Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012140.1 Kokia drynarioides strain JFW-HI SEQ_127139, 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: 2619
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Found at i:171 original size:17 final size:17
Alignment explanation
Indices: 145--193 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
135 TCTGGGCCCA
*
145 ATAAACTTAAATTTATT
1 ATAAAATTAAATTTATT
* *
162 TTAAAATTAAGTTTATT
1 ATAAAATTAAATTTATT
*
179 ATAAATTTAAATTTA
1 ATAAAATTAAATTTA
194 AAATTTATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
ATAAAATTAAATTTATT
Found at i:1377 original size:30 final size:30
Alignment explanation
Indices: 1350--1618 Score: 295
Period size: 30 Copynumber: 9.2 Consensus size: 30
1340 TAATTTTGAG
* *
1350 AGTTTCGAGGTTTAAAATGAAATTTTTGGA
1 AGTTTCGAGGTTAAAAATGGAATTTTTGGA
* *
1380 AGTTT-G-GGATAAAAATGGAATTTTTAGA
1 AGTTTCGAGGTTAAAAATGGAATTTTTGGA
*
1408 AGTTTC-AGGGTCAAAAATGGAATTTTTGGA
1 AGTTTCGA-GGTTAAAAATGGAATTTTTGGA
* *
1438 AG-TTCGAGGGTAAAAATGGAGTTTTTGGA
1 AGTTTCGAGGTTAAAAATGGAATTTTTGGA
* *
1467 AGTTTTGGGGTTAAAAATGGAATTTTTGGA
1 AGTTTCGAGGTTAAAAATGGAATTTTTGGA
* ** *
1497 AG-TTCGGGGGCATAAATGGAATTTTTGGA
1 AGTTTCGAGGTTAAAAATGGAATTTTTGGA
* *
1526 AGTTTTGAGGTTAATAATGGAATTTTTGGA
1 AGTTTCGAGGTTAAAAATGGAATTTTTGGA
*
1556 AGTTTCGAGGTCAAAAATGGAATTTTTGGA
1 AGTTTCGAGGTTAAAAATGGAATTTTTGGA
*
1586 AG-TTCTG-GG--GAAAATGGAATTTTTGGA
1 AGTTTC-GAGGTTAAAAATGGAATTTTTGGA
1613 CAGTTT
1 -AGTTT
1619 AGGGACCTCC
Statistics
Matches: 202, Mismatches: 28, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
27 17 0.08
28 25 0.12
29 57 0.28
30 103 0.51
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.36
Consensus pattern (30 bp):
AGTTTCGAGGTTAAAAATGGAATTTTTGGA
Found at i:1471 original size:59 final size:59
Alignment explanation
Indices: 1275--1617 Score: 316
Period size: 59 Copynumber: 5.9 Consensus size: 59
1265 TCTCGAGGAC
* * * * * * *
1275 AAAATGGTAATTTTGGGAAG-TTCGGGGTTAAATATGAAATTCTTAGATA-TTCGGGGGT-
1 AAAATGG-AATTTTTGGAAGTTTCTGGGTTAAAAATGGAATTTTTGGA-AGTTCGAGGGTA
* * * * *
1333 AAAAGGGTAA-TTTT-GAGAGTTTC-GAGGTTTAAAATGAAATTTTTGGAAGTTTG-GGATA
1 AAAATGG-AATTTTTGGA-AGTTTCTG-GGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTA
* * *
1391 AAAATGGAATTTTTAGAAGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCTGGGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTA
* * *
1450 AAAATGGAGTTTTTGGAAGTTT-TGGGGTTAAAAATGGAATTTTTGGAAGTTCGGGGGCA
1 AAAATGGAATTTTTGGAAGTTTCT-GGGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTA
* *
1509 TAAATGGAATTTTTGGAAGTTT-TGAGGTTAATAATGGAATTTTTGGAAGTTTCGA-GGTCA
1 AAAATGGAATTTTTGGAAGTTTCTG-GGTTAAAAATGGAATTTTTGGAAG-TTCGAGGGT-A
*
1569 AAAATGGAATTTTTGGAAG-TTCTGGG--GAAAATGGAATTTTTGGACAGTT
1 AAAATGGAATTTTTGGAAGTTTCTGGGTTAAAAATGGAATTTTTGGA-AGTT
1618 TAGGGACCTC
Statistics
Matches: 242, Mismatches: 28, Indels: 31
0.80 0.09 0.10
Matches are distributed among these distances:
56 2 0.01
57 30 0.12
58 76 0.31
59 109 0.45
60 25 0.10
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTTCTGGGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTA
Found at i:1545 original size:89 final size:87
Alignment explanation
Indices: 1275--1618 Score: 344
Period size: 89 Copynumber: 3.9 Consensus size: 87
1265 TCTCGAGGAC
* * * * * * * * *
1275 AAAATGGTAATTTTGGGAAG-TTCGGGGTTAAATATGAAATTCTTAGATA-TTCGGGGGTAAAAG
1 AAAATGG-AATTTTTGGAAGTTTTGGGGTTAAAAATGGAATTTTTGGA-AGTTCAGGGGCAAAAT
1338 GGTAA-TTTT-GAGAGTTTCGAGGTTT
64 GG-AATTTTTGGA-AGTTTCGAGG-TT
* * * *
1363 AAAATGAAATTTTTGGAAG-TTT-GGGATAAAAATGGAATTTTTAGAAGTTTCAGGGTCAAAAAT
1 AAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGAATTTTTGGAAG-TTCAGGGGC-AAAAT
*
1426 GGAATTTTTGGAAG-TTCGAGGGTA
64 GGAATTTTTGGAAGTTTCGA-GGTT
* *
1450 AAAATGGAGTTTTTGGAAGTTTTGGGGTTAAAAATGGAATTTTTGGAAGTTCGGGGGCATAAATG
1 AAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGAATTTTTGGAAGTTCAGGGGCA-AAATG
*
1515 GAATTTTTGGAAGTTTTGAGGTT
65 GAATTTTTGGAAGTTTCGAGGTT
* * * *
1538 AATAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCTGGGG-AAAATG
1 AA-AATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGAATTTTTGGAAGTTCAGGGGCAAAATG
1602 GAATTTTTGGACAGTTT
65 GAATTTTTGGA-AGTTT
1619 AGGGACCTCC
Statistics
Matches: 219, Mismatches: 25, Indels: 24
0.82 0.09 0.09
Matches are distributed among these distances:
85 1 0.00
86 19 0.09
87 61 0.28
88 59 0.27
89 79 0.36
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (87 bp):
AAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGAATTTTTGGAAGTTCAGGGGCAAAATGG
AATTTTTGGAAGTTTCGAGGTT
Found at i:2483 original size:16 final size:16
Alignment explanation
Indices: 2464--2495 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2454 TTAATTAATG
2464 TTATTATTAATATTAT
1 TTATTATTAATATTAT
*
2480 TTATTATTAATGTTAT
1 TTATTATTAATATTAT
2496 CATTATTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
TTATTATTAATATTAT
Done.