Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002461.1 Kokia drynarioides strain JFW-HI SEQ_114589, 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: 22098
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:157 original size:18 final size:19
Alignment explanation
Indices: 94--160 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 19
84 TTTTTTAATT
* *
94 AATTAAATTTTAAA-TTCA
1 AATTAAAGTTTAAACTTTA
*
112 AATT-AATTTTAAAC-TTA
1 AATTAAAGTTTAAACTTTA
129 AGA--AAAGTTTAAACTTTA
1 A-ATTAAAGTTTAAACTTTA
147 AATTAAA-TTTAAAC
1 AATTAAAGTTTAAAC
161 CCAAAATGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
17 22 0.54
18 16 0.39
19 3 0.07
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (19 bp):
AATTAAAGTTTAAACTTTA
Found at i:1567 original size:19 final size:21
Alignment explanation
Indices: 1529--1568 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
1519 TCTCCTCAAC
1529 TACAATAAAAGTAAACAAAGA
1 TACAATAAAAGTAAACAAAGA
*
1550 TACAA-AAAAG-AAAGAAAGA
1 TACAATAAAAGTAAACAAAGA
1569 AAATCTCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 5 0.28
21 5 0.28
ACGTcount: A:0.70, C:0.07, G:0.12, T:0.10
Consensus pattern (21 bp):
TACAATAAAAGTAAACAAAGA
Found at i:3156 original size:3 final size:3
Alignment explanation
Indices: 3148--3191 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
3138 CTTTTGTCCT
* ** *
3148 ATA ATA ATA ATA ATA ATA ACA ATA ACG ATA ACA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3192 CTAAAAGTTC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:3165 original size:12 final size:12
Alignment explanation
Indices: 3148--3190 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
3138 CTTTTGTCCT
*
3148 ATAATAATAATA
1 ATAATAACAATA
3160 ATAATAACAATA
1 ATAATAACAATA
**
3172 ACGATAACAATA
1 ATAATAACAATA
3184 ATAATAA
1 ATAATAA
3191 TCTAAAAGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (12 bp):
ATAATAACAATA
Found at i:4019 original size:23 final size:24
Alignment explanation
Indices: 3975--4019 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
3965 CAAAATTATT
***
3975 TAAAAATTAAATAATTTTAAATAA
1 TAAAAATTAAATAATAAAAAATAA
3999 TAAAAATT-AATAATAAAAAAT
1 TAAAAATTAAATAATAAAAAAT
4020 TATTATGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 10 0.56
24 8 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
TAAAAATTAAATAATAAAAAATAA
Found at i:4240 original size:9 final size:9
Alignment explanation
Indices: 4226--4292 Score: 57
Period size: 9 Copynumber: 7.4 Consensus size: 9
4216 GTATATATAG
4226 TTTTTAAAA
1 TTTTTAAAA
4235 TTTTTAATAA
1 TTTTTAA-AA
4245 --TTTAAAA
1 TTTTTAAAA
*
4252 TTTTAAAAA
1 TTTTTAAAA
*
4261 TTATTTAAAT
1 TT-TTTAAAA
**
4271 TTTTTATGA
1 TTTTTAAAA
*
4280 TTCTTAAAA
1 TTTTTAAAA
4289 TTTT
1 TTTT
4293 AAATAATTCT
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
7 2 0.05
8 5 0.11
9 28 0.64
10 9 0.20
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:4301 original size:19 final size:19
Alignment explanation
Indices: 4229--4302 Score: 73
Period size: 19 Copynumber: 4.1 Consensus size: 19
4219 TATATAGTTT
*
4229 TTAAAATTTTTAATAA-T-
1 TTAAAATTTTAAATAATTC
*
4246 TTAAAATTTTAAA-AATTA
1 TTAAAATTTTAAATAATTC
* ** *
4264 TTTAAATTTTTTATGATTC
1 TTAAAATTTTAAATAATTC
4283 TTAAAATTTTAAATAATTC
1 TTAAAATTTTAAATAATTC
4302 T
1 T
4303 ATATACTTAA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
16 2 0.05
17 13 0.30
18 10 0.23
19 19 0.43
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (19 bp):
TTAAAATTTTAAATAATTC
Found at i:4455 original size:10 final size:9
