Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014362.1 Corchorus capsularis cultivar CVL-1 contig14383, 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: 45115
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:1282 original size:24 final size:24
Alignment explanation
Indices: 1255--1301 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1245 CTAAATTTAT
1255 TTTCGACACAAAATATTTTTTTTG
1 TTTCGACACAAAATATTTTTTTTG
* * *
1279 TTTCGACGCAAATTTTTTTTTTT
1 TTTCGACACAAAATATTTTTTTT
1302 TAGAAAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.13, G:0.09, T:0.55
Consensus pattern (24 bp):
TTTCGACACAAAATATTTTTTTTG
Found at i:6557 original size:14 final size:14
Alignment explanation
Indices: 6538--6564 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6528 CTCTTACTAA
6538 ACTTAATTACCTTT
1 ACTTAATTACCTTT
6552 ACTTAATTACCTT
1 ACTTAATTACCTT
6565 GAATTAAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.22, G:0.00, T:0.48
Consensus pattern (14 bp):
ACTTAATTACCTTT
Found at i:6592 original size:35 final size:34
Alignment explanation
Indices: 6550--6853 Score: 410
Period size: 35 Copynumber: 8.7 Consensus size: 34
6540 TTAATTACCT
* *
6550 TTACTTAATTACCTTGAATTAAGTTACTTATTGAC
1 TTACTTAATTACCCTGAATTAAGTTA-TTACTGAC
* *
6585 TTGCTTAATTACCCTGAATCAAGTTGATTACTGAC
1 TTACTTAATTACCCTGAATTAAGTT-ATTACTGAC
* * *
6620 TCACTTAATCACCCTGAATTAAGTTTATTACTAAC
1 TTACTTAATTACCCTGAATTAAG-TTATTACTGAC
6655 TTACTTAATTACCCTGAATTAAGTTGATTACTGAC
1 TTACTTAATTACCCTGAATTAAGTT-ATTACTGAC
* *
6690 TTACTTAATTACCCTGAATTAAGTTAATTACTAAA
1 TTACTTAATTACCCTGAATTAAGTT-ATTACTGAC
* * *
6725 TTACTTAATTACCCTGAATTAAGTTAATCACTAAA
1 TTACTTAATTACCCTGAATTAAGTT-ATTACTGAC
*
6760 TTACTTAATTACTCTGAATTAAGTTAATTACTGAC
1 TTACTTAATTACCCTGAATTAAGTT-ATTACTGAC
*
6795 TCACTTAATTACCCTGAATTAAGTTTATTACTGAC
1 TTACTTAATTACCCTGAATTAAG-TTATTACTGAC
6830 TTACTTAATTACCCTGAATTAAGT
1 TTACTTAATTACCCTGAATTAAGT
6854 CAATAATGAT
Statistics
Matches: 242, Mismatches: 23, Indels: 9
0.88 0.08 0.03
Matches are distributed among these distances:
34 3 0.01
35 234 0.97
36 5 0.02
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (34 bp):
TTACTTAATTACCCTGAATTAAGTTATTACTGAC
Found at i:16508 original size:158 final size:155
Alignment explanation
Indices: 16260--16622 Score: 355
Period size: 156 Copynumber: 2.3 Consensus size: 155
16250 CTTCTCACCT
* * *
16260 CAAACTGTCCGTAAATGAAAAACTAGCATAAGTTTTTCATTCTTAGTCTAAATGAGCTGAAACTT
1 CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTAAACGAGCTG-AACTT
* * **
16325 TGTCAAGGGACTTACAATATTTCCAT-GAGACTATGGAAAAAAAATCCCAAGTAAAACCGTGCTC
65 TGTCAAGGGACTTACAATATCTCCATAAAG-CTATGG--AAAAAATCCCAAGTAAAACCGAACTC
* * * *
16389 TCCTTG-ATGGTGAACTAGGTTTCTCTCCC
127 T-CTAGCATAGAGAACTAGGTTTCACTCCC
** * *
16418 TGAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAACGAAGCTG-A-TT
1 CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTAAACG-AGCTGAACTT
* *
16480 T-TCCACCAGTAGG-CTTA-AATTATCTCCATAAAGCTATGGAAAAAATTCTAAGTAAAACCGAA
65 TGT-CA--AG--GGACTTACAA-TATCTCCATAAAGCTATGGAAAAAATCCCAAGTAAAACCGAA
* * *
16542 CTCTCTAGCATAGAGAAGTTGGTTTGACTCCC
124 CTCTCTAGCATAGAGAACTAGGTTTCACTCCC
* * *
16574 CAAACTATCCTTAATTGAAAAACTAGCATAAGTTTTTCATACTAAGTCT
1 CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCT
16623 GCTTGAGATG
Statistics
Matches: 169, Mismatches: 26, Indels: 21
0.78 0.12 0.10
Matches are distributed among these distances:
154 1 0.01
155 8 0.05
156 83 0.49
157 7 0.04
158 66 0.39
159 4 0.02
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.31
Consensus pattern (155 bp):
CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTAAACGAGCTGAACTTT
GTCAAGGGACTTACAATATCTCCATAAAGCTATGGAAAAAATCCCAAGTAAAACCGAACTCTCTA
GCATAGAGAACTAGGTTTCACTCCC
Found at i:30004 original size:13 final size:13
Alignment explanation
Indices: 29986--30013 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29976 ATATATTTAC
29986 ATTTGCTAGACAA
1 ATTTGCTAGACAA
29999 ATTTGCTAGACAA
1 ATTTGCTAGACAA
30012 AT
1 AT
30014 CTGCCTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (13 bp):
ATTTGCTAGACAA
