Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022938.1 Corchorus olitorius cultivar O-4 contig22971, 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: 31357
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Found at i:10913 original size:8 final size:8
Alignment explanation
Indices: 10890--10990 Score: 57
Period size: 8 Copynumber: 11.9 Consensus size: 8
10880 GTGAAAAAAA
10890 TTTAT-TT
1 TTTATATT
10897 TTCTATATT
1 TT-TATATT
10906 TTTATATT
1 TTTATATT
*
10914 ATTAT-TT
1 TTTATATT
10921 AATTTAATATT
1 --TTT-ATATT
10932 TTTATATT
1 TTTATATT
*
10940 ATTAT-TT
1 TTTATATT
10947 AATTTAATATT
1 --TTT-ATATT
10958 TTTATATT
1 TTTATATT
*
10966 ATTAT-TT
1 TTTATATT
10973 AATTTAATATT
1 --TTT-ATATT
10984 TTTATAT
1 TTTATAT
10991 CATTATTTAA
Statistics
Matches: 74, Mismatches: 6, Indels: 27
0.69 0.06 0.25
Matches are distributed among these distances:
7 8 0.11
8 35 0.47
9 19 0.26
10 6 0.08
11 6 0.08
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTATATT
Found at i:10930 original size:18 final size:18
Alignment explanation
Indices: 10909--10988 Score: 71
Period size: 18 Copynumber: 4.6 Consensus size: 18
10899 CTATATTTTT
10909 ATATTATTATTTAATTTA
1 ATATTATTATTTAATTTA
*
10927 ATATTTTTATATTATTATTTA
1 ATATTATTAT-TTA--ATTTA
*
10948 AT-TTAATA-TT--TTT-
1 ATATTATTATTTAATTTA
10961 ATATTATTATTTAATTTA
1 ATATTATTATTTAATTTA
*
10979 ATATTTTTAT
1 ATATTATTAT
10989 ATCATTATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
13 2 0.04
14 8 0.16
15 2 0.04
17 3 0.06
18 20 0.41
19 3 0.06
20 4 0.08
21 7 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATATTATTATTTAATTTA
Found at i:11014 original size:26 final size:26
Alignment explanation
Indices: 10901--11007 Score: 196
Period size: 26 Copynumber: 4.1 Consensus size: 26
10891 TTATTTTTCT
10901 ATATTTTTATATTATTATTTAATTTA
1 ATATTTTTATATTATTATTTAATTTA
10927 ATATTTTTATATTATTATTTAATTTA
1 ATATTTTTATATTATTATTTAATTTA
10953 ATATTTTTATATTATTATTTAATTTA
1 ATATTTTTATATTATTATTTAATTTA
* *
10979 ATATTTTTATATCATTATTTAATTAA
1 ATATTTTTATATTATTATTTAATTTA
11005 ATA
1 ATA
11008 AAATTATGAA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 79 1.00
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (26 bp):
ATATTTTTATATTATTATTTAATTTA
Found at i:11327 original size:18 final size:18
Alignment explanation
Indices: 11304--11338 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11294 ACAAAAACTG
11304 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
11322 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
11339 TGTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:11582 original size:35 final size:35
Alignment explanation
Indices: 11536--11610 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
11526 TTATATAAAC
*
11536 GAACACTTAAATGAACAATAAACGAGGCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
11571 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
11606 GAACA
1 GAACA
11611 TAAACGAACT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (35 bp):
GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
Found at i:18275 original size:18 final size:19
Alignment explanation
Indices: 18252--18288 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
18242 GCACCGAATC
18252 ATCATCA-TGAAGAAAAAA
1 ATCATCATTGAAGAAAAAA
*
18270 ATCATCATTGATGAAAAAA
1 ATCATCATTGAAGAAAAAA
18289 TTCCAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.22
Consensus pattern (19 bp):
ATCATCATTGAAGAAAAAA
Found at i:21622 original size:49 final size:49
Alignment explanation
Indices: 21503--21647 Score: 161
Period size: 50 Copynumber: 3.0 Consensus size: 49
21493 GAGCGTGCCA
* *
21503 ATCAATTTTGTCA-AAAAATTGATAAAAAAATGCGATGAAAATTAAAAG
1 ATCAATTTTGTCATAAAAATTGATAAAAAAATGCAATGAAAAATAAAAG
* * *
21551 ATCAATTTTGTCTTTAAAAATTGAGAAAAAGATGCAA-GTAAAAATAAAAG
1 ATCAATTTTGTC-ATAAAAATTGATAAAAAAATGCAATG-AAAAATAAAAG
* * * *
21601 TTCAATTTTGT-AGTAAAAATTGATAAAAAAGTGCAGTGAAAAGTAAA
1 ATCAATTTTGTCA-TAAAAATTGATAAAAAAATGCAATGAAAAATAAA
21648 TGATTGCTTG
Statistics
Matches: 80, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
48 12 0.15
49 28 0.35
50 40 0.50
ACGTcount: A:0.52, C:0.06, G:0.14, T:0.28
Consensus pattern (49 bp):
ATCAATTTTGTCATAAAAATTGATAAAAAAATGCAATGAAAAATAAAAG
Found at i:22945 original size:9 final size:9
Alignment explanation
Indices: 22927--22964 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
22917 TTAATTCATT
22927 TAATTT-CA
1 TAATTTCCA
22935 TAATTTCCA
1 TAATTTCCA
*
22944 TAATTTCCT
1 TAATTTCCA
*
22953 TGATTTCCA
1 TAATTTCCA
22962 TAA
1 TAA
22965 GTAATTTGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
8 6 0.24
9 19 0.76
ACGTcount: A:0.32, C:0.18, G:0.03, T:0.47
Consensus pattern (9 bp):
TAATTTCCA
Found at i:30005 original size:48 final size:49
Alignment explanation
Indices: 29930--30071 Score: 161
Period size: 49 Copynumber: 3.0 Consensus size: 49
29920 GAGCGTGCCA
* * * *
29930 ATCAATTTTATC-CAAAAATTGATAAAAAG-TGCAA-TGAAAATTAAAAG
1 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGT-AAAAATAAAAG
29977 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG
1 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG
* *
30026 TTCAATTTTGT-TGTAAAAATTGAGAAAAA-ATAC-AGTAAAAAGTAAA
1 ATCAATTTTGTCT-TAAAAATTGAGAAAAAGATGCAAGTAAAAA-TAAA
30072 GGATTGCTTG
Statistics
Matches: 84, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
47 19 0.23
48 23 0.27
49 41 0.49
50 1 0.01
ACGTcount: A:0.53, C:0.06, G:0.13, T:0.28
Consensus pattern (49 bp):
ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG
Done.