Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010315.1 Kokia drynarioides strain JFW-HI SEQ_125177, 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: 26910
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Warning! 101 characters in sequence are not A, C, G, or T
Found at i:4162 original size:26 final size:27
Alignment explanation
Indices: 4128--4205 Score: 70
Period size: 26 Copynumber: 2.8 Consensus size: 27
4118 TAATGGGATT
*
4128 ATTATTAAATATAATTTAATAAAAATG
1 ATTAATAAATATAATTTAATAAAAATG
* *
4155 A-TAATAAATAATTATATTTTAAT-ATAATT
1 ATTAATAAAT-A-TA-A-TTTAATAAAAATG
*
4184 ATTATTAAATATAATTTAATAA
1 ATTAATAAATATAATTTAATAA
4206 CATTTTTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
26 13 0.32
27 4 0.10
28 4 0.10
29 7 0.17
30 13 0.32
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (27 bp):
ATTAATAAATATAATTTAATAAAAATG
Found at i:4181 original size:16 final size:16
Alignment explanation
Indices: 4162--4199 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
4152 ATGATAATAA
*
4162 ATAATTA-TATTTTAAT
1 ATAATTATTA-TTAAAT
4178 ATAATTATTATTAAAT
1 ATAATTATTATTAAAT
4194 ATAATT
1 ATAATT
4200 TAATAACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATAATTATTATTAAAT
Found at i:4216 original size:56 final size:53
Alignment explanation
Indices: 4125--4244 Score: 145
Period size: 56 Copynumber: 2.2 Consensus size: 53
4115 ATATAATGGG
4125 ATTATTATTAAATATAATTTAATAAAAATGATAATAAATAATTATATTT-TAATATA
1 ATTATTATTAAATATAATTTAATAAAAATGATAAT--ATAATTAT-TTTAT-ATATA
* * ** *
4181 ATTATTATTAAATATAATTTAATAACATTTTTAATATAATTATTTTATATTTA
1 ATTATTATTAAATATAATTTAATAAAAATGATAATATAATTATTTTATATATA
4234 ATTA-TATTAAA
1 ATTATTATTAAA
4245 ATATTCTAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
52 7 0.12
53 11 0.19
54 9 0.16
56 31 0.53
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (53 bp):
ATTATTATTAAATATAATTTAATAAAAATGATAATATAATTATTTTATATATA
Found at i:7161 original size:55 final size:55
Alignment explanation
Indices: 7077--7180 Score: 163
Period size: 55 Copynumber: 1.9 Consensus size: 55
7067 AAAATTTTTA
* *
7077 TTAGCACTATATACGAATCATCAAAATAATTTATATATGTTGATTATGTCAGTAG
1 TTAGCACTATATACGAATAATCAAAATAATTGATATATGTTGATTATGTCAGTAG
* **
7132 TTAGCATTATATTTGAATAATCAAAATAATTGATATATGTTGATTATGT
1 TTAGCACTATATACGAATAATCAAAATAATTGATATATGTTGATTATGT
7181 TAATTAGTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.41
Consensus pattern (55 bp):
TTAGCACTATATACGAATAATCAAAATAATTGATATATGTTGATTATGTCAGTAG
Found at i:8253 original size:12 final size:12
Alignment explanation
Indices: 8232--8260 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
8222 ATTGTTTCTT
8232 AAAT-GACCACG
1 AAATAGACCACG
8243 AAATAGACCACG
1 AAATAGACCACG
8255 AAATAG
1 AAATAG
8261 CCCCTGTGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.52, C:0.21, G:0.17, T:0.10
Consensus pattern (12 bp):
AAATAGACCACG
Found at i:12182 original size:18 final size:18
Alignment explanation
Indices: 12159--12203 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
12149 GTTACTTATT
12159 ATTTATAAAATTTATCAC
1 ATTTATAAAATTTATCAC
* *
12177 ATTTATAAATTTTATCAT
1 ATTTATAAAATTTATCAC
*
12195 ACTTATAAA
1 ATTTATAAA
12204 TAAAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTATAAAATTTATCAC
Found at i:20982 original size:3 final size:3
Alignment explanation
Indices: 20974--21006 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
20964 GGAAATTGTT
