Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014622.1 Kokia drynarioides strain JFW-HI SEQ_129661, 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: 29620
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:7410 original size:58 final size:58
Alignment explanation
Indices: 7320--7435 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
7310 AGCATGGTCT
*
7320 ATTTATAAGGATTCAATAAAGGCACATTGAATACCATCAAGAGCGTAAGGACTGCATG
1 ATTTATAAGGATTCAATAAAGGCACATTGAATACCATCAAGAGCATAAGGACTGCATG
7378 ATTTATAAGGATTCAATAAAGGCACATTGAATACCATCAAGAGCATAAGGACTGCATG
1 ATTTATAAGGATTCAATAAAGGCACATTGAATACCATCAAGAGCATAAGGACTGCATG
7436 CAGAATTAGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.24
Consensus pattern (58 bp):
ATTTATAAGGATTCAATAAAGGCACATTGAATACCATCAAGAGCATAAGGACTGCATG
Found at i:12329 original size:20 final size:22
Alignment explanation
Indices: 12298--12343 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
12288 ATTTACTTAA
12298 TAAATTTAATATTTT-ATTGAG
1 TAAATTTAATATTTTAATTGAG
*
12319 TAAATTT-ATATTTTAATTTAG
1 TAAATTTAATATTTTAATTGAG
12340 TAAA
1 TAAA
12344 AAGGAAGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (22 bp):
TAAATTTAATATTTTAATTGAG
Found at i:12500 original size:25 final size:25
Alignment explanation
Indices: 12454--12501 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
12444 TAAATTAGTT
* *
12454 AAATATTTTATAATATTTTTAATTA
1 AAATATTTTACAATATTATTAATTA
12479 AAATAATTTTACAAT-TTATTAAT
1 AAAT-ATTTTACAATATTATTAAT
12502 GATTTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
AAATATTTTACAATATTATTAATTA
Found at i:16864 original size:116 final size:116
Alignment explanation
Indices: 16723--16957 Score: 461
Period size: 116 Copynumber: 2.0 Consensus size: 116
16713 GTTTAAATAT
16723 CAAATTATTTATCAATAAATTTGATTTTGATTGAGTTTTGAATATTATTATTTTATCTTAATATT
1 CAAATTATTTATCAATAAATTTGATTTTGATTGAGTTTTGAATATTATTATTTTATCTTAATATT
*
16788 TTAGGGAGGTTCTTATATTATGCATTTTTAGCCGATTTAGTCCCTCTATTA
66 TTAGGGAGGTTCTTATATTATGCATTTTTAGACGATTTAGTCCCTCTATTA
16839 CAAATTATTTATCAATAAATTTGATTTTGATTGAGTTTTGAATATTATTATTTTATCTTAATATT
1 CAAATTATTTATCAATAAATTTGATTTTGATTGAGTTTTGAATATTATTATTTTATCTTAATATT
16904 TTAGGGAGGTTCTTATATTATGCATTTTTAGACGATTTAGTCCCTCTATTA
66 TTAGGGAGGTTCTTATATTATGCATTTTTAGACGATTTAGTCCCTCTATTA
16955 CAA
1 CAA
16958 TTTGAATACT
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 118 1.00
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.49
Consensus pattern (116 bp):
CAAATTATTTATCAATAAATTTGATTTTGATTGAGTTTTGAATATTATTATTTTATCTTAATATT
TTAGGGAGGTTCTTATATTATGCATTTTTAGACGATTTAGTCCCTCTATTA
Found at i:23107 original size:25 final size:25
Alignment explanation
Indices: 23057--23116 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 25
23047 AAAACAAAAA
* *
23057 ATAAAAAGTAAACTACTTATATTAT
1 ATAAAAAGTAAACTACTAATAATAT
*
23082 ATAAAAATTAAATCTA-TAATAATAT
1 ATAAAAAGTAAA-CTACTAATAATAT
*
23107 AACAAAAAGT
1 -ATAAAAAGT
23117 TAGATCATCT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 18 0.64
26 10 0.36
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.32
Consensus pattern (25 bp):
ATAAAAAGTAAACTACTAATAATAT
Found at i:26727 original size:18 final size:18
Alignment explanation
Indices: 26704--26746 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
26694 GAATAAATTT
26704 TTAATTAAATAAGTTT-AA
1 TTAATTAAA-AAGTTTAAA
*
26722 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAGTTTAAA
26740 TTAATTA
1 TTAATTA
26747 CAATTGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAGTTTAAA
Found at i:28189 original size:8 final size:10
Alignment explanation
Indices: 28152--28188 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
28142 TTTTAGGAAT
28152 TATATAAAAA
1 TATATAAAAA
*
28162 -ATCTAAAAA
1 TATATAAAAA
28171 TATATAAAAA
1 TATATAAAAA
28181 TA-ATAAAA
1 TATATAAAA
28189 TCTATTGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 14 0.58
10 10 0.42
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (10 bp):
TATATAAAAA
Found at i:28274 original size:19 final size:18
Alignment explanation
Indices: 28247--28283 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
28237 TTTAATATAA
*
28247 TTTTTATAATTTCCTATT
1 TTTTTATAATTTCATATT
28265 TTTTTAATAATTTCATATT
1 TTTTT-ATAATTTCATATT
28284 GTTTAAAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTTATAATTTCATATT
Found at i:28755 original size:22 final size:22
Alignment explanation
Indices: 28729--28781 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
28719 TCATTTAATA
28729 TTTACTAATTA-TATATATATCT
1 TTTACTAATTATTATATATAT-T
*
28751 TTTAC-ACTTATTATATATATT
1 TTTACTAATTATTATATATATT
*
28772 TTTATTAATT
1 TTTACTAATT
28782 TTTTAAACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTACTAATTATTATATATATT
Found at i:29512 original size:6 final size:6
Alignment explanation
Indices: 29505--29545 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
29495 AGTATCCTCT
*
29505 CTCTCT CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTC
29546 ATTCTTTTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (6 bp):
CTCTCC
Done.