Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012268.1 Corchorus olitorius cultivar O-4 contig12301, 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: 31844
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:634 original size:36 final size:36
Alignment explanation
Indices: 587--656 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
577 GGGATTTTGG
*
587 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATTACAAAAAATGTAATA
623 AGAAATATGATAACCAAAATTACAAAAAATGTAA
1 AGAAATATGATAACCAAAATTACAAAAAATGTAA
657 GGTTATTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.61, C:0.07, G:0.09, T:0.23
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATTACAAAAAATGTAATA
Found at i:3046 original size:98 final size:98
Alignment explanation
Indices: 2930--3114 Score: 327
Period size: 98 Copynumber: 1.9 Consensus size: 98
2920 AAATTGATAA
*
2930 TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATATTTAACTTCGTTCTTTAATAGT
1 TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTGACTAATATTTAACTTCGTTC-TTAATAGT
2995 CCTGTAG-TTTTTTAGTAAATTCTTTCTTCTTCT
65 CCTGTAGTTTTTTTAGTAAATTCTTTCTTCTTCT
*
3028 TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTGACTAATGTTTAACTTCGTTCTTAATAGTC
1 TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTGACTAATATTTAACTTCGTTCTTAATAGTC
*
3093 TTGTAGTTTTTTTAGTAAATTC
66 CTGTAGTTTTTTTAGTAAATTC
3115 AAATAAGAAA
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
97 14 0.17
98 69 0.83
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.48
Consensus pattern (98 bp):
TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTGACTAATATTTAACTTCGTTCTTAATAGTC
CTGTAGTTTTTTTAGTAAATTCTTTCTTCTTCT
Found at i:8923 original size:31 final size:31
Alignment explanation
Indices: 8883--8961 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
8873 ATTTTTAGCC
* *
8883 ACCAATTTGAGCCTAAATCTTTCAAAAGTTG
1 ACCAATTTGAGCCTAAACCTTTCAAAAATTG
*
8914 -CTCAATTTGAGTCTAAACCTTTCAAAAATTG
1 AC-CAATTTGAGCCTAAACCTTTCAAAAATTG
*
8945 ACCAATTTAAGCCTAAA
1 ACCAATTTGAGCCTAAA
8962 AACAAAAACG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 1 0.02
31 39 0.95
32 1 0.02
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (31 bp):
ACCAATTTGAGCCTAAACCTTTCAAAAATTG
Found at i:9466 original size:2 final size:2
Alignment explanation
Indices: 9461--9486 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9451 CTCTCTATAT
9461 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
9487 GAAAATTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:10971 original size:21 final size:18
Alignment explanation
Indices: 10926--10964 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
10916 GATGAAGAAG
*
10926 CAAAGAAAGTTGAAGCAA
1 CAAAGAAAGTAGAAGCAA
* *
10944 CACAGAAAGTAGAAGCTA
1 CAAAGAAAGTAGAAGCAA
10962 CAA
1 CAA
10965 CAAAGAAGAA
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.15, G:0.21, T:0.10
Consensus pattern (18 bp):
CAAAGAAAGTAGAAGCAA
Found at i:18948 original size:12 final size:10
Alignment explanation
Indices: 18921--18951 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
18911 AGTTTAAAGG
18921 TTGAGAGAAT
1 TTGAGAGAAT
18931 TTGAGAGAAT
1 TTGAGAGAAT
18941 TTGAGAGAAT
1 TTGAGAGAAT
18951 T
1 T
18952 GAAAAGTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
TTGAGAGAAT
Found at i:20214 original size:93 final size:93
