Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009488.1 Kokia drynarioides strain JFW-HI SEQ_124197, 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: 22454
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Found at i:5299 original size:21 final size:21
Alignment explanation
Indices: 5275--5314 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5265 TATTTATGTC
*
5275 AATAT-TTTATATTATAAAATT
1 AATATATTTAT-TCATAAAATT
5296 AATATATTTATTCATAAAA
1 AATATATTTATTCATAAAA
5315 AATATTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
AATATATTTATTCATAAAATT
Found at i:5746 original size:24 final size:25
Alignment explanation
Indices: 5719--5767 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
5709 TCTTGTGGCA
*
5719 ATTAAATTT-ATTTAAAATAAAAAC
1 ATTAAATTTAATTAAAAATAAAAAC
5743 ATTAAATTTAAATTAAAAATAAAAA
1 ATTAAATTT-AATTAAAAATAAAAA
5768 AATAAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.41
26 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
ATTAAATTTAATTAAAAATAAAAAC
Found at i:6026 original size:30 final size:32
Alignment explanation
Indices: 5962--6042 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 32
5952 ATAAAATCTA
*
5962 TTTATAAAATTCAAAAATATATAATTATAAAT
1 TTTAAAAAATTCAAAAATATATAATTATAAAT
5994 TTTGAAAAAATTC-AAAATA-AT-A-TATAAAAT
1 TTT-AAAAAATTCAAAAATATATAATTAT-AAAT
*
6024 TTTAAAAATATTAAAAAAT
1 TTTAAAAA-ATTCAAAAAT
6043 GGACTAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
29 8 0.19
30 11 0.26
31 7 0.16
32 9 0.21
33 8 0.19
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.37
Consensus pattern (32 bp):
TTTAAAAAATTCAAAAATATATAATTATAAAT
Found at i:20147 original size:50 final size:50
Alignment explanation
Indices: 20052--20147 Score: 147
Period size: 50 Copynumber: 1.9 Consensus size: 50
20042 TTGAAACCGT
* * *
20052 AATGGCAAATCTCATACACCTAAAGCTATAGAGGGGCAGAATGAAGCTAC
1 AATGGCAAATCTCATAAACCTAAAGCTATAGAGGAGAAGAATGAAGCTAC
* *
20102 AATGGCAAATCTCATAAACCTAAAGCTGTAGAGGAGAAGATTGAAG
1 AATGGCAAATCTCATAAACCTAAAGCTATAGAGGAGAAGAATGAAG
20148 TCAGAAAGAC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.19
Consensus pattern (50 bp):
AATGGCAAATCTCATAAACCTAAAGCTATAGAGGAGAAGAATGAAGCTAC
Found at i:20422 original size:79 final size:79
Alignment explanation
Indices: 20201--20662 Score: 572
Period size: 79 Copynumber: 5.8 Consensus size: 79
20191 AGTTACAACC
* * * *
20201 TCCAATCTTTTACCTTAACCAGAGGGTAGATTGAAGACCATCCGATCTCTTACCCCGATCAT-AG
1 TCCAATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGAG
*
20265 GACAGATTAAAGCAA
66 G-CAGATTGAAGCAA
* * * * *
20280 TCCAATCTTTTACCCTAACCAGAGGGCATGATTGAAAACCATCCAATCTCTTACCCTGATCATGA
1 TCCAATCTTTTACCCTAACTAGAGGGCA-GATTGAAGACCATCCGATCTCTTACCCCGACCATGA
* *
20345 GGCAAATTGAAGAAA
65 GGCAGATTGAAGCAA
* * * * *
20360 TCCAATATTTTACCCTAACTAGAGGGTAGATTGAAGACCATCCGATCTCTTACTCCGATCATGGG
1 TCCAATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGAG
20425 GCAGATTGAAGCAA
66 GCAGATTGAAGCAA
* * * *
20439 TCCAATCTTTTACCCTAGCTAAAGGGCAAATTGAAGACCATCCGATCTCTTACCCCGACCATAAG
