Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010261.1 Kokia drynarioides strain JFW-HI SEQ_125099, 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: 29444
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Warning! 135 characters in sequence are not A, C, G, or T
Found at i:2226 original size:2 final size:2
Alignment explanation
Indices: 2219--2246 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2209 ACCATGCATG
2219 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2247 TATATAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:17439 original size:30 final size:30
Alignment explanation
Indices: 17375--17435 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
17365 AATAAATGTT
*
17375 AATTAATTCAATTAATTGATCAACCACGTT
1 AATTAATTCAATTAATTGATCAACCACGTA
*
17405 AATTAATTCAATTAATTGATCAATCAC-TA
1 AATTAATTCAATTAATTGATCAACCACGTA
17434 AA
1 AA
17436 ATTAGTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 3 0.10
30 26 0.90
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (30 bp):
AATTAATTCAATTAATTGATCAACCACGTA
Found at i:18362 original size:96 final size:96
Alignment explanation
Indices: 18185--18369 Score: 241
Period size: 96 Copynumber: 1.9 Consensus size: 96
18175 GAAAAGGATA
** *
18185 TTTGATTATCTCGATTCGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTAAGAATCGA
1 TTTGATTATCTCGATTCGAAGAAAGAATGCACCTAGTAAGTTAAGGCACAATATTTAAGAATCGA
18250 AGATAAGGAAACATTGCCTCGATTAAGGGTG
66 AGATAAGGAAACATTGCCTCGATTAAGGGTG
* * * **
18281 TTTGATTATTTCGATTTGAAGAAAGAATGCACCTAGTGAGTTAAGGCACAA-ATTTTCGAAACTC
1 TTTGATTATCTCGATTCGAAGAAAGAATGCACCTAGTAAGTTAAGGCACAATATTTAAG-AA-TC
*
18345 GAA-ATAAAGG-AATATTGCCTCGATT
64 GAAGAT-AAGGAAACATTGCCTCGATT
18370 TTTTTTAAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
95 5 0.06
96 63 0.82
97 9 0.12
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.30
Consensus pattern (96 bp):
TTTGATTATCTCGATTCGAAGAAAGAATGCACCTAGTAAGTTAAGGCACAATATTTAAGAATCGA
AGATAAGGAAACATTGCCTCGATTAAGGGTG
Found at i:18638 original size:59 final size:58
Alignment explanation
Indices: 18557--18718 Score: 252
Period size: 59 Copynumber: 2.7 Consensus size: 58
18547 ATCGGAGTTC
* * *
18557 AAAACGAGACTTTTCGGAAGTTCGGGGCTAAAATGATAATTTTTAGAAGGTTCGGGGTCA
1 AAAATGAGA-TTTTTGGAAGTTCGGGG-TAAAATGGTAATTTTTAGAAGGTTCGGGGTCA
*
18617 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCA
1 AAAATGAGATTTTTGGAAGTTC-GGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCA
18676 AAAATGAGATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTT
1 AAAATGAGATTTTTGGAAGTTC-GGGGTAAAATGGTAATTTTT
18719 TGAAAAGTTT
Statistics
Matches: 95, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
59 84 0.88
60 11 0.12
ACGTcount: A:0.31, C:0.07, G:0.30, T:0.32
Consensus pattern (58 bp):
AAAATGAGATTTTTGGAAGTTCGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCA
Found at i:18720 original size:30 final size:28
Alignment explanation
Indices: 18567--18718 Score: 148
Period size: 30 Copynumber: 5.2 Consensus size: 28
18557 AAAACGAGAC
* *
18567 TTTTCGGAAGTTCGGGGCTAAAATGATAA
1 TTTTTGGAAGTTCGGGG-TAAAATGGTAA
* *
18596 TTTTTAGAAGGTTCGGGGTCAAAAATGG-GA
1 TTTTTGGAA-GTTCGGGGT--AAAATGGTAA
18626 TTTTTGGAAGTTCGGGGGTAAAATGGTAA
1 TTTTTGGAAGTTC-GGGGTAAAATGGTAA
*
18655 TTTTTAGAAGGTTCGGGGTCAAAAAT-G-AGA
1 TTTTTGGAA-GTTCGGGGT--AAAATGGTA-A
18685 TTTTTGGAAGTTCAGGGGTAAAATGGTAA
1 TTTTTGGAAGTTC-GGGGTAAAATGGTAA
18714 TTTTT
1 TTTTT
18719 TGAAAAGTTT
Statistics
Matches: 103, Mismatches: 8, Indels: 24
0.76 0.06 0.18
Matches are distributed among these distances:
28 12 0.12
29 38 0.37
30 42 0.41
31 11 0.11
ACGTcount: A:0.30, C:0.06, G:0.30, T:0.34
Consensus pattern (28 bp):
TTTTTGGAAGTTCGGGGTAAAATGGTAA
