Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010553.1 Kokia drynarioides strain JFW-HI SEQ_125473, 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, 1000
Length: 2143
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:313 original size:29 final size:30
Alignment explanation
Indices: 275--350 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
265 ATAGGGTTAA
* *
275 AAAATG-AATTTTTGG-AGAATTTAGG-GTC
1 AAAATGTAATTTTTGGAAAAAATT-GGTGTC
303 AAAATGTAA-TTTTGGAAAAAATTGGTGTC
1 AAAATGTAATTTTTGGAAAAAATTGGTGTC
*
332 AAAATGTAATTTTAGGAAA
1 AAAATGTAATTTTTGGAAA
351 GTTTGATGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 14 0.34
29 19 0.46
30 8 0.20
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAAAAATTGGTGTC
Found at i:397 original size:30 final size:30
Alignment explanation
Indices: 294--623 Score: 248
Period size: 29 Copynumber: 11.2 Consensus size: 30
284 TTTTGGAGAA
* * *
294 TTTA-GGGTCAAAATGTAATTTTGGAAAAA
1 TTTAGGGGTCAAAATGTGATTTTGGGAAAG
* * * *
323 ATT-GGTGTCAAAATGTAATTTTAGGAAAG
1 TTTAGGGGTCAAAATGTGATTTTGGGAAAG
** * *
352 TTT-GATGTTAAAATATGATTTTGGGAAAG
1 TTTAGGGGTCAAAATGTGATTTTGGGAAAG
*
381 TTTAGGGGTCAAAATATGATTTTGGG-AAG
1 TTTAGGGGTCAAAATGTGATTTTGGGAAAG
* *
410 TTTAGGGGTC-AAATTTGATTTTGGAAAAG
1 TTTAGGGGTCAAAATGTGATTTTGGGAAAG
* * * *
439 TTTAGAGGT-GAAATATGATTTTGAGAAAG
1 TTTAGGGGTCAAAATGTGATTTTGGGAAAG
* * *
468 TTTTA-GGGTTATAATGTGATTTTGGGAAAT
1 -TTTAGGGGTCAAAATGTGATTTTGGGAAAG
* *
498 TTTAGGGTTTAAAATGTGATTTTGGGAAAG
1 TTTAGGGGTCAAAATGTGATTTTGGGAAAG
* * * *
528 TTGAGGGGT-AAAAGTGTAATTTTGGAAAAA
1 TTTAGGGGTCAAAA-TGTGATTTTGGGAAAG
* * * * *
558 TTTATGGGTGAGAATGTAATTTT-GAAAAG
1 TTTAGGGGTCAAAATGTGATTTTGGGAAAG
* * *
587 TTT-GAGTGTCAAAATATGATTTTTGGAAAG
1 TTTAG-GGGTCAAAATGTGATTTTGGGAAAG
617 TTTAGGG
1 TTTAGGG
624 ACCTTTTGGG
Statistics
Matches: 243, Mismatches: 46, Indels: 23
0.78 0.15 0.07
Matches are distributed among these distances:
28 13 0.05
29 121 0.50
30 105 0.43
31 4 0.02
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.38
Consensus pattern (30 bp):
TTTAGGGGTCAAAATGTGATTTTGGGAAAG
Found at i:403 original size:59 final size:59
Alignment explanation
Indices: 329--623 Score: 256
Period size: 59 Copynumber: 5.0 Consensus size: 59
