Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008534.1 Kokia drynarioides strain JFW-HI SEQ_123211, 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: 48688
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:12063 original size:19 final size:17
Alignment explanation
Indices: 12029--12075 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
12019 GATTAGGCAG
12029 TAAAAGAAAAAGAAGAA
1 TAAAAGAAAAAGAAGAA
12046 TAAAAGAAAAGGAGAAGAA
1 TAAAAGAAAA--AGAAGAA
* *
12065 GAAGAGAAAAA
1 TAAAAGAAAAA
12076 TTCTAGAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 11 0.42
19 15 0.58
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.04
Consensus pattern (17 bp):
TAAAAGAAAAAGAAGAA
Found at i:13435 original size:24 final size:24
Alignment explanation
Indices: 13406--13462 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
13396 ATCCCACTAC
*
13406 ATATCCTACTACATGGATTGTGGT
1 ATATCCTACTACATGGATTATGGT
*
13430 ATATCCAACTACATGGATTATGGT
1 ATATCCTACTACATGGATTATGGT
13454 ATATCCTAC
1 ATATCCTAC
13463 ATCAATCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (24 bp):
ATATCCTACTACATGGATTATGGT
Found at i:16121 original size:30 final size:29
Alignment explanation
Indices: 16060--16162 Score: 75
Period size: 30 Copynumber: 3.4 Consensus size: 29
16050 AAAATCCAAC
* * *
16060 TTAACCATCAAATTTTAATAAAAGTTGAAA
1 TTAACCCTTAAATTTT-ATAAAAGTTCAAA
16090 TTAACCCTTAAATTTTATTAAAA-TTACAAA
1 TTAACCCTTAAATTTTA-TAAAAGTT-CAAA
* * * *
16120 TTAGTCCC-TAAATTTTACAAAATTTCCAAT
1 TTA-ACCCTTAAATTTTATAAAAGTT-CAAA
*
16150 TTAATCCTTAAAT
1 TTAACCCTTAAAT
16163 AAATTTTGGG
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
29 9 0.15
30 47 0.80
31 3 0.05
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.39
Consensus pattern (29 bp):
TTAACCCTTAAATTTTATAAAAGTTCAAA
Found at i:19293 original size:349 final size:351
Alignment explanation
Indices: 18617--19310 Score: 955
Period size: 349 Copynumber: 2.0 Consensus size: 351
18607 CACAGTCTAA
18617 TAATATGAATAGAATATCAACATGCGATACGCATCACGGAATAAAATGATACAAATATCACAACA
1 TAATATGAATAGAATATCAACATGCGATACGCATCACGGAATAAAATGATACAAATATCACAACA
* * *
18682 CATAATAATATCACACAAGGTGTGGAACACCGTCACACAACAAAATGTAGCACAGGAAGAAACAC
66 CAGAAGAATATCACACAAGGTATGGAACACCGTCACACAACAAAATGTAGCACAGGAAGAAACAC
* * *
18747 ACCTTTAGCGGGTAAAAGCTTTAAAGTCATGAAGGACGCCTCTCACACTTAGATCTAACTTCGAC
131 ACCTCTAGCGGGCAAAAGCTCTAAAGTCATGAAGGACGCCTCTCACACTTAGATCTAACTTCGAC
** * * * * *
18812 TCTAGTTGAATTAGGACTTATGAGAATAAACTCTGCATTAAAATCTATCACTAGGCCACTTACTA
196 TCTAACTGAATTAAGACCTATGACAATAAACTCTACATTAAAATCTATCACTAGGCCACCTACTA
* * * * *
18877 ACACAATACTAAATTGAATACGCTCATGTGCAGCACTCGTAACTCGTGCAGGGGTAGTCAACATA
261 ACACAATACTAAATCGAATACACTCATGTGCAGCACTCGTAACTCGTGCAAGAGCAGTCAACATA
18942 GGT-GA-AGGAGGTAACTTGTCAGCC