1 TCCAATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGAG
20504 GCAGATTGAAGGTC-A
66 GCAGATTGAA-G-CAA
** * * *
20519 TCTGATCTTTTA-CCTCGACTAGAGGGCAGATTGAAAATCATCCGATCTCTTACCCCGACCATGA
1 TCCAATCTTTTACCCT-AACTAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGA
20583 GGCAGATTGAAGCAA
65 GGCAGATTGAAGCAA
** * *
20598 TCCAATCACTTACCCTAA-TCGAAGGGCAGATTGAAGACCATTCGATCTCTTACCCCGACCATGA
1 TCCAATCTTTTACCCTAACTAG-AGGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGA
20662 G
65 G
20663 ATAAATTGAA
Statistics
Matches: 330, Mismatches: 45, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
78 3 0.01
79 190 0.58
80 133 0.40
81 4 0.01
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (79 bp):
TCCAATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGAG
GCAGATTGAAGCAA
Found at i:20631 original size:238 final size:238
Alignment explanation
Indices: 20201--20660 Score: 608
Period size: 238 Copynumber: 1.9 Consensus size: 238
20191 AGTTACAACC
* * * * *
20201 TCCAATCTTTTACCTTAACCAGAGGGTAGATTGAAGACCATCCGATCTCTTACCCCGATCATAGG
1 TCCAATCTTTTACCCTAACCAAAGGGCAAATTGAAGACCATCCGATCTCTTACCCCGACCATAGG
20266 ACAGATTAAAGCAATCCAATCTTTTACCCTAACCAGAGGGCATGATTGAAAACCATCCAATCTCT
66 ACAGATTAAAGCAATCCAATCTTTTACCCTAACCAGAGGGCATGATTGAAAACCATCCAATCTCT
* * * * *
20331 TACCCTGATCATGAGGCAAATTGAAGAAATCCAATATTTTACCCTAACTAGAGGGTAGATTGAAG
131 TACCCCGACCATGAGGCAAATTGAAGAAATCCAATATCTTACCCTAACGAGAGGGCAGATTGAAG
* *
20396 ACCATCCGATCTCTTACTCCGATCATGGGGCAGATTGAAGCAA
196 ACCATCCGATCTCTTACCCCGACCATGGGGCAGATTGAAGCAA
* *
20439 TCCAATCTTTTACCCTAGCTAAAGGGCAAATTGAAGACCATCCGATCTCTTACCCCGACCATAAG
1 TCCAATCTTTTACCCTAACCAAAGGGCAAATTGAAGACCATCCGATCTCTTACCCCGACCAT-AG
* ** * * * *
20504 G-CAGATTGAAGGTC-ATCTGATCTTTTA-CCTCGACTAGAGGGCA-GATTGAAAATCATCCGAT
65 GACAGATT-AAAG-CAATCCAATCTTTTACCCT-AACCAGAGGGCATGATTGAAAACCATCCAAT
* *
20565 CTCTTACCCCGACCATGAGGCAGATTGAAGCAATCCAATCA-CTTACCCTAATCGA-AGGGCAGA
127 CTCTTACCCCGACCATGAGGCAAATTGAAGAAATCCAAT-ATCTTACCCTAA-CGAGAGGGCAGA
*
20628 TTGAAGACCATTCGATCTCTTACCCCGACCATG
190 TTGAAGACCATCCGATCTCTTACCCCGACCATG
20661 AGATAAATTG
Statistics
Matches: 192, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
238 161 0.84
239 30 0.16
240 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (238 bp):
TCCAATCTTTTACCCTAACCAAAGGGCAAATTGAAGACCATCCGATCTCTTACCCCGACCATAGG
ACAGATTAAAGCAATCCAATCTTTTACCCTAACCAGAGGGCATGATTGAAAACCATCCAATCTCT
TACCCCGACCATGAGGCAAATTGAAGAAATCCAATATCTTACCCTAACGAGAGGGCAGATTGAAG
ACCATCCGATCTCTTACCCCGACCATGGGGCAGATTGAAGCAA
Found at i:20671 original size:159 final size:157
Alignment explanation
Indices: 20201--20672 Score: 597
Period size: 159 Copynumber: 3.0 Consensus size: 157
20191 AGTTACAACC
* *
20201 TCCAATCTTTTACCTTAACCAGAGGGTAGATTGAAGACCATCCGATCTCTTACCCCGATCAT-AG
1 TCCAATCTTTTACCTCAACTAGAGGGTAGATTGAAGACCATCCGATCTCTTACCCCGATCATGAG
* * * *
20265 GACAGATTAAAGCAATCCAATCTTTTACCCTAACCAGAGGGCATGATTGAAAACCATCCAATCTC
66 G-CAGATTGAAGCAATCCAATCTTTTACCCTAA-CAAAGGGCA-GATTGAAGACCATCCGATCTC
