Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019480.1 Corchorus olitorius cultivar O-4 contig19513, 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: 46430
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2248 original size:42 final size:43
Alignment explanation
Indices: 2197--2290 Score: 111
Period size: 45 Copynumber: 2.2 Consensus size: 43
2187 AGTGTATTAT
* * *
2197 CTAA-ATTCTA-CTCCATCTCTGGGTAATTCATCAAAGTAAAA
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
* *
2238 CTAATATTCTACTCCTCCATCTCTAGATGATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAA
2283 CTAATATT
1 CTAATATT
2291 AATTGTTGCT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.14
45 34 0.77
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:22061 original size:17 final size:16
Alignment explanation
Indices: 22021--22069 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
22011 CATGTAATCT
*
22021 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
22037 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
22054 TTAGATCACTAGTGAT
1 TT-GATCACTGGTGAT
22070 ATGGGGGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:23997 original size:22 final size:26
Alignment explanation
Indices: 23972--24022 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
23962 TAAAAGAATG
*
23972 AAATA-TATT-ATTATTTAA-T-AGT
1 AAATACTATTAATTAATTAAGTAAGT
23994 AAATACTATTAATTAATTAAGTAAGT
1 AAATACTATTAATTAATTAAGTAAGT
24020 AAA
1 AAA
24023 AAATATTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.21
23 4 0.17
24 8 0.33
25 1 0.04
26 6 0.25
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (26 bp):
AAATACTATTAATTAATTAAGTAAGT
Found at i:24029 original size:26 final size:23
Alignment explanation
Indices: 23976--24029 Score: 54
Period size: 26 Copynumber: 2.2 Consensus size: 23
23966 AGAATGAAAT
* *
23976 ATATTATTATTTAATAGTAAATA
1 ATATTATTAATTAATAGTAAAAA
*
23999 CTATTAATTAATTAAGTAAGTAAAAA
1 ATATT-ATTAATTAA-T-AGTAAAAA
24025 ATATT
1 ATATT
24030 TAGTATTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 4 0.17
24 8 0.33
25 1 0.04
26 11 0.46
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.43
Consensus pattern (23 bp):
ATATTATTAATTAATAGTAAAAA
Found at i:32290 original size:8 final size:8
Alignment explanation
Indices: 32277--32309 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
32267 TATAAGTGCC
32277 TCTTTTTT
1 TCTTTTTT
32285 TCTTTTTT
1 TCTTTTTT
32293 TCTTTTTT
1 TCTTTTTT
32301 TCTTTTTT
1 TCTTTTTT
32309 T
1 T
32310 TTCTGGTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TCTTTTTT
Found at i:44824 original size:2 final size:2
Alignment explanation
Indices: 44817--44844 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44807 GATGTACCAA
44817 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44845 CTAAAATTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.