Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014954.1 Kokia drynarioides strain JFW-HI SEQ_129998, 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: 252428
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 875 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:206554 original size:24 final size:24
Alignment explanation
Indices: 206302--206553 Score: 236
Period size: 24 Copynumber: 10.5 Consensus size: 24
206292 ACAACAACTC
* *
206302 ATATACGTTTACACTCGTTAGCTT
1 ATATACGTTTACGCTCGTCAGCTT
** * * * *
206326 GCACACATTTACTCTCATC-GACTT
1 ATATACGTTTACGCTCGTCAG-CTT
*
206350 ATATACGTTTACGCTCATCAGCTT
1 ATATACGTTTACGCTCGTCAGCTT
*
206374 ATATTCGTTTACGCTCGTCAGCTT
1 ATATACGTTTACGCTCGTCAGCTT
*
206398 ATATACATTTACGCTCGTCAGCTT
1 ATATACGTTTACGCTCGTCAGCTT
** * *
206422 GCACACATTTACGCTCGTCAGCTT
1 ATATACGTTTACGCTCGTCAGCTT
*
206446 ATATACGTTTACGCTCGTCAACTT
1 ATATACGTTTACGCTCGTCAGCTT
** * * *
206470 GCACACGTTTACGCTCATCAACTT
1 ATATACGTTTACGCTCGTCAGCTT
*
206494 ATATACATTTACGCTCGTCAGCTT
1 ATATACGTTTACGCTCGTCAGCTT
** * * *
206518 GCATACATTTACACTCGTCAACTT
1 ATATACGTTTACGCTCGTCAGCTT
*
206542 ATATATGTTTAC
1 ATATACGTTTAC
206554 AATATTTCAT
Statistics
Matches: 184, Mismatches: 42, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
23 1 0.01
24 182 0.99
25 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.12, T:0.37
Consensus pattern (24 bp):
ATATACGTTTACGCTCGTCAGCTT
Found at i:212009 original size:21 final size:21
Alignment explanation
Indices: 211983--212028 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
211973 CGAGCTTGGT
* * *
211983 TTTAAAGTTTGTGGTTCATGG
1 TTTAAAGTTTGAGGATCAGGG
212004 TTTAAAGTTTGAGGATCAGGG
1 TTTAAAGTTTGAGGATCAGGG
212025 TTTA
1 TTTA
212029 GGGTTTAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.04, G:0.28, T:0.43
Consensus pattern (21 bp):
TTTAAAGTTTGAGGATCAGGG
Found at i:234969 original size:19 final size:19
Alignment explanation
Indices: 234947--234986 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
234937 TTTTACTTTT
*
234947 ATTATACTTTTCT-ATTCTA
1 ATTAAACTTTT-TGATTCTA
234966 ATTAAACTTTTTGATTCTA
1 ATTAAACTTTTTGATTCTA
234985 AT
1 AT
234987 AATAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (19 bp):
ATTAAACTTTTTGATTCTA
Found at i:236014 original size:15 final size:15
Alignment explanation
Indices: 235990--236038 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
235980 GATCTTTTTG
* *
235990 ACATTCTAATTCCGT
1 ACATTATAATTCCAT
236005 ACATTATAATTCCAT
1 ACATTATAATTCCAT
236020 ACATTATAATTCCAT
1 ACATTATAATTCCAT
236035 ACAT
1 ACAT
236039 AGACATAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.37, C:0.22, G:0.02, T:0.39
Consensus pattern (15 bp):
ACATTATAATTCCAT
Found at i:240231 original size:19 final size:19
Alignment explanation
Indices: 240209--240248 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
240199 TTTTACTTTT
*
240209 ATTATACTTTTCT-ATTCTA
1 ATTAAACTTTT-TGATTCTA
240228 ATTAAACTTTTTGATTCTA
1 ATTAAACTTTTTGATTCTA
240247 AT
1 AT
240249 AATAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (19 bp):
ATTAAACTTTTTGATTCTA
Found at i:241276 original size:15 final size:15
Alignment explanation
Indices: 241252--241300 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
241242 GATCTTTTTG
* *
241252 ACATTCTAATTCCGT
1 ACATTATAATTCCAT
241267 ACATTATAATTCCAT
1 ACATTATAATTCCAT
241282 ACATTATAATTCCAT
1 ACATTATAATTCCAT
241297 ACAT
1 ACAT
241301 AGACATAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.37, C:0.22, G:0.02, T:0.39
Consensus pattern (15 bp):
ACATTATAATTCCAT
Found at i:246463 original size:14 final size:14
Alignment explanation
Indices: 246444--246471 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
246434 TATATTAGTA
246444 TTTTCTATTCTATT
1 TTTTCTATTCTATT
246458 TTTTCTATTCTATT
1 TTTTCTATTCTATT
246472 AGTATTAGAT
