Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007886.1 Hibiscus syriacus cultivar Beakdansim tig00110266_pilon, 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: 1254954
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:145955 original size:19 final size:19
Alignment explanation
Indices: 145940--146001 Score: 99
Period size: 19 Copynumber: 3.2 Consensus size: 19
145930 ATTAATAAAC
145940 ATAATAATAATAAATAATA
1 ATAATAATAATAAATAATA
145959 ATAATAATAATAAATAATA
1 ATAATAATAATAAATAATA
145978 ATAA-ATATATATAAATAATA
1 ATAATA-ATA-ATAAATAATA
145998 ATAA
1 ATAA
146002 AAAAAGACCC
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
18 1 0.02
19 26 0.63
20 14 0.34
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAATAATAATAAATAATA
Found at i:145957 original size:10 final size:10
Alignment explanation
Indices: 145942--146002 Score: 99
Period size: 10 Copynumber: 6.2 Consensus size: 10
145932 TAATAAACAT
145942 AATAATAATA
1 AATAATAATA
145952 AATAATAAT-
1 AATAATAATA
145961 AATAATAATA
1 AATAATAATA
145971 AATAATAATA
1 AATAATAATA
145981 AAT-ATATATA
1 AATAATA-ATA
145991 AATAATAATA
1 AATAATAATA
146001 AA
1 AA
146003 AAAAGACCCG
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
9 12 0.25
10 33 0.69
11 3 0.06
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AATAATAATA
Found at i:145959 original size:16 final size:16
Alignment explanation
Indices: 145940--146002 Score: 76
Period size: 16 Copynumber: 3.9 Consensus size: 16
145930 ATTAATAAAC
145940 ATAATAATAATAAATA
1 ATAATAATAATAAATA
145956 ATAATAATAAT-AATAA
1 ATAATAATAATAAAT-A
*
145972 ATAATAATAA-ATATA
1 ATAATAATAATAAATA
145987 TATAAATAATAATAAA
1 -AT-AATAATAATAAA
146003 AAAAGACCCG
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
15 4 0.10
16 26 0.65
17 8 0.20
18 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAATAATAATAAATA
Found at i:152681 original size:4 final size:4
Alignment explanation
Indices: 152672--152708 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
152662 GTGTTAATAT
152672 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG A
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG A
152709 CCCATCTCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.27, C:0.00, G:0.49, T:0.24
Consensus pattern (4 bp):
AGTG
Found at i:158179 original size:10 final size:10
Alignment explanation
Indices: 158149--158189 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
158139 TTTTTAAATG
158149 AAAAATATTT
1 AAAAATATTT
*
158159 AATAATA--T
1 AAAAATATTT
158167 AAAAATATTT
1 AAAAATATTT
158177 AAAAAT-TTT
1 AAAAATATTT
158186 AAAA
1 AAAA
158190 GATTTTATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
8 7 0.26
9 7 0.26
10 13 0.48
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
AAAAATATTT
Found at i:159182 original size:9 final size:9
Alignment explanation
Indices: 159168--159241 Score: 58
Period size: 9 Copynumber: 8.0 Consensus size: 9
159158 AATAAATATT
159168 AAAAAATAA
1 AAAAAATAA
*
159177 AAAAAATTA
1 AAAAAATAA
*
159186 AAGAAATAA
1 AAAAAATAA
*
159195 AGAAAAAGAA
1 A-AAAAATAA
*
159205 GAAAAATATA
1 AAAAAATA-A
* *
159215 TATAAATAA
1 AAAAAATAA
*
159224 AACAAATAA
1 AAAAAATAA
*
159233 ATAAAATAA
1 AAAAAATAA
159242 TAATAAAAAA
Statistics
Matches: 50, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
9 37 0.74
10 13 0.26
ACGTcount: A:0.77, C:0.01, G:0.05, T:0.16
Consensus pattern (9 bp):
AAAAAATAA
Found at i:159183 original size:19 final size:19
Alignment explanation
Indices: 159155--159201 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
159145 AAATAGTAAG
*
159155 TAAAATAAATATTAAA-AAA
1 TAAAA-AAAAATTAAAGAAA
159174 T-AAAAAAAATTAAAGAAA
1 TAAAAAAAAATTAAAGAAA
*
159192 TAAAGAAAAA
1 TAAAAAAAAA
159202 GAAGAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 9 0.38
18 7 0.29
19 8 0.33
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (19 bp):
TAAAAAAAAATTAAAGAAA
Found at i:159194 original size:18 final size:17
Alignment explanation
Indices: 159155--159201 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 17
159145 AAATAGTAAG
159155 TAAAATAAATATTAAAAAA
1 TAAAA-AAA-ATTAAAAAA
159174 TAAAAAAAATTAAAGAAA
1 TAAAAAAAATTAAA-AAA
159192 TAAAGAAAAA
1 TAAA-AAAAA
159202 GAAGAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.23
18 10 0.38
19 10 0.38
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (17 bp):
TAAAAAAAATTAAAAAA
Found at i:159240 original size:47 final size:49
Alignment explanation
Indices: 159171--159267 Score: 114
Period size: 47 Copynumber: 2.0 Consensus size: 49
159161 AAATATTAAA
*
159171 AAATAAAAAAAATTAAAGAAATAA-AGA-AAAAGAAG-AAAAAT-ATATAT
1 AAATAAAAAAAATTAAAAAAATAATA-ATAAAA-AAGTAAAAATAATATAT
*
159218 AAATAAAACAAA-TAAATAAAATAATAATAAAAAAGTAAAAATAATATAT
1 AAATAAAAAAAATTAAA-AAAATAATAATAAAAAAGTAAAAATAATATAT
159267 A
1 A
159268 TATATATAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
46 4 0.09
47 21 0.49
48 11 0.26
49 7 0.16
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.20
Consensus pattern (49 bp):
AAATAAAAAAAATTAAAAAAATAATAATAAAAAAGTAAAAATAATATAT
Found at i:159286 original size:51 final size:50
Alignment explanation
Indices: 159092--159286 Score: 125
Period size: 51 Copynumber: 3.8 Consensus size: 50
159082 TAATTAAATT
* * * * *
159092 AAAATGAAGAAAAA-ATAAATTAAATAAAA-GATAAGATAAAGAAAGTAAAG
1 AAAAAGAAGAAAAATATATA-TAAATAAAACAAAAAAATAAAGAAA-TAAAG
* *
159142 ATAAAATAGTAAGTAAAATAAATATTAAA-AAATA-AAAAAAATTAAAGAAATAAAG
1 --AAAA-AG-AAGAAAAATATATA-TAAATAAA-ACAAAAAAA-TAAAGAAATAAAG
*
159197 AAAAAGAAGAAAAATATATATAAATAAAACAAATAAATAAA-ATAATAATA-
1 AAAAAGAAGAAAAATATATATAAATAAAACAAAAAAATAAAGA-AATAA-AG
* * *
159247 AAAAAGTAA-AAATAATATATATATATATAATAAAAAAATA
1 AAAAAG-AAGAAA-AATATATATAAATAAAACAAAAAAATA
159287 GTAAAAATAT
Statistics
Matches: 118, Mismatches: 14, Indels: 23
0.76 0.09 0.15
Matches are distributed among these distances:
49 1 0.01
50 23 0.19
51 47 0.40
52 6 0.05
53 5 0.04
54 10 0.08
55 18 0.15
56 8 0.07
ACGTcount: A:0.71, C:0.01, G:0.07, T:0.21
Consensus pattern (50 bp):
AAAAAGAAGAAAAATATATATAAATAAAACAAAAAAATAAAGAAATAAAG
Found at i:159299 original size:34 final size:35
Alignment explanation
Indices: 159238--159375 Score: 126
Period size: 34 Copynumber: 3.8 Consensus size: 35
159228 AATAAATAAA
159238 ATAA-TAATAAAAAAGTAAAAATAATATATATATAT
1 ATAATTAATAAAAAAGTAAAAAT-ATATATATATAT
159273 ATAA-TAA-AAAAATAGTAAAAATATATATATATAT
1 ATAATTAATAAAAA-AGTAAAAATATATATATATAT
*
159307 A-AATTAATAAAACTGATAATAAAATAATATATATATATATGT
1 ATAATTAATAAAA---A-AGT-AAA-AATATATATATATA--T
159349 ATAATCTAA-AAAAAA-TAAAAATATATA
1 ATAAT-TAATAAAAAAGTAAAAATATATA
159376 CTAAAGTAAA
Statistics
Matches: 90, Mismatches: 1, Indels: 23
0.79 0.01 0.20
Matches are distributed among these distances:
33 2 0.02
34 21 0.23
35 20 0.22
36 8 0.09
37 3 0.03
38 5 0.06
39 4 0.04
40 15 0.17
42 2 0.02
43 7 0.08
44 3 0.03
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (35 bp):
ATAATTAATAAAAAAGTAAAAATATATATATATAT
Found at i:159337 original size:36 final size:35
Alignment explanation
Indices: 159236--159343 Score: 121
Period size: 36 Copynumber: 3.0 Consensus size: 35
159226 CAAATAAATA
*
159236 AAATAATAATAAAAA-AGTAAAAATAATATATATAT
1 AAATAATAA-AAAAATAATAAAAATAATATATATAT
* *
159271 ATATAATAAAAAAATAGTAAAAATATATATATATAT
1 AAATAATAAAAAAATAATAAAAATA-ATATATATAT
**
159307 AAATTAATAAAACTGATAAT-AAAATAATATATATAT
1 AAA-TAATAAAA-AAATAATAAAAATAATATATATAT
159343 A
1 A
159344 TATGTATAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
34 5 0.08
35 18 0.28
36 23 0.36
37 14 0.22
38 4 0.06
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (35 bp):
AAATAATAAAAAAATAATAAAAATAATATATATAT
Found at i:160570 original size:33 final size:34
Alignment explanation
Indices: 160499--160582 Score: 125
Period size: 35 Copynumber: 2.5 Consensus size: 34
160489 CGAGGGTTTC
* *
160499 GTGTTTCAAGAGAAATATTTTCAAAGGTTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGG-TTTTTTT
160534 GTGTTTCAAGAGAAACAATTTCAAAGG-TTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTT
*
160567 GTGTTTCAATAGAAAC
1 GTGTTTCAAGAGAAAC
160583 TGTATTCAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 21 0.46
35 25 0.54
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (34 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTT
Found at i:160649 original size:36 final size:36
Alignment explanation
Indices: 160600--160709 Score: 125
Period size: 36 Copynumber: 3.1 Consensus size: 36
160590 AAAGATTGAA
*
160600 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* *
160636 GTTTCAAGAGAAACTGTCTTAAGAGAGACAAAA--A
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* * * * * *
160670 CTTCCAAAAGAAACTGTCTCAAGGGAGACGAGATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
160706 GTTT
1 GTTT
160710 AACGTAAAAC
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
34 26 0.44
36 33 0.56
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.25
Consensus pattern (36 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:160682 original size:34 final size:35
Alignment explanation
Indices: 160609--160698 Score: 110
Period size: 34 Copynumber: 2.6 Consensus size: 35
160599 AGTTTCAAGG
** * *
160609 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAA-TACTTCCAAAA
*
160645 GAAACTGTCTTAAGAGAGACAAAA-ACTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAATACTTCCAAAA
*
160679 GAAACTGTCTCAAGGGAGAC
1 GAAACTGTCTCAAGAGAGAC
160699 GAGATTTGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
34 24 0.51
36 23 0.49
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (35 bp):
GAAACTGTCTCAAGAGAGACAAAATACTTCCAAAA
Found at i:160814 original size:36 final size:36
Alignment explanation
Indices: 160767--161054 Score: 126
Period size: 36 Copynumber: 8.3 Consensus size: 36
160757 AAGTTTATGC
* *
160767 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
* * * **
