Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002740.1 Kokia drynarioides strain JFW-HI SEQ_115046, 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, 841
Length: 1403
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Found at i:377 original size:29 final size:30
Alignment explanation
Indices: 330--386 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
320 ATCGGAGTTC
*
330 AAAATGAGACTTTTCGGATTCTCGGGGGAA
1 AAAATGAGAATTTTCGGATTCTCGGGGGAA
*
360 AAAATGATAATTTT-GGATTCTCGGGGG
1 AAAATGAGAATTTTCGGATTCTCGGGGG
387 TGAAACAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.30
Consensus pattern (30 bp):
AAAATGAGAATTTTCGGATTCTCGGGGGAA
Found at i:476 original size:30 final size:28
Alignment explanation
Indices: 430--783 Score: 318
Period size: 30 Copynumber: 12.0 Consensus size: 28
420 AATGGGATTA
*
430 GGGGTAAAAATGGGATTTTTAGAAGTTTC
1 GGGGTAAAAAT-GGATTTTTGGAAGTTTC
*
459 GAGGTAAAAAATAGGATTTTTGGAAG-TTC
1 GGGGT-AAAAAT-GGATTTTTGGAAGTTTC
* * *
488 AGGGGTAAAAATAGAATTTTTAGAAGTTTT
1 -GGGGTAAAAAT-GGATTTTTGGAAGTTTC
518 GGGGTCAAAAATGGAATTTTTGGAAG-TTC
1 GGGGT-AAAAATGG-ATTTTTGGAAGTTTC
* *
547 GAGAGTAAAAATGGAATTTTTGGAAGTTTT
1 G-GGGTAAAAATGG-ATTTTTGGAAGTTTC
* *
577 AGGGTCTAAAATGGGATTTTTGGAAGTTTC
1 GGGGT-AAAAAT-GGATTTTTGGAAGTTTC
*
607 GGGGTCGAAAATGAGATTTTTGGAAG-TTC
1 GGGGT-AAAAATG-GATTTTTGGAAGTTTC
636 GGGGGTAAAAATGGAATTTTTGGAAGTTTC
1 -GGGGTAAAAATGG-ATTTTTGGAAGTTTC
* * *
666 TGTGTTAAAAATGAGATTTTTGGAAGTTTA
1 -GGGGTAAAAATG-GATTTTTGGAAGTTTC
* *
696 GGGGTAAAAATAGAATTTTGGGAAGTTTC
1 GGGGTAAAAAT-GGATTTTTGGAAGTTTC
* *
725 GAGGTCAAAAATGAGATTTTTGGAAGTTTG
1 GGGGT-AAAAATG-GATTTTTGGAAGTTTC
* *
755 GGGGTAAAAACGAAATTTTTGGACAGTTT
1 GGGGTAAAAATG-GATTTTTGGA-AGTTT
784 AGGGACCTCC
Statistics
Matches: 272, Mismatches: 35, Indels: 35
0.80 0.10 0.10
Matches are distributed among these distances:
28 1 0.00
29 121 0.44
30 147 0.54
31 3 0.01
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (28 bp):
GGGGTAAAAATGGATTTTTGGAAGTTTC
Found at i:497 original size:59 final size:57
Alignment explanation
Indices: 430--783 Score: 340
Period size: 59 Copynumber: 6.0 Consensus size: 57
420 AATGGGATTA
* * *
430 GGGGTAAAAATGGGATTTTTAGAAGTTTCGAGGTAAAAAATAGGATTTTTGGAAG-TTC
1 GGGGTAAAAATGAGATTTTTGGAAGTTTCGGGGT-AAAAAT-GGATTTTTGGAAGTTTC
* *
488 AGGGGTAAAAAT-AGAATTTTTAGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAG-TTC
