Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021528.1 Corchorus olitorius cultivar O-4 contig21561, 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: 38236
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:12546 original size:25 final size:25
Alignment explanation
Indices: 12512--12600 Score: 63
Period size: 25 Copynumber: 3.5 Consensus size: 25
12502 TTGGATCGGA
12512 TGGTTAGATCGGAAAATATTTGAAC
1 TGGTTAGATCGGAAAATATTTGAAC
* * *** * *
12537 TGGTTGGATCAGATGGTTAGATTGGA-
1 TGGTTAGATCGGA-AAATA-TTTGAAC
* *
12563 TGGTTAGACCGAAAAATATTTGAAC
1 TGGTTAGATCGGAAAATATTTGAAC
*
12588 TGGTTGGATCGGA
1 TGGTTAGATCGGA
12601 GTTGAACTCA
Statistics
Matches: 42, Mismatches: 19, Indels: 6
0.63 0.28 0.09
Matches are distributed among these distances:
24 4 0.10
25 23 0.55
26 11 0.26
27 4 0.10
ACGTcount: A:0.30, C:0.08, G:0.30, T:0.31
Consensus pattern (25 bp):
TGGTTAGATCGGAAAATATTTGAAC
Found at i:16278 original size:23 final size:23
Alignment explanation
Indices: 16239--16282 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
16229 CTAAAAAATA
16239 AAAAAAATCAAAAATTTATTTTT
1 AAAAAAATCAAAAATTTATTTTT
*
16262 AAAAATAT-AAAATATTTATTT
1 AAAAAAATCAAAA-ATTTATTT
16283 AAAATAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
AAAAAAATCAAAAATTTATTTTT
Found at i:18285 original size:17 final size:18
Alignment explanation
Indices: 18258--18291 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
18248 ATGCTTCCTT
*
18258 TCAACTCTTCAGTTTTGA
1 TCAACTCTTCAGGTTTGA
18276 TCAA-TCTTCAGGTTTG
1 TCAACTCTTCAGGTTTG
18292 CTAAAAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.44
Consensus pattern (18 bp):
TCAACTCTTCAGGTTTGA
Found at i:26724 original size:7 final size:7
Alignment explanation
Indices: 26712--26736 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
26702 GTAGTATTAA
26712 ATATATG
1 ATATATG
26719 ATATATG
1 ATATATG
26726 ATATATG
1 ATATATG
26733 ATAT
1 ATAT
26737 GTTAATTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (7 bp):
ATATATG
Found at i:26968 original size:60 final size:60
Alignment explanation
Indices: 26848--27010 Score: 195
Period size: 60 Copynumber: 2.8 Consensus size: 60
26838 CAAATAGATT
* * * **
26848 CTTATTTGGCTAAATTAAATGATCGGA--TCTATTTGAGCATTTTCGATAACGTTAGGCC
1 CTTATTTGGCTAAATTAAAAGATCGGACCTTTATTTGAGCATTTTCGATAACATTAAACC
* * * *
26906 CTTATTTGACCAAATTAAAAGATCGGACCTTTATTTGAGTATTTTCGATAATATTAAACC
1 CTTATTTGGCTAAATTAAAAGATCGGACCTTTATTTGAGCATTTTCGATAACATTAAACC
* ** *
26966 CTTATTTGGTTAAATTAAAAGATCAAACCTTTATTTGAACATTTT
1 CTTATTTGGCTAAATTAAAAGATCGGACCTTTATTTGAGCATTTT
27011 GGTAAATGTT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
58 24 0.28
60 63 0.72
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (60 bp):
CTTATTTGGCTAAATTAAAAGATCGGACCTTTATTTGAGCATTTTCGATAACATTAAACC
Found at i:27028 original size:60 final size:60
Alignment explanation
Indices: 26877--27043 Score: 183
Period size: 60 Copynumber: 2.8 Consensus size: 60
26867 TGATCGGATC
* * **
26877 TATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCGGACCTT
1 TATTTGAACATTTTCGATAATGTTAGGCCCTTATTTGACCAAATTAAAAGATCAAACCTT
** * ** ***
26937 TATTTGAGTATTTTCGATAATATTAAACCCTTATTTGGTTAAATTAAAAGATCAAACCTT
1 TATTTGAACATTTTCGATAATGTTAGGCCCTTATTTGACCAAATTAAAAGATCAAACCTT
* *
26997 TATTTGAACATTTT-GGTAAATGTTAGGCCCTTATTTGAGCAATATTA
1 TATTTGAACATTTTCGAT-AATGTTAGGCCCTTATTTGACCAA-ATTA
27044 TCCATACTTG
Statistics
Matches: 86, Mismatches: 19, Indels: 3
0.80 0.18 0.03
Matches are distributed among these distances:
59 2 0.02
60 80 0.93
61 4 0.05
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (60 bp):
TATTTGAACATTTTCGATAATGTTAGGCCCTTATTTGACCAAATTAAAAGATCAAACCTT
Found at i:31701 original size:20 final size:20
Alignment explanation
Indices: 31678--31715 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31668 TTAAGGATGT
*
31678 TTTTTCTTCCTTCTTTTTTC
1 TTTTTCTACCTTCTTTTTTC
*
31698 TTTTTCTACCTTGTTTTT
1 TTTTTCTACCTTCTTTTT
31716 CTATATATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.74
Consensus pattern (20 bp):
TTTTTCTACCTTCTTTTTTC
Found at i:34270 original size:16 final size:18
Alignment explanation
Indices: 34236--34272 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
34226 ATTTTCCTTT
34236 TTTATTTCGTTTATACAC
1 TTTATTTCGTTTATACAC
34254 TTTATTTC-TTT-TACAC
1 TTTATTTCGTTTATACAC
34270 TTT
1 TTT
34273 CTTTTGTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
17 3 0.16
18 8 0.42
ACGTcount: A:0.19, C:0.16, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTATTTCGTTTATACAC
Found at i:34915 original size:43 final size:44
Alignment explanation
Indices: 34853--34935 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 44
34843 AATGTCTCTC
* *
34853 TATGATCAAATATCCAATGAAAAATTACATATACAAACCATTTT
1 TATGATCAAATATCCAATGAAAAATCACAAATACAAACCATTTT
* * *
34897 TATGCTCAAA-ATCTAATGAGAAATCACAAATACAAACCA
1 TATGATCAAATATCCAATGAAAAATCACAAATACAAACCA
34936 CATCCACTGC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
43 25 0.74
44 9 0.26
ACGTcount: A:0.49, C:0.18, G:0.06, T:0.27
Consensus pattern (44 bp):
TATGATCAAATATCCAATGAAAAATCACAAATACAAACCATTTT
Done.