Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006629.1 Kokia drynarioides strain JFW-HI SEQ_121219, 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, 648
Length: 1081
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.29
Found at i:413 original size:30 final size:28
Alignment explanation
Indices: 374--577 Score: 96
Period size: 29 Copynumber: 7.0 Consensus size: 28
364 TTTTAAAAAA
*
374 ATCGGGATAAAAAACGGAATTTTTGGAC
1 ATCGGGATAAAAAATGGAATTTTTGGAC
*
402 ATCCGGGGAT--AAAATGGTAATTTTTAGGAAA
1 AT-C-GGGATAAAAAATGG-AATTTTT-GG-AC
*
433 ATCGAGATAAAAAATGGAATTTTTGGAC
1 ATCGGGATAAAAAATGGAATTTTTGGAC
* *
461 ATTCAGGGGT--AAAATGGTAATTTTTGAAGGC
1 A-TC-GGGATAAAAAATGG-AATTTTTG--GAC
* * * *
492 TTCGGGGTCAAAAATGGAAATTTTGGA-
1 ATCGGGATAAAAAATGGAATTTTTGGAC
* * *
519 AGTTCGTGGGT-AAAAATGTAATTTTTGGAA
1 A--TCG-GGATAAAAAATGGAATTTTTGGAC
* * *
549 ATTTCGGGGTTAAAAATAGAATTTTTGGA
1 A--TCGGGATAAAAAATGGAATTTTTGGA
578 AGTTTGGGGC
Statistics
Matches: 141, Mismatches: 16, Indels: 36
0.73 0.08 0.19
Matches are distributed among these distances:
28 18 0.13
29 52 0.37
30 52 0.37
31 19 0.13
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.31
Consensus pattern (28 bp):
ATCGGGATAAAAAATGGAATTTTTGGAC
Found at i:505 original size:59 final size:59
Alignment explanation
Indices: 294--695 Score: 233
Period size: 59 Copynumber: 6.8 Consensus size: 59
284 ACTTTGAGGA
* * * * * *
294 AAAATGGTAATTTTGGGAAAG-TTCGAGGTTAAAAATGGAATTTATAGACACTCAGGGGT
1 AAAATGGTAATTTT-TGAAAGATTCGGGGTAAAAAATGGAATTTTTGGACATTCAGGGGT
* * * * * * * *
353 AAAACGGTAACTTTTAAAAAAATCGGGATAAAAAACGGAATTTTTGGACA-TCCGGGGAT
1 AAAATGGTAATTTTTGAAAGATTCGGGGTAAAAAATGGAATTTTTGGACATTCAGGGG-T
* *
412 AAAATGGTAATTTTTAGGAAA-A-TCGAGATAAAAAATGGAATTTTTGGACATTCAGGGGT
1 AAAATGGTAATTTTT--GAAAGATTCGGGGTAAAAAATGGAATTTTTGGACATTCAGGGGT
* * * *
471 AAAATGGTAATTTTTGAAGGCTTCGGGGTCAAAAATGGAAATTTTGGA-AGTTC-GTGGGT
1 AAAATGGTAATTTTTGAAAGATTCGGGGTAAAAAATGGAATTTTTGGACA-TTCAG-GGGT
* * * *
530 AAAAAT-GTAATTTTTGGAAA-TTTCGGGGTTAAAAATAGAATTTTTGGA-AGTT-TGGGGCT
1 -AAAATGGTAATTTTT-GAAAGATTCGGGGTAAAAAATGGAATTTTTGGACA-TTCAGGGG-T
** * * * * *
589 AAAA-AATAATTTTTTGAAA-TTTTGGGGTCAAAAATAGAATTTTT-GAAAGTTC-GAGGGT
1 AAAATGGTAA-TTTTTGAAAGATTCGGGGTAAAAAATGGAATTTTTGGACA-TTCAG-GGGT
* * ** * *
647 AAAAT-ATAATTTTT-AAAAATTTTAGGATCAAAAATGGAATTTTTGGACA
1 AAAATGGTAATTTTTGAAAGA-TTCGGGGTAAAAAATGGAATTTTTGGACA
696 GTTTAGGGAC
Statistics
Matches: 283, Mismatches: 38, Indels: 44
0.78 0.10 0.12
Matches are distributed among these distances:
56 3 0.01
57 10 0.04
58 83 0.29
59 169 0.60
60 15 0.05
61 3 0.01
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (59 bp):
AAAATGGTAATTTTTGAAAGATTCGGGGTAAAAAATGGAATTTTTGGACATTCAGGGGT
Found at i:505 original size:118 final size:119
Alignment explanation
Indices: 293--577 Score: 310
