Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013801.1 Kokia drynarioides strain JFW-HI SEQ_128829, 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: 1823
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Found at i:245 original size:60 final size:60
Alignment explanation
Indices: 141--461 Score: 236
Period size: 59 Copynumber: 5.4 Consensus size: 60
131 GGAGGTCCCT
* * * * *
141 AAACTGTCCGAAAATTACATTTTTG-CCCCCAAACTTCAAAAAATTCCATTTTCGACCTCA
1 AAACT-TCCAAAAATTCCATTTTTGACCCCAAAACTTCTAAAAATTCCATTTTCGACCCCA
* * *
201 AAACTTCTAAAAATTCCATTTTCGACCCCAAAACTTCTAAAAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCTAAAAATTCCATTTTCGACCCCA
*
261 AAACTTCCAAAAATTCCATTTTTAACCCCAAAACTT-TCAAAAATTACCATTTT-G-CCCTC-
1 AAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCT-AAAAATT-CCATTTTCGACCC-CA
* * * * * *
320 GAA-TGTCCAAAATTTCCATTTTTAACCTCGAAGCTT-TCAAAAATTACCATTTT-G-CCCTC-
1 AAACT-TCCAAAAATTCCATTTTTGACCCCAAAACTTCT-AAAAATT-CCATTTTCGACCC-CA
* * * * * * * *
379 GAA-TGTCCAAAAATTCCTTTTTTAACCCGAAAACTTCCAAAAATTCAATTTT-TACCCCT
1 AAACT-TCCAAAAATTCCATTTTTGACCCCAAAACTTCTAAAAATTCCATTTTCGACCCCA
*
438 AAA-TGTCTAAAAATTCCATCTTTT
1 AAACT-TCCAAAAATTCCAT-TTTT
462 AACCTCGAAC
Statistics
Matches: 224, Mismatches: 28, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
58 8 0.04
59 127 0.57
60 82 0.37
61 7 0.03
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.33
Consensus pattern (60 bp):
AAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCTAAAAATTCCATTTTCGACCCCA
Found at i:330 original size:29 final size:29
Alignment explanation
Indices: 298--393 Score: 115
Period size: 29 Copynumber: 3.3 Consensus size: 29
288 CCAAAACTTT
298 CAAAAATTACCATTTTGCCCTCGAATGTC
1 CAAAAATTACCATTTTGCCCTCGAATGTC
* ** *
327 C-AAAATTTCCATTTTTAACCTCGAA-GCTTT
1 CAAAAATTACCA-TTTTGCCCTCGAATG--TC
357 CAAAAATTACCATTTTGCCCTCGAATGTC
1 CAAAAATTACCATTTTGCCCTCGAATGTC
386 CAAAAATT
1 CAAAAATT
394 CCTTTTTTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
28 10 0.19
29 21 0.39
30 13 0.24
31 10 0.19
ACGTcount: A:0.33, C:0.25, G:0.08, T:0.33
Consensus pattern (29 bp):
CAAAAATTACCATTTTGCCCTCGAATGTC
Found at i:357 original size:59 final size:58
Alignment explanation
Indices: 209--508 Score: 286
Period size: 59 Copynumber: 5.1 Consensus size: 58
199 CAAAACTTCT
** * * * *
209 AAAAATTCCATTTTCGACCCCAAAACTTCTAAAAATT-CCATTTTTGACCCCAAAACT-TCC
1 AAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTACCA-TTTTG-CCCC-GAA-TGTCC
* * *
269 AAAAATTCCATTTTTAACCCCAAAACTTTCAAAAATTACCATTTTGCCCTCGAATGTCC
1 AAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTACCATTTTGCCC-CGAATGTCC
* * *
328 AAAATTTCCATTTTTAACCTCGAAGCTTTCAAAAATTACCATTTTGCCCTCGAATGTCC
1 AAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTACCATTTTGCCC-CGAATGTCC
* * * * *
387 AAAAATTCCTTTTTTAACC-CGAAAACTTCCAAAAATT-CAATTTTTACCCCTAAATGTCT
1 AAAAATTCCATTTTTAACCTCG-AAACTTCCAAAAATTACCA-TTTTGCCCC-GAATGTCC
* * *
446 AAAAATTCCATCTTTTAACCTCG-AACTTCCCCAAAATTACCATCTTGCCCCGAAAGTCC
1 AAAAATTCCAT-TTTTAACCTCGAAACTT-CCAAAAATTACCATTTTGCCCCGAATGTCC
505 AAAA
1 AAAA
509 TTAGCATTTT
Statistics
Matches: 205, Mismatches: 25, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
58 6 0.03
59 130 0.63
60 62 0.30
61 7 0.03
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.32
Consensus pattern (58 bp):
AAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTACCATTTTGCCCCGAATGTCC
Found at i:420 original size:30 final size:31
Alignment explanation
Indices: 141--470 Score: 221
Period size: 30 Copynumber: 11.0 Consensus size: 31
131 GGAGGTCCCT
* * **
141 AAACTGTCCGAAAATTACATTTTTG-CC-CCC
1 AAACT-TCCAAAAATTCCATTTTTGACCTCGA
* *
171 AAACTTCAAAAAATTCCATTTTCGACCTC-A
1 AAACTTCCAAAAATTCCATTTTTGACCTCGA
* * *
201 AAACTTCTAAAAATTCCATTTTCGACC-CCA
1 AAACTTCCAAAAATTCCATTTTTGACCTCGA
* *
231 AAACTTCTAAAAATTCCATTTTTGACC-CCA
1 AAACTTCCAAAAATTCCATTTTTGACCTCGA
* *
261 AAACTTCCAAAAATTCCATTTTTAACC-CCA
1 AAACTTCCAAAAATTCCATTTTTGACCTCGA
* *
291 AAACTTTCAAAAATTACCA-TTTTGCCCTCG-
1 AAACTTCCAAAAATT-CCATTTTTGACCTCGA
* *
321 -AA-TGTCCAAAATTTCCATTTTTAACCTCG-
1 AAACT-TCCAAAAATTCCATTTTTGACCTCGA
* * *
350 AAGCTTTCAAAAATTACCA-TTTTGCCCTCG-
1 AAACTTCCAAAAATT-CCATTTTTGACCTCGA
* *
380 -AA-TGTCCAAAAATTCCTTTTTTAACC-CGA
1 AAACT-TCCAAAAATTCCATTTTTGACCTCGA
* **
409 AAACTTCCAAAAATTCAATTTTT-ACC-CCT
1 AAACTTCCAAAAATTCCATTTTTGACCTCGA
* *
438 AAA-TGTCTAAAAATTCCATCTTTTAACCTCGA
1 AAACT-TCCAAAAATTCCAT-TTTTGACCTCGA
470 A
1 A
471 CTTCCCCAAA
Statistics
Matches: 246, Mismatches: 35, Indels: 36
0.78 0.11 0.11
Matches are distributed among these distances:
28 10 0.04
29 70 0.28
30 151 0.61
31 13 0.05
32 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (31 bp):
AAACTTCCAAAAATTCCATTTTTGACCTCGA
Done.