Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023054.1 Corchorus olitorius cultivar O-4 contig23087, 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: 30217
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Found at i:1129 original size:12 final size:11
Alignment explanation
Indices: 1102--1134 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
1092 AACCGTTTAA
1102 TAATTATATAT
1 TAATTATATAT
1113 T-ATTATATAT
1 TAATTATATAT
1123 GTAATTATATAT
1 -TAATTATATAT
1135 ATCTAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 9 0.45
11 2 0.10
12 9 0.45
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
TAATTATATAT
Found at i:1163 original size:21 final size:22
Alignment explanation
Indices: 1130--1170 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1120 TATGTAATTA
**
1130 TATATATCTAATAT-TATTTTT
1 TATATATAAAATATATATTTTT
1151 TATATATAAAATATATATTT
1 TATATATAAAATATATATTT
1171 AATTATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TATATATAAAATATATATTTTT
Found at i:1176 original size:23 final size:23
Alignment explanation
Indices: 1102--1182 Score: 78
Period size: 23 Copynumber: 3.6 Consensus size: 23
1092 AACCGTTTAA
* *
1102 TAATTATATAT-TATTATATATG
1 TAATTATATATATAATATATATT
1124 TAATTATATATATCTAATAT-TATT
1 TAATTATATATA--TAATATATATT
* *
1148 T-TTTATATATAAAATATATATT
1 TAATTATATATATAATATATATT
*
1170 TAATTATAAATAT
1 TAATTATATATAT
1183 TACTAAACGG
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
21 5 0.11
22 16 0.34
23 17 0.36
24 4 0.09
25 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (23 bp):
TAATTATATATATAATATATATT
Found at i:10802 original size:5 final size:5
Alignment explanation
Indices: 10794--10825 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
10784 TAGACACGAC
10794 AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG AG
1 AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG AG
10826 CTGAAGAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (5 bp):
AGAAG
Found at i:18172 original size:29 final size:30
Alignment explanation
Indices: 18116--18177 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
18106 CATTTTTGAC
**
18116 CAAACCATTGTGGTTATTAAAAATAATTCT
1 CAAACCATTGTACTTATTAAAAATAATTCT
*
18146 CAAACCATTGTACTT-TTAAAATTAATTCT
1 CAAACCATTGTACTTATTAAAAATAATTCT
18175 CAA
1 CAA
18178 TCTCCTGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.37
Consensus pattern (30 bp):
CAAACCATTGTACTTATTAAAAATAATTCT
Found at i:22812 original size:13 final size:13
Alignment explanation
Indices: 22794--22820 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
22784 CCAGTTTGAG
22794 AAACAACCCATTA
1 AAACAACCCATTA
22807 AAACAACCCATTA
1 AAACAACCCATTA
22820 A
1 A
22821 GCCCATTTTT
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:0.56, C:0.30, G:0.00, T:0.15
Consensus pattern (13 bp):
AAACAACCCATTA
Found at i:29771 original size:19 final size:18
Alignment explanation
Indices: 29747--29782 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
29737 TGAAGACTTA
29747 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
29766 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
29783 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:29789 original size:30 final size:30
Alignment explanation
Indices: 29735--29794 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
29725 GAAGTTCGTG
* *
29735 TTTGAAGACTTATTGAAGACAATTTGAAGA
1 TTTGAAGACTCATTGAAGACAATTTCAAGA
*
29765 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA
29795 GCAAGAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (30 bp):
TTTGAAGACTCATTGAAGACAATTTCAAGA
Done.