Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005486.1 Kokia drynarioides strain JFW-HI SEQ_119547, 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, 802
Length: 1337
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Found at i:350 original size:30 final size:29
Alignment explanation
Indices: 310--577 Score: 142
Period size: 30 Copynumber: 9.1 Consensus size: 29
300 AAAGGTCCCT
310 AAACTATCCAAAAATTCCATTTTCCACCTCG
1 AAACT-TCCAAAAATTCCATTTT-CACCTCG
* * *
341 AAACTTCCAAAAATTTCATTTTTGACCTCA
1 AAACTTCCAAAAATTCCA-TTTTCACCTCG
* * *
371 AAACTTTCAAAAATTCCATTTTTATCCCCG
1 AAACTTCCAAAAATTCCATTTTCA-CCTCG
* * *
401 -AACTTCCAAAAATTCTAATTTTAACC-CTA
1 AAACTTCCAAAAATTC-CATTTTCACCTC-G
* * *
430 AAACTTTCAAAAATTCCATTTTTACCCCCG
1 AAACTTCCAAAAATTCCATTTTCA-CCTCG
* * * *
460 -AACCTCCAAAATTTCCATTTTTGACC-CTA
1 AAACTTCCAAAAATTCCA-TTTTCACCTC-G
* * * *
489 AAACTTTCAAAAAATACCA-TTTCACCCCC
1 AAAC-TTCCAAAAATTCCATTTTCACCTCG
*
518 AAA-TGTCC-AAAACTCCATTTTCGACCTCG
1 AAACT-TCCAAAAATTCCATTTTC-ACCTCG
547 AAAC-TCTC-AAAATTACCATTTTGC-CCTCG
1 AAACTTC-CAAAAATT-CCATTTT-CACCTCG
576 AA
1 AA
578 TATCCAAAAT
Statistics
Matches: 185, Mismatches: 33, Indels: 40
0.72 0.13 0.16
Matches are distributed among these distances:
27 8 0.04
28 10 0.05
29 72 0.39
30 74 0.40
31 21 0.11
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTCACCTCG
Found at i:404 original size:29 final size:28
Alignment explanation
Indices: 311--486 Score: 145
Period size: 30 Copynumber: 5.9 Consensus size: 28
301 AAGGTCCCTA
* *
311 AACTATCCAAAAATTCCATTTTCCACCTCG
1 AACT-TCCAAAAATTCCATTTT-TACCCCG
* **
341 AAACTTCCAAAAATTTCATTTTTGACCTCAA
1 -AACTTCCAAAAATTCCATTTTT-ACC-CCG
*
372 AACTTTCAAAAATTCCATTTTTATCCCCG
1 AACTTCCAAAAATTCCATTTTTA-CCCCG
* * **
401 AACTTCCAAAAATTCTAATTTTAACCCTAA
1 AACTTCCAAAAATTC-CATTTTTACCC-CG
*
431 AACTTTCAAAAATTCCATTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTA-CCCCG
* *
460 AACCTCCAAAATTTCCATTTTTGACCC
1 AACTTCCAAAAATTCCATTTTT-ACCC
487 TAAAACTTTC
Statistics
Matches: 116, Mismatches: 22, Indels: 16
0.75 0.14 0.10
Matches are distributed among these distances:
29 47 0.41
30 65 0.56
31 4 0.03
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (28 bp):
AACTTCCAAAAATTCCATTTTTACCCCG
Found at i:434 original size:59 final size:58
Alignment explanation
Indices: 318--510 Score: 237
Period size: 59 Copynumber: 3.2 Consensus size: 58
308 CTAAACTATC
* *
318 CAAAAATTCCATTTTCCACCTCGAAACTTCCAAAAATT-TCATTTTTGA-CCTCAAAACTTT
1 CAAAAATTCCATTTT-TACCCCG-AACTTCCAAAAATTCT-ATTTTTGACCCT-AAAACTTT
* *
378 CAAAAATTCCATTTTTATCCCCGAACTTCCAAAAATTCTAATTTTAACCCTAAAACTTT
1 CAAAAATTCCATTTTTA-CCCCGAACTTCCAAAAATTCTATTTTTGACCCTAAAACTTT
* * *
437 CAAAAATTCCATTTTTACCCCCGAACCTCCAAAATTTCCATTTTTGACCCTAAAACTTT
1 CAAAAATTCCATTTTTA-CCCCGAACTTCCAAAAATTCTATTTTTGACCCTAAAACTTT
*
496 CAAAAAATACCATTT
1 C-AAAAATTCCATTT
511 CACCCCCAAA
Statistics
Matches: 118, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
59 83 0.70
60 35 0.30
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (58 bp):
CAAAAATTCCATTTTTACCCCGAACTTCCAAAAATTCTATTTTTGACCCTAAAACTTT
Found at i:527 original size:59 final size:58
Alignment explanation
Indices: 318--594 Score: 217
Period size: 59 Copynumber: 4.7 Consensus size: 58
308 CTAAACTATC
* * *
318 CAAAAATTCCATTTTCCACCTCGAAACTTCCAAAAATTT-CATTTTTGA-CCTCAAAACTTT
1 CAAAAATTCCATTTT-TACCCCCAAA-TTCC-AAAATTTCCATTTTTGACCCT-AAAACTTT
* * * * * *
378 CAAAAATTCCATTTTTATCCCCGAACTTCCAAAAATTCTAATTTTAACCCTAAAACTTT
1 CAAAAATTCCATTTTTA-CCCCCAAATTCCAAAATTTCCATTTTTGACCCTAAAACTTT
**
437 CAAAAATTCCATTTTTACCCCCGAACCTCCAAAATTTCCATTTTTGACCCTAAAACTTT
1 CAAAAATTCCATTTTTACCCCC-AAATTCCAAAATTTCCATTTTTGACCCTAAAACTTT
* * * * * *
496 CAAAAAATACCA-TTTCACCCCCAAATGTCCAAAA-CTCCATTTTCGA-CCTCGAAACTCT
1 C-AAAAATTCCATTTTTACCCCCAAAT-TCCAAAATTTCCATTTTTGACCCT-AAAACTTT
* * * *
554 C-AAAATTACCA-TTTTGCCCTCGAATATCCAAAATTACCATT
1 CAAAAATT-CCATTTTTACCCCCAAAT-TCCAAAATTTCCATT
595 CCTCCCTCCG
Statistics
Matches: 179, Mismatches: 29, Indels: 20
0.79 0.13 0.09
Matches are distributed among these distances:
56 5 0.03
57 23 0.13
58 34 0.19
59 84 0.47
60 33 0.18
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (58 bp):
CAAAAATTCCATTTTTACCCCCAAATTCCAAAATTTCCATTTTTGACCCTAAAACTTT
Found at i:588 original size:28 final size:29
Alignment explanation
Indices: 523--594 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
513 CCCCCAAATG
*
523 TCCAAAACT-CCATTTTCGACCTCGAAAC
1 TCCAAAATTACCATTTTCGACCTCGAAAC
*
551 TCTCAAAATTACCATTTT-GCCCTCGAATA-
1 TC-CAAAATTACCATTTTCGACCTCGAA-AC
580 TCCAAAATTACCATT
1 TCCAAAATTACCATT
595 CCTCCCTCCG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 15 0.38
29 16 0.41
30 8 0.21
ACGTcount: A:0.33, C:0.31, G:0.06, T:0.31
Consensus pattern (29 bp):
TCCAAAATTACCATTTTCGACCTCGAAAC
Done.