Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021395.1 Corchorus olitorius cultivar O-4 contig21428, 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: 34879
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Found at i:1128 original size:16 final size:14
Alignment explanation
Indices: 1100--1135 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
1090 TGGAATTGAT
1100 AAAAAAAAAATAAA
1 AAAAAAAAAATAAA
1114 AAAAATAAAAGATAAA
1 AAAAA-AAAA-ATAAA
1130 AAAAAA
1 AAAAAA
1136 TCACTGCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 5 0.25
16 10 0.50
ACGTcount: A:0.89, C:0.00, G:0.03, T:0.08
Consensus pattern (14 bp):
AAAAAAAAAATAAA
Found at i:6098 original size:31 final size:31
Alignment explanation
Indices: 6004--6100 Score: 87
Period size: 31 Copynumber: 3.2 Consensus size: 31
5994 TAACCAATTC
* * * *
6004 AGGATGTAACGTTTACCCGAAAA-ATCAATTC
1 AGGATATAACG-TTACCCAAAAAGATCAAATA
*
6035 AGGATATAACGTT--TCAAAAACG-TC-AATAA
1 AGGATATAACGTTACCCAAAAA-GATCAAAT-A
6064 AGGATATAACGTTACCCAAAAAGATCAAATA
1 AGGATATAACGTTACCCAAAAAGATCAAATA
6095 AGGATA
1 AGGATA
6101 ATTGTGGACG
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
28 7 0.13
29 15 0.28
30 3 0.06
31 25 0.47
32 3 0.06
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (31 bp):
AGGATATAACGTTACCCAAAAAGATCAAATA
Found at i:6187 original size:12 final size:12
Alignment explanation
Indices: 6140--6187 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
6130 CACGCGCAAT
6140 TAAGTATGCCACG
1 TAAG-ATGCCACG
* *
6153 TAGGATGCCATG
1 TAAGATGCCACG
*
6165 TAACATGCCACG
1 TAAGATGCCACG
*
6177 TAAGATTCCAC
1 TAAGATGCCAC
6188 ATGTAAAATA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
12 25 0.89
13 3 0.11
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (12 bp):
TAAGATGCCACG
Found at i:6223 original size:19 final size:20
Alignment explanation
Indices: 6199--6248 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
6189 TGTAAAATAA
*
6199 AAATTAAAAAATTAA-GAAT
1 AAATTAAAAAATTAATAAAT
* *
6218 AAATTAAGAATTTAATAAAT
1 AAATTAAAAAATTAATAAAT
*
6238 AAAGTAAAAAA
1 AAATTAAAAAA
6249 ATGGTAAAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (20 bp):
AAATTAAAAAATTAATAAAT
Found at i:10456 original size:21 final size:21
Alignment explanation
Indices: 10430--10470 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
10420 CATTAACTCG
10430 ACCACCAGCAAGACCTTCTCA
1 ACCACCAGCAAGACCTTCTCA
*
10451 ACCACCAGGAAGACCTTCTC
1 ACCACCAGCAAGACCTTCTC
10471 CTTCCACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.41, G:0.12, T:0.15
Consensus pattern (21 bp):
ACCACCAGCAAGACCTTCTCA
Found at i:12862 original size:21 final size:21
Alignment explanation
Indices: 12834--12902 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
12824 ATCATTCAAA
12834 GCCC-ATGGACTTTAGATTCG
1 GCCCAATGGACTTTAGATTCG
* * * *
12854 GTCCAATGGACTTTGGCTTTG
1 GCCCAATGGACTTTAGATTCG
* *
12875 GGCCAATGGA-TTTTGAATTCG
1 GCCCAATGGACTTTAG-ATTCG
12896 GCCCAAT
1 GCCCAAT
12903 TATCAACAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
20 7 0.18
21 31 0.82
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.32
Consensus pattern (21 bp):
GCCCAATGGACTTTAGATTCG
Found at i:13086 original size:2 final size:2
Alignment explanation
Indices: 13079--13104 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13069 TAGACATTGT
13079 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
13105 GTTTAAAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20177 original size:10 final size:10
Alignment explanation
Indices: 20143--20190 Score: 57
Period size: 10 Copynumber: 5.1 Consensus size: 10
20133 ACCGACCTTC
20143 TAATATATAT
1 TAATATATAT
* *
20153 TATTAT-TAA
1 TAATATATAT
20162 TAATATATAT
1 TAATATATAT
20172 TAATATATA-
1 TAATATATAT
20181 T-ATATATAT
1 TAATATATAT
20190 T
1 T
20191 CCGTTAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
8 7 0.22
9 9 0.28
10 16 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TAATATATAT
Done.