20974 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
21007 TAGACAGACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:21115 original size:137 final size:137
Alignment explanation
Indices: 20869--21268 Score: 592
Period size: 125 Copynumber: 3.0 Consensus size: 137
20859 TGGTATTTGA
* * * *
20869 ATAGACAGATCGATCGCAGAAAGATTTATTCTAAACAAAGTTACGAAATAATTTCAAATTTTGTA
1 ATAGACAGACCGATCGCAGAAAGATTTATTCTAAACAAAGTCATGAAATAATTTCAAATTTTGCA
* *
20934 ACTGCAC-AAAAATTTCAGATGTTATATATAGGAAATTGTTATAATAATAATAATAATAATAATA
66 ACAGCACAAAAAATTT-AGATGTTATATATAGGTAATTGTTATAATAATAATAATAATAATAATA
20998 ATAATAAT
130 ATAATAAT
*
21006 ATAGACAGACCGATCGCAAAAAGATTTATTCTAAACAAAGTCATGAAATAATTTCAAATTTTGCA
1 ATAGACAGACCGATCGCAGAAAGATTTATTCTAAACAAAGTCATGAAATAATTTCAAATTTTGCA
*
21071 ACAGCACAAAAAATTTAGATGTTATATATAGTTAATTG---------T--T-ATAATAATAATAA
66 ACAGCACAAAAAATTTAGATGTTATATATAGGTAATTGTTATAATAATAATAATAATAATAATAA
21124 TAATAAT
131 TAATAAT
21131 ATAGACAGACCGATCGCAGAAAGATTTATTCTAAACAAAGTCATGAAATAATTTCAAATTTTGCA
1 ATAGACAGACCGATCGCAGAAAGATTTATTCTAAACAAAGTCATGAAATAATTTCAAATTTTGCA
* * * *
21196 ACAGCACAAAAATTTTAAATGTTATATATAGGTAATTGTTATAATAATAATAATAAGAATAACAA
66 ACAGCACAAAAAATTTAGATGTTATATATAGGTAATTGTTATAATAATAATAATAATAATAATAA
21261 TAATAAT
131 TAATAAT
21268 A
1 A
21269 ACAATAATAA
Statistics
Matches: 236, Mismatches: 14, Indels: 26
0.86 0.05 0.09
Matches are distributed among these distances:
125 119 0.50
126 1 0.00
128 1 0.00
134 1 0.00
136 1 0.00
137 105 0.44
138 8 0.03
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.32
Consensus pattern (137 bp):
ATAGACAGACCGATCGCAGAAAGATTTATTCTAAACAAAGTCATGAAATAATTTCAAATTTTGCA
ACAGCACAAAAAATTTAGATGTTATATATAGGTAATTGTTATAATAATAATAATAATAATAATAA
TAATAAT
Found at i:21244 original size:3 final size:3
Alignment explanation
Indices: 21236--21310 Score: 105
Period size: 3 Copynumber: 25.0 Consensus size: 3
21226 GGTAATTGTT
* * * *
21236 ATA ATA ATA ATA ATA AGA ATA ACA ATA ATA ATA ACA ATA ATA ACA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
21284 ATA ATA ACA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
21311 TTTGAGACAG
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.67, C:0.05, G:0.01, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:21264 original size:21 final size:21
Alignment explanation
Indices: 21238--21310 Score: 119
Period size: 21 Copynumber: 3.5 Consensus size: 21
21228 TAATTGTTAT
* *
21238 AATAATAATAATAAGAATAAC
1 AATAATAATAACAATAATAAC
21259 AATAATAATAACAATAATAAC
1 AATAATAATAACAATAATAAC
*
21280 AATAATAATAACAATAATAAT
1 AATAATAATAACAATAATAAC
21301 AATAATAATA
1 AATAATAATA
21311 TTTGAGACAG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.67, C:0.05, G:0.01, T:0.26
Consensus pattern (21 bp):
AATAATAATAACAATAATAAC
Found at i:23000 original size:3 final size:3
Alignment explanation
Indices: 22992--23027 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
22982 CAGAAGACTA
22992 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
23028 GATGATGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:24967 original size:18 final size:17
Alignment explanation
Indices: 24937--24973 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
24927 TTTTGAACAA
24937 TTTAATTTTTTTATTTC
1 TTTAATTTTTTTATTTC
*
24954 TTTATTTTTCTTTATTTC
1 TTTAATTTT-TTTATTTC
24972 TT
1 TT
24974 CCCCTTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTAATTTTTTTATTTC
Done.