Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009581.1 Hibiscus syriacus cultivar Beakdansim tig00116958_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: 2551150
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 13
Found at i:986451 original size:19 final size:20
Alignment explanation
Indices: 986382--986464 Score: 69
Period size: 22 Copynumber: 3.9 Consensus size: 20
986372 GGGAAAAACA
* *
986382 AAATAAAATAAGTAATAAAA
1 AAATAAAATAAATAATAAAT
986402 ATAATAATAATAAATAATGATAAT
1 A-AATAA-AATAAATAAT-A-AAT
986426 -AATAATAATAAATAAATAAAT
1 AAATAA-AATAAAT-AATAAAT
*
986447 AAATAAAACTATATAATA
1 AAATAAAA-TAAATAATA
986465 TACATTTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
20 1 0.02
21 14 0.26
22 32 0.60
23 4 0.08
24 2 0.04
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.28
Consensus pattern (20 bp):
AAATAAAATAAATAATAAAT
Found at i:986542 original size:30 final size:31
Alignment explanation
Indices: 986506--986594 Score: 130
Period size: 31 Copynumber: 2.9 Consensus size: 31
986496 CTATATACTA
986506 TATATAAATTTTC-AAAAT-TTTTAAAAAAAC
1 TATAT-AATTTTCAAAAATGTTTTAAAAAAAC
*
986536 TATATAATTTTCAAAAAATGTTTT-CAAAAAC
1 TATATAATTTTC-AAAAATGTTTTAAAAAAAC
986567 TATATAATTTTCAAAAATGTTTTAAAAA
1 TATATAATTTTCAAAAATGTTTTAAAAA
986595 TTATATATTA
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
29 7 0.13
30 16 0.30
31 26 0.49
32 4 0.08
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (31 bp):
TATATAATTTTCAAAAATGTTTTAAAAAAAC
Found at i:986659 original size:38 final size:38
Alignment explanation
Indices: 986567--986803 Score: 200
Period size: 39 Copynumber: 6.2 Consensus size: 38
986557 TTTCAAAAAC
*
986567 TATATAA-TTTTCAAAAATGTTTTAAAAATTA-TATATTATT
1 TATATAAGTTTTCAAAAATGATTTAAAAA--ACTATA-TA-T
* *
986607 ATATATAAGTTTTCAAAAATGCTTTAAAAAATTATATAT
1 -TATATAAGTTTTCAAAAATGATTTAAAAAACTATATAT
* *
986646 TATATAAGTTTTCAAAAAATGATTTTAAAAACCATATAT
1 TATATAAGTTTTC-AAAAATGATTTAAAAAACTATATAT
** *
986685 TATATATTTTTTCTAAAAAT-ATTTTAAAAACTATATAT
1 TATATAAGTTTTC-AAAAATGATTTAAAAAACTATATAT
** * * *
986723 TATA-CCGTTTTCAAAAATG-TTTTAAAATCTATATAC
1 TATATAAGTTTTCAAAAATGATTTAAAAAACTATATAT
* *
986759 TATATTCA-TTTTC-AAAATGCCTTTAAAAAAACTATATAT
1 TATA-TAAGTTTTCAAAAATG-ATTT-AAAAAACTATATAT
986798 TATATA
1 TATATA
986804 TGTATTTTCA
Statistics
Matches: 168, Mismatches: 19, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
36 31 0.18
37 10 0.06
38 39 0.23
39 54 0.32
40 3 0.02
41 11 0.07
42 20 0.12
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (38 bp):
TATATAAGTTTTCAAAAATGATTTAAAAAACTATATAT
Found at i:996989 original size:5 final size:5
Alignment explanation
Indices: 996956--996988 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
996946 CATGCATGAA
*
996956 CATAT CATAT CATAT CATAT CATAT CATGT CAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CAT
996989 GCTATCACAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.39
Consensus pattern (5 bp):
CATAT
Found at i:1000079 original size:32 final size:32
Alignment explanation
Indices: 1000038--1000145 Score: 96
Period size: 32 Copynumber: 3.4 Consensus size: 32
1000028 AGTCAAGGGT
*
1000038 TTACCTATGTTCTACGGAATATATAAACAGAA
1 TTACCTATGTTCTACGGAACATATAAACAGAA
* * * *
1000070 TTACCTATG-TCTTTCGGGACATATGAACAGTA
1 TTACCTATGTTC-TACGGAACATATAAACAGAA
* * *
1000102 -TACCTATGTTCTAAGGGAACATATAGACA-AT
1 TTACCTATGTTCT-ACGGAACATATAAACAGAA
*
1000133 TTACCTAGGTTCT
1 TTACCTATGTTCT
1000146 TCGGGACCTA
Statistics
Matches: 59, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
31 11 0.19
32 48 0.81
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (32 bp):
TTACCTATGTTCTACGGAACATATAAACAGAA
Found at i:1000138 original size:63 final size:63
Alignment explanation
Indices: 1000039--1000163 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
1000029 GTCAAGGGTT
* *
1000039 TACCTATGTTCTACGGAATATATAAACAGAATTACCTATG-TCTTTCGGGACATATGAACAGTA
