Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009591.1 Corchorus capsularis cultivar CVL-1 contig09612, 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: 48576
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:726 original size:18 final size:18
Alignment explanation
Indices: 684--728 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
674 GGAGGAAGAA
* *
684 GAAGAAGAAGACGATGAC
1 GAAGAAGAAGACCATAAC
* *
702 GATGAAGAAGACCATAAT
1 GAAGAAGAAGACCATAAC
720 GAAGAAGAA
1 GAAGAAGAA
729 CCCAACATTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.53, C:0.09, G:0.29, T:0.09
Consensus pattern (18 bp):
GAAGAAGAAGACCATAAC
Found at i:9609 original size:30 final size:30
Alignment explanation
Indices: 9573--9630 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
9563 AGAAACAGGC
9573 TTTGAACGACCGGCTTCAAATACCTTGAAG
1 TTTGAACGACCGGCTTCAAATACCTTGAAG
*
9603 TTTGAACGATCGGCTTCAAATACCTTGA
1 TTTGAACGACCGGCTTCAAATACCTTGA
9631 GAGCAAGCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (30 bp):
TTTGAACGACCGGCTTCAAATACCTTGAAG
Found at i:9820 original size:30 final size:30
Alignment explanation
Indices: 9784--9856 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
9774 CTTGCCAATA
*
9784 GGGCTTATTTGACTTTTTTTAAGAGTTCAG
1 GGGCTTATTTGACTTTTTTTAAAAGTTCAG
*
9814 GGGCTTATTTGGCTTTTTTTAAAAGTTCAG
1 GGGCTTATTTGACTTTTTTTAAAAGTTCAG
9844 GGGCTTATTTGAC
1 GGGCTTATTTGAC
9857 GGTTCGGTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.19, C:0.11, G:0.25, T:0.45
Consensus pattern (30 bp):
GGGCTTATTTGACTTTTTTTAAAAGTTCAG
Found at i:14175 original size:1 final size:1
Alignment explanation
Indices: 14169--14198 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
14159 TGAACAATGC
14169 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
14199 AACATTTGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:19477 original size:29 final size:30
Alignment explanation
Indices: 19435--19496 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
19425 TTTTGCAAAG
* * *
19435 AAGTATATTATTTT-TTTTTGAGAAAAAAA
1 AAGTATATTATTTTACTTTTCAAAAAAAAA
19464 AAGTATATTATTTTACTTTTCAAAAAAAAA
1 AAGTATATTATTTTACTTTTCAAAAAAAAA
19494 AAG
1 AAG
19497 CCTATCCATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 14 0.48
30 15 0.52
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.40
Consensus pattern (30 bp):
AAGTATATTATTTTACTTTTCAAAAAAAAA
Found at i:26363 original size:2 final size:2
Alignment explanation
Indices: 26351--26397 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
26341 TTACTGCCGT
* *
26351 TA TA GA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26393 TA TA T
1 TA TA T
26398 CATCATTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:29255 original size:31 final size:31
Alignment explanation
Indices: 29220--29281 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
29210 AAAGATTCGA
29220 ATCCAAAATCTTTTTTAAGAATAATCTAAGT
1 ATCCAAAATCTTTTTTAAGAATAATCTAAGT
29251 ATCCAAAATCTTTTTTAAGAATAATCTAAGT
1 ATCCAAAATCTTTTTTAAGAATAATCTAAGT
29282 CCAATACATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (31 bp):
ATCCAAAATCTTTTTTAAGAATAATCTAAGT
Found at i:35161 original size:3 final size:3
Alignment explanation
Indices: 35153--35184 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
35143 AATTGAAGCT
*
35153 GAA GAA GAA GGA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
35185 GGACGGTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:38429 original size:21 final size:21
Alignment explanation
Indices: 38386--38429 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
38376 AAGTTGGGGG
* *
38386 TTGCTAAATACCGTCCTAGTT
1 TTGCTAAATACCGCCCCAGTT
*
38407 TTGCTAAATACCGCCCCATTT
1 TTGCTAAATACCGCCCCAGTT
38428 TT
1 TT
38430 TACACTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.27, G:0.11, T:0.39
Consensus pattern (21 bp):
TTGCTAAATACCGCCCCAGTT
Found at i:38764 original size:32 final size:32
Alignment explanation
Indices: 38614--38750 Score: 168
Period size: 32 Copynumber: 4.2 Consensus size: 32
38604 AAAATAGCCG
*
38614 AGCCGCCCCACCGGGGCGGCCTGCCGTGGCGA
1 AGCCTCCCCACCGGGGCGGCCTGCCGTGGCGA
*
38646 AGCCTCCCCACCAGGGCGGCCTGCCGTGGCGA
1 AGCCTCCCCACCGGGGCGGCCTGCCGTGGCGA
* * *
38678 AGCCTCCCCACCGGGACGGCCTGCCCATGGGGA
1 AGCCTCCCCACCGGGGCGGCCTG-CCGTGGCGA
* ** *
38711 AGCCGCCCTC-TTGGGGCGGCTTGCCGTGGCGA
1 AGCCTCCC-CACCGGGGCGGCCTGCCGTGGCGA
38743 AGCCTCCC
1 AGCCTCCC
38751 AAGTGGGGCG
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
32 65 0.73
33 23 0.26
34 1 0.01
ACGTcount: A:0.11, C:0.42, G:0.36, T:0.11
Consensus pattern (32 bp):
AGCCTCCCCACCGGGGCGGCCTGCCGTGGCGA
Found at i:46381 original size:18 final size:18
Alignment explanation
Indices: 46355--46409 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 18
46345 ATCACCTCCA
*
46355 AAAGAAAAAGAGAAAAGG
1 AAAGGAAAAGAGAAAAGG
*
46373 AAAGGAAAAGA-AAAAGA
1 AAAGGAAAAGAGAAAAGG
* *
46390 AAAAGAAAA-AGAAAAAG
1 AAAGGAAAAGAGAAAAGG
46407 AAA
1 AAA
46410 AGCAAAACCC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 1 0.03
17 20 0.65
18 10 0.32
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (18 bp):
AAAGGAAAAGAGAAAAGG
Found at i:46416 original size:6 final size:6
Alignment explanation
Indices: 46354--46410 Score: 80
Period size: 6 Copynumber: 9.5 Consensus size: 6
46344 CATCACCTCC
* *
46354 AAAAGA AAAAGA GAAAAG- GAAAGG AAAAGA AAAAGA AAAAGA AAAAGA
1 AAAAGA AAAAGA -AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
46402 AAAAGA AAA
1 AAAAGA AAA
46411 GCAAAACCCA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
5 4 0.09
6 37 0.80
7 5 0.11
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AAAAGA
Done.