Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018153.1 Corchorus olitorius cultivar O-4 contig18186, 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: 80215
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:3211 original size:21 final size:20
Alignment explanation
Indices: 3187--3226 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3177 TATGGTCTTC
3187 GGCTAATGGCTAATGGCTTAT
1 GGCTAATGGCTAAT-GCTTAT
* *
3208 GGCTTATGGCTCATGCTTA
1 GGCTAATGGCTAATGCTTA
3227 ATTGGGAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (20 bp):
GGCTAATGGCTAATGCTTAT
Found at i:12130 original size:2 final size:2
Alignment explanation
Indices: 12123--12160 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
12113 GATGATCAAC
12123 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12161 GATCCAAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33143 original size:78 final size:78
Alignment explanation
Indices: 33047--33203 Score: 287
Period size: 78 Copynumber: 2.0 Consensus size: 78
33037 TATCTAACTC
* *
33047 TTTTGGCCTTTGGGTCAAAGTATTCCTAACTTTTACCCTTAATTATAAAAAAATTCAAATAATAT
1 TTTTGGCCTTTGGATCAAAATATTCCTAACTTTTACCCTTAATTATAAAAAAATTCAAATAATAT
33112 GTTTTGAAAAGCT
66 GTTTTGAAAAGCT
*
33125 TTTTGGCCTTTTGATCAAAATATTCCTAACTTTTACCCTTAATTATAAAAAAATTCAAATAATAT
1 TTTTGGCCTTTGGATCAAAATATTCCTAACTTTTACCCTTAATTATAAAAAAATTCAAATAATAT
33190 GTTTTGAAAAGCT
66 GTTTTGAAAAGCT
33203 T
1 T
33204 AAGATGAGGG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.41
Consensus pattern (78 bp):
TTTTGGCCTTTGGATCAAAATATTCCTAACTTTTACCCTTAATTATAAAAAAATTCAAATAATAT
GTTTTGAAAAGCT
Found at i:35648 original size:100 final size:100
Alignment explanation
Indices: 35475--35674 Score: 400
Period size: 100 Copynumber: 2.0 Consensus size: 100
35465 CACTATGGAG
35475 TTACGGACAATTTTGAAAGGAGAAAATTCTTAATTTAAGTCAAATCCTAGGAGTGGAAAAACACC
1 TTACGGACAATTTTGAAAGGAGAAAATTCTTAATTTAAGTCAAATCCTAGGAGTGGAAAAACACC
35540 CAGAGCTCTTCTAATCTCTACAACTACCAAGTCCA
66 CAGAGCTCTTCTAATCTCTACAACTACCAAGTCCA
35575 TTACGGACAATTTTGAAAGGAGAAAATTCTTAATTTAAGTCAAATCCTAGGAGTGGAAAAACACC
1 TTACGGACAATTTTGAAAGGAGAAAATTCTTAATTTAAGTCAAATCCTAGGAGTGGAAAAACACC
35640 CAGAGCTCTTCTAATCTCTACAACTACCAAGTCCA
66 CAGAGCTCTTCTAATCTCTACAACTACCAAGTCCA
35675 ATTGCTGCTC
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (100 bp):
TTACGGACAATTTTGAAAGGAGAAAATTCTTAATTTAAGTCAAATCCTAGGAGTGGAAAAACACC
CAGAGCTCTTCTAATCTCTACAACTACCAAGTCCA
Found at i:37441 original size:14 final size:16
Alignment explanation
Indices: 37422--37455 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
37412 TCCATAACAA
37422 AATTAGT-A-CCAATT
1 AATTAGTCATCCAATT
37436 AATTAGTCATCCAATT
1 AATTAGTCATCCAATT
37452 AATT
1 AATT
37456 TTTTCAGGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 1 0.06
16 10 0.56
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (16 bp):
AATTAGTCATCCAATT
Found at i:37767 original size:23 final size:23
Alignment explanation
Indices: 37741--37787 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
37731 TCCCTAAGGA
* *
37741 ATACATGTCATTCTTCTAAA-TCC
1 ATACATG-CAATCTGCTAAACTCC
37764 ATACATGCAATCTGCTAAACTCC
1 ATACATGCAATCTGCTAAACTCC
37787 A
1 A
37788 CTGACAGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.32
Consensus pattern (23 bp):
ATACATGCAATCTGCTAAACTCC
Found at i:49001 original size:22 final size:18
Alignment explanation
Indices: 48939--48988 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 18
48929 AAAATGGTTA
48939 AGTTTGTTTGGGTAAGTAGGTC
1 AGTTTGTTTGGGT-AG-A--TC
48961 AGTTTGTTTGGGTAGATC
1 AGTTTGTTTGGGTAGATC
48979 AGTTTGTTTG
1 AGTTTGTTTG
48989 AGGTTCCAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 12 0.43
20 1 0.04
21 2 0.07
22 13 0.46
ACGTcount: A:0.16, C:0.04, G:0.34, T:0.46
Consensus pattern (18 bp):
AGTTTGTTTGGGTAGATC
Found at i:60711 original size:15 final size:16
Alignment explanation
Indices: 60691--60721 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
60681 TTGAGTTATT
60691 CCATTCA-CAGCATCA
1 CCATTCACCAGCATCA
60706 CCATTCACCAGCATCA
1 CCATTCACCAGCATCA
60722 AAACAGTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.32, C:0.42, G:0.06, T:0.19
Consensus pattern (16 bp):
CCATTCACCAGCATCA
Found at i:68578 original size:21 final size:20
Alignment explanation
Indices: 68515--68578 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
68505 TTGACACTGT
68515 TTAACAACTGTACAGATGAGA
1 TTAAC-ACTGTACAGATGAGA
* *
68536 TT-ACACTGTACAGATTAAA
1 TTAACACTGTACAGATGAGA
*
68555 TTAAGTACTGTACAGATGAGA
1 TTAA-CACTGTACAGATGAGA
68576 TTA
1 TTA
68579 TTAGAGCAGC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 15 0.42
20 3 0.08
21 18 0.50
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (20 bp):
TTAACACTGTACAGATGAGA
Done.