Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013810.1 Corchorus olitorius cultivar O-4 contig13843, 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: 26923
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:2867 original size:52 final size:53
Alignment explanation
Indices: 2799--2904 Score: 196
Period size: 52 Copynumber: 2.0 Consensus size: 53
2789 TCAAAACCTT
*
2799 TTTTTAATTTTCAAATTTTATTATGCAAAGAAAAGCAGGAAAACAAGTAAATC
1 TTTTTAATTTTCAAATTTTATTATGCAAACAAAAGCAGGAAAACAAGTAAATC
2852 TTTTT-ATTTTCAAATTTTATTATGCAAACAAAAGCAGGAAAACAAGTAAATC
1 TTTTTAATTTTCAAATTTTATTATGCAAACAAAAGCAGGAAAACAAGTAAATC
2904 T
1 T
2905 ACTCTAATCA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 47 0.90
53 5 0.10
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.35
Consensus pattern (53 bp):
TTTTTAATTTTCAAATTTTATTATGCAAACAAAAGCAGGAAAACAAGTAAATC
Found at i:7344 original size:13 final size:13
Alignment explanation
Indices: 7326--7353 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
7316 GAGAAATTCA
7326 TCTTTATAACCTG
1 TCTTTATAACCTG
7339 TCTTTATAACCTG
1 TCTTTATAACCTG
7352 TC
1 TC
7354 CTTCTTCACG
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:0.21, C:0.25, G:0.07, T:0.46
Consensus pattern (13 bp):
TCTTTATAACCTG
Found at i:11537 original size:45 final size:45
Alignment explanation
Indices: 11473--11626 Score: 184
Period size: 45 Copynumber: 3.4 Consensus size: 45
11463 TCACTGTTAT
*
11473 ACCCATCCAGATTTTCACCCCCATTATAGGCTCTAACTCCCTCAA
1 ACCCATCCAGATTTTCACCCCCATTATACGCTCTAACTCCCTCAA
* * * *
11518 ACCCATCAAGATTTTCACCCCCATTCTCCTCTCTAACTCCCTCAA
1 ACCCATCCAGATTTTCACCCCCATTATACGCTCTAACTCCCTCAA
* * * * * *
11563 ACCCATCCACATTTTCACCCTCATTCTCCTCTCTAACAT-TCTCAA
1 ACCCATCCAGATTTTCACCCCCATTATACGCTCTAAC-TCCCTCAA
*
11608 ACCCATCCACATTTTCACC
1 ACCCATCCAGATTTTCACC
11627 TTCTGCACCA
Statistics
Matches: 99, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
45 98 0.99
46 1 0.01
ACGTcount: A:0.25, C:0.43, G:0.03, T:0.29
Consensus pattern (45 bp):
ACCCATCCAGATTTTCACCCCCATTATACGCTCTAACTCCCTCAA
Found at i:13305 original size:11 final size:10
Alignment explanation
Indices: 13289--13322 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
13279 GATTTTACGA
13289 TTTTAATTTT
1 TTTTAATTTT
*
13299 CTTTTAATTAT
1 -TTTTAATTTT
13310 TTTTAATTTT
1 TTTTAATTTT
13320 TTT
1 TTT
13323 AACCCGCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTAATTTT
Found at i:13372 original size:20 final size:20
Alignment explanation
Indices: 13344--13391 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
13334 GACTTTATGG
* *
13344 CGTGTCCTCTGATAATTCCA
1 CGTGGCCTCTCATAATTCCA
13364 CGTGGCCTCTCATAATTCCA
1 CGTGGCCTCTCATAATTCCA
13384 CGTGGCCT
1 CGTGGCCT
13392 ATACGCATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.17, C:0.33, G:0.19, T:0.31
Consensus pattern (20 bp):
