Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold514
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: 183874
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:4203 original size:20 final size:21
Alignment explanation
Indices: 4163--4205 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4153 TACGTAATAC
*
4163 ATATAAATATAAAAATAAATT
1 ATATAAATAAAAAAATAAATT
*
4184 ATATAATTAAAAAAAT-AATT
1 ATATAAATAAAAAAATAAATT
4204 AT
1 AT
4206 GGCAAGCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
ATATAAATAAAAAAATAAATT
Found at i:4962 original size:19 final size:20
Alignment explanation
Indices: 4931--4969 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
4921 GGGGCGAGGG
4931 AAAGGGGGAGGAGG-GGAAA
1 AAAGGGGGAGGAGGCGGAAA
4950 AAAGGAGGG-GGAGGCGGAAA
1 AAAGG-GGGAGGAGGCGGAAA
4970 GGGGAGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.41, C:0.03, G:0.56, T:0.00
Consensus pattern (20 bp):
AAAGGGGGAGGAGGCGGAAA
Found at i:5186 original size:16 final size:15
Alignment explanation
Indices: 5167--5219 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
5157 AAAAAAGGTG
5167 GGGAAAAAACAAAAAA
1 GGGAAAAAA-AAAAAA
5183 GGGAAAAAAAAAAAA
1 GGGAAAAAAAAAAAA
*
5198 --AAAAAAAAAAATAA
1 GGGAAAAAAAAAA-AA
*
5212 AGGAAAAA
1 GGGAAAAA
5220 GGAAGCAGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 10 0.31
14 2 0.06
15 6 0.19
16 14 0.44
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (15 bp):
GGGAAAAAAAAAAAA
Found at i:7993 original size:3 final size:3
Alignment explanation
Indices: 7985--8019 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
7975 ATCAAAATTG
7985 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
8020 CTTTGCCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:9169 original size:33 final size:33
Alignment explanation
Indices: 9127--9193 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
9117 TCTCATAACT
9127 TAGACTTTTTCTTATATACAATGAAGGTCGCAA
1 TAGACTTTTTCTTATATACAATGAAGGTCGCAA
9160 TAGACTTTTTCTTATATACAATGAAGGTCGCAA
1 TAGACTTTTTCTTATATACAATGAAGGTCGCAA
9193 T
1 T
9194 TTAAGAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (33 bp):
TAGACTTTTTCTTATATACAATGAAGGTCGCAA
Found at i:9225 original size:21 final size:21
Alignment explanation
Indices: 9201--9240 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
9191 AATTTAAGAA
9201 TAAAAAATAAATTATAAATAT
1 TAAAAAATAAATTATAAATAT
** *
9222 TAAAATTTAAATTTTAAAT
1 TAAAAAATAAATTATAAAT
9241 TTTTTAAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAAAAATAAATTATAAATAT
Found at i:9677 original size:17 final size:18
Alignment explanation
Indices: 9655--9688 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
9645 AGTGGAACCC
*
9655 CATGGATCCAC-CATGCA
1 CATGGAGCCACACATGCA
9672 CATGGAGCCACACATGC
1 CATGGAGCCACACATGC
9689 TTGGTCTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.35, G:0.21, T:0.15
Consensus pattern (18 bp):
CATGGAGCCACACATGCA
Found at i:13068 original size:2 final size:2
Alignment explanation
Indices: 13061--13086 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13051 AAGTGAATGG
13061 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
13087 GAAAAAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13207 original size:16 final size:16
Alignment explanation
Indices: 13188--13218 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
13178 CGTATTAAAA
13188 ATATTATATATTCATT
1 ATATTATATATTCATT
13204 ATATTATATATTCAT
1 ATATTATATATTCAT
13219 GTAAACTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATTATATATTCATT
Found at i:14762 original size:2 final size:2
Alignment explanation
Indices: 14755--14786 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
14745 TGACACAATC
*
14755 CT CT CT CT CT CT CT CT AT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
14787 TGTTGCGTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:18294 original size:23 final size:23
Alignment explanation
Indices: 18264--18307 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
18254 TCAACTCCAC
*
18264 TGATTTTAAGTCATAAATCAATT
1 TGATTTTAAGTCACAAATCAATT
*
18287 TGATTTTAAGTCGCAAATCAA
1 TGATTTTAAGTCACAAATCAA
18308 AATCCCCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (23 bp):
TGATTTTAAGTCACAAATCAATT
Found at i:20180 original size:41 final size:39
Alignment explanation
Indices: 20135--20227 Score: 89
Period size: 42 Copynumber: 2.3 Consensus size: 39
20125 ATAATTGTTT
* *
20135 ATAAAATAAAATAAAATAATATTTTTATTTTAATTTT-AATA
1 ATAAAATAAAATAAAAT-AT-TTTTAATATT-ATTTTAAATA
* *
20176 ATAAATATTAATATTTAAATATTTTTAATATTATTTTAAATA
1 ATAAA-A-TAA-AATAAAATATTTTTAATATTATTTTAAATA
20218 ATAAAATAAA
1 ATAAAATAAA
20228 GTTTTGAATC
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
39 1 0.02
40 3 0.07
41 11 0.25
42 18 0.41
43 5 0.11
44 6 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (39 bp):
ATAAAATAAAATAAAATATTTTTAATATTATTTTAAATA
Found at i:20225 original size:20 final size:20
Alignment explanation
Indices: 20164--20222 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
20154 TATTTTTATT
20164 TTAATTTT-AATAATAAATA
1 TTAATTTTAAATAATAAATA
* *
20183 TTAATATTTAAATATTTTTAATA
1 TTAAT-TTTAAATA--ATAAATA
20206 TT-ATTTTAAATAATAAA
1 TTAATTTTAAATAATAAA
20223 ATAAAGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
19 8 0.25
20 3 0.09
21 12 0.38
22 2 0.06
23 7 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAATTTTAAATAATAAATA
Found at i:20892 original size:11 final size:11
Alignment explanation
Indices: 20876--20927 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
20866 ACGTTTAACA
20876 AATATAAAAAT
1 AATATAAAAAT
20887 AATATAATAAAT
1 AATATAA-AAAT
* *
20899 -ATAATTAATAT
1 AAT-ATAAAAAT
*
20910 GATATAAAAAT
1 AATATAAAAAT
20921 AATATAA
1 AATATAA
20928 TAATGTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
11 24 0.73
12 9 0.27
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:20930 original size:14 final size:14
Alignment explanation
Indices: 20879--20930 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 14
20869 TTTAACAAAT
20879 ATAAAAATAATATA
1 ATAAAAATAATATA
20893 ATAAATATAATTAATATGA
1 AT-AA-A-AA-TAATAT-A
20912 TATAAAAATAATATA
1 -ATAAAAATAATATA
20927 ATAA
1 ATAA
20931 TGTAATACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
14 6 0.19
15 3 0.09
16 7 0.22
17 4 0.12
18 7 0.22
19 3 0.09
20 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
ATAAAAATAATATA
Found at i:24034 original size:1 final size:1
Alignment explanation
Indices: 24028--24053 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
24018 GCGAGATTTT
24028 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
24054 ATGGACAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:24942 original size:17 final size:17
Alignment explanation
Indices: 24912--24944 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
24902 AAAATCAGAT
24912 TATTTCATTTTTTTATG
1 TATTTCATTTTTTTATG
24929 TATTT-ATTTATTTTAT
1 TATTTCATTT-TTTTAT
24945 ATGTTTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.73
Consensus pattern (17 bp):
TATTTCATTTTTTTATG
Found at i:36464 original size:17 final size:17
Alignment explanation
Indices: 36442--36476 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
36432 ATTGTGTATA
36442 TTATTTTGAATTTAAAT
1 TTATTTTGAATTTAAAT
36459 TTATTTTGAATTTAAAT
1 TTATTTTGAATTTAAAT
36476 T
1 T
36477 ATCTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (17 bp):
TTATTTTGAATTTAAAT
Found at i:36547 original size:16 final size:16
Alignment explanation
Indices: 36499--36559 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
36489 TGTTATTTAC
36499 TTTAAATATTTTTAAA
1 TTTAAATATTTTTAAA
* *
36515 TTCAAACTA-TTTCAAA
1 TTTAAA-TATTTTTAAA
36531 TTTAAATATTTTTAAA
1 TTTAAATATTTTTAAA
*
36547 -TTAAATATCTTTA
1 TTTAAATATTTTTA
36560 GATTATGATC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
15 14 0.37
16 22 0.58
17 2 0.05
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTAAATATTTTTAAA
Found at i:36550 original size:15 final size:15
Alignment explanation
Indices: 36500--36564 Score: 69
Period size: 15 Copynumber: 4.2 Consensus size: 15
36490 GTTATTTACT
36500 TTAAATATTTTTAAA
1 TTAAATATTTTTAAA
*
36515 TTCAAACTA-TTTCAAA
1 TT-AAA-TATTTTTAAA
36531 TTTAAATATTTTTAAA
1 -TTAAATATTTTTAAA
* *
36547 TTAAATATCTTTAGA
1 TTAAATATTTTTAAA
36562 TTA
1 TTA
36565 TGATCGTTAG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
15 20 0.48
16 18 0.43
17 4 0.10
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (15 bp):
TTAAATATTTTTAAA
Found at i:36774 original size:6 final size:6
Alignment explanation
