Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002421.1 Kokia drynarioides strain JFW-HI SEQ_114519, 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: 43965
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 118 characters in sequence are not A, C, G, or T
Found at i:2309 original size:62 final size:62
Alignment explanation
Indices: 2229--2439 Score: 266
Period size: 62 Copynumber: 3.4 Consensus size: 62
2219 GAAAAAAAAA
* * *
2229 TTCAAAATTTTTTGGTGTTGGCCATGCAATGATCGACACCCCCTGTTCTCGGATAAAAAATT
1 TTCAAATTTTTTTGGTGTTGGCCATGCAATGACCGACACCCCCTGTTATCGGATAAAAAATT
* * * * **
2291 TTTAAATTTTTTTGGTGTTGGCCATACAATG-GCGACA-CCCCTATTTATTTGATAAAAAAATT
1 TTCAAATTTTTTTGGTGTTGGCCATGCAATGACCGACACCCCCT-GTTATCGGAT-AAAAAATT
* *
2353 TTCAAA-TTTTTTGGATGTTGGCCATGCAATGACCGATACCCCCTGTTATCGGATAAAAAAAT
1 TTCAAATTTTTTTGG-TGTTGGCCATGCAATGACCGACACCCCCTGTTATCGGATAAAAAATT
*
2415 TTCAAATTTTTTTGATGTTGGCCAT
1 TTCAAATTTTTTTGGTGTTGGCCAT
2440 TGCCTAGGGA
Statistics
Matches: 126, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
60 5 0.04
61 19 0.15
62 79 0.63
63 18 0.14
64 5 0.04
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (62 bp):
TTCAAATTTTTTTGGTGTTGGCCATGCAATGACCGACACCCCCTGTTATCGGATAAAAAATT
Found at i:2630 original size:59 final size:56
Alignment explanation
Indices: 2508--2748 Score: 218
Period size: 59 Copynumber: 4.2 Consensus size: 56
2498 CCGAGAACAG
* * * * * *
2508 GGCCAACACCAAAAAATTTTGATTTTTTT-T-GAATAAGGGGGTGTCTGTCATTGCAT
1 GGCCAACACCCAAAAA-TGTAATTTTTTTATCGAA-AAAGGGGTGTCGGCCATTGCAT
* *
2564 GGTCAACACCCAAAAATGTAATTTTTTTATCCGAGAAAAGAGAGTGTCGGCCATTGCAT
1 GGCCAACACCCAAAAATGTAATTTTTTTAT-CGA-AAAAG-GGGTGTCGGCCATTGCAT
* * *
2623 GGCCAACACCCAAAAATGCAATTTTTTAATCAGATAAATAGGGGTGTCGGCCATTGTAT
1 GGCCAACACCCAAAAATGTAATTTTTTTATC-GA-AAA-AGGGGTGTCGGCCATTGCAT
** * * *
2682 GGCCAACACAAAAAAATAGTATTTTTATCTTAT-TAAAAAGGGGTGTCGACCATTGCAT
1 GGCCAACACCCAAAAAT-GTAATTTT-T-TTATCGAAAAAGGGGTGTCGGCCATTGCAT
2740 GGCCAACAC
1 GGCCAACAC
2749 TTCAAATTTT
Statistics
Matches: 153, Mismatches: 22, Indels: 18
0.79 0.11 0.09
Matches are distributed among these distances:
55 10 0.07
56 15 0.10
58 33 0.22
59 82 0.54
60 9 0.06
61 1 0.01
62 3 0.02
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (56 bp):
GGCCAACACCCAAAAATGTAATTTTTTTATCGAAAAAGGGGTGTCGGCCATTGCAT
Found at i:22821 original size:39 final size:39
Alignment explanation
Indices: 22766--22843 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
22756 TGTCTCAAAC
*
22766 AAGTTTATAATCTCACCCATATTTTTAAATTATTATGCT
1 AAGTTTATAATCTCACCCATATTTTCAAATTATTATGCT
* *
22805 AAGTTTCTAATTTCACCCATATTTTCAAATTATTATGCT
1 AAGTTTATAATCTCACCCATATTTTCAAATTATTATGCT
22844 TACATTAATG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.32, C:0.17, G:0.05, T:0.46
Consensus pattern (39 bp):
AAGTTTATAATCTCACCCATATTTTCAAATTATTATGCT
Found at i:32829 original size:30 final size:30
Alignment explanation
Indices: 32795--32859 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
32785 ACTTATTTTA
* *
32795 TTGTTAATTTTGTTATTATTTTAAAGGTAT
1 TTGTTAATTTTGTTACTATTTTAAAGGCAT
*
32825 TTGTTAATTTTGTTACTATTTTAGAGGCAT
1 TTGTTAATTTTGTTACTATTTTAAAGGCAT
32855 TTGTT
1 TTGTT
32860 TGTTAAGTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.23, C:0.03, G:0.15, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTTTAAAGGCAT
Found at i:43891 original size:4 final size:4
Alignment explanation
Indices: 43882--43951 Score: 61
Period size: 4 Copynumber: 17.2 Consensus size: 4
43872 AAATAAACGG
* * * * *
43882 GAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA GAAG GAGAG GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA GA-AA GAAA
*
43932 GAAA G-AA GAAG GAAA GAAA G
1 GAAA GAAA GAAA GAAA GAAA G
43952 GTAATGTGTT
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
3 3 0.05
4 44 0.80
5 8 0.15
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:43914 original size:17 final size:17
Alignment explanation
Indices: 43894--43951 Score: 93
Period size: 17 Copynumber: 3.5 Consensus size: 17
43884 AAGAAAGAAA
*
43894 GAAAGGAAGAAGGAGAG
1 GAAAGAAAGAAGGAGAG
43911 GAAAGAAAGAAGGAGAG
1 GAAAGAAAGAAGGAGAG
43928 GAAAGAAAGAA-GA-AG
1 GAAAGAAAGAAGGAGAG
43943 GAAAGAAAG
1 GAAAGAAAG
43952 GTAATGTGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
15 11 0.28
16 2 0.05
17 27 0.68
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAGGAGAG
Found at i:43914 original size:29 final size:32
Alignment explanation
Indices: 43883--43951 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 32
43873 AATAAACGGG
*
43883 AAAGAAAGAAAGAAAGG-AAG-AAGGAG-AGG
1 AAAGAAAGAAAGAAAGGAAAGAAAGAAGAAGG
* *
43912 AAAGAAAGAAGGAGAGGAAAGAAAGAAGAAGG
1 AAAGAAAGAAAGAAAGGAAAGAAAGAAGAAGG
43944 AAAGAAAG
1 AAAGAAAG
43952 GTAATGTGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 15 0.44
30 3 0.09
31 5 0.15
32 11 0.32
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (32 bp):
AAAGAAAGAAAGAAAGGAAAGAAAGAAGAAGG
Done.