Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015911.1 Corchorus capsularis cultivar CVL-1 contig15932, 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: 24424
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Found at i:1988 original size:22 final size:22
Alignment explanation
Indices: 1960--2008 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
1950 AGTCTTTATA
1960 AAAATTAC-AAAGAATAGTAATC
1 AAAATTACAAAAG-ATAGTAATC
*
1982 AAAATTACAAAAGATTGTAATC
1 AAAATTACAAAAGATAGTAATC
2004 AAAAT
1 AAAAT
2009 CTCGTAAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.24
Consensus pattern (22 bp):
AAAATTACAAAAGATAGTAATC
Found at i:2094 original size:43 final size:42
Alignment explanation
Indices: 2044--2190 Score: 118
Period size: 43 Copynumber: 3.4 Consensus size: 42
2034 TTAATGGAGC
*
2044 TTATCAAAATTACAAAAGATAGTTACCAATATTTCATATGAGA
1 TTATCAAAATTACAAAAGATCGTTACCAA-ATTTCATATGAGA
* * * * *
2087 TTATCAAAATTA-TAAAGAGTCGTTATCAAAATTACATATGGTGG
1 TTATCAAAATTACAAAAGA-TCGTTA-CCAAATTTCATAT-GAGA
* * * * *
2131 TTATCAAAATTTATATAAGGTCGTTATCGAAATTTCA-ATCAGGA
1 TTATCAAAA-TTACAAAAGATCGTTA-CCAAATTTCATATGA-GA
2175 TTATCAAAATTACAAA
1 TTATCAAAATTACAAA
2191 TAGCGGATAT
Statistics
Matches: 82, Mismatches: 16, Indels: 12
0.75 0.15 0.11
Matches are distributed among these distances:
42 5 0.06
43 30 0.37
44 26 0.32
45 18 0.22
46 3 0.04
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.34
Consensus pattern (42 bp):
TTATCAAAATTACAAAAGATCGTTACCAAATTTCATATGAGA
Found at i:2165 original size:23 final size:22
Alignment explanation
Indices: 2087--2164 Score: 95
Period size: 22 Copynumber: 3.5 Consensus size: 22
2077 TCATATGAGA
2087 TTATCAAAATTATA-AAGAGTCG
1 TTATCAAAATTATATAAG-GTCG
* * *
2109 TTATCAAAATTACATATGGTGG
1 TTATCAAAATTATATAAGGTCG
2131 TTATCAAAATTTATATAAGGTCG
1 TTATCAAAA-TTATATAAGGTCG
*
2154 TTATCGAAATT
1 TTATCAAAATT
2165 TCAATCAGGA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
22 27 0.57
23 20 0.43
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTATATAAGGTCG
Found at i:2184 original size:21 final size:21
Alignment explanation
Indices: 2154--2254 Score: 57
Period size: 22 Copynumber: 4.7 Consensus size: 21
2144 TATAAGGTCG
*
2154 TTATCGAAATTTCAAT-CAGGA
1 TTATCAAAATTTCAATAC-GGA
*
2175 TTATCAAAATTACAAATAGCGGA
1 TTATCAAAATTTC-AATA-CGGA
* *
2198 -TATCAAAATTTCAA-ATGGTGG
1 TTATCAAAATTTCAATA-CG-GA
* *
2219 TTTTCAAAATTTC-AGACGGTA
1 TTATCAAAATTTCAATACGG-A
2240 GTTATCAAAATTTCA
1 -TTATCAAAATTTCA
2255 TAGGACGGTT
Statistics
Matches: 61, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
20 3 0.05
21 16 0.26
22 38 0.62
23 3 0.05
24 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.34
Consensus pattern (21 bp):
TTATCAAAATTTCAATACGGA
Found at i:2225 original size:22 final size:22
Alignment explanation
Indices: 2198--2254 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
2188 AAATAGCGGA
* *
2198 TATCAAAATTTCAAATGGTGGT
1 TATCAAAATTTCAAACGGTAGT
* *
2220 TTTCAAAATTTCAGACGGTAGT
1 TATCAAAATTTCAAACGGTAGT
2242 TATCAAAATTTCA
1 TATCAAAATTTCA
2255 TAGGACGGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCAAACGGTAGT
Found at i:3062 original size:1 final size:1
Alignment explanation
Indices: 3056--3082 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
3046 TTGCTAAGAG
3056 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
3083 AAATTCCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:4065 original size:166 final size:166
Alignment explanation
Indices: 3746--4076 Score: 452
Period size: 166 Copynumber: 2.0 Consensus size: 166
3736 TCATTTGTCA
* *
3746 ATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATAAAAAATTAGGACATTTAA
1 ATTGAGAAATGACCAAAAAGATTACTTATTTAATCCCCTCAAGAATAAAAAATTAGGACATTTAA
* * ** * * ** * *
3811 GTAATCTGCCAAGTAGGTAAAGACGAAAAATGTTAGTTCTCTAGCTCATCATCAATTCTTGATGA
