Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010024.1 Kokia drynarioides strain JFW-HI SEQ_124789, 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, 686
Length: 1144
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Found at i:567 original size:30 final size:29
Alignment explanation
Indices: 506--846 Score: 226
Period size: 30 Copynumber: 11.9 Consensus size: 29
496 GTCCTTAAAC
* **
506 CTTCCAAAAAT-TCCGTTTTTACCCCCGAA
1 CTTCCAAAAATCT-CATTTTTACCCCAAAA
*
535 CTTCCAAAAATCTCATTTTTGACCCCGAAA
1 CTTCCAAAAATCTCATTTTT-ACCCCAAAA
**
565 CTTCCAAAAAT-TCCATTTTTACCCCCGAA
1 CTTCCAAAAATCT-CATTTTTACCCCAAAA
*
594 CTTCC----A--T--TTTTGACCCCAAAA
1 CTTCCAAAAATCTCATTTTTACCCCAAAA
* *
615 C-TCCAAAAAAT-TCCTTTTTTACCCCTAAA
1 CTTCC-AAAAATCT-CATTTTTACCCCAAAA
* * *
644 CTTCTAAAAATCCCATTTTTAACCTCAAAA
1 CTTCCAAAAATCTCATTTTT-ACCCCAAAA
* * *
674 CTTCTAAAAATCACATTTTTGACCCTAAAA
1 CTTCCAAAAATCTCATTTTT-ACCCCAAAA
** *
704 CTTCTTAAAAT-TCTATTTTTACCCCTAAA
1 CTTCCAAAAATCTC-ATTTTTACCCCAAAA
*
733 CTTCCAAAAATCCCATTTTTTACCCCAAAA
1 CTTCCAAAAATCTCA-TTTTTACCCCAAAA
**
763 CTTCCAAAAAT-TCTATTTTTACCCCCGAA
1 CTTCCAAAAATCTC-ATTTTTACCCCAAAA
* * *
792 CTTCCAAAAATCCCATTTTTGACCTCAAATT
1 CTTCCAAAAATCTCATTTTT-ACCCCAAA-A
* * *
823 TTTCCAAAAATATC-GTTTTACCCC
1 CTTCCAAAAATCTCATTTTTACCCC
847 CGGGTATCCG
Statistics
Matches: 250, Mismatches: 40, Indels: 44
0.75 0.12 0.13
Matches are distributed among these distances:
20 3 0.01
21 12 0.05
24 1 0.00
25 2 0.01
26 1 0.00
29 107 0.43
30 113 0.45
31 11 0.04
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (29 bp):
CTTCCAAAAATCTCATTTTTACCCCAAAA
Found at i:598 original size:59 final size:58
Alignment explanation
Indices: 506--846 Score: 267
Period size: 59 Copynumber: 5.9 Consensus size: 58
496 GTCCTTAAAC
* ** *
506 CTTCCAAAAATTCCGTTTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCCGAAA
1 CTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATCTCATTTTT-ACCCCAAAA
** *
565 CTTCCAAAAATTCCATTTTTACCCCCGAACTTCC----A--T--TTTTGACCCCAAAA
1 CTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATCTCATTTTTACCCCAAAA
* * * * *
615 C-TCCAAAAAATTCCTTTTTTACCCCTAAACTTCTAAAAATCCCATTTTTAACCTCAAAA
1 CTTCC-AAAAATTCCATTTTTACCCCAAAACTTCCAAAAATCTCATTTTT-ACCCCAAAA
* * ** *
674 CTTCTAAAAA-TCACATTTTTGACCCTAAAACTTCTTAAAAT-TCTATTTTTACCCCTAAA
1 CTTCCAAAAATTC-CATTTTT-ACCCCAAAACTTCCAAAAATCTC-ATTTTTACCCCAAAA
* **
733 CTTCCAAAAATCCCATTTTTTACCCCAAAACTTCCAAAAAT-TCTATTTTTACCCCCGAA
1 CTTCCAAAAATTCCA-TTTTTACCCCAAAACTTCCAAAAATCTC-ATTTTTACCCCAAAA
* * ** * *
792 CTTCCAAAAATCCCATTTTTGACCTCAAATTTTTCCAAAAATATC-GTTTTACCCC
1 CTTCCAAAAATTCCATTTTT-ACCCCAAA-ACTTCCAAAAATCTCATTTTTACCCC
847 CGGGTATCCG
Statistics
Matches: 234, Mismatches: 29, Indels: 38
0.78 0.10 0.13
Matches are distributed among these distances:
49 3 0.01
50 34 0.15
51 4 0.02
53 1 0.00
54 1 0.00
55 1 0.00
58 11 0.05
59 136 0.58
60 41 0.18
61 2 0.01
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (58 bp):
CTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATCTCATTTTTACCCCAAAA
Found at i:616 original size:21 final size:20
Alignment explanation
Indices: 568--616 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
558 CCCGAAACTT
*
568 CCAAAAATTCCATTTTTACC
1 CCAAAACTTCCATTTTTACC
**
588 CCCGAACTTCCATTTTTGACC
1 CCAAAACTTCCATTTTT-ACC
609 CCAAAACT
1 CCAAAACT
617 CCAAAAAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.31, C:0.35, G:0.04, T:0.31
Consensus pattern (20 bp):
CCAAAACTTCCATTTTTACC
Found at i:646 original size:50 final size:50
Alignment explanation
Indices: 548--647 Score: 148
Period size: 50 Copynumber: 2.0 Consensus size: 50
538 CCAAAAATCT
* *
548 CATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTC
1 CATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTC
* *
598 CATTTTTGACCCCAAAAC-TCCAAAAAATTCCTTTTTTACCCCTAAACTTC
1 CATTTTTGACCCCAAAACTTCC-AAAAATTCCATTTTTACCCCCAAACTTC
648 TAAAAATCCC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 3 0.07
50 42 0.93
ACGTcount: A:0.30, C:0.33, G:0.04, T:0.33
Consensus pattern (50 bp):
CATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTC
Found at i:782 original size:89 final size:89
Alignment explanation
Indices: 598--773 Score: 264
Period size: 89 Copynumber: 2.0 Consensus size: 89
588 CCCGAACTTC
*
598 CATTTTTGACCCCAAAACTCCAAAAAATTCCTTTTTTACCCCTAAACTTCTAAAAATCCCATTTT
1 CATTTTTGACCCCAAAACTCCAAAAAATTCCTTTTTTACCCCTAAACTTCCAAAAATCCCATTTT
* *
663 TAACCTCAAAACTTCTAAAAATCA
66 TAACCCCAAAACTTCCAAAAATCA
* * **
687 CATTTTTGACCCTAAAACTTCTTAAAATT-CTATTTTTACCCCTAAACTTCCAAAAATCCCATTT
1 CATTTTTGACCCCAAAACTCCAAAAAATTCCT-TTTTTACCCCTAAACTTCCAAAAATCCCATTT
*
751 TTTACCCCAAAACTTCCAAAAAT
65 TTAACCCCAAAACTTCCAAAAAT
774 TCTATTTTTA
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
88 2 0.03
89 76 0.97
ACGTcount: A:0.37, C:0.28, G:0.01, T:0.34
Consensus pattern (89 bp):
CATTTTTGACCCCAAAACTCCAAAAAATTCCTTTTTTACCCCTAAACTTCCAAAAATCCCATTTT
TAACCCCAAAACTTCCAAAAATCA
Done.