Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024796.1 Corchorus olitorius cultivar O-4 contig24829, 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: 31952
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:12828 original size:28 final size:27
Alignment explanation
Indices: 12794--12883 Score: 108
Period size: 28 Copynumber: 3.3 Consensus size: 27
12784 GGAATTTTGG
* *
12794 GTCATTTTCAAAATCCAGGGGCATTTTG
1 GTCATTTTC-ACATCCAGGGGCATTTTA
* * *
12822 GTCATTTGCACATTCAGGGGTATTTTA
1 GTCATTTTCACATCCAGGGGCATTTTA
*
12849 GTCATTTTGCACGTCCAGGGGCATTTTA
1 GTCATTTT-CACATCCAGGGGCATTTTA
12877 GTCATTT
1 GTCATTT
12884 CTACTCCATT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
27 21 0.40
28 31 0.60
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (27 bp):
GTCATTTTCACATCCAGGGGCATTTTA
Found at i:12846 original size:27 final size:27
Alignment explanation
Indices: 12806--12883 Score: 111
Period size: 28 Copynumber: 2.9 Consensus size: 27
12796 CATTTTCAAA
*
12806 ATCCAGGGGCATTTTGGTCATTTGCAC
1 ATCCAGGGGCATTTTAGTCATTTGCAC
* *
12833 ATTCAGGGGTATTTTAGTCATTTTGCAC
1 ATCCAGGGGCATTTTAGTCA-TTTGCAC
*
12861 GTCCAGGGGCATTTTAGTCATTT
1 ATCCAGGGGCATTTTAGTCATTT
12884 CTACTCCATT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
27 20 0.45
28 24 0.55
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.38
Consensus pattern (27 bp):
ATCCAGGGGCATTTTAGTCATTTGCAC
Found at i:13100 original size:44 final size:44
Alignment explanation
Indices: 13036--13121 Score: 154
Period size: 44 Copynumber: 2.0 Consensus size: 44
13026 CATTTGCATC
13036 TACATGATCTCAATTAGTAATTGAACCTTGATACTTTGGTCATT
1 TACATGATCTCAATTAGTAATTGAACCTTGATACTTTGGTCATT
* *
13080 TACATGATCTCAATTTGTAATTGAGCCTTGATACTTTGGTCA
1 TACATGATCTCAATTAGTAATTGAACCTTGATACTTTGGTCA
13122 GTAGGTTTAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (44 bp):
TACATGATCTCAATTAGTAATTGAACCTTGATACTTTGGTCATT
Found at i:20278 original size:16 final size:16
Alignment explanation
Indices: 20242--20279 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
20232 GACGCTTCTC
*
20242 CCTTCTTCTTCCTCGA
1 CCTTCTTCTTCCTCAA
*
20258 GCTTCTTCTTCCTCAA
1 CCTTCTTCTTCCTCAA
20274 CCTTCT
1 CCTTCT
20280 CCCTTCACCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.08, C:0.42, G:0.05, T:0.45
Consensus pattern (16 bp):
CCTTCTTCTTCCTCAA
Found at i:23254 original size:28 final size:28
Alignment explanation
Indices: 23213--23278 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
23203 CACTGAATTA
***
23213 AAAATGCCCCGCCAATGTGCCAATGACC
1 AAAATGCCCCGCCAATGTAAAAATGACC
*
23241 GAAATGCCCCGCCAATGTAAAAATGACC
1 AAAATGCCCCGCCAATGTAAAAATGACC
23269 AAAATGCCCC
1 AAAATGCCCC
23279 TAGGTGACCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.36, C:0.33, G:0.17, T:0.14
Consensus pattern (28 bp):
AAAATGCCCCGCCAATGTAAAAATGACC
Found at i:24824 original size:40 final size:40
Alignment explanation
Indices: 24717--25214 Score: 347
Period size: 40 Copynumber: 11.7 Consensus size: 40
24707 GCAGACTTAA
24717 ACAACACCTTCCGGTGGGGAAGGGCAAACTGAG-AATTTAG
1 ACAACACCTTCCGGTGGGGAAGGGCAAACT-AGTAATTTAG
* *
24757 ACAACACCTT-CGGTGGGGAAGGACAAACTAGTGATTTAG
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTAGTAATTTAG
* * *
24796 ACAACACCTTCCGGTGGGGATGGGCAAACTGGTACACTATAGTTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTAGT--A--AT--TTAG
*
24842 ACAACACC-TCCGGGTGGGGAAGGGCAAACTAGGAATTTAG
1 ACAACACCTTCC-GGTGGGGAAGGGCAAACTAGTAATTTAG
*