Indices: 36761--36789 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
36751 TAAAATTTTA
36761 AAAT-T AAATAT AAATAT AAATAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT
36790 TTATAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AAATAT
Found at i:37377 original size:29 final size:29
Alignment explanation
Indices: 37342--37399 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
37332 ATAATTAATA
37342 ATTTTTTTCATCATTCCAA-CACATTATAT
1 ATTTTTTTCATCATT-CAATCACATTATAT
37371 ATTTTTTTCATCATTCAATCACATTATAT
1 ATTTTTTTCATCATTCAATCACATTATAT
37400 GAAGAAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 3 0.11
29 25 0.89
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (29 bp):
ATTTTTTTCATCATTCAATCACATTATAT
Found at i:38011 original size:2 final size:2
Alignment explanation
Indices: 38004--38048 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
37994 TCAGATTTGT
38004 TA TA TA 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 TA TA TA
38046 TA T
1 TA T
38049 GAAGTATTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39811 original size:5 final size:5
Alignment explanation
Indices: 39801--39868 Score: 63
Period size: 5 Copynumber: 14.0 Consensus size: 5
39791 CGATAATTTA
* *
39801 TATAT TATAT T-TAT T-TAT T-TAT TTTAT TATAT TATAAT TATATT TAAAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT-AT TATA-T TATAT
*
39850 TATTT TAT-T TATAT TATAT
1 TATAT TATAT TATAT TATAT
39869 AAAACTTAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
4 16 0.29
5 30 0.55
6 9 0.16
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
TATAT
Found at i:39824 original size:25 final size:27
Alignment explanation
Indices: 39796--39868 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 27
39786 CTAAACGATA
*
39796 ATTTATATATTATATT-TATTT-ATTT
1 ATTTATATATTATATTATATTTAAATT
39821 ATTTTATTATATTATAATTATATTTAAATT
1 A-TTTA-TATATTAT-ATTATATTTAAATT
39851 ATTT-TAT-TTATATTATAT
1 ATTTATATATTATATTATAT
39869 AAAACTTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
25 8 0.19
26 8 0.19
27 11 0.26
28 3 0.07
29 8 0.19
30 4 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (27 bp):
ATTTATATATTATATTATATTTAAATT
Found at i:39842 original size:11 final size:10
Alignment explanation
Indices: 39804--39864 Score: 52
Period size: 11 Copynumber: 5.8 Consensus size: 10
39794 TAATTTATAT
39804 ATTATATTTA
1 ATTATATTTA
* *
39814 TTTATTTATTTT
1 ATTA--TATTTA
39826 ATTATATTATA
1 ATTATATT-TA
39837 ATTATATTTAA
1 ATTATATTT-A
39848 ATTAT-TTTA
1 ATTATATTTA
*
39857 TTTATATT
1 ATTATATT
39865 ATATAAAACT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
9 5 0.12
10 13 0.32
11 15 0.37
12 8 0.20
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
ATTATATTTA
Found at i:39865 original size:14 final size:15
Alignment explanation
Indices: 39801--39868 Score: 81
Period size: 14 Copynumber: 4.7 Consensus size: 15
39791 CGATAATTTA
39801 TATATTATATTTATT
1 TATATTATATTTATT
39816 TAT-TTAT-TTTA-T
1 TATATTATATTTATT
39828 TATATTATAATTATATT
1 TATATTAT-ATT-TATT
*
39845 TAAATTAT-TTTATT
1 TATATTATATTTATT
39859 TATATTATAT
1 TATATTATAT
39869 AAAACTTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
12 4 0.09
13 8 0.18
14 15 0.33
15 8 0.18
16 2 0.04
17 8 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATATTATATTTATT
Found at i:39869 original size:27 final size:27
Alignment explanation
Indices: 39798--39869 Score: 74
Period size: 30 Copynumber: 2.5 Consensus size: 27
39788 AAACGATAAT
*
39798 TTATATATTATATTTATTTATTTATTTTA
1 TTATATATTATA--TATTTAATTATTTTA
*
39827 TTATATTATAATTATATTTAAATTATTTTA
1 TTATA-TATTA-TATATTT-AATTATTTTA
39857 TT-TATATTATATA
1 TTATATATTATATA
39870 AAACTTAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
27 4 0.11
28 4 0.11
29 12 0.32
30 15 0.41
31 2 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (27 bp):
TTATATATTATATATTTAATTATTTTA
Found at i:39878 original size:30 final size:31
Alignment explanation
Indices: 39819--39896 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 31
39809 ATTTATTTAT
* * *
39819 TTATTTTA-TTATATTATAATTATATTTAAA
1 TTATTTTATTTATATTATAATAAAACTTAAA
39849 TTATTTTATTTATATTAT-ATAAAACTTAAA
1 TTATTTTATTTATATTATAATAAAACTTAAA
*
39879 ATATTTTATATTTATATT
1 TTA-TTT-TATTTATATT
39897 GTATTTATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 19 0.46
31 12 0.29
32 10 0.24
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (31 bp):
TTATTTTATTTATATTATAATAAAACTTAAA
Found at i:41063 original size:22 final size:22
Alignment explanation
Indices: 41023--41064 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
41013 AATAAAATAT
*
41023 TATTTTTATATTAATATTTATA
1 TATTTTTAAATTAATATTTATA
41045 TATTTTTAAAATTAA-ATTTA
1 TATTTTT-AAATTAATATTTA
41065 AATAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTTTAAATTAATATTTATA
Found at i:42125 original size:18 final size:19
Alignment explanation
Indices: 42085--42132 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
42075 TACATGTCTG
* **
42085 CCTTTGTTTTGTTTCTTTT
1 CCTTTGTTTTCTTTCTTCC
42104 CCTTTG-TTTCTTTCTTCC
1 CCTTTGTTTTCTTTCTTCC
*
42122 CCTTTTTTTTC
1 CCTTTGTTTTC
42133 CCTCTTTTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.00, C:0.25, G:0.06, T:0.69
Consensus pattern (19 bp):
CCTTTGTTTTCTTTCTTCC
Found at i:43396 original size:3 final size:3
Alignment explanation
Indices: 43388--43428 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
43378 TTCAGTCACT
43388 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
43429 GTTAAACCCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:43773 original size:14 final size:14
Alignment explanation
Indices: 43741--43777 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
43731 AATTATTAAA
43741 ATATTAAA-AT-TT
1 ATATTAAATATATT
43753 ATATTAAATATATT
1 ATATTAAATATATT
*
43767 ATTTTAAATAT
1 ATATTAAATAT
43778 GATATGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 8 0.36
13 2 0.09
14 12 0.55
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATTAAATATATT
Found at i:48054 original size:2 final size:2
Alignment explanation
Indices: 48042--48085 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
48032 GAAATATAGT
*
48042 GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
48084 GA
1 GA
48086 ATGAGAAAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:52281 original size:60 final size:60
Alignment explanation
Indices: 52191--52311 Score: 188
Period size: 60 Copynumber: 2.0 Consensus size: 60
52181 GGTGTAGGGG
* *
52191 AATAATATTAGTTTCACTTTTTGGTTTTGATATAAGAAAAACCAGTAAATGTCATTCAAT
1 AATAATATTAGTTTCACTTTTTGGTTTTGATATAAGAAAAACCAGAAAATGTCATACAAT
* * **
52251 AATAATGTTTGTTTCACTTTTTGGTTTTGATATAAGAAAAACTTGAAAATGTCATACAAT
1 AATAATATTAGTTTCACTTTTTGGTTTTGATATAAGAAAAACCAGAAAATGTCATACAAT
52311 A
1 A
52312 TTACTTTTCT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.40
Consensus pattern (60 bp):
AATAATATTAGTTTCACTTTTTGGTTTTGATATAAGAAAAACCAGAAAATGTCATACAAT
Found at i:59886 original size:15 final size:17
Alignment explanation
Indices: 59866--59897 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
59856 TTAATTAAAT
59866 ATTTAAA-AAA-ATTTA
1 ATTTAAATAAATATTTA
59881 ATTTAAATAAATATTTA
1 ATTTAAATAAATATTTA
59898 TATTATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTAAATAAATATTTA
Found at i:64369 original size:20 final size:20
Alignment explanation
Indices: 64341--64415 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
64331 TTTTACCCAG
64341 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
64361 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
64381 ATGTATTGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
64401 ATGTATCGATACATT
1 ATGTATCGATACATT
64416 CTATTTTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:78290 original size:9 final size:9
Alignment explanation
Indices: 78276--78349 Score: 69
Period size: 9 Copynumber: 7.6 Consensus size: 9
78266 CTTTACACCA
78276 AAAAAAAAC
1 AAAAAAAAC
78285 AAAAAAAA-
1 AAAAAAAAC
78293 AATAAAAAAC
1 AA-AAAAAAC
78303 AAAAAAAAC
1 AAAAAAAAC
*
78312 AAGAAAACCAAG
1 AA-AAAA--AAC
78324 AAAAAAATAGC
1 AAAAAAA-A-C
78335 AAAAAAAAC
1 AAAAAAAAC
78344 AGAAAA
1 A-AAAA
78350 GGGGTCTAGA
Statistics
Matches: 55, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
8 2 0.04
9 26 0.47
10 12 0.22
11 11 0.20
12 4 0.07
ACGTcount: A:0.82, C:0.09, G:0.05, T:0.03
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:78292 original size:12 final size:12
Alignment explanation
Indices: 78275--78342 Score: 50
Period size: 12 Copynumber: 5.5 Consensus size: 12
78265 CCTTTACACC
78275 AAAAAAAAACAA
