Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005929.1 Kokia drynarioides strain JFW-HI SEQ_120307, 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, 738
Length: 1230
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Found at i:624 original size:59 final size:57
Alignment explanation
Indices: 555--926 Score: 265
Period size: 59 Copynumber: 6.3 Consensus size: 57
545 ACTCAGGGGC
* * *
555 AAAATGGTAATTTTT-ACAAGTTTCGGGATTAAAAATGTAATTTTTGGAAGTTTAGGGGTA
1 AAAAT-GTAATTTTTGA-AATTTTAGGG-TTAAAAATGGAATTTTTGGAAGTTT-GGGGTA
* * *
615 AAAATGTAATTTTTTGAAATTTTTGAGGTTAAAAATGGAATTTTTTGAAGTTTGGGGGTT
1 AAAATGTAA-TTTTTGAAATTTTAG-GGTTAAAAATGGAATTTTTGGAAGTTT-GGGGTA
675 AAAATGTAATTTTTGGAAATTTTAGGGTTAAAAATGGAA-TTTTGGAAAGTTTGGCGGTA
1 AAAATGTAATTTTT-GAAATTTTAGGGTTAAAAATGGAATTTTTGG-AAGTTTGG-GGTA
** ** * *
734 AAAATGCATTTTTTTGTGAAA--TCGGGGTCAAAAATGGAA-TTTTGGAATATTTAGGGGTA
1 AAAATG--TAATTTT-TGAAATTTTAGGGTTAAAAATGGAATTTTTGGAA-GTTT-GGGGTA
* * ** * * *
793 AAATTGTTATTTTTGGAAAAATTAGGGTCAAAAATAGAA-TTTTGGAAAGTTCGAGGGTA
1 AAAATGTAATTTTT-GAAATTTTAGGGTTAAAAATGGAATTTTTGG-AAGTTTG-GGGTA
* * * *
852 AAAATGTAATTTTTTGAAAGTTTAGGGGTCAAAAT--ATATTTTTGGAGAAGTTTAGGGGTT
1 AAAATGTAA-TTTTTGAAATTTTAGGGTTAAAAATGGA-ATTTTT-G-GAAGTTT-GGGGTA
*
912 AAAATATAATTTTTG
1 AAAATGTAATTTTTG
927 GACAATTTAG
Statistics
Matches: 258, Mismatches: 32, Indels: 45
0.77 0.10 0.13
Matches are distributed among these distances:
56 1 0.00
57 11 0.04
58 11 0.04
59 131 0.51
60 89 0.34
61 14 0.05
62 1 0.00
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.39
Consensus pattern (57 bp):
AAAATGTAATTTTTGAAATTTTAGGGTTAAAAATGGAATTTTTGGAAGTTTGGGGTA
Found at i:807 original size:118 final size:118
Alignment explanation
Indices: 645--938 Score: 316
Period size: 118 Copynumber: 2.5 Consensus size: 118
635 TTTTGAGGTT
* * * ** *
645 AAAAATGGAATTTTTTGAAGTTTGGGGGTTAAAATGTAATTTTTGGAAATTTTAGGGTTAAAAAT
1 AAAAATGGAATTTTTGGAAATTTAGGGGTTAAAATGTAATTTTTGGAAAAATTAGGGTCAAAAAT
* * *
710 GGAATTTTGGAAAGTTTG-GCGGTAAAAATGCATTTTTTTGTGAAATCGGGGTC
66 AGAATTTTGGAAAGTTCGAG-GGTAAAAATGCAATTTTTTGTGAAATCGGGGTC
*
763 AAAAATGGAA-TTTTGGAATATTTAGGGG-TAAAATTGTTATTTTTGGAAAAATTAGGGTCAAAA
1 AAAAATGGAATTTTTGGAA-ATTTAGGGGTTAAAA-TGTAATTTTTGGAAAAATTAGGGTCAAAA
* *
826 ATAGAATTTTGGAAAGTTCGAGGGTAAAAATGTAA-TTTTT-TGAAAGTTTAGGGGTC
64 ATAGAATTTTGGAAAGTTCGAGGGTAAAAATGCAATTTTTTGTGAAA---TCGGGGTC
* * *
882 -AAAAT--ATATTTTTGGAGAAGTTTAGGGGTTAAAATATAATTTTTGGACAATTTAGGG
1 AAAAATGGA-ATTTTTGGA-AA-TTTAGGGGTTAAAATGTAATTTTTGGAAAAATTAGGG
939 AACTTTAAGG
Statistics
Matches: 149, Mismatches: 16, Indels: 21
0.80 0.09 0.11
Matches are distributed among these distances:
116 6 0.04
117 18 0.12
118 84 0.56
119 36 0.24
120 5 0.03
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (118 bp):
AAAAATGGAATTTTTGGAAATTTAGGGGTTAAAATGTAATTTTTGGAAAAATTAGGGTCAAAAAT
AGAATTTTGGAAAGTTCGAGGGTAAAAATGCAATTTTTTGTGAAATCGGGGTC
Found at i:936 original size:30 final size:29
Alignment explanation
Indices: 586--938 Score: 176
Period size: 30 Copynumber: 11.9 Consensus size: 29
576 TTCGGGATTA
* * *
586 AAAATGTAATTTTTGGAAGTTTAGGGGTA
1 AAAATATAATTTTTGGAAATTTAGGGGTT
* * * *
615 AAAATGTAATTTTTTGAAATTTTTGAGGTT
1 AAAATATAATTTTTGGAAA-TTTAGGGGTT
* * *
645 AAAA-ATGGAATTTTTTGAAGTTTGGGGGTT
1 AAAATAT--AATTTTTGGAAATTTAGGGGTT
*
675 AAAATGTAATTTTTGGAAATTTTA-GGGTT
1 AAAATATAATTTTTGGAAA-TTTAGGGGTT
*
704 AAAA-ATGGAA-TTTTGGAAAGTTT-GGCGGTA
1 AAAATAT--AATTTTTGGAAA-TTTAGG-GGTT
* * *
734 AAAATGCAT-TTTTTTGTGAAA--TCGGGGTC
1 AAAAT--ATAATTTTTG-GAAATTTAGGGGTT
763 AAAA-ATGGAA-TTTTGGAATATTTAGGGG-T
1 AAAATAT--AATTTTTGGAA-ATTTAGGGGTT
* * * *
792 AAAATTGTTATTTTTGGAAAAATTA-GGGTC
1 AAAA-TATAATTTTTGG-AAATTTAGGGGTT
* * * *
822 AAAA-ATAGAATTTTGGAAAGTTCGAGGGTA
1 AAAATATA-ATTTTTGGAAATTTAG-GGGTT
* * *
852 AAAATGTAATTTTTTGAAAGTTTAGGGGTC
1 AAAATATAATTTTTGGAAA-TTTAGGGGTT
882 AAAATAT-ATTTTTGGAGAAGTTTAGGGGTT
1 AAAATATAATTTTTGGA-AA-TTTAGGGGTT
912 AAAATATAATTTTTGGACAATTTAGGG
1 AAAATATAATTTTTGGA-AATTTAGGG
939 AACTTTAAGG
Statistics
Matches: 250, Mismatches: 41, Indels: 65
0.70 0.12 0.18
Matches are distributed among these distances:
26 2 0.01
27 3 0.01
28 13 0.05
29 81 0.32
30 109 0.44
31 36 0.14
32 4 0.02
33 2 0.01
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.38
Consensus pattern (29 bp):
AAAATATAATTTTTGGAAATTTAGGGGTT
Done.