CGTGGCCTCTCATAATTCCA
Found at i:15698 original size:27 final size:24
Alignment explanation
Indices: 15650--15698 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 24
15640 TAACAATTAA
*
15650 AAAGAAAGAAATTATACTAGATAC
1 AAAGAAAGAAATTAAACTAGATAC
15674 AAAGCAAAGTAAATTAAATCTAGAT
1 AAAG-AAAG-AAATTAAA-CTAGAT
15699 CTATGGCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 4 0.19
26 7 0.33
27 6 0.29
ACGTcount: A:0.57, C:0.08, G:0.12, T:0.22
Consensus pattern (24 bp):
AAAGAAAGAAATTAAACTAGATAC
Found at i:16453 original size:11 final size:11
Alignment explanation
Indices: 16437--16462 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
16427 CCTTGCCTAA
16437 AAAACTAGAAG
1 AAAACTAGAAG
16448 AAAACTAGAAG
1 AAAACTAGAAG
16459 AAAA
1 AAAA
16463 GAAACTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:26587 original size:298 final size:298
Alignment explanation
Indices: 26051--26648 Score: 1142
Period size: 298 Copynumber: 2.0 Consensus size: 298
26041 GATCACGAAT
*
26051 TAAATGAGTTTGGTTATATTTGTTATGCATATGTGAAAATTGATCTTAATGCTTTGTTCATGACA
1 TAAATGAGTTTGGTTATATTTGTTATGCATATGTGAAAATTCATCTTAATGCTTTGTTCATGACA
26116 TACTAATGGATTGGTAATACAATGGTTAGTTGTTTTGAATAAAAGGGATAATTTAAGCTGGTAAA
66 TACTAATGGATTGGTAATACAATGGTTAGTTGTTTTGAATAAAAGGGATAATTTAAGCTGGTAAA
26181 TAAGTAATTTTATCTAATATGCATGTTAGAGATTTCTCTAGACCAATTGTTAAATTGAGAGAATA
131 TAAGTAATTTTATCTAATATGCATGTTAGAGATTTCTCTAGACCAATTGTTAAATTGAGAGAATA
26246 TTAAATTCATCTTTTAAATCAATGATCCATAGTTAAATTGATTGATTTCTACCATTGGAGAAGAA
196 TTAAATTCATCTTTTAAATCAATGATCCATAGTTAAATTGATTGATTTCTACCATTGGAGAAGAA
* * *
26311 GTATGCTTTCTTATTATTGTTTTCTTTATTAATTGCCA
261 GTATGATATCTTATTATTGTTTTCTTTATTAATTGACA
*
26349 TAAATGAGTTTGGTTATATTTGTTATGCATGTGTGAAAATTCATCTTAATGCTTTGTTCATGACA
1 TAAATGAGTTTGGTTATATTTGTTATGCATATGTGAAAATTCATCTTAATGCTTTGTTCATGACA
*
26414 TACTAATGGATTGGTAATACAATGGTTAGTTGTTTTGAATAAAATGGATAATTTAAGCTGGTAAA
66 TACTAATGGATTGGTAATACAATGGTTAGTTGTTTTGAATAAAAGGGATAATTTAAGCTGGTAAA
26479 TAAGTAATTTTATCTAATATGCATGTTAGAGATTTCTCTAGACCAATTGTTAAATTGAGAGAATA
131 TAAGTAATTTTATCTAATATGCATGTTAGAGATTTCTCTAGACCAATTGTTAAATTGAGAGAATA
26544 TTAAATTCATCTTTTAAATCAATGATCCATAGTTAAATTGATTGATTTCTACCATTGGAGAAGAA
196 TTAAATTCATCTTTTAAATCAATGATCCATAGTTAAATTGATTGATTTCTACCATTGGAGAAGAA
26609 GTATGATATCTTATTATTGTTTTCTTTATTAATTGACA
261 GTATGATATCTTATTATTGTTTTCTTTATTAATTGACA
26647 TA
1 TA
26649 TTTTAGATTT
Statistics
Matches: 294, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
298 294 1.00
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (298 bp):
TAAATGAGTTTGGTTATATTTGTTATGCATATGTGAAAATTCATCTTAATGCTTTGTTCATGACA
TACTAATGGATTGGTAATACAATGGTTAGTTGTTTTGAATAAAAGGGATAATTTAAGCTGGTAAA
TAAGTAATTTTATCTAATATGCATGTTAGAGATTTCTCTAGACCAATTGTTAAATTGAGAGAATA
TTAAATTCATCTTTTAAATCAATGATCCATAGTTAAATTGATTGATTTCTACCATTGGAGAAGAA
GTATGATATCTTATTATTGTTTTCTTTATTAATTGACA
Done.