Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007911.1 Hibiscus syriacus cultivar Beakdansim tig00110307_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: 1972160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 9
Found at i:1021744 original size:18 final size:18
Alignment explanation
Indices: 1021721--1021755 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1021711 TTCCATCCGG
*
1021721 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1021739 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1021756 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1023072 original size:18 final size:18
Alignment explanation
Indices: 1023051--1023091 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1023041 CGACGGTCAA
*
1023051 CGGGTCAACAGGTCGGGT
1 CGGGTAAACAGGTCGGGT
*
1023069 CGGGTAAACGGGTCGGGT
1 CGGGTAAACAGGTCGGGT
1023087 CGGGT
1 CGGGT
1023092 TGTGACCGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.20, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTAAACAGGTCGGGT
Found at i:1026847 original size:18 final size:18
Alignment explanation
Indices: 1026824--1026858 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1026814 TTCCATCCGG
*
1026824 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1026842 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1026859 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1028163 original size:15 final size:17
Alignment explanation
Indices: 1028133--1028166 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
1028123 GGTCAACAGT
1028133 GGTCAACGACGGTCAAC
1 GGTCAACGACGGTCAAC
1028150 GGTCAAC-A-GGTCAAC
1 GGTCAACGACGGTCAAC
1028165 GG
1 GG
1028167 GTCGGGTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 1 0.06
17 7 0.41
ACGTcount: A:0.29, C:0.26, G:0.32, T:0.12
Consensus pattern (17 bp):
GGTCAACGACGGTCAAC
Found at i:1028181 original size:18 final size:18
Alignment explanation
Indices: 1028158--1028227 Score: 96
Period size: 18 Copynumber: 4.2 Consensus size: 18
1028148 ACGGTCAACA
1028158 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
1028176 GGTCAA-----CGGGTCG
1 GGTCAACGGGTCGGGTCG
1028189 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
1028207 GGTCAACTGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
1028225 GGT
1 GGT
1028228 TGTGACCGGT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
13 13 0.28
18 33 0.72
ACGTcount: A:0.11, C:0.21, G:0.49, T:0.19
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:1028196 original size:31 final size:31
Alignment explanation
Indices: 1028158--1028223 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
1028148 ACGGTCAACA
1028158 GGTCAACGGGTCGGGTCGGGTCAACGGGTCG
1 GGTCAACGGGTCGGGTCGGGTCAACGGGTCG
*
1028189 GGTCAACGGGTCGGGTCGGGTCAACTGGTCG
1 GGTCAACGGGTCGGGTCGGGTCAACGGGTCG
1028220 GGTC
1 GGTC
1028224 GGGTTGTGAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.12, C:0.23, G:0.47, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCGGGTCAACGGGTCG
Found at i:1028223 original size:13 final size:13
Alignment explanation
Indices: 1028169--1028205 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
1028159 GTCAACGGGT
1028169 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
1028182 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
1028195 CGGGTCGGGTC
1 CGGGTCGGGTC
1028206 GGGTCAACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.11, C:0.24, G:0.49, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:1029777 original size:26 final size:26
Alignment explanation
Indices: 1029726--1029777 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
1029716 CTTTTCCTCT
* *
1029726 TTTAATATTTATTTTAGTTTTTATTA
1 TTTAATATTTAATTTAGTTTTGATTA
*
1029752 TTTAATCTTTAATTTA-TATTTGATTA
1 TTTAATATTTAATTTAGT-TTTGATTA
1029778 ACATTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (26 bp):
TTTAATATTTAATTTAGTTTTGATTA
Found at i:1031893 original size:4 final size:4
Alignment explanation
Indices: 1031884--1032185 Score: 500
Period size: 4 Copynumber: 76.0 Consensus size: 4
1031874 TTAAGAAGTT
* *
1031884 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ACAC ACAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * *
1031932 ACAC ATAC --AC ACAC ATAC ATAC ATAC ATGC ATAC ATAT ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1031978 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1032026 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1032074 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * *
1032122 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ACAC ACAC ACAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
1032170 ACAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC
1032186 CAATTTTGAT
Statistics
Matches: 287, Mismatches: 9, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
2 2 0.01
4 285 0.99
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAC
Found at i:1031941 original size:10 final size:10
Alignment explanation
Indices: 1031914--1031950 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
1031904 ATACATACAT
*
1031914 ACATACATAC
1 ACATACACAC
*
1031924 ACACACACAC
1 ACATACACAC
1031934 ACATACACAC
1 ACATACACAC
1031944 ACATACA
1 ACATACA
1031951 TACATACATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.51, C:0.38, G:0.00, T:0.11
Consensus pattern (10 bp):
ACATACACAC
Found at i:1031943 original size:14 final size:14
Alignment explanation
Indices: 1031924--1031954 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1031914 ACATACATAC
1031924 ACACACACACACAT
1 ACACACACACACAT
*
1031938 ACACACACATACAT
1 ACACACACACACAT
1031952 ACA
1 ACA
1031955 TACATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.39, G:0.00, T:0.10
Consensus pattern (14 bp):
ACACACACACACAT
Found at i:1034015 original size:37 final size:36
Alignment explanation
Indices: 1033956--1034075 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
1033946 ATCCCATTAT
* *
1033956 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
1033992 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1034028 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1034063 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
1034076 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 35 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:1034031 original size:21 final size:21
Alignment explanation
Indices: 1034007--1034067 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1033997 TTCAAAGAAA
1034007 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
1034028 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
1034042 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
1034063 CATTT
1 CATTT
1034068 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:1034084 original size:35 final size:36
Alignment explanation
Indices: 1033958--1034102 Score: 142
Period size: 35 Copynumber: 4.1 Consensus size: 36
1033948 CCCATTATCA
*
1033958 TTTTTCAACA-AACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
*
1033993 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*
1034030 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
***
1034066 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
1034100 TTT
1 TTT
1034103 AATAATTTCA
Statistics
Matches: 98, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
34 14 0.14
35 45 0.46
36 8 0.08
37 30 0.31
38 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:1038624 original size:37 final size:36
Alignment explanation
Indices: 1038565--1038684 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
1038555 ATCCCATTAT
* *
1038565 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
1038601 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1038637 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1038672 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
1038685 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 35 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:1038640 original size:21 final size:21
Alignment explanation
Indices: 1038616--1038676 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1038606 TTCAAAGAAA
1038616 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
1038637 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
1038651 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
1038672 CATTT
1 CATTT
1038677 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:1038693 original size:35 final size:36
Alignment explanation
Indices: 1038567--1038711 Score: 142
Period size: 35 Copynumber: 4.1 Consensus size: 36
1038557 CCCATTATCA
*
1038567 TTTTTCAACA-AACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
*
1038602 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*
1038639 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
***
1038675 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
1038709 TTT
1 TTT
1038712 AATAATTTCA
Statistics
Matches: 98, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
34 14 0.14
35 45 0.46
36 8 0.08
37 30 0.31
38 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:1039739 original size:21 final size:21
Alignment explanation
Indices: 1039707--1039748 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1039697 TGTCATTATC
1039707 TATATATGTTTATTATATTTT
1 TATATATGTTTATTATATTTT
*
1039728 TATA-ATGTTTTATTTTATTTT
1 TATATATG-TTTATTATATTTT
1039749 AATTTGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (21 bp):
TATATATGTTTATTATATTTT
Found at i:1040187 original size:60 final size:61
Alignment explanation
Indices: 1040101--1040218 Score: 177
Period size: 60 Copynumber: 2.0 Consensus size: 61
1040091 TAGCCACATA
* *
1040101 TTTATACGTGCAATATTTTCTAAATTTTAGTTTCCTAAACTAAGGCACTAA-CCACTAATAT
1 TTTATACGTGCAATACTTTCTAAATTTTAATTTCC-AAACTAAGGCACTAATCCACTAATAT
* *
1040162 TTTATACGTGGAATACTTT-TAAATTTTAATTTCCAAACTAAGGTACTAATCCACTAA
1 TTTATACGTGCAATACTTTCTAAATTTTAATTTCCAAACTAAGGCACTAATCCACTAA
1040219 GGCAATACTA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 14 0.27
60 21 0.40
61 17 0.33
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (61 bp):
TTTATACGTGCAATACTTTCTAAATTTTAATTTCCAAACTAAGGCACTAATCCACTAATAT
Found at i:1041696 original size:6 final size:6
Alignment explanation
Indices: 1041685--1041745 Score: 95
Period size: 6 Copynumber: 10.2 Consensus size: 6
1041675 GACACGTATT
* * *
1041685 ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCTCG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1041733 ACCACG ACCACG A