24882 ACAACACCTTCCGGTGGGGAAGGGCAAACTAGTAAACTAAACTTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTAGT-AA-T----TTAG
* * * * *
24928 ACAACACCTTGCGGTGGGGAAGGGCAATTCGGTAAACTATACTTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAA-AC--T--AGTA-ATTTAG
* *
24974 ACAACACCTTCCGGTGGGG-AGGGCAAATTAGAAATTTAG
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTAGTAATTTAG
* * ** * *
25013 ACAACACCTTCTGGTAGGGAAGGGCAAGTTGGGTAAAGTGGACTTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAACT-AGT-AA-T----TTAG
* * * * * * *
25060 ACAACATCTTCCGATGAGGAAGGGCAAATTGGGAATTTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTAGTAATTTAG
* * *
25100 ACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAATATACTTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAACT-AGT---A-AT--TTAG
* * * *
25147 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAG
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTAGTAATTTAG
*
25187 ACAACACCTACCGGTGGGGAAGGGCAAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAA
25215 TTGGGTAAAG
Statistics
Matches: 372, Mismatches: 49, Indels: 74
0.75 0.10 0.15
Matches are distributed among these distances:
38 2 0.01
39 55 0.15
40 130 0.35
41 8 0.02
42 8 0.02
43 2 0.01
44 5 0.01
45 14 0.04
46 84 0.23
47 59 0.16
49 1 0.00
50 1 0.00
51 3 0.01
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.19
Consensus pattern (40 bp):
ACAACACCTTCCGGTGGGGAAGGGCAAACTAGTAATTTAG
Found at i:24867 original size:46 final size:47
Alignment explanation
Indices: 24796--25301 Score: 336
Period size: 40 Copynumber: 11.6 Consensus size: 47
24786 AGTGATTTAG
* * *
24796 ACAACACCTTCCGGTGGGGATGGGCAAACT-GGTACACTATAGTTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTAGGTAAACTATACTTAA
*
24842 ACAACACC-TCCGGGTGGGGAAGGGCAAACTAGG---A--AT--TTAG
1 ACAACACCTTCC-GGTGGGGAAGGGCAAACTAGGTAAACTATACTTAA
*
24882 ACAACACCTTCCGGTGGGGAAGGGCAAACTA-GTAAACTAAACTTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTAGGTAAACTATACTTAA
* * *
24928 ACAACACCTTGCGGTGGGGAAGGGC-AATTCGGTAAACTATACTTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTAGGTAAACTATACTTAA
* *
24974 ACAACACCTTCCGGTGGGG-AGGGCAAATTA-G--AA--AT--TTAG
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTAGGTAAACTATACTTAA
* * ** * * **
25013 ACAACACCTTCTGGTAGGGAAGGGCAAGTTGGGTAAAGTGGACTTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTAGGTAAACTATACTTAA
* * * * *
25060 ACAACATCTTCCGATGAGGAAGGGCAAA-TTGG--GA--AT--TTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTAGGTAAACTATACTTAA
* * *
25100 ACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAATATACTTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTAGGTAAACTATACTTAA
* * * *
25147 ACAACACCTTCCGATGAGGAAGGGCAAACT-GG--GA--AT--TTAG
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTAGGTAAACTATACTTAA
* * * * **
25187 ACAACACCTACCGGTGGGGAAGGGCAAATTGGGTAAAGTGGACTTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTAGGTAAACTATACTTAA
* * * * *
25234 ACAATACCTTCCGATGAGGAAAGGCAAACTTGG---A--AT-C-TAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTAGGTAAACTATACTTAA
**
25274 ACAACACCTTCATGTGGGGAAGGGCAAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAA
25302 TTGGGTATTT
Statistics
Matches: 365, Mismatches: 61, Indels: 74
0.73 0.12 0.15
Matches are distributed among these distances:
39 21 0.06
40 122 0.33
41 12 0.03
42 5 0.01
43 6 0.02
44 5 0.01
45 14 0.04
46 93 0.25
47 87 0.24
