Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024738.1 Corchorus olitorius cultivar O-4 contig24771, 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: 26713
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Found at i:533 original size:252 final size:255
Alignment explanation
Indices: 86--617 Score: 926
Period size: 252 Copynumber: 2.1 Consensus size: 255
76 TAAAAGTTAG
*
86 ACAGGGATCTCCCGGGTACTTTTACCAAAATAAATTTCAATAAAATAAAATATATTAAAAAAATA
1 ACAGGGACCTCCCGGGTACTTTTACCAAAATAAATTTCAATAAAATAAAATATATTAAAAAAATA
* * *
151 TTTAATTTTTATTCCACGTGTCACCTGTCACGTCAGCAAAAAAGACGGTGTTAGTGCCATGTCAG
66 TTTAATTTTTATTCCACGTGTCACCTGCCACGTCAGCAAAAAAGACGGTATTAGTGCCACGTCAG
** *
216 CATATTTGACGGGTCTGTCACGGCATGCTAACGTAAGGGATCTCGGGTGATAGGTTCTGATAGTA
131 CATATTTGACGGGTCTGTCACGGCACACTAACGTAAGGGACCTCGGGTGATAGGTTCTGATAGTA
*
281 GAGGGACGAATTTGTAG-AAAAAAAAAAGTACAGGGACCAAAATCAACATTTCGTATAGT
196 GAGGAACGAATTTGTAGAAAAAAAAAAAGTACAGGGACCAAAATCAACATTTCGTATAGT
340 ACAGGGACCTCCCGGGTACTTTTACCAAAATAAATTTCAATAAAAT-AAATATATT-AAAAAATA
1 ACAGGGACCTCCCGGGTACTTTTACCAAAATAAATTTCAATAAAATAAAATATATTAAAAAAATA
403 TTTAATTTTTATTCCACGTGTCACCTGCCACGTCAGCAAAAAAGACGGTATTAGTGCCACGTCAG
66 TTTAATTTTTATTCCACGTGTCACCTGCCACGTCAGCAAAAAAGACGGTATTAGTGCCACGTCAG
* *
468 CATATTTGACGGGTCTGTCACGGTACACTAACGTGAGGGACCTCGGGTGATAGGTTCTGATAGTA
131 CATATTTGACGGGTCTGTCACGGCACACTAACGTAAGGGACCTCGGGTGATAGGTTCTGATAGTA
*
533 GAGGAACGAATTTGTAGTAAAAAAAAAAAGTATAGGGACCAAAATCAACATTTCGTATAGT
196 GAGGAACGAATTTGTAG-AAAAAAAAAAAGTACAGGGACCAAAATCAACATTTCGTATAGT
*
594 ACAGGGACCTCCCGGATACTTTTA
1 ACAGGGACCTCCCGGGTACTTTTA
618 TCGCTTGTTT
Statistics
Matches: 264, Mismatches: 12, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
252 146 0.55
253 9 0.03
254 109 0.41
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (255 bp):
ACAGGGACCTCCCGGGTACTTTTACCAAAATAAATTTCAATAAAATAAAATATATTAAAAAAATA
TTTAATTTTTATTCCACGTGTCACCTGCCACGTCAGCAAAAAAGACGGTATTAGTGCCACGTCAG
CATATTTGACGGGTCTGTCACGGCACACTAACGTAAGGGACCTCGGGTGATAGGTTCTGATAGTA
GAGGAACGAATTTGTAGAAAAAAAAAAAGTACAGGGACCAAAATCAACATTTCGTATAGT
Found at i:7412 original size:24 final size:25
Alignment explanation
Indices: 7380--7428 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
7370 GACATCTCTT
*
7380 CCGCCGCAGCAAA-GGAAGAAGAAA
1 CCGCAGCAGCAAAGGGAAGAAGAAA
7404 CCGCAGCAGCAAAGGGAAGAAGAAA
1 CCGCAGCAGCAAAGGGAAGAAGAAA
7429 GAAATGGAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.47, C:0.22, G:0.31, T:0.00
Consensus pattern (25 bp):
CCGCAGCAGCAAAGGGAAGAAGAAA
Found at i:8820 original size:30 final size:30
Alignment explanation
Indices: 8753--8813 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
8743 ACTTTAGATA
8753 CACTGCTAACCTTGACCTCTGTGATGTAAT
1 CACTGCTAACCTTGACCTCTGTGATGTAAT
8783 CACTGCTAACCTTGACCTCTGTGATGTAAT
1 CACTGCTAACCTTGACCTCTGTGATGTAAT
8813 C
1 C
8814 CATGCTAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (30 bp):
CACTGCTAACCTTGACCTCTGTGATGTAAT
Found at i:9309 original size:25 final size:25
Alignment explanation
Indices: 9261--9335 Score: 143
Period size: 25 Copynumber: 3.0 Consensus size: 25
9251 GTCCGGTTTG
9261 CTTTATAATGAAGC-TCTTTTTGGT
1 CTTTATAATGAAGCTTCTTTTTGGT
9285 CTTTATAATGAAGCTTCTTTTTGGT
1 CTTTATAATGAAGCTTCTTTTTGGT
9310 CTTTATAATGAAGCTTCTTTTTGGT
1 CTTTATAATGAAGCTTCTTTTTGGT
9335 C
1 C
9336 ATACATTCCA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
24 14 0.28
25 36 0.72
ACGTcount: A:0.20, C:0.13, G:0.16, T:0.51
Consensus pattern (25 bp):
CTTTATAATGAAGCTTCTTTTTGGT
