Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011047.1 Kokia drynarioides strain JFW-HI SEQ_126018, 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: 5942
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Found at i:1757 original size:205 final size:206
Alignment explanation
Indices: 1251--1948 Score: 907
Period size: 205 Copynumber: 3.4 Consensus size: 206
1241 AAAGCGAGCA
* *
1251 AAATCTTCGAATCC-TAGCTT-CTTGATGAGACATTGAGAG-GCAGGTCGAAGCAATAAAAGGTT
1 AAATCTTCGAA-CCACAGCTTCCTT-ATGAGACACTGAGAGAGCAGGTCGAAGCAATAAAAGGTT
* *
1313 AGCTTCCTGATGAGATATTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGA
64 AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGA
* * * *
1378 ATTGAAACAAACGACGCGGTCATCTTCCTGATGAGACACTGAGAAGAAG-AC---CCAAA-CGAG
129 ATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGAACAAATCAAATCCAC
** * * *
1438 GCTTAAAGCGAGC
194 GCTCGATGTGAAC
* * *
1451 AAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGA-AAAGCAGGTCGAAGCAATAAAAGGTTA
1 -AAATCTTCGAACCACAGCTTCCTTATGAGACACTGAGAGAGCAGGTCGAAGCAATAAAAGGTTA
* *
1515 GCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTGATGAGATACAGATAAGCGAA
65 GCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAA
* * * *
1580 TTGAAAGAAAGGACGCGGTCATCTTCCAGATGAGATATTGAGAAGAAGAACAAATCAAATCCACG
130 TTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGAACAAATCAAATCCACG
1645 CTCGATGTGAAC
195 CTCGATGTGAAC
* *
1657 AAATCTTCGAACCACAGTTTCCTTATGAGACACTGAGAGA-CAGGTCGAAGCGATAAAAGGTTAG
1 AAATCTTCGAACCACAGCTTCCTTATGAGACACTGAGAGAGCAGGTCGAAGCAATAAAAGGTTAG
* * * * * *
1721 CTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAGGAGGAT
66 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAAT
* * *
1786 TGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGATCAAATCAAATACACGC
131 TGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGAACAAATCAAATCCACGC
*
1851 TCGATGTGAAT
196 TCGATGTGAAC
* ** * * *
1862 AAATCTTTGAACCATGGCTT-CTTGATGAAACACTAAGA-AGCAGGTCGAAGCAATAAATGGTTA
1 AAATCTTCGAACCACAGCTTCCTT-ATGAGACACTGAGAGAGCAGGTCGAAGCAATAAAAGGTTA
*
1925 GTTTCCTGATGAGATACTGAGAAG
65 GCTTCCTGATGAGATACTGAGAAG
1949 AAGACAAAGT
Statistics
Matches: 434, Mismatches: 52, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
200 3 0.01
201 155 0.36
202 4 0.01
204 4 0.01
205 256 0.59
206 12 0.03
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.22
Consensus pattern (206 bp):
AAATCTTCGAACCACAGCTTCCTTATGAGACACTGAGAGAGCAGGTCGAAGCAATAAAAGGTTAG
CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAAT
TGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGAACAAATCAAATCCACGC
TCGATGTGAAC
Found at i:2285 original size:6 final size:6
Alignment explanation
Indices: 2274--2354 Score: 59
Period size: 6 Copynumber: 14.2 Consensus size: 6
2264 CGGGCCCAAC
* * *
2274 AAATTT AAATTT -ATTTT AAAATT AAGTTT --ATTCT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATT-T AAATTT AAATTT
2320 --ATTT AAATTT --ATTAT AAATTT AAATTT AAAATTT A
1 AAATTT AAATTT AAATT-T AAATTT AAATTT -AAATTT A
2355 TTTAAATAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
4 9 0.15
5 6 0.10
6 32 0.54
7 12 0.20
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:2330 original size:27 final size:25
Alignment explanation
Indices: 2294--2361 Score: 86
Period size: 27 Copynumber: 2.7 Consensus size: 25
2284 TTATTTTAAA
*
2294 ATTAAGTTTATTCTAAATTTAAATTT
1 ATTAAATTTATT-TAAATTTAAATTT
2320 ATTTAAATTTATTATAAATTTAAATTT
1 A-TTAAATTTATT-TAAATTTAAATTT
2347 A--AAATTTATTTAAAT
1 ATTAAATTTATTTAAAT
2362 AATGTCCAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
23 5 0.13
