Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013768.1 Kokia drynarioides strain JFW-HI SEQ_128796, 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: 40474
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:918 original size:8 final size:8
Alignment explanation
Indices: 896--946 Score: 50
Period size: 9 Copynumber: 6.1 Consensus size: 8
886 TTAGTCCCTC
896 TAAAAATAA
1 TAAAAAT-A
905 TAAAAATTA
1 TAAAAA-TA
914 TAAAAATA
1 TAAAAATA
*
922 T-AAACTA
1 TAAAAATA
*
929 TTAAAATGA
1 TAAAAAT-A
938 TAAAAATA
1 TAAAAATA
946 T
1 T
947 TTTTTTACTA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
7 6 0.17
8 9 0.25
9 20 0.56
10 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (8 bp):
TAAAAATA
Found at i:5825 original size:21 final size:23
Alignment explanation
Indices: 5783--5831 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
5773 TTTCATTATG
*
5783 TATATTTATTTCAATAATAAAAA
1 TATAATTATTTCAATAATAAAAA
*
5806 TATAATTA-TTCATTAA-AAAAA
1 TATAATTATTTCAATAATAAAAA
*
5827 GATAA
1 TATAA
5832 AATTAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 9 0.39
22 7 0.30
23 7 0.30
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (23 bp):
TATAATTATTTCAATAATAAAAA
Found at i:5835 original size:23 final size:22
Alignment explanation
Indices: 5792--5836 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
5782 GTATATTTAT
* *
5792 TTCAATAATAAAAATATAATTA
1 TTCAATAAAAAAAATAAAATTA
*
5814 TTCATTAAAAAAAGATAAAATTA
1 TTCAATAAAAAAA-ATAAAATTA
5837 ATATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (22 bp):
TTCAATAAAAAAAATAAAATTA
Found at i:20288 original size:17 final size:18
Alignment explanation
Indices: 20252--20295 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
20242 TTTTCAACTT
20252 TTTATTTATAAAATATTA
1 TTTATTTATAAAATATTA
20270 TTTATTT-T-AAATATATA
1 TTTATTTATAAAATAT-TA
*
20287 TTTAATTAT
1 TTTATTTAT
20296 TATTATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 6 0.26
17 9 0.39
18 8 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTATTTATAAAATATTA
Found at i:33561 original size:2 final size:2
Alignment explanation
Indices: 33554--33589 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
33544 CTAAGACAGC
33554 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33590 TAATATACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39600 original size:2 final size:2
Alignment explanation
Indices: 39593--39626 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
39583 TTTGTATTTA
39593 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39627 TAAAATATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40319 original size:4 final size:4
Alignment explanation
Indices: 40295--40352 Score: 75
Period size: 4 Copynumber: 14.8 Consensus size: 4
40285 GGGGACCAAC
* *
40295 GAAA -AAA GAAG GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA
40342 GAAA GAAA GAA
1 GAAA GAAA GAA
40353 GGAAGAAGGA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
3 6 0.13
4 38 0.81
5 3 0.06
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:40321 original size:21 final size:22
Alignment explanation
Indices: 40296--40347 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
40286 GGGACCAACG
40296 AAAAAAGAAGGAAA-AAAGAAAG-
1 AAAAAAG-A-GAAAGAAAGAAAGA
40318 AAAAAAGAGAAAGAAAGAAAGA
1 AAAAAAGAGAAAGAAAGAAAGA
*
40340 AAGAAAGA
1 AAAAAAGA
40348 AAGAAGGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 4 0.15
21 9 0.33
22 14 0.52
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (22 bp):
AAAAAAGAGAAAGAAAGAAAGA
Found at i:40364 original size:11 final size:11
Alignment explanation
Indices: 40299--40366 Score: 57
Period size: 11 Copynumber: 6.2 Consensus size: 11
40289 ACCAACGAAA
*
40299 AAAGAAGGAAA
1 AAAGAAGGAAG
* *
40310 AAAGAAAGAAA
1 AAAGAAGGAAG
*
40321 AAAG-AGAAAG
1 AAAGAAGGAAG
*
40331 AAAGAAAGAAAG
1 AAAG-AAGGAAG
*
40343 AAAGAAAGAAG
1 AAAGAAGGAAG
*
40354 GAAGAAGGAAG
1 AAAGAAGGAAG
40365 AA
1 AA
40367 GGAGAAGAAG
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
10 7 0.15
11 29 0.63
12 10 0.22
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (11 bp):
AAAGAAGGAAG
Done.