319 AAAAATTGGT
* *
329 GTCAAAATGTAATTTTAGGAAAGTTTGA-TGTTAAAATATGATTTTGGGAAAGTTTAGGG
1 GTCAAAATGTGATTTT-GGAAAGTTTGAGGGTTAAAATATGATTTTGGGAAAGTTTAGGG
* * * * * * *
388 GTCAAAATATGATTTTGGGAAGTTT-AGGGGTCAAATTTGATTTTGGAAAAGTTTAGAG
1 GTCAAAATGTGATTTTGGAAAGTTTGAGGGTTAAAATATGATTTTGGGAAAGTTTAGGG
* * * * * *
446 GT-GAAATATGATTTTGAGAAAGTTTTAGGGTTATAATGTGATTTTGGGAAATTTTAGGG
1 GTCAAAATGTGATTTTG-GAAAGTTTGAGGGTTAAAATATGATTTTGGGAAAGTTTAGGG
* * * * * * * *
505 TTTAAAATGTGATTTTGGGAAAG-TTGAGGGGTAAAAGTGTAATTTTGGAAAAATTTATGG
1 GTCAAAATGTGATTTT-GGAAAGTTTGAGGGTTAAAA-TATGATTTTGGGAAAGTTTAGGG
* * * * * * *
565 GTGAGAATGTAATTTTGAAAAGTTTGAGTGTCAAAATATGATTTTTGGAAAGTTTAGGG
1 GTCAAAATGTGATTTTGGAAAGTTTGAGGGTTAAAATATGATTTTGGGAAAGTTTAGGG
624 ACCTTTTGGG
Statistics
Matches: 187, Mismatches: 42, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
57 14 0.07
58 42 0.22
59 73 0.39
60 57 0.30
61 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.27, T:0.38
Consensus pattern (59 bp):
GTCAAAATGTGATTTTGGAAAGTTTGAGGGTTAAAATATGATTTTGGGAAAGTTTAGGG
Found at i:574 original size:60 final size:58
Alignment explanation
Indices: 266--623 Score: 230
Period size: 59 Copynumber: 6.1 Consensus size: 58
256 AAATAAAAAA
* * * * **
266 TAGGGTTAAAAAATGAATTTTTGGAGAA-TTTA-GGGTCAAAATGTAATTTTGGAAAAAAT
1 TAGGGTGAAAATATG-ATTTTGGGA-AAGTTTAGGGGT-AAAATGTGATTTTGGAAAAGTT
* * * * * * * *
325 T-GGTGTCAAAATGTAATTTTAGGAAAGTTT-GATGTTAAAATATGATTTTGGGAAAGTT
1 TAGG-GTGAAAATATGATTTTGGGAAAGTTTAG-GGGTAAAATGTGATTTTGGAAAAGTT
* * *
383 TAGGGGTCAAAATATGATTTTGGG-AAGTTTAGGGGTCAAATTTGATTTTGGAAAAGTT
1 TA-GGGTGAAAATATGATTTTGGGAAAGTTTAGGGGTAAAATGTGATTTTGGAAAAGTT
* * * * *
441 TAGAGGTG-AAATATGATTTTGAGAAAGTTTTAGGGTTATAATGTGATTTTGGGAAATTT
1 TAG-GGTGAAAATATGATTTTGGGAAAG-TTTAGGGGTAAAATGTGATTTTGGAAAAGTT
* * * * *
500 TAGGGTTTAAAATGTGATTTTGGGAAAGTTGAGGGGTAAAAGTGTAATTTTGGAAAAATT
1 TAGGG-TGAAAATATGATTTTGGGAAAGTTTAGGGGTAAAA-TGTGATTTTGGAAAAGTT
* * * * * *
560 TATGGGTGAGAATGTAATTTT-GAAAAGTTT-GAGTGTCAAAATATGATTTTTGG-AAAGTT
1 TA-GGGTGAAAATATGATTTTGGGAAAGTTTAG-GGGT-AAAATGTGA-TTTTGGAAAAGTT
619 TAGGG
1 TAGGG
624 ACCTTTTGGG
Statistics
Matches: 236, Mismatches: 46, Indels: 35
0.74 0.15 0.11
Matches are distributed among these distances:
