Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011959.1 Kokia drynarioides strain JFW-HI SEQ_126957, 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: 397225
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 35 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:382258 original size:168 final size:170
Alignment explanation
Indices: 381981--382313 Score: 564
Period size: 168 Copynumber: 2.0 Consensus size: 170
381971 ATACCTTCAA
*
381981 TTGAACTCCTAATACTTCTCCTAATAAAATAAGTAATAAATTAATCTAAATAATTAATTTGACTT
1 TTGAACTCCTAATACCTCTCCTAATAAAATAAGTAATAAATTAATCTAAATAATTAATTTGACTT
*
382046 CTAACATAAAACCTTTCACCTAGATAAAACGAAGTATTTCAACTCTTCGCAGAAATCAC-AAATA
66 CTAACATAAAACCTTTCACCTAGATAAAACGAAGTATTTCAACTCTTCACAGAAATCACAAAATA
* *
382110 TGATGTAAACCTCAAATGCAT-T-AGAGAGAGAGAGAGAT
131 TGATGGAAACCTCAAATGCATCTCAAAGAGAGAGAGAGAT
382148 TTGAACTCCTAATACCTCTCCTAATAAAATAAGTAATAAATTAATCTAAAATAATTAATTTGACT
1 TTGAACTCCTAATACCTCTCCTAATAAAATAAGTAATAAATTAATCT-AAATAATTAATTTGACT
* * *
382213 TCTAACATAAAACGTTTCACCTAGATAACATGAAGTATTTCAACTCTTCACAGAAATCACAAAAT
65 TCTAACATAAAACCTTTCACCTAGATAAAACGAAGTATTTCAACTCTTCACAGAAATCACAAAAT
*
382278 ATGCTGGAAACCTCAAATGCATCTCAAAGAGAGAGA
130 ATGATGGAAACCTCAAATGCATCTCAAAGAGAGAGA
382314 AAGAGAGAGA
Statistics
Matches: 154, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
167 46 0.30
168 73 0.47
169 24 0.16
170 1 0.01
171 10 0.06
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (170 bp):
TTGAACTCCTAATACCTCTCCTAATAAAATAAGTAATAAATTAATCTAAATAATTAATTTGACTT
CTAACATAAAACCTTTCACCTAGATAAAACGAAGTATTTCAACTCTTCACAGAAATCACAAAATA
TGATGGAAACCTCAAATGCATCTCAAAGAGAGAGAGAGAT
Found at i:385166 original size:12 final size:12
Alignment explanation
Indices: 385149--385175 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
385139 ATTCTTATCG
385149 TTCCTATTCTTA
1 TTCCTATTCTTA
385161 TTCCTATTCTTA
1 TTCCTATTCTTA
385173 TTC
1 TTC
385176 TCGTCTAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.26, G:0.00, T:0.59
Consensus pattern (12 bp):
TTCCTATTCTTA
Found at i:386227 original size:27 final size:26
Alignment explanation
Indices: 386183--386241 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
386173 CGAGATTAAG
*
386183 TGGGTCTGAGGACCCTTGAGTTCGAGA
1 TGGGTCAGAGGACCCTTGAGTTCGA-A
*
386210 TGGGTCAGAGG-CCTCTTGAGTTTGAA
1 TGGGTCAGAGGACC-CTTGAGTTCGAA
386236 TGGGTC
1 TGGGTC
386242 TAAAAACCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 9 0.31
27 20 0.69
ACGTcount: A:0.17, C:0.17, G:0.37, T:0.29
Consensus pattern (26 bp):
TGGGTCAGAGGACCCTTGAGTTCGAA
Found at i:386267 original size:26 final size:26
Alignment explanation
Indices: 386228--386293 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
386218 AGGCCTCTTG
* * *
386228 AGTTTGAATGGGTCTAAAAACCCTTA
1 AGTTTGAGTTGGTCGAAAAACCCTTA
* **
386254 AGTTTGAGTTGGTCGGAGGACCCTTA
1 AGTTTGAGTTGGTCGAAAAACCCTTA
*
386280 AGTTTAAGTTGGTC
