Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016861.1 Corchorus olitorius cultivar O-4 contig16894, 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: 32152
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:395 original size:13 final size:13
Alignment explanation
Indices: 365--410 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
355 CCCGTTGAGG
365 AAATG-TTT-TAT
1 AAATGCTTTATAT
*
376 AACTGCTTTATAT
1 AAATGCTTTATAT
389 AAATGCTTTATA-
1 AAATGCTTTATAT
*
401 AAATGTTTTA
1 AAATGCTTTA
411 GTAAATATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
11 4 0.13
12 12 0.40
13 14 0.47
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (13 bp):
AAATGCTTTATAT
Found at i:3878 original size:22 final size:21
Alignment explanation
Indices: 3850--3901 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
3840 GTGGAAAAAA
*
3850 AAAAGAAAAAAAAAATGAAAG
1 AAAAGAAAAAAAAAATCAAAG
* *
3871 AAANAGAAGAAAGAAATCAAAG
1 AAA-AGAAAAAAAAAATCAAAG
3893 AAAATGAAA
1 AAAA-GAAA
3902 TCAAGAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.75, C:0.02, G:0.15, T:0.06
Consensus pattern (21 bp):
AAAAGAAAAAAAAAATCAAAG
Found at i:5078 original size:3 final size:3
Alignment explanation
Indices: 5060--5104 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
5050 CCGGCCACCG
* *
5060 GAA GAA GAG GAG GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
5105 AGAAAGAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:6601 original size:12 final size:12
Alignment explanation
Indices: 6550--6601 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
6540 TTCTAACTGC
*
6550 TTTATATAAATGC
1 TTTA-ATAAATGT
6563 TTT-ATAAAATGT
1 TTTAAT-AAATGT
*
6575 TTCAATAAATGT
1 TTTAATAAATGT
6587 TTTAATAAATGT
1 TTTAATAAATGT
6599 TTT
1 TTT
6602 GGGTGAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
11 2 0.06
12 27 0.79
13 5 0.15
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (12 bp):
TTTAATAAATGT
Found at i:10347 original size:21 final size:23
Alignment explanation
Indices: 10321--10364 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
10311 AGGGTATATG
10321 GACAGAGAAG-AAG-AAGTAAAA
1 GACAGAGAAGAAAGAAAGTAAAA
*
10342 GACAGAGATGAAAGAAAGTAAAA
1 GACAGAGAAGAAAGAAAGTAAAA
10365 TGGTTTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 3 0.15
23 8 0.40
ACGTcount: A:0.61, C:0.05, G:0.27, T:0.07
Consensus pattern (23 bp):
GACAGAGAAGAAAGAAAGTAAAA
Found at i:17232 original size:10 final size:10
Alignment explanation
Indices: 17219--17260 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
17209 GGGGCACGTG
17219 CGGGCCACCA
1 CGGGCCACCA
*
17229 CGGGCCACCG
1 CGGGCCACCA
17239 CGGGCCACCA
1 CGGGCCACCA
*
17249 TGGGCCATCCA
1 CGGGCCA-CCA
17260 C
1 C
17261 ATTTTCAGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
10 24 0.89
11 3 0.11
ACGTcount: A:0.17, C:0.48, G:0.31, T:0.05
Consensus pattern (10 bp):
CGGGCCACCA
Found at i:17241 original size:20 final size:20
Alignment explanation
Indices: 17218--17255 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
17208 GGGGGCACGT
17218 GCGGGCCACCACGGGCCACC
1 GCGGGCCACCACGGGCCACC
*
17238 GCGGGCCACCATGGGCCA
1 GCGGGCCACCACGGGCCA
17256 TCCACATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.45, G:0.37, T:0.03
Consensus pattern (20 bp):
GCGGGCCACCACGGGCCACC
Found at i:18935 original size:18 final size:19
Alignment explanation
Indices: 18900--18937 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
18890 AAAGAAAAGT
18900 AATTGATTAAGTAGCCCAA
1 AATTGATTAAGTAGCCCAA
*
18919 AATTTATTAAG-AGCCCAA
1 AATTGATTAAGTAGCCCAA
18937 A
1 A
18938 GACAAAGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (19 bp):
AATTGATTAAGTAGCCCAA
Done.