Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017191.1 Corchorus olitorius cultivar O-4 contig17224, 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: 25714
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2324 original size:11 final size:11
Alignment explanation
Indices: 2308--2347 Score: 55
Period size: 10 Copynumber: 3.5 Consensus size: 11
2298 TTTAACCTTT
2308 AATTATAAAAA
1 AATTATAAAAA
2319 AATTATATAAAAA
1 AA-T-TATAAAAA
2332 AATT-TAAAAA
1 AATTATAAAAA
2342 AATTAT
1 AATTAT
2348 GTTTTGATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 10 0.38
11 4 0.15
12 2 0.08
13 10 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AATTATAAAAA
Found at i:2329 original size:13 final size:13
Alignment explanation
Indices: 2311--2347 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
2301 AACCTTTAAT
2311 TATAAAAAAATTA
1 TATAAAAAAATTA
2324 TATAAAAAAA-T-
1 TATAAAAAAATTA
2335 T-TAAAAAAATTA
1 TATAAAAAAATTA
2347 T
1 T
2348 GTTTTGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 8 0.36
11 2 0.09
12 2 0.09
13 10 0.45
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TATAAAAAAATTA
Found at i:4877 original size:53 final size:53
Alignment explanation
Indices: 4814--4971 Score: 289
Period size: 53 Copynumber: 3.0 Consensus size: 53
4804 AATCATGATT
4814 AAGGGAGTGGTCAAGGGAGCTAAGAGTTTCTTACCTAGCCTTCCCACAGCCCG
1 AAGGGAGTGGTCAAGGGAGCTAAGAGTTTCTTACCTAGCCTTCCCACAGCCCG
*
4867 AAGGGAGTGGTCAAGGGAGCTAAGAGTTTCTTACCTAGCCTTCCCACAACCCG
1 AAGGGAGTGGTCAAGGGAGCTAAGAGTTTCTTACCTAGCCTTCCCACAGCCCG
* *
4920 AAGGGGGTGGTCAAGGGAGCTAAAAGTTTCTTACCTAGCCTTCCCACAGCCC
1 AAGGGAGTGGTCAAGGGAGCTAAGAGTTTCTTACCTAGCCTTCCCACAGCCC
4972 ACTGTAATAC
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 101 1.00
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.21
Consensus pattern (53 bp):
AAGGGAGTGGTCAAGGGAGCTAAGAGTTTCTTACCTAGCCTTCCCACAGCCCG
Found at i:5005 original size:27 final size:27
Alignment explanation
Indices: 4967--5051 Score: 152
Period size: 27 Copynumber: 3.1 Consensus size: 27
4957 GCCTTCCCAC
4967 AGCCCACTGTAATACGTGGCAGTATAA
1 AGCCCACTGTAATACGTGGCAGTATAA
4994 AGCCCACTGTAATACGTGGCAGTATAA
1 AGCCCACTGTAATACGTGGCAGTATAA
* *
5021 AGCCCGCTGTAATACGTGGCAATATAA
1 AGCCCACTGTAATACGTGGCAGTATAA
5048 AGCC
1 AGCC
5052 AACTATGTGG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (27 bp):
AGCCCACTGTAATACGTGGCAGTATAA
Found at i:14178 original size:12 final size:13
Alignment explanation
Indices: 14160--14189 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
14150 GTTTTCTTTA
14160 ATTTTCTTGATTG
1 ATTTTCTTGATTG
14173 -TTTTCTTGATTG
1 ATTTTCTTGATTG
14185 ATTTT
1 ATTTT
14190 AATTGCTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (13 bp):
ATTTTCTTGATTG
Found at i:15670 original size:20 final size:18
Alignment explanation
Indices: 15645--15681 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
15635 GATTTGGTTT
15645 GTTTTGATATTTGATATTGG
1 GTTTTGAT-TTTGA-ATTGG
15665 GTTTTGATTTTGAATTG
1 GTTTTGATTTTGAATTG
15682 ATTTGGTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.19, C:0.00, G:0.24, T:0.57
Consensus pattern (18 bp):
GTTTTGATTTTGAATTGG
Found at i:19046 original size:10 final size:10
Alignment explanation
Indices: 19031--19059 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
