Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015661.1 Corchorus capsularis cultivar CVL-1 contig15682, 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: 12927
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:489 original size:18 final size:19
Alignment explanation
Indices: 468--510 Score: 79
Period size: 18 Copynumber: 2.3 Consensus size: 19
458 TAATTAATAT
468 AGATAAGGATAAAGAT-AA
1 AGATAAGGATAAAGATAAA
486 AGATAAGGATAAAGATAAA
1 AGATAAGGATAAAGATAAA
505 AGATAA
1 AGATAA
511 AAAAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.63, C:0.00, G:0.21, T:0.16
Consensus pattern (19 bp):
AGATAAGGATAAAGATAAA
Found at i:508 original size:7 final size:6
Alignment explanation
Indices: 468--525 Score: 66
Period size: 6 Copynumber: 9.8 Consensus size: 6
458 TAATTAATAT
* *
468 AGATAA GGATAA AGATAA AGATAA GGATAA AGATAAA AGATAA A-A-AA
1 AGATAA AGATAA AGATAA AGATAA AGATAA AGAT-AA AGATAA AGATAA
*
515 AAATAA AGATA
1 AGATAA AGATA
526 TATATATTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
4 3 0.07
5 2 0.05
6 33 0.75
7 6 0.14
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.16
Consensus pattern (6 bp):
AGATAA
Found at i:2744 original size:19 final size:18
Alignment explanation
Indices: 2720--2781 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
2710 TATATAGTAG
2720 GTGAGTATGGCCTTACTAA
1 GTGAGTATGG-CTTACTAA
* *
2739 GTGAGTATTG--TACTAG
1 GTGAGTATGGCTTACTAA
**
2755 GTGAGTATGGCTTTTGTAA
1 GTGAGTATGGC-TTACTAA
2774 GTGAGTAT
1 GTGAGTAT
2782 CTCACTATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 14 0.41
19 20 0.59
ACGTcount: A:0.24, C:0.08, G:0.31, T:0.37
Consensus pattern (18 bp):
GTGAGTATGGCTTACTAA
Found at i:2810 original size:16 final size:17
Alignment explanation
Indices: 2775--2816 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
2765 CTTTTGTAAG
*
2775 TGAGTATCTCACTATAAA
1 TGAGTATTTCAC-ATAAA
2793 TGAGTATTTCAC-TAAA
1 TGAGTATTTCACATAAA
2809 TGAGTATT
1 TGAGTATT
2817 GTACCGGGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.52
18 11 0.48
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (17 bp):
TGAGTATTTCACATAAA
Found at i:2828 original size:16 final size:16
Alignment explanation
Indices: 2809--2846 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2799 TTTCACTAAA
2809 TGAGTATTGTACCGGG
1 TGAGTATTGTACCGGG
**
2825 TGAGTATTGTATTGGG
1 TGAGTATTGTACCGGG
2841 TGAGTA
1 TGAGTA
2847 AGGTAGGAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.21, C:0.05, G:0.37, T:0.37
Consensus pattern (16 bp):
TGAGTATTGTACCGGG
Found at i:3258 original size:46 final size:46
Alignment explanation
Indices: 3207--3304 Score: 126
Period size: 46 Copynumber: 2.1 Consensus size: 46
3197 ATGGCTTCTT
*
3207 AGGGAGCG-TTCCGCGCAAGAGCTGGGTGAGTCTCCGCACGAGAGTA
1 AGGGAGCGCTT-CGCGCAAGAGCTGGGTGAGTCTCCGCACAAGAGTA
* * * * *
3253 GGGGAGTGCTTCGTGCAAGAGTTGGGTGAGTCTCCGCGCAAGAGTA
