Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000833.1 Kokia drynarioides strain JFW-HI SEQ_111928, 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: 34545
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:10572 original size:72 final size:72
Alignment explanation
Indices: 10448--10588 Score: 194
Period size: 72 Copynumber: 2.0 Consensus size: 72
10438 CCTTTATTCA
* ** *
10448 TACCTCCATGATGGGGTAAAACATGAGCAGGAGAGGGAGACTGAGATAAAACAGGACCAGGTGAG
1 TACCACCATGATGGGGTAAAACATGAGCAGGAGAGACAGACTGAGATAAAACAGGACCAGGTGAA
10513 GCAGTCC
66 GCAGTCC
* * * *
10520 TACCACCATGATGGGGTGAAACA-GAAGCAGGAGAGACAGGCTGAGGTGAAACAGGACCAGGTGA
1 TACCACCATGATGGGGTAAAACATG-AGCAGGAGAGACAGACTGAGATAAAACAGGACCAGGTGA
10584 AGCAG
65 AGCAG
10589 CCAGATATTC
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 1 0.02
72 59 0.98
ACGTcount: A:0.35, C:0.18, G:0.35, T:0.12
Consensus pattern (72 bp):
TACCACCATGATGGGGTAAAACATGAGCAGGAGAGACAGACTGAGATAAAACAGGACCAGGTGAA
GCAGTCC
Found at i:25864 original size:16 final size:15
Alignment explanation
Indices: 25839--25870 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
25829 GTGTGTATAT
25839 ATTGATATTCTAATC
1 ATTGATATTCTAATC
25854 ATTGCATATTCTAATC
1 ATTG-ATATTCTAATC
25870 A
1 A
25871 CTTATTCCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (15 bp):
ATTGATATTCTAATC
Found at i:32018 original size:92 final size:92
Alignment explanation
Indices: 31861--32043 Score: 330
Period size: 92 Copynumber: 2.0 Consensus size: 92
31851 AGTTGTATAT
*
31861 ATTATTAGATGAATTTAGCTGCATCTATGTATCTATATGATGCTTTTATTCTGTTGTTCATGATG
1 ATTATTAGATGAATTTAGCTGCATCTATGTATCTATATGATGCTTTTATTCTGTTGGTCATGATG
*
31926 GATGAGATGGAGATGCCTAGCACAGCC
66 GATGAGATGGAGATGACTAGCACAGCC
* *
31953 ATTATTTGATGAATTTAGCTGCATTTATGTATCTATATGATGCTTTTATTCTGTTGGTCATGATG
1 ATTATTAGATGAATTTAGCTGCATCTATGTATCTATATGATGCTTTTATTCTGTTGGTCATGATG
32018 GATGAGATGGAGATGACTAGCACAGC
66 GATGAGATGGAGATGACTAGCACAGC
32044 TATGAAAGAG
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 87 1.00
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (92 bp):
ATTATTAGATGAATTTAGCTGCATCTATGTATCTATATGATGCTTTTATTCTGTTGGTCATGATG
GATGAGATGGAGATGACTAGCACAGCC
Found at i:34151 original size:13 final size:13
Alignment explanation
Indices: 34122--34155 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
34112 GGTTTTTTTC
34122 AAAAAAATACGAT
1 AAAAAAATACGAT
34135 --AAAAATACGAT
1 AAAAAAATACGAT
34146 AAAAAAATAC
1 AAAAAAATAC
34156 CGGACACCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.58
13 8 0.42
ACGTcount: A:0.71, C:0.09, G:0.06, T:0.15
Consensus pattern (13 bp):
AAAAAAATACGAT
Found at i:34395 original size:11 final size:11
Alignment explanation
Indices: 34379--34435 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
34369 GGGGACCAAC
* *
34379 GAAAAATGAAG
1 GAAAAAAGAAA
34390 GAAAAAAGAAA
1 GAAAAAAGAAA
34401 GAAAAAAAAGAAA
1 G--AAAAAAGAAA
34414 GAAAGAAAGAAA
1 GAAA-AAAGAAA
*
34426 GAAAGAAGAA
1 GAAAAAAGAA
34436 GGAAGAATGA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 18 0.45
12 11 0.28
13 11 0.28
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:34403 original size:4 final size:4
Alignment explanation
Indices: 34390--34432 Score: 61
Period size: 4 Copynumber: 10.8 Consensus size: 4
34380 AAAAATGAAG
*
34390 GAAA -AAA GAAA GAAAA AAAA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GAAA GAA
34433 GAAGGAAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 29 0.83
5 3 0.09
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:34405 original size:21 final size:21
Alignment explanation
Indices: 34390--34435 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 21
34380 AAAAATGAAG
34390 GAAA-AAAGAAAGAAAAAAAA
1 GAAAGAAAGAAAGAAAAAAAA
34410 GAAAGAAAGAAAGAAAGAAAGAA
1 GAAAGAAAGAAAGAAA-AAA-AA
34433 GAA
1 GAA
34436 GGAAGAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.17
21 11 0.48
22 3 0.13
23 5 0.22
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGAAAGAAAAAAAA
Done.