Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015671.1 Corchorus capsularis cultivar CVL-1 contig15692, 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: 9034
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Found at i:2334 original size:22 final size:23
Alignment explanation
Indices: 2299--2360 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 23
2289 AAATACTAAT
**
2299 AAAATAGGGTAAAAACATATATA
1 AAAATAGCTTAAAAACATATATA
*
2322 AAAGTAG--TAAAAA-ATATATA
1 AAAATAGCTTAAAAACATATATA
2342 AAAATAGCTATAAAAACAT
1 AAAATAGCT-TAAAAACAT
2361 GCATAATTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
20 13 0.39
21 6 0.18
23 12 0.36
24 2 0.06
ACGTcount: A:0.63, C:0.05, G:0.10, T:0.23
Consensus pattern (23 bp):
AAAATAGCTTAAAAACATATATA
Found at i:2627 original size:59 final size:62
Alignment explanation
Indices: 2556--2676 Score: 185
Period size: 63 Copynumber: 2.0 Consensus size: 62
2546 TGGACCTTAT
* *
2556 ATAATTGATTATATT-A-AT-ATCCTTATTTAATCAGTTAATCAAGCACCACTCTAAAACAA
1 ATAATTGATTATATTAATATCATCCTTATTCAATCAGTTAATCAAGCACCACTATAAAACAA
*
2615 ATAATTGATTATATTAATATCGATCCTTATTCAATCAGTTAATCAAGCATCACTATAAAACA
1 ATAATTGATTATATTAATATC-ATCCTTATTCAATCAGTTAATCAAGCACCACTATAAAACA
2677 GAAAATGCCC
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
59 15 0.27
60 1 0.02
61 2 0.04
63 37 0.67
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.36
Consensus pattern (62 bp):
ATAATTGATTATATTAATATCATCCTTATTCAATCAGTTAATCAAGCACCACTATAAAACAA
Found at i:6342 original size:20 final size:19
Alignment explanation
Indices: 6308--6367 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
6298 TTAGTGTGTG
*
6308 TAATTT-ATTTCTTAATAA
1 TAATTTAATTTTTTAATAA
*
6326 TATTTATAATTTTTTAATAA
1 TAATT-TAATTTTTTAATAA
6346 TAATTTAATTATTTTCAATAA
1 TAATTTAATT-TTTT-AATAA
6367 T
1 T
6368 TAAAACCTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 4 0.11
19 6 0.17
20 19 0.54
21 6 0.17
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
TAATTTAATTTTTTAATAA
Found at i:6360 original size:21 final size:19
Alignment explanation
Indices: 6312--6367 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
6302 TGTGTGTAAT
6312 TTATTTCTTAATAATATTTA
1 TTATTT-TTAATAATATTTA
*
6332 TAATTTTTTAATAATAATTTAA
1 TTA-TTTTTAATAAT-ATTT-A
*
6354 TTATTTTCAATAAT
1 TTATTTTTAATAAT
6368 TAAAACCTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 10 0.33
21 17 0.57
22 3 0.10
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATTTTTAATAATATTTA
Found at i:7362 original size:143 final size:143
Alignment explanation
Indices: 7104--7397 Score: 457
Period size: 143 Copynumber: 2.0 Consensus size: 143
7094 TACTACATAT
* * *
7104 TATTTTTGTATACCAGGGAATTTACTGAAGGTCCCTTCCAACTTTTAACATGGGAGAACATTTTC
1 TATTTTTGTACACCAGGGAATTTACTGAAGGCCCCTTCCAACGTTTAACATGGGAGAACATTTTC
* * *
7169 GCCATATTTTAGTCTTTTCTCAAAAGGCTTATTACTTTAAAATTCTTCTAATCTTAACCCTTTTA
66 GCCACATTTTAGTCTTTTCTCAAAA-GCTTATTACTTTAAAATCCTTCTAATCCTAACCCTTTTA
7234 TTTAAAATGCA-TG
130 TTTAAAATGCATTG
*
7247 TATTTTTGTACACCAGGGAATTTACTGAAGGCCCCTTCCAACGTTTAACGTGGGAGAACATTTTC
1 TATTTTTGTACACCAGGGAATTTACTGAAGGCCCCTTCCAACGTTTAACATGGGAGAACATTTTC
* *
7312 GCCCCGTTTTAGTCTTTTCTCAAGTAA-CTTATTACTTTAAAATCCTTCTAATCCTAACCCTTTT
66 GCCACATTTTAGTCTTTTCTCAA--AAGCTTATTACTTTAAAATCCTTCTAATCCTAACCCTTTT
7376 ATTTAAAATGCATTG
129 ATTTAAAATGCATTG
*
7391 TCTTTTT
1 TATTTTT
7398 ATGTAATTTT
Statistics
Matches: 138, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
143 128 0.93
144 8 0.06
145 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (143 bp):
TATTTTTGTACACCAGGGAATTTACTGAAGGCCCCTTCCAACGTTTAACATGGGAGAACATTTTC
GCCACATTTTAGTCTTTTCTCAAAAGCTTATTACTTTAAAATCCTTCTAATCCTAACCCTTTTAT
TTAAAATGCATTG
Found at i:8011 original size:31 final size:31
Alignment explanation
Indices: 7940--8011 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
7930 ATCTATCAGC
*
7940 TTTTAATTTGTTTAATTTAATACTTTCATTT
1 TTTTAATTTGTTTAATTTAATACTTTAATTT
** * *
7971 TAATGATTTGTTTAATTTAATGC-TTAATTT
1 TTTTAATTTGTTTAATTTAATACTTTAATTT
8001 GTTTTAATTTG
1 -TTTTAATTTG
8012 CAATAATTTA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
30 6 0.19
31 26 0.81
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAATACTTTAATTT
Found at i:8568 original size:70 final size:70
Alignment explanation
Indices: 8486--8718 Score: 288
Period size: 70 Copynumber: 3.2 Consensus size: 70
8476 TTGTTTAGGT
* *
8486 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATT
8550 ATTTTA
65 ATTTTA
* *
8556 TTTTATTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAACATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATAT-CTT-T-A-TA
*
8621 TTATATTTTACCA
62 AT-TATTTT---A
* * *
8634 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA
*
8699 TTATA
66 TTTTA
*
8704 TTTTACAATTTTACT
1 TTTTACTATTTTACT
8719 ATTTTAGTTA
Statistics
Matches: 142, Mismatches: 12, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
70 63 0.44
71 5 0.04
72 1 0.01
73 6 0.04
74 5 0.04
75 7 0.05
76 1 0.01
77 2 0.01
78 52 0.37
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.49
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA
TTTTA
Found at i:8568 original size:78 final size:77
Alignment explanation
Indices: 8486--8724 Score: 332
Period size: 78 Copynumber: 3.2 Consensus size: 77
8476 TTGTTTAGGT
* *
8486 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATAT-CTT-T-A-TA
1 TTTTATA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
*
8547 AT-TATTTT---A
65 TTATATTTTACCA
*
8556 TTTTATTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAACATCCTTATAACTA
1 TTTTA-TATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
8621 TTATATTTTACCA
65 TTATATTTTACCA
*
8634 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTA-TATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
*
8699 TTATATTTTACAA
65 TTATATTTTACCA
8712 TTTTACTATTTTA
1 TTTTA-TATTTTA
8725 GTTAAAAAAA
Statistics
Matches: 152, Mismatches: 8, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
70 48 0.32
71 5 0.03
72 1 0.01
73 1 0.01
74 3 0.02
75 6 0.04
78 88 0.58
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (77 bp):
TTTTATATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTAT
TATATTTTACCA
Done.