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (47 bp):
ACAACACCTTCCGGTGGGGAAGGGCAAACTAGGTAAACTATACTTAA
Found at i:24928 original size:86 final size:85
Alignment explanation
Indices: 24757--24954 Score: 283
Period size: 86 Copynumber: 2.3 Consensus size: 85
24747 GAGAATTTAG
* *
24757 ACAACACCTTC-GGTGGGGAAGGACAAACTAGTGATTTAGACAACACCTTCCGGTGGGGATGGGC
1 ACAACACC-TCGGGTGGGGAAGGGCAAACTAGTGATTTAGACAACACCTTCCGGTGGGGAAGGGC
* * * *
24821 AAACTGGTACACTATAGTTAA
65 AAACTAGTAAACTAAACTTAA
24842 ACAACACCTCCGGGTGGGGAAGGGCAAACTAG-GAATTTAGACAACACCTTCCGGTGGGGAAGGG
1 ACAACACCT-CGGGTGGGGAAGGGCAAACTAGTG-ATTTAGACAACACCTTCCGGTGGGGAAGGG
24906 CAAACTAGTAAACTAAACTTAA
64 CAAACTAGTAAACTAAACTTAA
*
24928 ACAACACCTTGCGGTGGGGAAGGGCAA
1 ACAACACCTCG-GGTGGGGAAGGGCAA
24955 TTCGGTAAAC
Statistics
Matches: 102, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
84 1 0.01
85 11 0.11
86 90 0.88
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.18
Consensus pattern (85 bp):
ACAACACCTCGGGTGGGGAAGGGCAAACTAGTGATTTAGACAACACCTTCCGGTGGGGAAGGGCA
AACTAGTAAACTAAACTTAA
Found at i:25083 original size:47 final size:44
Alignment explanation
Indices: 24666--25308 Score: 316
Period size: 40 Copynumber: 14.9 Consensus size: 44
24656 GCAGGTAAAC
* ** *
24666 TAAAAAACACCTTCCGGCGAGGAAGGGCAAATTGGGGTAAAGCAGACT
1 TAAACAACACCTTCCGATGAGGAAGGGCAAATT-GGGT-AA--ATACT
* * * *
24714 TAAACAACACCTTCCGGTGGGGAAGGGCAAACTGAG--AAT--T
1 TAAACAACACCTTCCGATGAGGAAGGGCAAATTGGGTAAATACT
* * * * * * *
24754 TAGACAACACCTT-CGGTGGGGAAGGACAAACT-AGT-GAT--T
1 TAAACAACACCTTCCGATGAGGAAGGGCAAATTGGGTAAATACT
* * * * * *
24793 TAGACAACACCTTCCGGTGGGGATGGGCAAACT-GGTACACTATAGT
1 TAAACAACACCTTCCGATGAGGAAGGGCAAATTGGGTA-A--ATACT
* * * *
24839 TAAACAACACC-TCCGGGTGGGGAAGGGCAAACTAGG--AAT--T
1 TAAACAACACCTTCC-GATGAGGAAGGGCAAATTGGGTAAATACT
* * * * *
24879 TAGACAACACCTTCCGGTGGGGAAGGGCAAACT-AGTAAACTAAACT
1 TAAACAACACCTTCCGATGAGGAAGGGCAAATTGGGTAAA-T--ACT
* * * *
24925 TAAACAACACCTTGCGGTGGGGAAGGGC-AATTCGGTAAACTATACT
1 TAAACAACACCTTCCGATGAGGAAGGGCAAATTGGGT-AA--ATACT
* * *
24971 TAAACAACACCTTCCGGTG-GGGAGGGCAAATT-AG-AAAT--T
1 TAAACAACACCTTCCGATGAGGAAGGGCAAATTGGGTAAATACT
* * * *
25010 TAGACAACACCTTCTGGT-AGGGAAGGGCAAGTTGGGTAAAGTGGACT
1 TAAACAACACCTTCCGATGA-GGAAGGGCAAATTGGGTAAA-T--ACT
*
25057 TAAACAACATCTTCCGATGAGGAAGGGCAAATTGGG--AAT--T
1 TAAACAACACCTTCCGATGAGGAAGGGCAAATTGGGTAAATACT
* *
25097 TAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAATATACT
1 TAAACAACACCTTCCGATGAGGAAGGGCAAATTGGGT--AA-ATACT
*
25144 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGG--AAT--T
1 TAAACAACACCTTCCGATGAGGAAGGGCAAATTGGGTAAATACT
* * * *
25184 TAGACAACACCTACCGGTGGGGAAGGGCAAATTGGGTAAAGTGGACT
1 TAAACAACACCTTCCGATGAGGAAGGGCAAATTGGGTAAA-T--ACT
* *
25231 TAAACAATACCTTCCGATGAGGAAAGGCAAACTT-GG--AAT-C-
1 TAAACAACACCTTCCGATGAGGAAGGGCAAA-TTGGGTAAATACT
* *
25271 TAAACAACACCTTCATG-TGGGGAAGGGCAAATTGGGTA
1 TAAACAACACCTTC-CGATGAGGAAGGGCAAATTGGGTA
25309 TTTAGACAAG
Statistics
Matches: 488, Mismatches: 55, Indels: 110
0.75 0.08 0.17
Matches are distributed among these distances:
38 2 0.00
39 54 0.11
40 165 0.34
41 10 0.02
42 11 0.02
43 5 0.01
44 7 0.01
45 20 0.04
46 82 0.17
47 98 0.20
48 33 0.07
49 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.19
Consensus pattern (44 bp):
TAAACAACACCTTCCGATGAGGAAGGGCAAATTGGGTAAATACT
Found at i:25107 original size:87 final size:87
Alignment explanation
Indices: 24924--25308 Score: 515
Period size: 87 Copynumber: 4.4 Consensus size: 87
