Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012837.1 Corchorus olitorius cultivar O-4 contig12870, 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: 70280
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1398 original size:17 final size:17
Alignment explanation
Indices: 1378--1410 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1368 TCAACCTAAT
*
1378 TAAAACGTGCACGTGAC
1 TAAAACGTACACGTGAC
1395 TAAAACGTACACGTGA
1 TAAAACGTACACGTGA
1411 ATGAATCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (17 bp):
TAAAACGTACACGTGAC
Found at i:7687 original size:318 final size:318
Alignment explanation
Indices: 7110--7746 Score: 1256
Period size: 318 Copynumber: 2.0 Consensus size: 318
7100 AGTTTAAGAA
*
7110 CTTCAATGGTATATCTTTCATGGACCCCTCTTTATTTGGTTGAACTAATCTGTACATATATTCAT
1 CTTCAATGGTATATCTTTCATGAACCCCTCTTTATTTGGTTGAACTAATCTGTACATATATTCAT
7175 GCCTCTATTGGGATTTTCTGGAAATTTCTAGTTTCTATCTTATCTATATCTTTTGTCTTCTAACC
66 GCCTCTATTGGGATTTTCTGGAAATTTCTAGTTTCTATCTTATCTATATCTTTTGTCTTCTAACC
7240 TTATTCTGGACTTAACTTATAATGTTATGATATTGATTTGATATATTGCCCTGATTAATTCTGAA
131 TTATTCTGGACTTAACTTATAATGTTATGATATTGATTTGATATATTGCCCTGATTAATTCTGAA
7305 TCTAGATGGCATGAATTTAGGGGGAGTTCTATCTTACTATATTAATTCCCAATATTCTGTTAGCT
196 TCTAGATGGCATGAATTTAGGGGGAGTTCTATCTTACTATATTAATTCCCAATATTCTGTTAGCT
*
7370 ATTTTTCTCAATTCAGGGTTAGTTTTTTCATCATCAAAAAAGGGGGAGATTGTTGAAC
261 ATTTTTCTCAATTCAGGGTTAGTTTTGTCATCATCAAAAAAGGGGGAGATTGTTGAAC
7428 CTTCAATGGTATATCTTTCATGAACCCCTCTTTATTTGGTTGAACTAATCTGTACATATATTCAT
1 CTTCAATGGTATATCTTTCATGAACCCCTCTTTATTTGGTTGAACTAATCTGTACATATATTCAT
7493 GCCTCTATTGGGATTTTCTGGAAATTTCTAGTTTCTATCTTATCTATATCTTTTGTCTTCTAACC
66 GCCTCTATTGGGATTTTCTGGAAATTTCTAGTTTCTATCTTATCTATATCTTTTGTCTTCTAACC
7558 TTATTCTGGACTTAACTTATAATGTTATGATATTGATTTGATATATTGCCCTGATTAATTCTGAA
131 TTATTCTGGACTTAACTTATAATGTTATGATATTGATTTGATATATTGCCCTGATTAATTCTGAA
7623 TCTAGATGGCATGAATTTAGGGGGAGTTCTATCTTACTATATTAATTCCCAATATTCTGTTAGCT
196 TCTAGATGGCATGAATTTAGGGGGAGTTCTATCTTACTATATTAATTCCCAATATTCTGTTAGCT
7688 ATTTTTCTCAATTCAGGGTTAGTTTTGTCATCATCAAAAAAGGGGGAGATTGTTGAAC
261 ATTTTTCTCAATTCAGGGTTAGTTTTGTCATCATCAAAAAAGGGGGAGATTGTTGAAC
7746 C
1 C
7747 CTGTTGTTTT
Statistics
Matches: 317, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
318 317 1.00
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43
Consensus pattern (318 bp):
CTTCAATGGTATATCTTTCATGAACCCCTCTTTATTTGGTTGAACTAATCTGTACATATATTCAT
GCCTCTATTGGGATTTTCTGGAAATTTCTAGTTTCTATCTTATCTATATCTTTTGTCTTCTAACC
TTATTCTGGACTTAACTTATAATGTTATGATATTGATTTGATATATTGCCCTGATTAATTCTGAA
TCTAGATGGCATGAATTTAGGGGGAGTTCTATCTTACTATATTAATTCCCAATATTCTGTTAGCT
ATTTTTCTCAATTCAGGGTTAGTTTTGTCATCATCAAAAAAGGGGGAGATTGTTGAAC
Found at i:8566 original size:29 final size:29
Alignment explanation
Indices: 8505--8567 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
8495 TTTCTGATTT
* * * * *
8505 TTGTTTAAGTGCGGGTTGTGCATTTGTGT
1 TTGTTCAAGTGCGGGTTGTACACTTGGGA
*
8534 TTGTTCAAGTGTGGGTTGTACACTTGGGA
1 TTGTTCAAGTGCGGGTTGTACACTTGGGA
8563 TTGTT
1 TTGTT
8568 TTGAGTGTAG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.13, C:0.08, G:0.33, T:0.46
Consensus pattern (29 bp):
TTGTTCAAGTGCGGGTTGTACACTTGGGA
Found at i:14397 original size:14 final size:14
Alignment explanation
Indices: 14378--14406 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
14368 CATTTGCATT
14378 TCATCTTTCATGTG
1 TCATCTTTCATGTG
14392 TCATCTTTCATGTG
