Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003193.1 Kokia drynarioides strain JFW-HI SEQ_115806, 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: 22001
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:6239 original size:43 final size:43
Alignment explanation
Indices: 6191--6297 Score: 112
Period size: 43 Copynumber: 2.5 Consensus size: 43
6181 TATTTTTTAA
* *
6191 ATAAAAATCATAAAATTTCTACAAAT-TCTACAAAT-AAAAAATT
1 ATAAAAATCATAAAATAT-AACAAATAT-TACAAATAAAAAAATT
* *
6234 ATAAAAAT-AAAAAATATAACATATATTACAAATACAAAAAATT
1 ATAAAAATCATAAAATATAACAAATATTACAAATA-AAAAAATT
*
6277 ATATAAAGTCATAAAATATAA
1 ATA-AAAATCATAAAATATAA
6298 AAAAATCATT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
41 12 0.23
42 8 0.15
43 19 0.36
44 4 0.08
45 10 0.19
ACGTcount: A:0.63, C:0.08, G:0.01, T:0.28
Consensus pattern (43 bp):
ATAAAAATCATAAAATATAACAAATATTACAAATAAAAAAATT
Found at i:6251 original size:15 final size:16
Alignment explanation
Indices: 6222--6252 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6212 CAAATTCTAC
6222 AAATAAAAAATTATAA
1 AAATAAAAAATTATAA
6238 AAATAAAAAA-TATAA
1 AAATAAAAAATTATAA
6253 CATATATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATAAAAAATTATAA
Found at i:6347 original size:10 final size:10
Alignment explanation
Indices: 6334--6393 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
6324 ATAAAATGTA
6334 AAAAAATTAT
1 AAAAAATTAT
6344 AAAACAATTAT
1 AAAA-AATTAT
* **
6355 AACAAGCTAT
1 AAAAAATTAT
6365 AAAAAATT-T
1 AAAAAATTAT
6374 ATAAAAATTATT
1 A-AAAAATTA-T
6386 AAAAAATT
1 AAAAAATT
6394 CATATATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
9 2 0.05
10 20 0.50
11 16 0.40
12 2 0.05
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:6388 original size:21 final size:20
Alignment explanation
Indices: 6335--6393 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
6325 TAAAATGTAA
6335 AAAAATTATAAAACAA-TTAT
1 AAAAATTATAAAA-AATTTAT
**
6355 AACAAGCTATAAAAAATTTAT
1 AA-AAATTATAAAAAATTTAT
6376 AAAAATTATTAAAAAATT
1 AAAAATTA-TAAAAAATT
6394 CATATATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 8 0.25
21 24 0.75
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAAATTATAAAAAATTTAT
Found at i:12224 original size:23 final size:23
Alignment explanation
Indices: 12191--12235 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
12181 AGTGAAAAGA
*
12191 ACAAAACGAAAATGAGT-AGAAAT
1 ACAAAAAGAAAA-GAGTAAGAAAT
12214 ACAAAAAGAAAAGAGTAAGAAA
1 ACAAAAAGAAAAGAGTAAGAAA
12236 AAGTGTAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.67, C:0.07, G:0.18, T:0.09
Consensus pattern (23 bp):
ACAAAAAGAAAAGAGTAAGAAAT
Found at i:15759 original size:18 final size:18
Alignment explanation
Indices: 15738--15781 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
15728 ATGCGGTCTA
**
15738 AATATGCTCTTACGAGCC
1 AATATGCTCAAACGAGCC
15756 AATATGCTCAAACGAGCC
1 AATATGCTCAAACGAGCC
15774 AATATGCT
1 AATATGCT
15782 ATTCCTCCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (18 bp):
AATATGCTCAAACGAGCC
Found at i:17445 original size:15 final size:15
Alignment explanation
Indices: 17421--17451 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17411 CAGTATCAGA
17421 TTCAGATTCCACTAT
1 TTCAGATTCCACTAT
*
17436 TTCAGTTTCCACTAT
1 TTCAGATTCCACTAT
17451 T
1 T
17452 CAAACATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.26, G:0.06, T:0.45
Consensus pattern (15 bp):
TTCAGATTCCACTAT
Found at i:19613 original size:18 final size:18
Alignment explanation
Indices: 19584--19649 Score: 78
Period size: 18 Copynumber: 3.6 Consensus size: 18
19574 GCGAAAGAAA
*
19584 GAGCATACTGGCTCGTTT
1 GAGCATACTGGCTCATTT
* *
19602 GGGCATATTGGCTCATTT
1 GAGCATACTGGCTCATTT
**
19620 GAGCATACTGGCTCATAA
1 GAGCATACTGGCTCATTT
19638 GAGCATTACTGG
1 GAGCA-TACTGG
19650 ATCGCATGAG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
18 34 0.85
19 6 0.15
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (18 bp):
GAGCATACTGGCTCATTT
Done.