1 AAAAAAAAACAA
78287 AAAAAAAATA-AA
1 AAAAAAAA-ACAA
78299 AAACAAAAAA-AA
1 AAA-AAAAAACAA
* * *
78311 CAAGAAAACCAA
1 AAAAAAAAACAA
*
78323 GAAAAAAATAGCAA
1 -AAAAAAA-AACAA
78337 AAAAAA
1 AAAAAA
78343 CAGAAAAGGG
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
11 4 0.09
12 20 0.44
13 17 0.38
14 4 0.09
ACGTcount: A:0.84, C:0.09, G:0.04, T:0.03
Consensus pattern (12 bp):
AAAAAAAAACAA
Found at i:79631 original size:28 final size:29
Alignment explanation
Indices: 79563--80755 Score: 1175
Period size: 28 Copynumber: 42.1 Consensus size: 29
79553 TGTTCATCCC
* *
79563 TTTCAAAGCCCACAAGTTAGTGGCACTTT
1 TTTCAAAGCCCACAAGTCAGTGGCACCTT
**
79592 TTTCAAAGCCCATGAGTCAGTGGCACCTT
1 TTTCAAAGCCCACAAGTCAGTGGCACCTT
* *
79621 TTT-AAAGCCCACAAGTC-GTCAAG-AGCTT
1 TTTCAAAGCCCACAAGTCAGT--GGCACCTT
* *
79649 TTGTC-TAG---A-ATGTTCA-T--C-CC--
1 TT-TCAAAGCCCACAAG-TCAGTGGCACCTT
79669 TTTCAAAGCCCACAAGTCAGTGGCA-CTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT-T
**
79698 TTTCAAAGCCCATGAGTCAGTGGCACCTT
1 TTTCAAAGCCCACAAGTCAGTGGCACCTT
*
79727 TTT-AAAGCCCATAAGTCAGTGGCACAC--
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CTT
79754 TTTCAAAGCCCACAAGTCAGTGGCACAC-T
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CTT
*
79783 TTTCAAAGCCCACAAGTTAGTGGCACAC-T
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CTT
*
79812 TTTCAAAGCCCACAAGTCAGTGGCACC-C
1 TTTCAAAGCCCACAAGTCAGTGGCACCTT
79840 TTTCAAAGCCCACAAGTCAGTGGCA-CTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT-T
* *
79869 TTTCAAAGCTCACAAGTCAGTGGCACC-C
1 TTTCAAAGCCCACAAGTCAGTGGCACCTT
79897 TTTCAAAGCCCACAAGTCAGTGGCACC-T
1 TTTCAAAGCCCACAAGTCAGTGGCACCTT
* *
79925 TGTCAAAACCCACAAGTCAGTGGCA-CTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT-T
* *
79954 TTTCAAAGCTCACACGTCAGTGGCA-CTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT-T
*
79983 TTTCAAAGCCCACAAGTTAGTGGCATCC--
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCTT
*
80011 TTTCAAAGCCCACAAGTCAGTGGCACC-C
1 TTTCAAAGCCCACAAGTCAGTGGCACCTT
* *
80039 TTTCAAAGCCCACTAGTCAGTGGCACC-C
1 TTTCAAAGCCCACAAGTCAGTGGCACCTT
* *
80067 TTTCAAAGCCCACCAGTCAGTGGCACC-C
1 TTTCAAAGCCCACAAGTCAGTGGCACCTT
*
80095 TTTCAAAGCCCACAAGTCAGTGGCA-CTC
1 TTTCAAAGCCCACAAGTCAGTGGCACCTT
*
80123 TTTCAAAGCCCACAAGTCAATGGCA-CTAT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT-T
* *
80152 TTTCAAAGCCTACAAGTCAGTGGCA-TTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT-T
*
80181 TTTCAAAGCCCACAAGTTAGTGGCATCC-T
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCTT
*
80210 TTT-AAAGCCCACAAGTCAGTGGCACC-C
1 TTTCAAAGCCCACAAGTCAGTGGCACCTT
* *
80237 TTTCAAAGCTCAGC-AGTCAGTGGCACC-C
1 TTTCAAAGCCCA-CAAGTCAGTGGCACCTT
* * *
80265 TTTCAAAGCCTACGAGTCAGTGGCACC-C
1 TTTCAAAGCCCACAAGTCAGTGGCACCTT
*
80293 TTTCAAAGCCCACGAGTCAGTGGCA-CTT
1 TTTCAAAGCCCACAAGTCAGTGGCACCTT
80321 TTTCAAAGCCCACAAGTCAGTGGCATCC--
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCTT
*
80349 TTTCAAAGCCTACAAGTCAGTGGCACC-T
1 TTTCAAAGCCCACAAGTCAGTGGCACCTT
**
80377 TTTCAAAGCCTGCAAGTCAGTGGCA-CTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT-T
80406 TTTCAAAGCCCACAAGTCAGTGGCA-CTAT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT-T
*
80435 TTTCAAAGCCTACAAGTCAGTGGCA-CTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT-T
* * *
80464 TTTCAAACCCCACAAGTTAATGGCATCC--
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCTT
*
80492 TTTCAAAGCCCACAAGTCAGTGGCACC-C
1 TTTCAAAGCCCACAAGTCAGTGGCACCTT
* *
80520 TTTCAAAGCCCACAAGTCAGTGGTA-CTA
1 TTTCAAAGCCCACAAGTCAGTGGCACCTT
80548 TTTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CTT
* *
80578 TTTC-AAGCCCACGAGTCAGTAGCA-CTT
1 TTTCAAAGCCCACAAGTCAGTGGCACCTT
* *
80605 TTTCAAAGCCCACAAGTTATTGGCATCC--
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCTT
* *
80633 TTTCTAAGCCTACAAGTCAGTGGCACC-T
1 TTTCAAAGCCCACAAGTCAGTGGCACCTT
* * *
80661 TTTCAAAGCCCACAAGTCAATGGTAACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT-T
* * * * *
80691 TTTCAATGCCCACACGTGTCGGTGGTAACTTT
1 TTTCAAAGCCCACA--AGTCAGTGG-CACCTT
* *
80723 TTTCAAAGCTACACAAGTCAGTGGCACTTT
1 TTTCAAAGC-CCACAAGTCAGTGGCACCTT
80753 TTT
1 TTT
80756 TTTTAAAAAA
Statistics
Matches: 1004, Mismatches: 100, Indels: 119
0.82 0.08 0.10
Matches are distributed among these distances:
19 2 0.00
20 4 0.00
22 1 0.00
23 4 0.00
24 3 0.00
25 2 0.00
26 6 0.01
27 32 0.03
28 556 0.55
29 331 0.33
30 33 0.03
31 9 0.01
32 15 0.01
33 6 0.01
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.25
Consensus pattern (29 bp):
TTTCAAAGCCCACAAGTCAGTGGCACCTT
Found at i:79667 original size:106 final size:106
Alignment explanation
Indices: 79530--79743 Score: 392
Period size: 106 Copynumber: 2.0 Consensus size: 106
79520 CAAGAAATTA
* *
79530 TCGTCAAGAACTTTTGTCTAGAATGTTCATCCCTTTCAAAGCCCACAAGTTAGTGGCACTTTTTT
1 TCGTCAAGAACTTTTGTCTAGAATGTTCATCCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTT
79595 CAAAGCCCATGAGTCAGTGGCACCTTTTTAAAGCCCACAAG
66 CAAAGCCCATGAGTCAGTGGCACCTTTTTAAAGCCCACAAG
*
79636 TCGTCAAGAGCTTTTGTCTAGAATGTTCATCCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTT
1 TCGTCAAGAACTTTTGTCTAGAATGTTCATCCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTT
*
79701 CAAAGCCCATGAGTCAGTGGCACCTTTTTAAAGCCCATAAG
66 CAAAGCCCATGAGTCAGTGGCACCTTTTTAAAGCCCACAAG
79742 TC
1 TC
79744 AGTGGCACAC
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 104 1.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (106 bp):
TCGTCAAGAACTTTTGTCTAGAATGTTCATCCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTT
CAAAGCCCATGAGTCAGTGGCACCTTTTTAAAGCCCACAAG
Found at i:81336 original size:20 final size:19
Alignment explanation
Indices: 81311--81378 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 19
81301 TACCCAGATG
81311 TATCGATATACTTTTCAATA
1 TATCGATATA-TTTTCAATA
* * * *
81331 TATCGATACATGTATGAATC
1 TATCGATATAT-TTTCAATA
81351 TATCGATATATTCTTCAATA
1 TATCGATATATT-TTCAATA
81371 TATCGATA
1 TATCGATA
81379 CATTCTGTCT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 2 0.05
20 36 0.95
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (19 bp):
TATCGATATATTTTCAATA
Found at i:86642 original size:2 final size:2
Alignment explanation
Indices: 86592--86630 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
86582 TCCATGTTGA
*
86592 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
86631 CTGCTAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:87449 original size:18 final size:18
Alignment explanation
Indices: 87409--87443 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
87399 TCGGGCCTCT
87409 AGGAGGTTTAGGCGGCGC
1 AGGAGGTTTAGGCGGCGC
87427 AGGAGGTTTAGGCGGCG
1 AGGAGGTTTAGGCGGCG
87444 GTGGAGCAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.14, G:0.51, T:0.17
Consensus pattern (18 bp):
AGGAGGTTTAGGCGGCGC
Found at i:88894 original size:22 final size:24
Alignment explanation
Indices: 88868--88925 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
88858 ATAAATGATA
88868 AAATTTAATATAAATAT-AATTTT
1 AAATTTAATATAAATATAAATTTT
*
88891 AATTATTTAATA-ATATATAAATTTT
1 AA--ATTTAATATAAATATAAATTTT
88916 -AATTTAATAT
1 AAATTTAATAT
88926 CATTAATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
22 8 0.27
23 2 0.07
24 6 0.20
25 14 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
AAATTTAATATAAATATAAATTTT
Found at i:88898 original size:25 final size:25
Alignment explanation
Indices: 88870--88919 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
88860 AAATGATAAA
88870 ATTTAATATAAATAT-AATTTTAATT
1 ATTTAATA-AAATATAAATTTTAATT
*
88895 ATTTAATAATATATAAATTTTAATT
1 ATTTAATAAAATATAAATTTTAATT
88920 TAATATCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTTAATAAAATATAAATTTTAATT
Found at i:88970 original size:32 final size:32
Alignment explanation
Indices: 88915--88976 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
88905 ATATAAATTT
88915 TAATTTAATATCATTAATAATTATTTTTATTA
1 TAATTTAATATCATTAATAATTATTTTTATTA
* *
88947 TAATTT-ATTTCATTATATTATTATTTTTAT
1 TAATTTAATATCATTA-ATAATTATTTTTAT
88977 ATTTAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 8 0.30
32 19 0.70
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (32 bp):
TAATTTAATATCATTAATAATTATTTTTATTA
Found at i:89030 original size:21 final size:21
Alignment explanation
Indices: 88989--89067 Score: 64
Period size: 21 Copynumber: 4.1 Consensus size: 21
88979 TTAAATATAT
*
88989 ATTTAATCA--ATAAT-TTTA
1 ATTTAATCATTATAATAATTA
*
89007 ATTTTATCATTATAATAATTA
1 ATTTAATCATTATAATAATTA
* *
89028 ATTTAATTATTATAATTATT-
1 ATTTAATCATTATAATAATTA
*
89048 -TTTAATC-TTATCA-AATTA