160803 TTCAAGGGAAACTATCTCATGAGTGACAAAATTCAT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
* * * *
160839 GTCAAGGGAAA-TGTTTTC-A-A-TG-----TTTATGT
1 TTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT-TGT
* *
160868 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGT
* * **
160905 TTCAAGGGAACCTATCTCAAGAGAGACAAAATTCAT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
* * * *
160941 CTCAAGGGAAA-TGTTTTC-A-A-TG-----TTTATGT
1 TTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT-TGT
* * *
160970 TTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGT
* ** * * *
161007 TCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
161043 TTCAAGGGAAAC
1 TTCAAGGGAAAC
161055 AGATTCAAAG
Statistics
Matches: 176, Mismatches: 52, Indels: 48
0.64 0.19 0.17
Matches are distributed among these distances:
28 4 0.02
29 26 0.15
30 5 0.03
31 1 0.01
32 2 0.01
33 3 0.02
34 2 0.01
35 3 0.02
36 69 0.39
37 57 0.32
38 4 0.02
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.27
Consensus pattern (36 bp):
TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
Found at i:160880 original size:101 final size:102
Alignment explanation
Indices: 160743--161084 Score: 429
Period size: 102 Copynumber: 3.4 Consensus size: 102
160733 TTGTTTTAAA
* *
160743 GGAAACTGTTTTCAAAGTTTATGCTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCA
1 GGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCA
* * *
160807 AGGGAAACTATCTCATGAGTGACAAAATTCATGTCAAG
65 AGGGAAACTATCTCAAGAGAGACAAAATTCATCTCAAG
160845 GGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAA
1 GGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAA
*
160910 GGGAACCTATCTCAAGAGAGACAAAATTCATCTCAAG
66 GGGAAACTATCTCAAGAGAGACAAAATTCATCTCAAG
* * * * *
160947 GGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAA
1 GGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAA
** * * * * ** *
161012 AAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAG
66 GGGAAACTATCTCAAGAGAGACAAAATTCATCTCAAG
* * *
161049 GGAAACAG-ATTCAAAGATTT-TGTTTCAAGAGAAACT
1 GGAAA-TGTTTTCAATG-TTTATGTTTCAAGAGAAACT
161085 TGGAAATTGT
Statistics
Matches: 213, Mismatches: 24, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
101 47 0.22
102 162 0.76
103 4 0.02
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (102 bp):
GGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAA
GGGAAACTATCTCAAGAGAGACAAAATTCATCTCAAG
Found at i:160923 original size:37 final size:37
Alignment explanation
Indices: 160865--160937 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
160855 TCAATGTTTA
* *
160865 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
* *
160902 TGTTTCAAGGGAACCTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
160938 CATCTCAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
Found at i:161419 original size:106 final size:106
Alignment explanation
Indices: 161232--161554 Score: 441
Period size: 106 Copynumber: 3.0 Consensus size: 106
161222 TGTATTGTTC
* * * **
161232 CGAGTCCAATATCCTCCGCCGTGAAGTTAAAATTGGCTCTGGAA-CTAAGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGGAATC-GGGAAATTGTTTGTTGAC
* * * *
161296 AGCCAGCCACCCCTTCGTTGTGAAGTTGAGCTTGTGCTGTCT
65 AACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
161338 CGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGGAATCGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACA
* * *
161403 ACCAGCCATCCATTCGTTGTGAATTTGAACTTGTATTGTCT
66 ACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * *
161444 CGAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACA
* *
161509 ACCAGCCGTCCCTTCGTTGTGGAGTTGAACTTGTGTTGTCT
66 ACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
161550 CGAGT
1 CGAGT
161555 GGCACGATAT
Statistics
Matches: 190, Mismatches: 26, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
106 189 0.99
107 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACA
ACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:162249 original size:32 final size:31
Alignment explanation
Indices: 162132--162250 Score: 132
Period size: 32 Copynumber: 3.7 Consensus size: 31
162122 TTTGCATCAG
* * *
162132 GATGTTGAATTCCCAAAGATGCCCCAATATTT
1 GATGTTGAA-TCTCAAAAATGCCCCAACATTT
162164 GATGTTGAATCTCAAAAAATG-CCCAACATTT
1 GATGTTGAATCTC-AAAAATGCCCCAACATTT
* **
162195 GATGTTAAATCAAAAATAATGCCCCAACATTT
1 GATGTTGAATCTCAAA-AATGCCCCAACATTT
*
162227 GATGTTGAATCTTCAAAGATGCCC
1 GATGTTGAATC-TCAAAAATGCCC
162251 TCATTGTTCC
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
30 3 0.04
31 26 0.36
32 41 0.56
33 3 0.04
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.29
Consensus pattern (31 bp):
GATGTTGAATCTCAAAAATGCCCCAACATTT
Found at i:163321 original size:13 final size:14
Alignment explanation
Indices: 163291--163328 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
163281 TTTTTCTTCA
163291 ATTTTC-CTTTGTT
1 ATTTTCTCTTTGTT
*
163304 TTTTTCTCTTT-TT
1 ATTTTCTCTTTGTT
163317 ATTTTCTCTTTG
1 ATTTTCTCTTTG
163329 CTTTTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.74
Consensus pattern (14 bp):
ATTTTCTCTTTGTT
Found at i:166414 original size:5 final size:5
Alignment explanation
Indices: 166388--166567 Score: 52
Period size: 5 Copynumber: 34.2 Consensus size: 5
166378 AAAATGTAAG
* * * *
166388 AAAT- AAATA AATTA AATTA AAATA AAATGA AGAA-A AAA-C AAATT AAATAA
1 AAATA AAATA AAATA AAATA AAATA AAAT-A A-AATA AAATA AAATA AAAT-A
* * * *
166438 AAGATA AGAT- AAAGA AAGTA AAGATA AAATA GTAAGTA AAATAA AAATA
1 AA-ATA AAATA AAATA AAATA AA-ATA AAATA --AAATA AAAT-A AAATA
* * *
166487 AAA-A AATAAA AAATA AAGA-A AAAGTA GAAAAA AATATA TAAATA AAA-C
1 AAATA AA-ATA AAATA AA-ATA AAA-TA -AAATA AA-ATA -AAATA AAATA
166535 AAAT- AAATA AAATA ATAATAA AAAGTA AAATA A
1 AAATA AAATA AAATA A-AAT-A AAA-TA AAATA A
166568 TATATATATA
Statistics
Matches: 135, Mismatches: 17, Indels: 47
0.68 0.09 0.24
Matches are distributed among these distances:
4 22 0.16
5 62 0.46
6 35 0.26
7 16 0.12
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:166453 original size:32 final size:32
Alignment explanation
Indices: 166385--166459 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
166375 ATAAAAATGT
* * *
166385 AAGAAATAAATAAATTAAATTAAAATAAAATG
1 AAGAAATAAACAAATTAAATAAAAATAAAATA
*
166417 AAGAAA-AAACAAATTAAATAAAAGATAAGATA
1 AAGAAATAAACAAATTAAATAAAA-ATAAAATA
166449 AAGAAAGTAAA
1 AAGAAA-TAAA
166460 GATAAAATAG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
31 15 0.42
32 18 0.50
34 3 0.08
ACGTcount: A:0.71, C:0.01, G:0.09, T:0.19
Consensus pattern (32 bp):
AAGAAATAAACAAATTAAATAAAAATAAAATA
Found at i:166493 original size:8 final size:8
Alignment explanation
Indices: 166480--166549 Score: 52
Period size: 8 Copynumber: 8.0 Consensus size: 8
166470 TAAGTAAAAT
166480 AAAAATAA
1 AAAAATAA
166488 AAAAAT-A
1 AAAAATAA
166495 AAAAATAAA
1 AAAAAT-AA
166504 GAAAAAGTAGAA
1 -AAAAA-T--AA
*
166516 AAAAATAT
1 AAAAATAA
*
166524 ATAAATAA
1 AAAAATAA
166532 AACAAATAA
1 AA-AAATAA
166541 ATAAAATAA
1 A-AAAATAA
166550 TAATAAAAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
7 7 0.14
8 14 0.28
9 14 0.28
10 7 0.14
11 6 0.12
12 2 0.04
ACGTcount: A:0.79, C:0.01, G:0.04, T:0.16
Consensus pattern (8 bp):
AAAAATAA
Found at i:166501 original size:21 final size:22
Alignment explanation
Indices: 166475--166557 Score: 64
Period size: 21 Copynumber: 3.7 Consensus size: 22
166465 AATAGTAAGT
166475 AAAATAAAAATAAAA-AAATAA
1 AAAATAAAAATAAAACAAATAA
*
166496 AAAATAAAGAA-AAAGTAGAAA-AA
1 AAAATAAA-AATAAA--ACAAATAA
* *
166519 AATATATAAATAAAACAAATAAA
1 AAAATAAAAATAAAACAAAT-AA
*
166542 TAAAATAATAATAAAA
1 -AAAATAAAAATAAAA
166558 AGTAAAATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
21 15 0.31
22 4 0.08
23 14 0.29
24 15 0.31
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.17
Consensus pattern (22 bp):
AAAATAAAAATAAAACAAATAA
Found at i:166539 original size:38 final size:37
Alignment explanation
Indices: 166471--166569 Score: 96
Period size: 37 Copynumber: 2.6 Consensus size: 37
166461 ATAAAATAGT
166471 AAGTAAAATAAAAATAAAAAAATAAAAAATAAAGAAA
1 AAGTAAAATAAAAATAAAAAAATAAAAAATAAAGAAA
* * * *
166508 AAGTAGAA-AAAAATATATAAATAAAACAAATAAA-TAA
1 AAGTAAAATAAAAATAAAAAAAT-AAA-AAATAAAGAAA
*
166545 AA-TAATAATAAAAAGTAAAATAATA
1 AAGTAA-AATAAAAA-TAAAAAAATA
166570 TATATATATA
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
36 14 0.29
37 16 0.33
38 13 0.27
39 6 0.12
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (37 bp):
AAGTAAAATAAAAATAAAAAAATAAAAAATAAAGAAA
Found at i:166544 original size:17 final size:16
Alignment explanation
Indices: 166482--166601 Score: 65
Period size: 15 Copynumber: 7.8 Consensus size: 16
166472 AGTAAAATAA
166482 AAATAAAAAAATAAA-
1 AAATAAAAAAATAAAT
* *
166497 AAATAAAGAAA-AAGT
1 AAATAAAAAAATAAAT
* *
166512 --AGAAAAAAATATAT
1 AAATAAAAAAATAAAT
166526 AAATAAAACAAATAAAT
1 AAATAAAA-AAATAAAT
* *
166543 AAA-ATAATAATAAA-
1 AAATAAAAAAATAAAT
* * *
166557 AAGTAAAATAATATAT
1 AAATAAAAAAATAAAT
* * *
166573 ATATATATATAATAAAT
1 AAATA-AAAAAATAAAT
166590 AAA-AAAAAAATA
1 AAATAAAAAAATA
166602 GTAAATATAT
Statistics
Matches: 77, Mismatches: 20, Indels: 16
0.68 0.18 0.14
Matches are distributed among these distances:
13 7 0.09
14 6 0.08
15 31 0.40
16 12 0.16
17 21 0.27
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.22
Consensus pattern (16 bp):
AAATAAAAAAATAAAT
Found at i:166549 original size:18 final size:17
Alignment explanation
Indices: 166388--166567 Score: 59
Period size: 20 Copynumber: 9.9 Consensus size: 17
166378 AAAATGTAAG
*
166388 AAATAAATAAATTAAATTA
1 AAATAAATAAAATAAA--A
166407 AAATAAAATGAAGAA-AAAA
1 AAAT-AAAT-AA-AATAAAA
*
166426 CAAATTAAATAAAAGATAAGAT
1 -AAA-TAAAT-AAA-ATAA-AA
*
166448 AAAGAAAGTAAAGATAAAA
1 AAATAAA-TAAA-ATAAAA
* * *
166467 TAGTAAGTAAAAT--AA
1 AAATAAATAAAATAAAA
166482 AAATAAA-AAAAT-AAA
1 AAATAAATAAAATAAAA
*
166497 AAATAAAGAAAAAGTAGAAA
1 AAATAAA-TAAAA-TA-AAA
*
