Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024205.1 Corchorus olitorius cultivar O-4 contig24238, 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: 22391
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:9026 original size:2 final size:2
Alignment explanation
Indices: 9019--9068 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
9009 GGTAAACAAC
9019 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
9061 TG TG TG TG
1 TG TG TG TG
9069 AGCATTTTCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:18028 original size:47 final size:47
Alignment explanation
Indices: 17957--18062 Score: 194
Period size: 47 Copynumber: 2.2 Consensus size: 47
17947 ATTTTCTACT
17957 TCTTGGATCAATGTGTTTGATAAAGAACTCATTAAAAATGTTGTTTTTG
1 TCTT-GAT-AATGTGTTTGATAAAGAACTCATTAAAAATGTTGTTTTTG
18006 TCTTGATAATGTGTTTGATAAAGAACTCATTAAAAATGTTGTTTTTG
1 TCTTGATAATGTGTTTGATAAAGAACTCATTAAAAATGTTGTTTTTG
18053 TCTTGATAAT
1 TCTTGATAAT
18063 ATATACATCT
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
47 50 0.88
48 3 0.05
49 4 0.07
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (47 bp):
TCTTGATAATGTGTTTGATAAAGAACTCATTAAAAATGTTGTTTTTG
Found at i:18675 original size:12 final size:12
Alignment explanation
Indices: 18658--18711 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
18648 AAAAAAAAAA
18658 AAACAAACAAAC
1 AAACAAACAAAC
18670 AAACAAACAAAC
1 AAACAAACAAAC
18682 AAAC-AA-AAAC
1 AAACAAACAAAC
* *
18692 AAAAAAAAAAAC
1 AAACAAACAAAC
*
18704 AAAAAAAC
1 AAACAAAC
18712 GGGGAAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
10 7 0.18
11 4 0.11
12 27 0.71
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (12 bp):
AAACAAACAAAC
Found at i:18711 original size:8 final size:8
Alignment explanation
Indices: 18648--18711 Score: 67
Period size: 8 Copynumber: 7.9 Consensus size: 8
18638 GCAAGCAAGG
18648 AAAAAA-A
1 AAAAAACA
18655 AAAAAACA
1 AAAAAACA
*
18663 AACAAACA
1 AAAAAACA
*
18671 AACAAACA
1 AAAAAACA
*
18679 AACAAACAA
1 AAAAAAC-A
*
18688 AAACAAAAA
1 AAA-AAACA
18697 AAAAAACA
1 AAAAAACA
18705 AAAAAAC
1 AAAAAAC
18712 GGGGAAAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
7 6 0.12
8 34 0.68
9 7 0.14
10 3 0.06
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAACA
Found at i:20957 original size:29 final size:31
Alignment explanation
Indices: 20925--20991 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
20915 ATGCAATTTG
20925 GGATATAACGTTAC-AAAA-CAAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
**
20954 GGATATAACGTTACGAAAAGTGAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
20985 GGATATA
1 GGATATA
20992 GTCCGTTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 14 0.41
30 4 0.12
31 16 0.47
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.22
Consensus pattern (31 bp):
GGATATAACGTTACGAAAAGCAAGCAATTAA
Found at i:21158 original size:31 final size:31
Alignment explanation
Indices: 21123--21201 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
21113 CTAACTGATT
*
21123 ATATCCTTAATTGCTTGAAATCGAAAACGTC
1 ATATCCTTAATTGCTTGAAATAGAAAACGTC
*
21154 ATATCCTTAATTGCTTGAAATAGAAAACGTT
1 ATATCCTTAATTGCTTGAAATAGAAAACGTC
21185 ATATCCTTAATTGCTTG
1 ATATCCTTAATTGCTTG
21202 TTTTGTAACG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (31 bp):
ATATCCTTAATTGCTTGAAATAGAAAACGTC
Found at i:21227 original size:60 final size:62
Alignment explanation
Indices: 21121--21257 Score: 161
Period size: 60 Copynumber: 2.2 Consensus size: 62
21111 CCCTAACTGA
*
21121 TTATATCCTTAATTGCTTGAAATCGAAAACGTCATATCCTTAATTGCTTGAAATAGAAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACGTCATATCCTTAATTGCTTGAAAGAGAAAACG
** * * * *** *
21183 TTATATCCTTAATTGCTTG-TTTTG-TAACGTTATATCCTTAATTGCTTGTGGGAGCAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACGTCATATCCTTAATTGCTTGAAAGAGAAAACG
*
21243 TTATATCCTAAATTG
1 TTATATCCTTAATTG
21258 ATTATTTGGC
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 43 0.67
61 2 0.03
62 19 0.30
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (62 bp):
TTATATCCTTAATTGCTTGAAATCGAAAACGTCATATCCTTAATTGCTTGAAAGAGAAAACG
Found at i:21246 original size:31 final size:29
Alignment explanation
Indices: 21121--21257 Score: 130
Period size: 31 Copynumber: 4.5 Consensus size: 29
21111 CCCTAACTGA
* *
21121 TTATATCCTTAATTGCTTGAAATCGAAAACG
1 TTATATCCTTAATTGCTTG-TATAG-AAACG
* *
21152 TCATATCCTTAATTGCTTGAAATAGAAAACG
1 TTATATCCTTAATTGCTTG-TATAG-AAACG
* * *
21183 TTATATCCTTAATTGCTTGTTTTGTAACG
1 TTATATCCTTAATTGCTTGTATAGAAACG
**
21212 TTATATCCTTAATTGCTTGTGGGAGCAAACG
1 TTATATCCTTAATTGCTTGT-ATAG-AAACG
*
21243 TTATATCCTAAATTG
1 TTATATCCTTAATTG
21258 ATTATTTGGC
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
29 24 0.26
30 3 0.03
31 65 0.71
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (29 bp):
TTATATCCTTAATTGCTTGTATAGAAACG
Found at i:22342 original size:31 final size:31
Alignment explanation
Indices: 22243--22382 Score: 133
Period size: 31 Copynumber: 4.6 Consensus size: 31
22233 ATATGATAAG
* ***
22243 CAAGCAATTTAGGATATAACGTTTTCTG-CCG
1 CAAGCAATTAAGGATATAACGTTTTC-GATTT
* * ***
22274 CAAGCAATTAAGGATATAAC-ATTAC-AAAA
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
*
22303 CAAGCAATTAAGGATATAACGTTTTTGATTT
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
* * *
22334 TAAGCAATTAAGGATATGATGTTTTCGATTT
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
22365 CAAGCAATTAAGGATATA
1 CAAGCAATTAAGGATATA
22383 GACATATAG
Statistics
Matches: 88, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
29 20 0.23
30 5 0.06
31 63 0.72
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.32
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACGTTTTCGATTT
Done.