Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009345.1 Corchorus capsularis cultivar CVL-1 contig09366, 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: 66074
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:608 original size:21 final size:21
Alignment explanation
Indices: 582--628 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
572 GGTTGCTTTC
*
582 TTGTGGTGGAAATTGGTGACA
1 TTGTGGTGGAAATTGATGACA
603 TTGTGGTGGAAATTGATGACA
1 TTGTGGTGGAAATTGATGACA
624 TTGTG
1 TTGTG
629 TTAGTAGGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.23, C:0.04, G:0.36, T:0.36
Consensus pattern (21 bp):
TTGTGGTGGAAATTGATGACA
Found at i:1215 original size:2 final size:2
Alignment explanation
Indices: 1208--1232 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1198 ATTTTATTGG
1208 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 T
1233 TAGTTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4039 original size:18 final size:18
Alignment explanation
Indices: 4016--4057 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
4006 AAATAATATT
* * *
4016 TATATATTATATATTTTA
1 TATATATTACAGAATTTA
4034 TATATATTACAGAATTTA
1 TATATATTACAGAATTTA
4052 TATATA
1 TATATA
4058 CATTTAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
TATATATTACAGAATTTA
Found at i:5345 original size:3 final size:3
Alignment explanation
Indices: 5302--5395 Score: 70
Period size: 3 Copynumber: 31.3 Consensus size: 3
5292 CTAAAAAAGT
* *
5302 ATA ATTA ATA TTA ATCA AT- ATA TTA ATA A-A A-A ATA AT- ATA ATA
1 ATA A-TA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
5345 ATA ATA ATA TATT ATA ATA ATA GTA ATA GTA ATA GTA ATA TATA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
5392 ATA A
1 ATA A
5396 AAATTCCTTC
Statistics
Matches: 72, Mismatches: 12, Indels: 14
0.73 0.12 0.14
Matches are distributed among these distances:
2 8 0.11
3 53 0.74
4 11 0.15
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:10067 original size:36 final size:36
Alignment explanation
Indices: 10015--10095 Score: 153
Period size: 36 Copynumber: 2.2 Consensus size: 36
10005 AAGCCAAACT
*
10015 AAATGATCTAGCCTAAAGATCAAATTGCTTAGTTGA
1 AAATCATCTAGCCTAAAGATCAAATTGCTTAGTTGA
10051 AAATCATCTAGCCTAAAGATCAAATTGCTTAGTTGA
1 AAATCATCTAGCCTAAAGATCAAATTGCTTAGTTGA
10087 AAATCATCT
1 AAATCATCT
10096 TCATGCAACT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.31
Consensus pattern (36 bp):
AAATCATCTAGCCTAAAGATCAAATTGCTTAGTTGA
Found at i:12199 original size:6 final size:6
Alignment explanation
Indices: 12188--12216 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
12178 AAGAACCGCC
12188 TGCTTG TGCTTG TGCTTG TGCTTG TGCTT
1 TGCTTG TGCTTG TGCTTG TGCTTG TGCTT
12217 TCATATATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.31, T:0.52
Consensus pattern (6 bp):
TGCTTG
Found at i:20244 original size:21 final size:22
Alignment explanation
Indices: 20190--20244 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
20180 CTAAAAACAC
*
20190 TATTTTCATTTAAATAAATTCAA
1 TATTTT-ATCTAAATAAATTCAA
20213 TATTTTATTATCTAAA-AAATTCAA
1 TA--TT-TTATCTAAATAAATTCAA
20237 TATTTTAT
1 TATTTTAT
20245 AATTATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
21 4 0.14
22 2 0.07
23 2 0.07
24 10 0.36
25 8 0.29
26 2 0.07
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (22 bp):
