Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009412.1 Kokia drynarioides strain JFW-HI SEQ_124119, 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: 43891
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:10593 original size:58 final size:58
Alignment explanation
Indices: 10503--10619 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
10493 TTATTCATGC
10503 ATAGAATTATTTAGGTCACATAGGGCTTTTTGGCTTGTAACGTGTTGAGGCTTAAGAT
1 ATAGAATTATTTAGGTCACATAGGGCTTTTTGGCTTGTAACGTGTTGAGGCTTAAGAT
10561 ATAGAATTATTTAGGTCACATAGGGCTTTTTGGCTTGTAACGTGTTGAGGCTTAAGAT
1 ATAGAATTATTTAGGTCACATAGGGCTTTTTGGCTTGTAACGTGTTGAGGCTTAAGAT
10619 A
1 A
10620 GGTATGAATT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (58 bp):
ATAGAATTATTTAGGTCACATAGGGCTTTTTGGCTTGTAACGTGTTGAGGCTTAAGAT
Found at i:11817 original size:16 final size:16
Alignment explanation
Indices: 11796--11831 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
11786 AAATAATCCC
*
11796 AAAATTACAAGTCTCA
1 AAAATTAAAAGTCTCA
*
11812 AAAATTAAAATTCTCA
1 AAAATTAAAAGTCTCA
11828 AAAA
1 AAAA
11832 ACACTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.58, C:0.14, G:0.03, T:0.25
Consensus pattern (16 bp):
AAAATTAAAAGTCTCA
Found at i:19248 original size:26 final size:26
Alignment explanation
Indices: 19219--19385 Score: 165
Period size: 26 Copynumber: 6.4 Consensus size: 26
19209 ATCGTAAACA
*
19219 AATAAATAGCAGGCCTTAAGCCGGTG
1 AATAAATAGCAGGCCTTGAGCCGGTG
* *
19245 AATAAATAGCAAGCCTCGAGCCGGTG
1 AATAAATAGCAGGCCTTGAGCCGGTG
* * * *
19271 AATATATAGCAGGCTTTAAGCCGATG
1 AATAAATAGCAGGCCTTGAGCCGGTG
* * *
19297 AATAAATAGCAAGCCATGAGCCGATG
1 AATAAATAGCAGGCCTTGAGCCGGTG
* *
19323 AATATATAGCAGGCCTTGAGTCGGTG
1 AATAAATAGCAGGCCTTGAGCCGGTG
* * * *
19349 AATAATTAGCAAG-CTTCGACCCGATG
1 AATAAATAGCAGGCCTT-GAGCCGGTG
*
19375 ATTAAATAGCA
1 AATAAATAGCA
19386 AGCTTCGTGC
Statistics
Matches: 113, Mismatches: 27, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
25 3 0.03
26 110 0.97
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.22
Consensus pattern (26 bp):
AATAAATAGCAGGCCTTGAGCCGGTG
Found at i:19281 original size:52 final size:52
Alignment explanation
Indices: 19219--19385 Score: 219
Period size: 52 Copynumber: 3.2 Consensus size: 52
19209 ATCGTAAACA
*
19219 AATAAATAGCAGGCCTTAAGCCGGTGAATAAATAGCAAGCCTCGAGCCGGTG
1 AATAAATAGCAGGCCTTAAGCCGGTGAATAAATAGCAAGCCTCGAGCCGATG
* * *
19271 AATATATAGCAGGCTTTAAGCCGATGAATAAATAGCAAGCCAT-GAGCCGATG
1 AATAAATAGCAGGCCTTAAGCCGGTGAATAAATAGCAAGCC-TCGAGCCGATG
* * * * * *
19323 AATATATAGCAGGCCTTGAGTCGGTGAATAATTAGCAAGCTTCGACCCGATG
1 AATAAATAGCAGGCCTTAAGCCGGTGAATAAATAGCAAGCCTCGAGCCGATG
*
19375 ATTAAATAGCA
1 AATAAATAGCA
19386 AGCTTCGTGC
Statistics
Matches: 100, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
51 1 0.01
52 98 0.98
53 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.22
Consensus pattern (52 bp):
AATAAATAGCAGGCCTTAAGCCGGTGAATAAATAGCAAGCCTCGAGCCGATG
Found at i:19400 original size:78 final size:78
Alignment explanation
Indices: 19219--19388 Score: 207
Period size: 78 Copynumber: 2.2 Consensus size: 78
19209 ATCGTAAACA
* * * * *
19219 AATAAATAGCAGGCCTTAAGCCGGTGAATAAATAGCAAGCCTCGAGCCGGTGAATATATAGCAGG
1 AATAAATAGCAAGCCATGAGCCGATGAATAAATAGCAAGCCTCGAGCCGGTGAATATATAGCAAG
* *
19284 CTTTAAGCCGATG
66 CTTCAACCCGATG
* * * *
19297 AATAAATAGCAAGCCATGAGCCGATGAATATATAGCAGGCCTTGAGTCGGTGAATA-ATTAGCAA
1 AATAAATAGCAAGCCATGAGCCGATGAATAAATAGCAAGCCTCGAGCCGGTGAATATA-TAGCAA
*
19361 GCTTCGACCCGATG
65 GCTTCAACCCGATG
*
19375 ATTAAATAGCAAGC
1 AATAAATAGCAAGC
19389 TTCGTGCCGA
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
77 1 0.01
78 77 0.99
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (78 bp):
AATAAATAGCAAGCCATGAGCCGATGAATAAATAGCAAGCCTCGAGCCGGTGAATATATAGCAAG
CTTCAACCCGATG
Found at i:20118 original size:12 final size:12
Alignment explanation
Indices: 20101--20132 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
20091 AGTACAGGGT
20101 ACATGGGCAAAC
1 ACATGGGCAAAC
20113 ACATGGGCAAAC
1 ACATGGGCAAAC
20125 ACATGGGC
1 ACATGGGC
20133 TGGGACACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.38, C:0.25, G:0.28, T:0.09
Consensus pattern (12 bp):
ACATGGGCAAAC
Found at i:32137 original size:7 final size:7
Alignment explanation
Indices: 32125--32155 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
32115 AAATCCAATT
32125 GTGTTGA
1 GTGTTGA
32132 GTGTTGA
1 GTGTTGA
*
32139 GTGTGGA
1 GTGTTGA
32146 GTGTTGA
1 GTGTTGA
32153 GTG
1 GTG
32156 CTGAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.13, C:0.00, G:0.48, T:0.39
Consensus pattern (7 bp):
GTGTTGA
Found at i:36582 original size:27 final size:28
Alignment explanation
Indices: 36548--36604 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
36538 TAGACATTTT
* *
36548 TAGGGGTTTG-TCACGACGTAGACATGC
1 TAGGGGTTTGTTCACGACATAGAAATGC
*
36575 TAGGGGTTTGTTCGCGACATAGAAATGC
1 TAGGGGTTTGTTCACGACATAGAAATGC
36603 TA
1 TA
36605 TGTTGCGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.25, C:0.16, G:0.32, T:0.28
Consensus pattern (28 bp):
TAGGGGTTTGTTCACGACATAGAAATGC
Done.