1 ACCACG ACCACG A
1041746 GCCGAGCCGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.30, C:0.49, G:0.16, T:0.05
Consensus pattern (6 bp):
ACCACG
Found at i:1041753 original size:5 final size:5
Alignment explanation
Indices: 1041743--1041796 Score: 72
Period size: 5 Copynumber: 10.8 Consensus size: 5
1041733 ACCACGACCA
* * * *
1041743 CGAGC CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGA
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
1041793 CGAG
1 CGAG
1041797 ACGGACGGAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.17, C:0.37, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:1047330 original size:12 final size:12
Alignment explanation
Indices: 1047313--1047343 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1047303 GACACATATT
1047313 ACCACGACCACC
1 ACCACGACCACC
1047325 ACCACGACCACC
1 ACCACGACCACC
1047337 ACCACGA
1 ACCACGA
1047344 GCCGAGCCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.55, G:0.10, T:0.00
Consensus pattern (12 bp):
ACCACGACCACC
Found at i:1047351 original size:5 final size:5
Alignment explanation
Indices: 1047341--1047394 Score: 63
Period size: 5 Copynumber: 10.8 Consensus size: 5
1047331 ACCACCACCA
* * * * *
1047341 CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGTGC CGAGC CGAGC CGAGA
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
1047391 CGAG
1 CGAG
1047395 ACGGACGGAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.15, C:0.37, G:0.41, T:0.07
Consensus pattern (5 bp):
CGAGC
Found at i:1047367 original size:15 final size:15
Alignment explanation
Indices: 1047344--1047387 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
1047334 ACCACCACGA
1047344 GCCGAGCCGAGCCGT
1 GCCGAGCCGAGCCGT
* *
1047359 GCCGTGCCGTGCCGT
1 GCCGAGCCGAGCCGT
1047374 GCCGAGCCGAGCCG
1 GCCGAGCCGAGCCG
1047388 AGACGAGACG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.09, C:0.41, G:0.41, T:0.09
Consensus pattern (15 bp):
GCCGAGCCGAGCCGT
Found at i:1056328 original size:20 final size:20
Alignment explanation
Indices: 1056290--1056330 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1056280 GATGGTAAAG
* * *
1056290 AAAGAAAAAGAAGATGAAGA
1 AAAGAAAAACAAAAAGAAGA
1056310 AAAGAAAAACAAAAAGAAGA
1 AAAGAAAAACAAAAAGAAGA
1056330 A
1 A
1056331 TGAGGTATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (20 bp):
AAAGAAAAACAAAAAGAAGA
Found at i:1056848 original size:20 final size:20
Alignment explanation
Indices: 1056814--1056862 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1056804 AATGATTTTC
* * *
1056814 TTTTG-AAAGCAAAATTAGA
1 TTTTGAAAAACAAAATGAAA
1056833 TTTTGAAAAACAAAATGAAA
1 TTTTGAAAAACAAAATGAAA
1056853 TTTTGAAAAA
1 TTTTGAAAAA
1056863 TGATTTTGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.53, C:0.04, G:0.12, T:0.31
Consensus pattern (20 bp):
TTTTGAAAAACAAAATGAAA
Found at i:1061282 original size:22 final size:22
Alignment explanation
Indices: 1061248--1061315 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
1061238 CTCATTTCAG
* *
1061248 TGCTAA-GTCACTTT-GTATTAG
1 TGCTAATG-CACTTTAGTATCAA
**
1061269 TGCATAATGCACTTTCTTATCAA
1 TGC-TAATGCACTTTAGTATCAA
1061292 TGCTAATGCACTTTAGTATCAA
1 TGCTAATGCACTTTAGTATCAA
1061314 TG
1 TG
1061316 GCAAGGCACT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 3 0.08
22 28 0.72
23 8 0.21
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.40
Consensus pattern (22 bp):
TGCTAATGCACTTTAGTATCAA
Found at i:1061324 original size:22 final size:22
Alignment explanation
Indices: 1061248--1061326 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 22
1061238 CTCATTTCAG
* * *
1061248 TGCTAAGTCACTTT-GTATTAG
1 TGCTAAGGCACTTTAGTATCAA
* **
1061269 TGCATAATGCACTTTCTTATCAA
1 TGC-TAAGGCACTTTAGTATCAA
*
1061292 TGCTAATGCACTTTAGTATCAA
1 TGCTAAGGCACTTTAGTATCAA
1061314 TGGC-AAGGCACTT
1 T-GCTAAGGCACTT
1061327 CCGTTAATCG
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
21 3 0.06
22 35 0.74
23 9 0.19
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (22 bp):
TGCTAAGGCACTTTAGTATCAA
Found at i:1062373 original size:6 final size:6
Alignment explanation
Indices: 1062359--1062483 Score: 72
Period size: 6 Copynumber: 20.3 Consensus size: 6
1062349 CATGTTATTA
* * * * *
1062359 TAGTAG TAGTGG TAGTGG TAACAGTAG TAGTGG TAGTAG AAGTGG T-GATAG
1 TAGTGG TAGTGG TAGTGG T---AGTGG TAGTGG TAGTGG TAGTGG TAG-TGG
** * * * * * *
1062410 TAGTAA TGGTGG TAGTGG TGGTAG TGGTGG TAGTGA TAGTGG TGGTGG
1 TAGTGG TAGTGG TAGTGG TAGTGG TAGTGG TAGTGG TAGTGG TAGTGG
* *
1062458 TGGTGG TAGTAG TAGTGG TAGTGG TA
1 TAGTGG TAGTGG TAGTGG TAGTGG TA
1062484 ATGACAGTTT
Statistics
Matches: 91, Mismatches: 23, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
5 1 0.01
6 84 0.92
7 1 0.01
9 5 0.05
ACGTcount: A:0.22, C:0.01, G:0.45, T:0.32
Consensus pattern (6 bp):
TAGTGG
Found at i:1062396 original size:9 final size:9
Alignment explanation
Indices: 1062382--1062483 Score: 62
Period size: 9 Copynumber: 11.3 Consensus size: 9
1062372 AGTGGTAACA
1062382 GTAGTAGTG
1 GTAGTAGTG
**
1062391 GTAGTAGAA
1 GTAGTAGTG
* *
1062400 GTGGT-GATA
1 GTAGTAG-TG
*
1062409 GTAGTAATG
1 GTAGTAGTG
*
1062418 GTGGTAGTG
1 GTAGTAGTG
*
1062427 GTGGTAGTG
1 GTAGTAGTG
*
1062436 GTGGTAGTG
1 GTAGTAGTG
* *
1062445 ATAGTGGTG
1 GTAGTAGTG
* *
1062454 GTGGTGGTG
1 GTAGTAGTG
*
1062463 GTAGTAGTA
1 GTAGTAGTG
*
1062472 GTGGTAGTG
1 GTAGTAGTG
1062481 GTA
1 GTA
1062484 ATGACAGTTT
Statistics
Matches: 71, Mismatches: 20, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
8 1 0.01
9 70 0.99
ACGTcount: A:0.21, C:0.00, G:0.47, T:0.32
Consensus pattern (9 bp):
GTAGTAGTG
Found at i:1062410 original size:24 final size:24
Alignment explanation
Indices: 1062382--1062476 Score: 84
Period size: 24 Copynumber: 4.0 Consensus size: 24
1062372 AGTGGTAACA
1062382 GTAGTAGTGGTAGTAGAAGTGGTG
1 GTAGTAGTGGTAGTAGAAGTGGTG
* ** * * *
1062406 ATAGTAGTAATGGTGGTAGTGGTG
1 GTAGTAGTGGTAGTAGAAGTGGTG
*
1062430 GTAGTGGTGGTAGT-GATAGTGGTG
1 GTAGTAGTGGTAGTAGA-AGTGGTG
* * *
1062454 GTGGTGGTGGTAGTAGTAGTGGT
1 GTAGTAGTGGTAGTAGAAGTGGT
1062477 AGTGGTAATG
Statistics
Matches: 55, Mismatches: 14, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
23 1 0.02
24 53 0.96
25 1 0.02
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (24 bp):
GTAGTAGTGGTAGTAGAAGTGGTG
Found at i:1062422 original size:3 final size:3
Alignment explanation
Indices: 1062416--1062464 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
1062406 ATAGTAGTAA
* * * * *
1062416 TGG TGG TAG TGG TGG TAG TGG TGG TAG TGA TAG TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
1062464 T
1 T
1062465 AGTAGTAGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.10, C:0.00, G:0.55, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:1063463 original size:17 final size:17
Alignment explanation
Indices: 1063441--1063489 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
1063431 GTTAGTGTTA
1063441 GGATTTGAGAATTTTAG
1 GGATTTGAGAATTTTAG
1063458 GGATTTGAGAATTTTAG
1 GGATTTGAGAATTTTAG
*
1063475 GGATTTGAGTATTTT
1 GGATTTGAGAATTTT
1063490 TAAAAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.45
Consensus pattern (17 bp):
GGATTTGAGAATTTTAG
Found at i:1064117 original size:31 final size:31
Alignment explanation
Indices: 1064082--1064142 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
1064072 CAATACAATC
* *
1064082 CCCCAATATTTAGTCCGTTTGCAATATGGTT
1 CCCCAACATTTAGTCCATTTGCAATATGGTT
*
1064113 CCCCAACATTTAGTCTATTTGCAATATGGT
1 CCCCAACATTTAGTCCATTTGCAATATGGT
1064143 CCTCGACGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.38
Consensus pattern (31 bp):
CCCCAACATTTAGTCCATTTGCAATATGGTT
Found at i:1065797 original size:30 final size:31
Alignment explanation
Indices: 1065761--1065835 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 31
1065751 TTACGTCGAG
1065761 GACCATATTACAAACAAACTAAATATTA-GA
1 GACCATATTACAAACAAACTAAATATTAGGA
**
1065791 GACCATATTACAAACGGACTAAATATTAGGA
1 GACCATATTACAAACAAACTAAATATTAGGA
**
1065822 GACTGTATTACAAA
1 GACCATATTACAAA
1065836 TTTTAAAAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 26 0.65
31 14 0.35
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (31 bp):
GACCATATTACAAACAAACTAAATATTAGGA
Found at i:1077735 original size:20 final size:20
Alignment explanation
Indices: 1077707--1077745 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1077697 TTTATCATAT
*
1077707 ATTTTATTATCTA-TTAGAAA
1 ATTTAATTAT-TATTTAGAAA
1077727 ATTTAATTATTATTTAGAA
1 ATTTAATTATTATTTAGAA
1077746 TTTTTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (20 bp):
ATTTAATTATTATTTAGAAA
Found at i:1080473 original size:177 final size:175
Alignment explanation
Indices: 1080179--1080522 Score: 670
Period size: 177 Copynumber: 2.0 Consensus size: 175
1080169 TGCAGGCATA
1080179 CCAAGAGCTTCCAGAACAGTAATAAAAAATTGCCAATCCACTAAATCAAGTCTTATGCAATCCAA
1 CCAAGAGCTTCCAGAACAGTAATAAAAAATTGCCAATCCACTAAATCAAGTCTTATGCAATCCAA
1080244 TTTCAAAACACATCTAGGAGATAGGGAAGATCTATTATACCCCTAAACCAACTCTTGAGCCATCA
66 TTTCAAAACACATCTAGGAGATAGGGAAGATCTATTATACCCCTAAACCAACTCTTGAGCCATCA
1080309 AAGTATAGTCTCAAATGCTATGTCTAGGAATAAAATCCACTAAAT
131 AAGTATAGTCTCAAATGCTATGTCTAGGAATAAAATCCACTAAAT
1080354 CCAAGAGCTTCCAGAACAGTAATAAAAAATTGCCAATCCACTAAATCAAAAGTCTTATGCAATCC
1 CCAAGAGCTTCCAGAACAGTAATAAAAAATTGCCAATCCACTAAATC--AAGTCTTATGCAATCC
1080419 AATTTCAAAACACATCTAGGAGATAGGGAAGATCTATTATACCCCTAAACCAACTCTTGAGCCAT
64 AATTTCAAAACACATCTAGGAGATAGGGAAGATCTATTATACCCCTAAACCAACTCTTGAGCCAT
1080484 CAAAGTATAGTCTCAAATGCTATGTCTAGGAATAAAATC
129 CAAAGTATAGTCTCAAATGCTATGTCTAGGAATAAAATC
1080523 ACCTCAGCTT
Statistics
Matches: 167, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
175 47 0.28
177 120 0.72
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (175 bp):
CCAAGAGCTTCCAGAACAGTAATAAAAAATTGCCAATCCACTAAATCAAGTCTTATGCAATCCAA
TTTCAAAACACATCTAGGAGATAGGGAAGATCTATTATACCCCTAAACCAACTCTTGAGCCATCA
AAGTATAGTCTCAAATGCTATGTCTAGGAATAAAATCCACTAAAT
Found at i:1082096 original size:39 final size:38
Alignment explanation
Indices: 1082050--1082149 Score: 119
Period size: 39 Copynumber: 2.6 Consensus size: 38
1082040 CAAAAAAAAT
* *
1082050 TTAATTATCACTATTAGATTAATAAATTTACTTTCTATA
1 TTAATTATAAC-ATTAGATTAATAAATTCACTTTCTATA
** *
1082089 TTAATTATGAACATTAGATTAATAAATTCGTTTTCTATT
1 TTAATTAT-AACATTAGATTAATAAATTCACTTTCTATA
*
1082128 TTAATTATGACCATTAGATTAA
1 TTAATTAT-AACATTAGATTAA
1082150 AAAAATTGAT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
39 52 0.96
40 2 0.04
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (38 bp):
