Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003735.1 Kokia drynarioides strain JFW-HI SEQ_116692, 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: 48513
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:8469 original size:6 final size:6
Alignment explanation
Indices: 8458--8483 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
8448 ATATATTAAA
8458 AAAAAG AAAAAG AAAAAG AAAAAG AA
1 AAAAAG AAAAAG AAAAAG AAAAAG AA
8484 TCCTACCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:16403 original size:11 final size:11
Alignment explanation
Indices: 16387--16430 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
16377 TTTTTTATAT
16387 AAAATATTAAA
1 AAAATATTAAA
16398 AAAATATATAAA
1 AAAATAT-TAAA
*
16410 GAAATTATTAAA
1 -AAAATATTAAA
16422 AAATATATT
1 AAA-ATATT
16431 TTTTAACAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 10 0.36
12 12 0.43
13 6 0.21
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (11 bp):
AAAATATTAAA
Found at i:25829 original size:16 final size:17
Alignment explanation
Indices: 25798--25830 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
25788 AAAAACAAAA
25798 TTATATAATAAATATAT
1 TTATATAATAAATATAT
*
25815 TTATA-AATAATTATAT
1 TTATATAATAAATATAT
25831 AATTATAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTATATAATAAATATAT
Found at i:27163 original size:22 final size:22
Alignment explanation
Indices: 27137--27182 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
27127 TCATTACCAG
*
27137 ATCTGAATATTAAGGGTATATA
1 ATCTGAATATTAAGGGGATATA
*
27159 ATCTGGATATTAAGGGGATATA
1 ATCTGAATATTAAGGGGATATA
27181 AT
1 AT
27183 ATAAGTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (22 bp):
ATCTGAATATTAAGGGGATATA
Found at i:30179 original size:18 final size:17
Alignment explanation
Indices: 30152--30186 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
30142 AAGTGTTAGG
30152 AATAATAAATAGTATAT
1 AATAATAAATAGTATAT
*
30169 AATATATAAATATTATAT
1 AATA-ATAAATAGTATAT
30187 TCTTCATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
AATAATAAATAGTATAT
Found at i:33777 original size:19 final size:21
Alignment explanation
Indices: 33742--33783 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
33732 TAGATATATA
*
33742 TTTTTAAAAATTTTAT-AATT
1 TTTTTAAAAATTATATAAATT
33762 TTTTTAAAAA-TATATAAATT
1 TTTTTAAAAATTATATAAATT
33782 TT
1 TT
33784 AGAATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTTAAAAATTATATAAATT
Found at i:33795 original size:20 final size:19
Alignment explanation
Indices: 33774--33848 Score: 73
Period size: 18 Copynumber: 3.9 Consensus size: 19
33764 TTTAAAAATA
*
33774 TATAAAT-TTTAGAATTTT
1 TATAAATATTTTGAATTTT
33792 TATAAATATTTTGAA-TTT
1 TATAAATATTTTGAATTTT
* *
33810 TAAAAATTATTTTAAATTTT
1 TATAAA-TATTTTGAATTTT
*
33830 TGAAAAAATATTTTGAATT
1 T--ATAAATATTTTGAATT
33849 GTTTTTTTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
18 15 0.31
19 14 0.29
20 4 0.08
21 10 0.21
22 5 0.10
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:33797 original size:18 final size:19
Alignment explanation
Indices: 33774--33810 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
33764 TTTAAAAATA
33774 TATAAAT-TTTAGAATTTT
1 TATAAATATTTAGAATTTT
*
33792 TATAAATATTTTGAATTTT
1 TATAAATATTTAGAATTTT
33811 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:33809 original size:19 final size:19
Alignment explanation
Indices: 33779--33848 Score: 79
Period size: 19 Copynumber: 3.5 Consensus size: 19
33769 AAATATATAA
*
33779 ATTTTAGAATTTTTATAAAT
1 ATTTT-GAATTTTTAAAAAT
33799 ATTTTGAA-TTTTAAAAATT
1 ATTTTGAATTTTTAAAAA-T
*
33818 ATTTTAAATTTTTGAAAAAAT
1 ATTTTGAATTTTT--AAAAAT
33839 ATTTTGAATT
1 ATTTTGAATT
33849 GTTTTTTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
18 8 0.19
19 11 0.26
20 9 0.21
21 10 0.23
22 5 0.12
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (19 bp):
ATTTTGAATTTTTAAAAAT
Found at i:40261 original size:37 final size:37
Alignment explanation
Indices: 40219--40293 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
40209 GTCGCGACAT
40219 TAAAGGGTTGTTGTCACGACGTTGAAGCCCAAAACTA
1 TAAAGGGTTGTTGTCACGACGTTGAAGCCCAAAACTA
40256 TAAAGGGTTGTTGTCACGACGTTGAAGCCCAAAACTA
1 TAAAGGGTTGTTGTCACGACGTTGAAGCCCAAAACTA
40293 T
1 T
40294 CTTTGGAGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (37 bp):
TAAAGGGTTGTTGTCACGACGTTGAAGCCCAAAACTA
Found at i:46783 original size:20 final size:20
Alignment explanation
Indices: 46750--46791 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
46740 TATTTTTTAA
46750 TGTAACTATGTTAATTTAGTT
1 TGTAACTATGTTAATTT-GTT
46771 TGTAACT-TGTTAATTTGTT
1 TGTAACTATGTTAATTTGTT
46790 TG
1 TG
46792 GTTATGATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.24
20 9 0.43
21 7 0.33
ACGTcount: A:0.24, C:0.05, G:0.17, T:0.55
Consensus pattern (20 bp):
TGTAACTATGTTAATTTGTT
Done.