Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012943.1 Kokia drynarioides strain JFW-HI SEQ_127961, 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: 110443
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 280 characters in sequence are not A, C, G, or T
Found at i:236 original size:20 final size:19
Alignment explanation
Indices: 206--257 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
196 AAATTATAAA
206 AAAAATT-AAAATAATTTT
1 AAAAATTCAAAATAATTTT
224 CAAAAATTCAAAATAATTTT
1 -AAAAATTCAAAATAATTTT
*
244 TAAAATTCAAAATA
1 AAAAATTCAAAATA
258 TTCATAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 20 0.65
20 11 0.35
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:269 original size:19 final size:19
Alignment explanation
Indices: 207--275 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
197 AATTATAAAA
207 AAAATT-AAAATAATTTTCA-
1 AAAATTCAAAATAA--TTCAT
**
226 AAAATTCAAAATAATTTTT
1 AAAATTCAAAATAATTCAT
245 AAAATTCAAAAT-ATTCAT
1 AAAATTCAAAATAATTCAT
*
263 AATAATTCCAAAT
1 AA-AATTCAAAAT
276 TTTATAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
18 8 0.19
19 27 0.64
20 7 0.17
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATTCAAAATAATTCAT
Found at i:2286 original size:2 final size:2
Alignment explanation
Indices: 2281--2308 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2271 ACACACACAC
2281 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
2309 CTAGACTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10183 original size:20 final size:20
Alignment explanation
Indices: 10146--10183 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
10136 AGTTTATTTA
*
10146 ATTTATTTTAATATATTATT
1 ATTTATTTAAATATATTATT
10166 ATTTAGTTTAAATA-ATTA
1 ATTTA-TTTAAATATATTA
10184 ATCGTTAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
ATTTATTTAAATATATTATT
Found at i:14547 original size:42 final size:42
Alignment explanation
Indices: 14500--14616 Score: 128
Period size: 42 Copynumber: 2.8 Consensus size: 42
14490 TCGTGCAAGG
* *
14500 TCAAGATCCAAATCAAAATCACCCCTTAGTTATCGGAGAAGA
1 TCAAGATCCAAATCAAGATCACCCATTAGTTATCGGAGAAGA
* * *
14542 TCAAGAT-CAAAGTCTAGATCACCGATTAGTTATCGGCGAAGA
1 TCAAGATCCAAA-TCAAGATCACCCATTAGTTATCGGAGAAGA
* * * * *
14584 ACAAGGTCCAAGTCAAGATCACCAATCAGTTAT
1 TCAAGATCCAAATCAAGATCACCCATTAGTTAT
14617 AGGCGAAGGA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 55 0.89
43 3 0.05
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.22
Consensus pattern (42 bp):
TCAAGATCCAAATCAAGATCACCCATTAGTTATCGGAGAAGA
Found at i:14622 original size:42 final size:42
Alignment explanation
Indices: 14527--14633 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 42
14517 ATCACCCCTT
* * * * * *
14527 AGTTATCGGAGAAGATCAAGATCAAAGTCTAGATCACCGATT
1 AGTTATCGGCGAAGAACAAGGTCAAAGTCAAGATCACCAATC
*
14569 AGTTATCGGCGAAGAACAAGGTCCAAGTCAAGATCACCAATC
1 AGTTATCGGCGAAGAACAAGGTCAAAGTCAAGATCACCAATC
* * *
14611 AGTTATAGGCGAAGGAGAAGGTC
1 AGTTATCGGCGAAGAACAAGGTC
14634 TCGCTCTTAC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (42 bp):
AGTTATCGGCGAAGAACAAGGTCAAAGTCAAGATCACCAATC
Found at i:15419 original size:45 final size:45
Alignment explanation
Indices: 15345--15442 Score: 151
Period size: 45 Copynumber: 2.2 Consensus size: 45
15335 ATAAGAAATC
* * *
15345 TAAGCATCGGGATAGAAGGCGGTCGAGGTCAAGATCTGCTGATGG
1 TAAGCATCGGGATAGAAAGAGGTCAAGGTCAAGATCTGCTGATGG
*
15390 TAAGCATCGGGATAGAAAGAGGTCAAGGTCAAGATCTTCTGATGG
1 TAAGCATCGGGATAGAAAGAGGTCAAGGTCAAGATCTGCTGATGG