TTAATTATAACATTAGATTAATAAATTCACTTTCTATA
Found at i:1082566 original size:39 final size:39
Alignment explanation
Indices: 1082511--1082611 Score: 148
Period size: 39 Copynumber: 2.6 Consensus size: 39
1082501 TTTAAAAAAA
*
1082511 ATTAATTATGAGTATTAGATTAATAAATTTACTTTCTAT
1 ATTAATTATGAATATTAGATTAATAAATTTACTTTCTAT
**
1082550 ATTAATTATGAATATTAGATTAATAAATTTGTTTTCTAT
1 ATTAATTATGAATATTAGATTAATAAATTTACTTTCTAT
* * *
1082589 TTTAATTCTGAACATTAGATTAA
1 ATTAATTATGAATATTAGATTAA
1082612 AAAAATTGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.49
Consensus pattern (39 bp):
ATTAATTATGAATATTAGATTAATAAATTTACTTTCTAT
Found at i:1082611 original size:462 final size:455
Alignment explanation
Indices: 1082031--1082953 Score: 1517
Period size: 462 Copynumber: 2.0 Consensus size: 455
1082021 TAGATTCCAA
*
1082031 TAATTAATTCAAAAAAAATTTAATTATCACTATTAGATTAATAAATTTACTTTCTATATTAATTA
1 TAATAAATTCAAAAAAAATTTAATTATCACTATTAGATTAATAAATTTACTTTCTATATTAATTA
*
1082096 TGAACATTAGATTAATAAATTCGTTTTCTATTTTAATTATGACCATTAGATTAAAAAAATTGATT
66 TGAACATTAGATTAATAAATTCGTTTTCTATTTTAATTATGAACATTAGATTAAAAAAATTGATT
*
1082161 ATAACCATTAAATTAATTTTATTAAATGATTTATTTATTTATTATTAGTTTTATTAGATTAAAAA
131 ATAACCATTAAATTAATTTTATTAAATGATTTATTTATTTATTATTAATTTTATTAGATTAAAAA
*
1082226 TTAGATTATATAAAATGATTTTAAAAACTGTTAAGTTTAAATCATTATTATGATATAATAATTAA
196 TTAGATTATATAAAATGATTTTAAAAACTGTTAAGTTTAAATCACTATTATGATATAATAATTAA
*
1082291 TTAATAATTTAACTTAGAATTTTAATATATATATATATAACTTGTAAGTTATAAAACTTTTAATT
261 TTAATAATTTAACTTAG-A----AATATA-ATATATATAACTCGTAAGTTAT-AAACTTTTAATT
*
1082356 GGCAACTGATATTATAATATGACAACTAACAAAATAATTATTCACCATTGAAAGCACATGATTAA
319 GGAAACTGATATTATAATATGACAACTAACAAAATAATTATTCACCATTGAAAGCACATGATTAA
1082421 TTATGATAATTAGATTAATAAATTTATTTTTGA-TAAGTTGATATATAAATATATTCAAAAGTGT
384 TTATGATAATTAGATTAATAAATTTATTTTTGATTAA-TTGATATATAAATATATTCAAAAGTGT
1082485 AATAAAATT
448 AATAAAA-T
* * *
1082494 TAATAAATTTAAAAAAAA-TTAATTATGAGTATTAGATTAATAAATTTACTTTCTATATTAATTA
1 TAATAAATTCAAAAAAAATTTAATTATCACTATTAGATTAATAAATTTACTTTCTATATTAATTA
* * *
1082558 TGAATATTAGATTAATAAATTTGTTTTCTATTTTAATTCTGAACATTAGATTAAAAAAATTGATT
66 TGAACATTAGATTAATAAATTCGTTTTCTATTTTAATTATGAACATTAGATTAAAAAAATTGATT
* *
1082623 ATAACTATTAAATTAATTTTATTAAATGATTTATTTATTTATTATTAATTTTATTAGATTAGAAA
131 ATAACCATTAAATTAATTTTATTAAATGATTTATTTATTTATTATTAATTTTATTAGATTAAAAA
* *
1082688 TTAGATTATATAAAATGATTTTAAAAACTTTTAAGTTTAAATCACTATTATGATATAATAATTGA
196 TTAGATTATATAAAATGATTTTAAAAACTGTTAAGTTTAAATCACTATTATGATATAATAATTAA
* * * *
1082753 TTAATAATTTAAGTTAGAAATTTAATATATATAACTCGTAAGTTGTAAACTTTTAATTGGAAATT
261 TTAATAATTTAACTTAGAAATATAATATATATAACTCGTAAGTTATAAACTTTTAATTGGAAACT
* * * ** *
1082818 GATATTATAATATTACAACTAACAAAATAATTATTCGCCATTTAAAGTGCATGATTCATTATGAT
326 GATATTATAATATGACAACTAACAAAATAATTATTCACCATTGAAAGCACATGATTAATTATGAT
1082883 AATTAGATTAATAAATTTATTTTTGATTAATTGATATATAAATATATTCAAAAGTGTAATAAAAT
391 AATTAGATTAATAAATTTATTTTTGATTAATTGATATATAAATATATTCAAAAGTGTAATAAAAT
1082948 TAATAA
1 TAATAA
1082954 TTAATGGTTG
Statistics
Matches: 433, Mismatches: 26, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
454 7 0.02
455 136 0.31
456 23 0.05
457 5 0.01
461 1 0.00
462 245 0.57
463 16 0.04
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.43
Consensus pattern (455 bp):
TAATAAATTCAAAAAAAATTTAATTATCACTATTAGATTAATAAATTTACTTTCTATATTAATTA
TGAACATTAGATTAATAAATTCGTTTTCTATTTTAATTATGAACATTAGATTAAAAAAATTGATT
ATAACCATTAAATTAATTTTATTAAATGATTTATTTATTTATTATTAATTTTATTAGATTAAAAA
TTAGATTATATAAAATGATTTTAAAAACTGTTAAGTTTAAATCACTATTATGATATAATAATTAA
TTAATAATTTAACTTAGAAATATAATATATATAACTCGTAAGTTATAAACTTTTAATTGGAAACT
GATATTATAATATGACAACTAACAAAATAATTATTCACCATTGAAAGCACATGATTAATTATGAT
AATTAGATTAATAAATTTATTTTTGATTAATTGATATATAAATATATTCAAAAGTGTAATAAAAT
Found at i:1089624 original size:21 final size:21
Alignment explanation
Indices: 1089600--1089639 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1089590 CTCCCTTTGA
*
1089600 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1089621 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1089640 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1096348 original size:2 final size:2
Alignment explanation
Indices: 1096341--1096383 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1096331 TTCAGTTATA
* *
1096341 TG TG TG TG TG TG TG TG TG TG TG CG TG TA TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1096383 T
1 T
1096384 TGAACATAAA
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:0.02, C:0.02, G:0.47, T:0.49
Consensus pattern (2 bp):
TG
Found at i:1101937 original size:3 final size:3
Alignment explanation
Indices: 1101929--1101967 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1101919 TCTTATTCTT
1101929 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1101968 TTATTATTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1105991 original size:26 final size:27
Alignment explanation
Indices: 1105937--1105993 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
1105927 TTCTGTATCC
* *
1105937 ATTTTCATTTTCATTTTACATTCACAT
1 ATTTACATTTGCATTTTACATTCACAT
* *
1105964 ATTTACATTTGCA-TTTGCATTTACAT
1 ATTTACATTTGCATTTTACATTCACAT
1105990 ATTT
1 ATTT
1105994 GCATAGTTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.26, C:0.16, G:0.04, T:0.54
Consensus pattern (27 bp):
ATTTACATTTGCATTTTACATTCACAT
Found at i:1106481 original size:40 final size:40
Alignment explanation
Indices: 1106399--1106481 Score: 148
Period size: 40 Copynumber: 2.1 Consensus size: 40
1106389 TAGCTGATGC
* *
1106399 AATGAAAACAAATGACTAAGAACTTGTCAAGGAATGTGGA
1 AATGAAAACAAATGACTAAGAACTTGTCAAGGAATATCGA
1106439 AATGAAAACAAATGACTAAGAACTTGTCAAGGAATATCGA
1 AATGAAAACAAATGACTAAGAACTTGTCAAGGAATATCGA
1106479 AAT
1 AAT
1106482 CCAATAAGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.20
Consensus pattern (40 bp):
AATGAAAACAAATGACTAAGAACTTGTCAAGGAATATCGA
Found at i:1108898 original size:92 final size:91
Alignment explanation
Indices: 1108706--1108970 Score: 313
Period size: 92 Copynumber: 2.9 Consensus size: 91
1108696 ACTCATATTA
* **
1108706 TATTACTATTT-TATACAATAAAGCTTGAGTTATCCCCCTAAAGCAATTGGTTAATCGCCCCAGT
1 TATTACTATTTATATACAATAAAGCTTGAGTTGTCCCCCTAAAGCAATTGGTTAATCGCCCCAAC
* *
1108770 TTTATGGATAATATTCAACTAGCATG
66 TTTATGGATAATATTCAACGAACATG
* *
1108796 -ATATATTATTATATATATAATAAAGCTTGAGTTGTCCCCCTAAAGCAATTGGTTAATCGCCCCA
1 TAT-TACTATT-TATATACAATAAAGCTTGAGTTGTCCCCCTAAAGCAATTGGTTAATCGCCCCA
* * *
1108860 ACTTTATGGATAATATTTAGCGAACTTG
64 ACTTTATGGATAATATTCAACGAACATG
* * * * * * * *
1108888 TATTACTA-TTATATGCAATAAAGATTGAGCTGTCCCTCTAGAGCAATTGGTTAATAGCTCCGAC
1 TATTACTATTTATATACAATAAAGCTTGAGTTGTCCCCCTAAAGCAATTGGTTAATCGCCCCAAC
1108952 TTTATGGATAAGT-TTCAAC
66 TTTATGGATAA-TATTCAAC
1108971 TAGCCTGATT
Statistics
Matches: 148, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
89 2 0.01
90 67 0.45
91 3 0.02
92 74 0.50
93 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Consensus pattern (91 bp):
TATTACTATTTATATACAATAAAGCTTGAGTTGTCCCCCTAAAGCAATTGGTTAATCGCCCCAAC
TTTATGGATAATATTCAACGAACATG
Found at i:1112341 original size:126 final size:123
Alignment explanation
Indices: 1111606--1112634 Score: 1517
Period size: 123 Copynumber: 8.3 Consensus size: 123
1111596 TAGGATGTTT
* * * *
1111606 TCAACATTTCCA-AAAGAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCAAAA
1 TCAACATTTCCAGAAGGAGTTTATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* *** * *
1111670 TGAGAAGAACTTGTTCAACCTTTTACTCAACTCTATTGTAGAAGGAGATAGGTCAGCA
66 TGAGAAGAACTTGTTCAACCTTTTGCTCAACTCTATCACAGAAGGAGATAGATCAACA
* * *
1111728 TCAACATTTCCAGAAGGAGTTCATAATTAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTTATAA
1 TCAACATTTCCAGAAGGAGTTTATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* * * *
1111793 TGAAAAGAACTTGTTCAACCTTTTACTCGA-TGCTATCACAGAAGGAGATAGATCAATA
66 TGAGAAGAACTTGTTCAACCTTTTGCTCAACT-CTATCACAGAAGGAGATAGATCAACA
* * *
1111851 TCAATATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAA
1 TCAACATTTCCAGAAGGAGTTTATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* * *
1111916 TGAGAAAAACTTGTTCAACCTTTTGCTCATCTTTATCACAGAAGGAGATAGATCAACA
66 TGAGAAGAACTTGTTCAACCTTTTGCTCAACTCTATCACAGAAGGAGATAGATCAACA
* * *
1111974 TCAACAATTCTAGAAGAAGTTTATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
1 TCAACATTTCCAGAAGGAGTTTATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* * * *
1112039 TGAGAAGAACTTATTCAACCTTTTTCTCAACTCTATCACAGAAAGAGATAAATCAACA
66 TGAGAAGAACTTGTTCAACCTTTTGCTCAACTCTATCACAGAAGGAGATAGATCAACA
*
1112097 TCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
1 TCAACATTTCCAGAAGGAGTTTATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
** * * *
1112162 TGAGAAGAACTTGTTCATTCTTTTGTTCAACTCTATCATAGAAGGAGATAGATCATCA
66 TGAGAAGAACTTGTTCAACCTTTTGCTCAACTCTATCACAGAAGGAGATAGATCAACA
* *
1112220 TCAACATTTCTAGAAGGAGTTTATAATGAGAAGAACTCATCTAAAGAGGAAGAAGAAGAAGTTCA
1 TCAACATTTCCAGAAGGAGTTTATAATGAGAAGAACTCATCTGAAGA-G--GAAGAAGAAGTTCA
*
1112285 TAATGAGAAGAACTTGTTCAACCTTTTGCTCGAA-TCTATCACAGAAAGAGATAGATCAACA
63 TAATGAGAAGAACTTGTTCAACCTTTTGCTC-AACTCTATCACAGAAGGAGATAGATCAACA
* *
1112346 TCAACATTTCCAGAAAGAGTTTATAATGAGAAGAACTCATCTAAAGAGAAAGAAGAAGAAGTTCA
1 TCAACATTTCCAGAAGGAGTTTATAATGAGAAGAACTCATCTGAAGAG---GAAGAAGAAGTTCA
*
1112411 TAATGAGAAGAACTTGTTCAACCTTTTGCTCGAA-TCTATCACAGAAAGAGATAGATCAACA
63 TAATGAGAAGAACTTGTTCAACCTTTTGCTC-AACTCTATCACAGAAGGAGATAGATCAACA
*
1112472 TCAACATTTCCAGAAGGAGTTTATAATGAGAAGAACTCATCTGAAGAGGAAAAAGAAGTTCATAA
1 TCAACATTTCCAGAAGGAGTTTATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* * *
1112537 TGAGAAGAACGTGTTCAACCTTTTTCTCAACTCTATCACAGAAGGAGATAGATAAACA
66 TGAGAAGAACTTGTTCAACCTTTTGCTCAACTCTATCACAGAAGGAGATAGATCAACA
* *
1112595 TCAACATTTCTAGAAGGAGTTTATAATGAGAATAACTCAT
1 TCAACATTTCCAGAAGGAGTTTATAATGAGAAGAACTCAT
1112635 ATGAGAAGTC
Statistics
Matches: 828, Mismatches: 70, Indels: 17
0.90 0.08 0.02
Matches are distributed among these distances:
122 15 0.02
123 574 0.69
124 2 0.00
125 1 0.00
126 234 0.28
127 2 0.00
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (123 bp):
TCAACATTTCCAGAAGGAGTTTATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTTGCTCAACTCTATCACAGAAGGAGATAGATCAACA
Found at i:1113290 original size:28 final size:28
Alignment explanation
Indices: 1113258--1113317 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
1113248 TAATTTATTC
1113258 CAAAT-TTGATAAATTACATCATAAAT-TT
1 CAAATCTT-ATAAATTACATCAT-AATCTT
*
1113286 CAAATCTTATAAATTATATCATAATCTT
1 CAAATCTTATAAATTACATCATAATCTT
1113314 CAAA
