Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010761.1 Kokia drynarioides strain JFW-HI SEQ_125720, 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, 606
Length: 1010
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.39
Found at i:491 original size:29 final size:29
Alignment explanation
Indices: 458--756 Score: 197
Period size: 30 Copynumber: 10.3 Consensus size: 29
448 CTAAACTATT
458 CAAAAATTACATTTTTACCCTCGAACTTC
1 CAAAAATTACATTTTTACCCTCGAACTTC
* *
487 CAAAAATTCCATTTTTGA-CCTTGAAACTTC
1 CAAAAATTACATTTTT-ACCCTCG-AACTTC
* * ***
517 CAAAAATTCCATTTTAACCCAAAAACTTC
1 CAAAAATTACATTTTTACCCTCGAACTTC
* *
546 CAAAAATTATATTTTTACCCCCCGAACTTC
1 CAAAAATTACATTTTTA-CCCTCGAACTTC
* *
576 CAAAAATTCCATTTTTAACCC-CAAAACTTC
1 CAAAAATTACATTTTT-ACCCTC-GAACTTC
* * *
606 CAAAAATTTCATTTTT-CCCCCGAACCTC
1 CAAAAATTACATTTTTACCCTCGAACTTC
* * *
634 CAAAAATTCCATTTTGA-CCTCGAAACTTT
1 CAAAAATTACATTTTTACCCTCG-AACTTC
*
663 C-AAAATTAC-TATTTCACCC-CGAA-TGTC
1 CAAAAATTACAT-TTTTACCCTCGAACT-TC
* * **
690 CAAAAATTTCATTTTTCATCC-CGATTTTC
1 CAAAAATTACATTTTT-ACCCTCGAACTTC
* *
719 TTAAAAATTACCA-TTTTACTCTCGAA-TGTC
1 -CAAAAATTA-CATTTTTACCCTCGAACT-TC
749 CAAAAATT
1 CAAAAATT
757 CCGTTTTTTA
Statistics
Matches: 214, Mismatches: 36, Indels: 40
0.74 0.12 0.14
Matches are distributed among these distances:
26 1 0.00
27 5 0.02
28 49 0.23
29 68 0.32
30 88 0.41
31 3 0.01
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (29 bp):
CAAAAATTACATTTTTACCCTCGAACTTC
Found at i:517 original size:30 final size:29
Alignment explanation
Indices: 458--705 Score: 222
Period size: 30 Copynumber: 8.6 Consensus size: 29
448 CTAAACTATT
*
458 CAAAAATTACATTTTTACCCTCG-AACTTC
1 CAAAAATTCCATTTTTACCC-CGAAACTTC
**
487 CAAAAATTCCATTTTTGACCTTGAAACTTC
1 CAAAAATTCCATTTTT-ACCCCGAAACTTC
* **
517 CAAAAATTCCATTTTAACCCAAAAACTTC
1 CAAAAATTCCATTTTTACCCCGAAACTTC
**
546 CAAAAATTATATTTTTACCCCCCG-AACTTC
1 CAAAAATTCCATTTTTA--CCCCGAAACTTC
*
576 CAAAAATTCCATTTTTAACCCCAAAACTTC
1 CAAAAATTCCATTTTT-ACCCCGAAACTTC
* * *
606 CAAAAATTTCATTTTTCCCCCG-AACCTC
1 CAAAAATTCCATTTTTACCCCGAAACTTC
* * *
634 CAAAAATTCCATTTTGACCTCGAAACTTT
1 CAAAAATTCCATTTTTACCCCGAAACTTC
* *
663 C-AAAATTAC-TATTTCACCCCG-AA-TGTC
1 CAAAAATTCCAT-TTTTACCCCGAAACT-TC
*
690 CAAAAATTTCATTTTT
1 CAAAAATTCCATTTTT
706 CATCCCGATT
Statistics
Matches: 177, Mismatches: 31, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
26 1 0.01
27 5 0.03
28 48 0.27
29 54 0.31
30 65 0.37
31 4 0.02
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.33
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCCGAAACTTC
Found at i:550 original size:59 final size:57
Alignment explanation
Indices: 458--704 Score: 232
Period size: 59 Copynumber: 4.3 Consensus size: 57
448 CTAAACTATT
* * *** * **
458 CAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTTGAAACTTC
1 CAAAAATTCCATTTTAACCCAAAAACTTCCAAAAATTACATTTTT-ACCCCG-AACTTC
*
517 CAAAAATTCCATTTTAACCCAAAAACTTCCAAAAATTATATTTTTACCCCCCGAACTTC
1 CAAAAATTCCATTTTAACCCAAAAACTTCCAAAAATTACATTTTTA--CCCCGAACTTC
* * * *
576 CAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTTCATTTTTCCCCCGAACCTC
1 CAAAAATTCCA-TTTTAACCCAAAAACTTCCAAAAATTACATTTTTACCCCGAACTTC
* * * *
634 CAAAAATTCCATTTTGACCTC-GAAACTTTC-AAAATTAC-TATTTCACCCCGAA-TGTC
1 CAAAAATTCCATTTTAACC-CAAAAACTTCCAAAAATTACAT-TTTTACCCCGAACT-TC
*
690 CAAAAATTTCATTTT
1 CAAAAATTCCATTTT
705 TCATCCCGAT
Statistics
Matches: 160, Mismatches: 22, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
55 1 0.01
56 33 0.21
57 14 0.09
58 23 0.14
59 55 0.34
60 34 0.21
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.33
Consensus pattern (57 bp):
CAAAAATTCCATTTTAACCCAAAAACTTCCAAAAATTACATTTTTACCCCGAACTTC
Found at i:753 original size:59 final size:58
Alignment explanation
Indices: 565--823 Score: 183
Period size: 59 Copynumber: 4.5 Consensus size: 58
555 TATTTTTACC
* * * * * *
565 CCCCGAACT-TCCAAAAATTCCATTTTTAACCCCAAAAC-TTCCAAAAATT-TCATTTTTC
1 CCCCGAA-TGTCCAAAAATTCCATTTTTCATCCC-AATCTTTTCAAAAATTACCA-TTTTA
** * * * *
623 CCCCGAACCTCCAAAAATTCCA-TTTTGA-CCTCGAAAC-TTTC-AAAATTACTATTTCA
1 CCCCGAATGTCCAAAAATTCCATTTTTCATCC-C-AATCTTTTCAAAAATTACCATTTTA
* * *
679 CCCCGAATGTCCAAAAATTTCATTTTTCATCCCGAT-TTTCTTAAAAATTACCATTTTA
1 CCCCGAATGTCCAAAAATTCCATTTTTCATCCCAATCTTT-TCAAAAATTACCATTTTA
* * * * *
737 CTCTCGAATGTCCAAAAATTCCGTTTTTTATCCCAATCTTTTCAAAAGTTATCATTTTA
1 C-CCCGAATGTCCAAAAATTCCATTTTTCATCCCAATCTTTTCAAAAATTACCATTTTA
** *
796 CCACCGGGTGTCTAAAAATTCCATTTTT
1 CC-CCGAATGTCCAAAAATTCCATTTTT
824 AACCCCATAC
Statistics
Matches: 160, Mismatches: 30, Indels: 21
0.76 0.14 0.10
Matches are distributed among these distances:
56 33 0.21
57 21 0.13
58 37 0.23
59 66 0.41
60 3 0.02
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.36
Consensus pattern (58 bp):
CCCCGAATGTCCAAAAATTCCATTTTTCATCCCAATCTTTTCAAAAATTACCATTTTA
Done.