Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014761.1 Corchorus capsularis cultivar CVL-1 contig14782, 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: 17200
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:4502 original size:15 final size:15
Alignment explanation
Indices: 4471--4514 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
4461 GGAGGGAGGG
*
4471 AAGTAGGGAGCAAAGA
1 AAGT-GGGAGGAAAGA
4487 AA-TGGTGAGGAAAGA
1 AAGTGG-GAGGAAAGA
4502 AAGTGGGAGGAAA
1 AAGTGGGAGGAAA
4515 ATGAAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 2 0.08
15 18 0.72
16 5 0.20
ACGTcount: A:0.48, C:0.02, G:0.41, T:0.09
Consensus pattern (15 bp):
AAGTGGGAGGAAAGA
Found at i:7215 original size:25 final size:23
Alignment explanation
Indices: 7187--7233 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 23
7177 ATATTTTTTA
7187 ATAAATCCTCTATATCCTTGAACTT
1 ATAAATCCTCTATA-CCTT-AACTT
7212 ATAAATCCTCTATACCTTAACT
1 ATAAATCCTCTATACCTTAACT
7234 AGATATAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 4 0.18
24 4 0.18
25 14 0.64
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.38
Consensus pattern (23 bp):
ATAAATCCTCTATACCTTAACTT
Found at i:8210 original size:3 final size:3
Alignment explanation
Indices: 8202--8325 Score: 61
Period size: 3 Copynumber: 41.3 Consensus size: 3
8192 CAGACGCTTT
* * * * * * *
8202 CTC CTC CTC CTC CTC CTC GTT CTC CCC CTC CAC CAC CAC CTT CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
* * * * * * *
8250 CTC CTC CTC CTC GTTC C-C CCC CTC CAC CAC CAC CTT CTC CTT CTC
1 CTC CTC CTC CTC -CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
* * * * *
8295 CTC CAC CAC CAC CTT CTC CTT CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C
8326 CCCACCTTCT
Statistics
Matches: 94, Mismatches: 25, Indels: 4
0.76 0.20 0.03
Matches are distributed among these distances:
2 2 0.02
3 90 0.96
4 2 0.02
ACGTcount: A:0.07, C:0.62, G:0.02, T:0.29
Consensus pattern (3 bp):
CTC
Found at i:8250 original size:24 final size:24
Alignment explanation
Indices: 8223--8335 Score: 94
Period size: 24 Copynumber: 5.0 Consensus size: 24
8213 CCTCCTCGTT
8223 CTCCCCCTCCACCACCACCTTCTC
1 CTCCCCCTCCACCACCACCTTCTC
* * * *
8247 CT---CCTCCTCCTCC-TCGT-TC
1 CTCCCCCTCCACCACCACCTTCTC
8266 C-CCCCCTCCACCACCACCTTCTC
1 CTCCCCCTCCACCACCACCTTCTC
* *
8289 CTTCTCCTCCACCACCACCTTCTC
1 CTCCCCCTCCACCACCACCTTCTC
* * * *
8313 CTTCTCCTCCTCCCCCACCTTCT
1 CTCCCCCTCCACCACCACCTTCT
8336 TTTTGCCCTG
Statistics
Matches: 71, Mismatches: 12, Indels: 12
0.75 0.13 0.13
Matches are distributed among these distances:
19 3 0.04
20 2 0.03
21 18 0.25
22 2 0.03
23 3 0.04
24 43 0.61
ACGTcount: A:0.09, C:0.63, G:0.01, T:0.27
Consensus pattern (24 bp):
CTCCCCCTCCACCACCACCTTCTC
Found at i:8259 original size:42 final size:42
Alignment explanation
Indices: 8200--8298 Score: 180
Period size: 42 Copynumber: 2.4 Consensus size: 42
8190 CTCAGACGCT
*
8200 TTCTCCTCCTCCTCCTCCTCGTTCTCCCCCTCCACCACCACC
1 TTCTCCTCCTCCTCCTCCTCGTTCCCCCCCTCCACCACCACC
8242 TTCTCCTCCTCCTCCTCCTCGTTCCCCCCCTCCACCACCACC
1 TTCTCCTCCTCCTCCTCCTCGTTCCCCCCCTCCACCACCACC
*
8284 TTCTCCTTCTCCTCC
1 TTCTCCTCCTCCTCC
8299 ACCACCACCT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.06, C:0.62, G:0.02, T:0.30
Consensus pattern (42 bp):
TTCTCCTCCTCCTCCTCCTCGTTCCCCCCCTCCACCACCACC
Found at i:9017 original size:13 final size:13
Alignment explanation
Indices: 8999--9023 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8989 TTAGCTTACT
8999 CTTCTTCTTCTTC
1 CTTCTTCTTCTTC
9012 CTTCTTCTTCTT
1 CTTCTTCTTCTT
9024 TTTAAATTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (13 bp):
CTTCTTCTTCTTC
Found at i:10859 original size:21 final size:21
Alignment explanation
Indices: 10834--10876 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
10824 TATCTTAGAT
10834 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
10855 ATAATAAATATATTTTAAATAA
1 ATAAT-AATATATTTTAAATAA
10877 TAAATCATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 8 0.40
23 7 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:14943 original size:20 final size:20
Alignment explanation
Indices: 14920--14969 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
14910 ATGAAAGAGC
*
14920 CTAATTAAATCT-AATTAAGT
1 CTAATTAAATCTCAAATAA-T
*
14940 CTAATCAAATCTCAAATAAT
1 CTAATTAAATCTCAAATAAT
*
14960 CTAAATAAAT
1 CTAATTAAAT
14970 TATTAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.34
Consensus pattern (20 bp):
CTAATTAAATCTCAAATAAT
Done.