166517 AAA-ATATATAAATAAAA
1 AAATAAATA-AAATAAAA
166534 CAAATAAATAAAATAATAA
1 -AAATAAATAAAATAA-AA
*
166553 TAAA-AAGTAAAATAA
1 -AAATAAATAAAATAA
166568 TATATATATA
Statistics
Matches: 125, Mismatches: 17, Indels: 39
0.69 0.09 0.22
Matches are distributed among these distances:
14 5 0.04
15 15 0.12
17 9 0.07
18 27 0.22
19 24 0.19
20 31 0.25
21 12 0.10
22 2 0.02
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.19
Consensus pattern (17 bp):
AAATAAATAAAATAAAA
Found at i:166560 original size:49 final size:50
Alignment explanation
Indices: 166476--166629 Score: 147
Period size: 49 Copynumber: 3.1 Consensus size: 50
166466 ATAGTAAGTA
* *
166476 AAATAAAAATAAAAAAATAAAAAATAAAGAAAAAGTAGAAA-AA-A-ATATAT
1 AAAT-AAAATAAATAAATAAAAAAT-AATAAAAAGTA-AAATAATATATATAT
*
166526 AAATAAAACAAATAAATAAAATAATAATAAAAAGTAAAATAATATATATAT
1 AAATAAAATAAATAAATAAAA-AATAATAAAAAGTAAAATAATATATATAT
* * * * * *
166577 ATATATAATAAATAAAAAAAAAATAGTAAATA-T-ATATATATATATATAT
1 AAATAAAATAAATAAATAAAAAATAATAAAAAGTAAAATA-ATATATATAT
166626 AAAT
1 AAAT
166630 TAATAAAATG
Statistics
Matches: 88, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
48 7 0.08
49 41 0.47
50 17 0.19
51 23 0.26
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (50 bp):
AAATAAAATAAATAAATAAAAAATAATAAAAAGTAAAATAATATATATAT
Found at i:166566 original size:12 final size:11
Alignment explanation
Indices: 166396--166567 Score: 53
Period size: 11 Copynumber: 16.0 Consensus size: 11
166386 AGAAATAAAT
* *
166396 AAATTAAATTA
1 AAATAAAATAA
*
166407 AAATAAAATGA
1 AAATAAAATAA
* *
166418 AGA-AAAA-AC
1 AAATAAAATAA
*
166427 AAATTAAATAA
1 AAATAAAATAA
*
166438 AAGATAAGAT--
1 AA-ATAAAATAA
* *
166448 AAAGAAAGTAA
1 AAATAAAATAA
* *
166459 AGATAAAATAGT
1 AAATAAAATA-A
*
166471 AAGTAAAATAA
1 AAATAAAATAA
166482 AAATAAAA-AA
1 AAATAAAATAA
166492 ATAA-AAAATAA
1 A-AATAAAATAA
*
166503 AGAA-AAAGTAGA
1 A-AATAAAATA-A
*
166515 AAA-AAATATAT
1 AAATAAA-ATAA
*
166526 AAAT-AAA-AC
1 AAATAAAATAA
166535 AAAT-AAAT-A
1 AAATAAAATAA
166544 AAATAATAATAA
1 AAATAA-AATAA
166556 AAAGTAAAATAA
1 AAA-TAAAATAA
166568 TATATATATA
Statistics
Matches: 118, Mismatches: 27, Indels: 31
0.67 0.15 0.18
Matches are distributed among these distances:
9 18 0.15
10 18 0.15
11 53 0.45
12 26 0.22
13 3 0.03
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.19
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:166569 original size:18 final size:17
Alignment explanation
Indices: 166452--166567 Score: 64
Period size: 18 Copynumber: 6.7 Consensus size: 17
166442 TAAGATAAAG
*
166452 AAAGTAAAGATAAAATAG
1 AAAGTAAA-ATAAAATAA
* *
166470 TAAGTAAAATAAAA-AT
1 AAAGTAAAATAAAATAA
166486 AAA--AAAATAAAA-AA
1 AAAGTAAAATAAAATAA
*
166500 TAAAGAAAAAGTAGAAA-AA
1 -AAAGTAAAA-TA-AAATAA
*
166519 AATA-TATAAATAAAACAA
1 AA-AGTA-AAATAAAATAA
*
166537 ATAAATAAAATAATAATAA
1 A-AAGTAAAATAA-AATAA
166556 AAAGTAAAATAA
1 AAAGTAAAATAA
166568 TATATATATA
Statistics
Matches: 80, Mismatches: 7, Indels: 22
0.73 0.06 0.20
Matches are distributed among these distances:
14 10 0.12
15 3 0.04
16 3 0.04
17 13 0.16
18 34 0.43
19 17 0.21
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.18
Consensus pattern (17 bp):
AAAGTAAAATAAAATAA
Found at i:166612 original size:41 final size:43
Alignment explanation
Indices: 166544--166685 Score: 159
Period size: 41 Copynumber: 3.4 Consensus size: 43
166534 CAAATAAATA
* *
166544 AAATAATAATAAAA-AGTAAAATAATATATATATATATATAAT
1 AAATAAAAAAAAAATAGTAAAATAATATATATATATATATAAT
166586 AAATAAAAAAAAAATAGT-AAAT-ATATATATATATATAT-AT
1 AAATAAAAAAAAAATAGTAAAATAATATATATATATATATAAT
* ** * *
166626 AAATTAATAAAATGATAATAAAATAATATATATATATATATATCT
1 AAA-TAAAAAAAAAATAGTAAAATAATATATATATATATATA-AT
*
166671 AAA-AAAATAAAAATA
1 AAATAAAAAAAAAATA
166686 TATACTAAAG
Statistics
Matches: 83, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
40 5 0.06
41 27 0.33
42 20 0.24
43 27 0.33
45 4 0.05
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (43 bp):
AAATAAAAAAAAAATAGTAAAATAATATATATATATATATAAT
Found at i:166654 original size:45 final size:42
Alignment explanation
Indices: 166544--166683 Score: 160
Period size: 45 Copynumber: 3.3 Consensus size: 42
166534 CAAATAAATA
*
166544 AAATAATAATAAAAAGTAAAATAATATATATATATATATA-AT
1 AAATAATAA-AAAAAATAAAATAATATATATATATATATATAT
**
166586 AAATAA-AAAAAAAATAGTA-AATATATATATATATATATAT
1 AAATAATAAAAAAAATAAAATAATATATATATATATATATAT
* *
166626 AAATTAATAAAATGATAATAAAATAATATATATATATATATATCT
1 AAA-TAATAAAA--AAAATAAAATAATATATATATATATATATAT
*
166671 AAAAAAATAAAAA
1 -AAATAATAAAAA
166684 TATATACTAA
Statistics
Matches: 83, Mismatches: 8, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
39 18 0.22
40 13 0.16
41 5 0.06
42 10 0.12
43 1 0.01
44 6 0.07
45 27 0.33
46 3 0.04
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (42 bp):
AAATAATAAAAAAAATAAAATAATATATATATATATATATAT
Found at i:168115 original size:11 final size:11
Alignment explanation
Indices: 168101--168137 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
168091 TTTTTAAATT
168101 TTTTAATAATG
1 TTTTAATAATG
168112 TTTTAAT--T-
1 TTTTAATAATG
168120 TTTTAATAATG
1 TTTTAATAATG
168131 TTTTAAT
1 TTTTAAT
168138 TTTTAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 7 0.30
9 1 0.04
10 1 0.04
11 14 0.61
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (11 bp):
TTTTAATAATG
Found at i:168143 original size:18 final size:19
Alignment explanation
Indices: 168092--168141 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
168082 ATGCATGTTT
168092 TTTTAAATTTTTTAATAATG
1 TTTT-AATTTTTTAATAATG
168112 TTTTAATTTTTTAATAATG
1 TTTTAATTTTTTAATAATG
168131 TTTTAATTTTT
1 TTTTAATTTTT
168142 AAAAAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 26 0.87
20 4 0.13
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (19 bp):
TTTTAATTTTTTAATAATG
Found at i:168365 original size:33 final size:33
Alignment explanation
Indices: 168323--168390 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
168313 GATATTAAGC
*
168323 CTTTTAATAATCAT-AAGACTCAACAAAGTAACA
1 CTTTTAATAATC-TGAAGACTCAACAAAGCAACA
*
168356 CTTTTAATAATCTGAAGACTCAATAAAGCAACA
1 CTTTTAATAATCTGAAGACTCAACAAAGCAACA
168389 CT
1 CT
168391 ATAATGTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 1 0.03
33 31 0.97
ACGTcount: A:0.46, C:0.19, G:0.07, T:0.28
Consensus pattern (33 bp):
CTTTTAATAATCTGAAGACTCAACAAAGCAACA
Found at i:169410 original size:16 final size:17
Alignment explanation
Indices: 169391--169423 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
169381 AATAAATTTG
169391 AAAT-AAAAATTAAATA
1 AAATAAAAAATTAAATA
169407 AAATAAAAAATTAAATA
1 AAATAAAAAATTAAATA
169424 TTGAAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAAAATTAAATA
Found at i:169476 original size:2 final size:2
Alignment explanation
Indices: 169469--169511 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
169459 CAAATAAGAA
* *
169469 AT AT AT AT AT AT GT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
169511 A
1 A
169512 AATAAAAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:171173 original size:84 final size:84
Alignment explanation
Indices: 171067--171854 Score: 769
Period size: 84 Copynumber: 9.5 Consensus size: 84
171057 AAAGTCTTTA
* *
171067 GCAGATAACCCTTCTCTACTTAAGTTATGATGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGA
171132 ACTCGAAGGTCTTTGGTTG
66 ACTCGAAGGTCTTTGGTTG
* *
171151 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGA
* * *
171216 ACTCAAAAGTCTTTTGTTG
66 ACTCGAAGGTCTTTGGTTG
* * * * * * * *
171235 ACAGATAACCC-TCATAGCCTTGAGTTATGCTGTAAATGATGTGTCCTCGAAGCTGAGTGTAATC
1 GCAGATAACCCTTC-TCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGTGTAGTC
*
171299 GAACTCGAGGGTC--T--TTG
64 GAACTCGAAGGTCTTTGGTTG
* * * * * **
171316 GCAGATAACCCTTCTCGACTTAAGCTGTGCTGTAAATGATGTGTCTTGAAGCTGAGCATAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGA
*
171381 ACTCGAAGGCCTTTGGTTG
66 ACTCGAAGGTCTTTGGTTG
* * *
171400 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATAATATGCCTTGGAGCTGAGCGTAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGA
*
171465 ACTCGAAGGTCTTTTGTTG
66 ACTCGAAGGTCTTTGGTTG
* * * * * * * ** * * * * *
171484 ACAGATAACCTTTTTAGCCTTGAGTAATGCTATAAATGATGTACCCTCGAAACTGAGTGTAATCG
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT-GCCTTGGAGCTGAGTGTAGTCG
*
171549 AACTCGAGGGTC--T--TTG
65 AACTCGAAGGTCTTTGGTTG
* * * * *
171565 GCAGATATCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTAGAGCTGAGCGTAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGA
* *
171630 ACTCAAAGGCCTTTTGG-TG
66 ACTCGAAGGTC-TTTGGTTG
* * * * * * * * * *
171649 ACAAATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGTGTAGTCG
*
171714 AACTCTTCG-AGAG-C-CT--TTG
65 AA--C-TCGAAG-GTCTTTGGTTG
* ** * * *
171733 GCAGATAGCTATTCTCGACTTAAGCTATGCTGCAAATGATGTACCTTGGAGCTGAGTATAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGA
171798 ACTCGAAGGTCTTTGGTTG
66 ACTCGAAGGTCTTTGGTTG
* *
171817 ACAGATAACCCTTCTCGACTTAAGTTATGCAGCAAATG
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
171855 TTTAAAAAAT
Statistics
Matches: 561, Mismatches: 119, Indels: 48
0.77 0.16 0.07
Matches are distributed among these distances:
80 54 0.10
81 76 0.14
82 4 0.01
83 24 0.04
84 324 0.58
85 72 0.13
87 4 0.01
88 3 0.01
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (84 bp):
GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGA
ACTCGAAGGTCTTTGGTTG
Found at i:171355 original size:165 final size:164
Alignment explanation
Indices: 171068--171854 Score: 613
Period size: 165 Copynumber: 4.7 Consensus size: 164
171058 AAGTCTTTAG
** *
171068 CAGATAACCCTTCTCTACTTAAGTTATGATGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAA
*
171133 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTT
66 CTCGAAGGTC--T--TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTT
* * * *
171198 GGAGCTGAGCGTAGTCGAACTCAAAAGTCTTTTGTTGA