Found at i:9688 original size:17 final size:17
Alignment explanation
Indices: 9666--9698 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
9656 CCGGTATGCC
9666 TGTTCCATTGAAAGGCT
1 TGTTCCATTGAAAGGCT
9683 TGTTCCATTGAAAGGC
1 TGTTCCATTGAAAGGC
9699 GGTTACATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (17 bp):
TGTTCCATTGAAAGGCT
Found at i:9764 original size:11 final size:11
Alignment explanation
Indices: 9748--9784 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
9738 GGTATCGGAA
9748 GTTTCGAACTT
1 GTTTCGAACTT
9759 GTTTCG-AC-T
1 GTTTCGAACTT
*
9768 ATTTCGAACTT
1 GTTTCGAACTT
9779 GTTTCG
1 GTTTCG
9785 GCATTATCCG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 6 0.27
10 4 0.18
11 12 0.55
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.46
Consensus pattern (11 bp):
GTTTCGAACTT
Found at i:11539 original size:30 final size:30
Alignment explanation
Indices: 11496--11553 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
11486 TTTGACATCC
*
11496 TTGAACTTCATGGTTGGGGTGGCATGTTCA
1 TTGAAATTCATGGTTGGGGTGGCATGTTCA
*
11526 TTGAAATTTATGGTTGGGGTGGCATGTT
1 TTGAAATTCATGGTTGGGGTGGCATGTT
11554 TGGGCAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.17, C:0.09, G:0.34, T:0.40
Consensus pattern (30 bp):
TTGAAATTCATGGTTGGGGTGGCATGTTCA
Found at i:24563 original size:52 final size:53
Alignment explanation
Indices: 24485--24587 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 53
24475 TAGTGAACAA
*
24485 ACATTTTGGGTATTCCTCTATTTTATTATTTTAGTTGGGTCTT-TTTTTTTCT
1 ACATTTTGGGCATTCCTCTATTTTATTATTTTAGTTGGGTCTTCTTTTTTTCT
24537 ACATTTTGGGCATTCCTCTATTTTATTATTTTAGTTGGGTCTTCTTTTTTT
1 ACATTTTGGGCATTCCTCTATTTTATTATTTTAGTTGGGTCTTCTTTTTTT
24588 TTTCATTCTT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 42 0.86
53 7 0.14
ACGTcount: A:0.14, C:0.13, G:0.14, T:0.60
Consensus pattern (53 bp):
ACATTTTGGGCATTCCTCTATTTTATTATTTTAGTTGGGTCTTCTTTTTTTCT
Found at i:24574 original size:29 final size:29
Alignment explanation
Indices: 24490--24575 Score: 71
Period size: 29 Copynumber: 3.2 Consensus size: 29
24480 AACAAACATT
*
24490 TTGGGTATTCCTCTATTTTATTATTTTAG
1 TTGGGCATTCCTCTATTTTATTATTTTAG
**
24519 TTGGGTC-TT--T-T-TTTT-TCTACATT--
1 TTGGG-CATTCCTCTATTTTAT-TATTTTAG
24542 TTGGGCATTCCTCTATTTTATTATTTTAG
1 TTGGGCATTCCTCTATTTTATTATTTTAG
24571 TTGGG
1 TTGGG
24576 TCTTCTTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 20
0.63 0.07 0.30
Matches are distributed among these distances:
22 1 0.02
23 7 0.17
24 1 0.02
25 9 0.21
26 2 0.05
27 9 0.21
28 1 0.02
29 12 0.29
ACGTcount: A:0.14, C:0.12, G:0.16, T:0.58
Consensus pattern (29 bp):
TTGGGCATTCCTCTATTTTATTATTTTAG
Found at i:24598 original size:15 final size:15
Alignment explanation
Indices: 24578--24620 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
24568 TAGTTGGGTC
24578 TTCTTTTTTTTTTCA
1 TTCTTTTTTTTTTCA
*
24593 TTCTTTTTCTTTTCA
1 TTCTTTTTTTTTTCA
24608 TT-TTTCTTTTTTT
1 TTCTTT-TTTTTTT
24621 TTCTAGTTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 3 0.12
15 22 0.88
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (15 bp):
TTCTTTTTTTTTTCA
Found at i:24801 original size:21 final size:21
Alignment explanation
Indices: 24775--24817 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
24765 CCAAGTTTGT
24775 TTTACAAATGCAAAAATTACA
1 TTTACAAATGCAAAAATTACA
24796 TTTACAAATGCAAAAATTACA
1 TTTACAAATGCAAAAATTACA
24817 T
1 T
24818 GCCAGATGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (21 bp):
TTTACAAATGCAAAAATTACA
Done.