Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012121.1 Corchorus olitorius cultivar O-4 contig12154, 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: 33612
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:6630 original size:49 final size:49
Alignment explanation
Indices: 6558--6656 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
6548 TATGCGGGCG
* *
6558 ATAAATTGATAATTTGAGAGATCTATTGCTAAGTCAGGCGGTACAGTTA
1 ATAAATTAATAATTTGAGAGATCTACTGCTAAGTCAGGCGGTACAGTTA
*
6607 ATAAATTAATAATTTGAGAGATCTACTGCTAAGTCAGGTGGTACAGTTA
1 ATAAATTAATAATTTGAGAGATCTACTGCTAAGTCAGGCGGTACAGTTA
6656 A
1 A
6657 CCCTCGAGTC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.32
Consensus pattern (49 bp):
ATAAATTAATAATTTGAGAGATCTACTGCTAAGTCAGGCGGTACAGTTA
Found at i:7112 original size:15 final size:16
Alignment explanation
Indices: 7079--7118 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
7069 TTACTTTGCT
7079 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
7095 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
7110 TTGCTTTCT
1 TTGTTTTCT
7119 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:10926 original size:15 final size:16
Alignment explanation
Indices: 10893--10932 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
10883 TTACTTTGCT
10893 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
10909 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
10924 TTGCTTTCT
1 TTGTTTTCT
10933 TTCAACCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:11282 original size:46 final size:46
Alignment explanation
Indices: 11132--11263 Score: 210
Period size: 46 Copynumber: 2.9 Consensus size: 46
11122 AAAGAGCTTT
* * *
11132 GAGCCGATGGTGTAAAAAAAATTATGCCATCGGGATGGAGAAATTG
1 GAGCCGATGGTGTAAAGAAATTTATACCATCGGGATGGAGAAATTG
*
11178 GAGCCGATGGTGAAAAGAAATTTATACCATCGGGATGGAGAAATTG
1 GAGCCGATGGTGTAAAGAAATTTATACCATCGGGATGGAGAAATTG
* *
11224 GAGCCGATGGTGTAAAGAAATTTATTCCATCGGGAGGGAG
1 GAGCCGATGGTGTAAAGAAATTTATACCATCGGGATGGAG
11264 TAGTGTATAC
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.35, C:0.11, G:0.32, T:0.22
Consensus pattern (46 bp):
GAGCCGATGGTGTAAAGAAATTTATACCATCGGGATGGAGAAATTG
Found at i:11515 original size:24 final size:24
Alignment explanation
Indices: 11483--11535 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
11473 CTAAGAATTT
**
11483 TCTTCACTCTTGCCATCATCACCA
1 TCTTCACTCTCACCATCATCACCA
*
11507 TCTTCACTCTCACCATCATCACCG
1 TCTTCACTCTCACCATCATCACCA
11531 TCTTC
1 TCTTC
11536 CTGGCTCGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.19, C:0.43, G:0.04, T:0.34
Consensus pattern (24 bp):
TCTTCACTCTCACCATCATCACCA
Found at i:17791 original size:50 final size:50
Alignment explanation
Indices: 17658--18048 Score: 584
Period size: 50 Copynumber: 7.7 Consensus size: 50
17648 ATGTTTGAAC
* * * *
17658 TGACTCGTATGGAAATGAGTTCGACTTGTGGAAAAGCCTACGTGGCTTGGATAGT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA--T-G-TT-GATAAT
* * * *
17713 TGACTCGTACGGAAACAAGTTTGACTTGTGGAAAAGCTTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
17763 TGACTCGTATGGAAACGAGCTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* *
17813 TGACTCGTATGGAAACGAGCTTGGCTTGTGGAAAAGCCCATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* * * *
17863 TGACTCGTATGGAAATGAGCTTCGCTTGTGGAAAAGCCCATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
17913 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
17963 TGACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
18013 TGACTCGTATGGAAACGAGTTTGGCTTATGGAAAAG
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG
18049 TCAAAGCATT
Statistics
Matches: 315, Mismatches: 21, Indels: 5
0.92 0.06 0.01
Matches are distributed among these distances:
50 276 0.88
51 2 0.01
52 1 0.00
53 1 0.00
55 35 0.11
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30
Consensus pattern (50 bp):
TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
Found at i:18238 original size:91 final size:91
Alignment explanation
Indices: 18135--18328 Score: 316
Period size: 91 Copynumber: 2.1 Consensus size: 91
18125 ATACCTTTGG
* *
18135 AAAATAACTCTGAATCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAATG
1 AAAATAACTCTGAATCTGATGTTGTAACTGAAAACTTCTAGATCGATGATGAAAAAGGACCAATG
