Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006330.1 Corchorus capsularis cultivar CVL-1 contig06351, 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: 15654
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Found at i:1263 original size:61 final size:61
Alignment explanation
Indices: 1168--1285 Score: 191
Period size: 61 Copynumber: 1.9 Consensus size: 61
1158 GATTGGGTGC
* ** *
1168 AGTGTGTGCTAGTGTGTTGATTCTTATTGAATTGAGACTGTGACTAAATGTTGCTTAGTAT
1 AGTGTGTGCTAGGGTACTGATCCTTATTGAATTGAGACTGTGACTAAATGTTGCTTAGTAT
*
1229 AGTGTGTGCTAGGGTACTGATCCTTATTGAATTGAGATTGTGACTAAATGTTGCTTA
1 AGTGTGTGCTAGGGTACTGATCCTTATTGAATTGAGACTGTGACTAAATGTTGCTTA
1286 ATGTGAATGC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (61 bp):
AGTGTGTGCTAGGGTACTGATCCTTATTGAATTGAGACTGTGACTAAATGTTGCTTAGTAT
Found at i:2586 original size:13 final size:13
Alignment explanation
Indices: 2568--2624 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
2558 AATACCAAAT
2568 TACTAAATGAAAA
1 TACTAAATGAAAA
*
2581 TACTAATTGAAAA
1 TACTAAATGAAAA
* * *
2594 CACCATAATGCCAAA
1 TACTA-AATG-AAAA
2609 TCACTAAATGAAAA
1 T-ACTAAATGAAAA
2623 TA
1 TA
2625 TGCAAAAACT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
13 16 0.48
14 7 0.21
15 7 0.21
16 3 0.09
ACGTcount: A:0.54, C:0.16, G:0.07, T:0.23
Consensus pattern (13 bp):
TACTAAATGAAAA
Found at i:2753 original size:27 final size:27
Alignment explanation
Indices: 2723--2791 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
2713 AGGTGAACTT
*
2723 AAAAATGAATAAAATGCCCCT-GAGTGC
1 AAAAATGAACAAAATGCCCCTGGA-TGC
*
2750 AAAAATGACCAAAATGCCCCTGGATGC
1 AAAAATGAACAAAATGCCCCTGGATGC
* *
2777 AAAAAAGACCAAAAT
1 AAAAATGAACAAAAT
2792 ACCCTTGGGC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 36 0.95
28 2 0.05
ACGTcount: A:0.49, C:0.20, G:0.16, T:0.14
Consensus pattern (27 bp):
AAAAATGAACAAAATGCCCCTGGATGC
Found at i:9654 original size:18 final size:18
Alignment explanation
Indices: 9627--9661 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9617 GCACGAGCCA
9627 TCCGGCCACAACCGGCCT
1 TCCGGCCACAACCGGCCT
*
9645 TCCGGGCACAACCGGCC
1 TCCGGCCACAACCGGCC
9662 ACTTGATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.49, G:0.26, T:0.09
Consensus pattern (18 bp):
TCCGGCCACAACCGGCCT
Found at i:12188 original size:33 final size:32
Alignment explanation
Indices: 12093--12195 Score: 134
Period size: 33 Copynumber: 3.1 Consensus size: 32
12083 GAAAAGAGAC
* *
12093 TTTTAGATGTTGTTTGCGATGATACTAAACCTAA
1 TTTTAG-TGTTGTTTGCGATGATACTAAATCT-G
* *
12127 TTTTAGTGTTGTTTGCAATGACACTAAATCTG
1 TTTTAGTGTTGTTTGCGATGATACTAAATCTG
*
12159 TTTTAAGTGTTGTTTGTGATGATACTAAATCTG
1 TTTT-AGTGTTGTTTGCGATGATACTAAATCTG
12192 TTTT
1 TTTT
12196 GGATGCTAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
32 4 0.07
33 51 0.84
34 6 0.10
ACGTcount: A:0.25, C:0.10, G:0.18, T:0.47
Consensus pattern (32 bp):
TTTTAGTGTTGTTTGCGATGATACTAAATCTG
Found at i:12255 original size:33 final size:33
Alignment explanation
Indices: 12211--12296 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
12201 CTAATTGTTA
* *
12211 TGAAAACAAATCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAAATCTGTTTTGGTTGATCATAACAT
*
12244 TGCAAATAAATCTGTTTTGGTTGATCATAACAT
1 TGAAAATAAATCTGTTTTGGTTGATCATAACAT
*
12277 TGAAAATAATTCTGTTTTGG
1 TGAAAATAAATCTGTTTTGG
12297 GTGAAAAGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (33 bp):
TGAAAATAAATCTGTTTTGGTTGATCATAACAT
Found at i:15309 original size:20 final size:20
Alignment explanation
Indices: 15273--15310 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
15263 TTCTGGTCGA
* *
15273 AATTTTTTTTTTTTTTTTTG
1 AATTTTTTTTATATTTTTTG
15293 AATTTTTTTTATATTTTT
1 AATTTTTTTTATATTTTT
15311 CGATATAACT
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:0.16, C:0.00, G:0.03, T:0.82
Consensus pattern (20 bp):
AATTTTTTTTATATTTTTTG
Done.