Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005435.1 Corchorus capsularis cultivar CVL-1 contig05453, 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: 28612
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:18185 original size:39 final size:36
Alignment explanation
Indices: 18142--18330 Score: 129
Period size: 33 Copynumber: 5.5 Consensus size: 36
18132 TAATATATAT
*
18142 TGACACCAGGAGTTGTCACAATTTATTTTACTCTCCAAA
1 TGACACCAGAAGTTGTCACAA-TTA--TTACTCTCCAAA
* * *
18181 TGACACCAGAAGTTGT--C-ATGATAAATCTCCAAA
1 TGACACCAGAAGTTGTCACAATTATTACTCTCCAAA
* *
18214 TGACACCAGAAGTTGTC-TAA-TA-TA---T---AT
1 TGACACCAGAAGTTGTCACAATTATTACTCTCCAAA
*
18241 TGACACCAGGAGTTGTCACAATTTATTTTACTCTCCAAA
1 TGACACCAGAAGTTGTCACAA-TTA--TTACTCTCCAAA
* * *
18280 TGACACCAGAAGTTGT--C-ATGATAAATCTCCAAA
1 TGACACCAGAAGTTGTCACAATTATTACTCTCCAAA
18313 TGACACCAGAAGTTGTCA
1 TGACACCAGAAGTTGTCA
18331 TGATCTTGCA
Statistics
Matches: 119, Mismatches: 15, Indels: 36
0.70 0.09 0.21
Matches are distributed among these distances:
27 17 0.14
28 2 0.02
30 3 0.03
33 55 0.46
34 1 0.01
35 5 0.04
36 3 0.03
37 2 0.02
39 31 0.26
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (36 bp):
TGACACCAGAAGTTGTCACAATTATTACTCTCCAAA
Found at i:18215 original size:33 final size:33
Alignment explanation
Indices: 18173--18364 Score: 177
Period size: 33 Copynumber: 5.9 Consensus size: 33
18163 TTTATTTTAC
18173 TCTCCAAATGACACCAGAAGTTGTCATGATAAA
1 TCTCCAAATGACACCAGAAGTTGTCATGATAAA
*
18206 TCTCCAAATGACACCAGAAGTTGTC-T-A-ATA
1 TCTCCAAATGACACCAGAAGTTGTCATGATAAA
* * * * * *
18236 TAT---ATTGACACCAGGAGTTGTCACAATTTATTTTAC
1 TCTCCAAATGACACCAGAAGTTGT--C-A-TGA--TAAA
18272 TCTCCAAATGACACCAGAAGTTGTCATGATAAA
1 TCTCCAAATGACACCAGAAGTTGTCATGATAAA
*
18305 TCTCCAAATGACACCAGAAGTTGTCATGAT--C
1 TCTCCAAATGACACCAGAAGTTGTCATGATAAA
* *
18336 T-TGCAATTGACACCAGAAGTTGTCATGAT
1 TCTCCAAATGACACCAGAAGTTGTCATGAT
18365 TTTGCAATTG
Statistics
Matches: 131, Mismatches: 16, Indels: 27
0.75 0.09 0.16
Matches are distributed among these distances:
27 16 0.12
29 1 0.01
30 30 0.23
31 2 0.02
32 2 0.02
33 58 0.44
35 2 0.02
36 3 0.02
37 1 0.01
39 16 0.12
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.29
Consensus pattern (33 bp):
TCTCCAAATGACACCAGAAGTTGTCATGATAAA
Found at i:18302 original size:99 final size:99
Alignment explanation
Indices: 18131--18329 Score: 398
Period size: 99 Copynumber: 2.0 Consensus size: 99
18121 ATTATTAACG
18131 CTAATATATATTGACACCAGGAGTTGTCACAATTTATTTTACTCTCCAAATGACACCAGAAGTTG
1 CTAATATATATTGACACCAGGAGTTGTCACAATTTATTTTACTCTCCAAATGACACCAGAAGTTG
18196 TCATGATAAATCTCCAAATGACACCAGAAGTTGT
66 TCATGATAAATCTCCAAATGACACCAGAAGTTGT
18230 CTAATATATATTGACACCAGGAGTTGTCACAATTTATTTTACTCTCCAAATGACACCAGAAGTTG
1 CTAATATATATTGACACCAGGAGTTGTCACAATTTATTTTACTCTCCAAATGACACCAGAAGTTG
18295 TCATGATAAATCTCCAAATGACACCAGAAGTTGT
66 TCATGATAAATCTCCAAATGACACCAGAAGTTGT
18329 C
1 C
18330 ATGATCTTGC
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (99 bp):
CTAATATATATTGACACCAGGAGTTGTCACAATTTATTTTACTCTCCAAATGACACCAGAAGTTG
TCATGATAAATCTCCAAATGACACCAGAAGTTGT
Found at i:18410 original size:32 final size:30
Alignment explanation
Indices: 18280--18421 Score: 160