127 GAAGCTGAGCATAGTCGAACTCAAAAGCCTTTGGTTGA
* * * * * *
171236 CAGATAACCC-TCATAGCCTTGAGTTATGCTGTAAATGATGTGTCCTCGAAGCTGAGTGTAATCG
1 CAGATAACCCTTC-TAGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGTGTAGTCG
* * * * *
171300 AACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTGTGCTGTAAATGATGTGTCTTGA
64 AACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGA
* * *
171365 AGCTGAGCATAGTCGAACTCGAAGGCCTTTGGTTGG
129 AGCTGAGCATAGTCGAACTCAAAAGCCTTTGGTTGA
* * * *
171401 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATAATATGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAA
* * * * * ** * *
171466 CTCGAAGGTCTTTTGTTGACAGATAACCTTTTTAGCCTTGAG-TAATGCTATAAATGATGTACCC
66 CTCGAAGGTC-TTTG--G-CAGATAACCCTTCTCGACTTAAGCT-ATGCTGCAAATGATAT-GCC
* * ** * * ** *
171530 TCGAAACTGAGTGTAATCGAACTCGAGGGTCTTT-G--G-
125 TTGAAGCTGAGCATAGTCGAACTCAAAAGCCTTTGGTTGA
* * * * * *
171566 CAGATATCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAA
* * * * * * * * * *
171631 CTCAAAGGCCTTTTGGTGACAAATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCT
66 CTCGAAGGTC-TTT-G-G-CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATG-CCT
* ** * * *
171696 CGAAGCTGAGTGTAATCGAACTCTTCGAGAGCCTTT-G--G-
126 TGAAGCTGAGCATAGTCGAA--C-TCAAAAGCCTTTGGTTGA
* ** * * * *
171734 CAGATAGCTATTCTCGACTTAAGCTATGCTGCAAATGATGTACCTTGGAGCTGAGTATAGTCGAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAA
* *
171799 CTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCAGCAAATG
66 CTCGAAGGTCTTT-G--G-CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
171855 TTTAAAAAAT
Statistics
Matches: 520, Mismatches: 83, Indels: 32
0.82 0.13 0.05
Matches are distributed among these distances:
164 28 0.05
165 243 0.47
166 5 0.01
167 11 0.02
168 176 0.34
169 57 0.11
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (164 bp):
CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAA
CTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGAAG
CTGAGCATAGTCGAACTCAAAAGCCTTTGGTTGA
Found at i:171483 original size:249 final size:248
Alignment explanation
Indices: 171001--171718 Score: 965
Period size: 249 Copynumber: 2.9 Consensus size: 248
170991 AGCCCTTCTT
* * * * * **
171001 GCCTTGAGCTATGCTGTAAGATTGATTTGCCTCTG-AGTTGAATATAATCGAACTCGAAAGTCTT
1 GCCTTGAGTTATGCTGTAA-A-TGATGTGCCTC-GAAGCTGAGTGTAATCGAACTCGAGGGTCTT
* * * * * * *
171065 TAGCAGATAACCCTTCTCTACTTAAGTTATGATGCAAATGATGTGCCTTGGAGCTGAGTGTAGTC
63 TGGCAGATAACCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTGAAGCTGAGCGTAGTC
*
171130 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGC
128 GAACTCGAAGGCCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGC
171195 CTTGGAGCTGAGCGTAGTCGAACTCAAAAGTCTTTTGTTGACAGATAACCCTCATA
193 CTTGGAGCTGAGCGTAGTCGAACTCAAAAGTCTTTTGTTGACAGATAACCCTCATA
171251 GCCTTGAGTTATGCTGTAAATGATGTGTCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTG
1 GCCTTGAGTTATGCTGTAAATGATGTG-CCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTG
* * *
171316 GCAGATAACCCTTCTCGACTTAAGCTGTGCTGTAAATGATGTGTCTTGAAGCTGAGCATAGTCGA
65 GCAGATAACCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTGAAGCTGAGCGTAGTCGA
*
171381 ACTCGAAGGCCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATAATATGCCT
130 ACTCGAAGGCCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCT
* * * **
171446 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGACAGATAACCTTTTTA
195 TGGAGCTGAGCGTAGTCGAACTCAAAAGTCTTTTGTTGACAGATAACCCTCATA
* * * *
171500 GCCTTGAGTAATGCTATAAATGATGTACCCTCGAAACTGAGTGTAATCGAACTCGAGGGTCTTTG
1 GCCTTGAGTTATGCTGTAAATGATGT-GCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTG
*
171565 GCAGATATCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTT-AGAGCTGAGCGTAGTCG
65 GCAGATAACCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTGA-AGCTGAGCGTAGTCG
* * * * * * * * *
171629 AACTCAAAGGCCTTTTGG-TGACAAATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGC
129 AACTCGAAGGCC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG-
* * * *
171693 CCTCGAAGCTGAGTGTAATCGAACTC
192 CCTTGGAGCTGAGCGTAGTCGAACTC
171719 TTCGAGAGCC
Statistics
Matches: 416, Mismatches: 46, Indels: 12
0.88 0.10 0.03
Matches are distributed among these distances:
248 8 0.02
249 363 0.87
250 45 0.11
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (248 bp):
GCCTTGAGTTATGCTGTAAATGATGTGCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
CAGATAACCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAA
CTCGAAGGCCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTT
GGAGCTGAGCGTAGTCGAACTCAAAAGTCTTTTGTTGACAGATAACCCTCATA
Found at i:171772 original size:249 final size:243
Alignment explanation
Indices: 170996--171846 Score: 938
Period size: 249 Copynumber: 3.4 Consensus size: 243
170986 TAGATAGCCC
* * * * * * *
170996 TTCTTGCCTTGAGCTATGCTGTAAGATTGATTTGCCTCTG-AGTTGAATATAATCGAACTCGAAA
1 TTCTAGCCTTGAG-TATGCTGTAA-A-TGATGTACCTC-GAAGCTGAGTGTAATCGAACTCGAAG
* * * * * *
171060 GTCTTTAGCAGATAACCCTTCTCTACTTAAGTTATGATGCAAATGATGTGCCTTGGAGCTGAGTG
62 GTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTT-GAGCTGAGCG
*
171125 TAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
126 TAGTCGAACTCGAAGGCCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
* *
171190 TATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAAGTCTTTTGTTGACAGATAACC
191 TATGCCTTGGAGCTGAGCGTAGTCGAACTC-GAAGTCTTTTG-TGACAGATAACT
* * *
171245 CTCATAGCCTTGAGTTATGCTGTAAATGATGTGTCCTCGAAGCTGAGTGTAATCGAACTCGAGGG
1 TTC-TAGCCTTGAG-TATGCTGTAAATGATGT-ACCTCGAAGCTGAGTGTAATCGAACTCGAAGG
* * *
171310 TCTTTGGCAGATAACCCTTCTCGACTTAAGCTGTGCTGTAAATGATGTGTCTTGAAGCTGAGCAT
63 TCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTG-AGCTGAGCGT
*
171375 AGTCGAACTCGAAGGCCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATAAT
127 AGTCGAACTCGAAGGCCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
171440 ATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGACAGATAACCT
192 ATGCCTTGGAGCTGAGCGTAGTCGAACTCGAA-GTCTTTTG-TGACAGATAA-CT
* * * *
171495 TTTTAGCCTTGAGTAATGCTATAAATGATGTACCCTCGAAACTGAGTGTAATCGAACTCGAGGGT
1 TTCTAGCCTTGAGT-ATGCTGTAAATGATGTA-CCTCGAAGCTGAGTGTAATCGAACTCGAAGGT
*
171560 CTTTGGCAGATATCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTAGAGCTGAGCGTA
64 CTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTT-GAGCTGAGCGTA
* * * * * * * *
171625 GTCGAACTCAAAGGCCTTTTGG-TGACAAATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGAT
128 GTCGAACTCGAAGGCC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
* * * * * * *
171689 GTGCCCTCGAAGCTGAGTGTAATCGAACTCTTCGAGAG-CCTTTG-G-CAGATAGCT
192 ATG-CCTTGGAGCTGAGCGTAGTCGAA--C-TCGA-AGTCTTTTGTGACAGATAACT
* * * * * * * *
171743 ATTCTCGACTTAAGCTATGCTGCAAATGATGTACCTTGGAGCTGAGTATAGTCGAACTCGAAGGT
1 -TTCTAGCCTTGAG-TATGCTGTAAATGATGTACCTCGAAGCTGAGTGTAATCGAACTCGAAGGT
*
171808 CTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGC
64 CTTT-G--G-CAGATAACCCTTCTCGACTTAAGCTATGC
171847 AGCAAATGTT
Statistics
Matches: 519, Mismatches: 62, Indels: 39
0.84 0.10 0.06
Matches are distributed among these distances:
248 42 0.08
249 389 0.75
250 48 0.09
251 1 0.00
252 33 0.06
253 5 0.01
254 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (243 bp):
TTCTAGCCTTGAGTATGCTGTAAATGATGTACCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCT
TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTGAGCTGAGCGTAGTC
GAACTCGAAGGCCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGC
CTTGGAGCTGAGCGTAGTCGAACTCGAAGTCTTTTGTGACAGATAACT
Found at i:175847 original size:23 final size:23
Alignment explanation
Indices: 175821--175864 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
175811 ATAATAAATC
*
175821 AAAAAAGAAAGAGGAAAAATAAA
1 AAAAAAGAAAAAGGAAAAATAAA
175844 AAAAAAGAAAAAGGAAAAATA
1 AAAAAAGAAAAAGGAAAAATA
175865 TGAGATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.05
Consensus pattern (23 bp):
AAAAAAGAAAAAGGAAAAATAAA
Found at i:178706 original size:18 final size:18
Alignment explanation
Indices: 178678--178732 Score: 62
Period size: 16 Copynumber: 3.2 Consensus size: 18
178668 TTGTGATTAG
178678 TTTTTTATTGTTTATTTGA
1 TTTTTT-TTGTTTATTTGA
178697 TTTTTTTTG-TT-TTTGA
1 TTTTTTTTGTTTATTTGA
**
178713 TTAATTTT-TTTATTTGA
1 TTTTTTTTGTTTATTTGA
178730 TTT
1 TTT
178733 GAAATAGGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 13 0.42
17 9 0.29
18 3 0.10
19 6 0.19
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (18 bp):
TTTTTTTTGTTTATTTGA
Found at i:179431 original size:131 final size:131
Alignment explanation
Indices: 179191--179454 Score: 347
Period size: 131 Copynumber: 2.0 Consensus size: 131
179181 ATCAAATCTG
* * * *
179191 AAAAGAGATCTGCTATGCTACTTTTCAGGGTAAATCAATCTGGAAACTTTGATTCACTTCACTAC
1 AAAAGAGATATGCTATGCTACTCTTCAGGGTAAATCAATCTAGAAACGTTGATTCACTTCACTAC
* *
179256 TCTTCAGGGAAGATTGAATCGAGGTAGATTTTCTTCACATCTCTTTAGAAAATATCAAATCTAAA
66 TCTTCAGAGAAGATTGAATCGAGGTAGATTTGCTTCACATCTCTTTAGAAAATATCAAATCTAAA
179321 A
131 A
* * *
179322 AAAAG-GATATGCTCTGTTACTCTTCAGGGTAGATCAAATCTAGAAACGTTGATTCGA-TTCACT
1 AAAAGAGATATGCTATGCTACTCTTCAGGGTAAATC-AATCTAGAAACGTTGATTC-ACTTCACT
* * * *
179385 ATTCTTCTGAGAAGATTGAATCGAGGTTA-ATTTGCTTCAC-TGCTCTTTATAGAATATCAAATC
64 ACTCTTCAGAGAAGATTGAATCGAGG-TAGATTTGCTTCACAT-CTCTTTAGAAAATATCAAATC
179448 TAAAA
127 TAAAA
179453 AA
1 AA
179455 GGGATTTGTT
Statistics
Matches: 116, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
130 26 0.22
131 87 0.75
132 3 0.03
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (131 bp):
AAAAGAGATATGCTATGCTACTCTTCAGGGTAAATCAATCTAGAAACGTTGATTCACTTCACTAC
TCTTCAGAGAAGATTGAATCGAGGTAGATTTGCTTCACATCTCTTTAGAAAATATCAAATCTAAA
A
Found at i:180568 original size:45 final size:45
Alignment explanation
Indices: 180506--181359 Score: 894
Period size: 45 Copynumber: 19.0 Consensus size: 45
180496 ATTTAAGTTG
* *
180506 AGAATGACATCACTAAAAGGTTGACTCCTCTTC-CTGAGAAAGTTA