*
15435 CAAGCATC
1 TAAGCATC
15443 ACAGAGGAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.31, C:0.16, G:0.33, T:0.20
Consensus pattern (45 bp):
TAAGCATCGGGATAGAAAGAGGTCAAGGTCAAGATCTGCTGATGG
Found at i:20050 original size:20 final size:22
Alignment explanation
Indices: 20009--20051 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
19999 ATAAAATTAT
20009 TAAATATTAAAAGAATATAATA
1 TAAATATTAAAAGAATATAATA
*
20031 TAAATTTTAAAA-AA-ATAATA
1 TAAATATTAAAAGAATATAATA
20051 T
1 T
20052 GGGCCGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 2 0.10
22 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
TAAATATTAAAAGAATATAATA
Found at i:20504 original size:21 final size:21
Alignment explanation
Indices: 20467--20506 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20457 AAATTGACCA
*
20467 TTATATTAACATATTTAATAT
1 TTATATTAAAATATTTAATAT
20488 TTATATTTAAAAT-TTTAAT
1 TTATA-TTAAAATATTTAAT
20507 TTACATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TTATATTAAAATATTTAATAT
Found at i:30979 original size:35 final size:36
Alignment explanation
Indices: 30940--31036 Score: 115
Period size: 36 Copynumber: 2.6 Consensus size: 36
30930 TTTATGTTTA
* *
30940 ATTTTAAAAAATTATTTAATTAAACCAGATAAATC-
1 ATTTTAAAAAATTATTTAACTAAACCAGACAAATCG
*
30975 ATTTTAAAAAAATTATTGAACTAAACCAGACAAATCG
1 ATTTT-AAAAAATTATTTAACTAAACCAGACAAATCG
*
31012 ATATTCAATAAAATTAGTTTAACTA
1 AT-TTTAA-AAAATTA-TTTAACTA
31037 TTAATTCGAT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
35 5 0.10
36 27 0.52
37 4 0.08
38 9 0.17
39 7 0.13
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (36 bp):
ATTTTAAAAAATTATTTAACTAAACCAGACAAATCG
Found at i:33136 original size:2 final size:2
Alignment explanation
Indices: 33129--33161 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
33119 AATTAAAATT
33129 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33162 ATTAGGTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33165 original size:8 final size:9
Alignment explanation
Indices: 33128--33165 Score: 53
Period size: 8 Copynumber: 4.3 Consensus size: 9
33118 AAATTAAAAT
33128 TTATATATA
1 TTATATATA
33137 -TATATATA
1 TTATATATA
33145 TATATATATA
1 T-TATATATA
33155 TTATATA-A
1 TTATATATA
33163 TTA
1 TTA
33166 GGTTTATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 12 0.44
9 6 0.22
10 9 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TTATATATA
Found at i:43579 original size:26 final size:26
Alignment explanation
Indices: 43530--43579 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
43520 TCTGTTTAAA
**
43530 TTTGAATTTATTTAATAATTTTTATG
1 TTTGAATTTATTTAATAAGGTTTATG
*
43556 TTTGAATTTATTTAATGAGGTTTA
1 TTTGAATTTATTTAATAAGGTTTA
43580 GCTAATGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (26 bp):
TTTGAATTTATTTAATAAGGTTTATG
Found at i:46077 original size:16 final size:17
Alignment explanation
Indices: 46058--46095 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
46048 ATATTTTTTA
46058 AAAATATTT-AATATAT
1 AAAATATTTAAATATAT
46074 AAAATATTTAAATATAT
1 AAAATATTTAAATATAT
*
46091 CAAAT
1 AAAAT
46096 GAATTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATATTTAAATATAT
Found at i:46876 original size:17 final size:17
Alignment explanation
Indices: 46854--46887 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
46844 CTTACAATAA
*
46854 TTAAATAATATTTAAAT
1 TTAAATAACATTTAAAT
46871 TTAAATAACATTTAAAT
1 TTAAATAACATTTAAAT
46888 GAATTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATAACATTTAAAT
Found at i:47315 original size:27 final size:27
Alignment explanation
Indices: 47277--47335 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
47267 TCCGTATCAA
*
47277 TTTTTTTAATTTATTATT-TAAATAAT
1 TTTTTTTAATTTAATATTATAAATAAT
* *
47303 TTTTTATTTATTTAATATTAATAAATTAT
1 TTTTT-TTAATTTAATATT-ATAAATAAT
47332 TTTT
1 TTTT
47336 ATGTCAGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 5 0.19
27 11 0.41
29 11 0.41
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
TTTTTTTAATTTAATATTATAAATAAT
Found at i:47318 original size:16 final size:16
Alignment explanation
Indices: 47276--47318 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
47266 ATCCGTATCA
*
47276 ATTTTTTTAATTTATT
1 ATTTATTTAATTTATT
** *
47292 ATTTAAATAATTTTTT
1 ATTTATTTAATTTATT
47308 ATTTATTTAAT
1 ATTTATTTAAT
47319 ATTAATAAAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTATTTAATTTATT
Found at i:53871 original size:25 final size:26
Alignment explanation
Indices: 53819--53869 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
53809 TATAAATGCA
*
53819 ATTTTTTATTATAAAATATATAATAT
1 ATTTTATATTATAAAATATATAATAT
53845 ATTTTATATT-TAAAAT-T-TAATAT
1 ATTTTATATTATAAAATATATAATAT
53868 AT
1 AT
53870 ATAATTTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 8 0.33
24 1 0.04
25 6 0.25
26 9 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
ATTTTATATTATAAAATATATAATAT
Found at i:55433 original size:2 final size:2
Alignment explanation
Indices: 55426--55461 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
55416 TAAATTGTGT
55426 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55462 AACTACACCC
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):
TA
Found at i:59265 original size:13 final size:12
Alignment explanation
Indices: 59240--59304 Score: 60
Period size: 13 Copynumber: 5.2 Consensus size: 12
59230 TGTTTGGCAT
*
59240 AAATTTAAATTA
1 AAATTTAATTTA
*
59252 AATATTTTATTT-
1 AA-ATTTAATTTA
59264 AAATTTAATTATA
1 AAATTTAATT-TA
*
59277 AAATATAATTTA
1 AAATTTAATTTA
*
59289 AATATTTTATTTA
1 AA-ATTTAATTTA
59302 AAA
1 AAA
59305 AAATAAAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
11 7 0.16
12 10 0.23
13 26 0.60
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
AAATTTAATTTA
Found at i:59265 original size:18 final size:18
Alignment explanation
Indices: 59242--59303 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
59232 TTTGGCATAA
59242 ATTTAAATTAAATATTTT
1 ATTTAAATTAAATATTTT
* ***
59260 ATTTAAATTTAATTATAAA
1 ATTTAAA-TTAAATATTTT
* *
59279 ATATAATTTAAATATTTT
1 ATTTAAATTAAATATTTT
59297 ATTTAAA
1 ATTTAAA
59304 AAAATAAAAT
Statistics
Matches: 31, Mismatches: 12, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
18 19 0.61
19 12 0.39
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTTAAATTAAATATTTT
Found at i:62740 original size:23 final size:24
Alignment explanation
Indices: 62686--62730 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
62676 ACAATTATTT
*
62686 TTTAATAAACATATTCATTTAAAG
1 TTTAATAAACAAATTCATTTAAAG
62710 TTT-ATAAACAAATTCATTTAA
1 TTTAATAAACAAATTCATTTAA
62731 TTTAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (24 bp):
TTTAATAAACAAATTCATTTAAAG
Found at i:63672 original size:29 final size:32
Alignment explanation
Indices: 63613--63672 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 32
63603 ATCATAAAAA
*
63613 TATGAGTTATTAAAATATTAAAATTTCATTTT
1 TATGAGTTATTAAAATATTAAAATTTAATTTT
*
63645 TATGA-TTA-TAAAA-ATTACAATTTAATTT
1 TATGAGTTATTAAAATATTAAAATTTAATTT