1 TACCTATGTTCTACGGAACATATAAACAGAATTACCTAGGTTC-TTCGGGACATATGAACAGTA
* * * * *
1000102 TACCTATGTTCTAAGGGAACATATAGACA-ATTTACCTAGGTTCTTCGGGACCTATGGACAGT
1 TACCTATGTTCT-ACGGAACATATAAACAGAATTACCTAGGTTCTTCGGGACATATGAACAGT
1000164 TGCCGAGGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
63 38 0.72
64 15 0.28
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (63 bp):
TACCTATGTTCTACGGAACATATAAACAGAATTACCTAGGTTCTTCGGGACATATGAACAGTA
Found at i:1001762 original size:2 final size:2
Alignment explanation
Indices: 1001755--1001783 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1001745 CATCATTTGT
1001755 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1001784 GTGTGAACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1005470 original size:2 final size:2
Alignment explanation
Indices: 1005463--1005494 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1005453 TATTGGGAAT
1005463 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
1005495 TTACATCATC
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1006904 original size:37 final size:37
Alignment explanation
Indices: 1006853--1006936 Score: 100
Period size: 37 Copynumber: 2.3 Consensus size: 37
1006843 CCCGACCCGA
*
1006853 TCGGGTCGGATTTTTTTAAA-AAAAT-TTCGGGTTCGGG
1 TCGGGTCGG-GTTTTTTAAATAAAATGTTCGGG-TCGGG
** *
1006890 TCGGGTCGGGTTTTTTAAATGTACTGTTCGGGTCGGG
1 TCGGGTCGGGTTTTTTAAATAAAATGTTCGGGTCGGG
1006927 TCGGGTCGGG
1 TCGGGTCGGG
1006937 ATTAGGGTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
36 9 0.22
37 26 0.63
38 6 0.15
ACGTcount: A:0.14, C:0.13, G:0.37, T:0.36
Consensus pattern (37 bp):
TCGGGTCGGGTTTTTTAAATAAAATGTTCGGGTCGGG
Found at i:1008298 original size:14 final size:16
Alignment explanation
Indices: 1008268--1008299 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1008258 TTTTTATCAA
1008268 AAGATATTAATTAATT
1 AAGATATTAATTAATT
1008284 AAGATA-TAA-TAATT
1 AAGATATTAATTAATT
1008298 AA
1 AA
1008300 ATCAATTGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 3 0.19
16 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (16 bp):
AAGATATTAATTAATT
Found at i:1011685 original size:2 final size:2
Alignment explanation
Indices: 1011672--1011701 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1011662 CATCAATGTC
*
1011672 AT AT AT AG 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
1011702 CTTTATACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1015606 original size:24 final size:24
Alignment explanation
Indices: 1015572--1015622 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
1015562 CATATATCAG
* *
1015572 TTTATAGCCGTTGCTGTAATTGCT
1 TTTATACCCGTTGCTGTAACTGCT
1015596 TTTATACCCGTTGCTGTAACTGCT
1 TTTATACCCGTTGCTGTAACTGCT
1015620 TTT
1 TTT
1015623 GTTAAATCCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.47
Consensus pattern (24 bp):
TTTATACCCGTTGCTGTAACTGCT
Found at i:1016139 original size:21 final size:21
Alignment explanation
Indices: 1016113--1016161 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1016103 TCATCTTCAT
* *
1016113 CTTCACCATCTCCACCTCCAC
1 CTTCACCATCACCACCACCAC
*
1016134 CTTCACCATCACCACCACCAT
1 CTTCACCATCACCACCACCAC
1016155 CTTCACC
1 CTTCACC
1016162 TCCGCTAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.55, G:0.00, T:0.22
Consensus pattern (21 bp):
CTTCACCATCACCACCACCAC
Found at i:1017302 original size:65 final size:63
Alignment explanation
Indices: 1017184--1017393 Score: 221
Period size: 65 Copynumber: 3.3 Consensus size: 63
1017174 TTTTTCAGAG
* * *
1017184 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATT-AAACATCGAATGC
1 TGATGCATCGATGCA-CAA-CCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATGC
1017246 ATT
61 ATT
* *
1017249 TCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCAT
1017313 T
63 T
* * * *
1017314 TGATGCATCGATGCACCAACCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
*
1017378 TGATGCATCGTTGCAC