1 AGAATGACATCACTAAAAGATTGACTCCTCTTCAC-GAGAAAGTCA
* *
180551 AGAATGACATCATTAAAAGGTTGACTCCTCTTCACGAGAAAGTCA
1 AGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
* * *
180596 AGAATCACATCACTAAAAGGTTAACTCCTCTT-AGCGAGAAAGTCA
1 AGAATGACATCACTAAAAGATTGACTCCTCTTCA-CGAGAAAGTCA
* * * * *
180641 AGAATGACATAACTATAACATTGACTCATCTTCGCGAGAAAGTCA
1 AGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
* * *
180686 AGAATGACATCACTAAAAGGTTGTCTCCTCTTCACGAAAAAGTCA
1 AGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
* * * *
180731 ATAATGACAACACTAAAGGATCT-ACTCCTCTTCATGAGAAAGTCA
1 AGAATGACATCACTAAAAGAT-TGACTCCTCTTCACGAGAAAGTCA
* * * ** *
180776 AGAATGACAACACCAAAAGATTAACTTATCTTCACGATAAAGTCA
1 AGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
* * * *
180821 AGAATAACATCAATAAAAGGTTGACTCCTCTT-TCGAGAAAGTCA
1 AGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
* * * * * * *
180865 ATAAGGACAACACTAAATGATTGACTCATATTCGCGAGAAAGTCA
1 AGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
* * **
180910 AGAAAGACAACACTAAAAGATTGACTCCTCTTTGCGAGAAAGTCA
1 AGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
* * * * * *
180955 AGAATAACATCACTAAAAGGTTGAGTTCTCTTCATGAGAAACTCA
1 AGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
* * * *
181000 AGAATCACATCACTAAAATATTGACTCCTCTTCATGAGAAATTCA
1 AGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
* * * **
181045 AGAAGGACAACACTAAAAGATCGACTCCTCTTCGTGAGAAAGTCA
1 AGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
* * * * *
181090 AGAAGGATAAT-ACTAAAATATTGACTCCTCTTCGCGAAAAAGTCA
1 AGAATGA-CATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
*
181135 AGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
1 AGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
* * * *
181180 AAAATGACAACACT-AAAGATTGACTCCTCTTCACAAGAAAGTTA
1 AGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
* * * *
181224 AGAAGGACAACACTAAAAG-TTGACTCATGTTCACGAGAAAGTCA
1 AGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
* * * * * *
181268 AGAATGACAACATTAAAAGATTTACTCTTCTTCACAAGAAATTCA
1 AGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
* * * ** *
181313 ATAATGACATCACTAAAAGTTTGAATTTTCTTCACGAAAAAGTCA
1 AGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
181358 AG
1 AG
181360 TTGAGGTTTC
Statistics
Matches: 676, Mismatches: 123, Indels: 20
0.83 0.15 0.02
Matches are distributed among these distances:
44 114 0.17
45 559 0.83
46 3 0.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (45 bp):
AGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
Found at i:181596 original size:19 final size:20
Alignment explanation
Indices: 181564--181601 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
181554 AAAATTTATC
181564 ATGTATGTATGAAATGATGA
1 ATGTATGTATGAAATGATGA
181584 ATGTATG-ATGAAATGATG
1 ATGTATGTATGAAATGATG
181602 CAAATTCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.26, T:0.34
Consensus pattern (20 bp):
ATGTATGTATGAAATGATGA
Found at i:182852 original size:3 final size:3
Alignment explanation
Indices: 182844--182869 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
182834 TTTGTTCTCT
182844 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
182870 TTTTCTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:182881 original size:1 final size:1
Alignment explanation
Indices: 182877--183061 Score: 127
Period size: 1 Copynumber: 185.0 Consensus size: 1
182867 CTTTTTTCTC
* * * * * * * * * *
182877 TTTTTATTTTATTTTATTTTATTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * *
182942 TTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * *
183007 ATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
183062 CTATCTTTTA
Statistics
Matches: 130, Mismatches: 54, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 130 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (1 bp):
T
Found at i:183074 original size:7 final size:7
Alignment explanation
Indices: 182883--183072 Score: 337
Period size: 7 Copynumber: 26.9 Consensus size: 7
182873 TCTCTTTTTA
182883 TTTTATT
1 TTTTATT
182890 TTATT-TT
1 TT-TTATT
182897 ATTTTATT
1 -TTTTATT
182905 TTTTATT
1 TTTTATT
182912 TTTTATT
1 TTTTATT
182919 TTTTATT
1 TTTTATT
182926 TTTTATT
1 TTTTATT
182933 TTTTATT
1 TTTTATT
182940 TTTTATT
1 TTTTATT
182947 TTTTATT
1 TTTTATT
182954 TTTTATT
1 TTTTATT
182961 TTTTATT
1 TTTTATT
182968 TTTTATT
1 TTTTATT
182975 TTTTATT
1 TTTTATT
182982 TTTTATT
1 TTTTATT
182989 TTTTATT
1 TTTTATT
182996 TTTTATT
1 TTTTATT
183003 TTTTATT
1 TTTTATT
183010 TTTTATT
1 TTTTATT
183017 TTTTATT
1 TTTTATT
183024 TTTTATT
1 TTTTATT
183031 TTTTATT
1 TTTTATT
183038 TTTTATT
1 TTTTATT
183045 TTTTATT
1 TTTTATT
183052 TTTTATT
1 TTTTATT
*
183059 TTTCTATC
1 TTT-TATT
183067 TTTTAT
1 TTTTAT
183073 CTCTCTTTTT
Statistics
Matches: 178, Mismatches: 1, Indels: 8
0.95 0.01 0.04
Matches are distributed among these distances:
7 166 0.93
8 12 0.07
ACGTcount: A:0.15, C:0.01, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTATT
Found at i:186897 original size:17 final size:17
Alignment explanation
Indices: 186861--186893 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
186851 AAAACATGAA
186861 ATACGACAAATAATATT
1 ATACGACAAATAATATT
186878 ATAC-ACAAATAATATT
1 ATACGACAAATAATATT
186894 TATAACATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (17 bp):
ATACGACAAATAATATT
Found at i:187003 original size:2 final size:2
Alignment explanation
Indices: 186996--187045 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
186986 AACACTTAAC
186996 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
187038 AT AT AT AT
1 AT AT AT AT
187046 GAAGGAAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:188087 original size:18 final size:18
Alignment explanation
Indices: 188064--188098 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
188054 TATTAGTTTT
*
188064 TTTATTGTTTTTTTATTA
1 TTTATTGATTTTTTATTA
188082 TTTATTGATTTTTTATT
1 TTTATTGATTTTTTATT
188099 TGATTTTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (18 bp):
TTTATTGATTTTTTATTA
Found at i:188509 original size:31 final size:31
Alignment explanation
Indices: 188469--188535 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
188459 TGTAATACAA
*
188469 TCCCCCAACATTTAGTCTATTTGCAATATAG
1 TCCCCCAACATTTAGTCCATTTGCAATATAG
* *
188500 TCCCTCAACATTTAGTCCATTTGCAATATGG
1 TCCCCCAACATTTAGTCCATTTGCAATATAG
188531 TCCCC
1 TCCCC
188536 GACGTAACTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.30, G:0.10, T:0.34
Consensus pattern (31 bp):
TCCCCCAACATTTAGTCCATTTGCAATATAG
Found at i:189971 original size:31 final size:30
Alignment explanation
Indices: 189920--189996 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 30
189910 TCCCCAACTC
*
189920 TTGCAATATAATCCCCAACATTTAGTCCGT
1 TTGCAATATAGTCCCCAACATTTAGTCCGT
* *
189950 TTGTAATATAGTCCCTCAACATTTAGTCTGT
1 TTGCAATATAGTCCC-CAACATTTAGTCCGT
*
189981 TTGCAATATGGTCCCC
1 TTGCAATATAGTCCCC
189997 GACGTAATAG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
30 14 0.34
31 27 0.66
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (30 bp):
TTGCAATATAGTCCCCAACATTTAGTCCGT
Found at i:190144 original size:22 final size:23
Alignment explanation
Indices: 190116--190162 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
190106 CATTACTATA
190116 CTTTACCC-T-AAATAGAAAGATG
1 CTTTACCCATAAAATA-AAAGATG
190138 CTTTACCCAATAAAATAAAAGATG
1 CTTTACCC-ATAAAATAAAAGATG
190162 C
1 C
190163 ATATGAGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
24 9 0.41
25 5 0.23
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (23 bp):
CTTTACCCATAAAATAAAAGATG
Found at i:195368 original size:2 final size:2
Alignment explanation
Indices: 195361--195485 Score: 205
Period size: 2 Copynumber: 62.5 Consensus size: 2
195351 TAGACAACAT
* *
195361 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TG 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
* * *
195403 TA TA CA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
195445 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
195486 TGTGTCTTAG
Statistics
Matches: 113, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 113 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:197154 original size:20 final size:16
Alignment explanation
Indices: 197107--197147 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
197097 TTTAACAAGG
197107 AATATATTATTTTCGA
1 AATATATTATTTTCGA
197123 AATATATTATTTTCGA
1 AATATATTATTTTCGA
*
197139 AAAATATTA
1 AATATATTA
197148 ATTATTTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (16 bp):
AATATATTATTTTCGA
Found at i:200950 original size:3 final size:3
Alignment explanation
Indices: 200942--200972 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
200932 TTAATCCGAG
200942 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
200973 ATATTATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:201415 original size:21 final size:20
Alignment explanation
Indices: 201391--201488 Score: 70
Period size: 21 Copynumber: 4.7 Consensus size: 20
201381 AAATGTTAAG
*
201391 ACCTTTCGATGAAAGGACTTA
1 ACCTTTTGATGAAAGGA-TTA
* * *
201412 ACCTTTTGATTAAAAGATTTC
1 ACCTTTTGATGAAAGGA-TTA
*
201433 TCCTTTTGATGAAAGGGATTA
1 ACCTTTTGATGAAA-GGATTA
* *
201454 ACCTTTTTTATAAAAGGATTTA
1 ACC-TTTTGATGAAAGGA-TTA
* *
201476 ATCTTTTCATGAA
1 ACCTTTTGATGAA
201489 GAGAATTGTT
Statistics
Matches: 59, Mismatches: 15, Indels: 6
0.74 0.19 0.08
Matches are distributed among these distances:
21 43 0.73
22 16 0.27
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (20 bp):
ACCTTTTGATGAAAGGATTA
Found at i:201468 original size:42 final size:43
Alignment explanation
Indices: 201392--201474 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 43
201382 AATGTTAAGA
201392 CCTTTCGATGAAAGGACTTAACCTTTTGATTAAAA-GATTTCT
1 CCTTTCGATGAAAGGACTTAACCTTTTGATTAAAAGGATTTCT
* *
201434 CCTTTTGATGAAAGGGA-TTAACCTTTT-TTATAAAAGGATTT