1 ATTTAATCATTATAATAATTA
89066 AT
1 AT
89068 CTTACTATCT
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
17 3 0.06
18 13 0.27
19 7 0.15
20 5 0.10
21 20 0.42
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTAATCATTATAATAATTA
Found at i:90038 original size:109 final size:106
Alignment explanation
Indices: 89821--90042 Score: 261
Period size: 109 Copynumber: 2.1 Consensus size: 106
89811 AAATTAAATT
* *
89821 AAAAAAGATTTATTATTATTATTTTTAATAAAATTAAAAATAATATTTAATTAAGTTTTAAAAAA
1 AAAAAAGATTTATTATTATTATTTTTAATAAAATGAAAAATAATATTTAATTAAATTTTAAAAAA
* * * * * * **
89886 TTACATTAACAAATTAAAATATTAATTATTATGTTTTTATAA
66 TTAAATTAAAAAATTAAAAAATAAATTATAAAG-TAATATAA
*
89928 AAAAAAGTATTTATTATTATTATTTTTTAATAAAATGAAAAATGATATTTAATTAAATTTTAAAA
1 AAAAAAG-ATTTATTATTATTA-TTTTTAATAAAATGAAAAATAATATTTAATTAAATTTT-AAA
89993 AAATTAAATTAAAAAATTTTAAAAAATAACATT-TAAAG-AAT-TAA
63 AAATTAAATTAAAAAA--TTAAAAAATAA-ATTATAAAGTAATATAA
90037 AAAAAA
1 AAAAAA
90043 TTATCATCAT
Statistics
Matches: 98, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
107 7 0.07
108 14 0.14
109 44 0.45
110 18 0.18
112 12 0.12
113 3 0.03
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (106 bp):
AAAAAAGATTTATTATTATTATTTTTAATAAAATGAAAAATAATATTTAATTAAATTTTAAAAAA
TTAAATTAAAAAATTAAAAAATAAATTATAAAGTAATATAA
Found at i:90039 original size:23 final size:23
Alignment explanation
Indices: 89986--90045 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
89976 TTAATTAAAT
89986 TTTAAAAAAATTAAATTAAAAAA
1 TTTAAAAAAATTAAATTAAAAAA
* *
90009 TTTTAAAAAA-TAACATTTAAAGAA
1 TTTAAAAAAATTAA-A-TTAAAAAA
*
90033 TTAAAAAAAATTA
1 TTTAAAAAAATTA
90046 TCATCATTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 3 0.10
23 10 0.33
24 15 0.50
25 2 0.07
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (23 bp):
TTTAAAAAAATTAAATTAAAAAA
Found at i:91394 original size:88 final size:87
Alignment explanation
Indices: 91271--92417 Score: 1184
Period size: 88 Copynumber: 13.1 Consensus size: 87
91261 AAAAAAAAAG
* * * *
91271 AAAAA-TTGATTGATTGTAAATGTCAGACTTAAGGATTAGACTAATCCATTAATTATATCTGAGA
1 AAAAAGTTGACTGATTGTAAATGTCAGACTGAAGGATTAGACTAATGCATGAATTATATCTGAGA
91335 ATTAGATTCTTTTTTATAGAAAA
66 ATTAGATTCTTTTTTATAG-AAA
* ** *
91358 AAAAAGTTGACTGATTTTGGATGTCAGACTGCAGGATTAGACTAATGCATGAATTATATCTGAGA
1 AAAAAGTTGACTGATTGTAAATGTCAGACTGAAGGATTAGACTAATGCATGAATTATATCTGAGA
* *
91423 ATCAGATTATTTTTTATAGAAA
66 ATTAGATTCTTTTTTATAGAAA
* *
91445 AAAAAGTTGACTGATTGTAAATGTTAGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAG
1 AAAAAGTTGACTGATTGTAAATGTCAGACTG-AAGGATTAGACTAATGCATGAATTATATCTGAG
91510 AATTAGATTCTTTTTTATAGAAAA
65 AATTAGATTCTTTTTTATAG-AAA
* ** *
91534 AAAAAGTTGACTGATTTTGGATGTCAGACTGCAGGATTAGACTAATGCATGAATTATATCTGAGA
1 AAAAAGTTGACTGATTGTAAATGTCAGACTGAAGGATTAGACTAATGCATGAATTATATCTGAGA
* *
91599 ATCAGATTATTTTTTATAGAAA
66 ATTAGATTCTTTTTTATAGAAA
* *
91621 AAAAAGTTGACTGATTGTAAATGTTAGACTGCAAAGATTAGACTAATGCATGAATTATATCTGAG
1 AAAAAGTTGACTGATTGTAAATGTCAGACTG-AAGGATTAGACTAATGCATGAATTATATCTGAG
*
91686 AATTAGA-T-TTTTTTATAGCAA
65 AATTAGATTCTTTTTTATAGAAA
* * * ** * * *
91707 AAAAAGACTGATTGATTGTAAATGTCAGACTATAAATATTAAAATAATGCATGAATTATATCTAA
1 AAAAAG-TTGACTGATTGTAAATGTCAGACT-GAAGGATTAGACTAATGCATGAATTATATCTGA
* *
91772 CAATCA-ATT-TTTTTTATAG-AA
64 GAATTAGATTCTTTTTTATAGAAA
* * * * * * *
91793 AAAAAGCTGATTGATTGTAAATGTCAGACTACAAGGATTTGACTAATGCATGAATTAAATTTGAA
1 AAAAAGTTGACTGATTGTAAATGTCAGACT-GAAGGATTAGACTAATGCATGAATTATATCTGAG
91858 AATT-GAATTCTTTTTTATAGAGAAAA
65 AATTAG-ATTCTTTTTTAT--AG-AAA
* * *
91884 AGAAAAGTTGACTGATTGTAAATGTCAGACTGCAATGATTAGAGTAATGCATTAATTATATCTGA
1 A-AAAAGTTGACTGATTGTAAATGTCAGACTG-AAGGATTAGACTAATGCATGAATTATATCTGA
*
91949 GAA-TCGAATTCTTTTTTATAG--A
64 GAATTAG-ATTCTTTTTTATAGAAA
* * * * * * *
91971 AAAAAGTTGAATAATTGTAAATATCAGGCTGAAAAGATTAGACTAAT-CATGAATTATATTTAAG
1 AAAAAGTTGACTGATTGTAAATGTCAGACTG-AAGGATTAGACTAATGCATGAATTATATCTGAG
** * *
92035 AATCGGATT-TTTTTTTTATAAA
65 AATTAGATTCTTTTTTATAGAAA
* * * *
92057 AAAAAGACTGATTGATTGTAAATGTCAGACTGTAAGGATTAGACTAATGTATAAATTATATCTGA
1 AAAAAG-TTGACTGATTGTAAATGTCAGACTG-AAGGATTAGACTAATGCATGAATTATATCTGA
*
92122 GAATCAGATTC--TTTTATAG--A
64 GAATTAGATTCTTTTTTATAGAAA
* * *
92142 AAAAAG-TGACTGATTGTAAATGTCAGGCTATAAGGATTAAACTAATGCATGAATTATATCTGAG
1 AAAAAGTTGACTGATTGTAAATGTCAGACT-GAAGGATTAGACTAATGCATGAATTATATCTGAG
* *
92206 AA-TCGAATTCTTTTTTATAAAAAAA
65 AATTAG-ATTCTTTTTTAT--AGAAA
* * * * * *
92231 AAGAAAGACTGATTGATTGTAAGTGTCATATTGTAAAGG-TTAGACTAATGCATGAATTATATTT
1 AA-AAAG-TTGACTGATTGTAAATGTCAGACTG--AAGGATTAGACTAATGCATGAATTATATCT
* * * *
92295 AAGAATCAGATTATTTTTATATAAAAA
62 GAGAATTAGATTCTTTTT-TATAGAAA
* *
92322 AAGAAAGATTGATTGATTGTAAATGTCAGACTATAAGGATTAGACTAATGCATGAATTATATCTG
1 AA-AAAG-TTGACTGATTGTAAATGTCAGACT-GAAGGATTAGACTAATGCATGAATTATATCTG
*
92387 AGAA-TCGAATT-TTTTTTATAAGAAA
63 AGAATTAG-ATTCTTTTTTAT-AGAAA
92412 AAAAAG
1 AAAAAG
92418 ACTACAAGAA
Statistics
Matches: 894, Mismatches: 124, Indels: 82
0.81 0.11 0.07
Matches are distributed among these distances:
82 1 0.00
83 57 0.06
84 8 0.01
85 84 0.09
86 77 0.09
87 181 0.20
88 224 0.25
89 42 0.05
90 22 0.02
91 68 0.08
92 122 0.14
93 8 0.01
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (87 bp):
AAAAAGTTGACTGATTGTAAATGTCAGACTGAAGGATTAGACTAATGCATGAATTATATCTGAGA
ATTAGATTCTTTTTTATAGAAA
Found at i:92470 original size:67 final size:66
Alignment explanation
Indices: 92349--92484 Score: 168
Period size: 67 Copynumber: 2.0 Consensus size: 66
92339 TGTAAATGTC
* * *
92349 AGACTATAAGGATTAGACTAATGCATGAATTATATCTGAGAATCGAATTTTTTTTATAAGAAAAA
1 AGACTACAAGAATTAGACTAATGCATGAATTATATCTGAGAATCGAATTTTTTTTAGAA-AAAAA
92414 AA
65 AA
* * * *
92416 AGACTACAAGAATTAGACTAATGTATGAATTGTA-CATGAGAATC-AGTTTTTTTTTGGAAAAAA
1 AGACTACAAGAATTAGACTAATGCATGAATTATATC-TGAGAATCGA-ATTTTTTTTAGAAAAAA
92479 AAA
64 AAA
92482 AGA
1 AGA
92485 AAAGTTGGTT
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
66 12 0.20
67 48 0.80
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.32
Consensus pattern (66 bp):
AGACTACAAGAATTAGACTAATGCATGAATTATATCTGAGAATCGAATTTTTTTTAGAAAAAAAA
A
Found at i:96680 original size:27 final size:27
Alignment explanation
Indices: 96622--96681 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
96612 ATTAATGTAA
* *
96622 ATTTTTTAAAAATTAATTAAATATTAT
1 ATTTTTTAAAAAATAATTAAATAATAT
* *
96649 TTTTTATTAAAAAATAA-TAATTAATAT
1 ATTTT-TTAAAAAATAATTAAATAATAT
96676 ATTTTT
1 ATTTTT
96682 ATTTTTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
26 1 0.04
27 16 0.59
28 10 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
ATTTTTTAAAAAATAATTAAATAATAT
Found at i:96690 original size:31 final size:29
Alignment explanation
Indices: 96622--96690 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 29
96612 ATTAATGTAA
*
96622 ATTTTTTAAAAATTAATTAAATATTATTT
1 ATTTTTAAAAAATTAATTAAATATTATTT
96651 -TTTATTAAAAAATAATAATTAATATATT-TTT
1 ATTT-TTAAAAAAT--TAATTAA-ATATTATTT
96682 ATTTTTAAA
1 ATTTTTAAA
96691 TTTTTTAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
28 3 0.09
29 8 0.24
31 15 0.44
32 8 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
ATTTTTAAAAAATTAATTAAATATTATTT
Found at i:96691 original size:28 final size:32
Alignment explanation
Indices: 96624--96691 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 32
96614 TAATGTAAAT
96624 TTTTTAAA-AATTAATTAAATATTATTTTTTA
1 TTTTTAAATAATTAATTAAATATTATTTTTTA
***
96655 TTAAAAAATAA-TAATT-AATA-TA-TTTTTA
1 TTTTTAAATAATTAATTAAATATTATTTTTTA
96683 TTTTTAAAT
1 TTTTTAAAT
96692 TTTTTAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
28 12 0.40
29 2 0.07
30 4 0.13
31 10 0.33
32 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (32 bp):
TTTTTAAATAATTAATTAAATATTATTTTTTA
Found at i:104012 original size:28 final size:28
Alignment explanation
Indices: 103975--104037 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
103965 ATTTAAAATT
*
103975 GATTATGATTTGATTTTTTTAAATTTAA
1 GATTATGATTTGATTTTTTAAAATTTAA
* * *
104003 GATTTTGATTTTATTTTTTAAAATTTTA
1 GATTATGATTTGATTTTTTAAAATTTAA
104031 GATTATG
1 GATTATG
104038 TTTTAACACC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (28 bp):
GATTATGATTTGATTTTTTAAAATTTAA
Found at i:115688 original size:27 final size:27
Alignment explanation
Indices: 115633--115696 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
115623 AATAAAAAAA
*
115633 TAATTTAAAATTATTTAAATTTAATTT
1 TAATTTAAAATTATATAAATTTAATTT
*
115660 TAATTTAAAAATTA-ATAATTTTGAATTT
1 TAATTT-AAAATTATATAAATTT-AATTT
* *
115688 AAACTTAAA
1 TAATTTAAA
115697 TAATTTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
27 15 0.48