57 17 0.07
58 72 0.31
59 86 0.36
60 58 0.25
61 3 0.01
ACGTcount: A:0.35, C:0.01, G:0.27, T:0.37
Consensus pattern (58 bp):
TAGGGTGAAAATATGATTTTGGGAAAGTTTAGGGGTAAAATGTGATTTTGGAAAAGTT
Found at i:776 original size:30 final size:30
Alignment explanation
Indices: 732--957 Score: 180
Period size: 30 Copynumber: 7.6 Consensus size: 30
722 NNNNNNNNNN
* *
732 ATTTTGG-GAAGTTTAGGGGTCAAAATTTG
1 ATTTTGGAAAAGTTTAGGGGTCAAAATGTG
* * *
761 ATTTTGGAAAAGTTTAGAGGTGAAAATATG
1 ATTTTGGAAAAGTTTAGGGGTCAAAATGTG
* *
791 ATTTT-GAGAAAGTTTTA-GGGTTATAATGTG
1 ATTTTGGA-AAAG-TTTAGGGGTCAAAATGTG
* * * *
821 ATTTTGGGAAATTTTAGGGTTTAAAATGTG
1 ATTTTGGAAAAGTTTAGGGGTCAAAATGTG
* *
851 ATTTTGGGAAAGTTTAGGGGT-AAAAGTGTA
1 ATTTTGGAAAAGTTTAGGGGTCAAAA-TGTG
* * * * *
881 ATTTTGGAAAAATTTATGGGTGAGAATGTA
1 ATTTTGGAAAAGTTTAGGGGTCAAAATGTG
*
911 ATTTT-GAAAAGTTT-GAGGGTC-AAATATG
1 ATTTTGGAAAAGTTTAG-GGGTCAAAATGTG
939 ATTTTTGG-AAAGTTTAGGG
1 A-TTTTGGAAAAGTTTAGGG
958 ACCTTTTGGG
Statistics
Matches: 161, Mismatches: 25, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
28 5 0.03
29 42 0.26
30 106 0.66
31 8 0.05
ACGTcount: A:0.33, C:0.01, G:0.28, T:0.38
Consensus pattern (30 bp):
ATTTTGGAAAAGTTTAGGGGTCAAAATGTG
Found at i:909 original size:90 final size:89
Alignment explanation
Indices: 732--957 Score: 219
Period size: 90 Copynumber: 2.5 Consensus size: 89
722 NNNNNNNNNN
* * * * * *
732 ATTTTGGG-AAGTTTAGGGGTCAAAATTTGATTTTGGAAAAGTTTAGAGGTGAAAATATGATTTT
1 ATTTTGGGAAATTTTA-GGGTTAAAATATGATTTTGGGAAAGTTTAGGGGTGAAAATATAATTTT
** * * *
796 GAGAAAGTTTTAGGGTTATAATGTG
65 GAGAAAAATTTAGGGTGAGAATGTA
* *
821 ATTTTGGGAAATTTTAGGGTTTAAAATGTGATTTTGGGAAAGTTTAGGGGT-AAAAGTGTAATTT
1 ATTTTGGGAAATTTTAGGG-TTAAAATATGATTTTGGGAAAGTTTAGGGGTGAAAA-TATAATTT
885 TG-GAAAAATTTATGGGTGAGAATGTA
64 TGAGAAAAATTTA-GGGTGAGAATGTA
* * * *
911 ATTTT-GAAAAGTTTGAGGG-TCAAATATGATTTTTGGAAAGTTTAGGG
1 ATTTTGGGAAA-TTTTAGGGTTAAAATATGATTTTGGGAAAGTTTAGGG
958 ACCTTTTGGG
Statistics
Matches: 115, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
88 25 0.22
89 27 0.23
90 63 0.55
ACGTcount: A:0.33, C:0.01, G:0.28, T:0.38
Consensus pattern (89 bp):
ATTTTGGGAAATTTTAGGGTTAAAATATGATTTTGGGAAAGTTTAGGGGTGAAAATATAATTTTG
AGAAAAATTTAGGGTGAGAATGTA
Done.