TATTTTATCTAAATAAATTCAA
Found at i:20555 original size:28 final size:27
Alignment explanation
Indices: 20523--20581 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
20513 TACTTGTATA
20523 ATTTTACT-CAACTAAAAACTCTATTTTT
1 ATTTTACTGCAA--AAAAACTCTATTTTT
* * *
20551 ATTTTTCTGTAAAAAAATTCTATTTTT
1 ATTTTACTGCAAAAAAACTCTATTTTT
20578 ATTT
1 ATTT
20582 AATTAAATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 18 0.67
28 7 0.26
29 2 0.07
ACGTcount: A:0.34, C:0.12, G:0.02, T:0.53
Consensus pattern (27 bp):
ATTTTACTGCAAAAAAACTCTATTTTT
Found at i:20588 original size:25 final size:27
Alignment explanation
Indices: 20536--20588 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
20526 TTACTCAACT
**
20536 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTCTATTTTTATTTTAATGTAA
*
20563 AAAAATTCTATTTTTA-TTTAAT-TAA
1 AAAAACTCTATTTTTATTTTAATGTAA
20588 A
1 A
20589 TCTAATATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 15 0.65
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.51
Consensus pattern (27 bp):
AAAAACTCTATTTTTATTTTAATGTAA
Found at i:20689 original size:26 final size:26
Alignment explanation
Indices: 20660--20709 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
20650 CATATTAGAA
**
20660 TTTTTA-AAATATTCTTTTACAATTT
1 TTTTTAGAAATAAACTTTTACAATTT
20685 TTTTTAGAAATAAACTTTTACAATT
1 TTTTTAGAAATAAACTTTTACAATT
20710 ATATTCTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.54
Consensus pattern (26 bp):
TTTTTAGAAATAAACTTTTACAATTT
Found at i:24369 original size:30 final size:31
Alignment explanation
Indices: 24302--24376 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
24292 ATAACTTGTT
24302 TGTATCCTGAATTGACACAAGACAATAACGG
1 TGTATCCTGAATTGACACAAGACAATAACGG
* ***
24333 TATATCCTGAATTGACACAAG-TGGTAACGG
1 TGTATCCTGAATTGACACAAGACAATAACGG
*
24363 TGTATCCTTAATTG
1 TGTATCCTGAATTG
24377 CATTTTCGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
30 18 0.47
31 20 0.53
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.29
Consensus pattern (31 bp):
TGTATCCTGAATTGACACAAGACAATAACGG
Found at i:29032 original size:23 final size:24
Alignment explanation
Indices: 28999--29044 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
28989 CCTGACCTGG
28999 TAATGTGACTTGCCGAACTTGTGC
1 TAATGTGACTTGCCGAACTTGTGC
* *
29023 TAATG-GACTTGCTGAATTTGTG
1 TAATGTGACTTGCCGAACTTGTG
29045 GCCATAGAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.37
Consensus pattern (24 bp):
TAATGTGACTTGCCGAACTTGTGC
Found at i:42772 original size:135 final size:135
Alignment explanation
Indices: 42526--42821 Score: 441
Period size: 135 Copynumber: 2.2 Consensus size: 135
42516 AAGACTTGGA
* * ** *
42526 GGGG-AAAACCAACAACTGCTTGGTGCCCAGCCCGGTGCTCTGCCTTTTCAACAAGTCAACCATT
1 GGGGCAAAACCAACAACTGCTTGGTGCCCAGCCCAGTCCTCTGCCCCTTCAACAAGTCAACCATC
*
42590 AGGTGAACAACCCACAAGTCATGGCTTAGATTGGTCTCATCGATGAAAAACTTGGGGGGCAAGGA
66 AGGTGAACAACCAACAAGTCATGGCTTAGATTGGTCTCATCGATGAAAAACTTGGGGGGCAAGGA
42655 CTCGG
131 CTCGG
* * *
42660 GGGGCAAAACCAACAACTGCTTGGTGCCCAGCCCAGTCCTCTTCCCCTTCGACAAGTCAACTATC
1 GGGGCAAAACCAACAACTGCTTGGTGCCCAGCCCAGTCCTCTGCCCCTTCAACAAGTCAACCATC
* * * * *
42725 AGGTGAACAATCAACAGGTCATGGCTTAGGTTGGTCTGATCGATGAAAGACTTGGGGGGCAAGGA
66 AGGTGAACAACCAACAAGTCATGGCTTAGATTGGTCTCATCGATGAAAAACTTGGGGGGCAAGGA
42790 CTCGG