326 GGTAGAGAGGAGGTAACTTGTCAGCC
* * * * *
18966 TAATATGTATGGAATATTAACATGTGATACGCATCACGGAATAAAATGATATAAATATCACAACA
1 TAATATGAATAGAATATCAACATGCGATACGCATCACGGAATAAAATGATACAAATATCACAACA
* * *
19031 CAGAAGAATATCACACAAGGTATGGAACATCGTCACACAATAAAATGTAGCACATGAAGAAACAC
66 CAGAAGAATATCACACAAGGTATGGAACACCGTCACACAACAAAATGTAGCACAGGAAGAAACAC
* * * * * * * *
19096 ACCTCTAGTGGGCAGAAGCTCTAACGTCGTGGAGGACGCCTCTCATAGTTAGATCTAAC-TCTGG
131 ACCTCTAGCGGGCAAAAGCTCTAAAGTCATGAAGGACGCCTCTCACACTTAGATCTAACTTC-GA
* * *
19160 GTCTAACTGAATTAAGACCTATGACAATAAACTTTACATTAAAATCTAAT-ACTATGCCACCTAC
195 CTCTAACTGAATTAAGACCTATGACAATAAACTCTACATTAAAATCT-ATCACTAGGCCACCTAC
* * * **
19224 TAACATAATACTAAATCGAATACACTCATGTGCAGTACTTGTAACTCGTGCAAGAGCAGTCCGCA
259 TAACACAATACTAAATCGAATACACTCATGTGCAGCACTCGTAACTCGTGCAAGAGCAGTCAACA
19289 TAGGTAGAGGAGGAGGTAACTT
324 TAGGTAGA-GAGGAGGTAACTT
19311 ATTGGCTTTA
Statistics
Matches: 298, Mismatches: 42, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
348 2 0.01
349 280 0.94
350 4 0.01
352 12 0.04
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (351 bp):
TAATATGAATAGAATATCAACATGCGATACGCATCACGGAATAAAATGATACAAATATCACAACA
CAGAAGAATATCACACAAGGTATGGAACACCGTCACACAACAAAATGTAGCACAGGAAGAAACAC
ACCTCTAGCGGGCAAAAGCTCTAAAGTCATGAAGGACGCCTCTCACACTTAGATCTAACTTCGAC
TCTAACTGAATTAAGACCTATGACAATAAACTCTACATTAAAATCTATCACTAGGCCACCTACTA
ACACAATACTAAATCGAATACACTCATGTGCAGCACTCGTAACTCGTGCAAGAGCAGTCAACATA
GGTAGAGAGGAGGTAACTTGTCAGCC
Found at i:28898 original size:33 final size:33
Alignment explanation
Indices: 28856--28918 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
28846 GAAAGAAGTA
28856 AGAGTACAAAAGATGGAGATAAAAACTAAATCC
1 AGAGTACAAAAGATGGAGATAAAAACTAAATCC
28889 AGAGTACAAAAGATGGAGATAAAAACTAAA
1 AGAGTACAAAAGATGGAGATAAAAACTAAA
28919 CCCTAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.57, C:0.10, G:0.19, T:0.14
Consensus pattern (33 bp):
AGAGTACAAAAGATGGAGATAAAAACTAAATCC
Found at i:43080 original size:17 final size:16
Alignment explanation
Indices: 43040--43080 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
43030 TTGTCTTTCT
43040 TGCAATGTAAACGTCC
1 TGCAATGTAAACGTCC
*
43056 TCGTAATGTAAACGTTCC
1 T-GCAATGTAAACG-TCC
43074 TGCAATG
1 TGCAATG
43081 CCACATAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 16 0.76
18 4 0.19
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (16 bp):
TGCAATGTAAACGTCC
Found at i:43174 original size:16 final size:16
Alignment explanation
Indices: 43153--43186 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
43143 CTATGCATGC
*
43153 AAAATATAAAAGACAT
1 AAAATACAAAAGACAT
43169 AAAATACAAAAGACAT
1 AAAATACAAAAGACAT
43185 AA
1 AA
43187 TAGTGAACTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.09, G:0.06, T:0.15
Consensus pattern (16 bp):
AAAATACAAAAGACAT
Done.