Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014907.1 Kokia drynarioides strain JFW-HI SEQ_129950, 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: 425439
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 158 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:371396 original size:13 final size:13
Alignment explanation
Indices: 371374--371414 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
371364 TGATTTTTTT
371374 AAGAGAAAAA-AA
1 AAGAGAAAAACAA
371386 AAGATGAAAAACAA
1 AAGA-GAAAAACAA
371400 AA-ACGAAAAACAA
1 AAGA-GAAAAACAA
371413 AA
1 AA
371415 CCCTAACTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 4 0.15
13 18 0.69
14 4 0.15
ACGTcount: A:0.78, C:0.07, G:0.12, T:0.02
Consensus pattern (13 bp):
AAGAGAAAAACAA
Found at i:372378 original size:17 final size:18
Alignment explanation
Indices: 372351--372393 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
372341 TGCTCCTAAA
*
372351 AAAAAGT-TTTTGGA-AT
1 AAAAAGTATTTTCGAGAT
372367 AAAAAGTATTTTCGAGAT
1 AAAAAGTATTTTCGAGAT
372385 AAAAA-TATT
1 AAAAAGTATT
372394 GTCAAAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 7 0.29
17 10 0.42
18 7 0.29
ACGTcount: A:0.49, C:0.02, G:0.14, T:0.35
Consensus pattern (18 bp):
AAAAAGTATTTTCGAGAT
Found at i:375346 original size:156 final size:156
Alignment explanation
Indices: 375181--375496 Score: 596
Period size: 156 Copynumber: 2.0 Consensus size: 156
375171 CTCTTTAGGT
375181 TAAATTCGTTCACCCAATATGATCTTATTTTATCTCATGAAAACTATTACATCATTCTTCATAAA
1 TAAATTCGTTCACCCAATATGATCTTATTTTATCTCATGAAAACTATTACATCATTCTTCATAAA
* * *
375246 AAAATCAATTATTAAAAAATAGTAATTAAATCATTTATCCTAGATAAATGATCTGTGATCACATT
66 AAAATCAATTACTAAAAAATAGTAATTAAATCATTTATCCTAGATAAATAATCCGTGATCACATT
375311 ACTTTCTATCTATCATGTAATGCCAA
131 ACTTTCTATCTATCATGTAATGCCAA
*
375337 TAAATTCGTTCACCCAATATGATCTTATTTTATCTCATGAAAATTATTACATCATTCTTCATAAA
1 TAAATTCGTTCACCCAATATGATCTTATTTTATCTCATGAAAACTATTACATCATTCTTCATAAA
375402 AAAATCAATTACTAAAAAATAGTAATTAAATCATTTATCCTAGATAAATAATCCGTGATCACATT
66 AAAATCAATTACTAAAAAATAGTAATTAAATCATTTATCCTAGATAAATAATCCGTGATCACATT
375467 ACTTTCTATCTATCATGTAATGCCAA
131 ACTTTCTATCTATCATGTAATGCCAA
375493 TAAA
1 TAAA
375497 AAATATCATT
Statistics
Matches: 156, Mismatches: 4, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
156 156 1.00
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (156 bp):
TAAATTCGTTCACCCAATATGATCTTATTTTATCTCATGAAAACTATTACATCATTCTTCATAAA
AAAATCAATTACTAAAAAATAGTAATTAAATCATTTATCCTAGATAAATAATCCGTGATCACATT
ACTTTCTATCTATCATGTAATGCCAA
Found at i:376375 original size:150 final size:150
Alignment explanation
Indices: 376104--376409 Score: 612
Period size: 150 Copynumber: 2.0 Consensus size: 150
376094 CTCATTGTGA
376104 GGAGCTTGGATTGAAAATTATGTCCTTAAAGGAAGAAATATCATGTTGAAATCCCTTCGGAGCAG
1 GGAGCTTGGATTGAAAATTATGTCCTTAAAGGAAGAAATATCATGTTGAAATCCCTTCGGAGCAG
376169 AGTTAGAGCTGGTGCTTGAAGAAAATACTGGAAATGAGAGGTAGATTCACCAAAAGCATGCAACT
66 AGTTAGAGCTGGTGCTTGAAGAAAATACTGGAAATGAGAGGTAGATTCACCAAAAGCATGCAACT
376234 ACAAGATAGTCAGTCCTCAT
131 ACAAGATAGTCAGTCCTCAT
376254 GGAGCTTGGATTGAAAATTATGTCCTTAAAGGAAGAAATATCATGTTGAAATCCCTTCGGAGCAG
1 GGAGCTTGGATTGAAAATTATGTCCTTAAAGGAAGAAATATCATGTTGAAATCCCTTCGGAGCAG
376319 AGTTAGAGCTGGTGCTTGAAGAAAATACTGGAAATGAGAGGTAGATTCACCAAAAGCATGCAACT
66 AGTTAGAGCTGGTGCTTGAAGAAAATACTGGAAATGAGAGGTAGATTCACCAAAAGCATGCAACT
376384 ACAAGATAGTCAGTCCTCAT
131 ACAAGATAGTCAGTCCTCAT
376404 GGAGCT
1 GGAGCT
376410 AGAATGGATC
Statistics
Matches: 156, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
150 156 1.00
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.25