1 AGGGAGCGCTTCGCGCAAGAGCTGGGTGAGTCTCCGCACAAGAGTA
3299 AGGGAG
1 AGGGAG
3305 TGCTCCACAC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
46 42 0.95
47 2 0.05
ACGTcount: A:0.21, C:0.19, G:0.42, T:0.17
Consensus pattern (46 bp):
AGGGAGCGCTTCGCGCAAGAGCTGGGTGAGTCTCCGCACAAGAGTA
Found at i:3305 original size:46 final size:46
Alignment explanation
Indices: 3221--3308 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 46
3211 AGCGTTCCGC
* *
3221 GCAAGAGCTGGGTGAGTCTCCGCACGAGAGTAGGGGAGTGCTTCGT
1 GCAAGAGCTGGGTGAGTCTCCGCACAAGAGTAAGGGAGTGCTTCGT
* *
3267 GCAAGAGTTGGGTGAGTCTCCGCGCAAGAGTAAGGGAGTGCT
1 GCAAGAGCTGGGTGAGTCTCCGCACAAGAGTAAGGGAGTGCT
3309 CCACACAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.22, C:0.18, G:0.41, T:0.19
Consensus pattern (46 bp):
GCAAGAGCTGGGTGAGTCTCCGCACAAGAGTAAGGGAGTGCTTCGT
Found at i:3310 original size:23 final size:23
Alignment explanation
Indices: 3216--3310 Score: 88
Period size: 23 Copynumber: 4.1 Consensus size: 23
3206 TAGGGAGCGT
3216 TCCGCGCAAGAGCT-GGGTGAGT-C
1 TCCGCGCAAGAG-TAGGG-GAGTGC
* *
3239 TCCGCACGAGAGTAGGGGAGTGC
1 TCCGCGCAAGAGTAGGGGAGTGC
* * *
3262 TTCGTGCAAGAGTTGGGTGAGT-C
1 TCCGCGCAAGAGTAGGG-GAGTGC
*
3285 TCCGCGCAAGAGTAAGGGAGTGC
1 TCCGCGCAAGAGTAGGGGAGTGC
3308 TCC
1 TCC
3311 ACACAAAAGC
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
22 9 0.16
23 44 0.77
24 4 0.07
ACGTcount: A:0.20, C:0.22, G:0.39, T:0.19
Consensus pattern (23 bp):
TCCGCGCAAGAGTAGGGGAGTGC
Found at i:3395 original size:2 final size:2
Alignment explanation
Indices: 3388--3419 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3378 AAAACAACTC
3388 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3420 GTACAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3931 original size:25 final size:24
Alignment explanation
Indices: 3777--4019 Score: 150
Period size: 25 Copynumber: 9.9 Consensus size: 24
3767 TAGGTTGGGG
* * *
3777 GAGTCTCTCCTAGCGCACAGTAGAT
1 GAGTCTCACCTAGCGCATAGCAG-T
* * *
3802 GAGTCTCACCTAGTGCGTAGCAAGG
1 GAGTCTCACCTAGCGCATAGC-AGT
* * * *
3827 GAATCTCCCCCAGTGCATAGCA-T
1 GAGTCTCACCTAGCGCATAGCAGT
* *
3850 GAGTCTCACCTAGCGCACAGTAGAT
1 GAGTCTCACCTAGCGCATAGCAG-T
*
3875 GAGTCTCACCTAGCGCACAGCAGAT
1 GAGTCTCACCTAGCGCATAGCAG-T
* *
3900 GAGTCTCACCTAGCGCGTAGCAAGG
1 GAGTCTCACCTAGCGCATAGC-AGT
* * * *
3925 GAATCTCCCCCAGTGCATAGCA-T
1 GAGTCTCACCTAGCGCATAGCAGT
* *
3948 GAGTCTCATCTAGCGCATAGTAAAG-
1 GAGTCTCACCTAGCGCATAG--CAGT
* *** *
3973 GAGTCTCCCCTAATACACAGCAGGT
1 GAGTCTCACCTAGCGCATAGCA-GT
*
3998 GAGTCTCACCTAGTGCATAGCA
1 GAGTCTCACCTAGCGCATAGCA
4020 AGGGACTCTC
Statistics
Matches: 165, Mismatches: 44, Indels: 18
0.73 0.19 0.08
Matches are distributed among these distances:
23 32 0.19
24 3 0.02
25 126 0.76
26 4 0.02
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.21
Consensus pattern (24 bp):
GAGTCTCACCTAGCGCATAGCAGT
Found at i:3946 original size:98 final size:98