1 CAAA
1113318 CTCTATTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 3 0.10
28 24 0.83
29 2 0.07
ACGTcount: A:0.47, C:0.13, G:0.02, T:0.38
Consensus pattern (28 bp):
CAAATCTTATAAATTACATCATAATCTT
Found at i:1113446 original size:4 final size:4
Alignment explanation
Indices: 1113437--1113622 Score: 363
Period size: 4 Copynumber: 46.5 Consensus size: 4
1113427 TACGCATGAT
1113437 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1113485 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1113533 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
1113581 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1113623 GTAAACCATG
Statistics
Matches: 180, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 180 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:1114800 original size:43 final size:43
Alignment explanation
Indices: 1114751--1115112 Score: 449
Period size: 43 Copynumber: 8.4 Consensus size: 43
1114741 TGCATTAACG
* * * *
1114751 GTAAGGTCTTACCCTTTCACACAACAAAAGAGCCT-GAGAAAC-
1 GTAAGG-CTTACCCTTGCACACAACAAAGGAACCTGGGGAAACT
* * * *
1114793 GATAAGGTCTTACCCTTGCACATAGCAAAGGAGCATGGGGAAACT
1 G-TAAGG-CTTACCCTTGCACACAACAAAGGAACCTGGGGAAACT
* *
1114838 GTAAGGCTTATCCTTGCACACAACAAAGGAACCTGGGGAAATT
1 GTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACT
* * *
1114881 GTAAGGCTTACCGTTGCACACAATAAAGGAACCTGGAGAAACT
1 GTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACT
** *
1114924 GTAAGGCTTACCCTTATACACAACAAAGAAACCTGGGGAAACT
1 GTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACT
* * * *
1114967 ATAAGGTTTACCCTTGCACACAACAATGAAACCTGGGGAAACT
1 GTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACT
* **
1115010 GTAAGGCTTACCCTTTCACACCTCAAAGGAACCTGGGGAAACT
1 GTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACT
* *
1115053 GTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGAGAATCT
1 GTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACT
1115096 GTAAGGGCTTACCCTTG
1 GTAA-GGCTTACCCTTG
1115113 TACATAGCAG
Statistics
Matches: 276, Mismatches: 40, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
42 1 0.00
43 251 0.91
44 23 0.08
45 1 0.00
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (43 bp):
GTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACT
Found at i:1119479 original size:43 final size:42
Alignment explanation
Indices: 1119431--1119872 Score: 471
Period size: 43 Copynumber: 10.4 Consensus size: 42
1119421 TGCAAAAATA
* ** * * *
1119431 GTAAGGTCTTACCCTTGCACATAGCAAAATAGCCTGAGAAACA
1 GTAAGGT-TTACCCTTGCACACAGCAAAGGAACCTGGGAAACT
* * * *
1119474 GTAAGGTCGTACCCTTTCACATAGCAAAGGAGCCTGTGGAAACT
1 GTAAGGT-TTACCCTTGCACACAGCAAAGGAACCTG-GGAAACT
*
1119518 GTAAGGTTTACCCTTGCACACAGGAAAGGAACCTGGGGAAACT
1 GTAAGGTTTACCCTTGCACACAGCAAAGGAACCT-GGGAAACT
* * *
1119561 GTAAGGCTTACCCTTGCTCACAGCAAAGAAACCTAGGGAAACT
1 GTAAGGTTTACCCTTGCACACAGCAAAGGAACCT-GGGAAACT
* *
1119604 GTAAGATTTACCCTCGCACACAGCAAAGGAACCTGAGGAAACT
1 GTAAGGTTTACCCTTGCACACAGCAAAGGAACCTG-GGAAACT
* *
1119647 GTAAGGTTTACCCTCGCACACAACAAAGGAACCTGAGGAAACT
1 GTAAGGTTTACCCTTGCACACAGCAAAGGAACCTG-GGAAACT
* ** *
1119690 ATAAGGTTTACAGTTGCACACAACAAAGGAACCTAGGGAAACT
1 GTAAGGTTTACCCTTGCACACAGCAAAGGAACCT-GGGAAACT
* *
1119733 GTAAGGATTACCCTTACACACAGCAAAGGAACCTGGGGAAACT
1 GTAAGGTTTACCCTTGCACACAGCAAAGGAACCT-GGGAAACT
* *
1119776 GTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACT
1 GTAAGGTTTACCCTTGCACACAGCAAAGGAACCT-GGGAAACT
* **
1119819 GTAAGG-----CTTTGCACACAGCAAATAAACCTGGGGAAACT
1 GTAAGGTTTACCCTTGCACACAGCAAAGGAACCT-GGGAAACT
*
1119857 GTAAGGGCTTACCCTT
1 GTAA-GGTTTACCCTT
1119873 ACATATAATA
Statistics
Matches: 347, Mismatches: 42, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
38 32 0.09
39 2 0.01
42 1 0.00
43 295 0.85
44 17 0.05
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (42 bp):
GTAAGGTTTACCCTTGCACACAGCAAAGGAACCTGGGAAACT
Found at i:1122217 original size:17 final size:17
Alignment explanation
Indices: 1122197--1122239 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1122187 AAAGTCAATG
*
1122197 GTCAGCGGCGGTCAACA
1 GTCAACGGCGGTCAACA
* *
1122214 GTCAATGGTGGTCAACA
1 GTCAACGGCGGTCAACA
1122231 GTCAACGGC
1 GTCAACGGC
1122240 TCAGTCCAGG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.33, T:0.16
Consensus pattern (17 bp):
GTCAACGGCGGTCAACA
Found at i:1125104 original size:18 final size:18
Alignment explanation
Indices: 1125081--1125118 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1125071 AGCTAAAACT
*
1125081 CAAATTCAATATGCAACC
1 CAAATTCAATATACAACC
*
1125099 CAAATTTAATATACAACC
1 CAAATTCAATATACAACC
1125117 CA
1 CA
1125119 TATCCAATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.26, G:0.03, T:0.24
Consensus pattern (18 bp):
CAAATTCAATATACAACC
Found at i:1127679 original size:39 final size:39
Alignment explanation
Indices: 1127636--1127714 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
1127626 CACTTGGATA
*
1127636 TGGATTGTGATGATTATATGTTAATAATCTCAAATGTAT
1 TGGATTGTGATGATTATATGTTAATAAACTCAAATGTAT
*
1127675 TGGATTGTGATGATTATATGTTAATAAACTCAAGTGTAT
1 TGGATTGTGATGATTATATGTTAATAAACTCAAATGTAT
1127714 T
1 T
1127715 ATGTAAGATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (39 bp):
TGGATTGTGATGATTATATGTTAATAAACTCAAATGTAT
Found at i:1129087 original size:18 final size:18
Alignment explanation
Indices: 1129064--1129108 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1129054 ATCTAGCTAA
*
1129064 AACCCAAATTCAATATGC
1 AACCCAAATTCAATATAC
*
1129082 AACCCAAATTTAATATAC
1 AACCCAAATTCAATATAC
*
1129100 AACCTAAAT
1 AACCCAAAT
1129109 CTAATACCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.49, C:0.24, G:0.02, T:0.24
Consensus pattern (18 bp):
AACCCAAATTCAATATAC
Found at i:1129113 original size:18 final size:18
Alignment explanation
Indices: 1129064--1129114 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
1129054 ATCTAGCTAA
*
1129064 AACCCAAAT-TCAATATGC
1 AACCCAAATCT-AATATAC
*
1129082 AACCCAAATTTAATATAC
1 AACCCAAATCTAATATAC
*
1129100 AACCTAAATCTAATA
1 AACCCAAATCTAATA
1129115 CCCTTAACAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 28 0.97
19 1 0.03
ACGTcount: A:0.49, C:0.24, G:0.02, T:0.25
Consensus pattern (18 bp):
AACCCAAATCTAATATAC
Found at i:1131764 original size:12 final size:12
Alignment explanation
Indices: 1131749--1131773 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1131739 ATTATTTAAA
1131749 CGGGTATCGGGC
1 CGGGTATCGGGC
1131761 CGGGTATCGGGC
1 CGGGTATCGGGC
1131773 C
1 C
1131774 AGTTATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.28, G:0.48, T:0.16
Consensus pattern (12 bp):
CGGGTATCGGGC
Found at i:1131796 original size:15 final size:16
Alignment explanation
Indices: 1131776--1131817 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
1131766 ATCGGGCCAG
1131776 TTATATATATTTAA-A
1 TTATATATATTTAATA
*
1131791 TTATATATA-TAAATA
1 TTATATATATTTAATA
1131806 TTATATATATTT
1 TTATATATATTT
1131818 TTTAATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 3 0.13
15 19 0.83
16 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATATATATTTAATA
Found at i:1131797 original size:13 final size:13
Alignment explanation
Indices: 1131779--1131868 Score: 53
Period size: 13 Copynumber: 7.0 Consensus size: 13
1131769 GGGCCAGTTA
*
1131779 TATATATTTAAAT
1 TATATATATAAAT
1131792 TATATATATAAA-
1 TATATATATAAAT
*
1131804 TAT-TATATATAT
1 TATATATATAAAT
* * *
1131816 TTTTTAATTTAAAT
1 TATAT-ATATAAAT
* *
1131830 TAAATTTATTAATAT
1 TATATATA-TAA-AT
*
1131845 TATATATATATA-
1 TATATATATAAAT
1131857 TATATATA-AAAT
1 TATATATATAAAT
1131869 AATTATTTTT
Statistics
Matches: 57, Mismatches: 14, Indels: 13
0.68 0.17 0.15
Matches are distributed among these distances:
11 9 0.16
12 13 0.23
13 14 0.25
14 13 0.23
15 8 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TATATATATAAAT
Found at i:1131981 original size:42 final size:42
Alignment explanation
Indices: 1131920--1132008 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
1131910 GATTACTAAA
* * *
1131920 CCCGTCCCCGTCCCTGTTTAACATAAACAGTTTTTTCCCGTC
1 CCCGTCCCCGTCCCCGTTTAACATAAACAGTTTTTCCCCATC
*
1131962 CCCGTCCCCGTCCCCGTTTAACATAAACGGTTTTTCCCCATC
1 CCCGTCCCCGTCCCCGTTTAACATAAACAGTTTTTCCCCATC
1132004 CCCGT
1 CCCGT
1132009 TTAATTCAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.16, C:0.42, G:0.12, T:0.30
Consensus pattern (42 bp):
CCCGTCCCCGTCCCCGTTTAACATAAACAGTTTTTCCCCATC
Found at i:1132446 original size:2 final size:2
Alignment explanation
Indices: 1132400--1132429 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1132390 AATCAAAATA
1132400 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
1132430 TAATACCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1132549 original size:78 final size:78
Alignment explanation
Indices: 1132420--1132571 Score: 198
Period size: 78 Copynumber: 1.9 Consensus size: 78
1132410 ATATATATAT
* *
1132420 ATATATATATTAATACCAAACATATATTAATAAATACTATATCAAAGAATTAAAATCTATAAACA
1 ATATATATATTAATACCAAACATAAATTAATAAATACTAAATCAAAGAATTAAAATCTATAAACA
*
1132485 CTAAATCAAAATC
66 CCAAATCAAAATC
** * * * * *
1132498 ATATATATATTAATACCAAACATAAATTTGTAAGT-GTCAAATCAAGGAATTAGAATCTATAAAT
1 ATATATATATTAATACCAAACATAAATTAATAAATACT-AAATCAAAGAATTAAAATCTATAAAC
1132562 ACCAAATCAA
65 ACCAAATCAA
1132572 TATATTATAT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
77 1 0.02
78 62 0.98
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (78 bp):
ATATATATATTAATACCAAACATAAATTAATAAATACTAAATCAAAGAATTAAAATCTATAAACA
CCAAATCAAAATC
Found at i:1132848 original size:21 final size:21
Alignment explanation
Indices: 1132824--1132866 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1132814 TATTTGAATT
*
1132824 AATTAATATATA-ACAAACATA
1 AATTAATAAATATAC-AACATA
*
1132845 AATTTATAAATATACAACATA
1 AATTAATAAATATACAACATA
1132866 A
1 A
1132867 TATCAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.30
Consensus pattern (21 bp):
AATTAATAAATATACAACATA
Found at i:1132888 original size:4 final size:4
Alignment explanation
Indices: 1132881--1133144 Score: 109
Period size: 4 Copynumber: 65.8 Consensus size: 4
1132871 AAAATTATAT
* * * * *
1132881 ATAG ATAG ATAG ATAG ATAG ATAG ATAA ATAG ATAT ACAAC ATA- ATATC
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG A-TAG ATAG ATA-G
* * * * * * * *
1132930 A-AA ATTAT ATAG ATAG ATAG ATAG ATAG ACAG ACAG ACAG ACAG ACAT
1 ATAG A-TAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
* * * * * * *
1132978 ATAG ATAG ACAG ATAG ATAG ATAG ACAT ATAG ATAT ACAG AGAG ACAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