Consensus pattern (150 bp):
GGAGCTTGGATTGAAAATTATGTCCTTAAAGGAAGAAATATCATGTTGAAATCCCTTCGGAGCAG
AGTTAGAGCTGGTGCTTGAAGAAAATACTGGAAATGAGAGGTAGATTCACCAAAAGCATGCAACT
ACAAGATAGTCAGTCCTCAT
Found at i:381185 original size:22 final size:22
Alignment explanation
Indices: 381157--381203 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
381147 AGGTCAATTG
*
381157 TTTCGTTGTTGTT-TTGTTATTA
1 TTTCGTTATT-TTATTGTTATTA
381179 TTTCGTTATTTTATTGTTATTA
1 TTTCGTTATTTTATTGTTATTA
381201 TTT
1 TTT
381204 AGATATTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.13, C:0.04, G:0.13, T:0.70
Consensus pattern (22 bp):
TTTCGTTATTTTATTGTTATTA
Found at i:386267 original size:30 final size:30
Alignment explanation
Indices: 386233--386290 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
386223 TAAAAATATA
* *
386233 ATTTTTAAAGGATTAAATTGAAATTTTATC
1 ATTTTTAAAGGATCAAAGTGAAATTTTATC
* *
386263 ATTTTTAGAGGGTCAAAGTGAAATTTTA
1 ATTTTTAAAGGATCAAAGTGAAATTTTA
386291 CCTTTACTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.43
Consensus pattern (30 bp):
ATTTTTAAAGGATCAAAGTGAAATTTTATC
Found at i:386317 original size:79 final size:79
Alignment explanation
Indices: 386229--386386 Score: 230
Period size: 80 Copynumber: 2.0 Consensus size: 79
386219 ATAGTAAAAA
* ** *
386229 TATAATTTTTAAAGGATTAAATTGAAATTTTATCATTTTTA-GAGGGTCAAAGTGA-AATTTTAC
1 TATAATTTTTAAAGAATTAAATCAAAATTTTACCA-TTTTAGGAGGGTCAAAGT-ATAATTTTAC
386292 CTTTACTAATTTAAAT
64 CTTTACTAATTTAAAT
*
386308 TATAATTTTTAAAGAATTAAATCAAAATTTTACCATTTTAGGGGGGGTCAAAGTATAATTTTACC
1 TATAATTTTTAAAGAATTAAATCAAAATTTTACCATTTTA-GGAGGGTCAAAGTATAATTTTACC
386373 TTTACTAATTTAAA
65 TTTACTAATTTAAA
386387 ATTTTCAAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
78 5 0.07
79 32 0.45
80 34 0.48
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (79 bp):
TATAATTTTTAAAGAATTAAATCAAAATTTTACCATTTTAGGAGGGTCAAAGTATAATTTTACCT
TTACTAATTTAAAT
Found at i:387230 original size:30 final size:29
Alignment explanation
Indices: 387196--387254 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
387186 AATTTACGAG
*
387196 AATTAAATAAAATTAAAATTTTATGTATAA
1 AATTAAACAAAATTAAAA-TTTATGTATAA
* *
387226 AATTACACAAATTTAAAATTTATGTATAA
1 AATTAAACAAAATTAAAATTTATGTATAA
387255 TTTTAAGGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.39
Consensus pattern (29 bp):
AATTAAACAAAATTAAAATTTATGTATAA
Found at i:393176 original size:23 final size:23
Alignment explanation
Indices: 393092--393240 Score: 108
Period size: 23 Copynumber: 6.5 Consensus size: 23
393082 TATACGGAAC
* *
393092 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
393114 -AACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * * *
393135 GGGCAACAGAGAACGCACACAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
393161 AAACAGAGAGTACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
**
393184 AATTAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * * *
393207 GATCAGAGGGCACGA-AACGTGCT
1 AAACAGAGAGCAC-ACAAAGTGCT
393230 AAACAGAGAGC
1 AAACAGAGAGC
393241 GCGATAGTGT
Statistics
Matches: 98, Mismatches: 22, Indels: 13
0.74 0.17 0.10
Matches are distributed among these distances:
21 17 0.17
23 63 0.64
24 1 0.01
25 11 0.11
26 6 0.06
ACGTcount: A:0.42, C:0.20, G:0.26, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:393214 original size:69 final size:68
Alignment explanation
Indices: 393092--393239 Score: 160
Period size: 69 Copynumber: 2.1 Consensus size: 68
393082 TATACGGAAC
* *
393092 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAACGCAC-ACA
