Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001537.1 Kokia drynarioides strain JFW-HI SEQ_113107, 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, 895
Length: 1493
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.37
Found at i:100 original size:60 final size:59
Alignment explanation
Indices: 2--239 Score: 252
Period size: 60 Copynumber: 4.0 Consensus size: 59
1 C
* *
2 AAACTTTTCAAAAATTATATTTTGA-CCTCCAAAGTTCTCCAAAATTATATTTTTGACTCT
1 AAACTTTTCAAAAATTACATTTTGACCCT-CAAACTTCTCCAAAATTATATTTTTGAC-CT
* ** *
62 GAACTTTTTGAAAATTACATTTTCACCCTCAAACTTCTCCAAAATTATATTTTTGACCTT
1 AAACTTTTCAAAAATTACATTTTGACCCTCAAACTTCTCCAAAATTATATTTTTGACC-T
* * *
122 AAACTTTTTCAAAAATTTCATTTTGACCCATCAAACTTC-CTTAAAATTATA-TTTTAACCCT
1 AAAC-TTTTCAAAAATTACATTTTGACCC-TCAAACTTCTC-CAAAATTATATTTTTGA-CCT
* * * *
183 AAACTTTCCAAAAATTACATTTTTACCCCCAAACTT-GCCAAAATT-TCATTTTTGACC
1 AAACTTTTCAAAAATTACATTTTGACCCTCAAACTTCTCCAAAATTAT-ATTTTTGACC
240 CGATTTTCCT
Statistics
Matches: 150, Mismatches: 19, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
57 1 0.01
58 9 0.06
59 14 0.09
60 72 0.48
61 34 0.23
62 20 0.13
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (59 bp):
AAACTTTTCAAAAATTACATTTTGACCCTCAAACTTCTCCAAAATTATATTTTTGACCT
Found at i:196 original size:29 final size:29
Alignment explanation
Indices: 2--240 Score: 155
Period size: 30 Copynumber: 8.0 Consensus size: 29
1 C
* *
2 AAACTTTTCAAAAATTATATTTTGACCTCC
1 AAACTTTCCAAAAATTATATTTTGACC-CT
* *
32 AAAGTTCTCC-AAAATTATATTTTTGACTCT
1 AAACTT-TCCAAAAATTATA-TTTTGACCCT
* *** * *
62 GAACTTTTTGAAAATTACATTTTCACCCT
1 AAACTTTCCAAAAATTATATTTTGACCCT
*
91 CAAACTTCTCC-AAAATTATATTTTTGACCTT
1 -AAACTT-TCCAAAAATTATA-TTTTGACCCT
*
122 AAACTTTTTCAAAAATT-TCATTTTGACCCAT
1 AAAC-TTTCCAAAAATTAT-ATTTTGACCC-T
* *
153 CAAAC-TTCCTTAAAATTATATTTTAACCCT
1 -AAACTTTCC-AAAAATTATATTTTGACCCT
* * *
183 AAACTTTCCAAAAATTACATTTTTACCCCC
1 AAACTTTCCAAAAATTATATTTTGA-CCCT
* *
213 AAACTTGCCAAAATTTCAT-TTTTGACCC
1 AAACTTTCCAAAAATT-ATATTTTGACCC
241 GATTTTCCTA
Statistics
Matches: 163, Mismatches: 30, Indels: 33
0.72 0.13 0.15
Matches are distributed among these distances:
29 29 0.18
30 85 0.52
31 44 0.27
32 5 0.03
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (29 bp):
AAACTTTCCAAAAATTATATTTTGACCCT
Found at i:254 original size:29 final size:28
Alignment explanation
Indices: 188--295 Score: 85
Period size: 29 Copynumber: 3.8 Consensus size: 28
178 ACCCTAAACT
* *
188 TTCCAAAAATTACATTTTT-ACCCCCAAAC
1 TTCCAAAAATTTCATTTTTGA--CCCGAAC
**
217 TTGCC-AAAATTTCATTTTTGACCCGATT
1 TT-CCAAAAATTTCATTTTTGACCCGAAC
***
245 TTCCTAAAAATTATCATTTTACCCCCGAAC
1 TTCC-AAAAATT-TCATTTTTGACCCGAAC
*
275 TTCCAAAAATTCCATTTTTGA
1 TTCCAAAAATTTCATTTTTGA
296 TCTTTTTCCA
Statistics
Matches: 61, Mismatches: 13, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
27 2 0.03
28 12 0.20
29 28 0.46
30 19 0.31
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (28 bp):
TTCCAAAAATTTCATTTTTGACCCGAAC
Found at i:254 original size:58 final size:55
Alignment explanation
Indices: 187--325 Score: 174
Period size: 58 Copynumber: 2.5 Consensus size: 55
177 AACCCTAAAC
*
187 TTTCCAAAAATTA-CATTTTTACCCCCAAACTTGCC-AAAATTTCATTTTTGACCCGAT
1 TTTCCAAAAATTACCA-TTTTACCCCCAAACTT-CCAAAAATTCCATTTTTGA-CC-AT
* * * *
244 TTTCCTAAAAATTATCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGATCTT
1 TTTCC-AAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCAT
300 TTTCCAAAAATTACCATTTTACCCCC
1 TTTCCAAAAATTACCATTTTACCCCC
326 GAATGTTTAA
Statistics
Matches: 74, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
55 20 0.27
56 6 0.08
57 8 0.11
58 38 0.51
59 2 0.03
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.38
Consensus pattern (55 bp):
TTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCAT
Found at i:356 original size:28 final size:29
Alignment explanation
Indices: 306--406 Score: 84
Period size: 28 Copynumber: 3.5 Consensus size: 29
296 TCTTTTTCCA
* *
306 AAAATTACCA-TTTTACCCCCGAATGTTT-
1 AAAATTACCATTTTTAACCACGAA-GTTTC
334 AAAATT-CCATTTTTAACCACGAAGTTTCCC
1 AAAATTACCATTTTTAACCACGAAGTTT--C
* * * * *
364 AAAATTACCATTTTT-CCCTCGAGGGTCC
1 AAAATTACCATTTTTAACCACGAAGTTTC
392 AAAATTACCATTTTT
1 AAAATTACCATTTTT
407 CCCCCCGGTA
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
27 7 0.11
28 33 0.54
30 13 0.21
31 8 0.13
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.36
Consensus pattern (29 bp):
AAAATTACCATTTTTAACCACGAAGTTTC
Done.