28 16 0.52
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
TAATTTAAAATTATATAAATTTAATTT
Found at i:115695 original size:21 final size:22
Alignment explanation
Indices: 115654--115702 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
115644 TATTTAAATT
115654 TAATTTTAATTTAAAAATT-AA
1 TAATTTTAATTTAAAAATTAAA
*
115675 TAATTTTGAATTT-AAACTTAAA
1 TAATTTT-AATTTAAAAATTAAA
115697 TAATTT
1 TAATTT
115703 AAAACTCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TAATTTTAATTTAAAAATTAAA
Found at i:115961 original size:24 final size:25
Alignment explanation
Indices: 115907--115963 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
115897 ATTTAATATT
* *
115907 AATTTTTATATAAGTTATATATTTT
1 AATTTTTATATAAGTTATATAATTA
115932 AA-TTTTATCA-AA-TTATATAATTA
1 AATTTTTAT-ATAAGTTATATAATTA
115955 AATTTTTAT
1 AATTTTTAT
115964 TATTAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 11 0.39
24 14 0.50
25 3 0.11
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (25 bp):
AATTTTTATATAAGTTATATAATTA
Found at i:115990 original size:22 final size:22
Alignment explanation
Indices: 115923--115992 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 22
115913 TATATAAGTT
* *
115923 ATATATTTTAATTTTATCAAATT-
1 ATATAATTAAATTTT-T-AAATTA
*
115946 ATATAATTAAATTTTTATTATTA
1 ATATAATTAAATTTTTA-AATTA
115969 ATA-AATTAAATTATTTAAATTA
1 ATATAATTAAATT-TTTAAATTA
115991 AT
1 AT
115993 TCTATTAAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 1 0.03
22 19 0.47
23 20 0.50
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATAATTAAATTTTTAAATTA
Found at i:116500 original size:21 final size:21
Alignment explanation
Indices: 116474--116517 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
116464 TTGAATTGAT
*
116474 TTAAAATAATAATA-AAAACTA
1 TTAAAAT-ATAAGAGAAAACTA
116495 TTAAAATATAAGAGAAAACTA
1 TTAAAATATAAGAGAAAACTA
116516 TT
1 TT
116518 TTTTTTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (21 bp):
TTAAAATATAAGAGAAAACTA
Found at i:118081 original size:86 final size:86
Alignment explanation
Indices: 117929--118089 Score: 205
Period size: 86 Copynumber: 1.9 Consensus size: 86
117919 CAGTAATAGC
** * * * * *** *
117929 ACATATTAGTCTTGTAATAATAATAAAGGTAATACGGTTAAAAATATATTTGTGATTATAAATTA
1 ACATATTAAACTTATAATAATAATAAAGATAATACGATCAAAAATATATTTACAATTACAAATTA
117994 AATATTTGATACAAGGATAAT
66 AATATTTGATACAAGGATAAT
* * *
118015 ACATATTAAACTTATAATAATAATAAATATAATACGATCAAAAATATATTTACAATTGCAAGTTA
1 ACATATTAAACTTATAATAATAATAAAGATAATACGATCAAAAATATATTTACAATTACAAATTA
118080 AATATTTGAT
66 AATATTTGAT
118090 CAGGAGTTTT
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
86 62 1.00
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.37
Consensus pattern (86 bp):
ACATATTAAACTTATAATAATAATAAAGATAATACGATCAAAAATATATTTACAATTACAAATTA
AATATTTGATACAAGGATAAT
Found at i:118937 original size:18 final size:17
Alignment explanation
Indices: 118916--118975 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
118906 ATGATTTGTT
118916 AAATCACTATGAATAATC
1 AAATCACTA-GAATAATC
*
118934 AAATCA-TGAAGACTAATC
1 AAATCACT--AGAATAATC
*
118952 AAATCACTAAAATTAATC
1 AAATCACTAGAA-TAATC
118970 AAATCA
1 AAATCA
118976 TGAAATCTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
17 3 0.09
18 30 0.86
19 2 0.06
ACGTcount: A:0.53, C:0.17, G:0.05, T:0.25
Consensus pattern (17 bp):
AAATCACTAGAATAATC
Found at i:139316 original size:10 final size:10
Alignment explanation
Indices: 139297--139339 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
139287 CAAACAAACA
139297 AAAAAAAAAG
1 AAAAAAAAAG
*
139307 AAAAAGAAAG
1 AAAAAAAAAG
*
139317 AAAAAAGCAAAA
1 AAAAAA--AAAG
139329 AAAAAAAAAG
1 AAAAAAAAAG
139339 A
1 A
139340 GTAAAAACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
10 18 0.67
12 9 0.33
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:139345 original size:17 final size:16
Alignment explanation
Indices: 139296--139346 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
139286 CCAAACAAAC
139296 AAAAAAAAAAGA-AAA
1 AAAAAAAAAAGAGAAA
*
139311 AGAAAGAAAAAAG-CAAA
1 A-AAA-AAAAAAGAGAAA
139328 AAAAAAAAAAGAGTAAA
1 AAAAAAAAAAGAG-AAA
139345 AA
1 AA
139347 CTTGAGTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
15 8 0.27
16 6 0.20
17 16 0.53
ACGTcount: A:0.84, C:0.02, G:0.12, T:0.02
Consensus pattern (16 bp):
AAAAAAAAAAGAGAAA
Found at i:140404 original size:21 final size:20
Alignment explanation
Indices: 140372--140432 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
140362 AAAAAAAAAA
140372 ATTC-CAAATGTATCGATAC
1 ATTCACAAATGTATCGATAC
***
140391 ATTTGTAGAATGTATCGATAC
1 ATTCACA-AATGTATCGATAC
140412 ATTCACAAATGTATCGATAC
1 ATTCACAAATGTATCGATAC
140432 A
1 A
140433 GGGTCCCAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 3 0.09
20 15 0.43
21 17 0.49
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (20 bp):
ATTCACAAATGTATCGATAC
Found at i:140424 original size:20 final size:19
Alignment explanation
Indices: 140372--140432 Score: 77
Period size: 20 Copynumber: 3.1 Consensus size: 19
140362 AAAAAAAAAA
140372 ATTCCAAATGTATCGATAC
1 ATTCCAAATGTATCGATAC
**
140391 ATTTGTAGAATGTATCGATAC
1 A-TTCCA-AATGTATCGATAC
140412 ATTCACAAATGTATCGATAC
1 ATTC-CAAATGTATCGATAC
140432 A
1 A
140433 GGGTCCCAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 1 0.03
20 19 0.54
21 15 0.43
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (19 bp):
ATTCCAAATGTATCGATAC
Found at i:140492 original size:19 final size:19
Alignment explanation
Indices: 140468--140535 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
140458 AATTCAACGA
140468 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
140487 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
140502 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
140519 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
140536 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:140506 original size:32 final size:32
Alignment explanation
Indices: 140470--140532 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
140460 TTCAACGATT
*
140470 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
140502 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
140533 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:140507 original size:13 final size:13
Alignment explanation
Indices: 140489--140513 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
140479 ACATAAGTTT
140489 TGTATCGATACAA
1 TGTATCGATACAA
140502 TGTATCGATACA
1 TGTATCGATACA
140514 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:140593 original size:13 final size:13
Alignment explanation
Indices: 140575--140600 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
140565 CATTTTTCTG
140575 TGTATCGATACAT
1 TGTATCGATACAT
140588 TGTATCGATACAT
1 TGTATCGATACAT
140601 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:140597 original size:33 final size:33
Alignment explanation
Indices: 140555--140621 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
140545 GCCAAGGAAA
***
140555 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
140588 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
140621 T
1 T
140622 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:143102 original size:27 final size:25
Alignment explanation
Indices: 143064--143139 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 25
143054 TTTCTTCACA
143064 ATCGGGGATACTCCAACCCCGTTGAT
1 ATCGGGGATACTCCAACCCCGTT-AT
*
143090 CATCGGGGATACTCTAACCCCGTTAT
1 -ATCGGGGATACTCCAACCCCGTTAT
*
143116 TTCCGAGGGGATACTCCAACCCCG
1 AT-C--GGGGATACTCCAACCCCG
143140 ACTTTATTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
25 1 0.02
26 3 0.07
27 22 0.51
28 17 0.40
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.22
Consensus pattern (25 bp):
ATCGGGGATACTCCAACCCCGTTAT
Found at i:143259 original size:52 final size:52
Alignment explanation
Indices: 142953--143309 Score: 225
Period size: 51 Copynumber: 6.8 Consensus size: 52
142943 TTCTCAATTC
* * *
142953 TCCACAATCGGGGATATTCCAACTCCGATTTTATTT-TCAAAACACTAA-TTT
1 TCCATAATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACACTAATTTT
* * * *
143004 TCTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACAAATTTCT
1 TCCATAATCGGGGATACTCCAACCCCGATTTTATTT-C-TAAAACACTAATTT-T
* * * ** * *
143059 T-CACAATCGGGGATACTCCAACCCCG--TTGATCATCGGGGATACTCTAACCCCGTTATT
1 TCCATAATCGGGGATACTCCAACCCCGATTTTAT-TTC--TAAAACACTAA-----TT-TT
* * * *
143117 TCC--GA--GGGGATACTCCAACCCCGACTTTATTTCTAAAATATTAATTTT
1 TCCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTT
* *