1 -GGGGTAAAAATGAG-ATTTTTGGAAGTTTCGGGGT-AAAAATGG-ATTTTTGGAAGTTTC
* ** *
547 GAGAGTAAAAATG-GAATTTTTGGAAGTTTTAGGGTCTAAAATGGGATTTTTGGAAGTTTC
1 G-GGGTAAAAATGAG-ATTTTTGGAAGTTTCGGGGT-AAAAAT-GGATTTTTGGAAGTTTC
*
607 GGGGTCGAAAATGAGATTTTTGGAAG-TTCGGGGGTAAAAATGGAATTTTTGGAAGTTTC
1 GGGGT-AAAAATGAGATTTTTGGAAGTTTC-GGGGTAAAAATGG-ATTTTTGGAAGTTTC
* * * * *
666 TGTGTTAAAAATGAGATTTTTGGAAGTTTAGGGGTAAAAATAGAATTTTGGGAAGTTTC
1 -GGGGTAAAAATGAGATTTTTGGAAGTTTCGGGGTAAAAAT-GGATTTTTGGAAGTTTC
* * * *
725 GAGGTCAAAAATGAGATTTTTGGAAGTTTGGGGGTAAAAACGAAATTTTTGGACAGTTT
1 GGGGT-AAAAATGAGATTTTTGGAAGTTTCGGGGTAAAAATG-GATTTTTGGA-AGTTT
784 AGGGACCTCC
Statistics
Matches: 255, Mismatches: 24, Indels: 31
0.82 0.08 0.10
Matches are distributed among these distances:
58 10 0.04
59 206 0.81
60 38 0.15
61 1 0.00
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (57 bp):
GGGGTAAAAATGAGATTTTTGGAAGTTTCGGGGTAAAAATGGATTTTTGGAAGTTTC
Found at i:588 original size:89 final size:88
Alignment explanation
Indices: 427--787 Score: 350
Period size: 89 Copynumber: 4.1 Consensus size: 88
417 CAAAATGGGA
* * *
427 TTAGGGGTAAAAATGGGATTTTTAGAAGTTTCGAGGTAAAAAATAGG-ATTTTTGGAAG-TTCAG
1 TTAGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTAAAAAAT-GGAATTTTTGGAAGTTTTA-
* *
490 GGGTAAAAATAGAATTTTTAGAAGT
64 GGGTTAAAATAGAATTTTTGGAAGT
*
515 TTTGGGGTCAAAAATGGAATTTTTGGAAG-TTCGAGAGT-AAAAATGGAATTTTTGGAAGTTTTA
1 TTAGGGGT-AAAAATGGAATTTTTGGAAGTTTCGAG-GTAAAAAATGGAATTTTTGGAAGTTTTA
* *
578 GGGTCTAAAATGGGATTTTTGGAAGT
64 GGGT-TAAAATAGAATTTTTGGAAGT
* * *
604 TTCGGGGTCGAAAAT-GAGATTTTTGGAAG-TTCGGGGGT-AAAAATGGAATTTTTGGAAGTTTC
1 TTAGGGGT-AAAAATGGA-ATTTTTGGAAGTTTC-GAGGTAAAAAATGGAATTTTTGGAAGTTT-
*
666 T-GTGTTAAAA-ATGAGATTTTTGGAAGT
62 TAGGGTTAAAATA-GA-ATTTTTGGAAGT
* * * *
693 TTAGGGGTAAAAATAGAATTTTGGGAAGTTTCGAGGTCAAAAAT-GAGATTTTTGGAAG-TTTGG
1 TTAGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTAAAAAATGGA-ATTTTTGGAAGTTTTAG
*
756 GGGTAAAA-ACGAAATTTTTGGACAGT
65 GGTTAAAATA-G-AATTTTTGGA-AGT
782 TTAGGG
1 TTAGGG
788 ACCTCCGGGG
Statistics
Matches: 235, Mismatches: 21, Indels: 33
0.81 0.07 0.11
Matches are distributed among these distances:
87 3 0.01
88 83 0.35
89 146 0.62
90 3 0.01
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (88 bp):
TTAGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTAAAAAATGGAATTTTTGGAAGTTTTAGG
GTTAAAATAGAATTTTTGGAAGT
Done.