19021 TTTATATATA
19031 ATATAGATAG
1 ATATAGATAG
19041 ATATAGATAG
1 ATATAGATAG
19051 ATATAGATA
1 ATATAGATA
19060 TATTTCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.17, T:0.31
Consensus pattern (10 bp):
ATATAGATAG
Found at i:20004 original size:349 final size:352
Alignment explanation
Indices: 19334--20032 Score: 1080
Period size: 349 Copynumber: 2.0 Consensus size: 352
19324 ACCAAGCCAG
* * * *
19334 ATGTCTTGAAGTCTAAATCTGATATTAATTCTTAGACCCAGTTCATTACTGTGGAAGCCCAAAGA
1 ATGTCTTGAAGACTAAATCTGA-ATTAATTCTTAGACCCAATTCATTAATATGGAAGCCCAAAGA
* * * *
19399 AGGAGTCCAAGTCCAATTAGTAATTATGATGCAGTAATGATTCAGCCCTAATGCAGCATTGTTAA
65 AGGAGTCCAAGTCCAATCAGTAATTAGGATGCAATAATGATTCAGCCCTAATGCAACATTGTTAA
* * * *
19464 ATCCTATTCAAAAGAGGACTTCACAATAGCAGTTTTGGAAGAAAATTCATAATTTTTGATCCGGA
130 ATCATATTCAAAAGAGGACTTCACAATAGCAGTTTTGGAAGAAAATTCATAACTTTTAATCCAGA
*
19529 GCTCAAAAAAATGCAAATGAGGTACCGTTGGAAAGAGGATTCCAAGATCTACAAATTTTATGCTT
195 GCTCAAAAAAATGCAAATGAGGTACCGTTCGAAAGAGGATTCCAAGATCTACAAATTTTATGCTT
* **
19594 ACCTCGAGACCTAATTCTGCAGTTCGGGTGGACGATTTTGCCTTTGAAATTTCTGGACAGAATTG
260 ACCTCGAGACCTAATTCTGCAGTTCCGGTAAACGATTTTGCCTTTGAAATTTCTGGACAGAATTG
*
19659 ATCTTCTCCTAAACCGGCTTGGAGAGCC
325 ATCTTCTCCTAAACCGACTTGGAGAGCC
* * *
19687 ATGTCTTGAAGACTAAATCTG-A-T-ATTCTTAGGCCCAATTCGTTAATATGGAAGCTCAAAGAA
1 ATGTCTTGAAGACTAAATCTGAATTAATTCTTAGACCCAATTCATTAATATGGAAGCCCAAAGAA
* * *
19749 GGAGTTCAAGTTCAATCAGTAATTAGGATGCAATAATGATTCAGCCCTGATGCAACATTGTTAAA
66 GGAGTCCAAGTCCAATCAGTAATTAGGATGCAATAATGATTCAGCCCTAATGCAACATTGTTAAA
* * *
19814 TCATATTCAATAGAGGACTTCACAATAGCTGTTTTGGAAGAAAATTCATAACTTTTAATCTAGAG
131 TCATATTCAAAAGAGGACTTCACAATAGCAGTTTTGGAAGAAAATTCATAACTTTTAATCCAGAG
* * *
19879 CTTAGAAAAATGCAAATGAGGTACCGTTCGAAAGAGGATTCCAAGATCTACAAGTTTTATGCTTA
196 CTCAAAAAAATGCAAATGAGGTACCGTTCGAAAGAGGATTCCAAGATCTACAAATTTTATGCTTA
* * *
19944 CCTCGAGACCTAATTCTGTAGTTCCGGTAAACGATTTTGCCTTTGAAATTTTTTGACAGAATTGA
261 CCTCGAGACCTAATTCTGCAGTTCCGGTAAACGATTTTGCCTTTGAAATTTCTGGACAGAATTGA
20009 TCTTCTCCTAAACCGACTTGGAGA
326 TCTTCTCCTAAACCGACTTGGAGA
20033 ATGTTTTGGA
Statistics
Matches: 314, Mismatches: 32, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
349 292 0.93
350 1 0.00
351 1 0.00
353 20 0.06
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (352 bp):
ATGTCTTGAAGACTAAATCTGAATTAATTCTTAGACCCAATTCATTAATATGGAAGCCCAAAGAA
GGAGTCCAAGTCCAATCAGTAATTAGGATGCAATAATGATTCAGCCCTAATGCAACATTGTTAAA
TCATATTCAAAAGAGGACTTCACAATAGCAGTTTTGGAAGAAAATTCATAACTTTTAATCCAGAG
CTCAAAAAAATGCAAATGAGGTACCGTTCGAAAGAGGATTCCAAGATCTACAAATTTTATGCTTA
CCTCGAGACCTAATTCTGCAGTTCCGGTAAACGATTTTGCCTTTGAAATTTCTGGACAGAATTGA
TCTTCTCCTAAACCGACTTGGAGAGCC
Found at i:20379 original size:2 final size:2
Alignment explanation
Indices: 20372--20400 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
20362 AAACTATTAC
20372 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20401 AATTATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24545 original size:21 final size:21
Alignment explanation
Indices: 24519--24559 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
24509 TTTAAACCCT
24519 ATTGGAGAC-AAGTGGTACTAA
1 ATTGGA-ACTAAGTGGTACTAA
*
24540 ATTGGATCTAAGTGGTACTA
1 ATTGGAACTAAGTGGTACTA
24560 GGGTTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
ATTGGAACTAAGTGGTACTAA
Done.