Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013515.1 Corchorus olitorius cultivar O-4 contig13548, 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: 27389
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Found at i:638 original size:58 final size:57
Alignment explanation
Indices: 542--655 Score: 174
Period size: 58 Copynumber: 2.0 Consensus size: 57
532 ATAGCATCAT
*
542 GCCTCGGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAA
1 GCCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAA
* * * *
599 GCCTTGGTCCGAAAACGTCTTTTTTTATGCATCTAATAAAGAACATGTCACTTGATA
1 GCCTCGGTCCGAAAACGTC-TTTTTTAGGCATCTAATAAAAAACATGTCACTCGATA
656 TTTGATTAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 17 0.33
58 34 0.67
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (57 bp):
GCCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAA
Found at i:7633 original size:2 final size:2
Alignment explanation
Indices: 7626--7658 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
7616 ATATAAAAGC
7626 AG AG AG AG AG AG AG AG AG AG AG AG -G AG -G AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
7659 CAGAAATTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:8697 original size:5 final size:5
Alignment explanation
Indices: 8689--8739 Score: 77
Period size: 5 Copynumber: 10.4 Consensus size: 5
8679 GGGAAGGAAG
* *
8689 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AA-AA AAAAA AATAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
8738 AA
1 AA
8740 ATTAGGGCTG
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
4 4 0.09
5 40 0.91
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (5 bp):
AAGAA
Found at i:9316 original size:15 final size:16
Alignment explanation
Indices: 9290--9319 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
9280 GGTTTTCGCT
9290 TCCTACTTCCTTTCCA
1 TCCTACTTCCTTTCCA
9306 TCCTA-TTCCTTTCC
1 TCCTACTTCCTTTCC
9320 TCCCTATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.10, C:0.43, G:0.00, T:0.47
Consensus pattern (16 bp):
TCCTACTTCCTTTCCA
Found at i:9657 original size:24 final size:24
Alignment explanation
Indices: 9630--9676 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
9620 AAAGGCCAAA
* *
9630 TGGTGGTCGTGAGATTCGGCCACG
1 TGGTGATCGTGAGATTCGACCACG
9654 TGGTGATCGTGAGATTCGACCAC
1 TGGTGATCGTGAGATTCGACCAC
9677 ATGAGAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.21, G:0.36, T:0.26
Consensus pattern (24 bp):
TGGTGATCGTGAGATTCGACCACG
Found at i:26320 original size:19 final size:18
Alignment explanation
Indices: 26287--26322 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
26277 TTGAAATTAT
26287 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
26305 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
26323 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:27136 original size:1 final size:1
Alignment explanation
Indices: 27130--27157 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
27120 CAACAATGGA
27130 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
27158 GAAATACCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:27203 original size:18 final size:18
Alignment explanation
Indices: 27180--27216 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
27170 CTCCTCTATC
*
27180 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
*
27198 ATGAAAACAATTTTTTTT
1 ATGAAAACAATTCTTTTT
27216 A
1 A
27217 ATTACCCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Done.