Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021704.1 Corchorus olitorius cultivar O-4 contig21737, 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: 21576
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Found at i:8156 original size:22 final size:21
Alignment explanation
Indices: 8121--8166 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 21
8111 TTTGCTTTTC
8121 TTGTTCTTGTTGGGCCTTG-A
1 TTGTTCTTGTTGGGCCTTGTA
8141 TTGTTACTTGGTTGGGCCTTGTA
1 TTGTT-CTT-GTTGGGCCTTGTA
8164 TTG
1 TTG
8167 AGATTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.22
21 3 0.13
22 11 0.48
23 4 0.17
ACGTcount: A:0.07, C:0.13, G:0.30, T:0.50
Consensus pattern (21 bp):
TTGTTCTTGTTGGGCCTTGTA
Found at i:8826 original size:35 final size:31
Alignment explanation
Indices: 8752--8839 Score: 106
Period size: 35 Copynumber: 2.7 Consensus size: 31
8742 AGTTTTTATG
*
8752 GGGAAAGTTCCCA-CTAGTTTTAAGTTAAATT
1 GGGAAAGTTCCCATC-AGTTTTAAGTTAAATC
8783 GGGAAAGTTCCCATCAGCTTTTAAGTTTTCAAATC
1 GGGAAAGTTCCCATCAG-TTTTAAG--TT-AAATC
8818 GGGAAAGTTCCCATTCAGTTTT
1 GGGAAAGTTCCCA-TCAGTTTT
8840 TCAAAGTTCT
Statistics
Matches: 50, Mismatches: 1, Indels: 8
0.85 0.02 0.14
Matches are distributed among these distances:
31 15 0.30
32 8 0.16
34 2 0.04
35 21 0.42
36 4 0.08
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Consensus pattern (31 bp):
GGGAAAGTTCCCATCAGTTTTAAGTTAAATC
Found at i:13082 original size:21 final size:21
Alignment explanation
Indices: 13058--13133 Score: 109
Period size: 21 Copynumber: 3.6 Consensus size: 21
13048 AGAATTAGTG
*
13058 CGCCGAGATGAAGAGGCGAAA
1 CGCCGAGAAGAAGAGGCGAAA
*
13079 CGCCGAGATGAAGAGGCGAAA
1 CGCCGAGAAGAAGAGGCGAAA
*
13100 TGCCGAGAAGAAGAGGC-AAA
1 CGCCGAGAAGAAGAGGCGAAA
13120 GCGCCGAGAAGAAG
1 -CGCCGAGAAGAAG
13134 CCACTAACGC
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.39, C:0.18, G:0.38, T:0.04
Consensus pattern (21 bp):
CGCCGAGAAGAAGAGGCGAAA
Found at i:13284 original size:21 final size:21
Alignment explanation
Indices: 13260--13299 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
13250 AGCTTGAATT
*
13260 TGACCGGAGCAAACTCAGGGC
1 TGACAGGAGCAAACTCAGGGC
* *
13281 TGACAGGGGCAAGCTCAGG
1 TGACAGGAGCAAACTCAGG
13300 CCTCACTAGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.25, G:0.38, T:0.10
Consensus pattern (21 bp):
TGACAGGAGCAAACTCAGGGC
Found at i:16638 original size:2 final size:2
Alignment explanation
Indices: 16631--16657 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16621 TTCTTCTTTC
16631 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 T
16658 TCTCTCTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21313 original size:37 final size:37
Alignment explanation
Indices: 21188--21573 Score: 636
Period size: 37 Copynumber: 10.5 Consensus size: 37
21178 AACAGGTCAA
21188 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
*
21225 CATTTATCAGAGTTGACTGGAAACAGGTCATCTTTTCA-
1 --TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
* *
21263 TTTATCAGAGTTGACTGGAAACAGGTCATCTCTTCAG
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
*
21300 TTTATCAAAGTTGACTGGAGACAGGTCATCTTTTCA-
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
21336 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
*
21373 TTTATCAAAGTTGACTGGAAACAGGTCATCTCTTCAG
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
* *
21410 TTTATCAAAGTTGACTGGAGACAGGTAATCTTTTCA-
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
21446 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
*