Found at i:20564 original size:17 final size:17
Alignment explanation
Indices: 20537--20620 Score: 89
Period size: 17 Copynumber: 4.9 Consensus size: 17
20527 TTAGACATTT
20537 TAAATTTTAAATTTATAA
1 TAAA-TTTAAATTTATAA
*
20555 TAAATTTAAATTTCA-AC
1 TAAATTTAAATTT-ATAA
*
20572 TAAATTTAAATTTAGAA
1 TAAATTTAAATTTATAA
* * *
20589 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTATAA
*
20606 TAAATTTAAGTTTAT
1 TAAATTTAAATTTAT
20621 TGGGCCCAGA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
16 1 0.02
17 50 0.89
18 5 0.09
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:20582 original size:34 final size:34
Alignment explanation
Indices: 20537--20620 Score: 105
Period size: 34 Copynumber: 2.4 Consensus size: 34
20527 TTAGACATTT
* * *
20537 TAAATTTTAAATTTATAATAAATTTAAATTTCAAC
1 TAAA-TTTAAATTTATAATAAACTTAAATTTAAAA
* *
20572 TAAATTTAAATTTAGAATAAACTTAATTTTAAAA
1 TAAATTTAAATTTATAATAAACTTAAATTTAAAA
*
20606 TAAATTTAAGTTTAT
1 TAAATTTAAATTTAT
20621 TGGGCCCAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
34 38 0.90
35 4 0.10
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (34 bp):
TAAATTTAAATTTATAATAAACTTAAATTTAAAA
Found at i:21551 original size:204 final size:203
Alignment explanation
Indices: 21017--21571 Score: 871
Period size: 203 Copynumber: 2.7 Consensus size: 203
21007 TTTCCTCAGG
* * * * *
21017 ATTTGGTTCACTTCTCGGTATCTCATCGGGGAGCTAACCACTTTATGGCTTCGACTTGCTTCTCA
1 ATTTGGTTCACTTCTCAGTACCTCATCAGGAAGCTAA-C-CTTTATTGCTTCGACTTGCTTCTCA
* * * ** * * *
21082 GTGTCTCATCAGGAAGCTGAGATTCGAAGA-TTTGCTCGTTTTAAGCCTCGTTTGGGTCTTTTTT
64 GTGTCTCATCAGGAAGCTGGGGTTCAAAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTC
***
21146 TCAGCACCTCATCAGGAAGATGATTACATCACTGTTTGTTTCAATTCGCTTCTCCGTATTTCATC
129 TCAGTGTCTCATCAGGAAGATGATTACATCACTGTTTGTTTCAATTCGCTTCTCCGTATTTCATC
21211 CGGAAGACGA
194 CGGAAGACGA
21221 ATTTGGTTCACTTCTCAGTACC-CATCAGGAAGCTAACCTTTTATTGCTTCGACTTGCTTCTCAG
1 ATTTGGTTCACTTCTCAGTACCTCATCAGGAAGCTAACC-TTTATTGCTTCGACTTGCTTCTCAG
*
21285 TGTCTCATCAAGAAGCTGGGGTTCAAAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCT
65 TGTCTCATCAGGAAGCTGGGGTTCAAAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCT
21350 CAGTGTCTCATCAGGAAGATGATTACATCACTGTTTGTTTCAATTCGCTTCTCCGTATTTCATCC
130 CAGTGTCTCATCAGGAAGATGATTACATCACTGTTTGTTTCAATTCGCTTCTCCGTATTTCATCC
21415 GGAAGACGA
195 GGAAGACGA
*
21424 ATTTGGTTCACTTCTCAGTACCTCATCAGGAAGCTAACCTTCTATTGCTTCGACCTGCTTCTCAG
1 ATTTGGTTCACTTCTCAGTACCTCATCAGGAAGCTAACCTT-TATTGCTTCGACTTGCTTCTCAG
* * *
21489 TGTCTCATCAGGAAGCTGGGGTTCAAAGACTTTACTCACTTTGAGCCTCGTTTAGATCTTCTTCT
65 TGTCTCATCAGGAAGCTGGGGTTCAAAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCT
21554 CAGTGTCTCATCAGGAAG
130 CAGTGTCTCATCAGGAAG
21572 CTAGGATTCG
Statistics
Matches: 325, Mismatches: 22, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
201 1 0.00
202 50 0.15
203 137 0.42
204 137 0.42
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.36
Consensus pattern (203 bp):
ATTTGGTTCACTTCTCAGTACCTCATCAGGAAGCTAACCTTTATTGCTTCGACTTGCTTCTCAGT
GTCTCATCAGGAAGCTGGGGTTCAAAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTC
AGTGTCTCATCAGGAAGATGATTACATCACTGTTTGTTTCAATTCGCTTCTCCGTATTTCATCCG
GAAGACGA
Found at i:22170 original size:27 final size:27
Alignment explanation
Indices: 22132--22191 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 27
22122 CCAAAAATTC
*
22132 TATT-AAAAGAGGATCGAAGGAAACAA
1 TATTAAAAAGAGGATCAAAGGAAACAA
22158 TATTAAAAAGAGGATCAAAGGAAACAA
1 TATTAAAAAGAGGATCAAAGGAAACAA
22185 TCATTAA
1 T-ATTAA
22192 TTGGAAATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 4 0.13
27 22 0.71
28 5 0.16
ACGTcount: A:0.55, C:0.08, G:0.18, T:0.18
Consensus pattern (27 bp):
TATTAAAAAGAGGATCAAAGGAAACAA
Done.