Alignment explanation
Indices: 4439--4489 Score: 50
Period size: 10 Copynumber: 5.3 Consensus size: 9
4429 ATTTCAATAT
4439 ATTTTTATA
1 ATTTTTATA
4448 ATTATTTATA
1 ATT-TTTATA
4458 ATTTTTAAATAA
1 ATTTTT--AT-A
4470 ATTTTTAT-
1 ATTTTTATA
*
4478 AGTTTTATA
1 ATTTTTATA
4487 ATT
1 ATT
4490 AAAAAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
8 7 0.20
9 8 0.23
10 11 0.31
11 2 0.06
12 7 0.20
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (9 bp):
ATTTTTATA
Found at i:4476 original size:21 final size:23
Alignment explanation
Indices: 4447--4492 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
4437 ATATTTTTAT
4447 AATTATTTATAATTTT-TAAATA
1 AATTATTTATAATTTTATAAATA
* *
4469 AATT-TTTATAGTTTTATAATTA
1 AATTATTTATAATTTTATAAATA
4491 AA
1 AA
4493 AAAAAAACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
AATTATTTATAATTTTATAAATA
Found at i:7291 original size:21 final size:20
Alignment explanation
Indices: 7265--7313 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
7255 AATTAAATAA
*
7265 AAATATAATGAATTTGTAAAT
1 AAATATAATAAATTT-TAAAT
* **
7286 AAATATTATAAATTTTATTT
1 AAATATAATAAATTTTAAAT
7306 AAATATAA
1 AAATATAA
7314 GTAATCGTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (20 bp):
AAATATAATAAATTTTAAAT
Found at i:9474 original size:12 final size:12
Alignment explanation
Indices: 9457--9481 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9447 AATTATTAAC
9457 TTCATATATATA
1 TTCATATATATA
9469 TTCATATATATA
1 TTCATATATATA
9481 T
1 T
9482 ATTCGATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TTCATATATATA
Found at i:9479 original size:14 final size:15
Alignment explanation
Indices: 9460--9490 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
9450 TATTAACTTC
9460 ATATATATATTC-AT
1 ATATATATATTCGAT
9474 ATATATATATTCGAT
1 ATATATATATTCGAT
9489 AT
1 AT
9491 TTGTGTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (15 bp):
ATATATATATTCGAT
Found at i:10352 original size:17 final size:18
Alignment explanation
Indices: 10313--10353 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
10303 AACAATAAAT
* *
10313 ATTTCGATTACTTAATTA
1 ATTTCGATTAATTAAGTA
10331 A-TTCGATTAATT-AGTA
1 ATTTCGATTAATTAAGTA
10347 ATTTCGA
1 ATTTCGA
10354 ACCAAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 4 0.20
17 15 0.75
18 1 0.05
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (18 bp):
ATTTCGATTAATTAAGTA
Found at i:19583 original size:46 final size:43
Alignment explanation
Indices: 19488--19583 Score: 102
Period size: 46 Copynumber: 2.2 Consensus size: 43
19478 AGAAAGGTTG
* **
19488 AAGGGTTCATTTTATAGAGTTACAAGTATAGTTGGTATGCTAT
1 AAGGTTTCATTTTATAGAGTTACAAGTATAGTTGACATGCTAT
* ** *
19531 ATGGTTTCATTTTATAGAGTTGTAGTAGATATAGTTGACATGTTAT
1 AAGGTTTCATTTTATAGAG-T-TACAAG-TATAGTTGACATGCTAT
19577 AAGGTTT
1 AAGGTTT
19584 GTTTCATAAG
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
43 17 0.40
44 1 0.02
45 4 0.10
46 20 0.48
ACGTcount: A:0.29, C:0.05, G:0.23, T:0.43
Consensus pattern (43 bp):
AAGGTTTCATTTTATAGAGTTACAAGTATAGTTGACATGCTAT
Found at i:20055 original size:7 final size:7
Alignment explanation
Indices: 20033--20067 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
20023 TTTATTTATA
20033 TTTATATT
1 TTTAT-TT
*
20041 TGTATTT
1 TTTATTT
20048 TTTATTT
1 TTTATTT
20055 TTTATTT
1 TTTATTT
20062 TTTATT
1 TTTATT
20068 ACACCCTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 21 0.84
8 4 0.16
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (7 bp):
TTTATTT
Done.