Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003532.1 Kokia drynarioides strain JFW-HI SEQ_116376, 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, 757
Length: 1263
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Found at i:244 original size:30 final size:30
Alignment explanation
Indices: 210--332 Score: 101
Period size: 29 Copynumber: 4.2 Consensus size: 30
200 ATTTTCCAAA
* *
210 AAACTTTTTTAAATTTACA-TTTTAGCCTCT
1 AAACTTTTTAAAAATTACACTTTTA-CCTCT
* *
240 AAACTTCTCAAAAATTACACTTTTACCTC-
1 AAACTTTTTAAAAATTACACTTTTACCTCT
* * * * *
269 GAAC-TTCTAAAAATTACATTTTTGCCCCT
1 AAACTTTTTAAAAATTACACTTTTACCTCT
* * *
298 AAAC-TTTTGAAAATTACATTTTTACCTCC
1 AAACTTTTTAAAAATTACACTTTTACCTCT
327 AAACTT
1 AAACTT
333 CCAAAAATCA
Statistics
Matches: 73, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
28 18 0.25
29 30 0.41
30 20 0.27
31 5 0.07
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.41
Consensus pattern (30 bp):
AAACTTTTTAAAAATTACACTTTTACCTCT
Found at i:281 original size:29 final size:29
Alignment explanation
Indices: 224--579 Score: 220
Period size: 29 Copynumber: 12.3 Consensus size: 29
214 TTTTTTAAAT
224 TTACA-TTTTAGCCTCTAAACTTCTCAAAAA
1 TTACATTTTTA-CCTC-AAACTTCTCAAAAA
* *
254 TTACACTTTTACCTCGAACTTCT-AAAAA
1 TTACATTTTTACCTCAAACTTCTCAAAAA
* * **
282 TTACATTTTTGCCCCTAAACTT-TTGAAAA
1 TTACATTTTTACCTC-AAACTTCTCAAAAA
311 TTACATTTTTACCTCCAAACTTC-CAAAAA
1 TTACATTTTTACCT-CAAACTTCTCAAAAA
*
340 TCACATTTTTACCCTCAAACTTC-CAAAAA
1 TTACATTTTTA-CCTCAAACTTCTCAAAAA
* * * * * *
369 TCATATTTTTGCCCCTGAACTT-GCAAAAA
1 TTACATTTTTACCTC-AAACTTCTCAAAAA
* *
398 TCACATTTTTACCCTCGATA-TTC-CAAAAA
1 TTACATTTTTA-CCTC-AAACTTCTCAAAAA
*
427 TTACA-TTTTACCCCTAAACTTC-CAAAAA
1 TTACATTTTTACCTC-AAACTTCTCAAAAA
* * *
455 TCATATTTTTACC-CTGAACTTCTCAAAAA
1 TTACATTTTTACCTC-AAACTTCTCAAAAA
* * * *
484 TCACTTTTTTACCCCAAAC-TCTCCCAAAA
1 TTACATTTTTACCTCAAACTTCT-CAAAAA
* * *
513 TGACATTTTTACCCTTAAAACTT-TCCAAAA
1 TTACATTTTTA-CC-TCAAACTTCTCAAAAA
* * *
543 TTACATTTTAACCCCAAAC-TCTCCAAAAC
1 TTACATTTTTACCTCAAACTTCT-CAAAAA
572 TT-CATTTT
1 TTACATTTT
580 AAACCTCATT
Statistics
Matches: 264, Mismatches: 42, Indels: 42
0.76 0.12 0.12
Matches are distributed among these distances:
27 6 0.02
28 60 0.23
29 152 0.58
30 35 0.13
31 10 0.04
32 1 0.00
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (29 bp):
TTACATTTTTACCTCAAACTTCTCAAAAA
Found at i:361 original size:87 final size:88
Alignment explanation
Indices: 229--551 Score: 322
Period size: 87 Copynumber: 3.7 Consensus size: 88
219 TAAATTTACA
* * * * * *
229 TTTTAGCCTCTAAACTTCTCAAAAATTACACTTTTA-CCTCGAACTTCTAAAAATTACATTTTTG
1 TTTTACCCTCCAAACTTC-CAAAAATTACATTTTTACCCTCAAACTTCCAAAAATCACATTTTTG
** *
293 CCCCTAAACTTTTGAAAATTACAT
65 CCCCTAAACTTTCAAAAATCACAT
* *
317 TTTTA-CCTCCAAACTTCCAAAAATCACATTTTTACCCTCAAACTTCCAAAAATCATATTTTTGC
1 TTTTACCCTCCAAACTTCCAAAAATTACATTTTTACCCTCAAACTTCCAAAAATCACATTTTTGC
