Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015636.1 Corchorus capsularis cultivar CVL-1 contig15657, 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: 10208
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:64 original size:15 final size:14
Alignment explanation
Indices: 29--79 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
19 AGTTCTCCTT
29 AAAGAGAAG-AGAG
1 AAAGAGAAGAAGAG
* *
42 ATCAGAGAAGTAGAG
1 A-AAGAGAAGAAGAG
57 AAATGAGAAAGAAGAG
1 AAA-GAG-AAGAAGAG
73 AAAGAGA
1 AAAGAGA
80 TTCTGGTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
13 1 0.03
14 9 0.29
15 11 0.35
16 10 0.32
ACGTcount: A:0.59, C:0.02, G:0.33, T:0.06
Consensus pattern (14 bp):
AAAGAGAAGAAGAG
Found at i:523 original size:6 final size:6
Alignment explanation
Indices: 512--539 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
502 AATTTTGATC
512 CAGGCT CAGGCT CAGGCT CAGGCT CAGG
1 CAGGCT CAGGCT CAGGCT CAGGCT CAGG
540 ATTAAGCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.32, G:0.36, T:0.14
Consensus pattern (6 bp):
CAGGCT
Found at i:974 original size:6 final size:6
Alignment explanation
Indices: 963--994 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
953 ATTCAGACGG
963 CTCTGC CTCTGC CTCTGC CTCTGC CTCTGC CT
1 CTCTGC CTCTGC CTCTGC CTCTGC CTCTGC CT
995 GCCCTTTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.16, T:0.34
Consensus pattern (6 bp):
CTCTGC
Found at i:1088 original size:2 final size:2
Alignment explanation
Indices: 1081--1111 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1071 TAATTACTAC
1081 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1112 CAAAGTTTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5346 original size:21 final size:22
Alignment explanation
Indices: 5302--5346 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
5292 AACTACTGAA
* * *
5302 TTGCTAAATACCGTCCCCATTT
1 TTGCTAAACACCATCCCCACTT
5324 TTGCTAAACACCAT-CCCACTT
1 TTGCTAAACACCATCCCCACTT
5345 TT
1 TT
5347 TACACTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.24, C:0.33, G:0.07, T:0.36
Consensus pattern (22 bp):
TTGCTAAACACCATCCCCACTT
Found at i:5810 original size:15 final size:16
Alignment explanation
Indices: 5792--5831 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
5782 ATTTCAAAAT
5792 TTAAATTAATAA-TAA
1 TTAAATTAATAATTAA
5807 TTAATATT--TAATTAA
1 TTAA-ATTAATAATTAA
5822 TTAAATTAAT
1 TTAAATTAAT
5832 TAAAAAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
14 6 0.29
15 11 0.52
16 4 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAATTAATAATTAA
Found at i:5840 original size:21 final size:21
Alignment explanation
Indices: 5816--5860 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5806 ATTAATATTT
*
5816 AATTAATTAAATTAATTAAAA
1 AATTAACTAAATTAATTAAAA
**
5837 AATTGCCTAAATTAATTAAAA
1 AATTAACTAAATTAATTAAAA
5858 AAT
1 AAT
5861 GGCCTAAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (21 bp):
AATTAACTAAATTAATTAAAA
Found at i:5865 original size:21 final size:21
Alignment explanation
Indices: 5823--5867 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
5813 TTTAATTAAT
*
5823 TAAATTAATTAAAAAATTGCC
1 TAAATTAATTAAAAAATGGCC
5844 TAAATTAATTAAAAAATGGCC
1 TAAATTAATTAAAAAATGGCC
5865 TAA
1 TAA
5868 GATTGACCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.31
Consensus pattern (21 bp):
TAAATTAATTAAAAAATGGCC
Found at i:6096 original size:33 final size:33
Alignment explanation
Indices: 5999--6099 Score: 132
Period size: 33 Copynumber: 3.1 Consensus size: 33
5989 AAAAATGCAT
*
5999 GTGCCGCCCTAGGAGGACGGCACGCCGTGGC-A
1 GTGCCGCCCTAGGAGGGCGGCACGCCGTGGCTA
* *
6031 TTTGCCGCCCCAGGAGGGCGGCACGCCGTGGCTA
1 -GTGCCGCCCTAGGAGGGCGGCACGCCGTGGCTA
* * *
6065 GTGTCGCCCTAGGAGGGCGGCATGTCGTGGCTA
1 GTGCCGCCCTAGGAGGGCGGCACGCCGTGGCTA
6098 GT
1 GT
6100 TATCAACCCC
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
33 58 0.98
34 1 0.02
ACGTcount: A:0.13, C:0.31, G:0.41, T:0.16
Consensus pattern (33 bp):
GTGCCGCCCTAGGAGGGCGGCACGCCGTGGCTA
Found at i:6769 original size:2 final size:2
Alignment explanation
Indices: 6762--6797 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
6752 ATTGGTTAAG
6762 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6798 CTACATATTA
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:6809 original size:19 final size:19
Alignment explanation
Indices: 6762--6809 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
6752 ATTGGTTAAG
*
6762 ATATATATATATATATATAT
1 ATATATAT-TATATATATAC
6782 ATATATATTATATATACTAC
1 ATATATATTATATATA-TAC
6802 ATAT-TATT
1 ATATATATT
6810 TGAATAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATATATTATATATATAC
Done.