63673 CGAACCCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 13 0.50
30 5 0.19
31 3 0.12
32 5 0.19
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (32 bp):
TATGAGTTATTAAAATATTAAAATTTAATTTT
Found at i:64690 original size:1 final size:1
Alignment explanation
Indices: 64643--64670 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
64633 TTAGCTTGCC
64643 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
64671 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:64691 original size:1 final size:1
Alignment explanation
Indices: 64681--64707 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
64671 NNNNNNNNNN
64681 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
64708 AAGAAAACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:65112 original size:20 final size:20
Alignment explanation
Indices: 65076--65117 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
65066 AGTGACTAGT
* *
65076 TTAAATTAGTCATTTTATTA
1 TTAAATTAGTCAATTTAATA
65096 TTAAA-TAGATCAATTTAATA
1 TTAAATTAG-TCAATTTAATA
65116 TT
1 TT
65118 TGAACTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (20 bp):
TTAAATTAGTCAATTTAATA
Found at i:72446 original size:17 final size:17
Alignment explanation
Indices: 72424--72457 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
72414 AGTAATTCCA
*
72424 TTAATTCTTTTTATTAT
1 TTAATTCTATTTATTAT
72441 TTAATTCTATTTATTAT
1 TTAATTCTATTTATTAT
72458 ATTGTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (17 bp):
TTAATTCTATTTATTAT
Found at i:75857 original size:11 final size:10
Alignment explanation
Indices: 75815--75862 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 10
75805 AGTCACGAAT
75815 TTTAAAATTAA
1 TTTAAAA-TAA
**
75826 TTTAATTTTAA
1 TTTAA-AATAA
75837 TTTAAAATAA
1 TTTAAAATAA
75847 TTTAAAGATAA
1 TTTAAA-ATAA
75858 TTTAA
1 TTTAA
75863 TTAAAATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
10 9 0.29
11 22 0.71
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (10 bp):
TTTAAAATAA
Found at i:75858 original size:21 final size:22
Alignment explanation
Indices: 75815--75862 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
75805 AGTCACGAAT
***
75815 TTTAAAATTAATTTAATTTTAA
1 TTTAAAATTAATTTAAAGATAA
75837 TTTAAAA-TAATTTAAAGATAA
1 TTTAAAATTAATTTAAAGATAA
75858 TTTAA
1 TTTAA
75863 TTAAAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTAAAATTAATTTAAAGATAA
Found at i:79013 original size:25 final size:25
Alignment explanation
Indices: 78983--79038 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
78973 AATTTGCTGA
78983 TTTATCCACAATAAAAGTTTAATTT
1 TTTATCCACAATAAAAGTTTAATTT
79008 TTTATCCACAATAAAAGTTTAATTT
1 TTTATCCACAATAAAAGTTTAATTT
79033 TCTTAT
1 T-TTAT
79039 TGTGATTGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 26 0.87
26 4 0.13
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (25 bp):
TTTATCCACAATAAAAGTTTAATTT
Found at i:79410 original size:20 final size:20
Alignment explanation
Indices: 79385--79426 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
79375 ACTTATACTG
79385 TTCTGTCATTCAACAAGTGA
1 TTCTGTCATTCAACAAGTGA
79405 TTCTGTCATTCAACAAGTGA
1 TTCTGTCATTCAACAAGTGA
79425 TT
1 TT
79427 GTGTTTTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (20 bp):
TTCTGTCATTCAACAAGTGA
Found at i:79736 original size:2 final size:2
Alignment explanation
Indices: 79729--79764 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
79719 AGCATTCCAG
79729 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
