Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014458.1 Corchorus capsularis cultivar CVL-1 contig14479, 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: 84999
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:574 original size:2 final size:2
Alignment explanation
Indices: 562--610 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
552 AATTCAATGA
* * *
562 AT AT TT AT AT AT AT AA AT AT AT AA 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 AT AT
604 AT AT AT A
1 AT AT AT A
611 CTCAAGTGGG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1036 original size:11 final size:11
Alignment explanation
Indices: 993--1030 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
983 CCTATATATA
*
993 AAATAAATTAT
1 AAATTAATTAT
1004 GAAA-TAATTAT
1 -AAATTAATTAT
1015 AAATTAATTAT
1 AAATTAATTAT
1026 AAATT
1 AAATT
1031 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:5699 original size:2 final size:2
Alignment explanation
Indices: 5692--5720 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5682 TACGATCTCC
5692 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 T
5721 TACTGGGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17806 original size:12 final size:12
Alignment explanation
Indices: 17789--17813 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17779 GAAGAATGAG
17789 AAATGAAGTTAT
1 AAATGAAGTTAT
17801 AAATGAAGTTAT
1 AAATGAAGTTAT
17813 A
1 A
17814 GAAAATTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (12 bp):
AAATGAAGTTAT
Found at i:26201 original size:21 final size:21
Alignment explanation
Indices: 26177--26223 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
26167 CTCGTCAAGG
*
26177 AAGGGTTCGAGACGGCGGAGA
1 AAGGGCTCGAGACGGCGGAGA
* *
26198 AAGGGCTGGAGACGGCTGAGA
1 AAGGGCTCGAGACGGCGGAGA
26219 AAGGG
1 AAGGG
26224 ATCATTACAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.49, T:0.09
Consensus pattern (21 bp):
AAGGGCTCGAGACGGCGGAGA
Found at i:48454 original size:1 final size:1
Alignment explanation
Indices: 48448--48476 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
48438 CCTAAAGTTC
48448 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
48477 AAAGTTCTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:49040 original size:22 final size:21
Alignment explanation
Indices: 48992--49040 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
48982 AGTTGGGGTT
* *
48992 TTGGGCCTGAATAGGGCCAAG
1 TTGGGCCTGAATAGGCCCAAA
*
49013 TATGGGCCTGAGTTAGGCCCAAA
1 T-TGGGCCTGA-ATAGGCCCAAA
49036 TTGGG
1 TTGGG
49041 ACCTAAGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 13 0.57
23 9 0.39
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.22
Consensus pattern (21 bp):
TTGGGCCTGAATAGGCCCAAA
Found at i:53927 original size:17 final size:17
Alignment explanation
Indices: 53905--53957 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
53895 CTTTTTCATT
53905 AAAACCCCATAAAATTG
1 AAAACCCCATAAAATTG
53922 AAAACCCC--AAAATTG
1 AAAACCCCATAAAATTG
*
53937 AAATTA-CCCATAAATTTG
1 AAA--ACCCCATAAAATTG
53955 AAA
1 AAA
53958 CCCAAAAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 10 0.32
16 3 0.10
17 9 0.29
18 9 0.29
ACGTcount: A:0.53, C:0.21, G:0.06, T:0.21
Consensus pattern (17 bp):
AAAACCCCATAAAATTG
Found at i:60490 original size:27 final size:27
Alignment explanation
Indices: 60452--60507 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
60442 CTTTCTTCCA
60452 TTTAATGTTTGCTAGAAATTTATCTGC
1 TTTAATGTTTGCTAGAAATTTATCTGC
* *
60479 TTTAATGTTTGCTAGATATTTGTCTGC
1 TTTAATGTTTGCTAGAAATTTATCTGC
60506 TT
1 TT
60508 GGTTTCGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.21, C:0.11, G:0.16, T:0.52
Consensus pattern (27 bp):
TTTAATGTTTGCTAGAAATTTATCTGC
Found at i:67502 original size:7 final size:7
Alignment explanation
Indices: 67490--67535 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
67480 ATACATGCCG
67490 AAAAGAA
1 AAAAGAA
67497 AAAAGAA
1 AAAAGAA
67504 AAAA-AA
1 AAAAGAA
67510 AGAAA-AA
1 A-AAAGAA
67517 AGAAA-AA
1 A-AAAGAA
67524 AAAAGAA
1 AAAAGAA
67531 AAAAG
1 AAAAG
67536 GAAGACATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
6 6 0.16
7 31 0.84
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:67512 original size:17 final size:17
Alignment explanation
Indices: 67490--67535 Score: 92
Period size: 17 Copynumber: 2.7 Consensus size: 17
67480 ATACATGCCG
67490 AAAAGAAAAAAGAAAAA
1 AAAAGAAAAAAGAAAAA
67507 AAAAGAAAAAAGAAAAA
1 AAAAGAAAAAAGAAAAA
67524 AAAAGAAAAAAG
1 AAAAGAAAAAAG
67536 GAAGACATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAAGAAAAA
Found at i:67540 original size:11 final size:10
Alignment explanation
Indices: 67495--67534 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
67485 TGCCGAAAAG
67495 AAAAAAGAAA
1 AAAAAAGAAA
67505 AAAAAAG---
1 AAAAAAGAAA
67512 AAAAAAGAAA
1 AAAAAAGAAA
67522 AAAAAAGAAA
1 AAAAAAGAAA
67532 AAA
1 AAA
67535 GGAAGACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 7 0.26
10 20 0.74
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:77601 original size:16 final size:16
Alignment explanation
Indices: 77576--77606 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
77566 CTAGGAGCCA
77576 AATTTCGATTGCTGCC
1 AATTTCGATTGCTGCC
*
77592 AATTTTGATTGCTGC
1 AATTTCGATTGCTGC
77607 TAGTCTCCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (16 bp):
AATTTCGATTGCTGCC
Done.