* * * * * * * * * *
1133026 ATAG AGAG ACAG ACAT ACAG ATAG ATAA ACAA ATAG ATAG AGAG AGAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
* * * * * * * *
1133074 ACAG ATAG AGAG ACAG ACAG ACAA ATAG ATAG ATAG ATAG ACAG ACAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
* * * *
1133122 AGAG ACAG ACAG ATAT ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATA
1133145 CTAAATCAAA
Statistics
Matches: 207, Mismatches: 48, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
3 4 0.02
4 198 0.96
5 5 0.02
ACGTcount: A:0.52, C:0.09, G:0.21, T:0.17
Consensus pattern (4 bp):
ATAG
Found at i:1132992 original size:40 final size:40
Alignment explanation
Indices: 1132936--1133144 Score: 202
Period size: 40 Copynumber: 5.2 Consensus size: 40
1132926 TATCAAAATT
*
1132936 ATATAGATAGATAGATAGATAGACAGACAGACAGACAGAC
1 ATATAGATAGATAGATAGACAGACAGACAGACAGACAGAC
* * * * * * *
1132976 ATATAGATAGACAGATAGATAGATAGACATATAGATATAC
1 ATATAGATAGATAGATAGACAGACAGACAGACAGACAGAC
* * * * * * * *
1133016 AGAGAGACAGATAGAGAGACAGACATACAGATAGATAAAC
1 ATATAGATAGATAGATAGACAGACAGACAGACAGACAGAC
* * * * *
1133056 AAATAGATAGAGAGAGAGACAGATAGAGAGACAGACAGAC
1 ATATAGATAGATAGATAGACAGACAGACAGACAGACAGAC
* * *
1133096 AAATAGATAGATAGATAGACAGACAGAGAGACAGACAGAT
1 ATATAGATAGATAGATAGACAGACAGACAGACAGACAGAC
1133136 ATATAGATA
1 ATATAGATA
1133145 CTAAATCAAA
Statistics
Matches: 138, Mismatches: 31, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 138 1.00
ACGTcount: A:0.52, C:0.10, G:0.23, T:0.15
Consensus pattern (40 bp):
ATATAGATAGATAGATAGACAGACAGACAGACAGACAGAC
Found at i:1133018 original size:52 final size:52
Alignment explanation
Indices: 1132940--1133134 Score: 228
Period size: 52 Copynumber: 3.8 Consensus size: 52
1132930 AAAATTATAT
* * * * * *
1132940 AGATAGATAGATAGATAGACAGACAGACAGACAGACATATAGATAGACAGAT
1 AGATAGATAGACAGATAGACAGACAGAGAGACAGACAGAGAGACAGACAGAC
* * * * *
1132992 AGATAGATAGACATATAGATATACAGAGAGACAGATAGAGAGACAGACATAC
1 AGATAGATAGACAGATAGACAGACAGAGAGACAGACAGAGAGACAGACAGAC
* * * * *
1133044 AGATAGATAAACAAATAGATAGAGAGAGAGACAGATAGAGAGACAGACAGAC
1 AGATAGATAGACAGATAGACAGACAGAGAGACAGACAGAGAGACAGACAGAC
* *
1133096 AAATAGATAGATAGATAGACAGACAGAGAGACAGACAGA
1 AGATAGATAGACAGATAGACAGACAGAGAGACAGACAGA
1133135 TATATAGATA
Statistics
Matches: 120, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 120 1.00
ACGTcount: A:0.52, C:0.11, G:0.25, T:0.13
Consensus pattern (52 bp):
AGATAGATAGACAGATAGACAGACAGAGAGACAGACAGAGAGACAGACAGAC
Found at i:1133027 original size:28 final size:28
Alignment explanation
Indices: 1132940--1133144 Score: 129
Period size: 28 Copynumber: 7.6 Consensus size: 28
1132930 AAAATTATAT
* *
1132940 AGATAGATAGATAGATAGACAGACAGAC
1 AGATAGACATATAGATAGACAGACAGAC
* * *
1132968 AGACAGACATATAGATAGACAGATAGAT
1 AGATAGACATATAGATAGACAGACAGAC
* *
1132996 AGATAGACATATAGATATACAGAGAGAC
1 AGATAGACATATAGATAGACAGACAGAC
* * * *
1133024 AGATAG----AGAGACAGACATACAGAT
1 AGATAGACATATAGATAGACAGACAGAC
* * * *
1133048 AGATAAACAAATAGATAGAGAGAGAGAC
1 AGATAGACATATAGATAGACAGACAGAC
* * * *
1133076 AGATAG----AGAGACAGACAGACAAAT
1 AGATAGACATATAGATAGACAGACAGAC
* * * *
1133100 AGATAGATAGATAGACAGACAGAGAGAC
1 AGATAGACATATAGATAGACAGACAGAC
* *
1133128 AGACAGATATATAGATA
1 AGATAGACATATAGATA
1133145 CTAAATCAAA
Statistics
Matches: 133, Mismatches: 36, Indels: 16
0.72 0.19 0.09
Matches are distributed among these distances:
24 35 0.26
28 98 0.74
ACGTcount: A:0.52, C:0.10, G:0.24, T:0.14
Consensus pattern (28 bp):
AGATAGACATATAGATAGACAGACAGAC
Found at i:1133203 original size:29 final size:26
Alignment explanation
Indices: 1133137--1133208 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 26
1133127 CAGACAGATA
* *
1133137 TATAGATACTAAATCAAAGAATTTTT
1 TATAAATACTAAATCAAAGAATTATT
**
1133163 TATGCATACTAAATCAAAGAATTAAAATT
1 TATAAATACTAAATCAAAGAATT---ATT
1133192 TATAAATACTAAATCAA
1 TATAAATACTAAATCAA
1133209 CATATATTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
26 21 0.55
29 17 0.45
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.33
Consensus pattern (26 bp):
TATAAATACTAAATCAAAGAATTATT
Found at i:1133320 original size:21 final size:21
Alignment explanation
Indices: 1133296--1133344 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1133286 AATTTGAATT
*
1133296 AATTAATATATATCAAACATA
1 AATTAATAAATATCAAACATA
* *
1133317 AATTTATAAATATCCAACATA
1 AATTAATAAATATCAAACATA
1133338 ATATTAA
1 A-ATTAA
1133345 AATAATACAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (21 bp):
AATTAATAAATATCAAACATA
Found at i:1137148 original size:64 final size:64
Alignment explanation
Indices: 1137074--1137204 Score: 262
Period size: 64 Copynumber: 2.0 Consensus size: 64
1137064 TACAAATGAT
1137074 GAGAGATGTGGGATGGAAATCTTTACTTGAAAAAGTTTCTTTGTTTTGCAAAAAGAATAAAATA
1 GAGAGATGTGGGATGGAAATCTTTACTTGAAAAAGTTTCTTTGTTTTGCAAAAAGAATAAAATA
1137138 GAGAGATGTGGGATGGAAATCTTTACTTGAAAAAGTTTCTTTGTTTTGCAAAAAGAATAAAATA
1 GAGAGATGTGGGATGGAAATCTTTACTTGAAAAAGTTTCTTTGTTTTGCAAAAAGAATAAAATA
1137202 GAG
1 GAG
1137205 GTTCCAAATA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 67 1.00
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (64 bp):
GAGAGATGTGGGATGGAAATCTTTACTTGAAAAAGTTTCTTTGTTTTGCAAAAAGAATAAAATA
Found at i:1138021 original size:30 final size:30
Alignment explanation
Indices: 1137980--1138049 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
1137970 GAACTTTCGA
* *
1137980 ATTATTTTTATTTTCTTCAT-TCT-GAATTAT
1 ATTATTATTATTTTCAT-ATATCTAGAATT-T
*
1138010 TTTATTATTATTTTCATATATCTAGAATTT
1 ATTATTATTATTTTCATATATCTAGAATTT
1138040 ATTATTATTA
1 ATTATTATTA
1138050 AAATATAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 2 0.06
30 27 0.79
31 5 0.15
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.61
Consensus pattern (30 bp):
ATTATTATTATTTTCATATATCTAGAATTT
Found at i:1139204 original size:27 final size:27
Alignment explanation
Indices: 1139174--1139230 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1139164 ATATATATAT
*
1139174 TAATAAAAAAAATAAAT-TAATAAATAC
1 TAATAAAAAAAATAAATCT-ATAAAGAC
* *
1139201 TAATAAAATAATTAAATCTATAAAGAC
1 TAATAAAAAAAATAAATCTATAAAGAC
1139228 TAA
1 TAA
1139231 ATCAAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (27 bp):
TAATAAAAAAAATAAATCTATAAAGAC
Found at i:1139297 original size:78 final size:77
Alignment explanation
Indices: 1139125--1139313 Score: 193
Period size: 78 Copynumber: 2.4 Consensus size: 77
1139115 AAGTTTACCT
*
1139125 TCAAAGAATTAAAATTTAT-AAGTACTAAATCAAAACAAAATATATATATTAATAAAAAAAATAA
1 TCAAAGAATT-AAATCTATAAAG-ACTAAATC-AAACAAAATATATATATTAATAAAAAAAATAA
1139189 ATTAATAAATACTAA
63 ATTAATAAATACTAA
* * * ** **
1139204 TAAAATAATTAAATCTATAAAGACTAAATCAAA-ATAATATATATATTAATACCAAACGTAAATT
1 TCAAAGAATTAAATCTATAAAGACTAAATCAAACAAAATATATATATTAATAAAAAAAATAAATT
* * *
1139268 ACTAAGTTCTAAA
66 AATAAATACT-AA
* * *
1139281 TCAAGGAATTAGAATCTAAAAATACTAAATCAA
1 TCAAAGAATTA-AATCTATAAAGACTAAATCAA
1139314 TATGTTATCA
Statistics
Matches: 91, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
76 33 0.36
77 13 0.14
78 34 0.37
79 11 0.12
ACGTcount: A:0.58, C:0.09, G:0.04, T:0.29
Consensus pattern (77 bp):
TCAAAGAATTAAATCTATAAAGACTAAATCAAACAAAATATATATATTAATAAAAAAAATAAATT
AATAAATACTAA
Found at i:1139392 original size:21 final size:21
Alignment explanation
Indices: 1139368--1139410 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1139358 TATTCTAATT
*
1139368 AATTCATAAATATCAAAAATA
1 AATTCATAAATACCAAAAATA
* *
1139389 AATTTATAAATACCAAACATA
1 AATTCATAAATACCAAAAATA
1139410 A
1 A
1139411 TATCAAAACA
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:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (21 bp):
AATTCATAAATACCAAAAATA
Found at i:1139517 original size:250 final size:250
Alignment explanation
Indices: 1139235--1139749 Score: 994
Period size: 250 Copynumber: 2.1 Consensus size: 250
1139225 GACTAAATCA
* *
1139235 AAATAATATATATATTAATACCAAACGTAAATTACTAAGTTCTAAATCAAGGAATTAGAATCTAA
1 AAATAAAATATATATTAATACCAAACGTAAATTACTAAGTACTAAATCAAGGAATTAGAATCTAA
1139300 AAATACTAAATCAATATGTTATCAAATCTGTAAATACATTCTAAAAATTAAAATAATATATTCTA
66 AAATACTAAATCAATATGTTATCAAATCTGTAAATACATTCTAAAAATTAAAATAATATATTCTA
*
1139365 ATTAATTCATAAATATCAAAAATAAATTTATAAATACCAAACATAATATCAAAACAATATATATA
131 ATTAATTCATAAATACCAAAAATAAATTTATAAATACCAAACATAATATCAAAACAATATATATA
1139430 CAAAATTAAAGAATTAAAATTTATAAATACTTAACGAACATATATTTGAATCACT
196 CAAAATTAAAGAATTAAAATTTATAAATACTTAACGAACATATATTTGAATCACT
*
1139485 AAATAAAATATATATTAATACCAAACGTAAATTACTAAGTACTAAATCAAGGAATTGGAATCTAA
1 AAATAAAATATATATTAATACCAAACGTAAATTACTAAGTACTAAATCAAGGAATTAGAATCTAA
1139550 AAATACTAAATCAATATGTTATCAAATCTGTAAATACATTCTAAAAATTAAAATAATATATTCTA
66 AAATACTAAATCAATATGTTATCAAATCTGTAAATACATTCTAAAAATTAAAATAATATATTCTA
1139615 ATTAATTCATAAATACCAAAAATAAATTTATAAATACCAAACATAATATCAAAACAATATATATA
131 ATTAATTCATAAATACCAAAAATAAATTTATAAATACCAAACATAATATCAAAACAATATATATA
1139680 CAAAATTAAAGAATTAAAATTTATAAATACTTAACGAACATATATTTGAATCACT
196 CAAAATTAAAGAATTAAAATTTATAAATACTTAACGAACATATATTTGAATCACT
1139735 AAATAAAATATATAT
1 AAATAAAATATATAT
1139750 CTCATATATT
Statistics
Matches: 261, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
250 261 1.00
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.32
Consensus pattern (250 bp):
AAATAAAATATATATTAATACCAAACGTAAATTACTAAGTACTAAATCAAGGAATTAGAATCTAA
AAATACTAAATCAATATGTTATCAAATCTGTAAATACATTCTAAAAATTAAAATAATATATTCTA
ATTAATTCATAAATACCAAAAATAAATTTATAAATACCAAACATAATATCAAAACAATATATATA
CAAAATTAAAGAATTAAAATTTATAAATACTTAACGAACATATATTTGAATCACT
Found at i:1139642 original size:21 final size:21
Alignment explanation
Indices: 1139618--1139660 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1139608 TATTCTAATT
1139618 AATTCATAAATACCAAAAATA
1 AATTCATAAATACCAAAAATA
* *
1139639 AATTTATAAATACCAAACATA
1 AATTCATAAATACCAAAAATA
1139660 A
1 A
1139661 TATCAAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (21 bp):
AATTCATAAATACCAAAAATA
Found at i:1143829 original size:5 final size:5
Alignment explanation
Indices: 1143819--1143844 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1143809 ACTACATACC
1143819 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
1143845 TACAAGTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:1143955 original size:29 final size:29
Alignment explanation
Indices: 1143923--1143999 Score: 127
Period size: 29 Copynumber: 2.7 Consensus size: 29
1143913 ACATGGGGCT
1143923 AAATTAAAATAAATTAAAATTACATGGAC
