Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004039.1 Kokia drynarioides strain JFW-HI SEQ_117179, 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, 754
Length: 1257
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Found at i:671 original size:59 final size:59
Alignment explanation
Indices: 579--979 Score: 488
Period size: 59 Copynumber: 6.8 Consensus size: 59
569 CCTAAACCTT
* * *
579 CAAAAATTACCATTTTA-CCCTCGAACTTCCAAAAATCACATTTTTGACCCTGAATCTTC
1 CAAAAATTACTATTTTACCCCT-GAACTTCCAAAAATCCCATTTTTGACCCCGAATCTTC
* * *
638 CAAAAATTACTATTTTACCCCTTAACTTCCAAAAATCCAATTTTTAACCCCGAATCTTC
1 CAAAAATTACTATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCGAATCTTC
* ** *
697 AAAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAATCTTC
1 CAAAAATTACTATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCGAATCTTC
* ** *
756 CAAAAAATACTATTTTA-CCCTCGAACTTCCAAAAATCCCATTTTAAACCCCGAACCTTC
1 CAAAAATTACTATTTTACCCCT-GAACTTCCAAAAATCCCATTTTTGACCCCGAATCTTC
* * ** * ***
815 TAAAAATTACCATTTTACCCCCAAACTTCTAAAAATCCCATTTTTGACATTGAATCTTC
1 CAAAAATTACTATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCGAATCTTC
* *
874 CAAAAATTACTATTTTCCCCCCGAA-TTCCCAAAAATCCCATTTTT-AGCCCCGAATCTTC
1 CAAAAATTACTATTTTACCCCTGAACTT-CCAAAAATCCCATTTTTGA-CCCCGAATCTTC
* *
933 CAAAAATTACCATTTTA-CCCTCGAACTTCCAAAAATCCTATTTTTGA
1 CAAAAATTACTATTTTACCCCT-GAACTTCCAAAAATCCCATTTTTGA
980 TTCCAAACAT
Statistics
Matches: 290, Mismatches: 44, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
58 9 0.03
59 271 0.93
60 10 0.03
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (59 bp):
CAAAAATTACTATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCGAATCTTC
Found at i:788 original size:118 final size:116
Alignment explanation
Indices: 576--979 Score: 569
Period size: 118 Copynumber: 3.4 Consensus size: 116
566 GTCCCTAAAC
* * *
576 CTTCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCACATTTTTGACC-CTGAATCTTCCA
1 CTTCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTC-GAATCTTCCA
* *
640 AAAATTACTATTTTACCCCTTAACTTCCAAAAATCCAATTTTTAACCCCGAAT
65 AAAATTACTATTTTACCCC-GAACTTCCAAAAATCCCATTTTTAACCCCGAAT
*
693 CTTCAAAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAATCTTCCA
1 CTTC-AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAATCTTCCA
* * *
758 AAAAATACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTAAACCCCGAAC
65 AAAATTACTATTTTACCC-CGAACTTCCAAAAATCCCATTTTTAACCCCGAAT
* * *
811 CTTCTAAAAATTACCATTTTACCCCCAAACTTCTAAAAATCCCATTTTTGACATTGAATCTTCCA
1 CTTC-AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAATCTTCCA
* *
876 AAAATTACTATTTTCCCCCCGAA-TTCCCAAAAATCCCATTTTTAGCCCCGAAT
65 AAAATTACTATTTT-ACCCCGAACTT-CCAAAAATCCCATTTTTAACCCCGAAT
* * *
929 CTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCTATTTTTGA
1 CTT-CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA
980 TTCCAAACAT
Statistics
Matches: 258, Mismatches: 23, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
117 6 0.02
118 246 0.95
119 6 0.02
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (116 bp):
CTTCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAATCTTCCAA
AAATTACTATTTTACCCCGAACTTCCAAAAATCCCATTTTTAACCCCGAAT
Found at i:886 original size:177 final size:177
Alignment explanation
Indices: 579--976 Score: 566
Period size: 177 Copynumber: 2.2 Consensus size: 177
569 CCTAAACCTT
* ** * *
579 CAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCACATTTTTGACCCTGAATCTTCCAAAAA
1 CAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTAAACCCCGAACCTTCCAAAAA
* ** *
644 TTACTATTTTACCCCTTAACTTCCAAAAATCCAATTTTTAACCCCGAATCTTCAAAAAATTACTA
66 TTACCATTTTACCCCCAAACTTCCAAAAATCCAATTTTTAACACCGAATCTTCAAAAAATTACTA
*
709 TTTTACCCCCAAACTT-CCAAAAATCCCATTTTT-GACCTCGAATCTTC
131 TTTTACCCCCAAA-TTCCCAAAAATCCCATTTTTAG-CCCCGAATCTTC
* * *
756 CAAAAAATACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTAAACCCCGAACCTTCTAAAAA
1 CAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTAAACCCCGAACCTTCCAAAAA
* * * ** *
821 TTACCATTTTACCCCCAAACTTCTAAAAATCCCATTTTTGACATTGAATCTTCCAAAAATTACTA
66 TTACCATTTTACCCCCAAACTTCCAAAAATCCAATTTTTAACACCGAATCTTCAAAAAATTACTA
* *
886 TTTTCCCCCCGAATTCCCAAAAATCCCATTTTTAGCCCCGAATCTTC
131 TTTTACCCCCAAATTCCCAAAAATCCCATTTTTAGCCCCGAATCTTC
*
933 CAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCTATTTT
1 CAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTT
977 TGATTCCAAA
Statistics
Matches: 195, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
176 2 0.01
177 192 0.98
178 1 0.01
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (177 bp):
CAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTAAACCCCGAACCTTCCAAAAA
TTACCATTTTACCCCCAAACTTCCAAAAATCCAATTTTTAACACCGAATCTTCAAAAAATTACTA
TTTTACCCCCAAATTCCCAAAAATCCCATTTTTAGCCCCGAATCTTC
Done.