1 CCTTTCGATGAAA-GGACTTAACCTTTTGAT-TAAAAGGATTT
201475 AATCTTTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
41 1 0.03
42 27 0.75
43 8 0.22
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (43 bp):
CCTTTCGATGAAAGGACTTAACCTTTTGATTAAAAGGATTTCT
Found at i:204249 original size:36 final size:36
Alignment explanation
Indices: 204209--204280 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
204199 AAATACGAAA
204209 CTTTTCCTTGTGTTGGAATTCGCATGAATACCTCGG
1 CTTTTCCTTGTGTTGGAATTCGCATGAATACCTCGG
204245 CTTTTCCTTGTGTTGGAATTCGCATGAATACCTCGG
1 CTTTTCCTTGTGTTGGAATTCGCATGAATACCTCGG
204281 ATTAAATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (36 bp):
CTTTTCCTTGTGTTGGAATTCGCATGAATACCTCGG
Found at i:204798 original size:21 final size:21
Alignment explanation
Indices: 204774--204828 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
204764 TCAATGAAAG
204774 GACTTAACCTTTTGATTAAAA
1 GACTTAACCTTTTGATTAAAA
** *
204795 GACTTCTCCTTTTGATTAAAG
1 GACTTAACCTTTTGATTAAAA
* *
204816 GGCTTAATCTTTT
1 GACTTAACCTTTT
204829 CATGTAAAGA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (21 bp):
GACTTAACCTTTTGATTAAAA
Found at i:205184 original size:31 final size:31
Alignment explanation
Indices: 205149--205210 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
205139 TATAAAATTA
205149 TGAGTCGAGTAGAATAAAAAAATCAATTTTT
1 TGAGTCGAGTAGAATAAAAAAATCAATTTTT
* * * *
205180 TGAGTCGAGTCGAGTAAAAAATTCAGTTTTT
1 TGAGTCGAGTAGAATAAAAAAATCAATTTTT
205211 CGACTCGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.34
Consensus pattern (31 bp):
TGAGTCGAGTAGAATAAAAAAATCAATTTTT
Found at i:206275 original size:22 final size:22
Alignment explanation
Indices: 206250--206299 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
206240 TTAATGGAAC
206250 CATTCAGCGTTGAATGTTGAAT
1 CATTCAGCGTTGAATGTTGAAT
206272 CATTCAGCGTTGAATGTTGAAT
1 CATTCAGCGTTGAATGTTGAAT
206294 CATTCA
1 CATTCA
206300 ACGCGTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (22 bp):
CATTCAGCGTTGAATGTTGAAT
Found at i:215948 original size:5 final size:5
Alignment explanation
Indices: 215940--215972 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
215930 AAGATATACT
215940 ATATA ATATA ATATA ATATA ATATA ATATA ATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATA
215973 GTTTAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:217227 original size:45 final size:45
Alignment explanation
Indices: 217177--217375 Score: 285
Period size: 45 Copynumber: 4.4 Consensus size: 45
217167 TATAAAATCT
* * *
217177 CTTACCATTTATCCCATAAGCTCGTAAGGTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
217222 CTTACCA-TTATTCCATAAGCTAGTAAGCTTATTTTATCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
217266 CTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTGTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT-TACCAATATA
*
217312 CTTACCATTTATTCCATAAGCACGTAAGCTTATTTTACCAATACT-
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATA-TA
**
217357 CTTGTCATTTATTCCATAA
1 CTTACCATTTATTCCATAA
217376 CCATATACCA
Statistics
Matches: 139, Mismatches: 12, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
44 39 0.28
45 57 0.41
46 43 0.31
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:217366 original size:91 final size:89
Alignment explanation
Indices: 217177--217375 Score: 285
Period size: 91 Copynumber: 2.2 Consensus size: 89
217167 TATAAAATCT
* *
217177 CTTACCATTTATCCCATAAGCTCGTAAGGTTATTTTACCAAAATACTTACCATTATTCCATAAGC
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTATTCCATAAGC
*
217242 TAGTAAGCTTATTTTATCAATATA
66 TAGTAAGCTTATTTTACCAATATA
* *
217266 CTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTGTACCAATATACTTACCATTTATTCCATAA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT-TACCAAAATACTTACCA-TTATTCCATAA
217331 GC-ACGTAAGCTTATTTTACCAATACT-
64 GCTA-GTAAGCTTATTTTACCAATA-TA
**
217357 CTTGTCATTTATTCCATAA
1 CTTACCATTTATTCCATAA
217376 CCATATACCA
Statistics
Matches: 98, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
89 32 0.33
90 17 0.17
91 48 0.49
92 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (89 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTATTCCATAAGC
TAGTAAGCTTATTTTACCAATATA
Found at i:217408 original size:20 final size:22
Alignment explanation
Indices: 217385--217427 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
217375 ACCATATACC
217385 ATAGACAATAG-CC-ATAAACA
1 ATAGACAATAGCCCAATAAACA
217405 ATAGACAATAGCCCAATAAACA
1 ATAGACAATAGCCCAATAAACA
217427 A
1 A
217428 CCCTGAGGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.52
21 2 0.10
22 8 0.38
ACGTcount: A:0.56, C:0.21, G:0.09, T:0.14
Consensus pattern (22 bp):
ATAGACAATAGCCCAATAAACA
Found at i:239852 original size:18 final size:18
Alignment explanation
Indices: 239829--239863 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
239819 ACTATTGCGA
239829 TCATTATGAATATCACCC
1 TCATTATGAATATCACCC
*
239847 TCATTATGGATATCACC
1 TCATTATGAATATCACC
239864 TTTGTGCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (18 bp):
TCATTATGAATATCACCC
Found at i:247113 original size:3 final size:3
Alignment explanation
Indices: 247100--247175 Score: 55
Period size: 3 Copynumber: 23.3 Consensus size: 3
247090 TTTGTTTAGT
* *
247100 ATA ATTA ATA ATA ATA ATG ATAA ACA ATA ATA ACTA ATA ATA ATA AGTA
1 ATA A-TA ATA ATA ATA ATA AT-A ATA ATA ATA A-TA ATA ATA ATA A-TA
*
247149 A-A AGTT ATA ATTA ATA ATA ATTA ATA A
1 ATA A-TA ATA A-TA ATA ATA A-TA ATA A
247176 ACGACAAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
2 2 0.03
3 40 0.68
4 17 0.29
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:247132 original size:29 final size:26
Alignment explanation
Indices: 247100--247169 Score: 86
Period size: 26 Copynumber: 2.6 Consensus size: 26
247090 TTTGTTTAGT
247100 ATAATTAATAATAATAATGATAAACAATA
1 ATAATTAATAATAATAA-G-TAAA-AATA
* * *
247129 ATAACTAATAATAATAAGTAAAAGTT
1 ATAATTAATAATAATAAGTAAAAATA
247155 ATAATTAATAATAAT
1 ATAATTAATAATAAT
247170 TAATAAACGA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 16 0.43
27 4 0.11
28 1 0.03
29 16 0.43
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (26 bp):
ATAATTAATAATAATAAGTAAAAATA
Found at i:247170 original size:10 final size:10
Alignment explanation
Indices: 247100--247175 Score: 56
Period size: 10 Copynumber: 8.1 Consensus size: 10
247090 TTTGTTTAGT
247100 ATAATTAATA
1 ATAATTAATA
*
247110 ATAA-TAATG
1 ATAATTAATA
**
247119 ATAAACAATA
1 ATAATTAATA
*
247129 ATAACTAATA
1 ATAATTAATA
247139 ATAA-TAAGTA
1 ATAATTAA-TA
*
247149 A-AAGT--T-
1 ATAATTAATA
247155 ATAATTAATA
1 ATAATTAATA
247165 ATAATTAATA
1 ATAATTAATA
247175 A
1 A
247176 ACGACAAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
6 1 0.02
7 4 0.08
9 14 0.26
10 34 0.64
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.33
Consensus pattern (10 bp):
ATAATTAATA
Found at i:249575 original size:16 final size:17
Alignment explanation
Indices: 249550--249583 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
249540 TCGAGGTGTC
249550 ACATTAACTTTT-CAAA
1 ACATTAACTTTTACAAA
*
249566 ACATTTACTTTTACAAA
1 ACATTAACTTTTACAAA
249583 A
1 A
249584 TAATTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (17 bp):
ACATTAACTTTTACAAA
Found at i:250253 original size:23 final size:22
Alignment explanation
Indices: 250190--250256 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
250180 GTGCCATATA
* *
250190 AATTGTCCCGAAAGACCCCGTAG
1 AATTGTCCCG-AAGACCACATAG
* *
250213 GATTGTCTCGAAGACCACATAG
1 AATTGTCCCGAAGACCACATAG
*
250235 AATTGTCCCTAAGGACCACATA
1 AATTGTCCCGAA-GACCACATA
250257 TATGTTCCAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 19 0.53
23 17 0.47
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (22 bp):
AATTGTCCCGAAGACCACATAG
Found at i:250278 original size:21 final size:21
Alignment explanation
Indices: 250245--250337 Score: 91
Period size: 21 Copynumber: 4.4 Consensus size: 21
250235 AATTGTCCCT
250245 AAGGACCACATATATGTTCCA
1 AAGGACCACATATATGTTCCA
* * * *
250266 AATGACCAAATATATATGT-CG
1 AAGGACCACATATATGT-TCCA
*
250287 AAGGACCTCATATATGTTCCA
1 AAGGACCACATATATGTTCCA
* *
250308 AAGGATCACATATATG-TCTCG
1 AAGGACCACATATATGTTC-CA
250329 AAGGACCAC
1 AAGGACCAC
250338 GTAGAACCCT
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
20 3 0.05
21 52 0.93
22 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.25
Consensus pattern (21 bp):
AAGGACCACATATATGTTCCA
Found at i:250292 original size:42 final size:42
Alignment explanation
Indices: 250245--250337 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
250235 AATTGTCCCT
* *
250245 AAGGACCACATATATGTTCCAAATGACCAAATATATATGTCG
1 AAGGACCACATATATGTTCCAAAGGACCAAATATATATCTCG
* * * *
250287 AAGGACCTCATATATGTTCCAAAGGATCACATATATGTCTCG
1 AAGGACCACATATATGTTCCAAAGGACCAAATATATATCTCG
250329 AAGGACCAC
1 AAGGACCAC
250338 GTAGAACCCT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.25
Consensus pattern (42 bp):
AAGGACCACATATATGTTCCAAAGGACCAAATATATATCTCG
Found at i:256192 original size:33 final size:33
Alignment explanation
Indices: 256150--256217 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
256140 CTAGCAAGCA
*
256150 TTTCATCTCGC-CCGTAACTCCCCTCGGTCAGAG
1 TTTCATCTCGCGCCGCAACT-CCCTCGGTCAGAG
* *
256183 TTTCATCTCGCGCCGCAACTTCCTTGGTCAGAG
1 TTTCATCTCGCGCCGCAACTCCCTCGGTCAGAG
256216 TT
1 TT
256218 CCCTTGCGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.15, C:0.35, G:0.19, T:0.31
Consensus pattern (33 bp):
TTTCATCTCGCGCCGCAACTCCCTCGGTCAGAG
Found at i:258826 original size:24 final size:25
Alignment explanation
Indices: 258784--258830 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
258774 CACCGAAGTT
258784 CCGCGTAGAAATTTATCCCGAAGAA
1 CCGCGTAGAAATTTATCCCGAAGAA
*
258809 CCGCGTAG-AATTTGTCCCGAAG
1 CCGCGTAGAAATTTATCCCGAAG
258831 GACCATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (25 bp):