1 AAATTAAAATAAATTAAAATTACATGGAC
*
1143952 AAATTAAAATAAATTAAAATTACATGGCC
1 AAATTAAAATAAATTAAAATTACATGGAC
* *
1143981 GAATTAAAATAAATAAAAA
1 AAATTAAAATAAATTAAAA
1144000 AACATATTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.26
Consensus pattern (29 bp):
AAATTAAAATAAATTAAAATTACATGGAC
Found at i:1145689 original size:42 final size:42
Alignment explanation
Indices: 1145651--1145737 Score: 102
Period size: 42 Copynumber: 2.1 Consensus size: 42
1145641 CTCGAAGGGT
*
1145651 TTAATCATCATGCTCAAAAGACTTACAGATAACCCGAAGGAC
1 TTAAACATCATGCTCAAAAGACTTACAGATAACCCGAAGGAC
* ** * * * *
1145693 TTAAACATTATGCTTGAAAGACTTACTGATTACCCAAACGAC
1 TTAAACATCATGCTCAAAAGACTTACAGATAACCCGAAGGAC
1145735 TTA
1 TTA
1145738 CCAACTTTGG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (42 bp):
TTAAACATCATGCTCAAAAGACTTACAGATAACCCGAAGGAC
Found at i:1145944 original size:42 final size:41
Alignment explanation
Indices: 1145875--1145970 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 41
1145865 TTGTGGATTG
* * *
1145875 CCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAAATGA
1 CCCGAAGGACTTAGCATCATGCTCGAAAGACTAACAAATGA
* ** *
1145916 CCCGAAGGATTTAAGCATCATGCTCGAAAGACTAACTGATGG
1 CCCGAAGGACTT-AGCATCATGCTCGAAAGACTAACAAATGA
1145958 CCCGAAGGACTTA
1 CCCGAAGGACTTA
1145971 TAAATTTTGG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 12 0.26
42 34 0.74
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (41 bp):
CCCGAAGGACTTAGCATCATGCTCGAAAGACTAACAAATGA
Found at i:1146076 original size:233 final size:233
Alignment explanation
Indices: 1145654--1147684 Score: 2703
Period size: 233 Copynumber: 8.7 Consensus size: 233
1145644 GAAGGGTTTA
* * * * * * *
1145654 ATCATCATGCTCAAAAGACTTACAGATAACCCGAAGGACTTAAACATTATGCTTGAAAGACTTAC
1 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
** * * ** * * *
1145719 TGATTACCCAAACGACTTACCAACTTTGGAAATAATTTACTAGGTAAGAAACTTTTCTTACTTTT
66 TGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT
* * *
1145784 CAAAAATTTCAATTTTCATATTTAAATGAGAAACCTTTCTCATTTTTCGAGAGACATGTGAAAAC
131 CAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTCATATTTCGATAGACATGTGAAAAC
* *
1145849 ATC-CGACCTGAAGGTCTTGTGGATTGCCCGAAGGACTT
196 ATCACG-CCCGAAGGTCTTATGGATTGCCCGAAGGACTT
* *
1145887 ATCATCTTGCTCGAAAGACTTACAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTAAC
1 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
* ** *
1145952 TGATGGCCCGAAGGACTTATAAATTTTGGAAATAATTTACTAGGTAAGAAAGTTTTCTTTCTTTT
66 TGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT
* *
1146017 CAAAAATTTCAATTTTCAAATTTAAATGATAAACCTTTCTCATATTTCGATAAACATGTG-AAAC
131 CAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTCATATTTCGATAGACATGTGAAAAC
** * *
1146081 ATC-CTATCCGAAGATCTTATGGATGGCCCGAAGGACTT
196 ATCAC-GCCCGAAGGTCTTATGGATTGCCCGAAGGACTT
* * * *
1146119 ATCATCTTGCTCGAAAGAATTACAAATGACACGAAGGATTTAAGCATCATGCTCGAAACACTTAC
1 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
* *
1146184 TGATGGCGATGGCCCGAATGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCAT
66 ---T---GATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTT
* * * * *
1146249 AATTTTCAAAAATTTCAAATTTCAAATTTAAATGAGAATCATTTCTCATATTTTGATAGACATGT
125 ACTTTTCAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTCATATTTCGATAGACATGT
* *
1146314 GAAAACATCATGCCCGAAGGTCTTATCGA-TGCCCCGAAGGACTT
190 GAAAACATCACGCCCGAAGGTCTTATGGATTG-CCCGAAGGACTT
* * * * *
1146358 ATCATCTTGCTCAAAAGACTTATATATAACCCGAAGGATTTAAGCATCATGCTCGAGAGACTTAC
1 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
* * * *
1146423 TAATGGCCCGAAGAACTTATAAACTTTGAAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT
66 TGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT
*
1146488 CAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTCATATTTCAATAGACATGTGAAAAC
131 CAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTCATATTTCGATAGACATGTGAAAAC
* * * * *
1146553 ATCATGTCCGAAGGTCTTATGGA-TGGCTGAAGAACTT
196 ATCACGCCCGAAGGTCTTATGGATTGCCCGAAGGACTT
* * * * * *
1146590 AGCATCTTTCTCAAAAGACTTATAGATGACTCGAAGGATTTAAGCATCATGCTCGAAAGACTTAT
1 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
* * *
1146655 TGATGGCCCAAAGGACTTAAAAATTTTAGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT
66 TGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT
** * *
1146720 CAAAAATTTCAAATTTT-TGATTTAAATAAGAAACATTTCTCATATTTCGATAGACATGTGAAAA
131 CAAAAATTTC-AATTTTCAAATTTAAATGAGAAACCTTTCTCATATTTCGATAGACATGTGAAAA
** *
1146784 CATCTTGCCCGAAGGTCTTATGGA-TGACCCGAAGGACAT
195 CATCACGCCCGAAGGTCTTATGGATTG-CCCGAAGGACTT
* * *
1146823 ATCATCTTGCTCGATAGACTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAGAGACTTAC
1 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
*
1146888 TGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGATAAGAAACCTTTCTTACTTTT
66 TGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT
* * * *
1146953 CAAAAAATTCAATTTTCAAATTTAAATTAGAAACATTTCTCATATTTCAATAGACATGTGAAAAC
131 CAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTCATATTTCGATAGACATGTGAAAAC
** * * * *
1147018 ATCTTGCCCGAAGGTCTTTTGGATAGACCGAAAGACTT
196 ATCACGCCCGAAGGTCTTATGGATTGCCCGAAGGACTT
* * *
1147056 ATCATCTTACTCGAAAGACTTACAGATGACTCGAAAGATTTAAGCATCATGCTCGAAAGACTTAC
1 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
* * *
1147121 TGATGGCTCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTATGAAACCTTTCTTATTTTT
66 TGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT
* * *
1147186 CAAAAATTTCAAATTTCATATTTAAATGAGAAACCTTTCTCATAATTCGATAGACATGTGAAAAC
131 CAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTCATATTTCGATAGACATGTGAAAAC
* ** * * * *
1147251 ATC-CTGCCCGATGAACTTATAGATAGTCCGAATGACTT
196 ATCAC-GCCCGAAGGTCTTATGGATTGCCCGAAGGACTT
* * * *
1147289 ATCATCTTGCTCAAAAGACTTACAGATTAGCCGAAGGATTTAAGCATCATGCTCGAAAGAATTAC
1 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
* * * *
1147354 TAATGGTCCGAAGGTCTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTGT
66 TGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT
* * * * * *
1147419 AAAAAATTTTAATTTTCAGATTTAAATGAGAAACGTTTCTCATATTTCGTTAGACATGTGAAAAT
131 CAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTCATATTTCGATAGACATGTGAAAAC
* * *
1147484 ATC-CTGCCTGAAGGTCTTATGGATTTCCTGAAGGACTT
196 ATCAC-GCCCGAAGGTCTTATGGATTGCCCGAAGGACTT
*
1147522 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCTTGCTCGAAAGACTTAC
1 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
* * *
1147587 TGATGACCCGAAGGACTTATAAATATTGGAAATAGTTTACTATGTAAGAAACCTTTCTTACTTTT
66 TGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT
* * *
1147652 CAGAAATTTCAAATTTCAGATTTAAATGAGAAA
131 CAAAAATTTCAATTTTCAAATTTAAATGAGAAA
1147685 TATTTTGTAA
Statistics
Matches: 1587, Mismatches: 196, Indels: 30
0.88 0.11 0.02
Matches are distributed among these distances:
232 303 0.19
233 1079 0.68
234 1 0.00
235 1 0.00
236 1 0.00
238 112 0.07
239 90 0.06
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (233 bp):
ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
TGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT
CAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTCATATTTCGATAGACATGTGAAAAC
ATCACGCCCGAAGGTCTTATGGATTGCCCGAAGGACTT
Found at i:1146845 original size:41 final size:41
Alignment explanation
Indices: 1146800--1146903 Score: 120
Period size: 42 Copynumber: 2.5 Consensus size: 41
1146790 GCCCGAAGGT
* * *
1146800 CTTATGGATGACCCGAAGGACAT-ATCATCTTGCTCGATAGA
1 CTTAT-GATGACCCGAAGGACATAAGCATCATGCTCGAGAGA
**
1146841 CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAGAGA
1 CTTAT-GATGACCCGAAGGACATAAGCATCATGCTCGAGAGA
*
1146883 CTTACTGATGGCCCGAAGGAC
1 CTTA-TGATGACCCGAAGGAC
1146904 TTATAAATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 20 0.38
42 32 0.60
43 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (41 bp):
CTTATGATGACCCGAAGGACATAAGCATCATGCTCGAGAGA
Found at i:1147089 original size:20 final size:20
Alignment explanation
Indices: 1147064--1147139 Score: 73
Period size: 20 Copynumber: 3.7 Consensus size: 20
1147054 TTATCATCTT
1147064 ACTCGAAAGACTTACAGATG
1 ACTCGAAAGACTTACAGATG
* *
1147084 ACTCGAAAGATTTA-AGCATC
1 ACTCGAAAGACTTACAG-ATG
*
1147104 ATGCTCGAAAGACTTACTGATG
1 A--CTCGAAAGACTTACAGATG
* *
1147126 GCTCGAAGGACTTA
1 ACTCGAAAGACTTA
1147140 TAAATTTTGG
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
19 2 0.04
20 28 0.62
22 14 0.31
23 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.24
Consensus pattern (20 bp):
ACTCGAAAGACTTACAGATG
Found at i:1149303 original size:6 final size:6
Alignment explanation
Indices: 1149294--1149372 Score: 59
Period size: 6 Copynumber: 13.2 Consensus size: 6
1149284 GTGTGTGTGT
* * * * * *
1149294 ATACAC ATACAC ATGCAC ATGCAC ATGCAC ATGCAC ATATAC ACACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
* * * * *
1149342 ACACAC ACACAC ACACAC ACACAC ACACAC A
1 ATACAC ATACAC ATACAC ATACAC ATACAC A
1149373 CACATATATA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.46, C:0.39, G:0.05, T:0.10
Consensus pattern (6 bp):
ATACAC
Found at i:1149341 original size:2 final size:2
Alignment explanation
Indices: 1149334--1149376 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1149324 ATGCACATAT
1149334 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1149376 A
1 A
1149377 TATATATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1149381 original size:2 final size:2
Alignment explanation
Indices: 1149376--1149405 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1149366 ACACACACAC
1149376 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1149406 ATCACCTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1158025 original size:3 final size:3
Alignment explanation
Indices: 1158017--1158046 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1158007 CATAAATAGA
1158017 AAT AAT AAT AAT AAT AAAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AA
1158047 AAGGCACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1158035 original size:16 final size:16
Alignment explanation
Indices: 1158016--1158046 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1158006 ACATAAATAG
1158016 AAATAATAATAATAAT
1 AAATAATAATAATAAT
1158032 AAATAATAATAATAA
1 AAATAATAATAATAA
1158047 AAGGCACAAA
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATAATAATAATAAT
Found at i:1158036 original size:13 final size:13
Alignment explanation
Indices: 1158020--1158047 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1158010 AAATAGAAAT
1158020 AATAATAATAATA