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:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:246483 original size:5 final size:6
Alignment explanation
Indices: 246468--246518 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
246458 TTTTCTATTC
* *
246468 TATTAG TATTAG -ATTAG TATT-C TATT-C TATTAG TATTAG -ATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
246512 TATTAG T
1 TATTAG T
246519 TAGTGATCCC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
5 19 0.47
6 21 0.52
ACGTcount: A:0.31, C:0.04, G:0.14, T:0.51
Consensus pattern (6 bp):
TATTAG
Found at i:246483 original size:11 final size:12
Alignment explanation
Indices: 246468--246518 Score: 56
Period size: 11 Copynumber: 4.6 Consensus size: 12
246458 TTTTCTATTC
246468 TATTAGTATTAG
1 TATTAGTATTAG
*
246480 -ATTAGTATT-C
1 TATTAGTATTAG
*
246490 TATT-CTATTAG
1 TATTAGTATTAG
246501 TATTAG-ATTAG
1 TATTAGTATTAG
246512 TATTAGT
1 TATTAGT
246519 TAGTGATCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
10 4 0.13
11 27 0.87
ACGTcount: A:0.31, C:0.04, G:0.14, T:0.51
Consensus pattern (12 bp):
TATTAGTATTAG
Found at i:246490 original size:27 final size:27
Alignment explanation
Indices: 246460--246515 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
246450 ATTCTATTTT
246460 TTCTATTCTATTAGTATTAGATTAGTA
1 TTCTATTCTATTAGTATTAGATTAGTA
246487 TTCTATTCTATTAGTATTAGATTAGTA
1 TTCTATTCTATTAGTATTAGATTAGTA
246514 TT
1 TT
246516 AGTTAGTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.54
Consensus pattern (27 bp):
TTCTATTCTATTAGTATTAGATTAGTA
Found at i:251141 original size:29 final size:29
Alignment explanation
Indices: 251109--251358 Score: 248
Period size: 29 Copynumber: 8.5 Consensus size: 29
251099 TAAAATGGTA
*
251109 ATTTTTGGAAGTTTCGGGGTCAAAATGAG
1 ATTTTTGGAAGTTTCGGGGTAAAAATGAG
251138 ATTTTTGGAAGTTT-GGGAGTAAAAAT-AG
1 ATTTTTGGAAGTTTCGGG-GTAAAAATGAG
**
251166 AATTTTTGGAAGTTTCATGGTAAAAAATGAG
1 -ATTTTTGGAAGTTTCGGGGT-AAAAATGAG
*
251197 ATTTTTGGAAG-TTCGAGGGTAAAAA-CAG
1 ATTTTTGGAAGTTTCG-GGGTAAAAATGAG
251225 ATTTTTTGGAAGTTTCGGGGTCAAAAATG-G
1 A-TTTTTGGAAGTTTCGGGGT-AAAAATGAG
*
251255 TATTTTTGGAAGTTTGAGGGGTAAAATAT-A-
1 -ATTTTTGGAAGTTT-CGGGGTAAAA-ATGAG
* *
251285 ATTTTTGGAAGTTTTGGGGTCAAAAATGTG
1 ATTTTTGGAAGTTTCGGGGT-AAAAATGAG
*
251315 ATTTTTGGAAG-TTCGAGGGTAAAAACG-G
1 ATTTTTGGAAGTTTCG-GGGTAAAAATGAG
251343 AATTTTTGGATAGTTT
1 -ATTTTTGGA-AGTTT
251359 AGGGACCTCC
Statistics
Matches: 188, Mismatches: 12, Indels: 40
0.78 0.05 0.17
Matches are distributed among these distances:
28 16 0.09
29 95 0.51
30 65 0.35
31 12 0.06
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.36
Consensus pattern (29 bp):
ATTTTTGGAAGTTTCGGGGTAAAAATGAG
Found at i:251202 original size:59 final size:59
Alignment explanation
Indices: 251108--251358 Score: 330
Period size: 59 Copynumber: 4.3 Consensus size: 59
251098 GTAAAATGGT
* *
251108 AATTTTTGGAAGTTTCGGGGTC-AAAATGAGATTTTTGGAAGTTTG-GGAGTAAAAATAG
1 AATTTTTGGAAGTTTCGGGGTCAAAAATGAGATTTTTGGAAGTTCGAGG-GTAAAAACAG
** *
251166 AATTTTTGGAAGTTTCATGGTAAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAAACAG
1 AATTTTTGGAAGTTTCGGGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAAACAG
* * * *
251225 ATTTTTTGGAAGTTTCGGGGTCAAAAATG-GTATTTTTGGAAGTTTGAGGGGT-AAAATAT
1 AATTTTTGGAAGTTTCGGGGTCAAAAATGAG-ATTTTTGGAAGTTCGA-GGGTAAAAACAG
* * *
251284 AATTTTTGGAAGTTTTGGGGTCAAAAATGTGATTTTTGGAAGTTCGAGGGTAAAAACGG
1 AATTTTTGGAAGTTTCGGGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAAACAG
251343 AATTTTTGGATAGTTT
1 AATTTTTGGA-AGTTT
251359 AGGGACCTCC
Statistics
Matches: 168, Mismatches: 18, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
58 24 0.14
59 132 0.79
60 12 0.07
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.36
Consensus pattern (59 bp):
AATTTTTGGAAGTTTCGGGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAAACAG
Done.