* *
20330 TTACCCTGATCATGAGGCAAATTGAAGAAA
128 TTACCCCGACCATGAGGCAAATTGAAGAAA
* * *
20360 TCCAATATTTTACC-CTAACTAGAGGGTAGATTGAAGACCATCCGATCTCTTACTCCGATCATGG
1 TCCAATCTTTTACCTC-AACTAGAGGGTAGATTGAAGACCATCCGATCTCTTACCCCGATCATGA
* *
20424 GGCAGATTGAAGCAATCCAATCTTTTACCCTAGCTAAAGGGCAAATTGAAGACCATCCGATCTCT
65 GGCAGATTGAAGCAATCCAATCTTTTACCCTAAC-AAAGGGCAGATTGAAGACCATCCGATCTCT
* * **
20489 TACCCCGACCATAAGGCAGATTGAAGGTCA
129 TACCCCGACCATGAGGCAAATTGAA-GAAA
** * * * * *
20519 TCTGATCTTTTACCTCGACTAGAGGGCAGATTGAAAATCATCCGATCTCTTACCCCGACCATGAG
1 TCCAATCTTTTACCTCAACTAGAGGGTAGATTGAAGACCATCCGATCTCTTACCCCGATCATGAG
** * *
20584 GCAGATTGAAGCAATCCAATCACTTACCCTAATCGAAGGGCAGATTGAAGACCATTCGATCTCTT
66 GCAGATTGAAGCAATCCAATCTTTTACCCTAA-CAAAGGGCAGATTGAAGACCATCCGATCTCTT
**
20649 ACCCCGACCATGAGATAAATTGAA
130 ACCCCGACCATGAGGCAAATTGAA
20673 ACAACCTTTT
Statistics
Matches: 270, Mismatches: 37, Indels: 12
0.85 0.12 0.04
Matches are distributed among these distances:
158 41 0.15
159 225 0.83
160 4 0.01
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (157 bp):
TCCAATCTTTTACCTCAACTAGAGGGTAGATTGAAGACCATCCGATCTCTTACCCCGATCATGAG
GCAGATTGAAGCAATCCAATCTTTTACCCTAACAAAGGGCAGATTGAAGACCATCCGATCTCTTA
CCCCGACCATGAGGCAAATTGAAGAAA
Found at i:22336 original size:23 final size:23
Alignment explanation
Indices: 22285--22454 Score: 186
Period size: 23 Copynumber: 7.3 Consensus size: 23
22275 TATACGGAAC
*
22285 AAACAGAGAGCACATA-AGTGCT
1 AAACAGAGAGCACACACAGTGCT
22307 GGAAAACAGAGAGCACACACAGTGCT
1 ---AAACAGAGAGCACACACAGTGCT
* *
22333 AAACAGAGAGCACACAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
*
22356 AATCAGAGAG--CACACAGTGCT
1 AAACAGAGAGCACACACAGTGCT
**
22377 AATTAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACACAGTGCT
*
22400 AATAACAGAGAGCACGAGAC-GTGCT
1 -A-AACAGAGAGCAC-ACACAGTGCT
22425 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACACAGTGCT
*
22448 AATCAGA
1 AAACAGA
Statistics
Matches: 126, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
21 18 0.14
22 3 0.02
23 64 0.51
24 2 0.02
25 30 0.24
26 9 0.07
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACACAGTGCT
Found at i:22437 original size:48 final size:47
Alignment explanation
Indices: 22285--22450 Score: 207
Period size: 48 Copynumber: 3.6 Consensus size: 47
22275 TATACGGAAC
*
22285 AAACAGAGAGCACATA-AGTGCTGGAA-AACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACACAGTGCT--AATAACAGAGAGCACACAC-GTGCT
* *
22333 AAACAGAGAGCACACAAAGTACTAAT--CAGAGAGCACACA-GTGCT
1 AAACAGAGAGCACACACAGTGCTAATAACAGAGAGCACACACGTGCT
** *
22377 AATTAGAGAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCT
1 AAACAGAGAGCACACACAGTGCTAATAACAGAGAGCAC-ACACGTGCT
22425 AAACAGAGAGCACACACAGTGCTAAT
1 AAACAGAGAGCACACACAGTGCTAAT
22451 CAGA
Statistics
Matches: 103, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
44 27 0.26
46 23 0.22
47 4 0.04
48 44 0.43
49 5 0.05
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (47 bp):
AAACAGAGAGCACACACAGTGCTAATAACAGAGAGCACACACGTGCT
Done.