Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023353.1 Corchorus olitorius cultivar O-4 contig23386, 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: 47217
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Found at i:531 original size:77 final size:77
Alignment explanation
Indices: 438--591 Score: 308
Period size: 77 Copynumber: 2.0 Consensus size: 77
428 CTTATAAAAA
438 TGCGACGCAAAAGAAAACAAACTTTACTAAAACTTCAAAATTTCATTAATAAAGAGATATGTACA
1 TGCGACGCAAAAGAAAACAAACTTTACTAAAACTTCAAAATTTCATTAATAAAGAGATATGTACA
503 AGTAGAAAAGAG
66 AGTAGAAAAGAG
515 TGCGACGCAAAAGAAAACAAACTTTACTAAAACTTCAAAATTTCATTAATAAAGAGATATGTACA
1 TGCGACGCAAAAGAAAACAAACTTTACTAAAACTTCAAAATTTCATTAATAAAGAGATATGTACA
580 AGTAGAAAAGAG
66 AGTAGAAAAGAG
592 ATAAACTTAT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.51, C:0.13, G:0.14, T:0.22
Consensus pattern (77 bp):
TGCGACGCAAAAGAAAACAAACTTTACTAAAACTTCAAAATTTCATTAATAAAGAGATATGTACA
AGTAGAAAAGAG
Found at i:622 original size:2 final size:2
Alignment explanation
Indices: 617--643 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
607 AAGGAATTTA
617 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 A
644 CACTACCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2193 original size:11 final size:12
Alignment explanation
Indices: 2166--2198 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
2156 AAAATCTTCA
2166 AGTCTTCAAATT
1 AGTCTTCAAATT
2178 AGTCTTCAAA-T
1 AGTCTTCAAATT
2189 AGTCTTCAAA
1 AGTCTTCAAA
2199 CACGAACTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (12 bp):
AGTCTTCAAATT
Found at i:5981 original size:32 final size:32
Alignment explanation
Indices: 5935--6016 Score: 101
Period size: 32 Copynumber: 2.6 Consensus size: 32
5925 CCAAATTTCA
* *
5935 TAATTATCAAATTCCATTTTTCACCTTTTCGT
1 TAATTATCAAATTCCATTTTACACCTTTACGT
* * * * *
5967 TAATTACCATATTCCATATTACTCCTTTACTT
1 TAATTATCAAATTCCATTTTACACCTTTACGT
5999 TAATTATCAAATTCCATT
1 TAATTATCAAATTCCATT
6017 CTATTCATTT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.29, C:0.22, G:0.01, T:0.48
Consensus pattern (32 bp):
TAATTATCAAATTCCATTTTACACCTTTACGT
Found at i:6064 original size:28 final size:28
Alignment explanation
Indices: 6024--6134 Score: 163
Period size: 28 Copynumber: 4.0 Consensus size: 28
6014 ATTCTATTCA
*
6024 TTTTACTTA-CCAAATTTCATTTTTACT
1 TTTTAATTACCCAAATTTCATTTTTACT
6051 TTTTAATTACCCAAATTTCATTTTTACT
1 TTTTAATTACCCAAATTTCATTTTTACT
*
6079 CTTTAATTACCCAAA-TTCATTTTTACT
1 TTTTAATTACCCAAATTTCATTTTTACT
* * *
6106 CTTTAATTACCCAAAATTCATTCTTACT
1 TTTTAATTACCCAAATTTCATTTTTACT
6134 T
1 T
6135 AATATCATTT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
27 35 0.45
28 43 0.55
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (28 bp):
TTTTAATTACCCAAATTTCATTTTTACT
Found at i:6089 original size:55 final size:55
Alignment explanation
Indices: 6025--6133 Score: 166
Period size: 55 Copynumber: 2.0 Consensus size: 55
6015 TTCTATTCAT
* * * *
6025 TTTACTTA-CCAAATTTCATTTTTACTTTTTAATTACCCAAATTTCATTTTTACTC
1 TTTAATTACCCAAA-TTCATTTTTACTCTTTAATTACCCAAAATTCATTCTTACTC
6080 TTTAATTACCCAAATTCATTTTTACTCTTTAATTACCCAAAATTCATTCTTACT
1 TTTAATTACCCAAATTCATTTTTACTCTTTAATTACCCAAAATTCATTCTTACT
6134 TAATATCATT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
55 44 0.90
56 5 0.10
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (55 bp):
TTTAATTACCCAAATTCATTTTTACTCTTTAATTACCCAAAATTCATTCTTACTC
Found at i:6199 original size:67 final size:67
Alignment explanation
Indices: 6089--6443 Score: 631
Period size: 67 Copynumber: 5.3 Consensus size: 67
6079 CTTTAATTAC
* * *
6089 CCAAA-TTCATTTTTACTCTTTAATTACCCAAAATTCATTCTTACTTAATATCATTTAACCTTAG
1 CCAAATTTCATTTTTACTTTTTAATTA-CCAAATTTCATTCTTACTTAATACCATTTAACCTTAG
6153 TTA
65 TTA
*
6156 CCAAATTTCATTTTTTCTTTTTAATTACCAAATTTCATTCTTACTTAATACCATTTAACCTTAGT
1 CCAAATTTCATTTTTACTTTTTAATTACCAAATTTCATTCTTACTTAATACCATTTAACCTTAGT
6221 TA
66 TA
*
6223 CCAAATTTCATTTTTACTTTTTAATTACCAAATTTTATTCTTACTTAATACCATTTAACCTTAGT
1 CCAAATTTCATTTTTACTTTTTAATTACCAAATTTCATTCTTACTTAATACCATTTAACCTTAGT
6288 TA
66 TA
*
6290 TCAAATTTCATTTTTACTTTTTAATTACCAAATTTCATTCTTACTTAATACCATTTAACCTTAGT
1 CCAAATTTCATTTTTACTTTTTAATTACCAAATTTCATTCTTACTTAATACCATTTAACCTTAGT
6355 TA
66 TA
*
6357 CCAAATTTCATTTTTACTTTTTAATTACCAAATTTCATTCTTACTTAATACTATTTAACCTTAGT
1 CCAAATTTCATTTTTACTTTTTAATTACCAAATTTCATTCTTACTTAATACCATTTAACCTTAGT
6422 TA
66 TA
6424 CCAAATTTCATTTTTACTTT
1 CCAAATTTCATTTTTACTTT
6444 ACCCCTTTTT
Statistics
Matches: 277, Mismatches: 10, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
67 258 0.93
68 19 0.07
ACGTcount: A:0.31, C:0.19, G:0.01, T:0.49
Consensus pattern (67 bp):
CCAAATTTCATTTTTACTTTTTAATTACCAAATTTCATTCTTACTTAATACCATTTAACCTTAGT
TA