1 TGATGCATCGATGCAC
1017394 TCTTAGTGTA
Statistics
Matches: 125, Mismatches: 12, Indels: 18
0.81 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 46 0.37
65 71 0.57
66 5 0.04
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:1023196 original size:24 final size:23
Alignment explanation
Indices: 1023164--1023244 Score: 71
Period size: 24 Copynumber: 3.6 Consensus size: 23
1023154 TCTGTGCTTA
1023164 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCAT-CCTTTGAAT
* *
1023188 GTGCATCGATTCATCATGTTG-A-
1 GTGCATCGATGCATCCT-TTGAAT
* *
1023210 -TGCACCGATGCAAGCC-TTGAAT
1 GTGCATCGATGC-ATCCTTTGAAT
1023232 GTGCATCGATGCA
1 GTGCATCGATGCA
1023245 CATGGTCATG
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
20 3 0.07
21 10 0.22
22 3 0.07
23 13 0.29
24 16 0.36
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (23 bp):
GTGCATCGATGCATCCTTTGAAT
Found at i:1023234 original size:44 final size:43
Alignment explanation
Indices: 1023182--1023264 Score: 121
Period size: 44 Copynumber: 1.9 Consensus size: 43
1023172 ATGCATCCCT
* * *
1023182 TTGAATGTGCATCGATTCATCATGTTGATGCACCGATGCAAGCC
1 TTGAATGTGCATCGATGCA-CATGGTCATGCACCGATGCAAGCC
*
1023226 TTGAATGTGCATCGATGCACATGGTCATGCATCGATGCA
1 TTGAATGTGCATCGATGCACATGGTCATGCACCGATGCA
1023265 TCCGTCGGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
43 17 0.49
44 18 0.51
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (43 bp):
TTGAATGTGCATCGATGCACATGGTCATGCACCGATGCAAGCC
Found at i:1024825 original size:21 final size:21
Alignment explanation
Indices: 1024783--1024826 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1024773 ACTTCGGGAG
* *
1024783 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
1024804 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
1024825 CT
1 CT
1024827 CCTCCAGCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:1026071 original size:64 final size:66
Alignment explanation
Indices: 1025914--1026073 Score: 184
Period size: 65 Copynumber: 2.5 Consensus size: 66
1025904 AATTAAATTG
* * *
1025914 AACATCGAATGCATTTCATGCATCGATGCA-CATACCATACACCGATGCGCTGAGGATTTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACCATACCATACACCGATGCACTCAGGATTTTATGA
1025978 A
66 A
* * * * * * *
1025979 AACATCGAATGTATTTGATACATCGATGCACCA-ACCATGCATCGATGTACTCTGGCTATTT-TG
1 AACATCGAATGCATTTGATGCATCGATGCACCATACCATACACCGATGCACTCAGGAT-TTTATG
1026042 -A
65 AA
*
1026043 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
1026074 TCTTAGTGCA
Statistics
Matches: 80, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
64 29 0.36
65 46 0.57
66 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (66 bp):
AACATCGAATGCATTTGATGCATCGATGCACCATACCATACACCGATGCACTCAGGATTTTATGA
A
Found at i:1026073 original size:17 final size:19
Alignment explanation
Indices: 1026045--1026093 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1026035 TATTTTGAAA
1026045 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1026063 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1026082 CACCGATGCACT
1 CATCGATGCACT
1026094 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1027782 original size:24 final size:24
Alignment explanation
Indices: 1027745--1027795 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1027735 CATATATCAG
* *
1027745 TTTATAGCCGTTGTTGTAACTGCT
1 TTTATACCCATTGTTGTAACTGCT
*
1027769 TTTATACCCATTGTTGTAACTGTT
1 TTTATACCCATTGTTGTAACTGCT
1027793 TTT
1 TTT
1027796 GTTAAATCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.51
Consensus pattern (24 bp):
TTTATACCCATTGTTGTAACTGCT
Found at i:1029896 original size:5 final size:5
Alignment explanation
Indices: 1029886--1029918 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1029876 TAGGGTCAAC
*
1029886 GGTCG GGTCG GGT-T GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
1029919 AGGCCGGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 22 0.88