1 AGTTTGAGTTGGTC
386294 AGAAGACCAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.26, C:0.14, G:0.27, T:0.33
Consensus pattern (26 bp):
AGTTTGAGTTGGTCGAAAAACCCTTA
Found at i:386301 original size:26 final size:26
Alignment explanation
Indices: 386247--386301 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
386237 GGGTCTAAAA
* * *
386247 ACCCTTAAGTTTGAGTTGGTCGGAGG
1 ACCCTTAAGTTTAAGTTGGTCAGAAG
386273 ACCCTTAAGTTTAAGTTGGTCAGAAG
1 ACCCTTAAGTTTAAGTTGGTCAGAAG
386299 ACC
1 ACC
386302 ATAAGCAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (26 bp):
ACCCTTAAGTTTAAGTTGGTCAGAAG
Found at i:391382 original size:13 final size:14
Alignment explanation
Indices: 391364--391469 Score: 72
Period size: 13 Copynumber: 8.1 Consensus size: 14
391354 TAAACTAAGT
391364 TTTTCAAAAGT-AC
1 TTTTCAAAAGTCAC
391377 TTTTCAAAA-TCAC
1 TTTTCAAAAGTCAC
*
391390 TTTTCCAAAG-CAC
1 TTTTCAAAAGTCAC
391403 ATTTT-AAAA-TCAC
1 -TTTTCAAAAGTCAC
*
391416 TTTTCCAAAG-CAC
1 TTTTCAAAAGTCAC
391429 ATTTT-AAAA-TCAC
1 -TTTTCAAAAGTCAC
* *
391442 TTCTCCAAAG-CAC
1 TTTTCAAAAGTCAC
391455 ATTTT-AAAA-TCAC
1 -TTTTCAAAAGTCAC
391468 TT
1 TT
391470 CTTAAAAAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 25
0.69 0.08 0.24
Matches are distributed among these distances:
12 10 0.14
13 52 0.71
14 11 0.15
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.36
Consensus pattern (14 bp):
TTTTCAAAAGTCAC
Found at i:391411 original size:26 final size:26
Alignment explanation
Indices: 391364--391469 Score: 169
Period size: 26 Copynumber: 4.1 Consensus size: 26
391354 TAAACTAAGT
* *
391364 TTTTCAAAAGTAC-TTTTCAAAATCAC
1 TTTTCCAAAGCACATTTT-AAAATCAC
391390 TTTTCCAAAGCACATTTTAAAATCAC
1 TTTTCCAAAGCACATTTTAAAATCAC
391416 TTTTCCAAAGCACATTTTAAAATCAC
1 TTTTCCAAAGCACATTTTAAAATCAC
*
391442 TTCTCCAAAGCACATTTTAAAATCAC
1 TTTTCCAAAGCACATTTTAAAATCAC
391468 TT
1 TT
391470 CTTAAAAAAA
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 72 0.95
27 4 0.05
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.36
Consensus pattern (26 bp):
TTTTCCAAAGCACATTTTAAAATCAC
Found at i:391901 original size:2 final size:2
Alignment explanation
Indices: 391896--391940 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
391886 ACATACATAC
* * * *
391896 AT AT AT AT AT AA AT AA AT AA AT AA AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
391938 AT A
1 AT A
391941 GTTTATAATT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (2 bp):
AT
Found at i:395254 original size:194 final size:193
Alignment explanation
Indices: 394925--395452 Score: 887
Period size: 194 Copynumber: 2.7 Consensus size: 193
394915 CAATCGATTG
394925 AAGTTGCCACATAAAACTTATCCTTATACTCCTTTTCACAATTGACGGCTTTCAAGAAAAACAC-
1 AAGTTGCCACATAAAACTTATCCTTATACTCCTTTTCACAATTGAC-GCTTTCAAGAAAAACACT
* * * *
394989 TCCACCTTCAGAAATGACTATAAAGTTAATTAATGGTCGTCTTTGTGCATTCGTCTATACATCAC
