Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008647.1 Corchorus capsularis cultivar CVL-1 contig08668, 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: 37671
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Found at i:2229 original size:24 final size:22
Alignment explanation
Indices: 2109--2469 Score: 302
Period size: 22 Copynumber: 16.0 Consensus size: 22
2099 AAGTTTCAAG
* *
2109 TACTGTTTTATGGTTAATTTGG
1 TACTGTTTTATGCTTAATTTGC
*
2131 TACTG-TTTATTGATTGAATTTGC
1 TACTGTTTTA-TGCTT-AATTTGC
* * *
2154 TTCTGTTTTATGATTGAATATGC
1 TACTGTTTTATGCTT-AATTTGC
* *
2177 TACTGTTTTATGATTGAATATGC
1 TACTGTTTTATGCTT-AATTTGC
2200 TACTGTTTCT-TGCTTATAATTTGC
1 TACTGTTT-TATGC-T-TAATTTGC
2224 TACTGTTTTATGCTTAATTTGC
1 TACTGTTTTATGCTTAATTTGC
* * * * *
2246 TACTATTTTAGGGTTCATGTAGC
1 TACTGTTTTATGCTTAAT-TTGC
2269 TACTGTTTTATGCTTAAATTT-C
1 TACTGTTTTATGCTT-AATTTGC
* * * *
2291 TACTGTTTTAGGGTTCATGTAGC
1 TACTGTTTTATGCTTAAT-TTGC
2314 TACTGTTTTATGCTTCAATTT-C
1 TACTGTTTTATGCTT-AATTTGC
* * * *
2336 TACTGTTTTAGGGTTCATGTAGC
1 TACTGTTTTATGCTTAAT-TTGC
2359 TACT-TTTTATGCTTAAATTT-C
1 TACTGTTTTATGCTT-AATTTGC
* * *
2380 TACTGTTTTAGGGTTCATTTGC
1 TACTGTTTTATGCTTAATTTGC
2402 TACTGTTTTATGCTTAATTTGC
1 TACTGTTTTATGCTTAATTTGC
* * * *
2424 TACTGTTTTAGGGTTCATGTAGC
1 TACTGTTTTATGCTTAAT-TTGC
2447 TACTGTTTTATGCTTAATTTGC
1 TACTGTTTTATGCTTAATTTGC
2469 T
1 T
2470 TCTATTTGTT
Statistics
Matches: 274, Mismatches: 47, Indels: 36
0.77 0.13 0.10
Matches are distributed among these distances:
21 17 0.06
22 117 0.43
23 112 0.41
24 27 0.10
25 1 0.00
ACGTcount: A:0.19, C:0.12, G:0.17, T:0.51
Consensus pattern (22 bp):
TACTGTTTTATGCTTAATTTGC
Found at i:2469 original size:45 final size:45
Alignment explanation
Indices: 2222--2463 Score: 411
Period size: 45 Copynumber: 5.4 Consensus size: 45
2212 CTTATAATTT
*
2222 GCTACTGTTTTATGCTT-AATTTGCTACTATTTTAGGGTTCATGTA
1 GCTACTGTTTTATGCTTAAATTT-CTACTGTTTTAGGGTTCATGTA
2267 GCTACTGTTTTATGCTTAAATTTCTACTGTTTTAGGGTTCATGTA
1 GCTACTGTTTTATGCTTAAATTTCTACTGTTTTAGGGTTCATGTA
*
2312 GCTACTGTTTTATGCTTCAATTTCTACTGTTTTAGGGTTCATGTA
1 GCTACTGTTTTATGCTTAAATTTCTACTGTTTTAGGGTTCATGTA
*
2357 GCTACT-TTTTATGCTTAAATTTCTACTGTTTTAGGGTTCAT-TT
1 GCTACTGTTTTATGCTTAAATTTCTACTGTTTTAGGGTTCATGTA
2400 GCTACTGTTTTATGCTT-AATTTGCTACTGTTTTAGGGTTCATGTA
1 GCTACTGTTTTATGCTTAAATTT-CTACTGTTTTAGGGTTCATGTA
2445 GCTACTGTTTTATGCTTAA
1 GCTACTGTTTTATGCTTAA
2464 TTTGCTTCTA
Statistics
Matches: 187, Mismatches: 5, Indels: 9
0.93 0.02 0.04
Matches are distributed among these distances:
43 12 0.06
44 63 0.34
45 106 0.57
46 6 0.03
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.50
Consensus pattern (45 bp):
GCTACTGTTTTATGCTTAAATTTCTACTGTTTTAGGGTTCATGTA
Found at i:2625 original size:21 final size:22
Alignment explanation
Indices: 2538--2627 Score: 130
Period size: 22 Copynumber: 4.1 Consensus size: 22
2528 CTAATTCTGT
* *
2538 AATTCTGTTTTTACTTAAGGTC
1 AATTCTGTTTTTGCTTAAGTTC
2560 AATTCTGTTTTTGCTTAAAG-TC
1 AATTCTGTTTTTGCTT-AAGTTC
2582 AATTCTGTTTTTGCTTAAGTTC