Found at i:8875 original size:15 final size:16
Alignment explanation
Indices: 8844--8883 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
8834 TTACTTTGCT
8844 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
8860 TTGTTTTCTA-TTTAA
1 TTGTTTTCTAGTTTAA
*
8875 TTGCTTTCT
1 TTGTTTTCT
8884 GTCAACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.15, C:0.10, G:0.10, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:15991 original size:2 final size:2
Alignment explanation
Indices: 15984--16010 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15974 AATACAAGAA
15984 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 A
16011 CACATGATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19222 original size:24 final size:24
Alignment explanation
Indices: 19193--19238 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
19183 TTTTTTGTTT
*
19193 TGAATTTCTGGATTTGTAACTGTC
1 TGAATTTCTGGATTCGTAACTGTC
*
19217 TGAATTTCTGGGTTCGTAACTG
1 TGAATTTCTGGATTCGTAACTG
19239 CATCAACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.20, C:0.13, G:0.24, T:0.43
Consensus pattern (24 bp):
TGAATTTCTGGATTCGTAACTGTC
Found at i:28548 original size:2 final size:2
Alignment explanation
Indices: 28541--28571 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28531 TTTTAGCTAA
28541 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
28572 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:30069 original size:5 final size:5
Alignment explanation
Indices: 30043--30103 Score: 94
Period size: 5 Copynumber: 13.0 Consensus size: 5
30033 GATCCTCCCA
30043 ATAT- ATAT- ATAT- ATAT- ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
30089 ATATC ATATC ATATC
1 ATATC ATATC ATATC
30104 CCCATAACCA
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 16 0.29
5 40 0.71
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.43
Consensus pattern (5 bp):
ATATC
Found at i:31115 original size:12 final size:12
Alignment explanation
Indices: 31080--31121 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
31070 AAGTGATTGT
*
31080 AAGAAAGGACAAA
1 AAGAAA-GAAAAA
31093 AAGAAAG-AAAA
1 AAGAAAGAAAAA
31104 AAGAAAGAAAAA
1 AAGAAAGAAAAA
31116 AAGAAA
1 AAGAAA
31122 TTGTAACCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 10 0.37
12 11 0.41
13 6 0.22
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (12 bp):
AAGAAAGAAAAA
Found at i:36451 original size:13 final size:13
Alignment explanation
Indices: 36433--36462 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
36423 ATACTTTAAT
36433 AAAAGGAAAAGAA
1 AAAAGGAAAAGAA
36446 AAAAGGAAAAGAA
1 AAAAGGAAAAGAA
36459 AAAA
1 AAAA
36463 AATTATTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAGGAAAAGAA
Found at i:38349 original size:2 final size:2
Alignment explanation
Indices: 38344--38368 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38334 AAAAAAAAAG
38344 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
38369 TAGGATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:45649 original size:15 final size:17
Alignment explanation
Indices: 45616--45658 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
45606 TTTAAAGTAT
45616 AATA-ATAATATAAATA
1 AATATATAATATAAATA
45632 AATATATAA-ATAAA-A
1 AATATATAATATAAATA
45647 AATATAATAATA
1 AATAT-ATAATA
45659 ATAATAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 6 0.25
16 13 0.54
17 5 0.21
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AATATATAATATAAATA
Found at i:45659 original size:15 final size:16
Alignment explanation
Indices: 45620--45659 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
45610 AAGTATAATA
45620 ATAAT-ATAAATAAAT
1 ATAATAATAAATAAAT
45635 AT-ATAAATAAA-AAAT
1 ATAAT-AATAAATAAAT
45650 ATAATAATAA
1 ATAATAATAA
45660 TAATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 2 0.09
15 13 0.59
16 7 0.32
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAATAATAAATAAAT
Found at i:45665 original size:12 final size:11
Alignment explanation
Indices: 45613--45669 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 11
45603 TTTTTTAAAG
45613 TATAATAATAA
1 TATAATAATAA
45624 TATAAATAA-ATA
1 TAT-AATAATA-A
*
45636 TATAAATAAAAAA
1 TAT-AAT-AATAA
45649 TATAATAATAA
1 TATAATAATAA
45660 TAATAATAAT
1 T-ATAATAAT
45670 TTCCTATCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
11 9 0.22
12 24 0.60
13 6 0.15
14 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TATAATAATAA
Found at i:47180 original size:2 final size:2
Alignment explanation
Indices: 47175--47214 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
47165 CTGTGAACTA
47175 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
47215 GAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.