143165 T-CATAATCGGGGATATTCCAACCCCGATTTTATTGCTAAAACACTAATTTT
1 TCCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTT
* * * * *
143216 TCCACAATCAGGGATACTCCAACCCCGGTTTTATTT-TCGAAACACCAA-TTT
1 TCCATAATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACACTAATTTT
* *** *
143267 TCCTTTAATCGGGGATACTCCAACTTTGATTTTATTTCCAAAA
1 TCC-ATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAA
143310 ATACCAATTT
Statistics
Matches: 235, Mismatches: 47, Indels: 47
0.71 0.14 0.14
Matches are distributed among these distances:
47 1 0.00
48 3 0.01
49 3 0.01
51 79 0.34
52 71 0.30
53 16 0.07
54 29 0.12
55 20 0.09
56 2 0.01
57 5 0.02
58 4 0.02
59 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (52 bp):
TCCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTT
Found at i:143363 original size:28 final size:28
Alignment explanation
Indices: 143331--143400 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
143321 TCACAGTTGA
** * **
143331 GGATACTCCAACCTTGTTATTTCATTGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
143359 GGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
143387 GGATACTCCAACCC
1 GGATACTCCAACCC
143401 TGGCTTTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCAGAGG
Found at i:143420 original size:263 final size:263
Alignment explanation
Indices: 142953--143453 Score: 706
Period size: 263 Copynumber: 1.9 Consensus size: 263
142943 TTCTCAATTC
* * * *
142953 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCAGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
*
143018 TACTCCAACTCCGATTTTATTTCCAAAAAACACAAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACAAATTTCTTCACAATCGAGGATACTCCAACCC
* *
143083 CGTTGATCATCGGGGATACTCTAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATT
131 CGTTGATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATT
* * *
143148 TCTAAAATATTAATTTTTCATAATCGGGGATA-TTCCAACCCCGATTTTATTGCTAAAACACTAA
196 CCCAAAATATTAATTTCTCATAATCGGGGATACTT-CAACCCCGATTTTATTGCTAAAACACTAA
143212 TTTT
260 TTTT
* * *
143216 TCCACAATCAGGGATACTCCAACCCCGGTTTTATTTTCGAAACACCAATTTTCCTTTAATCGGGG
1 TCCACAATCAGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGGG
** * *
143281 ATACTCCAACTTTGATTTTATTTCCAAAAATAC-C-AATTT-TTCACAGTTGAGGATACTCCAAC
65 ATACTCCAACTCCGATTTTATTTCCAAAAA-ACACAAATTTCTTCACAATCGAGGATACTCCAAC
** * * *
143343 CTTGTT-ATTTCATTGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCTGGCTT
129 CCCGTTGA--TCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTT
* *
143407 TATTCCCAAAATATTGATTTCTCATAATTGGGGATACTTCAACCCCG
192 TATTCCCAAAATATTAATTTCTCATAATCGGGGATACTTCAACCCCG
143454 TTATTTTCGA
Statistics
Matches: 209, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
261 1 0.00
262 24 0.11
263 140 0.67
264 42 0.20
265 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (263 bp):
TCCACAATCAGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACAAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTGATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATT
CCCAAAATATTAATTTCTCATAATCGGGGATACTTCAACCCCGATTTTATTGCTAAAACACTAAT
TTT
Found at i:143505 original size:79 final size:78
Alignment explanation
Indices: 143354--143558 Score: 223
Period size: 79 Copynumber: 2.6 Consensus size: 78
143344 TTGTTATTTC
* * *
143354 ATTGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCTGGCTTTATTCCCAAAAT
1 ATTGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCC-GACTTTATTCCCAAAAT
* *
143419 ATTGATTTCTCATA
65 ATCGATTTCTCACA
* * * ** *
143433 ATTGGGGATACTTCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTTC-TAAT
1 ATTGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAA-CCCGACTTTATTCCCAAAAT
143497 CATCGATTTCTCACA
65 -ATCGATTTCTCACA
** * * * *
143512 ACCGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCC
1 ATTGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCC
143559 CGTTATTATC
Statistics
Matches: 106, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
78 6 0.06
79 97 0.92
80 3 0.03
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (78 bp):
ATTGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCGACTTTATTCCCAAAATA
TCGATTTCTCACA
Found at i:155986 original size:10 final size:10
Alignment explanation
Indices: 155971--156022 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 10
155961 ACCTTCTCTT
155971 AAAAAAAA-A
1 AAAAAAAAGA
*
155980 AAAAAAAA-C
1 AAAAAAAAGA
*
155989 AAAACAAAGA
1 AAAAAAAAGA
* *
155999 AAAAGAGAGA
1 AAAAAAAAGA
156009 AAAAAAAAGA
1 AAAAAAAAGA
156019 AAAA
1 AAAA
156023 TCTGCTTAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
9 15 0.43
10 20 0.57
ACGTcount: A:0.87, C:0.04, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:157080 original size:55 final size:55
Alignment explanation
Indices: 156991--158053 Score: 1567
Period size: 55 Copynumber: 19.3 Consensus size: 55
156981 TCCGCTTTTT
156991 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
157046 AGTCCCCAAAGAGCAGGACACCT-TTCAAATCCCACCCAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
*
157101 AGTCCTCAAAGAGCAGGACACCACTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
157156 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
157211 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
157266 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
157321 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
157376 AGTCCTCAAAGAGTAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
*
157431 AGTCCTCAAAGAGGAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
157486 AGTCCCCAAAGAGTAGGACACCT-TTCAAAGCCCACCCAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
157541 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
157596 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
157651 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
* * *
157706 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* **
157761 AGTCCTCAAAGAGCAGGATACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
157816 AGTCCTCAAAGAACAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
*
157871 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCTACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
157926 ATTCCCCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
157981 AGTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* *
158036 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
158054 TACAGTTTAT
Statistics
Matches: 922, Mismatches: 65, Indels: 42
0.90 0.06 0.04
Matches are distributed among these distances:
54 27 0.03
55 870 0.94
56 25 0.03
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:157978 original size:29 final size:29
Alignment explanation
Indices: 157834--157981 Score: 89
Period size: 29 Copynumber: 5.3 Consensus size: 29
157824 AAGAACAGGA
157834 CACCTTTCAAAGCCCACACAAGTTGGTGG
1 CACCTTTCAAAGCCCACACAAGTTGGTGG
* * * * * **
157863 CA-TTTTC-CAGTCCTCA-AAG-AGCAGG
1 CACCTTTCAAAGCCCACACAAGTTGGTGG
*
157888 ACACCTCTT-AAAGCCTACACAAGTTGGTGG
1 -CACCT-TTCAAAGCCCACACAAGTTGGTGG
** * **
157918 CACCTTTC-ATTCCC-CA-AAG-AGCAGG
1 CACCTTTCAAAGCCCACACAAGTTGGTGG
157943 ACACCTTTCAAAGCCCACACAAGTTGGTGG
1 -CACCTTTCAAAGCCCACACAAGTTGGTGG
157973 CACCTTTCA
1 CACCTTTCA
157982 GTCCTCAAAG
Statistics
Matches: 81, Mismatches: 26, Indels: 24
0.62 0.20 0.18
Matches are distributed among these distances:
25 6 0.07
26 16 0.20
27 13 0.16
28 18 0.22
29 22 0.27
30 6 0.07
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.22
Consensus pattern (29 bp):
CACCTTTCAAAGCCCACACAAGTTGGTGG
Found at i:158687 original size:21 final size:20
Alignment explanation
Indices: 158655--158715 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
158645 AAAAAAAAAT
158655 ATTC-CAAATGTATCGATAC
1 ATTCACAAATGTATCGATAC
***
158674 ATTTGTAGAATGTATCGATAC
1 ATTCACA-AATGTATCGATAC
158695 ATTCACAAATGTATCGATAC
1 ATTCACAAATGTATCGATAC
158715 A
1 A
158716 GGGTCCCAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 3 0.09
20 15 0.43
21 17 0.49
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (20 bp):
ATTCACAAATGTATCGATAC
Found at i:158707 original size:20 final size:19
Alignment explanation
Indices: 158655--158715 Score: 77
Period size: 20 Copynumber: 3.1 Consensus size: 19
158645 AAAAAAAAAT
158655 ATTCCAAATGTATCGATAC
1 ATTCCAAATGTATCGATAC
**
158674 ATTTGTAGAATGTATCGATAC
1 A-TTCCA-AATGTATCGATAC
158695 ATTCACAAATGTATCGATAC
1 ATTC-CAAATGTATCGATAC
158715 A
1 A
158716 GGGTCCCAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 1 0.03
20 19 0.54
21 15 0.43
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (19 bp):
ATTCCAAATGTATCGATAC