131 CTCGG
* *
42795 TGGGCAAAACCAACAACCGCTTGGTGC
1 GGGGCAAAACCAACAACTGCTTGGTGC
42822 TCTGCCTCTG
Statistics
Matches: 145, Mismatches: 16, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
134 4 0.03
135 141 0.97
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.20
Consensus pattern (135 bp):
GGGGCAAAACCAACAACTGCTTGGTGCCCAGCCCAGTCCTCTGCCCCTTCAACAAGTCAACCATC
AGGTGAACAACCAACAAGTCATGGCTTAGATTGGTCTCATCGATGAAAAACTTGGGGGGCAAGGA
CTCGG
Found at i:47599 original size:156 final size:156
Alignment explanation
Indices: 47230--47599 Score: 403
Period size: 156 Copynumber: 2.4 Consensus size: 156
47220 CATCTCAAAG
* * * * *
47230 AGACTTAGTATGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAGTTTGGGGT-ATCAAACCAAC
1 AGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGAGGTGA-GAAACCAAC
* * * * * *
47294 TTCTCTATGCTAGAGAGTTCGGTTTTACTTAGAATTTTTCCCATAGCTTTATGGGGATAATCTAA
65 TTCACCATGCAAGAGAGCTCAGTTTTACTTAGAATTTTTACCATAGCTTTATGGGGATAATCTAA
*** *
47359 GTCTACTGGTGGAATATCAGCTTCGTT
130 GTCTACTGGAAAAATATCAGCTTCATT
* * *
47386 GGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTT-AGGGAGAGAAACCTAA
1 AGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGA-GGTGAGAAACC-AA
* * * **
47450 -TTCACCAT-CAAGGGAAGCTCAGTTTTACTTATAATTTTTACCATAG-TCTTATGTGGATCTTC
64 CTTCACCATGCAAGAG-AGCTCAGTTTTACTTAGAATTTTTACCATAGCT-TTATGGGGATAATC
* *
47512 TAAGT-TCCTTGGAAAAATTTCAGC-TCATT
127 TAAGTCTAC-TGGAAAAATATCAGCTTCATT
47541 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGAGGTGAGAA
1 -AGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGAGGTGAGAA
47600 GCTTAGTTTA
Statistics
Matches: 178, Mismatches: 28, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
155 11 0.06
156 163 0.92
157 4 0.02
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (156 bp):
AGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGAGGTGAGAAACCAACT
TCACCATGCAAGAGAGCTCAGTTTTACTTAGAATTTTTACCATAGCTTTATGGGGATAATCTAAG
TCTACTGGAAAAATATCAGCTTCATT
Found at i:54698 original size:39 final size:39
Alignment explanation
Indices: 54654--54731 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
54644 AACTGCAGCC
54654 TTCTTCAAATATGCATGGAATTGGCTTCTCTATTTAAGA
1 TTCTTCAAATATGCATGGAATTGGCTTCTCTATTTAAGA
*
54693 TTCTTCAAATATGCATGGAATTGGCTTTTCTATTTAAGA
1 TTCTTCAAATATGCATGGAATTGGCTTCTCTATTTAAGA
54732 ATATAGAGGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.42
Consensus pattern (39 bp):
TTCTTCAAATATGCATGGAATTGGCTTCTCTATTTAAGA
Found at i:59404 original size:24 final size:23
Alignment explanation
Indices: 59376--59434 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
59366 ACTAAAGTTA
59376 TTTATATATATTATATATTT-ATAT
1 TTTATATATATT-TA-ATTTGATAT
* *
59400 TTTATATTATATTTAATTTGTTTT
1 TTTATA-TATATTTAATTTGATAT
59424 TTTATATATAT
1 TTTATATATAT
59435 AGTATTATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 9 0.29
24 16 0.52
25 6 0.19
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
TTTATATATATTTAATTTGATAT
Found at i:64936 original size:19 final size:18
Alignment explanation
Indices: 64912--64947 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
64902 TGAAGATTTC
64912 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
64931 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
64948 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.