ACGTcount: A:0.00, C:0.18, G:0.58, T:0.24
Consensus pattern (5 bp):
GGTCG
Found at i:1029905 original size:14 final size:14
Alignment explanation
Indices: 1029886--1029912 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1029876 TAGGGTCAAC
1029886 GGTCGGGTCGGGTT
1 GGTCGGGTCGGGTT
1029900 GGTCGGGTCGGGT
1 GGTCGGGTCGGGT
1029913 CGGGTCAGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.59, T:0.26
Consensus pattern (14 bp):
GGTCGGGTCGGGTT
Found at i:1029927 original size:19 final size:19
Alignment explanation
Indices: 1029885--1029927 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1029875 GTAGGGTCAA
*
1029885 CGGTCGGGTCGGGTTGGTC
1 CGGTCGGGTCGGGTAGGTC
*
1029904 GGGTCGGGTCGGGTCAGG-C
1 CGGTCGGGTCGGGT-AGGTC
1029923 CGGTC
1 CGGTC
1029928 AAACCAGTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.02, C:0.23, G:0.53, T:0.21
Consensus pattern (19 bp):
CGGTCGGGTCGGGTAGGTC
Found at i:1034245 original size:8 final size:8
Alignment explanation
Indices: 1034234--1034263 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1034224 CTTGTATCCT
*
1034234 TAAGTCCG
1 TAAGTCCA
1034242 TAAGTCCA
1 TAAGTCCA
1034250 TAAGTCCA
1 TAAGTCCA
1034258 TAAGTC
1 TAAGTC
1034264 TATATAGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (8 bp):
TAAGTCCA
Found at i:1035128 original size:13 final size:14
Alignment explanation
Indices: 1035110--1035139 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1035100 TCAAAGGAGT
1035110 TCAACGGTC-ACGG
1 TCAACGGTCAACGG
1035123 TCAACGGTCAACGG
1 TCAACGGTCAACGG
1035137 TCA
1 TCA
1035140 GGTCGGGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.17
Consensus pattern (14 bp):
TCAACGGTCAACGG
Found at i:1035131 original size:7 final size:7
Alignment explanation
Indices: 1035110--1035139 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1035100 TCAAAGGAGT
1035110 TCAACGG
1 TCAACGG
1035117 TC-ACGG
1 TCAACGG
1035123 TCAACGG
1 TCAACGG
1035130 TCAACGG
1 TCAACGG
1035137 TCA
1 TCA
1035140 GGTCGGGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.17
Consensus pattern (7 bp):
TCAACGG
Found at i:1035169 original size:19 final size:18
Alignment explanation
Indices: 1035143--1035179 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1035133 ACGGTCAGGT
*
1035143 CGGGTCAGACCGGTCAAA
1 CGGGTCAGACCGATCAAA
1035161 CGGGTTCAGACCGATCAAA
1 CGGG-TCAGACCGATCAAA
1035180 ACCAGTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.30, C:0.27, G:0.30, T:0.14
Consensus pattern (18 bp):
CGGGTCAGACCGATCAAA
Found at i:1035888 original size:17 final size:17
Alignment explanation
Indices: 1035866--1035906 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1035856 ATTTAGTCCC
1035866 CATAATTTACCGATTTT
1 CATAATTTACCGATTTT
1035883 CATAATTTACCGATTTT
1 CATAATTTACCGATTTT
*
1035900 CACAATT
1 CATAATT
1035907 AAAACCTCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.44
Consensus pattern (17 bp):
CATAATTTACCGATTTT
Found at i:1042930 original size:6 final size:6
Alignment explanation
Indices: 1042921--1043054 Score: 268
Period size: 6 Copynumber: 22.3 Consensus size: 6
1042911 TATCTTGATT
1042921 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
1042969 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
1043017 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA AT
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA AT
1043055 TGTAAAATCT
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 128 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAA
Found at i:1047161 original size:21 final size:21
Alignment explanation
Indices: 1047135--1047179 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1047125 GATTTATGGG
* *
1047135 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1047156 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1047177 CAA
1 CAA
1047180 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1048308 original size:18 final size:18