Found at i:158779 original size:19 final size:18
Alignment explanation
Indices: 158755--158818 Score: 75
Period size: 19 Copynumber: 3.7 Consensus size: 18
158745 CAACGATTTA
158755 TATCGATACATAAGTTTTG
1 TATCGATACATAAG-TTTG
158774 TATCGATAC--AA---TG
1 TATCGATACATAAGTTTG
158787 TATCGATACATAAGTATTG
1 TATCGATACATAAGT-TTG
158806 TATCGATACATAA
1 TATCGATACATAA
158819 TTAGCTACTG
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
19 24 0.62
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (18 bp):
TATCGATACATAAGTTTG
Found at i:158790 original size:13 final size:13
Alignment explanation
Indices: 158772--158796 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
158762 ACATAAGTTT
158772 TGTATCGATACAA
1 TGTATCGATACAA
158785 TGTATCGATACA
1 TGTATCGATACA
158797 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:158791 original size:32 final size:32
Alignment explanation
Indices: 158755--158815 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
158745 CAACGATTTA
*
158755 TATCGATACATAAGTTTTGTATCGATACAATG
1 TATCGATACATAAGTATTGTATCGATACAATG
158787 TATCGATACATAAGTATTGTATCGATACA
1 TATCGATACATAAGTATTGTATCGATACA
158816 TAATTAGCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (32 bp):
TATCGATACATAAGTATTGTATCGATACAATG
Found at i:158876 original size:13 final size:13
Alignment explanation
Indices: 158858--158883 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
158848 CATTTTTCTG
158858 TGTATCGATACAT
1 TGTATCGATACAT
158871 TGTATCGATACAT
1 TGTATCGATACAT
158884 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:158880 original size:33 final size:33
Alignment explanation
Indices: 158838--158904 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
158828 GCCAAGGAAA
***
158838 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
158871 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
158904 T
1 T
158905 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:161428 original size:28 final size:27
Alignment explanation
Indices: 161358--161433 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 27
161348 TTTCTTCACA
161358 ATCGGGGATACTCCAACCCCGTTGATC
1 ATCGGGGATACTCCAACCCCGTTGATC
161385 ATCGGGGATACTCCAACCCCGTT-AT-
1 ATCGGGGATACTCCAACCCCGTTGATC
*
161410 TTCCGAGGGGATACTCCAACCCCG
1 AT-C--GGGGATACTCCAACCCCG
161434 ACTTTATTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 1 0.02
26 3 0.07
27 23 0.51
28 18 0.40
ACGTcount: A:0.22, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTGATC
Found at i:161559 original size:52 final size:51
Alignment explanation
Indices: 161249--161636 Score: 250
Period size: 51 Copynumber: 7.4 Consensus size: 51
161239 CTCAATTCTC
* * * * *
161249 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAA-TTTT
1 CACAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTT
* * *
161299 CTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
1 C-ACAATCGGGGATACTCCAACCCCGGTTTTATTTCC--AAAACACCAATTT-TT
* * ** * *
161354 CACAATCGGGGATACTCCAACCCC-G-TTGATCATCGGGGATACTCCAACCCCGTTATTT
1 CACAATCGGGGATACTCCAACCCCGGTTTTAT-TTC--CAAAACACCAA-----TT-TTT
* ** * * **
161412 C-CGA--GGGGATACTCCAACCCCGACTTTATTTCTAAAATATTAATTTTT
1 CACAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTT
* * * * *
161460 CATAATCGGGGATATTCCAACCCCGGTTTTA-TTGCTAAACACTAATTTTT
1 CACAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTT
* * * *
161510 CCACAATCGGGGATACTCTAACCCCGGTTTTATTTTCGAAACACCAATTTTC
1 -CACAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTT
** * * *
161562 CTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
1 C-ACAATCGGGGATACTCCAACCCCGGTTTTATTTCC-AAAACACCAATTTTT
* *
161615 CACAGTCGAGGATACTCCAACC
1 CACAATCGGGGATACTCCAACC
161637 TTGTTATTTC
Statistics
Matches: 260, Mismatches: 55, Indels: 44
0.72 0.15 0.12
Matches are distributed among these distances:
48 4 0.02
49 3 0.01
50 15 0.06
51 82 0.32
52 64 0.25
53 31 0.12
54 27 0.10
55 20 0.08
56 2 0.01
57 6 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (51 bp):
CACAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTT
Found at i:161656 original size:28 final size:28
Alignment explanation
Indices: 161624--161695 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
161614 TCACAGTCGA
** * **
161624 GGATACTCCAACCTTGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
161652 GGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
161680 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
161696 GCTTTATTCC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.25
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCAGAGG
Found at i:161713 original size:262 final size:262
Alignment explanation
Indices: 161247--161746 Score: 781
Period size: 262 Copynumber: 1.9 Consensus size: 262
161237 TTCTCAATTC
* * *
161247 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
*
161312 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
*
161377 CGTTGATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATT
131 CGTTGATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATT
* * * *
161442 TCTAAAATATTAATTTTTCATAATCGGGGATATTCCAACCCCGGTTTTATTGCTAAACACTAATT
196 CCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAACACTAATT
161507 TT
261 TT
* * * *
161509 TCCACAATCGGGGATACTCTAACCCCGGTTTTATTTTCGAAACACCAATTTTCCTTTAATCGGGG
1 TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGGG
* *
161574 ATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAGTCGAGGATACTCCAACC
65 ATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACC
** *
161637 TTGTT-ATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
130 CCGTTGA--TCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTT
*
161701 ATTCCCAAAATATTAATTTCTCATAATTGGGGATACTCCAACCCCG
193 ATTCCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCG
161747 TTATTTTCGA
Statistics
Matches: 216, Mismatches: 19, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
260 1 0.00
261 25 0.12
262 154 0.71
263 36 0.17
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (262 bp):
TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTGATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATT
CCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAACACTAATT
TT
Found at i:161761 original size:107 final size:107
Alignment explanation
Indices: 161570--161769 Score: 242
Period size: 107 Copynumber: 1.9 Consensus size: 107
161560 TCCTTTAATC
* * * *
161570 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAGTCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
**
161635 CCTTGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
66 CCCCGTTATTTCA-CGGGGATACTCCAACCCCGTTACTTCCGA
* * ** * * *
161678 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTAATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
161742 CCCCGTTATTTTCGA-GGGGATACTCCAA
66 CCCCGTTA-TTTC-ACGGGGATACTCCAA
161770 TCTCGATTTT
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
107 51 0.66
108 25 0.32
109 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTCACGGGGATACTCCAACCCCGTTACTTCCGA
Found at i:161799 original size:79 final size:79
Alignment explanation
Indices: 161649--161854 Score: 216
Period size: 79 Copynumber: 2.6 Consensus size: 79
161639 GTTATTTCAT
* * *
161649 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
* * *
161714 TAATTTCTCATAAT
66 CAATTTCTCACAAC
* * * * * ** *
161728 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCTCGATTTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAAT-A
*
161792 TCGATTTCTCACAAC
65 TCAATTTCTCACAAC
* * * *
161807 CGGGGATACTCCTAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 CGGGGATACTCC-AACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
161855 TTATTATCTC
Statistics
Matches: 103, Mismatches: 22, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
78 3 0.03
79 71 0.69
80 29 0.28
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.30
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
CAATTTCTCACAAC
Found at i:163171 original size:28 final size:31
Alignment explanation
Indices: 163115--163190 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 31
163105 AGAACTTTAC
* *
163115 TTCTTTGTCCTTAAAGAACAGGAAA-TTT-T
1 TTCTTTATCCTCAAAGAACAGGAAATTTTCT
* **
163144 TT-TTTATCCTCAAAGACCAGGATGTTTTCT
1 TTCTTTATCCTCAAAGAACAGGAAATTTTCT
*
163174 TTCTTTGTCCTCAAAGA
1 TTCTTTATCCTCAAAGA
163191 GTAGGGCTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
28 17 0.45
29 5 0.13
30 3 0.08
31 13 0.34
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.42
Consensus pattern (31 bp):
TTCTTTATCCTCAAAGAACAGGAAATTTTCT
