTTTTGGATT-ATA
18680 AA
1 AA
18682 CCATTTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 2 0.10
20 14 0.67
21 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (21 bp):
AATAATAATTTTTGGATTATA
Found at i:23908 original size:24 final size:26
Alignment explanation
Indices: 23860--23911 Score: 81
Period size: 24 Copynumber: 2.0 Consensus size: 26
23850 ATATTTAAGA
23860 AATATTAAACCATATCATCATGTATGT
1 AATATTAAACCA-ATCATCATGTATGT
23887 AATATTAAACC-AT-ATCATGTATGT
1 AATATTAAACCAATCATCATGTATGT
23911 A
1 A
23912 TATGGAGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 12 0.48
25 2 0.08
27 11 0.44
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (26 bp):
AATATTAAACCAATCATCATGTATGT
Found at i:33732 original size:2 final size:2
Alignment explanation
Indices: 33721--33766 Score: 67
Period size: 2 Copynumber: 22.5 Consensus size: 2
33711 TTCCACTATT
33721 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA
33764 TA T
1 TA T
33767 TATTTTTAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 1 0.02
2 36 0.88
3 4 0.10
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:34445 original size:8 final size:8
Alignment explanation
Indices: 34432--34464 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
34422 CTTATATAAT
34432 TTAATCAA
1 TTAATCAA
34440 TTAATCAA
1 TTAATCAA
34448 TTAATCAA
1 TTAATCAA
34456 TTAATCAA
1 TTAATCAA
34464 T
1 T
34465 CAAGTACCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (8 bp):
TTAATCAA
Found at i:34861 original size:5 final size:5
Alignment explanation
Indices: 34853--34898 Score: 92
Period size: 5 Copynumber: 9.2 Consensus size: 5
34843 AAAAAAATTA
34853 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT T
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT T
34899 GTTTAAAGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAAAT
Found at i:40420 original size:3 final size:3
Alignment explanation
Indices: 40412--40451 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
40402 AACCTTCTGC
40412 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG T
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG T
40452 GATAGTTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (3 bp):
TAG
Found at i:43028 original size:31 final size:31
Alignment explanation
Indices: 42992--43063 Score: 144
Period size: 31 Copynumber: 2.3 Consensus size: 31
42982 GATTGAATCT
42992 AATTAGGCCTAAAAGTTTGTGTCATCAACCA
1 AATTAGGCCTAAAAGTTTGTGTCATCAACCA
43023 AATTAGGCCTAAAAGTTTGTGTCATCAACCA
1 AATTAGGCCTAAAAGTTTGTGTCATCAACCA
43054 AATTAGGCCT
1 AATTAGGCCT
43064 TTTTTTGATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (31 bp):
AATTAGGCCTAAAAGTTTGTGTCATCAACCA
Found at i:53049 original size:11 final size:10
Alignment explanation
Indices: 53029--53090 Score: 52
Period size: 12 Copynumber: 5.4 Consensus size: 10
53019 AAATTCTAGG
53029 AAAATAATAA
1 AAAATAATAA
53039 AAAATATATAA
1 AAAATA-ATAA
53050 TAATAATAATAA
1 -AA-AATAATAA
53062 TAATAATAATAA
1 -AA-AATAATAA
53074 CAACAATAATTAA
1 -AA-AATAA-TAA
53087 AAAA
1 AAAA
53091 CAGAGTCATA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
10 6 0.13
11 6 0.13
12 27 0.59
13 7 0.15
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAATAATAA
Found at i:53052 original size:3 final size:3
Alignment explanation
Indices: 53031--53083 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
53021 ATTCTAGGAA
*
53031 AAT AAT AA- AA- AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAC
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
53075 AAC AAT AAT
1 AAT AAT AAT
53084 TAAAAAACAG
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 4 0.09
3 39 0.85
4 3 0.07
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Done.