1 TCATCTTTCATGTG
14406 T
1 T
14407 TAGATTACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.52
Consensus pattern (14 bp):
TCATCTTTCATGTG
Found at i:20144 original size:21 final size:21
Alignment explanation
Indices: 20118--20171 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
20108 AAGAATTGAT
* *
20118 ACCAAAAAACACACGATTCAC
1 ACCAAAAAACACACAACTCAC
* *
20139 ACCAAAAAAAACACAACTCAT
1 ACCAAAAAACACACAACTCAC
20160 ACCCAAAAAACA
1 A-CCAAAAAACA
20172 GTAGATACCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.59, C:0.31, G:0.02, T:0.07
Consensus pattern (21 bp):
ACCAAAAAACACACAACTCAC
Found at i:28779 original size:17 final size:17
Alignment explanation
Indices: 28752--28784 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28742 CCTGTGACAC
28752 TTCTGGGAGTTATTGAAT
1 TTCTGGGAGTT-TTGAAT
28770 TTCT-GGAGTTTTGAA
1 TTCTGGGAGTTTTGAA
28785 GCTTGGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.21, C:0.06, G:0.27, T:0.45
Consensus pattern (17 bp):
TTCTGGGAGTTTTGAAT
Found at i:45663 original size:15 final size:15
Alignment explanation
Indices: 45643--45672 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
45633 ATTCAATAAC
*
45643 AAAAAGGAAAGAAAA
1 AAAAAGAAAAGAAAA
45658 AAAAAGAAAAGAAAA
1 AAAAAGAAAAGAAAA
45673 GGGCTCTCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAGAAAA
Found at i:51453 original size:23 final size:23
Alignment explanation
Indices: 51427--51472 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
51417 ATGCTTATCT
*
51427 ATGGATGGGAAGAAGAAGGGGGC
1 ATGGATGGAAAGAAGAAGGGGGC
51450 ATGGATGGAAAGAAGAAGGGGGC
1 ATGGATGGAAAGAAGAAGGGGGC
51473 GGTGGCTCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.04, G:0.50, T:0.09
Consensus pattern (23 bp):
ATGGATGGAAAGAAGAAGGGGGC
Found at i:58287 original size:22 final size:21
Alignment explanation
Indices: 58235--58288 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
58225 TGCTTCTTGA
58235 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
58256 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
58275 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
58289 CATGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:64641 original size:65 final size:65
Alignment explanation
Indices: 64570--64700 Score: 253
Period size: 65 Copynumber: 2.0 Consensus size: 65
64560 TCTTGTTCTC
64570 TCTATTCTCTTATCTTTTCCATACTTCAATTCTCTACTCCCTTGCTTTATTTTGTTATCATTTCA
1 TCTATTCTCTTATCTTTTCCATACTTCAATTCTCTACTCCCTTGCTTTATTTTGTTATCATTTCA
*
64635 TCTATTCTCTTATCTTTTCCATACTTCAATTCTCTACTCTCTTGCTTTATTTTGTTATCATTTCA
1 TCTATTCTCTTATCTTTTCCATACTTCAATTCTCTACTCCCTTGCTTTATTTTGTTATCATTTCA
64700 T
1 T
64701 AACACGTTAT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.17, C:0.25, G:0.03, T:0.55
Consensus pattern (65 bp):
TCTATTCTCTTATCTTTTCCATACTTCAATTCTCTACTCCCTTGCTTTATTTTGTTATCATTTCA
Found at i:64885 original size:32 final size:33
Alignment explanation
Indices: 64844--64916 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
64834 ACAAAGTTTA
* *
64844 TTTAACATGCATAATC-CCTTCTTCTACCTTTC
1 TTTATCATGCATAATCTCCTCCTTCTACCTTTC
64876 TTTATCATGCATAATCTCCTCCTTCTACCTTTC
1 TTTATCATGCATAATCTCCTCCTTCTACCTTTC
64909 TTTATCAT
1 TTTATCAT
64917 TAAAAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 15 0.39
33 23 0.61
ACGTcount: A:0.21, C:0.30, G:0.03, T:0.47
Consensus pattern (33 bp):
TTTATCATGCATAATCTCCTCCTTCTACCTTTC
Done.