Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009855.1 Kokia drynarioides strain JFW-HI SEQ_124585, 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: 24572
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:696 original size:87 final size:87
Alignment explanation
Indices: 533--722 Score: 276
Period size: 87 Copynumber: 2.2 Consensus size: 87
523 CCCCGGAGGT
* ** *
533 CCCT-AAACTATCCAAAAATTACCATTTTACCCTTGAACTTCCAAAAATCCCATTTTTGACCCCA
1 CCCTCAAACT-TCCAAAAATTACCATTCTACCCCCGAACTTCCAAAAATCCAATTTTTGACCCCA
*
597 AACCTTCCAAAATTACCATTTTA
65 AACCTTCAAAAATTACCATTTTA
*
620 CCCTCAAACTTCCAAAAATTACCATTCTACCCCCGAACTTCCAAAAATCCAATTTTTGA-CCCGA
1 CCCTCAAACTTCCAAAAATTACCATTCTACCCCCGAACTTCCAAAAATCCAATTTTTGACCCCAA
684 ACCTTTCAAAAATTACCATTTTA
66 ACC-TTCAAAAATTACCATTTTA
* *
707 CCCCCGAACTTCCAAA
1 CCCTCAAACTTCCAAA
723 GGTCCCATTT
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
86 7 0.08
87 81 0.87
88 5 0.05
ACGTcount: A:0.35, C:0.33, G:0.03, T:0.28
Consensus pattern (87 bp):
CCCTCAAACTTCCAAAAATTACCATTCTACCCCCGAACTTCCAAAAATCCAATTTTTGACCCCAA
ACCTTCAAAAATTACCATTTTA
Found at i:774 original size:29 final size:29
Alignment explanation
Indices: 543--775 Score: 207
Period size: 29 Copynumber: 8.0 Consensus size: 29
533 CCCTAAACTA
*
543 TCCAAAAATTACCATTTTACCCTTGAA-CT
1 TCCAAAAATTACCATTTTACCC-CGAACCT
* *
572 TCCAAAAA-TCCCATTTTTGACCCCAAACCT
1 TCCAAAAATTACCA-TTTT-ACCCCGAACCT
*
602 TCC-AAAATTACCATTTTACCCTC-AAACT
1 TCCAAAAATTACCATTTTACCC-CGAACCT
*
630 TCCAAAAATTACCATTCTACCCCCGAA-CT
1 TCCAAAAATTACCATTTTA-CCCCGAACCT
659 TCCAAAAA-T-CCAATTTTTGA-CCCGAACCT
1 TCCAAAAATTACC-A-TTTT-ACCCCGAACCT
*
688 TTCAAAAATTACCATTTTACCCCCGAA-CT
1 TCCAAAAATTACCATTTTA-CCCCGAACCT
** *
717 TCC-AAAGGTCCCATTTTTGACCCCGAACCT
1 TCCAAAAATTACCA-TTTT-ACCCCGAACCT
*
747 TCCAAAAATTACCCTTTTACCCCGAACCT
1 TCCAAAAATTACCATTTTACCCCGAACCT
776 CCCATTTATT
Statistics
Matches: 168, Mismatches: 16, Indels: 40
0.75 0.07 0.18
Matches are distributed among these distances:
27 2 0.01
28 31 0.18
29 90 0.54
30 37 0.22
31 8 0.05
ACGTcount: A:0.33, C:0.34, G:0.05, T:0.29
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCCGAACCT
Found at i:2354 original size:17 final size:17
Alignment explanation
Indices: 2332--2365 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2322 GTAATAATTT
2332 AAAGAAAATAAATTTAA
1 AAAGAAAATAAATTTAA
* *
2349 AAAGAAACTCAATTTAA
1 AAAGAAAATAAATTTAA
2366 GTATCAGCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
AAAGAAAATAAATTTAA
Found at i:5915 original size:17 final size:17
Alignment explanation
Indices: 5893--5926 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5883 CTAAGAATTT
5893 AAAGAAAATAAATTTAA
1 AAAGAAAATAAATTTAA
* *
5910 AAAGAAACTCAATTTAA
1 AAAGAAAATAAATTTAA
5927 GTATCAGCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
AAAGAAAATAAATTTAA
Found at i:11832 original size:16 final size:17
Alignment explanation
Indices: 11799--11832 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
11789 ATTCCTTTTT
*
11799 GAATTTGAAAGTGAAAG
1 GAATTTAAAAGTGAAAG
11816 GAATTTAAAAG-GAAAG
1 GAATTTAAAAGTGAAAG
11832 G