Found at i:163188 original size:31 final size:29
Alignment explanation
Indices: 163080--163190 Score: 82
Period size: 30 Copynumber: 3.7 Consensus size: 29
163070 AACTTGACCC
** *
163080 TTTTTATCTTTGTCCTCAAAG-AGTGAGAAC
1 TTTTT-TCTTTGTCCTCAAAGAACAG-GAAA
* *
163110 TTTACTTCTTTGTCCTTAAAGAACAGGAAA
1 TTT-TTTCTTTGTCCTCAAAGAACAGGAAA
* * **
163140 TTTTTT-TTTATCCTCAAAGACCAGGATGT
1 TTTTTTCTTTGTCCTCAAAGAACAGGA-AA
163169 TTTCTTTCTTTGTCCTCAAAGA
1 TTT-TTTCTTTGTCCTCAAAGA
163191 GTAGGGCTTT
Statistics
Matches: 64, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
28 17 0.27
29 5 0.08
30 26 0.41
31 16 0.25
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (29 bp):
TTTTTTCTTTGTCCTCAAAGAACAGGAAA
Found at i:163322 original size:30 final size:30
Alignment explanation
Indices: 163283--163413 Score: 91
Period size: 30 Copynumber: 4.1 Consensus size: 30
163273 TATGACATTT
* *
163283 TTTTCCTTCTTTGTTCTCAAAGAGCAGGATG
1 TTTT-CTTCTTTGTCCTCAAAAAGCAGGATG
*
163314 TTTTCTTCTTTTCTTTGTCCTCAAAAAGCATGATG
1 --TT-TTC--TTCTTTGTCCTCAAAAAGCAGGATG
* * * * * **
163349 TTTTTTTCTTTGACCTCAAAGAGTAGAACA
1 TTTTCTTCTTTGTCCTCAAAAAGCAGGATG
* *
163379 TTTTCTTCTTTTGTCTTCAAAAAACAGGATG
1 TTTTCTTC-TTTGTCCTCAAAAAGCAGGATG
163410 TTTT
1 TTTT
163414 TTTTTTCTTT
Statistics
Matches: 74, Mismatches: 20, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
30 25 0.34
31 18 0.24
32 2 0.03
33 5 0.07
34 2 0.03
35 22 0.30
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.46
Consensus pattern (30 bp):
TTTTCTTCTTTGTCCTCAAAAAGCAGGATG
Found at i:163337 original size:35 final size:35
Alignment explanation
Indices: 163289--163648 Score: 164
Period size: 35 Copynumber: 11.1 Consensus size: 35
163279 ATTTTTTTCC
*
163289 TTCTTTGTTCTCAAAGAGCAGGATGTTTTCTTCTT
1 TTCTTTGTCCTCAAAGAGCAGGATGTTTTCTTCTT
* *
163324 TTCTTTGTCCTCAAAAAGCATGATG---T-TT-TT
1 TTCTTTGTCCTCAAAGAGCAGGATGTTTTCTTCTT
* * * **
163354 TTCTTTGACCTCAAAGAGTAGAACATTTTCTTC--
1 TTCTTTGTCCTCAAAGAGCAGGATGTTTTCTTCTT
* * *
163387 -T-TTTGTCTTCAAAAAACAGGATGTTTT-TT-TT
1 TTCTTTGTCCTCAAAGAGCAGGATGTTTTCTTCTT
* ** * * * *
163418 TTCTTTTTCCTTTAAGGGCATGATATTTTTTTCTT
1 TTCTTTGTCCTCAAAGAGCAGGATGTTTTCTTCTT
* *
163453 TTCTTTGTCTTC-AA-AGTAGGA-----T-TTC-T
1 TTCTTTGTCCTCAAAGAGCAGGATGTTTTCTTCTT
* * ** *
163479 TTCTTTGTCTTCAAAAAGC-GAGACATTTTCTTCAT
1 TTCTTTGTCCTCAAAGAGCAG-GATGTTTTCTTCTT
* * * * *
163514 TTCTTTATCCTCAAGGAGTATGATG-TTT-TTCCT
1 TTCTTTGTCCTCAAAGAGCAGGATGTTTTCTTCTT
* *
163547 TTCTTTGTCCTCAAGGAGCAAGATGTTTTCTTC--
1 TTCTTTGTCCTCAAAGAGCAGGATGTTTTCTTCTT
* * ** *
163580 --CTTTGTCCTCTAAGAGCAAGACATTTTCTTCCT
1 TTCTTTGTCCTCAAAGAGCAGGATGTTTTCTTCTT
* *
163613 TTCCTTGTCCTCAAAGAGCATGATGTTTTCTT-TT
1 TTCTTTGTCCTCAAAGAGCAGGATGTTTTCTTCTT
163647 TT
1 TT
163649 ATTCCCAAAA
Statistics
Matches: 241, Mismatches: 56, Indels: 57
0.68 0.16 0.16
Matches are distributed among these distances:
26 13 0.05
27 6 0.02
28 5 0.02
30 22 0.09
31 47 0.20
32 3 0.01
33 49 0.20
34 18 0.07
35 78 0.32
ACGTcount: A:0.21, C:0.18, G:0.14, T:0.47
Consensus pattern (35 bp):
TTCTTTGTCCTCAAAGAGCAGGATGTTTTCTTCTT
Found at i:163550 original size:33 final size:33
Alignment explanation
Indices: 163513--163641 Score: 113
Period size: 33 Copynumber: 3.9 Consensus size: 33
163503 ATTTTCTTCA
* *
163513 TTTCTTTATCCTCAAGGAGTATGATGTTTTTCC
1 TTTCTTTATCCTCAAGGAGCAAGATGTTTTTCC
*
163546 TTTCTTTGTCCTCAAGGAGCAAGATG-TTTT-C
1 TTTCTTTATCCTCAAGGAGCAAGATGTTTTTCC
* *
163577 TTCCTTTGTCCTCTAA-GAGCAAGACAT-TTTCTTCC
1 TTTCTTTATCCTC-AAGGAGCAAG--ATGTTT-TTCC
* * * *
163612 TTTCCTTGTCCTCAAAGAGCATGATGTTTT
1 TTTCTTTATCCTCAAGGAGCAAGATGTTTT
163642 CTTTTTTATT
Statistics
Matches: 81, Mismatches: 7, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
31 20 0.25
32 6 0.07
33 30 0.37
34 7 0.09
35 18 0.22
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (33 bp):
TTTCTTTATCCTCAAGGAGCAAGATGTTTTTCC
Found at i:163587 original size:31 final size:31
Alignment explanation
Indices: 163516--163644 Score: 116
Period size: 31 Copynumber: 4.0 Consensus size: 31
163506 TTCTTCATTT
* * * *
163516 CTTTATCCTCAAGGAGTATGATGTTTTTCCTTT
1 CTTTGTCCTCAAGGAGCAAGATG-TTTT-CTTC
163549 CTTTGTCCTCAAGGAGCAAGATGTTTTCTTC
1 CTTTGTCCTCAAGGAGCAAGATGTTTTCTTC
**
163580 CTTTGTCCTCTAA-GAGCAAGACATTTTCTTC
1 CTTTGTCCTC-AAGGAGCAAGATGTTTTCTTC
* *
163611 CTTTCCTTGTCCTCAAAGAGCATGATGTTTTCTT
1 C--T--TTGTCCTCAAGGAGCAAGATGTTTTCTT
163645 TTTTATTCCC
Statistics
Matches: 81, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
31 30 0.37
32 6 0.07
33 21 0.26
34 2 0.02
35 22 0.27
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (31 bp):
CTTTGTCCTCAAGGAGCAAGATGTTTTCTTC
Found at i:168818 original size:39 final size:38
Alignment explanation
Indices: 168748--168822 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 38
168738 TTTCTTGTTC
*
168748 TTGTTCTTTTATTCCTCCTCTTCCTTCTCTCATTCTCT
1 TTGTTCTTTTATTCCTCCTCTTCATTCTCTCATTCTCT
* *
168786 TTGTTCTCTTTGTTCCTCTTCTT-ATTCTTCTCATTCT
1 TTGTTCT-TTTATTCCTCCTCTTCATTC-TCTCATTCT
168823 TTTCTTTCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 10 0.31
39 22 0.69
ACGTcount: A:0.05, C:0.31, G:0.04, T:0.60
Consensus pattern (38 bp):
TTGTTCTTTTATTCCTCCTCTTCATTCTCTCATTCTCT
Found at i:168839 original size:14 final size:15
Alignment explanation
Indices: 168804--168843 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
168794 TTTGTTCCTC
168804 TTCTTATTC-TTCTCA
1 TTCTT-TTCTTTCTCA
168819 TTCTTTTCTTTCTCA
1 TTCTTTTCTTTCTCA
168834 TT-TTTTCTTT
1 TTCTTTTCTTT
168844 TTACTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.07, C:0.23, G:0.00, T:0.70
Consensus pattern (15 bp):
TTCTTTTCTTTCTCA
Found at i:168906 original size:9 final size:9
Alignment explanation
Indices: 168894--168936 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
168884 CTTTCTCTTA
168894 TTTTTTTCT
1 TTTTTTTCT
*
168903 TTTTCTTCT
1 TTTTTTTCT
**
168912 TTTACTTCT
1 TTTTTTTCT
*
168921 TCTTTTTCT
1 TTTTTTTCT
168930 TTTTTTT
1 TTTTTTT
168937 TATTTATTTG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:170950 original size:15 final size:15
Alignment explanation
Indices: 170932--170961 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
170922 TATTAAAAAA
*
170932 TAAATATATTTATAT
1 TAAATATATATATAT
170947 TAAATATATATATAT
1 TAAATATATATATAT
170962 ATATATCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAATATATATATAT
Found at i:170951 original size:19 final size:19
Alignment explanation
Indices: 170929--170965 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
170919 AAATATTAAA
*
170929 AAATAAATATATTTATATT
1 AAATAAATATATATATATT
*
170948 AAATATATATATATATAT
1 AAATAAATATATATATAT
170966 ATCTTTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAATAAATATATATATATT
Found at i:172281 original size:16 final size:16
Alignment explanation
Indices: 172262--172328 Score: 64
Period size: 16 Copynumber: 4.2 Consensus size: 16
172252 AGTGTTGTTG
*
172262 TTTTTTATTTAAATTA
1 TTTTATATTTAAATTA
* *
172278 TTTTGA-GTTTAAATCA
1 TTTT-ATATTTAAATTA
*
172294 TTTTATATTTGAATTA
1 TTTTATATTTAAATTA
* *
172310 TTTTAAATTTAAATAA
1 TTTTATATTTAAATTA
172326 TTT
1 TTT
172329 AGATTTAATA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
15 1 0.03
16 39 0.98
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.60
Consensus pattern (16 bp):
TTTTATATTTAAATTA
Found at i:172309 original size:32 final size:32
Alignment explanation
Indices: 172262--172336 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 32
172252 AGTGTTGTTG
* * * *
172262 TTTTTTATTTAAATTATTTTGAGTTTAAATCA
1 TTTTATATTTAAATTATTTTAAATTTAAATAA
*
172294 TTTTATATTTGAATTATTTTAAATTTAAATAA
1 TTTTATATTTAAATTATTTTAAATTTAAATAA
*
172326 -TTTAGATTTAA
1 TTTTATATTTAA
172337 TATTCAGATT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 9 0.25
32 27 0.75
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.57
Consensus pattern (32 bp):
TTTTATATTTAAATTATTTTAAATTTAAATAA
Found at i:173189 original size:17 final size:16
Alignment explanation
Indices: 173140--173180 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
173130 TAGGTGATTG
**
173140 AATTATTTCAAGTTTA
1 AATTATTTTGAGTTTA
173156 AATTATTTTGAGTTTA
1 AATTATTTTGAGTTTA
173172 AATTATTTT
1 AATTATTTT
173181 TAGATTTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.56
Consensus pattern (16 bp):
AATTATTTTGAGTTTA
Found at i:173610 original size:2 final size:2
Alignment explanation
Indices: 173603--173635 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
173593 GCAGTGCAGG
*
173603 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
173636 CTGTGTGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Done.