Alignment explanation
Indices: 1048285--1048320 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1048275 CGAGGGTCTA
1048285 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
1048303 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
1048321 ATATGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:1048512 original size:29 final size:30
Alignment explanation
Indices: 1048417--1048509 Score: 152
Period size: 30 Copynumber: 3.1 Consensus size: 30
1048407 ATGGTCTTTA
1048417 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1048447 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
1048477 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1048506 TGGA
1 TGGA
1048510 TAGGTCCTTC
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
29 18 0.30
30 42 0.70
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:1049390 original size:2 final size:2
Alignment explanation
Indices: 1049383--1049477 Score: 138
Period size: 2 Copynumber: 47.0 Consensus size: 2
1049373 GAGTTATGAG
1049383 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1049425 AT AT AT AT AT AT AT AT AT AT AT AT AT GT TT AT AT A- AT AT GAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
*
1049467 AG AT GAT AT AT
1 AT AT -AT AT AT
1049478 GAACATATAC
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
1 1 0.01
2 80 0.94
3 4 0.05
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1051383 original size:21 final size:21
Alignment explanation
Indices: 1051357--1051401 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1051347 GATTTCTGGG
* *
1051357 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1051378 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1051399 CAA
1 CAA
1051402 ACAAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1052542 original size:18 final size:19
Alignment explanation
Indices: 1052507--1052543 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1052497 CGAGGGTCTA
1052507 TGTGGTCCTTCGGGGACAT
1 TGTGGTCCTTCGGGGACAT
*
1052526 TGTGGTCTTTC-GGGACAT
1 TGTGGTCCTTCGGGGACAT
1052544 ATATGTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.11, C:0.19, G:0.35, T:0.35
Consensus pattern (19 bp):
TGTGGTCCTTCGGGGACAT
Found at i:1052729 original size:29 final size:30
Alignment explanation
Indices: 1052640--1052735 Score: 158
Period size: 30 Copynumber: 3.2 Consensus size: 30
1052630 GTGGTCTTTA
1052640 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
* *
1052670 TGGACAGTTACCGAGGATCTTTATAACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
1052700 TGGATAGTTACCG-GGGTCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
1052729 TGGATAG
1 TGGATAG
1052736 GTCATTCGGG
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
29 21 0.34
30 40 0.66
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATGACCTC
Found at i:1056381 original size:23 final size:24
Alignment explanation
Indices: 1056354--1056406 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1056344 TAAACACATG
* *
1056354 ATTTTAGGA-GACTAACTTCTAAA
1 ATTTTAGGAGGACAAACTTATAAA
*
1056377 ATTTTAGGAGGGCAAACTTATAAA
1 ATTTTAGGAGGACAAACTTATAAA
1056401 ATTTTA
1 ATTTTA
1056407 TGGGGCGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (24 bp):
ATTTTAGGAGGACAAACTTATAAA
Found at i:1057917 original size:25 final size:25
Alignment explanation
Indices: 1057868--1057917 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1057858 CACTGTATCT
**
1057868 TTTGTGACAATTGACATCAGGACAA
1 TTTGTGACAATTGACATCAAAACAA
1057893 TTTGTGACAATT-AGCATCAAAACAA
1 TTTGTGACAATTGA-CATCAAAACAA
1057918 AATATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (25 bp):
TTTGTGACAATTGACATCAAAACAA
Found at i:1058616 original size:18 final size:19
Alignment explanation
Indices: 1058581--1058617 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1058571 CACGGAATGT