21483 TTTATCAAAGTTGACTGGGAACAGGTCATCTTTTCA-
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
* *
21519 TTTATCGAAGTTGACTGGAAACAGGTCATCTTTTTAG
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
21556 TTTATCAAAGTTGACTGG
1 TTTATCAAAGTTGACTGG
21574 GAA
Statistics
Matches: 326, Mismatches: 17, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
36 137 0.42
37 154 0.47
39 35 0.11
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (37 bp):
TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
Found at i:21337 original size:73 final size:74
Alignment explanation
Indices: 21188--21573 Score: 636
Period size: 73 Copynumber: 5.2 Consensus size: 74
21178 AACAGGTCAA
*
21188 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCATTTATCAGAGTTGACTGGAAACAGGT
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG--TTTATCAAAGTTGACTGGAAACAGGT
21253 CATCTTTTCA-
64 CATCTTTTCAG
* * *
21263 TTTATCAGAGTTGACTGGAAACAGGTCATCTCTTCAGTTTATCAAAGTTGACTGGAGACAGGTCA
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGTTTATCAAAGTTGACTGGAAACAGGTCA
21328 TCTTTTCA-
66 TCTTTTCAG
21336 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGTTTATCAAAGTTGACTGGAAACAGGTCA
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGTTTATCAAAGTTGACTGGAAACAGGTCA
*
21401 TCTCTTCAG
66 TCTTTTCAG
* *
21410 TTTATCAAAGTTGACTGGAGACAGGTAATCTTTTCA-TTTATCAAAGTTGACTGGAAACAGGTCA
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGTTTATCAAAGTTGACTGGAAACAGGTCA
21474 TCTTTTCAG
66 TCTTTTCAG
* *
21483 TTTATCAAAGTTGACTGGGAACAGGTCATCTTTTCA-TTTATCGAAGTTGACTGGAAACAGGTCA
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGTTTATCAAAGTTGACTGGAAACAGGTCA
*
21547 TCTTTTTAG
66 TCTTTTCAG
21556 TTTATCAAAGTTGACTGG
1 TTTATCAAAGTTGACTGG
21574 GAA
Statistics
Matches: 294, Mismatches: 16, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
73 225 0.77
74 34 0.12
75 35 0.12
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (74 bp):
TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGTTTATCAAAGTTGACTGGAAACAGGTCA
TCTTTTCAG
Found at i:21410 original size:110 final size:110
Alignment explanation
Indices: 21188--21573 Score: 641
Period size: 110 Copynumber: 3.5 Consensus size: 110
21178 AACAGGTCAA
*
21188 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCATTTATCAGAGTTGACTGGAAACAGGT
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTT---CATTTATCAAAGTTGACTGGAAACAGGT
*
21253 CATCTTTTCA-TTTATCAGAGTTGACTGGAAACAGGTCATCTCTTCAG
63 CATCTTTTCAGTTTATCAAAGTTGACTGGAAACAGGTCATCTCTTCAG
*
21300 TTTATCAAAGTTGACTGGAGACAGGTCATCTTTTCATTTATCAAAGTTGACTGGAAACAGGTCAT
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCATTTATCAAAGTTGACTGGAAACAGGTCAT
21365 CTTTTCAGTTTATCAAAGTTGACTGGAAACAGGTCATCTCTTCAG
66 CTTTTCAGTTTATCAAAGTTGACTGGAAACAGGTCATCTCTTCAG
* *
21410 TTTATCAAAGTTGACTGGAGACAGGTAATCTTTTCATTTATCAAAGTTGACTGGAAACAGGTCAT
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCATTTATCAAAGTTGACTGGAAACAGGTCAT
* *
21475 CTTTTCAGTTTATCAAAGTTGACTGGGAACAGGTCATCTTTTCA-
66 CTTTTCAGTTTATCAAAGTTGACTGGAAACAGGTCATCTCTTCAG
* *
21519 TTTATCGAAGTTGACTGGAAACAGGTCATCTTTTTAGTTTATCAAAGTTGACTGG
1 TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCA-TTTATCAAAGTTGACTGG
21574 GAA
Statistics
Matches: 262, Mismatches: 10, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
109 69 0.26
110 160 0.61
112 33 0.13
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (110 bp):
TTTATCAAAGTTGACTGGAAACAGGTCATCTTTTCATTTATCAAAGTTGACTGGAAACAGGTCAT
CTTTTCAGTTTATCAAAGTTGACTGGAAACAGGTCATCTCTTCAG
Done.