*
18200 TGCGGTCAACTTGAAAAACAACTTGA
66 TGCGGTCAACCTGAAAAACAACTTGA
* * *
18226 AAAATAACTCTGAGTCTGATGTTGTGATTGAAAACTTCTAGATCGATGATGAAAAAGGACCAATG
1 AAAATAACTCTGAATCTGATGTTGTAACTGAAAACTTCTAGATCGATGATGAAAAAGGACCAATG
* *
18291 TGTGGTCAACCTGAAAAATAACTTGA
66 TGCGGTCAACCTGAAAAACAACTTGA
18317 AAAATAACTCTG
1 AAAATAACTCTG
18329 GTTTGATGTT
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 95 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (91 bp):
AAAATAACTCTGAATCTGATGTTGTAACTGAAAACTTCTAGATCGATGATGAAAAAGGACCAATG
TGCGGTCAACCTGAAAAACAACTTGA
Found at i:18808 original size:50 final size:50
Alignment explanation
Indices: 18754--18850 Score: 151
Period size: 50 Copynumber: 1.9 Consensus size: 50
18744 CTTAAATGCC
*
18754 CTTTGAAAAACGAATTTTGATATTG-GACTCACAAGTGGAATGCAATCCTA
1 CTTTGAAAAACGAATTTTGATATTGAG-CTCACAAATGGAATGCAATCCTA
* *
18804 CTTTGAAAAGCGAATTTTGATCTTGAGCTCACAAATGGAATGCAATC
1 CTTTGAAAAACGAATTTTGATATTGAGCTCACAAATGGAATGCAATC
18851 TTATTGTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 42 0.98
51 1 0.02
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (50 bp):
CTTTGAAAAACGAATTTTGATATTGAGCTCACAAATGGAATGCAATCCTA
Found at i:19444 original size:20 final size:19
Alignment explanation
Indices: 19401--19458 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 19
19391 ATCAATTCTC
*
19401 TTTTGATT--TTGATTTTG
1 TTTTGATTAATTGATTTTT
* *
19418 ATTTGATTAATTTATTTCTT
1 TTTTGATTAATTGATTT-TT
*
19438 TTTTGATTGATTGATTTTT
1 TTTTGATTAATTGATTTTT
19457 TT
1 TT
19459 GAATTTCTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
17 7 0.22
19 10 0.31
20 15 0.47
ACGTcount: A:0.17, C:0.02, G:0.12, T:0.69
Consensus pattern (19 bp):
TTTTGATTAATTGATTTTT
Found at i:23616 original size:26 final size:26
Alignment explanation
Indices: 23560--23621 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
23550 AAAAATCATG
* * * **
23560 CCCCCTTTTTATTATTGAATGACCATG
1 CCCCC-TTTTATCATTGAATAACAAAA
23587 CCCCCTTTTATCATTGAATAACAAAA
1 CCCCCTTTTATCATTGAATAACAAAA
*
23613 CCCCTTTTT
1 CCCCCTTTT
23622 TTATTTTCCA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
26 24 0.83
27 5 0.17
ACGTcount: A:0.26, C:0.29, G:0.06, T:0.39
Consensus pattern (26 bp):
CCCCCTTTTATCATTGAATAACAAAA
Found at i:25384 original size:76 final size:76
Alignment explanation
Indices: 25247--25398 Score: 193
Period size: 76 Copynumber: 2.0 Consensus size: 76
25237 ACAAGGACCC
* *
25247 CGACTCCACCTGGGTGCCCACATGGTTGACTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGTGCCCACATGGTTGACTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
25312 GGGCAGTGTCA
66 GGGCAGTGTCA
* * **
25323 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGTGCCCACATGG-TTGACTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
*
25385 GATGGGCTGTGTCA
63 GATGGGCAGTGTCA
25399 TAGCTCATCA
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
75 4 0.06
76 56 0.85
77 6 0.09
ACGTcount: A:0.18, C:0.28, G:0.29, T:0.25
Consensus pattern (76 bp):
CGACTCCACCTGGGTGCCCACATGGTTGACTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:30273 original size:16 final size:15
Alignment explanation
Indices: 30235--30276 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
30225 ATAGAGATTG
30235 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
30250 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
30265 ACTAGAAAACAA
1 AC-AGAAAACAA
30277 AGCAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:31054 original size:11 final size:11
Alignment explanation
Indices: 31038--31063 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
31028 CCTTTGCCTA
31038 AAAACTAGAAG
1 AAAACTAGAAG
31049 AAAACTAGAAG
1 AAAACTAGAAG
31060 AAAA
1 AAAA
31064 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:33580 original size:21 final size:21
Alignment explanation
Indices: 33556--33610 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
33546 GCTTGGAATT
* *
33556 GGTGATGGCACGGGCATGGCC
1 GGTGGTGGCACGGGCATGACC
*
33577 GGTGGTGGCACGGGCTTGACC
1 GGTGGTGGCACGGGCATGACC
33598 GGTGGTGGCACGG
1 GGTGGTGGCACGG
33611 TG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.11, C:0.22, G:0.51, T:0.16
Consensus pattern (21 bp):
GGTGGTGGCACGGGCATGACC
Done.