* *
381 CCCTGAACTTGCAAAAATCACAT
66 CCCTAAACTTTCAAAAATCACAT
* * *
404 TTTTACCCTCGATA-TTCCAAAAATTACA-TTTTACCC-CTAAACTTCCAAAAATCATATTTTT-
1 TTTTACCCTCCAAACTTCCAAAAATTACATTTTTACCCTC-AAACTTCCAAAAATCACATTTTTG
* * *
465 ACCCTGAACTTCTCAAAAATCACTT
65 CCCCTAAACTT-TCAAAAATCACAT
* * * *
490 TTTTA-CC-CCAAACTCTCCCAAAATGACATTTTTACCCTTAAAACTTTCC-AAAATTACATTTT
1 TTTTACCCTCCAAACT-TCCAAAAATTACATTTTTACCC-TCAAAC-TTCCAAAAATCACATTTT
552 AACCCCAAAC
Statistics
Matches: 200, Mismatches: 25, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
84 3 0.01
85 14 0.07
86 73 0.37
87 80 0.40
88 26 0.13
89 4 0.02
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (88 bp):
TTTTACCCTCCAAACTTCCAAAAATTACATTTTTACCCTCAAACTTCCAAAAATCACATTTTTGC
CCCTAAACTTTCAAAAATCACAT
Found at i:579 original size:58 final size:56
Alignment explanation
Indices: 229--570 Score: 303
Period size: 58 Copynumber: 5.9 Consensus size: 56
219 TAAATTTACA
* * * * * *
229 TTTTAGCCTCTAAACTTCTCAAAAATTACACTTTTACCTCGAACTTCTAAAAATTACAT
1 TTTTA-CC-CTAAACTT-TCCAAAATTACATTTTTACCCCAAACTTCCAAAAATCACAT
* **
288 TTTTGCCCCTAAACTTTTGAAAATTACATTTTTACCTCCAAACTTCCAAAAATCACAT
1 TTTT-ACCCTAAACTTTCCAAAATTACATTTTTACC-CCAAACTTCCAAAAATCACAT
* * * * *
346 TTTTACCCTCAAAC-TTCCAAAAATCATATTTTTGCCCCTGAACTTGCAAAAATCACAT
1 TTTTACCCT-AAACTTTCC-AAAATTACATTTTTACCCC-AAACTTCCAAAAATCACAT
** *
404 TTTTACCCTCGA-TATTCCAAAAATTACA-TTTTACCCCTAAACTTCCAAAAATCATAT
1 TTTTACCCTAAACT-TTCC-AAAATTACATTTTTACCCC-AAACTTCCAAAAATCACAT
* * * * * *
461 TTTTACCCTGAACTTCTCAAAAATCACTTTTTTACCCCAAACTCTCCCAAAATGACAT
1 TTTTACCCTAAACTT-TCCAAAATTACATTTTTACCCCAAACT-TCCAAAAATCACAT
*
519 TTTTACCCTTAAAACTTTCCAAAATTACATTTTAACCCCAAACTCTCCAAAA
1 TTTTACCC-T-AAACTTTCCAAAATTACATTTTTACCCCAAACT-TCCAAAA
571 CTTCATTTTA
Statistics
Matches: 232, Mismatches: 38, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
57 74 0.32
58 116 0.50
59 37 0.16
60 5 0.02
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (56 bp):
TTTTACCCTAAACTTTCCAAAATTACATTTTTACCCCAAACTTCCAAAAATCACAT
Found at i:998 original size:97 final size:97
Alignment explanation
Indices: 831--1021 Score: 285
Period size: 97 Copynumber: 2.0 Consensus size: 97
821 AAAATATTCA
* * * **
831 AAATCGAGGCAATATTCCTTTATTTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGACGTGAT
1 AAATCGAGGAAATATTCCTTTATCTCGGGTTTTGAAAATTTGTGCCCTAACTTACTAGACACGAT
*
896 ATTTCTTCAAACCGGGATAATCGAATACCCTT
66 ATTTCTTCAAACCAGGATAATCGAATACCCTT
*
928 AAATCGAGGAAATATTCCTTTATCTCGGGTTTTGAAAAATTT-TGCCCTAACTTACTAGGCACGA
1 AAATCGAGGAAATATTCCTTTATCTCGGGTTTTG-AAAATTTGTGCCCTAACTTACTAGACACGA
* *
992 TTTTTCTTCAAACCAGGATAATTGAATACC
65 TATTTCTTCAAACCAGGATAATCGAATACC
1022 TTTTTTTCAA
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
97 77 0.92
98 7 0.08
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (97 bp):
AAATCGAGGAAATATTCCTTTATCTCGGGTTTTGAAAATTTGTGCCCTAACTTACTAGACACGAT
ATTTCTTCAAACCAGGATAATCGAATACCCTT
Done.