1 AATTCTGTTTTTGCTTAAGTTC
*
2604 AATTCTGTTTATGCTT-AGTTC
1 AATTCTGTTTTTGCTTAAGTTC
2625 AAT
1 AAT
2628 ATTAGTTGAG
Statistics
Matches: 64, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
21 11 0.17
22 50 0.78
23 3 0.05
ACGTcount: A:0.22, C:0.13, G:0.13, T:0.51
Consensus pattern (22 bp):
AATTCTGTTTTTGCTTAAGTTC
Found at i:6159 original size:108 final size:104
Alignment explanation
Indices: 5938--6150 Score: 338
Period size: 108 Copynumber: 2.0 Consensus size: 104
5928 ATAATGTAAA
*
5938 AATTAATTAACAATATCCTTATCAATTTTTTTGTTTTTTTTCCGAATATCTCAGCCTTATAATTT
1 AATTAATTAACAATATCCTTATCAATTTTTTTGTTTTTTTTCCGAATATCCCAGCCTTATAATTT
6003 ATAATGTAAAGTCGGATTATTTTGTTCAAGAATTAATAT
66 ATAATGTAAAGTCGGATTATTTTGTTCAAGAATTAATAT
* *
6042 AATTAATTAACAATATCCTTAAATCAATTTGTTTGTTTTATTTTTTCCGAATATCCCAGTCTTA-
1 AATTAATTAACAATATCCTT--ATCAATTT-TTT-TGTT-TTTTTTCCGAATATCCCAGCCTTAT
*
6106 AATTTATAATGTAAAGTCGGATTATTTTGTTGAAGAATTAATAT
61 AATTTATAATGTAAAGTCGGATTATTTTGTTCAAGAATTAATAT
6150 A
1 A
6151 TCTGATTAAT
Statistics
Matches: 100, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
104 20 0.20
106 8 0.08
107 3 0.03
108 47 0.47
109 22 0.22
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (104 bp):
AATTAATTAACAATATCCTTATCAATTTTTTTGTTTTTTTTCCGAATATCCCAGCCTTATAATTT
ATAATGTAAAGTCGGATTATTTTGTTCAAGAATTAATAT
Found at i:11622 original size:1 final size:1
Alignment explanation
Indices: 11588--11612 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
11578 TTGTTGGGCA
11588 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
11613 TGTGTGGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:12525 original size:42 final size:42
Alignment explanation
Indices: 12466--12662 Score: 376
Period size: 42 Copynumber: 4.7 Consensus size: 42
12456 CAGATTCAGC
12466 AATCTTCTCAACAACTGGAAGGGGCTGCTGGACTTCCTCTGT
1 AATCTTCTCAACAACTGGAAGGGGCTGCTGGACTTCCTCTGT
*
12508 AATCTTCTCCACAACTGGAAGGGGCTGCTGGACTTCCTCTGT
1 AATCTTCTCAACAACTGGAAGGGGCTGCTGGACTTCCTCTGT
12550 AATCTTCTCAACAACTGGAAGGGGCTGCTGGACTTCCTCTGT
1 AATCTTCTCAACAACTGGAAGGGGCTGCTGGACTTCCTCTGT
*
12592 AATCTTCTCCACAACTGGAAGGGGCTGCTGGACTTCCTCTGT
1 AATCTTCTCAACAACTGGAAGGGGCTGCTGGACTTCCTCTGT
12634 AATCTTCTCAACAACTGGAAGGGGCTGCT
1 AATCTTCTCAACAACTGGAAGGGGCTGCT
12663 TATCTGCATT
Statistics
Matches: 151, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 151 1.00
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.28
Consensus pattern (42 bp):
AATCTTCTCAACAACTGGAAGGGGCTGCTGGACTTCCTCTGT
Found at i:13564 original size:50 final size:50
Alignment explanation
Indices: 13509--13609 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
13499 TAATTTCTTC
13509 ATTCTTCACCAAATATGTAATGCTTGATTAAATTTTACATAAAACAAATT
1 ATTCTTCACCAAATATGTAATGCTTGATTAAATTTTACATAAAACAAATT
13559 ATTCTTCACCAAATATGTAATGCTTGATTAAATTTTACATAAAACAAATT
1 ATTCTTCACCAAATATGTAATGCTTGATTAAATTTTACATAAAACAAATT
13609 A
1 A
13610 CTCAATAGAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.38
Consensus pattern (50 bp):
ATTCTTCACCAAATATGTAATGCTTGATTAAATTTTACATAAAACAAATT
Done.