79765 GTCTGTTTTA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:83581 original size:38 final size:39
Alignment explanation
Indices: 83539--83615 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
83529 ACTTTCAGGG
83539 TCATTTCCTGATATTT-AAATCTTAATAGGGTGTCTACT
1 TCATTTCCTGATATTTAAAATCTTAATAGGGTGTCTACT
83577 TCATTTCCTGATATTTAAAATCTTAATAGGGTGTCTACT
1 TCATTTCCTGATATTTAAAATCTTAATAGGGTGTCTACT
83616 GGTTCAGTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
38 16 0.42
39 22 0.58
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (39 bp):
TCATTTCCTGATATTTAAAATCTTAATAGGGTGTCTACT
Found at i:89574 original size:86 final size:88
Alignment explanation
Indices: 89412--89578 Score: 250
Period size: 91 Copynumber: 1.9 Consensus size: 88
89402 ACACATGTAC
89412 GTATCTTATGTTATGAATGACTTAAGACTAAGGAGTTAAAAAAAAAAAGAAAAAGAAAAAGGCCT
1 GTATCTTATGTTATGAATGACTTAAGACTAAGGAGTT-AAAAAAAAAAG--AAAGAAAAAGGCCT
89477 AATCGATACAATACAAAGACTTTCGA
63 AATCGATACAATACAAAGACTTTCGA
* * *
89503 GTATCTTATGTTATGAATGACTTAAGACTGAGGTGTT-TAAAAAAAAG-AAGAAATAA-GCCTAA
1 GTATCTTATGTTATGAATGACTTAAGACTAAGGAGTTAAAAAAAAAAGAAAGAAA-AAGGCCTAA
89565 TCGATACAATACAA
65 TCGATACAATACAA
89579 GTACATCGAG
Statistics
Matches: 72, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
86 26 0.36
87 2 0.03
89 9 0.12
91 35 0.49
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25
Consensus pattern (88 bp):
GTATCTTATGTTATGAATGACTTAAGACTAAGGAGTTAAAAAAAAAAGAAAGAAAAAGGCCTAAT
CGATACAATACAAAGACTTTCGA
Found at i:94808 original size:78 final size:78
Alignment explanation
Indices: 94647--94801 Score: 265
Period size: 78 Copynumber: 2.0 Consensus size: 78
94637 TCTCATTACA
* * *
94647 AACAACTCAAAGTAGTCAATAAAAACATGGCTATGGCTTCTTGAATTTGCCTGAAGAAAACAAGT
1 AACAACTCAAAGTAGTCAAGAAAAACATAGCTATGGCTTCTTGAATTTGCCTGAAGAAAACAAGC
94712 AATAACAAAACAG
66 AATAACAAAACAG
* *
94725 AACAACTCAAAGTAGTCAAGAAAAACATATCTATGGCTTCTTGAATTTGCCTGAAGAAAACAGGC
1 AACAACTCAAAGTAGTCAAGAAAAACATAGCTATGGCTTCTTGAATTTGCCTGAAGAAAACAAGC
94790 AATAACAAAACA
66 AATAACAAAACA
94802 TCACAACACA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 72 1.00
ACGTcount: A:0.46, C:0.17, G:0.15, T:0.21
Consensus pattern (78 bp):
AACAACTCAAAGTAGTCAAGAAAAACATAGCTATGGCTTCTTGAATTTGCCTGAAGAAAACAAGC
AATAACAAAACAG
Found at i:95510 original size:2 final size:2
Alignment explanation
Indices: 95503--95538 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
95493 ACATAGCTTT
95503 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
95539 ACAAGTGGGG
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):
TA
Found at i:101526 original size:2 final size:2
Alignment explanation
Indices: 101519--101553 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
101509 GCAGAAAAGA
101519 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
101554 AGGAGAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:102424 original size:29 final size:29
Alignment explanation
Indices: 102401--102465 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
102391 TTTTAGTTAT
* *
102401 TTATTTTTGAAATATTACGTTTTAATCAC
1 TTATGTTTGAAATATTACATTTTAATCAC
* **
102430 TTATGTTTGAAATGTTACATTTTTGTCAC
1 TTATGTTTGAAATATTACATTTTAATCAC
102459 TTATGTT
1 TTATGTT
102466 AGTATTTTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.54
Consensus pattern (29 bp):
TTATGTTTGAAATATTACATTTTAATCAC
Found at i:102562 original size:18 final size:20
Alignment explanation
Indices: 102539--102576 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