24 9 0.23
26 1 0.03
27 24 0.62
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (25 bp):
ATTAAATTTATTTAAATTTAAATTT
Found at i:2339 original size:11 final size:10
Alignment explanation
Indices: 2310--2361 Score: 68
Period size: 10 Copynumber: 4.8 Consensus size: 10
2300 TTTATTCTAA
2310 ATTTAAATTT
1 ATTTAAATTT
2320 ATTTAAATTT
1 ATTTAAATTT
2330 ATTATAAATTT
1 ATT-TAAATTT
2341 AAATTTAAAATTT
1 --ATTT-AAATTT
2354 ATTTAAAT
1 ATTTAAAT
2362 AATGTCCAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 17 0.45
11 11 0.29
12 1 0.03
13 9 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:2340 original size:17 final size:16
Alignment explanation
Indices: 2274--2361 Score: 95
Period size: 17 Copynumber: 5.2 Consensus size: 16
2264 CGGGCCCAAC
2274 AAATTTAAATTTATTTT
1 AAATTTAAATTTA-TTT
* *
2291 AAAATTAAGTTTATTCT
1 AAATTTAAATTTATT-T
2308 AAATTTAAATTTATTT
1 AAATTTAAATTTATTT
* **
2324 AAATTTATTATAAATTT
1 AAATTTA-AATTTATTT
2341 AAATTTAAAATTTATTT
1 AAATTT-AAATTTATTT
2358 AAAT
1 AAAT
2362 AATGTCCAGT
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
16 10 0.17
17 47 0.81
18 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (16 bp):
AAATTTAAATTTATTT
Found at i:4342 original size:30 final size:29
Alignment explanation
Indices: 4273--4571 Score: 303
Period size: 29 Copynumber: 10.2 Consensus size: 29
4263 TTGTTTTTAC
4273 CCCCG-AACTTCCAAAAATCCCATTTTT-A
1 CCCCGAAACTTCCAAAAAT-CCATTTTTGA
*
4301 CCCCCAAACTTCCAAAAATCCAATTTTTGA
1 CCCCGAAACTTCCAAAAATCC-ATTTTTGA
*
4331 CCTCGAAACTTCCAAAAATCCATTTTTGA
1 CCCCGAAACTTCCAAAAATCCATTTTTGA
*
4360 -CCCGAAACTTCTAAAAATTCCATTTTT-A
1 CCCCGAAACTTCCAAAAA-TCCATTTTTGA
* *
4388 CCCCTAAACTTCCAAAAATTTCATTTTT-A
1 CCCCGAAACTTCCAAAAA-TCCATTTTTGA
*
4417 CCCTC-AAACTTCAAAAAATCACATTTTTGA
1 CCC-CGAAACTTCCAAAAATC-CATTTTTGA
* *
4447 CCCCAAAACTTCCAAAAATTCCATTTTT-T
1 CCCCGAAACTTCCAAAAA-TCCATTTTTGA
* *
4476 CACTCG-AACTTCCAAAAATCCCATTTTTAA
1 C-CCCGAAACTTCCAAAAAT-CCATTTTTGA
4506 CCCTCG-AACTTCCAAAAATCCCATTTTTGA
1 CCC-CGAAACTTCCAAAAAT-CCATTTTTGA
* *
4536 CCCCAAAACTTCCAAAAATTACCA-TTTTGC
1 CCCCGAAACTTCCAAAAA-T-CCATTTTTGA
4566 CCCCGA
1 CCCCGA
4572 GTATCCGAAA
Statistics
Matches: 234, Mismatches: 21, Indels: 30
0.82 0.07 0.11
Matches are distributed among these distances:
28 24 0.10
29 107 0.46
30 97 0.41
31 6 0.03
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.30
Consensus pattern (29 bp):
CCCCGAAACTTCCAAAAATCCATTTTTGA
Found at i:4350 original size:59 final size:59
Alignment explanation
Indices: 4273--4554 Score: 317
Period size: 59 Copynumber: 4.8 Consensus size: 59
4263 TTGTTTTTAC
4273 CCCCG-AACTTCCAAAAATCCCATTTTTACCCCCAAACTTCCAAAAATCCAATTTTTGA
1 CCCCGAAACTTCCAAAAATCCCATTTTTACCCCCAAACTTCCAAAAATCCAATTTTTGA
* * *
4331 CCTCGAAACTTCCAAAAAT-CCATTTTTGA-CCCGAAACTTCTAAAAATTCC-ATTTTT-A
1 CCCCGAAACTTCCAAAAATCCCATTTTT-ACCCCCAAACTTCCAAAAA-TCCAATTTTTGA
* ** * *
4388 CCCCTAAACTTCCAAAAATTTCATTTTTACCCTCAAACTTCAAAAAAT-CACATTTTTGA
1 CCCCGAAACTTCCAAAAATCCCATTTTTACCCCCAAACTTCCAAAAATCCA-ATTTTTGA
* * * * * * * *
4447 CCCCAAAACTTCCAAAAATTCCATTTTTTCACTCGAACTTCCAAAAATCCCATTTTTAA
1 CCCCGAAACTTCCAAAAATCCCATTTTTACCCCCAAACTTCCAAAAATCCAATTTTTGA
*
4506 CCCTCG-AACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAAT
1 CCC-CGAAACTTCCAAAAATCCCATTTTT-ACCCCCAAACTTCCAAAAAT
4555 TACCATTTTG
Statistics
Matches: 189, Mismatches: 24, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
56 1 0.01
57 20 0.11
58 60 0.32
59 91 0.48
60 17 0.09
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.30
Consensus pattern (59 bp):
CCCCGAAACTTCCAAAAATCCCATTTTTACCCCCAAACTTCCAAAAATCCAATTTTTGA
Done.