CCGCGTAGAAATTTATCCCGAAGAA
Found at i:259077 original size:31 final size:30
Alignment explanation
Indices: 259023--259093 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 30
259013 ACATAATTCA
* *
259023 TATCGCATAGACATATCATTTCCATACCTT
1 TATCACATAAACATATCATTTCCATACCTT
*
259053 TATCACATAAACATTTCATTTTCCATACCTT
1 TATCACATAAACATATCA-TTTCCATACCTT
259084 TATCACATAA
1 TATCACATAA
259094 TTCATATAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 15 0.41
31 22 0.59
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (30 bp):
TATCACATAAACATATCATTTCCATACCTT
Found at i:259527 original size:21 final size:21
Alignment explanation
Indices: 259503--259545 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
259493 TCATATTCGT
* *
259503 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
259524 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
259545 T
1 T
259546 AGCCCAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:260012 original size:3 final size:3
Alignment explanation
Indices: 260004--260106 Score: 197
Period size: 3 Copynumber: 34.0 Consensus size: 3
259994 CTTCACGGTT
260004 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
260052 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
260100 GAGA GAA
1 GA-A GAA
260107 ATATCTGGAA
Statistics
Matches: 99, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 96 0.97
4 3 0.03
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:262603 original size:63 final size:64
Alignment explanation
Indices: 262468--262623 Score: 165
Period size: 64 Copynumber: 2.4 Consensus size: 64
262458 TTCGAGGTGT
* * * * **
262468 ATCGATGCACATGAAGTGCATCGATGCACTCTTTTAAAATACAAACATCGAATGTCATCAATGC
1 ATCGATGCATAAGGAGTGCATCGATGCACCCCCTTAAAATACAAACATCGAATGTCATCAATGC
* * **
262532 ATCGATGCATAAGGAGTGCATCGATGCACCCCCTT-AAATATAAACATCGAATAG-GATTTATGC
1 ATCGATGCATAAGGAGTGCATCGATGCACCCCCTTAAAATACAAACATCGAAT-GTCATCAATGC
*
262595 ATCGATGCAT-GGTGTAGTGCATCGATGCA
1 ATCGATGCATAAG-G-AGTGCATCGATGCA
262624 TACCTTCATT
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
62 1 0.01
63 33 0.42
64 44 0.56
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (64 bp):
ATCGATGCATAAGGAGTGCATCGATGCACCCCCTTAAAATACAAACATCGAATGTCATCAATGC
Found at i:263301 original size:23 final size:23
Alignment explanation
Indices: 263248--263308 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
263238 CAATCTTATA
* *
263248 TGGCACTACAGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
263271 CGGCACTTCGGTGTAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
263294 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
263309 TTTATATGAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:268212 original size:50 final size:50
Alignment explanation
Indices: 268137--268236 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
268127 GAACAAGTAG
268137 AAGTTCAACCTGATTTGACCTATGAAGAGGAACCAATACAAATTTTGGCT
1 AAGTTCAACCTGATTTGACCTATGAAGAGGAACCAATACAAATTTTGGCT
268187 AAGTTCAACCTGATTTGACCTATGAAGAGGAACCAATACAAATTTTGGCT
1 AAGTTCAACCTGATTTGACCTATGAAGAGGAACCAATACAAATTTTGGCT
268237 CACGAAGTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (50 bp):
AAGTTCAACCTGATTTGACCTATGAAGAGGAACCAATACAAATTTTGGCT
Found at i:270002 original size:23 final size:23
Alignment explanation
Indices: 269958--270002 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
269948 AATCTTATAT
*
269958 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
269981 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
270003 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:274402 original size:22 final size:22
Alignment explanation
Indices: 274377--274418 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
274367 TCGGTCGAAG
274377 TCAACAGTATGACCGATCAAAT
1 TCAACAGTATGACCGATCAAAT
* * *
274399 TCAACGGTCTGACCGGTCAA
1 TCAACAGTATGACCGATCAA
274419 CGATCAATGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (22 bp):
TCAACAGTATGACCGATCAAAT
Found at i:276592 original size:2 final size:2
Alignment explanation
Indices: 276585--276644 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
276575 CCTTCAGGAC
276585 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
276627 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
276645 CATTTGGAAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:279711 original size:22 final size:22
Alignment explanation
Indices: 279677--279718 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
279667 TCGGTCGAAG
279677 TCAACAGTATGACCGATCAAAT
1 TCAACAGTATGACCGATCAAAT
* * *
279699 TCAACGGTCTGACCGGTCAA
1 TCAACAGTATGACCGATCAA
279719 CGATTAATGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (22 bp):
TCAACAGTATGACCGATCAAAT
Found at i:297385 original size:22 final size:22
Alignment explanation
Indices: 297360--297401 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
297350 TTTTAGTATT
*
297360 GGATT-AAATGGTAATTATGGAA
1 GGATTGAAAGGGTAA-TATGGAA
297382 GGATTGAAAGGGTAATATGG
1 GGATTGAAAGGGTAATATGG
297402 TAATTTAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.33, T:0.29
Consensus pattern (22 bp):
GGATTGAAAGGGTAATATGGAA
Found at i:298108 original size:55 final size:55
Alignment explanation
Indices: 298017--298141 Score: 205
Period size: 55 Copynumber: 2.3 Consensus size: 55
298007 AAATGTTCAA
298017 AGTGTATCGATACCCTCAAAATATCGAATGCCATTTGTGTATCGGTACACTGAGG
1 AGTGTATCGATACCCTCAAAATATCGAATGCCATTTGTGTATCGGTACACTGAGG
* * * *
298072 AGTGTATCGATACCCTCAAAATATCGAGTGCTATTTGTGTATTGGTACACTGGGG
1 AGTGTATCGATACCCTCAAAATATCGAATGCCATTTGTGTATCGGTACACTGAGG
*
298127 AGTGCATCGATACCC
1 AGTGTATCGATACCC
298142 CCAAGTATGA
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 65 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (55 bp):
AGTGTATCGATACCCTCAAAATATCGAATGCCATTTGTGTATCGGTACACTGAGG
Found at i:298990 original size:18 final size:18
Alignment explanation
Indices: 298943--298991 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
298933 GTGTTCTATA
*
298943 TGGTCCTTCGAGACATAG
1 TGGTCCTTCGGGACATAG
298961 TGGTCCTTCGGGACATAG
1 TGGTCCTTCGGGACATAG
*
298979 TGGTCCTACGGGA
1 TGGTCCTTCGGGA
298992 AAAATTCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.18, C:0.22, G:0.33, T:0.27
Consensus pattern (18 bp):
TGGTCCTTCGGGACATAG
Found at i:301148 original size:22 final size:22
Alignment explanation
Indices: 301101--301173 Score: 103
Period size: 22 Copynumber: 3.3 Consensus size: 22
301091 TCAAGGATTC
301101 TATGTGGTCCTTCGGGACAAAAT
1 TATGTGGTCCTTCGGGAC-AAAT
301124 TATGTGGTCCTTCGGGACAAAT
1 TATGTGGTCCTTCGGGACAAAT
* *
301146 TATGTGGTACTTTGGTG-CAAAT
1 TATGTGGTCCTTCGG-GACAAAT
301168 TATGTG
1 TATGTG
301174 AGTTGTGGTG
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
22 28 0.60
23 19 0.40
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (22 bp):
TATGTGGTCCTTCGGGACAAAT
Found at i:304116 original size:2 final size:2
Alignment explanation
Indices: 304109--304151 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
304099 TCTTGTAGTT
* *
304109 TA TA TA TA TA TA TA TA TA TG TA TG 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
304151 T
1 T
304152 GAACAATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:316260 original size:20 final size:20
Alignment explanation
Indices: 316224--316274 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
316214 TTTCAATTCG
* *
316224 AGTCAACCTTTATATTTTCA
1 AGTCAACCATTAGATTTTCA
*
316244 AGTCGACCATTAGATTTTCA
1 AGTCAACCATTAGATTTTCA
*
316264 TGTCAACCATT
1 AGTCAACCATT
316275 TCTGTTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (20 bp):
AGTCAACCATTAGATTTTCA
Found at i:330104 original size:2 final size:2
Alignment explanation
Indices: 330097--330139 Score: 59
Period size: 2 Copynumber: 20.0 Consensus size: 2
330087 ATCTATTATG
330097 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AGT AGT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT A-T A-T AT AT AT
330140 CTGTTTTGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 32 0.82
3 7 0.18
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (2 bp):
AT
Found at i:339589 original size:2 final size:2
Alignment explanation
Indices: 339577--339615 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
339567 TCTTTTCTTT
339577 TA TA T- 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
339616 ATTTATATGG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:344619 original size:2 final size:2
Alignment explanation
Indices: 344612--344642 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
344602 AAACATGTGA
*
344612 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
344643 AAACAAGGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:345647 original size:21 final size:22
Alignment explanation
Indices: 345621--345680 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
345611 TCCTTAAAGA
*
345621 GTGGTCCTTCGGGACA-TCTAT
1 GTGGTCCTTCGGGACATTCTAC
*
345642 GTGGTCCTTCGAGACATTTCTAC
1 GTGGTCCTTCGGGACA-TTCTAC
*
345665 GTTGTCCTTCGGGACA
1 GTGGTCCTTCGGGACA
345681 AATTCTATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 15 0.45
23 18 0.55
ACGTcount: A:0.15, C:0.25, G:0.27, T:0.33
Consensus pattern (22 bp):
GTGGTCCTTCGGGACATTCTAC
Found at i:350569 original size:2 final size:2
Alignment explanation
Indices: 350562--350593 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
350552 GTCTTTTGGA
350562 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
350594 GTGTGATCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:350640 original size:21 final size:21
Alignment explanation
Indices: 350611--350668 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
350601 CCTTAAGGAC
* *
350611 TGGTTCTTCGAGACATCTATA
1 TGGTCCTTCGAGACATATATA
* * *
350632 TGGTCCTTCGGGATATATATG
1 TGGTCCTTCGAGACATATATA
350653 TGGTCCTTCGAGACAT
1 TGGTCCTTCGAGACAT
350669 TTCTACGCGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (21 bp):