66 GTAATCTGCCAAGTAAGAAAAGACGAAAAAAATAAATTCTCTAGCTCAAAAGCAAGTCTTGATGA
* *
3876 GGATCATTTATTAATTCCACTACTCTATTCAAGTTC
131 GGATCATTTAGTAATTCCACTACTCTATTAAAGTTC
* *
3912 ATTGAGAAATGACCAAAAAGATTACTTATTTAAT-CCCTCAAGAATCAAAAGTTAGGACATTTAA
1 ATTGAGAAATGACCAAAAAGATTACTTATTTAATCCCCTCAAGAATAAAAAATTAGGACATTTAA
*
3976 GTAATCTGCCAAGTAAGAAAAGACGAAAAAAATAAATTCTCT-GACTCAAAAAGCAAGTCTTGGT
66 GTAATCTGCCAAGTAAGAAAAGACGAAAAAAATAAATTCTCTAG-CTC-AAAAGCAAGTCTTGAT
*
4040 -AGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTT
129 GA-GGATCATTTAGTAATTCCACTACTCTATTAAAGTT
4077 TAGGACATTT
Statistics
Matches: 144, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
164 1 0.01
165 68 0.47
166 75 0.52
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.31
Consensus pattern (166 bp):
ATTGAGAAATGACCAAAAAGATTACTTATTTAATCCCCTCAAGAATAAAAAATTAGGACATTTAA
GTAATCTGCCAAGTAAGAAAAGACGAAAAAAATAAATTCTCTAGCTCAAAAGCAAGTCTTGATGA
GGATCATTTAGTAATTCCACTACTCTATTAAAGTTC
Found at i:11558 original size:66 final size:65
Alignment explanation
Indices: 11474--11881 Score: 636
Period size: 66 Copynumber: 6.2 Consensus size: 65
11464 GATGATTCGT
*
11474 GTTCAATTTTTGGCAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAACTTACGATTCAAGGAT
1 GTTCAATTTTTGACAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAA-TTACGATTCAAGGAT
11539 C
65 C
* * * * * *
11540 GTTCAATTTTTTATAAAACGTTATCGAGGGAGACATTTGTCTTACTTAATTCACGATTCAAGGAT
1 GTTCAATTTTTGACAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAATT-ACGATTCAAGGAT
11605 C
65 C
*
11606 GTTCAATTTTTGGCAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAACTTACGATTCAAGGAT
1 GTTCAATTTTTGACAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAA-TTACGATTCAAGGAT
11671 C
65 C
* * *
11672 GTTCAATTTTTTATAAAACGGTCTCGAGGGAGACGTTTGTCTTACTTAATTCACGATTCAAGGAT
1 GTTCAATTTTTGACAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAATT-ACGATTCAAGGAT
11737 C
65 C
*
11738 GTTCAATTTTTGGCAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAATTTACGATTCAAGGAT
1 GTTCAATTTTTGACAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAA-TTACGATTCAAGGAT
11803 C
65 C
* *
11804 GTTCAATTTTTTATAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAATTTACGATTCAAGGAT
1 GTTCAATTTTTGACAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAA-TTACGATTCAAGGAT
11869 C
65 C
11870 GTTCAATTTTTG
1 GTTCAATTTTTG
11882 GTCTTCAAGG
Statistics
Matches: 312, Mismatches: 26, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
65 4 0.01
66 304 0.97
67 4 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (65 bp):
GTTCAATTTTTGACAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAATTACGATTCAAGGATC
Found at i:11632 original size:132 final size:132
Alignment explanation
Indices: 11474--11882 Score: 764
Period size: 132 Copynumber: 3.1 Consensus size: 132
11464 GATGATTCGT
11474 GTTCAATTTTTGGCAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAACTTACGATTCAAGGAT
1 GTTCAATTTTTGGCAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAACTTACGATTCAAGGAT
* * *
11539 CGTTCAATTTTTTATAAAACGTTATCGAGGGAGACATTTGTCTTACTTAATTCACGATTCAAGGA
66 CGTTCAATTTTTTATAAAACGGTCTCGAGGGAGACGTTTGTCTTACTTAATTCACGATTCAAGGA
11604 TC
131 TC
11606 GTTCAATTTTTGGCAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAACTTACGATTCAAGGAT
1 GTTCAATTTTTGGCAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAACTTACGATTCAAGGAT
11671 CGTTCAATTTTTTATAAAACGGTCTCGAGGGAGACGTTTGTCTTACTTAATTCACGATTCAAGGA
66 CGTTCAATTTTTTATAAAACGGTCTCGAGGGAGACGTTTGTCTTACTTAATTCACGATTCAAGGA
11736 TC
131 TC
*
11738 GTTCAATTTTTGGCAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAATTTACGATTCAAGGAT
1 GTTCAATTTTTGGCAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAACTTACGATTCAAGGAT
* *
11803 CGTTCAATTTTTTATAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAATTTACGATTCAAGGA
66 CGTTCAATTTTTTATAAAACGGTCTCGAGGGAGACGTTTGTCTTACTTAATTCACGATTCAAGGA
11868 TC
131 TC
11870 GTTCAATTTTTGG
1 GTTCAATTTTTGG
11883 TCTTCAAGGA
Statistics
Matches: 271, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
132 271 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (132 bp):
GTTCAATTTTTGGCAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAACTTACGATTCAAGGAT
CGTTCAATTTTTTATAAAACGGTCTCGAGGGAGACGTTTGTCTTACTTAATTCACGATTCAAGGA
TC
Found at i:11807 original size:32 final size:32
Alignment explanation
Indices: 11771--11873 Score: 77
Period size: 32 Copynumber: 3.2 Consensus size: 32
11761 TCGAGGGAGA
11771 CGTTCGTCTTACTTAATTTACGATTCAAGGAT
1 CGTTCGTCTTACTTAATTTACGATTCAAGGAT
* * ** * * *
11803 CGTTCAAT-TT--TTTATAAAACGGTCTCGAGGGAGA
1 CGTTC-GTCTTACTTAAT-TTACGAT-TC-AAGGA-T
11837 CGTTCGTCTTACTTAATTTACGATTCAAGGAT
1 CGTTCGTCTTACTTAATTTACGATTCAAGGAT
11869 CGTTC
1 CGTTC
11874 AATTTTTGGT
Statistics
Matches: 49, Mismatches: 14, Indels: 16
0.62 0.18 0.20
Matches are distributed among these distances:
30 4 0.08
31 4 0.08
32 14 0.29
33 10 0.20
34 9 0.18
35 4 0.08
36 4 0.08
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (32 bp):
CGTTCGTCTTACTTAATTTACGATTCAAGGAT
Found at i:17447 original size:12 final size:12
Alignment explanation
Indices: 17430--17461 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
17420 TCCAAATGAG
*
17430 ATTCTCTTAAGA
1 ATTCTCTTAAAA
17442 ATTCTCTTAAAA
1 ATTCTCTTAAAA
17454 ATTCTCTT
1 ATTCTCTT
17462 GTTCAAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.31, C:0.19, G:0.03, T:0.47
Consensus pattern (12 bp):
ATTCTCTTAAAA
Found at i:22233 original size:24 final size:24
Alignment explanation
Indices: 22186--22236 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
22176 CTGTCATAGC
*
22186 CACGGCCACGATCACGATCGCGAT
1 CACGGCCACGATCACGATCACGAT
* * *
22210 CACGTCCACGATCACGGTTACGAT
1 CACGGCCACGATCACGATCACGAT
22234 CAC
1 CAC
22237 CATCATAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.37, G:0.22, T:0.16
Consensus pattern (24 bp):
CACGGCCACGATCACGATCACGAT
Found at i:22482 original size:19 final size:22
Alignment explanation
Indices: 22439--22483 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
22429 TTCACAGGTC
*
22439 AAAACATTGTTGATGATTGGTT
1 AAAACATTGTTGATAATTGGTT
22461 AAAACATTGTT-A-AATT-GTT
1 AAAACATTGTTGATAATTGGTT
22480 AAAA
1 AAAA
22484 GTGCAACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 3 0.14
21 1 0.05
22 11 0.50
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.38
Consensus pattern (22 bp):
AAAACATTGTTGATAATTGGTT
Found at i:22985 original size:133 final size:132
Alignment explanation
Indices: 22792--23050 Score: 389
Period size: 133 Copynumber: 2.0 Consensus size: 132
22782 TACTCGGTAA
* * *
22792 CAGCATGGCAGTGAAAACAAAGATACTGAAAAGCTTATAAACTAATGTAACTACCACCTTG-AGT
1 CAGCATGGAAGTGAAAACAAAGAAACTGAAAAGCTCATAAACTAATGTAACTACCACCTTGCA-T
22856 GAAAGATA-AGACGAAAAGAATATAATAATTGGTTTGACCAGGAGAAAATTCAATGATTCATATA
65 GAAAGATACA-AC-AAAAGAATATAATAATTGGTTTGACCAGGAGAAAATTCAATGATTCATATA
22920 AGTTT
128 AGTTT
** *
22925 CAGCATGGAAGTGAAAATGAAGAAACTGAAAAGCTCATAAGCTAATGTAACTATCC-CCTTGCAT
1 CAGCATGGAAGTGAAAACAAAGAAACTGAAAAGCTCATAAACTAATGTAACTA-CCACCTTGCAT
* *
22989 GAAAGATACAACAAAAGAATATAATAATTGGTTTGATCAGGAGAAAATTCAATGGTTCATAT
65 GAAAGATACAACAAAAGAATATAATAATTGGTTTGACCAGGAGAAAATTCAATGATTCATAT
23051 GTACATTCAA
Statistics
Matches: 115, Mismatches: 8, Indels: 7
0.88 0.06 0.05
Matches are distributed among these distances:
132 48 0.42
133 63 0.55
134 4 0.03
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.25
Consensus pattern (132 bp):
CAGCATGGAAGTGAAAACAAAGAAACTGAAAAGCTCATAAACTAATGTAACTACCACCTTGCATG
AAAGATACAACAAAAGAATATAATAATTGGTTTGACCAGGAGAAAATTCAATGATTCATATAAGT
TT
Done.