Alignment explanation
Indices: 20110--20294 Score: 307
Period size: 93 Copynumber: 2.0 Consensus size: 93
20100 TTGTTTAAAT
*
20110 TTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATCAAATCTAATATCCTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATCAAATCTAATATCCTTATAACTA
* *
20175 TTTTATTTTTACCATTTTACTATTTTAC
66 TTTTATTTTTACCATATTACTAATTTAC
* *
20203 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATCAAATCTAATATCCTTATAACTA
* *
20268 TTTTGTTTTTACCGTATTACTAATTTA
66 TTTTATTTTTACCATATTACTAATTTA
20295 ATTAAAAAGC
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 85 1.00
ACGTcount: A:0.32, C:0.14, G:0.03, T:0.51
Consensus pattern (93 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATCAAATCTAATATCCTTATAACTA
TTTTATTTTTACCATATTACTAATTTAC
Found at i:20407 original size:28 final size:29
Alignment explanation
Indices: 20352--20407 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
20342 GAAATTGTTT
* * **
20352 AAATTTTACAGTTTTTTTGTTACAAAATA
1 AAATTTTACAGTTATTCTACTACAAAATA
20381 AAATTTTACAGTTATTCTACTA-AAAAT
1 AAATTTTACAGTTATTCTACTACAAAAT
20408 TATATTTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (29 bp):
AAATTTTACAGTTATTCTACTACAAAATA
Found at i:20878 original size:31 final size:31
Alignment explanation
Indices: 20840--20912 Score: 146
Period size: 31 Copynumber: 2.4 Consensus size: 31
20830 TAATTTTCTT
20840 AGGTCATTCAGATTTCGGCTCATCTAGGTTC
1 AGGTCATTCAGATTTCGGCTCATCTAGGTTC
20871 AGGTCATTCAGATTTCGGCTCATCTAGGTTC
1 AGGTCATTCAGATTTCGGCTCATCTAGGTTC
20902 AGGTCATTCAG
1 AGGTCATTCAG
20913 GTCTGCGGGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (31 bp):
AGGTCATTCAGATTTCGGCTCATCTAGGTTC
Found at i:20914 original size:15 final size:15
Alignment explanation
Indices: 20865--20914 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
20855 CGGCTCATCT
20865 AGGTTCAGGTCATTC
1 AGGTTCAGGTCATTC
*
20880 AGATTTC-GGCTCA-TC
1 AG-GTTCAGG-TCATTC
20895 TAGGTTCAGGTCATTC
1 -AGGTTCAGGTCATTC
20911 AGGT
1 AGGT
20915 CTGCGGGTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
15 16 0.57
16 12 0.43
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (15 bp):
AGGTTCAGGTCATTC
Found at i:28942 original size:21 final size:21
Alignment explanation
Indices: 28918--29014 Score: 79
Period size: 21 Copynumber: 4.5 Consensus size: 21
28908 ACTATAGTCA
* *
28918 AAAATTTATAGGGAGATTAAC
1 AAAATTCATAGGGAGGTTAAC
* *
28939 AAAATCTCATAGAGAGGTTATC
1 AAAAT-TCATAGGGAGGTTAAC
* *
28961 AAAAATCATAGGAAGGTT-AC
1 AAAATTCATAGGGAGGTTAAC
* *
28981 AAAATTTCATAGGAAGGTTTATC
1 AAAA-TTCATAGGGAGG-TTAAC
29004 AAAATTTCATA
1 AAAA-TTCATA
29015 ATTAGTTTAT
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
20 5 0.08
21 27 0.44
22 18 0.29
23 12 0.19
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.29
Consensus pattern (21 bp):
AAAATTCATAGGGAGGTTAAC
Found at i:29075 original size:22 final size:22
Alignment explanation
Indices: 29050--29110 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
29040 CATAGGTAAA
* *
29050 TTATCAAAATTCCATAACG-TGG
1 TTATCAAAATTTCATAA-GATAG
*
29072 TTATCAAAATTTAATAAGATAG
1 TTATCAAAATTTCATAAGATAG
29094 TTATCAAAATTTCATAA
1 TTATCAAAATTTCATAA
29111 AATTATTCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 1 0.03
22 33 0.97
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGATAG
Done.