24914 TAAACTAAAC
* * * * *
24924 TTAAACAACACCTTGCGGTGGGGAAGGGC-AATTCGGTAAACTATACTTAAACAACACCTTCCGG
1 TTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAGTAGACTTAAACAACACCTTCCGA
* * *
24988 TG-GGGAGGGCAAATTAGAAAT
66 TGAGGAAGGGCAAATTGGGAAT
* * * * * *
25009 TTAGACAACACCTTCTGGTAGGGAAGGGCAAGTTGGGTAAAGTGGACTTAAACAACATCTTCCGA
1 TTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAGTAGACTTAAACAACACCTTCCGA
25074 TGAGGAAGGGCAAATTGGGAAT
66 TGAGGAAGGGCAAATTGGGAAT
* *
25096 TTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAATATACTTAAACAACACCTTCCGA
1 TTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAGTAGACTTAAACAACACCTTCCGA
*
25161 TGAGGAAGGGCAAACTGGGAAT
66 TGAGGAAGGGCAAATTGGGAAT
* * * *
25183 TTAGACAACACCTACCGGTGGGGAAGGGCAAATTGGGTAAAGTGGACTTAAACAATACCTTCCGA
1 TTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAGTAGACTTAAACAACACCTTCCGA
*
25248 TGAGGAAAGGCAAACTT-GGAAT
66 TGAGGAAGGGCAAA-TTGGGAAT
* **
25270 CTAAACAACACCTTCATGTGGGGAAGGGCAAATTGGGTA
1 TTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTA
25309 TTTAGACAAG
Statistics
Matches: 261, Mismatches: 36, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
85 25 0.10
86 30 0.11
87 205 0.79
88 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (87 bp):
TTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAGTAGACTTAAACAACACCTTCCGA
TGAGGAAGGGCAAATTGGGAAT
Found at i:25209 original size:174 final size:173
Alignment explanation
Indices: 24924--25308 Score: 576
Period size: 174 Copynumber: 2.2 Consensus size: 173
24914 TAAACTAAAC
* * * *
24924 TTAAACAACACCTTGCGGTGGGGAAGGGC-AATTCGGTAAACTATACTTAAACAACACCTTCCGG
1 TTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAATATACTTAAACAACACCTTCCGA
* * * * *
24988 TGGGGAGGGCAAATTAGAAATTTAGACAACACCTTCTGGTAGGGAAGGGCAAGTTGGGTAAAGTG
66 TGGGAAGGGCAAACTAGAAATTTAGACAACACCTACCGGTAGGGAAGGGCAAATTGGGTAAAGTG
* *
25053 GACTTAAACAACATCTTCCGATGAGGAAGGGCAAA-TTGGGAAT
131 GACTTAAACAACACCTTCCGATGAGGAAAGGCAAACTT-GGAAT
25096 TTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAATATACTTAAACAACACCTTCCGA
1 TTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAATATACTTAAACAACACCTTCCGA
* * *
25161 TGAGGAAGGGCAAACTGGGAATTTAGACAACACCTACCGGTGGGGAAGGGCAAATTGGGTAAAGT
66 TG-GGAAGGGCAAACTAGAAATTTAGACAACACCTACCGGTAGGGAAGGGCAAATTGGGTAAAGT
*
25226 GGACTTAAACAATACCTTCCGATGAGGAAAGGCAAACTTGGAAT
130 GGACTTAAACAACACCTTCCGATGAGGAAAGGCAAACTTGGAAT
* **
25270 CTAAACAACACCTTCATGTGGGGAAGGGCAAATTGGGTA
1 TTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTA
25309 TTTAGACAAG
Statistics
Matches: 192, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
172 28 0.15
173 34 0.18
174 128 0.67
175 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (173 bp):
TTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAATATACTTAAACAACACCTTCCGA
TGGGAAGGGCAAACTAGAAATTTAGACAACACCTACCGGTAGGGAAGGGCAAATTGGGTAAAGTG
GACTTAAACAACACCTTCCGATGAGGAAAGGCAAACTTGGAAT
Found at i:25377 original size:32 final size:32
Alignment explanation
Indices: 25336--25400 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
25326 TAATCTTTTG
25336 GATTTGACTTCTCAATTTCTGACCTACACTCT
1 GATTTGACTTCTCAATTTCTGACCTACACTCT
25368 GATTTGACTTCTCAATTTCTGACCTACACTCT
1 GATTTGACTTCTCAATTTCTGACCTACACTCT
25400 G
1 G
25401 CCAATGACTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.22, C:0.28, G:0.11, T:0.40
Consensus pattern (32 bp):
GATTTGACTTCTCAATTTCTGACCTACACTCT
Done.