1 AATAATAATAATA
1158033 AATAATAATAATA
1 AATAATAATAATA
1158046 AA
1 AA
1158048 AGGCACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:1158127 original size:24 final size:23
Alignment explanation
Indices: 1158070--1158165 Score: 95
Period size: 23 Copynumber: 4.1 Consensus size: 23
1158060 GGTGTCGACA
* *
1158070 TCACGAACATGTTCGTTTAATGT
1 TCACGAACGTGTTCATTTAATGT
1158093 TCACGAACGTGTTCATTTATATGT
1 TCACGAACGTGTTCATTTA-ATGT
* **
1158117 TCA-TAAGCGTGTTCATTTAGCGT
1 TCACGAA-CGTGTTCATTTAATGT
* * *
1158140 TCACGAACATGCTCATTTAGTGT
1 TCACGAACGTGTTCATTTAATGT
1158163 TCA
1 TCA
1158166 TTTATCATTA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
23 40 0.66
24 21 0.34
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.39
Consensus pattern (23 bp):
TCACGAACGTGTTCATTTAATGT
Found at i:1164159 original size:29 final size:29
Alignment explanation
Indices: 1164117--1164174 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
1164107 TGCAAAAAGG
*
1164117 GGGAGCTGAACATTTTCACATATTTTTCC
1 GGGAGCTGAACATTTTAACATATTTTTCC
*
1164146 GGGAGCTGAACATTTTAATATATTTTTCC
1 GGGAGCTGAACATTTTAACATATTTTTCC
1164175 AACAATTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (29 bp):
GGGAGCTGAACATTTTAACATATTTTTCC
Found at i:1170079 original size:19 final size:18
Alignment explanation
Indices: 1170039--1170083 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
1170029 ATTTAAATAT
*
1170039 TTTTTAAAAATATGATTT
1 TTTTTAAAAATATGATTA
1170057 TTTTTAAAAATGATCGA-TA
1 TTTTTAAAAAT-AT-GATTA
1170076 TTTTTAAA
1 TTTTTAAA
1170084 TGTTTTTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 11 0.46
19 11 0.46
20 2 0.08
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (18 bp):
TTTTTAAAAATATGATTA
Found at i:1174149 original size:2 final size:2
Alignment explanation
Indices: 1174142--1174179 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1174132 AATGCATTGT
1174142 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1174180 GACTAATGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1180687 original size:18 final size:18
Alignment explanation
Indices: 1180664--1180736 Score: 92
Period size: 18 Copynumber: 3.9 Consensus size: 18
1180654 AGGGATTATC
1180664 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
1180682 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
*
1180701 CAGTGGTCCTCCGGGACAT
1 -AGTGGTCCTTCGGGACAT
*
1180720 AGTGGTCATTCGGGACA
1 AGTGGTCCTTCGGGACA
1180737 AATATTTAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
18 29 0.63
19 4 0.09
20 13 0.28
ACGTcount: A:0.21, C:0.22, G:0.32, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1183218 original size:16 final size:15
Alignment explanation
Indices: 1183197--1183281 Score: 64
Period size: 16 Copynumber: 5.2 Consensus size: 15
1183187 TGTTAGAGGG
1183197 AAAAAAATGAATAAAT
1 AAAAAAATGAA-AAAT
*
1183213 AAAAAAATGAAGAAT
1 AAAAAAATGAAAAAT
*
1183228 AAAAATAAGTAAAAAAAT
1 AAAAA-AA-T-GAAAAAT
*
1183246 AAAATAAAAGGAAAAAT
1 -AAA-AAAATGAAAAAT
1183263 AAATAAAAT-AATAAAT
1 AAA-AAAATGAA-AAAT
1183279 AAA
1 AAA
1183282 TATTAAATAA
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
15 10 0.18
16 28 0.49
17 7 0.12
18 5 0.09
19 5 0.09
20 2 0.04
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.16
Consensus pattern (15 bp):
AAAAAAATGAAAAAT
Found at i:1183240 original size:25 final size:23
Alignment explanation
Indices: 1183206--1183283 Score: 79
Period size: 25 Copynumber: 3.3 Consensus size: 23
1183196 GAAAAAAATG
1183206 AATAAATAAAAAAATGAAGAATAAA
1 AATAAATAAAAAAAT-AA-AATAAA
*
1183231 AATAAGTAAAAAAATAAAAT-AA
1 AATAAATAAAAAAATAAAATAAA
** *
1183253 AAGGAA-AAATAAATAAAATAATA
1 AATAAATAAAAAAATAAAATAA-A
1183276 AATAAATA
1 AATAAATA
1183284 TTAAATAATA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
21 12 0.28
22 6 0.14
23 8 0.19
24 3 0.07
25 14 0.33
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (23 bp):
AATAAATAAAAAAATAAAATAAA
Found at i:1183243 original size:12 final size:12
Alignment explanation
Indices: 1183206--1183247 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
1183196 GAAAAAAATG
*
1183206 AATAAATAAAAA
1 AATAAGTAAAAA
1183218 AATGAAG-AATAAA
1 AAT-AAGTAA-AAA
1183231 AATAAGTAAAAA
1 AATAAGTAAAAA
1183243 AATAA
1 AATAA
1183248 AATAAAAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (12 bp):
AATAAGTAAAAA
Found at i:1183302 original size:18 final size:18
Alignment explanation
Indices: 1183259--1183293 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1183249 ATAAAAGGAA
1183259 AAATAAATA--AAATAAT
1 AAATAAATATTAAATAAT
1183275 AAATAAATATTAAATAAT
1 AAATAAATATTAAATAAT
1183293 A
1 A
1183294 TATATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
18 8 0.47
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATAAATATTAAATAAT
Found at i:1183579 original size:2 final size:2
Alignment explanation
Indices: 1183574--1183613 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1183564 TTAAAAAAAG
*
1183574 TA TA TA TA TA TA TA TA TA TA TA TA TA TC 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
1183614 AATAATAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1184186 original size:37 final size:37
Alignment explanation
Indices: 1184145--1184249 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
1184135 GTACTTGTGG
* *
1184145 ATCCTATATTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
* * * *
1184182 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
*
1184219 ATCCTATTTTTAGGAGTTTGAATCTTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAG
1184250 GACGAAAAGG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
Found at i:1187125 original size:149 final size:149
Alignment explanation
Indices: 1186855--1187150 Score: 592
Period size: 149 Copynumber: 2.0 Consensus size: 149
1186845 TTGACACCGA
1186855 CGGACTCGAAACGACACAAGGAACACGATGGTACAAGAGGTGTCGTAAACAGCGCAACGATCGGC
1 CGGACTCGAAACGACACAAGGAACACGATGGTACAAGAGGTGTCGTAAACAGCGCAACGATCGGC
1186920 GGTGAATTTAAGATTTTCCCGGTGATAGAGCTAACAAAAACGTCTAGACTTTGACTGTAAATTCT
66 GGTGAATTTAAGATTTTCCCGGTGATAGAGCTAACAAAAACGTCTAGACTTTGACTGTAAATTCT
1186985 CGATGTTTGGCAGCGTTGC
131 CGATGTTTGGCAGCGTTGC
1187004 CGGACTCGAAACGACACAAGGAACACGATGGTACAAGAGGTGTCGTAAACAGCGCAACGATCGGC
1 CGGACTCGAAACGACACAAGGAACACGATGGTACAAGAGGTGTCGTAAACAGCGCAACGATCGGC
1187069 GGTGAATTTAAGATTTTCCCGGTGATAGAGCTAACAAAAACGTCTAGACTTTGACTGTAAATTCT
66 GGTGAATTTAAGATTTTCCCGGTGATAGAGCTAACAAAAACGTCTAGACTTTGACTGTAAATTCT
1187134 CGATGTTTGGCAGCGTT
131 CGATGTTTGGCAGCGTT
1187151 TCGCTTCAAT
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 147 1.00
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (149 bp):
CGGACTCGAAACGACACAAGGAACACGATGGTACAAGAGGTGTCGTAAACAGCGCAACGATCGGC
GGTGAATTTAAGATTTTCCCGGTGATAGAGCTAACAAAAACGTCTAGACTTTGACTGTAAATTCT
CGATGTTTGGCAGCGTTGC
Found at i:1193808 original size:14 final size:14
Alignment explanation
Indices: 1193769--1193808 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
1193759 TCAAAGGAAG
*
1193769 TCAACGGTCAGCGA
1 TCAACGGTCAACGA
*
1193783 TC-ACGGTTAACGA
1 TCAACGGTCAACGA
1193796 TCAACGGTCAACG
1 TCAACGGTCAACG
1193809 GTCGGGTCGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.17
Consensus pattern (14 bp):
TCAACGGTCAACGA
Found at i:1193818 original size:5 final size:5
Alignment explanation
Indices: 1193808--1193845 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
1193798 AACGGTCAAC
* *
1193808 GGTCG GGTCG GGTCG GGTC- AGTCA GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
1193846 AGTCGAGTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
4 3 0.10
5 26 0.90
ACGTcount: A:0.05, C:0.21, G:0.53, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:1193837 original size:19 final size:19
Alignment explanation
Indices: 1193813--1193849 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1193803 TCAACGGTCG
1193813 GGTCGGGTCGGGTCAGTCA
1 GGTCGGGTCGGGTCAGTCA
1193832 GGTCGGGTCGGGTCAGTC
1 GGTCGGGTCGGGTCAGTC
1193850 GAGTCGGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.08, C:0.22, G:0.49, T:0.22
Consensus pattern (19 bp):
GGTCGGGTCGGGTCAGTCA
Found at i:1193855 original size:19 final size:19
Alignment explanation
Indices: 1193809--1193856 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
1193799 ACGGTCAACG
*
1193809 GTCGGGTCGGGTCGGGTCA
1 GTCGAGTCGGGTCGGGTCA
1193828 GTC-AGGTCGGGTCGGGTCA
1 GTCGA-GTCGGGTCGGGTCA
1193847 GTCGAGTCGG
1 GTCGAGTCGG
1193857 TCAGACCGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 25 0.96
20 1 0.04
ACGTcount: A:0.08, C:0.21, G:0.50, T:0.21
Consensus pattern (19 bp):
GTCGAGTCGGGTCGGGTCA
Found at i:1193881 original size:19 final size:18
Alignment explanation
Indices: 1193854--1193960 Score: 115
Period size: 19 Copynumber: 5.7 Consensus size: 18
1193844 TCAGTCGAGT
*
1193854 CGGTCAGACCGGTCAAAC
1 CGGTCAAACCGGTCAAAC
* * *
1193872 CGGTTCAGACTGATCAAAC
1 CGG-TCAAACCGGTCAAAC
*
1193891 CGGTCAAACCGGTTCAGAC
1 CGGTCAAACCGG-TCAAAC
* *
1193910 TGATCAAACCGGTCGAAAC
1 CGGTCAAACCGGTC-AAAC
1193929 CGGTCAAACCGGTCAGAAC
1 CGGTCAAACCGGTCA-AAC
1193948 CGGTCAAACCGGT
1 CGGTCAAACCGGT
1193961 TTCCAGCCCT
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
18 12 0.16
19 62 0.84
ACGTcount: A:0.30, C:0.30, G:0.25, T:0.15
Consensus pattern (18 bp):
CGGTCAAACCGGTCAAAC
Found at i:1193893 original size:28 final size:28
Alignment explanation
Indices: 1193861--1193961 Score: 150
Period size: 28 Copynumber: 3.6 Consensus size: 28
1193851 AGTCGGTCAG
1193861 ACCGGTCAAACCGGTTCAGACTGATCAA
1 ACCGGTCAAACCGGTTCAGACTGATCAA
1193889 ACCGGTCAAACCGGTTCAGACTGATCAA
1 ACCGGTCAAACCGGTTCAGACTGATCAA
* * *
1193917 ACCGGTCGAAACCGG-TCAAACCGGTCAGA
1 ACCGGTC-AAACCGGTTCAGACTGATCA-A
1193946 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
1193962 TCCAGCCCTC
Statistics
Matches: 67, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
28 51 0.76
29 16 0.24
ACGTcount: A:0.31, C:0.30, G:0.24, T:0.16
Consensus pattern (28 bp):
ACCGGTCAAACCGGTTCAGACTGATCAA
Found at i:1193930 original size:10 final size:9
Alignment explanation
Indices: 1193854--1193960 Score: 115
Period size: 9 Copynumber: 11.4 Consensus size: 9
1193844 TCAGTCGAGT
*
1193854 CGGTCAGAC
1 CGGTCAAAC
1193863 CGGTCAAAC
1 CGGTCAAAC
*
1193872 CGGTTCAGAC
1 CGG-TCAAAC
* *
1193882 TGATCAAAC
1 CGGTCAAAC
1193891 CGGTCAAAC
1 CGGTCAAAC
*
1193900 CGGTTCAGAC
1 CGG-TCAAAC
* *
1193910 TGATCAAAC
1 CGGTCAAAC
1193919 CGGTCGAAAC
1 CGGTC-AAAC
1193929 CGGTCAAAC
1 CGGTCAAAC
1193938 CGGTCAGAAC
1 CGGTCA-AAC
1193948 CGGTCAAAC
1 CGGTCAAAC
1193957 CGGT
1 CGGT