65 TCAACC-TCAGAAACGACCATAAAGTTAATTAATGGTCGTCTTTGTGCATTCGTCCATACATCAC
*
395054 GTACAAGACTAATACATTTTTCCCTCCATATTTCCTTTATAGGTATTAACAACCTCTCTATGTTA
129 GTACAAGACTAATACATTTTTCCCTCCACATTTCCTTTATAGGTATTAACAACCTCTCTATGTTA
395119 AAGTTGCCACATAAAACTTATCCTTATACTCCTTTTCACAATTGACAGCTTTCAAGAAAAACACT
1 AAGTTGCCACATAAAACTTATCCTTATACTCCTTTTCACAATTGAC-GCTTTCAAGAAAAACACT
*
395184 TCAACCTCAGAAACGACCATAAAGTTAATTAATGGTCGTCTTTGTGCATTCGTCCATTCATCACG
65 TCAACCTCAGAAACGACCATAAAGTTAATTAATGGTCGTCTTTGTGCATTCGTCCATACATCACG
395249 TACAAGACTAATACATTTTTCCCTCCACATTTCCTTTATAGGTATTAACAACCTCTCTATGTTA
130 TACAAGACTAATACATTTTTCCCTCCACATTTCCTTTATAGGTATTAACAACCTCTCTATGTTA
*
395313 AAGTTGCCACATAACACTTATCCTTATACTCCTTTTCACAATTGACGTCTTTCAAGAAAAACACT
1 AAGTTGCCACATAAAACTTATCCTTATACTCCTTTTCACAATTGACG-CTTTCAAGAAAAACACT
* * * * * *
395378 TCACCCTAAAAAACAACCATAAAGTTAATTAATGGTCGTCTTTGTGCATTCGTCCATCCATCACA
65 TCAACCTCAGAAACGACCATAAAGTTAATTAATGGTCGTCTTTGTGCATTCGTCCATACATCACG
*
395443 TATAAGACTA
130 TACAAGACTA
395453 GATTAGTTTA
Statistics
Matches: 317, Mismatches: 15, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
193 1 0.00
194 311 0.98
195 5 0.02
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (193 bp):
AAGTTGCCACATAAAACTTATCCTTATACTCCTTTTCACAATTGACGCTTTCAAGAAAAACACTT
CAACCTCAGAAACGACCATAAAGTTAATTAATGGTCGTCTTTGTGCATTCGTCCATACATCACGT
ACAAGACTAATACATTTTTCCCTCCACATTTCCTTTATAGGTATTAACAACCTCTCTATGTTA
Found at i:395516 original size:13 final size:13
Alignment explanation
Indices: 395469--395519 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
395459 TTTAGCATTA
395469 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
* *
395482 CTTTTAAAAAATG
1 CTTTTGAAAAGTG
* *
395495 -TGGTGGAAAAGTG
1 CT-TTTGAAAAGTG
395508 CTTTTGAAAAGT
1 CTTTTGAAAAGT
395520 TTGGTTAAAG
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
12 1 0.04
13 26 0.93
14 1 0.04
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:395733 original size:30 final size:30
Alignment explanation
Indices: 395697--395768 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
395687 ACTTATTGTT
395697 AATATTTTAATATATGAAATATTAA-T-TTTA
1 AATATTTTAATA-AT-AAATATTAATTATTTA
*
395727 AATATTTCTAAGTAATTAATATTAATTATTTA
1 AATATTT-TAA-TAATAAATATTAATTATTTA
395759 AA-ATTTTAAT
1 AATATTTTAAT
395769 TAGATTATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
29 1 0.03
30 18 0.49
31 10 0.27
32 8 0.22
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (30 bp):
AATATTTTAATAATAAATATTAATTATTTA
Found at i:396931 original size:22 final size:21
Alignment explanation
Indices: 396902--396945 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
396892 AAATAAAAAA
396902 TAAAAAATAAAAAAAAGTAAC
1 TAAAAAATAAAAAAAAGTAAC
* *
396923 TAAACAAATAAAATAATGTAAC
1 TAAA-AAATAAAAAAAAGTAAC
396945 T
1 T
396946 CATTCAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (21 bp):
TAAAAAATAAAAAAAAGTAAC
Done.