Period size: 30 Copynumber: 4.6 Consensus size: 30
18270 ACTCTCCAAA
* * *
18280 TGACACCAGAAGTTGTCATGATAAATCTCCAAA
1 TGACACCAGAAGTTGTCATGAT---TTTGCAAT
*
18313 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
18343 TGACACCAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
** *
18373 TGACACTTGAAGATT-TCATGATTTTATTCAAT
1 TGACACCAGAAG-TTGTCATGA-TTT-TGCAAT
18405 TGACACCAGAAGTTGTC
1 TGACACCAGAAGTTGTC
18422 CTATACACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
30 49 0.52
31 7 0.07
32 17 0.18
33 22 0.23
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATTTTGCAAT
Found at i:23135 original size:17 final size:17
Alignment explanation
Indices: 23093--23163 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 17
23083 AATGATCCTC
*
23093 ACACT-TTTTATGCTTT
1 ACACTATTTAATGCTTT
** *
23109 ATGCTATTTAATCCTTT
1 ACACTATTTAATGCTTT
*
23126 ACACTTTTTATATGCTTT
1 ACACTATTTA-ATGCTTT
** *
23144 ATGCTATTTAATTCTTT
1 ACACTATTTAATGCTTT
23161 ACA
1 ACA
23164 ATTATGGGTT
Statistics
Matches: 39, Mismatches: 14, Indels: 3
0.70 0.25 0.05
Matches are distributed among these distances:
16 3 0.08
17 23 0.59
18 13 0.33
ACGTcount: A:0.24, C:0.17, G:0.06, T:0.54
Consensus pattern (17 bp):
ACACTATTTAATGCTTT
Found at i:23146 original size:35 final size:33
Alignment explanation
Indices: 23093--23163 Score: 115
Period size: 35 Copynumber: 2.1 Consensus size: 33
23083 AATGATCCTC
23093 ACACTTTTTATGCTTTATGCTATTTAATCCTTT
1 ACACTTTTTATGCTTTATGCTATTTAATCCTTT
*
23126 ACACTTTTTATATGCTTTATGCTATTTAATTCTTT
1 ACAC-TTTT-TATGCTTTATGCTATTTAATCCTTT
23161 ACA
1 ACA
23164 ATTATGGGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 4 0.11
34 4 0.11
35 27 0.77
ACGTcount: A:0.24, C:0.17, G:0.06, T:0.54
Consensus pattern (33 bp):
ACACTTTTTATGCTTTATGCTATTTAATCCTTT
Found at i:24078 original size:25 final size:25
Alignment explanation
Indices: 24030--24078 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
24020 ATGTACTATT
*
24030 TATTTAGGTTAATTTATCATTTATC
1 TATTTAGGTTAATTTATCAATTATC
*
24055 TATTTAGTGTTAA-TTATGAATTAT
1 TATTTAG-GTTAATTTATCAATTAT
24079 TGAAATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.31, C:0.04, G:0.10, T:0.55
Consensus pattern (25 bp):
TATTTAGGTTAATTTATCAATTATC
Found at i:24200 original size:39 final size:40
Alignment explanation
Indices: 24116--24193 Score: 97
Period size: 39 Copynumber: 1.9 Consensus size: 40
24106 TTATTCATAG
* **
24116 ATAATCATGATAGATATCATTTGATTGTGTTCTGATGATAC
1 ATAATCATGATA-ATATCATTTGATTGTGTTATGAAAATAC
24157 ATAATCATGAT-ATATCATTTGATTAGTGTTAT-AAAAT
1 ATAATCATGATAATATCATTTGATT-GTGTTATGAAAAT
24194 GTATAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 16 0.48
40 6 0.18
41 11 0.33
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (40 bp):
ATAATCATGATAATATCATTTGATTGTGTTATGAAAATAC
Found at i:26686 original size:19 final size:19
Alignment explanation
Indices: 26659--26695 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
26649 GCATTTGAAT
*
26659 AAGATTTCAAATCCAACAG
1 AAGAATTCAAATCCAACAG
26678 AAGAATTCAAATCCAACA
1 AAGAATTCAAATCCAACA
26696 AATAGATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.22, G:0.08, T:0.19
Consensus pattern (19 bp):
AAGAATTCAAATCCAACAG
Done.