Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024683.1 Corchorus olitorius cultivar O-4 contig24716, 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: 19585
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:8408 original size:33 final size:33
Alignment explanation
Indices: 8366--8429 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
8356 AACTAATCCG
*
8366 GAGTCGACCTGAGTTACGCACCTAGGTTTGGTA
1 GAGTCGACCTGAGTCACGCACCTAGGTTTGGTA
*
8399 GAGTCGACCTGAGTCGCGCACCTAGGTTTGG
1 GAGTCGACCTGAGTCACGCACCTAGGTTTGG
8430 CGGGTGAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.19, C:0.23, G:0.33, T:0.25
Consensus pattern (33 bp):
GAGTCGACCTGAGTCACGCACCTAGGTTTGGTA
Found at i:8686 original size:128 final size:128
Alignment explanation
Indices: 8456--8707 Score: 450
Period size: 128 Copynumber: 2.0 Consensus size: 128
8446 GCGGCTGCGA
8456 ACGCAAGACAAGATCTCAAACCCTCACCTGCTTAATGAACGTGCTGGTTATCACTCATTCCAAAC
1 ACGCAAGACAAGATCTCAAACCCTCACCTGCTTAATGAACGTGCTGGTTATCACTCATTCCAAAC
* * *
8521 CGTTTACCACTCGGTCCAATCTTGCATTAGCTGTTTATCACTCGTTCCAATCACTCGTTGTGT
66 CGTTTACCACTCGATCCAACCTTGCATTAGCTATTTATCACTCGTTCCAATCACTCGTTGTGT
*
8584 ACGCAAGACAAGATCTCAAACCCTCACCTGCTTAATGAACGTGCTGGTTATCACTCGTTCCAAAC
1 ACGCAAGACAAGATCTCAAACCCTCACCTGCTTAATGAACGTGCTGGTTATCACTCATTCCAAAC
* *
8649 CGTTTACCATTCGATCCAACCTTGCATTGGCTATTTATCACTCGTTCCAATCACTCGTT
66 CGTTTACCACTCGATCCAACCTTGCATTAGCTATTTATCACTCGTTCCAATCACTCGTT
8708 CCAAACTGTT
Statistics
Matches: 118, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
128 118 1.00
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.30
Consensus pattern (128 bp):
ACGCAAGACAAGATCTCAAACCCTCACCTGCTTAATGAACGTGCTGGTTATCACTCATTCCAAAC
CGTTTACCACTCGATCCAACCTTGCATTAGCTATTTATCACTCGTTCCAATCACTCGTTGTGT
Found at i:8703 original size:13 final size:13
Alignment explanation
Indices: 8685--8711 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
8675 TTGGCTATTT
8685 ATCACTCGTTCCA
1 ATCACTCGTTCCA
8698 ATCACTCGTTCCA
1 ATCACTCGTTCCA
8711 A
1 A
8712 ACTGTTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.37, G:0.07, T:0.30
Consensus pattern (13 bp):
ATCACTCGTTCCA
Found at i:12611 original size:2 final size:2
Alignment explanation
Indices: 12604--12639 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
12594 TTTACACATA
12604 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
12640 AGAGAATCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:13432 original size:15 final size:14
Alignment explanation
Indices: 13414--13465 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
13404 AAGGGCTGGA
13414 ATTAATTAATTATT
1 ATTAATTAATTATT
13428 GATTAAATAATAATTATTT
1 -ATT-AAT--TAATTA-TT
*
13447 ATTAAATAATTATT
1 ATTAATTAATTATT
13461 ATTAA
1 ATTAA
13466 AAATCTTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
14 7 0.22
15 9 0.28
16 3 0.09
17 2 0.06
18 9 0.28
19 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
ATTAATTAATTATT
Found at i:13443 original size:18 final size:18
Alignment explanation
Indices: 13420--13463 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
13410 TGGAATTAAT
13420 TAATTATTGATTAAATAA
1 TAATTATTGATTAAATAA
*
13438 TAATTATTTATTAAATAA
1 TAATTATTGATTAAATAA
*
13456 TTATTATT
1 TAATTATT
13464 AAAAATCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TAATTATTGATTAAATAA
Found at i:15331 original size:10 final size:10
Alignment explanation
Indices: 15316--15340 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
15306 CTCTGCATAG
15316 CCGGCGATCC
1 CCGGCGATCC
15326 CCGGCGATCC
1 CCGGCGATCC
15336 CCGGC
1 CCGGC
15341 TCTCTTTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.52, G:0.32, T:0.08
Consensus pattern (10 bp):
CCGGCGATCC
Found at i:19159 original size:21 final size:21
Alignment explanation
Indices: 19133--19174 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
19123 TAAGGAAGAA
19133 GTTTCAAGCTCATCAGAGTTG
1 GTTTCAAGCTCATCAGAGTTG
*
19154 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCAGAGTTG
19175 TCTAAGATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (21 bp):
GTTTCAAGCTCATCAGAGTTG
Found at i:19308 original size:20 final size:21
Alignment explanation
Indices: 19285--19327 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
19275 ATCTTGAAGA
19285 ATTTAAAG-CCATCGGAGATC
1 ATTTAAAGCCCATCGGAGATC
* *
19305 ATTTGAAGCCCATTGGAGATC
1 ATTTAAAGCCCATCGGAGATC
19326 AT
1 AT
19328 CAACAAAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (21 bp):
ATTTAAAGCCCATCGGAGATC
Done.