Period size: 118 Copynumber: 2.4 Consensus size: 119
283 GACTTTGAGG
* * *
293 AAAAATGGTAATTTTGGGAAAGTTCGAGGTTAAAAATGGAATTTATAGACACTCAGGGGTAAAAC
1 AAAAATGGTAATTTTTGGAAAGTTCGAGGTTAAAAATGGAATTTTTGGACACTCAGGGGTAAAAC
*
358 GGTAACTTTTAAAAAAATCGGGATAAAAAACGGAATTTTTGGACA-TCCG-GGG-
66 GGTAACTTTTAAAAAAATCGGGATAAAAAACGGAAATTTTGGA-AGTCCGTGGGT
* * * *
410 ATAAAATGGTAATTTTTAGGAAA-ATCGAGATAAAAAATGGAATTTTTGGACATTCAGGGGTAAA
1 A-AAAATGGTAATTTTT-GGAAAGTTCGAGGTTAAAAATGGAATTTTTGGACACTCAGGGGTAAA
* * * **** * * * *
474 ATGGTAATTTTTGAAGGCTTCGGGGTCAAAAATGGAAATTTTGGAAGTTCGTGGGT
64 ACGGTAACTTTTAAAAAAATCGGGATAAAAAACGGAAATTTTGGAAGTCCGTGGGT
* * *
530 AAAAAT-GTAATTTTTGGAAATTTCGGGGTTAAAAATAGAATTTTTGGA
1 AAAAATGGTAATTTTTGGAAAGTTCGAGGTTAAAAATGGAATTTTTGGA
578 AGTTTGGGGC
Statistics
Matches: 138, Mismatches: 24, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
117 7 0.05
118 117 0.85
119 13 0.09
120 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (119 bp):
AAAAATGGTAATTTTTGGAAAGTTCGAGGTTAAAAATGGAATTTTTGGACACTCAGGGGTAAAAC
GGTAACTTTTAAAAAAATCGGGATAAAAAACGGAAATTTTGGAAGTCCGTGGGT
Found at i:586 original size:29 final size:29
Alignment explanation
Indices: 495--660 Score: 135
Period size: 29 Copynumber: 5.7 Consensus size: 29
485 TGAAGGCTTC
* * * *
495 GGGGTCAAAAATGGAAATTTTGGAAGTTC
1 GGGGTTAAAAATAGAATTTTTGGAAGTTT
*
524 GTGGG-TAAAAAT-GTAATTTTTGGAAATTT
1 G-GGGTTAAAAATAG-AATTTTTGGAAGTTT
553 CGGGGTTAAAAATAGAATTTTTGGAAGTTT
1 -GGGGTTAAAAATAGAATTTTTGGAAGTTT
* * * *
583 GGGGCTAAAAAATA-ATTTTTTGAAATTTT
1 GGGG-TTAAAAATAGAATTTTTGGAAGTTT
* * *
612 GGGGTCAAAAATAGAATTTTTGAAAGTTC
1 GGGGTTAAAAATAGAATTTTTGGAAGTTT
*
641 GAGGG-T-AAAATATAATTTTT
1 G-GGGTTAAAAATAGAATTTTT
661 AAAAATTTTA
Statistics
Matches: 114, Mismatches: 15, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
28 22 0.19
29 55 0.48
30 36 0.32
31 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (29 bp):
GGGGTTAAAAATAGAATTTTTGGAAGTTT
Found at i:608 original size:58 final size:58
Alignment explanation
Indices: 492--698 Score: 236
Period size: 58 Copynumber: 3.5 Consensus size: 58
482 TTTTGAAGGC
* * * * *
492 TTCGGGGTCAAAAATGGAAATTTTGGAAGTTCGTGGGTAAAAATGTAATTTTTGGAAAT
1 TTCGGGGTCAAAAATAGAATTTTTGGAAGTTCGAGGGTAAAAA-ATAATTTTTAGAAAT
* * *
551 TTCGGGGTTAAAAATAGAATTTTTGGAAGTTTG-GGGCTAAAAAATAATTTTTTGAAAT
1 TTCGGGGTCAAAAATAGAATTTTTGGAAGTTCGAGGG-TAAAAAATAATTTTTAGAAAT
* * * *
609 TTTGGGGTCAAAAATAGAATTTTTGAAAGTTCGAGGGTAAAATATAATTTTTAAAAAT
1 TTCGGGGTCAAAAATAGAATTTTTGGAAGTTCGAGGGTAAAAAATAATTTTTAGAAAT
** * *
667 TTTAGGATCAAAAATGGAATTTTTGGACAGTT
1 TTCGGGGTCAAAAATAGAATTTTTGGA-AGTT
699 TAGGGACCTC
Statistics
Matches: 128, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
58 86 0.67
59 42 0.33
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (58 bp):
TTCGGGGTCAAAAATAGAATTTTTGGAAGTTCGAGGGTAAAAAATAATTTTTAGAAAT
Done.