1 G
11833 CCGATTGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (17 bp):
GAATTTAAAAGTGAAAG
Found at i:12285 original size:22 final size:23
Alignment explanation
Indices: 12257--12310 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
12247 TCCATCCTTG
12257 CTGACTGGACC-TATAGAAGCTA
1 CTGACTGGACCTTATAGAAGCTA
* *
12279 CTGACTGGACCTTCTAGAAGCTG
1 CTGACTGGACCTTATAGAAGCTA
12302 CTGACTGGA
1 CTGACTGGA
12311 TGCCACATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 11 0.38
23 18 0.62
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (23 bp):
CTGACTGGACCTTATAGAAGCTA
Found at i:20227 original size:17 final size:17
Alignment explanation
Indices: 20205--20238 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20195 CTAAGAATTT
20205 AAAGAAAATAAATTTAA
1 AAAGAAAATAAATTTAA
* *
20222 AAAGAAACTCAATTTAA
1 AAAGAAAATAAATTTAA
20239 GTATCAGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
AAAGAAAATAAATTTAA
Found at i:20801 original size:28 final size:28
Alignment explanation
Indices: 20769--20826 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
20759 TTTAGAAAAT
20769 TAGCTGAGCATGATTATGGAAGAAATCA
1 TAGCTGAGCATGATTATGGAAGAAATCA
20797 TAGCTGAGCATGATTATGGAAGAAATCA
1 TAGCTGAGCATGATTATGGAAGAAATCA
20825 TA
1 TA
20827 CTCAACATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.26
Consensus pattern (28 bp):
TAGCTGAGCATGATTATGGAAGAAATCA
Found at i:21908 original size:13 final size:14
Alignment explanation
Indices: 21889--21924 Score: 65
Period size: 13 Copynumber: 2.6 Consensus size: 14
21879 ATTTTTCTTC
21889 TTCTTTTCTCTTTT
1 TTCTTTTCTCTTTT
21903 TT-TTTTCTCTTTT
1 TTCTTTTCTCTTTT
21916 TTCTTTTCT
1 TTCTTTTCT
21925 TTTCGAACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
TTCTTTTCTCTTTT
Found at i:21913 original size:20 final size:21
Alignment explanation
Indices: 21880--21927 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
21870 TAAGCAACCA
*
21880 TTTTTCTTCTTCTTTTCTCTT
1 TTTTTTTTCTTCTTTTCTCTT
*
21901 TTTTTTTTC-TCTTTTTTCTT
1 TTTTTTTTCTTCTTTTCTCTT
*
21921 TTCTTTT
1 TTTTTTT
21928 CGAACCTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTTTTTCTTCTTTTCTCTT
Found at i:21927 original size:21 final size:24
Alignment explanation
Indices: 21880--21927 Score: 66
Period size: 21 Copynumber: 2.1 Consensus size: 24
21870 TAAGCAACCA
*
21880 TTTTTCTTCTTCTTTTCTCTTTTT
1 TTTTTCTTCTTCTTTTCTCTTTCT
21904 TTTTTC-TCTT-TTTTCT-TTTCT
1 TTTTTCTTCTTCTTTTCTCTTTCT
21925 TTT
1 TTT
21928 CGAACCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 7 0.30
22 6 0.26
23 4 0.17
24 6 0.26
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (24 bp):
TTTTTCTTCTTCTTTTCTCTTTCT
Found at i:23979 original size:23 final size:23
Alignment explanation
Indices: 23926--23984 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
23916 TCATCCATCC
* * *
23926 TTGCTGACTAGACCTTCTAGAAG
1 TTGCTGACTGGATCTTCTACAAG
* *
23949 CTGTTGACTGGATCTTCTACAAG
1 TTGCTGACTGGATCTTCTACAAG
23972 TTGCTGACTGGAT
1 TTGCTGACTGGAT
23985 GCCACGGAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (23 bp):
TTGCTGACTGGATCTTCTACAAG
Done.