Alignment explanation
Indices: 3776--4032 Score: 388
Period size: 98 Copynumber: 2.6 Consensus size: 98
3766 ATAGGTTGGG
* *
3776 GGAGTCTCTCCTAGCGCACAGTAGATGAGTCTCACCTAGTGCGTAGCAAGGGAATCTCCCCCAGT
1 GGAGTCTCACCTAGCGCACAGCAGATGAGTCTCACCTAGTGCGTAGCAAGGGAATCTCCCCCAGT
*
3841 GCATAGCATGAGTCTCACCTAGCGCACAGTAGA
66 GCATAGCATGAGTCTCACCTAGCGCACAGTAAA
* *
3874 TGAGTCTCACCTAGCGCACAGCAGATGAGTCTCACCTAGCGCGTAGCAAGGGAATCTCCCCCAGT
1 GGAGTCTCACCTAGCGCACAGCAGATGAGTCTCACCTAGTGCGTAGCAAGGGAATCTCCCCCAGT
* *
3939 GCATAGCATGAGTCTCATCTAGCGCATAGTAAA
66 GCATAGCATGAGTCTCACCTAGCGCACAGTAAA
* *** * * *
3972 GGAGTCTCCCCTAATACACAGCAGGTGAGTCTCACCTAGTGCATAGCAAGGGACTCTCCCC
1 GGAGTCTCACCTAGCGCACAGCAGATGAGTCTCACCTAGTGCGTAGCAAGGGAATCTCCCC
4033 TAAGGGAGTT
Statistics
Matches: 143, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 143 1.00
ACGTcount: A:0.26, C:0.30, G:0.24, T:0.20
Consensus pattern (98 bp):
GGAGTCTCACCTAGCGCACAGCAGATGAGTCTCACCTAGTGCGTAGCAAGGGAATCTCCCCCAGT
GCATAGCATGAGTCTCACCTAGCGCACAGTAAA
Found at i:4120 original size:3 final size:3
Alignment explanation
Indices: 4114--4163 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
4104 TTTAATTATG
4114 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4162 TT
1 TT
4164 TAGAGCAGAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4573 original size:20 final size:20
Alignment explanation
Indices: 4549--4595 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
4539 AAAATAATAA
4549 TATTTATATTTTTC-TCTTT
1 TATTTATATTTTTCATCTTT
* *
4568 TGATTTTTCTTTTTCATCTTT
1 T-ATTTATATTTTTCATCTTT
4589 TATTTAT
1 TATTTAT
4596 GAGTTTAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 16 0.70
21 6 0.26
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.72
Consensus pattern (20 bp):
TATTTATATTTTTCATCTTT
Found at i:7430 original size:16 final size:16
Alignment explanation
Indices: 7409--7446 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
7399 AGTATCTCAC
7409 TGAGTATTGTACTAGG
1 TGAGTATTGTACTAGG
* *
7425 TGAGTATTGTATTGGG
1 TGAGTATTGTACTAGG
7441 TGAGTA
1 TGAGTA
7447 AGGTAGGAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.24, C:0.03, G:0.34, T:0.39
Consensus pattern (16 bp):
TGAGTATTGTACTAGG
Found at i:9470 original size:2 final size:2
Alignment explanation
Indices: 9463--9498 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
9453 AATTTGAGAG
9463 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9499 CATAATAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11197 original size:17 final size:17
Alignment explanation
Indices: 11175--11208 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11165 TCATTTTCTA
11175 ATCAAAACATCAAAAAT
1 ATCAAAACATCAAAAAT
*
11192 ATCAAAATATCAAAAAT
1 ATCAAAACATCAAAAAT
11209 TAATCCTGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.65, C:0.15, G:0.00, T:0.21
Consensus pattern (17 bp):
ATCAAAACATCAAAAAT
Done.