Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015202.1 Kokia drynarioides strain JFW-HI SEQ_130246, 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: 539317
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 763 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:482203 original size:23 final size:24
Alignment explanation
Indices: 482172--482228 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
482162 TTGCTGTTTT
* *
482172 TGTTTTTTTTAATGTTGTTTT-GC
1 TGTTATTTTTAATGCTGTTTTAGC
** *
482195 TGTTATTTTTGCTGCTGTTTTAGT
1 TGTTATTTTTAATGCTGTTTTAGC
482219 TGTTATTTTT
1 TGTTATTTTT
482229 GTTGTTTGGA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 17 0.61
24 11 0.39
ACGTcount: A:0.09, C:0.05, G:0.18, T:0.68
Consensus pattern (24 bp):
TGTTATTTTTAATGCTGTTTTAGC
Found at i:482232 original size:44 final size:43
Alignment explanation
Indices: 482143--482235 Score: 109
Period size: 44 Copynumber: 2.1 Consensus size: 43
482133 TTTTGGTTGA
* * *
482143 TGTTTTCGTGTTGTTTTTGTTGCTGTTTTTGTTTTTTTTAATGT
1 TGTTTTCGTGTTATTTTTGCTGCTGTTTTAGTTTTTTTT-ATGT
482187 TGTTTT-GCTGTTATTTTTGCTGCTGTTTTAGTTGTTATTTT-TGT
1 TGTTTTCG-TGTTATTTTTGCTGCTGTTTTAGTT-TT-TTTTATGT
482231 TGTTT
1 TGTTT
482236 GGATGTACTA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
43 1 0.02
44 36 0.84
45 2 0.05
46 4 0.09
ACGTcount: A:0.05, C:0.05, G:0.20, T:0.69
Consensus pattern (43 bp):
TGTTTTCGTGTTATTTTTGCTGCTGTTTTAGTTTTTTTTATGT
Found at i:482684 original size:26 final size:24
Alignment explanation
Indices: 482640--482701 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 24
482630 TTAAGATGAC
*
482640 TATATAAAAATTTTCAATAAATAAAA
1 TATAT-AAAATTTTAAAT-AATAAAA
*
482666 TATATAAAATTATTAAATATTAAAA
1 TATATAAAATT-TTAAATAATAAAA
*
482691 TAAAATAAAAT
1 T-ATATAAAAT
482702 AAAATAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 13 0.42
26 18 0.58
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
TATATAAAATTTTAAATAATAAAA
Found at i:510541 original size:3 final size:3
Alignment explanation
Indices: 510533--510572 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
510523 TTACATCATT
*
510533 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTG TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
510573 TTGGTTTGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:525244 original size:21 final size:20
Alignment explanation
Indices: 525213--525252 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
525203 TAAATTTCAA
525213 AATATTAAAAAAATCTAAAG
1 AATATTAAAAAAATCTAAAG
*
525233 AATATATAAAAAAATTTAAA
1 AATAT-TAAAAAAATCTAAA
525253 AAATCCTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (20 bp):
AATATTAAAAAAATCTAAAG
Found at i:529754 original size:53 final size:53
Alignment explanation
Indices: 529674--529778 Score: 174
Period size: 53 Copynumber: 2.0 Consensus size: 53
529664 GAGATTGAAG
* * *
529674 TTAATAGCTACATTTAATAAAGCTTGACCATTGGAAGATGGTAATAATAATTT
1 TTAATAGCCACATTTAATAAAGCTTGACAATTGGAAGATGGTAATAAAAATTT
*
529727 TTAATAGCCCCATTTAATAAAGCTTGACAATTGGAAGATGGTAATAAAAATT
1 TTAATAGCCACATTTAATAAAGCTTGACAATTGGAAGATGGTAATAAAAATT
529779 GTTGCACGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (53 bp):
TTAATAGCCACATTTAATAAAGCTTGACAATTGGAAGATGGTAATAAAAATTT
Found at i:536531 original size:39 final size:39
Alignment explanation
Indices: 536487--536570 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 39
536477 TGGGACAAGT
*
536487 CTCTTCCAAGAGGTAT-GTCCAATATGAAAAGGATTGTGA
1 CTCTTCCAAGAGGTATCATCCAATATG-AAAGGATTGTGA
* * * *
536526 CTCTT-CAATAGGTGTCCATCCAATTTGAAAGGGTTGTGA
1 CTCTTCCAAGAGGTAT-CATCCAATATGAAAGGATTGTGA
536565 CTCTTC
1 CTCTTC
536571 AAAAGGTGTC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
38 8 0.22
39 21 0.57
40 8 0.22
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.32
Consensus pattern (39 bp):
CTCTTCCAAGAGGTATCATCCAATATGAAAGGATTGTGA
Found at i:536571 original size:39 final size:40
Alignment explanation
Indices: 536504--536583 Score: 126
Period size: 39 Copynumber: 2.0 Consensus size: 40
536494 AAGAGGTATG
*
536504 TCCAATATGAAAAGGATTGTGACTCTTCAATAGGTGTCCA
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
* *
536544 TCCAATTTG-AAAGGGTTGTGACTCTTCAAAAGGTGTCCA
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
536583 T
1 T
536584 TAAGTGCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Consensus pattern (40 bp):
TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
Done.