Found at i:30306 original size:121 final size:120
Alignment explanation
Indices: 30139--30381 Score: 378
Period size: 121 Copynumber: 2.0 Consensus size: 120
30129 GTTAGCTCCT
* * *
30139 AATATTAGCTCTTAATTAAGTCTATGAAATTGACTACGAGCCCTCAATTGAGCCGATTTTGCAAC
1 AATATGAGCTCTTAATTAAGCCTATGAAATTGACTACGAGCCCTCAATTGAACCGATTTTGCAAC
* * * *
30204 GTTGGGCCATGATTTGAGTTTTTTTAATGATAGGTCTTAAATCGAGCATTTTCGC
66 GTTAGGCCATGATTTGAGGTTTTTGAATGATAGGCCTTAAATCGAGCATTTTCGC
* *
30259 AATATGAGCTCTTAATTTAAGCCTATGAAATTGACTGCGGGCCCTCAATTGAACCGATTTTGCAA
1 AATATGAGCTCTTAA-TTAAGCCTATGAAATTGACTACGAGCCCTCAATTGAACCGATTTTGCAA
* *
30324 TGTTAGGCCATGATTTGAGGTTTTTGAATGATAGGCCTTAAATTGAGCATTTTCGC
65 CGTTAGGCCATGATTTGAGGTTTTTGAATGATAGGCCTTAAATCGAGCATTTTCGC
30380 AA
1 AA
30382 ATATTGAACC
Statistics
Matches: 111, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
120 14 0.13
121 97 0.87
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.35
Consensus pattern (120 bp):
AATATGAGCTCTTAATTAAGCCTATGAAATTGACTACGAGCCCTCAATTGAACCGATTTTGCAAC
GTTAGGCCATGATTTGAGGTTTTTGAATGATAGGCCTTAAATCGAGCATTTTCGC
Found at i:34405 original size:20 final size:20
Alignment explanation
Indices: 34380--34421 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
34370 ATAAACTATG
*
34380 AACTAAAATTGAAATAATTA
1 AACTAAAATTCAAATAATTA
* *
34400 AACTAAATTTCAAGTAATTA
1 AACTAAAATTCAAATAATTA
34420 AA
1 AA
34422 ATAGAAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.31
Consensus pattern (20 bp):
AACTAAAATTCAAATAATTA
Found at i:35482 original size:22 final size:22
Alignment explanation
Indices: 35457--35512 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
35447 TTCTGAGGTT
35457 GCCCGCTCCCGGGCAAGGGGTC
1 GCCCGCTCCCGGGCAAGGGGTC
35479 GCCCGCTCCCGGGCAAGGGGTC
1 GCCCGCTCCCGGGCAAGGGGTC
35501 GCCCGCTCCCGG
1 GCCCGCTCCCGG
35513 ATTGCCTCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.07, C:0.45, G:0.39, T:0.09
Consensus pattern (22 bp):
GCCCGCTCCCGGGCAAGGGGTC
Found at i:39770 original size:6 final size:6
Alignment explanation
Indices: 39752--39781 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
39742 ATGTAGTTGT
39752 CATGAC TCATGAC CATGAC CATGAC CATGA
1 CATGAC -CATGAC CATGAC CATGAC CATGA
39782 TTATGATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (6 bp):
CATGAC
Found at i:42148 original size:11 final size:11
Alignment explanation
Indices: 42134--42171 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
42124 ATTCATAACA
42134 AATTTATAATT
1 AATTTATAATT
42145 AATTTATAATT
1 AATTTATAATT
42156 -ATTTGATAATT
1 AATTT-ATAATT
*
42167 TATTT
1 AATTT
42172 TATATAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:42557 original size:2 final size:2
Alignment explanation
Indices: 42550--42599 Score: 64
Period size: 2 Copynumber: 24.0 Consensus size: 2
42540 ATTTACTCTA
* *
42550 AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AC ACT AT AT AT ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T
42594 AT AT AT
1 AT AT AT
42600 TAATTTTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 39 0.93
3 3 0.07
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44874 original size:11 final size:11
Alignment explanation
Indices: 44858--44900 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
44848 TATATTATAT
44858 CTAATTAATAG
1 CTAATTAATAG
*
44869 CTAATTAATAT
1 CTAATTAATAG
44880 CTAATTAATAG
1 CTAATTAATAG
*
44891 TTAATTAATA
1 CTAATTAATA
44901 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:44879 original size:22 final size:22
Alignment explanation
Indices: 44854--44900 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
44844 CCATTATATT
44854 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
44876 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
44898 ATA
1 ATA
44901 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:44955 original size:2 final size:2
Alignment explanation
Indices: 44948--44975 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44938 TTATTATGGT
44948 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44976 GGATATTGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.