Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010300.1 Kokia drynarioides strain JFW-HI SEQ_125155, 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: 2938
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Found at i:2182 original size:218 final size:218
Alignment explanation
Indices: 1704--2366 Score: 1023
Period size: 218 Copynumber: 3.1 Consensus size: 218
1694 CTGAGAAGAT
*
1704 GGTTAGCTTCCTGACCATCTTCCTAATGAGGTATGGAGAAGTGGACCAAATTCGTCTTTCTGATG
1 GGTTAGCTTCCTGACCATCTTCCTAATGAGGTATGGAGAAGTGGACCAAATTCGTCTTCCTGATG
*
1769 GGATACAGAGAAGCGAATTGAAACAGACGACGTGGTCATCTTCCTGATGAGATACTGAGAAGAAG
66 AGATACAGAGAAGCGAATTGAAACAGACGACGTGGTCATCTTCCTGATGAGATACTGAGAAGAAG
*
1834 -----ACCAAACCCACGCTCGGTATGAGCAAATCTTCGAACCACAGCTTCCTGATGAGATACTGA
131 ACCAAACCAAACCCACGCTCGATATGAGCAAATCTTCGAACCACAGCTTCCTGATGAGATACTGA
1894 GAAGCAAGTCAAAGTAATAAAAC
196 GAAGCAAGTCAAAGTAATAAAAC
* * *
1917 GGTTAGCTTCCTGACCATTTTCCTAATGAGGTATGGAGAAATGGACCAAATTTGTCTTCCTGATG
1 GGTTAGCTTCCTGACCATCTTCCTAATGAGGTATGGAGAAGTGGACCAAATTCGTCTTCCTGATG
1982 AGATACAGAGAAGCGAATTGAAACAGACGACGTGGTCATCTTCCTGATGAGATACTGAGAAGAAG
66 AGATACAGAGAAGCGAATTGAAACAGACGACGTGGTCATCTTCCTGATGAGATACTGAGAAGAAG
* *
2047 ACCAAACCAAACCCACGCTCGATATGAGCGAATCCTCGAACCACAGCTTCCTGATGAGATACTGA
131 ACCAAACCAAACCCACGCTCGATATGAGCAAATCTTCGAACCACAGCTTCCTGATGAGATACTGA
*
2112 GAAGTAAGTCAAAGTAATAAAAC
196 GAAGCAAGTCAAAGTAATAAAAC
* *
2135 GGTTAGCTTCCTGACCATCTTCCTGATGAGGTACGGAGAAGTGGACCAAATTCGTCTTCCTGATG
1 GGTTAGCTTCCTGACCATCTTCCTAATGAGGTATGGAGAAGTGGACCAAATTCGTCTTCCTGATG
* * * * *
2200 AGATACAGAGAAGCGAATTGAAACAGATGACGTAGTCATCTTCCCGATGAGATACCGAGAAAAAG
66 AGATACAGAGAAGCGAATTGAAACAGACGACGTGGTCATCTTCCTGATGAGATACTGAGAAGAAG
* * * * * *
2265 ACCAAATCAAACTCACG-TCCGCTGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTG
131 ACCAAACCAAACCCACGCT-CGATATGAGCAAATCTTCGAACCACAGCTTCCTGATGAGATACTG
* * * *
2329 AGAAGCAGGTCGAAGCAATAAAGC
195 AGAAGCAAGTCAAAGTAATAAAAC
* *
2353 GATTAGCTCCCTGA
1 GGTTAGCTTCCTGA
2367 GGAGATACAA
Statistics
Matches: 410, Mismatches: 34, Indels: 7
0.91 0.08 0.02
Matches are distributed among these distances:
213 125 0.30
217 1 0.00
218 284 0.69
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (218 bp):
GGTTAGCTTCCTGACCATCTTCCTAATGAGGTATGGAGAAGTGGACCAAATTCGTCTTCCTGATG
AGATACAGAGAAGCGAATTGAAACAGACGACGTGGTCATCTTCCTGATGAGATACTGAGAAGAAG
ACCAAACCAAACCCACGCTCGATATGAGCAAATCTTCGAACCACAGCTTCCTGATGAGATACTGA
GAAGCAAGTCAAAGTAATAAAAC