102529 TCGTGAGAGT
102539 CCAACTAG-ATTTT-AAATG
1 CCAACTAGAATTTTCAAATG
*
102557 CCAACTTGAATTTTCAAATG
1 CCAACTAGAATTTTCAAATG
102577 GAATGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 5 0.29
20 5 0.29
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (20 bp):
CCAACTAGAATTTTCAAATG
Found at i:102972 original size:14 final size:14
Alignment explanation
Indices: 102953--102983 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
102943 TATGTTTAAA
102953 AAATTTAATTAATT
1 AAATTTAATTAATT
*
102967 AAATTTATTTAATT
1 AAATTTAATTAATT
102981 AAA
1 AAA
102984 AATATATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTTAATTAATT
Found at i:103572 original size:214 final size:214
Alignment explanation
Indices: 103200--103771 Score: 993
Period size: 214 Copynumber: 2.7 Consensus size: 214
103190 TAATTTACCT
103200 TTTTTATTTTGATTATTGAACAATAAAAAATTCAATTTAATTACTAAACTATTCGAATTTATTTT
1 TTTTTATTTTGATTATTGAACAATAAAAAATTCAATTTAATTACTAAACTATTCGAATTTATTTT
*
103265 TTGATTACTAATATAGGAATATTTAGTTAATCAATAAAATGAAGTTCGATAAGCTTACTTGAGAG
66 TTTATTACTAATATAGGAATATTTAGTTAATCAATAAAATGAAGTTCGATAAGCTTACTTGAGAG
*
103330 CAGGTCCATATCAAATCCATCACATTTGTCCCTGG-CACTTTTTAAAGAGTAAATTATTTAAATA
131 CAGGTCCATATCAAATCAATCACATTTGTCCC-GGACACTTTTTAAAGAGTAAATTATTTAAATA
103394 ATTATTAAACTTTTCACATG
195 ATTATTAAACTTTTCACATG
*
103414 TTTTTATTTTGATTATTGAACAATAAAAAATTCAATTTAATTACTAAACTATTCGAATTCATTTT
1 TTTTTATTTTGATTATTGAACAATAAAAAATTCAATTTAATTACTAAACTATTCGAATTTATTTT
* *
103479 TTTATTACTAACATAGGAATATTTAGTTAGTCAATAAAATGAAGTTCGATAAGCTTACTTGAGAG
66 TTTATTACTAATATAGGAATATTTAGTTAATCAATAAAATGAAGTTCGATAAGCTTACTTGAGAG
* * *
103544 CAGGTCCATATCAAATCAATCGCATTTGTCCCGGACACTTTTTAAAGAGTAAATTGTTTAAATAG
131 CAGGTCCATATCAAATCAATCACATTTGTCCCGGACACTTTTTAAAGAGTAAATTATTTAAATAA
103609 TTATTAAACTTTTCACATG
196 TTATTAAACTTTTCACATG
* *
103628 TTTTTATTTTGATTATTGAACAAAAAAAAATTCAATTTAATTACTAATCTATTCGAATTTATTTT
1 TTTTTATTTTGATTATTGAACAATAAAAAATTCAATTTAATTACTAAACTATTCGAATTTATTTT
* * * *
103693 TTTATTACTAATATAAGAATATTTAGTTAATCAATAAAATGAAATTCGATAAGCTTACCTAAGAG
66 TTTATTACTAATATAGGAATATTTAGTTAATCAATAAAATGAAGTTCGATAAGCTTACTTGAGAG
*
103758 CAGATCCATATCAA
131 CAGGTCCATATCAA
103772 TTTTATCTCT
Statistics
Matches: 339, Mismatches: 18, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
213 2 0.01
214 337 0.99
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (214 bp):
TTTTTATTTTGATTATTGAACAATAAAAAATTCAATTTAATTACTAAACTATTCGAATTTATTTT
TTTATTACTAATATAGGAATATTTAGTTAATCAATAAAATGAAGTTCGATAAGCTTACTTGAGAG
CAGGTCCATATCAAATCAATCACATTTGTCCCGGACACTTTTTAAAGAGTAAATTATTTAAATAA
TTATTAAACTTTTCACATG
Found at i:109420 original size:46 final size:46
Alignment explanation
Indices: 109320--109421 Score: 168
Period size: 46 Copynumber: 2.2 Consensus size: 46
109310 TTAGAACATG
*
109320 ACTAGACTGGTTAGTTGGATTGATAAGATCAAGAATCGACCGGTAT
1 ACTAGATTGGTTAGTTGGATTGATAAGATCAAGAATCGACCGGTAT
* *
109366 ACTAGATTGGTTAGTTGGATTGATAAGATCGAGAATCGACTGGTAT
1 ACTAGATTGGTTAGTTGGATTGATAAGATCAAGAATCGACCGGTAT
*
109412 ACTGGATTGG
1 ACTAGATTGG
109422 ATACTGCTCG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.30
Consensus pattern (46 bp):
ACTAGATTGGTTAGTTGGATTGATAAGATCAAGAATCGACCGGTAT
Found at i:109936 original size:4 final size:4
Alignment explanation
Indices: 109927--109952 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
109917 CTATTTCGTA
109927 ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT AT
109953 CACTTTGAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Done.