Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012501.1 Corchorus olitorius cultivar O-4 contig12534, 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: 28760
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:4978 original size:21 final size:21
Alignment explanation
Indices: 4937--5090 Score: 217
Period size: 21 Copynumber: 7.4 Consensus size: 21
4927 TGCTAGAAGT
4937 TCATTGGAGCAA-GTT-CAAGC
1 TCATTGGAG-AAGGTTCCAAGC
4957 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
4978 TCATTGGACAA-GTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
4998 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
5019 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
5040 TCATTGGAGAAGGTTCCAAGA
1 TCATTGGAGAAGGTTCCAAGC
*
5061 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
5082 TCATTGGAG
1 TCATTGGAG
5091 TTGCCTAAGA
Statistics
Matches: 126, Mismatches: 6, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
20 36 0.29
21 90 0.71
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:9173 original size:19 final size:18
Alignment explanation
Indices: 9140--9175 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
9130 TTGAAATTAT
9140 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
9158 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
9176 TAAATCTTCA
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:10945 original size:22 final size:21
Alignment explanation
Indices: 10920--10966 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
10910 TCCAAACTGA
10920 AATTCTCTTCAATTCAACTCTT
1 AATTCTCTTCAATTC-ACTCTT
* * *
10942 AATTGTGTTGAATTCACTCTT
1 AATTCTCTTCAATTCACTCTT
10963 AATT
1 AATT
10967 TGTAGCAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (21 bp):
AATTCTCTTCAATTCACTCTT
Found at i:17829 original size:29 final size:31
Alignment explanation
Indices: 17777--17856 Score: 101
Period size: 29 Copynumber: 2.6 Consensus size: 31
17767 TTTGTTGCTG
* *
17777 CAAGCAATTAAGGATATAACGTTA-CAAAAT
1 CAAGCAATTAAGGATAAAATGTTATCAAAAT
* **
17807 -AAGCAATTAAGGATAAAATGTTATCGATTT
1 CAAGCAATTAAGGATAAAATGTTATCAAAAT
17837 CAAGCAATTAAGGATAAAAT
1 CAAGCAATTAAGGATAAAAT
17857 TAAAGAGGGT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 21 0.49
30 3 0.07
31 19 0.44
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (31 bp):
CAAGCAATTAAGGATAAAATGTTATCAAAAT
Found at i:18598 original size:28 final size:25
Alignment explanation
Indices: 18562--18616 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 25
18552 CTGAGACTCA
18562 AACTAACTGACTCAACAAAACTGAACT
1 AACTAACTGACTCAA-AAAACTG-ACT
18589 AACTGAACTGACTCAAAAAACTGACT
1 AACT-AACTGACTCAAAAAACTGACT
18615 AA
1 AA
18617 ACCCAACAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 5 0.19
27 11 0.41
28 11 0.41
ACGTcount: A:0.49, C:0.24, G:0.09, T:0.18
Consensus pattern (25 bp):
AACTAACTGACTCAAAAAACTGACT
Found at i:19471 original size:2 final size:2
Alignment explanation
Indices: 19464--19499 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
19454 GCATTGCACA
19464 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19500 ATAGTTTTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19688 original size:32 final size:32
Alignment explanation
Indices: 19637--19701 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
19627 GCCCTCTCCA
19637 TTAGGAGGTAAATATGTCTTGAATTTGGAAAAT
1 TTAGGAGGTAAATATGTCTTGAATTT-GAAAAT
* *
19670 TTAGGTGGTTAAT-TGTCTTGAATTTGAAAAT
1 TTAGGAGGTAAATATGTCTTGAATTTGAAAAT
19701 T
1 T
19702 CAAGAAGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 7 0.23
32 12 0.40
33 11 0.37
ACGTcount: A:0.32, C:0.03, G:0.23, T:0.42
Consensus pattern (32 bp):
TTAGGAGGTAAATATGTCTTGAATTTGAAAAT
Found at i:22196 original size:15 final size:16
Alignment explanation
Indices: 22176--22212 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
22166 TCCCCTAGAA
22176 TATAAATTTAAAT-AT
1 TATAAATTTAAATAAT
*
22191 TATAAATTTAATTAAT
1 TATAAATTTAAATAAT
22207 TATAAA
1 TATAAA
22213 ATATGATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATAAATTTAAATAAT
Found at i:25351 original size:16 final size:15
Alignment explanation
Indices: 25311--25353 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
25301 CAGACCTGAG
25311 ACCCGAATGA-CCGA
1 ACCCGAATGAGCCGA
25325 ACCC-AGATGAGCCGAA
1 ACCCGA-ATGAGCCG-A
25341 ACCCGAATGAGCC
1 ACCCGAATGAGCC
25354 AAGAAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.04
14 8 0.32
15 3 0.12
16 12 0.48
17 1 0.04
ACGTcount: A:0.35, C:0.35, G:0.23, T:0.07
Consensus pattern (15 bp):
ACCCGAATGAGCCGA
Found at i:27451 original size:30 final size:30
Alignment explanation
Indices: 27415--27473 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
27405 TTGATGTCCT
27415 TGATAAGCCCTT-GGCGCATCATTCCCTCCA
1 TGATAAG-CCTTGGGCGCATCATTCCCTCCA
27445 TGATAAGCCTTGGGCGCATCATTCCCTCC
1 TGATAAGCCTTGGGCGCATCATTCCCTCC
27474 CCCTTTAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 4 0.14
30 24 0.86
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.27
Consensus pattern (30 bp):
TGATAAGCCTTGGGCGCATCATTCCCTCCA
Done.