Found at i:2856 original size:11 final size:10
Alignment explanation
Indices: 2803--2875 Score: 54
Period size: 10 Copynumber: 8.0 Consensus size: 10
2793 CCATACTCCC
2803 TTTAAATTTA
1 TTTAAATTTA
2813 TTTAAA---A
1 TTTAAATTTA
*
2820 ATTAAATTTA
1 TTTAAATTTA
2830 TTTAAA---A
1 TTTAAATTTA
*
2837 ATTAAATTTA
1 TTTAAATTTA
*
2847 TTTAAA-AT-
1 TTTAAATTTA
2855 TTTAAATTTA
1 TTTAAATTTA
2865 TTTTAAATTTA
1 -TTTAAATTTA
2876 AATTTATTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 17
0.68 0.08 0.24
Matches are distributed among these distances:
7 12 0.25
8 6 0.12
9 2 0.04
10 18 0.38
11 10 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TTTAAATTTA
Found at i:2861 original size:18 final size:17
Alignment explanation
Indices: 2803--2935 Score: 151
Period size: 17 Copynumber: 7.6 Consensus size: 17
2793 CCATACTCCC
2803 TTTAAATTTATTTAAAA
1 TTTAAATTTATTTAAAA
*
2820 ATTAAATTTATTTAAAA
1 TTTAAATTTATTTAAAA
*
2837 ATTAAATTTATTTAAAA
1 TTTAAATTTATTTAAAA
*
2854 TTTTAAATTTATTTTAAA
1 -TTTAAATTTATTTAAAA
2872 TTTAAATTTATTTTAAAA
1 TTTAAATTTA-TTTAAAA
* *
2890 TTTAAATTTAATTT-GAG
1 TTTAAATTT-ATTTAAAA
* *
2907 TTTAAAATTATTTTCAAA
1 TTTAAATTTA-TTTAAAA
2925 TTTAAAGTTTA
1 TTTAAA-TTTA
2936 AAA
Statistics
Matches: 100, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
16 1 0.01
17 55 0.55
18 40 0.40
19 4 0.04
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTAAAA
Found at i:2893 original size:24 final size:24
Alignment explanation
Indices: 2866--2915 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2856 TTAAATTTAT
*
2866 TTTAAATTTAAATTT-ATTTTAAAA
1 TTTAAATTT-AATTTGAGTTTAAAA
2890 TTTAAATTTAATTTGAGTTTAAAA
1 TTTAAATTTAATTTGAGTTTAAAA
2914 TT
1 TT
2916 ATTTTCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (24 bp):
TTTAAATTTAATTTGAGTTTAAAA
Found at i:2911 original size:35 final size:34
Alignment explanation
Indices: 2803--2936 Score: 153
Period size: 35 Copynumber: 3.8 Consensus size: 34
2793 CCATACTCCC
*
2803 TTTAAATTTATTTAAAAATTAAATTT-ATTTAAAA
1 TTTAAATTTATTTAAAATTTAAATTTAATTT-AAA
* *
2837 ATTAAATTTATTTAAAATTTTAAATTTATTTTAAA
1 TTTAAATTTATTTAAAA-TTTAAATTTAATTTAAA
* *
2872 TTTAAATTTATTTTAAAATTTAAATTTAATTTGAG
1 TTTAAATTTA-TTTAAAATTTAAATTTAATTTAAA
* *
2907 TTTAAAATTATTTTCAAATTTAAAGTTTAA
1 TTTAAATTTA-TTTAAAATTTAAA-TTTAA
2937 AA
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
34 16 0.18
35 56 0.64
36 15 0.17
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (34 bp):
TTTAAATTTATTTAAAATTTAAATTTAATTTAAA
Done.