TGGTCCTTCGAGACATATATA
Found at i:354725 original size:13 final size:13
Alignment explanation
Indices: 354707--354749 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
354697 TAAATGAATA
354707 AATTAATAGATTT
1 AATTAATAGATTT
* *
354720 AATTAA-ACA-TA
1 AATTAATAGATTT
354731 AATTAATAGATTT
1 AATTAATAGATTT
354744 AATTAA
1 AATTAA
354750 ACATAAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 7 0.29
12 4 0.17
13 13 0.54
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (13 bp):
AATTAATAGATTT
Found at i:354782 original size:24 final size:24
Alignment explanation
Indices: 354704--354777 Score: 125
Period size: 24 Copynumber: 3.2 Consensus size: 24
354694 ATATAAATGA
354704 ATAAATTAATAGATTTAATTAAAC
1 ATAAATTAATAGATTTAATTAAAC
354728 ATAAATTAATAGATTTAATTAAAC
1 ATAAATTAATAGATTTAATTAAAC
*
354752 ATAAATTAATAG-TGTAATTAAA-
1 ATAAATTAATAGATTTAATTAAAC
354774 ATAA
1 ATAA
354778 TAATTTATCA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
22 4 0.08
23 9 0.18
24 36 0.73
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.36
Consensus pattern (24 bp):
ATAAATTAATAGATTTAATTAAAC
Found at i:365612 original size:23 final size:23
Alignment explanation
Indices: 365586--365654 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
365576 CACCACAGCT
*
365586 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
365609 CGTAGAATTGCACC-AGAGTGCCG
1 CGTAGAATTGCACCGA-AGTGCCA
*
365632 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
365655 TATAATAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.03
23 39 0.98
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:366749 original size:20 final size:20
Alignment explanation
Indices: 366724--366769 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
366714 CTCTTTATAA
366724 ACATCTATTTCTATTTCCCT
1 ACATCTATTTCTATTTCCCT
*
366744 ATATCTATTTCTATTTCCCT
1 ACATCTATTTCTATTTCCCT
366764 ACATCT
1 ACATCT
366770 CTCGACTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.28, G:0.00, T:0.50
Consensus pattern (20 bp):
ACATCTATTTCTATTTCCCT
Found at i:370745 original size:3 final size:3
Alignment explanation
Indices: 370737--370785 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
370727 TCGCATTGGG
370737 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
370784 TA
1 TA
370786 CCTGGAATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:377382 original size:35 final size:31
Alignment explanation
Indices: 377325--377409 Score: 89
Period size: 35 Copynumber: 2.5 Consensus size: 31
377315 ACTTATATAC
*
377325 AATATATAAGTTTTAAAACATTTTGGAAATTATGT
1 AATATAT-AGTTTTAAAACATTTT-GAAA--ATAT
*
377360 AATATATAGTTTTGAAATCATTTTGAAAATAT
1 AATATATAGTTTT-AAAACATTTTGAAAATAT
*
377392 AATATATATTTTTTAAAA
1 AATATATA-GTTTTAAAA
377410 AAAACATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
32 14 0.32
33 4 0.09
34 10 0.23
35 16 0.36
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (31 bp):
AATATATAGTTTTAAAACATTTTGAAAATAT
Found at i:377483 original size:76 final size:71
Alignment explanation
Indices: 377339--377522 Score: 173
Period size: 71 Copynumber: 2.5 Consensus size: 71
377329 TATAAGTTTT
* * *
377339 AAAACATTTTGGAAATTATGTAATATATAGTTTTGAAATCATTTTGAAAATATAATATATATTTT
1 AAAACATTTTGGAAATTATATAATATATAGTTTTCAAAACATTTTGAAAATATAATATATATTTT
377404 TTAAAA
66 TTAAAA
*
377410 AAAACATTTTGGGAAAATTTATATAATATATCGTTTTAACAAAACATTTTGGAAAACT-T-ATAT
1 AAAACATTTT-GG-AAA-TTATATAATATATAGTTTT--CAAAACATTTT-GAAAA-TATAATAT
377473 A-ATATTTTT---A
59 ATAT-TTTTTAAAA
* * * *
377483 AAATCATTTTTGAAAACTATATAATATATAGTTTTGAAAA
1 AAAACA-TTTTGGAAATTATATAATATATAGTTTTCAAAA
377523 TGTTTTTATA
Statistics
Matches: 95, Mismatches: 9, Indels: 20
0.77 0.07 0.16
Matches are distributed among these distances:
69 4 0.04
71 27 0.28
72 5 0.05
73 10 0.11
74 21 0.22
75 2 0.02
76 19 0.20
77 6 0.06
78 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (71 bp):
AAAACATTTTGGAAATTATATAATATATAGTTTTCAAAACATTTTGAAAATATAATATATATTTT
TTAAAA
Found at i:377612 original size:5 final size:5
Alignment explanation
Indices: 377601--377638 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
377591 TATTATTAAT
* *
377601 ATTT- ATTTT ATTTC ATTTT ATTTC ATTTC ATTTC ATTT
1 ATTTC ATTTC ATTTC ATTTC ATTTC ATTTC ATTTC ATTT
377639 TATTAACTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (5 bp):
ATTTC
Found at i:377618 original size:10 final size:10
Alignment explanation
Indices: 377600--377642 Score: 70
Period size: 10 Copynumber: 4.4 Consensus size: 10
377590 TTATTATTAA
377600 TATTT-ATTT
1 TATTTCATTT
377609 TATTTCATTT
1 TATTTCATTT
377619 TATTTCATTT
1 TATTTCATTT
*
377629 CATTTCATTT
1 TATTTCATTT
377639 TATT
1 TATT
377643 AACTTAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
9 5 0.16
10 26 0.84
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (10 bp):
TATTTCATTT
Found at i:377620 original size:15 final size:15
Alignment explanation
Indices: 377602--377642 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
377592 ATTATTAATA
377602 TTTATTTTATTTCAT
1 TTTATTTTATTTCAT
*
377617 TTTATTTCATTTCAT
1 TTTATTTTATTTCAT
*
377632 TTCATTTTATT
1 TTTATTTTATT
377643 AACTTAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTATTTTATTTCAT
Found at i:378833 original size:8 final size:8
Alignment explanation
Indices: 378822--378876 Score: 53
Period size: 8 Copynumber: 7.0 Consensus size: 8
378812 AAATTTAACC
378822 TTTTATTA
1 TTTTATTA
378830 TTTTATTA
1 TTTTATTA
*
378838 TTTCT-TTC
1 TTT-TATTA
*
378846 TTTCATTA
1 TTTTATTA
378854 TTATTATTA
1 TT-TTATTA
378863 TTTT-TTA
1 TTTTATTA
378870 -TTTATTA
1 TTTTATTA
378877 GCATTTTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
6 3 0.08
7 6 0.15
8 22 0.56
9 8 0.21
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTATTA
Found at i:383012 original size:24 final size:24
Alignment explanation
Indices: 382985--383033 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
382975 AGAAAATAAC
382985 AAAATGAAGTAAAAA-AACAAAAATA
1 AAAAT-AA-TAAAAATAACAAAAATA
*
383010 AAAATCATAAAAATAACAAAAATA
1 AAAATAATAAAAATAACAAAAATA
383034 TATATGTAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 6 0.27
24 11 0.50
25 5 0.23
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.14
Consensus pattern (24 bp):
AAAATAATAAAAATAACAAAAATA
Found at i:386199 original size:2 final size:2
Alignment explanation
Indices: 386192--386219 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
386182 AAGTTACTTA
386192 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
386220 CATCTAGAAT
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:388024 original size:15 final size:15
Alignment explanation
Indices: 387993--388040 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
387983 ATCTGTTCCT
*
387993 AATAACACATATCCG
1 AATAACATATATCCG
388008 AATAACATATA-CTCG
1 AATAACATATATC-CG
* *
388023 AATATCATATATCTG
1 AATAACATATATCCG
388038 AAT
1 AAT
388041 TCCGATCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 1 0.04
15 26 0.93
16 1 0.04
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.29
Consensus pattern (15 bp):
AATAACATATATCCG
Found at i:390788 original size:30 final size:31
Alignment explanation
Indices: 390725--390790 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
390715 TTGGTCCCTA
*
390725 TACTATTTAACATTGGTTGGTTAAGCTCTTG
1 TACTATTTAACATTGGTTGGTCAAGCTCTTG
* *
390756 TACTATTTGACCTTGG-TGGTCAAG-TCCTTG
1 TACTATTTAACATTGGTTGGTCAAGCT-CTTG
390786 TACTA
1 TACTA
390791 GTTGGCGCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 1 0.03
30 16 0.52
31 14 0.45
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.42
Consensus pattern (31 bp):
TACTATTTAACATTGGTTGGTCAAGCTCTTG
Found at i:391153 original size:25 final size:24
Alignment explanation
Indices: 391116--391172 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
391106 GAAGTTTTGG
391116 AAATGCTTTATGAAAAAAATTT-AA
1 AAATG-TTTATGAAAAAAATTTGAA
* *
391140 ATAATGTTTAATGAAATAATTTTGAA
1 A-AATGTTT-ATGAAAAAAATTTGAA
391166 AAATGTT
1 AAATGTT
391173 CAATAAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 4 0.14
25 21 0.75
26 3 0.11
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.39
Consensus pattern (24 bp):
AAATGTTTATGAAAAAAATTTGAA
Found at i:396091 original size:23 final size:22
Alignment explanation
Indices: 396044--396120 Score: 88
Period size: 21 Copynumber: 3.5 Consensus size: 22
396034 TCGTGGGGTT
396044 ATCGATTCCC-T-AAAGGAGGGA
1 ATCGATTCCCTTCAAAGG-GGGA
396065 ATCGATTCCCATTCAAAGGGGGA
1 ATCGATTCCC-TTCAAAGGGGGA
* *
396088 ATCGGTTCCCCTTC-AAGGGGGT
1 ATCGATT-CCCTTCAAAGGGGGA
396110 ATCGATTCCCT
1 ATCGATTCCCT
396121 CTGCACTAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
21 14 0.29
22 13 0.27
23 14 0.29
24 8 0.16
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.25
Consensus pattern (22 bp):
ATCGATTCCCTTCAAAGGGGGA
Found at i:396108 original size:22 final size:23
Alignment explanation
Indices: 396044--396119 Score: 88
Period size: 23 Copynumber: 3.4 Consensus size: 23
396034 TCGTGGGGTT
396044 ATCGATTCCC--T-AAAGGAGGGA
1 ATCGATTCCCATTCAAAGG-GGGA
396065 ATCGATTCCCATTCAAAGGGGGA
1 ATCGATTCCCATTCAAAGGGGGA
* * *
396088 ATCGGTTCCCCTTC-AAGGGGGT
1 ATCGATTCCCATTCAAAGGGGGA
396110 ATCGATTCCC
1 ATCGATTCCC
396120 TCTGCACTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
21 10 0.21
22 16 0.33
23 17 0.35
24 5 0.10
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.24
Consensus pattern (23 bp):
ATCGATTCCCATTCAAAGGGGGA
Found at i:401971 original size:13 final size:14
Alignment explanation
Indices: 401948--401977 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
401938 GATTTTGAAG
401948 TTGTATCTTGGATC
1 TTGTATCTTGGATC
401962 TTGT-TCTTGGATC
1 TTGTATCTTGGATC
401975 TTG
1 TTG
401978 GATGTTGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.10, C:0.13, G:0.23, T:0.53
Consensus pattern (14 bp):
TTGTATCTTGGATC
Done.