1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCT-GGCAACAGAG--CGCACGAAA
393156 -GTGCT
63 CGTGCT
* * * *
393161 AAACAGAGAGTACACAAAGTGCTAATTAGAGAGCACACAAAGTGCT-G-ATCAGAGGGCACGAAA
1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGGCAACAGAGCGCACGAAA
393224 CGTGCT
63 CGTGCT
393230 AAACAGAGAG
1 AAACAGAGAG
393240 CGCGATAGTG
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
67 4 0.06
68 2 0.03
69 34 0.50
70 11 0.16
71 10 0.15
72 7 0.10
ACGTcount: A:0.43, C:0.20, G:0.26, T:0.12
Consensus pattern (68 bp):
AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGGCAACAGAGCGCACGAAACGT
GCT
Found at i:406886 original size:20 final size:20
Alignment explanation
Indices: 406861--406951 Score: 92
Period size: 20 Copynumber: 4.3 Consensus size: 20
406851 GTGCTTTTTT
406861 TTTTTTTACTGTTTTGGTTG
1 TTTTTTTACTGTTTTGGTTG
* *
406881 TTTTTTTTACTATTTTTATGTTG
1 -TTTTTTTACT-GTTTT-GGTTG
**
406904 TTGTTTTTACTGTTTTGGTAA
1 TT-TTTTTACTGTTTTGGTTG
*
406925 TTTTTTTGCTGTTTTGGTTG
1 TTTTTTTACTGTTTTGGTTG
*
406945 TTGTTTT
1 TTTTTTT
406952 CGTGTTGTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
20 21 0.37
21 14 0.25
22 10 0.18
23 12 0.21
ACGTcount: A:0.08, C:0.04, G:0.18, T:0.70
Consensus pattern (20 bp):
TTTTTTTACTGTTTTGGTTG
Found at i:407029 original size:24 final size:20
Alignment explanation
Indices: 406991--407055 Score: 76
Period size: 20 Copynumber: 3.0 Consensus size: 20
406981 TATTTTTTAA
*
406991 TGTTGTTTTGCTGTTATTTT
1 TGTTGTTTTGATGTTATTTT
407011 TGCTACTGTTTTGATTGTTATTTT
1 TG-T--TGTTTTGA-TGTTATTTT
*
407035 TGTTGTTTGGATGTTATTTT
1 TGTTGTTTTGATGTTATTTT
407055 T
1 T
407056 ATGCGTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
20 12 0.31
21 8 0.21
23 8 0.21
24 11 0.28
ACGTcount: A:0.09, C:0.05, G:0.20, T:0.66
Consensus pattern (20 bp):
TGTTGTTTTGATGTTATTTT
Found at i:407254 original size:39 final size:38
Alignment explanation
Indices: 407161--407254 Score: 93
Period size: 39 Copynumber: 2.4 Consensus size: 38
407151 AACTATCTTA
* * *
407161 ATATAAAT-TTTTTTTAATGTATTTTAAATTTATTTAT
1 ATATTAATATTTTTTTAATGTATCTTAAATGTATTTAT
* * *
407198 TTTTTAATGTTTATTTTAATGT-TCTTAAATGTATTTGAT
1 ATATTAATATTT-TTTTAATGTATCTTAAATGTATTT-AT
407237 ATATTATATATTTTTTTA
1 ATATTA-ATATTTTTTTA
407255 TTTTGTTGTC
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
37 5 0.11
38 15 0.33
39 20 0.44
40 5 0.11
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.63
Consensus pattern (38 bp):
ATATTAATATTTTTTTAATGTATCTTAAATGTATTTAT
Found at i:416291 original size:13 final size:13
Alignment explanation
Indices: 416273--416302 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
416263 CATCACTTAT
*
416273 TAAAAAAATAAAA
1 TAAAAAAACAAAA
416286 TAAAAAAACAAAA
1 TAAAAAAACAAAA
416299 TAAA
1 TAAA
416303 GGAATCTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (13 bp):
TAAAAAAACAAAA
Found at i:417157 original size:12 final size:12
Alignment explanation
Indices: 417140--417174 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
417130 AGCCGAAGCC
417140 TCCTCCTCCTCT
1 TCCTCCTCCTCT
*
417152 TCCTCCTCTTCT
1 TCCTCCTCCTCT
*
417164 TCGTCCTCCTC
1 TCCTCCTCCTC
417175 CTCCATCTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.54, G:0.03, T:0.43
Consensus pattern (12 bp):
TCCTCCTCCTCT
Found at i:424554 original size:14 final size:14
Alignment explanation
Indices: 424535--424562 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
424525 AGACAATGTC
424535 ACCATATCTCGAGA
1 ACCATATCTCGAGA
424549 ACCATATCTCGAGA
1 ACCATATCTCGAGA
424563 CATAACACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (14 bp):
ACCATATCTCGAGA
Done.