1193961 TTCCAGCCCT
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
9 51 0.63
10 30 0.37
ACGTcount: A:0.30, C:0.30, G:0.25, T:0.15
Consensus pattern (9 bp):
CGGTCAAAC
Found at i:1194916 original size:106 final size:106
Alignment explanation
Indices: 1194688--1196505 Score: 2786
Period size: 106 Copynumber: 17.2 Consensus size: 106
1194678 GGTTGTTACA
* * *
1194688 GAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
* * * * *
1194749 A-AT-TTTGTTGACAATCAGCCGCCCCTTCGTCGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * * *
1194788 GAGCTTGTGTTGTCTTGG-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGG
1 GAACTTGCGTTGTC-TGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
*
1194852 AAGTTGTTTATTGACAACCAGCGATCCCTTCGTCGTGAAGTT
65 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * * *
1194894 AAACTTGCGTTGTCTTGAGTCCAATATCCTACGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
* * *
1194959 AATTGTTTATTGACAACCAGCGGTCCCTTTGTCATGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * * **
1195000 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTAGCTCTAAAATTAAGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
* *
1195065 AGTTCTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
1195106 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
* * **
1195171 AGTTGTTTATTGACAACCAACGGTCTCTTTTTCGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * * *
1195212 GAACTTGCGTTGTATTGAGTTCAATATCCTTCGCTATGAAGTTGAAATTGGCTCTGAAATTGGGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
* * *
1195277 AATTGTTTGTTGACAACCAGCGGTCCCTTTGTCGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * *
1195318 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTAGCTCTGAAATTGAGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
*
1195383 AGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * * *
1195424 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGCGAAGTTGAAATTGGCTATGAAATTGAGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
*
1195489 AGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * * *
1195530 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGCGAAGTTGAAATTGGCTCTAAAATTGAGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
* * *
1195595 AGTTATTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* *
1195636 GAACTTGCGTTGTCTGGAGTCCAATATCCTTTGATGTGAAGTTGAAATTGGCTCTGAAATTGGGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
* *
1195701 AGTTGTTTATTGACAACCAACGGTCCCTTCTTCGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * *
1195742 GAACTTGCGTTGTCTTGAGTCCAATATCCTACGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
*
1195807 AATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * *
1195848 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
*
1195913 AGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
1195954 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
*
1196019 AGTTGTTTATTGACAACCAACGGTCCCTTCGTCGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * *
1196060 GAACTTGCGTTGTCTTGAGTCCAATATCATTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
*
1196125 AATTGTTTATTGACACATCCAGCGGTCCCTTCGTCGTGAAGTT
66 AGTTGTTTATTGACA-A-CCAGCGGTCCCTTCGTCGTGAAGTT
* * *
1196168 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAATTTGAAATTGGCTCTGAAATTGAGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
* *
1196233 AGTCGTTTATTGACAACCAGCGGTCCCTTCGTTGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
*
1196274 GAACTTGCGTTGTATGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
* *
1196339 AATTGTTTATTGACAACCAGAGGTCCCTTCGTCGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* *
1196380 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
* * *
1196445 AGTTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGATGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* *
1196486 GAACTTGTGTTGTCTTGAGT
1 GAACTTGCGTTGTCTGGAGT
1196506 GGCACGATAT
Statistics
Matches: 1575, Mismatches: 133, Indels: 14
0.91 0.08 0.01
Matches are distributed among these distances:
100 48 0.03
101 4 0.00
102 1 0.00
104 3 0.00
105 3 0.00
106 1418 0.90
107 2 0.00
108 96 0.06
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
Found at i:1198034 original size:172 final size:175
Alignment explanation
Indices: 1197736--1198085 Score: 521
Period size: 172 Copynumber: 2.0 Consensus size: 175
1197726 TAAATAGGCC
* *
1197736 CAAACAAGTATTTCAGGGTGTTGAACCAAGGATCAATTCATTCTGATTCCTTCAATCATGTCCTG
1 CAAACAAGTATTTCAGGGCGTTGAACCAAGGATCAATTCATTATGATTCCTTCAA-CA-GTCCTG
* * *
1197801 CTCAAACTGTCTCTGTCTTGATGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGA
64 CTCAAAATGTCTCTCTCTT-ATGATGCTCTATGATATTCGAGTGAAGTGATTCAGTGATTCGGGA
* *
1197866 ATGACTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
128 ATGACTGTGCTTGATCAATATCATAGTTTGAAGCTTGATGAGCCATTT
* *
1197914 CAAACAAGTGTTTTAGGGCGTTGAACCAAGGATCAATTCATTATGATGT-CTTC-A-A-TCCTGC
1 CAAACAAGTATTTCAGGGCGTTGAACCAAGGATCAATTCATTATGAT-TCCTTCAACAGTCCTGC
*
1197975 TCAAAATGTTTCTCTCTCT-TGATGCTCTATGATATTCGAGTGAAGTGATTCAGTGATTCGGGAA
65 TCAAAATGTCTCTCTCT-TATGATGCTCTATGATATTCGAGTGAAGTGATTCAGTGATTCGGGAA
*
1198039 TGATTGTGCTTGATCAATATCATAGTTTGAAGCTTGATGAGCCATTT
129 TGACTGTGCTTGATCAATATCATAGTTTGAAGCTTGATGAGCCATTT
1198086 GTCTTTAGGG
Statistics
Matches: 159, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
172 88 0.55
173 20 0.13
174 1 0.01
175 1 0.01
177 1 0.01
178 47 0.30
179 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (175 bp):
CAAACAAGTATTTCAGGGCGTTGAACCAAGGATCAATTCATTATGATTCCTTCAACAGTCCTGCT
CAAAATGTCTCTCTCTTATGATGCTCTATGATATTCGAGTGAAGTGATTCAGTGATTCGGGAATG
ACTGTGCTTGATCAATATCATAGTTTGAAGCTTGATGAGCCATTT
Found at i:1202551 original size:12 final size:12
Alignment explanation
Indices: 1202534--1202592 Score: 50
Period size: 13 Copynumber: 4.8 Consensus size: 12
1202524 AAAAATGAAT
1202534 AAATGAAAAAAA
1 AAATGAAAAAAA
*
1202546 AAATGAAGAATAA
1 AAATGAA-AAAAA
1202559 AAAT-AAGTAAAAA
1 AAATGAA--AAAAA
*
1202572 AAAT-AAAAATA
1 AAATGAAAAAAA
*
1202583 AAAGGAAAAA
1 AAATGAAAAA
1202593 TAAATAAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 7 0.18
12 14 0.36
13 18 0.46
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (12 bp):
AAATGAAAAAAA
Found at i:1202578 original size:9 final size:10
Alignment explanation
Indices: 1202554--1202612 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
1202544 AAAAATGAAG
1202554 AATAAAAATA
1 AATAAAAATA
*
1202564 AGTAAAAA-A
1 AATAAAAATA
1202573 AATAAAAATAA
1 AATAAAAAT-A
*
1202584 AAGGAAAAATA
1 AA-TAAAAATA
1202595 AAT--AAATA
1 AATAAAAATA
*
1202603 AATGAAAATA
1 AATAAAAATA
1202613 TTAAATATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
8 8 0.20
9 8 0.20
10 12 0.30
11 6 0.15
12 6 0.15
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (10 bp):
AATAAAAATA
Found at i:1202609 original size:19 final size:18
Alignment explanation
Indices: 1202526--1202610 Score: 64
Period size: 19 Copynumber: 4.5 Consensus size: 18
1202516 TAGAGGGAAA
*
1202526 AAATGAATAAATGAAAAAAA
1 AAATGAA-AAAT-AAAAAAT
*
1202546 AAATGAAGAAT-AAAAAT
1 AAATGAAAAATAAAAAAT
* * *
1202563 AAGTAAAAAAAATAAAAAT
1 AAATGAAAAATA-AAAAAT
*
1202582 AAAAGGAAAAATAAATAAAT
1 -AAATGAAAAATAAA-AAAT
1202602 AAATGAAAA
1 AAATGAAAA
1202611 TATTAAATAT
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
17 12 0.24
19 19 0.38
20 19 0.38
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.15
Consensus pattern (18 bp):
AAATGAAAAATAAAAAAT
Found at i:1202624 original size:2 final size:2
Alignment explanation
Indices: 1202617--1202641 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1202607 AAAATATTAA
1202617 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1202642 AATGAGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1202708 original size:13 final size:13
Alignment explanation
Indices: 1202685--1202745 Score: 52
Period size: 13 Copynumber: 4.6 Consensus size: 13
1202675 ATAATGATAG
*
1202685 TAATATGAAAATA
1 TAATATAAAAATA
*
1202698 TAATATAAAAAAA
1 TAATATAAAAATA
* *
1202711 AAATATATAAATCA
1 TAATATAAAAAT-A
*
1202725 -AATATAAAAGTA
1 TAATATAAAAATA
1202737 TACATATAA
1 TA-ATATAA
1202746 TGATAATTGC
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
12 1 0.03
13 30 0.79
14 7 0.18
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (13 bp):
TAATATAAAAATA
Found at i:1202880 original size:2 final size:2
Alignment explanation
Indices: 1202873--1202919 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
1202863 AAAATATTTA
1202873 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1202914 A- AT AT A
1 AT AT AT A
1202920 AAAAATAACC
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1202954 original size:21 final size:21
Alignment explanation
Indices: 1202914--1202954 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1202904 TATATATAAT
*
1202914 AATATAAAAAATAACCAAATG
1 AATATAAAAAATAACAAAATG
1202935 AATATAAATAAATAA-AAAAT
1 AATATAAA-AAATAACAAAAT
1202955 ATGTATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (21 bp):
AATATAAAAAATAACAAAATG
Found at i:1203450 original size:37 final size:37
Alignment explanation
Indices: 1203409--1203506 Score: 110
Period size: 37 Copynumber: 2.6 Consensus size: 37
1203399 GTGCTTGTGG
*
1203409 ATCCTATATTTAGGAGTTTAAAT-TATAGTAGAACTCT
1 ATCCTATATTTAGGAGTTTAAATCT-TAGTAAAACTCT
* * *
1203446 ATCCTATTTTTAGGAGTTTGAATCTTAGTAAAATTCT
1 ATCCTATATTTAGGAGTTTAAATCTTAGTAAAACTCT
* *
1203483 ATCCTA-ATTTTAAGAGTTTGAATC
1 ATCCTATA-TTTAGGAGTTTAAATC
1203507 CTAATAGGAC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
37 52 0.98
38 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (37 bp):
ATCCTATATTTAGGAGTTTAAATCTTAGTAAAACTCT
Found at i:1205686 original size:2 final size:2
Alignment explanation
Indices: 1205681--1205712 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1205671 AAGTGTGTCG
1205681 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
1205713 TTTTCTTCCT
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:1209174 original size:21 final size:20
Alignment explanation
Indices: 1209125--1209180 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
1209115 GTTTTTGTAA
1209125 TTTT-AAATAAA-TTTAGAT
1 TTTTAAAATAAATTTTAGAT
** *
1209143 TTTTATTATAAATTTTAAGTT
1 TTTTAAAATAAATTTT-AGAT
1209164 TTTTAAAATAAAATTTT
1 TTTTAAAAT-AAATTTT
1209181 CAAGAAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 4 0.14
19 5 0.17
20 3 0.10
21 10 0.34
22 7 0.24
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTTAAAATAAATTTTAGAT
Done.