1058581 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1058601 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1058618 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1058753 original size:18 final size:18
Alignment explanation
Indices: 1058732--1058779 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
1058722 CAAATTGTCC
*
1058732 TATTATATATTTGTATAA
1 TATTATATATTTGTAAAA
* *
1058750 TATTACA-AATTGTAAAA
1 TATTATATATTTGTAAAA
1058767 TATTTATATATTT
1 TA-TTATATATTT
1058780 TCTTTAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
17 10 0.43
18 10 0.43
19 3 0.13
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (18 bp):
TATTATATATTTGTAAAA
Found at i:1059898 original size:36 final size:36
Alignment explanation
Indices: 1059857--1059937 Score: 153
Period size: 36 Copynumber: 2.2 Consensus size: 36
1059847 TTTTTCGAGC
*
1059857 TCGAGTCAAGCTTGAAAATTTTAAGTTCGCGAGCTT
1 TCGAGTCAAGCTTGAAAATTTTAAGTTCACGAGCTT
1059893 TCGAGTCAAGCTTGAAAATTTTAAGTTCACGAGCTT
1 TCGAGTCAAGCTTGAAAATTTTAAGTTCACGAGCTT
1059929 TCGAGTCAA
1 TCGAGTCAA
1059938 TCCAAACTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (36 bp):
TCGAGTCAAGCTTGAAAATTTTAAGTTCACGAGCTT
Found at i:1060398 original size:15 final size:13
Alignment explanation
Indices: 1060377--1060417 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
1060367 TTTTACCGGA
1060377 TAAAAAACCGGTT
1 TAAAAAACCGGTT
1060390 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
1060404 TAAAAAACCGGTT
1 TAAAAAACCGGTT
1060417 T
1 T
1060418 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:1060408 original size:12 final size:12
Alignment explanation
Indices: 1060371--1060416 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
1060361 GGTTTTTTTT
*
1060371 ACCGGATAAAAA
1 ACCGGTTAAAAA
1060383 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
1060398 ACCGGTTAAAAA
1 ACCGGTTAAAAA
1060410 ACCGGTT
1 ACCGGTT
1060417 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:1062703 original size:21 final size:21
Alignment explanation
Indices: 1062679--1062718 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1062669 TTTATTTTAT
1062679 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
1062700 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
1062719 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:1062792 original size:33 final size:33
Alignment explanation
Indices: 1062713--1062810 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
1062703 TTTGTTTCAA
1062713 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1062745 TT-TCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
1062777 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1062810 T
1 T
1062811 ATGTTGAGTT
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
31 8 0.13
32 25 0.41
33 28 0.46
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.46
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:1062839 original size:13 final size:13
Alignment explanation
Indices: 1062796--1062844 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
1062786 TTGGAAGTAT
1062796 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
1062809 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
1062823 TTAAGTATTTCAA
1 TTAAGTATTTCAA
1062836 TTAAGTATT
1 TTAAGTATT
1062845 GAATTTATCG
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
12 3 0.10
13 16 0.55
14 7 0.24
15 3 0.10
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:1063411 original size:15 final size:17
Alignment explanation
Indices: 1063385--1063416 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1063375 TTCTATGGGA
1063385 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
1063401 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
1063417 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:1071163 original size:105 final size:104
Alignment explanation
Indices: 1070961--1071255 Score: 292
Period size: 105 Copynumber: 2.8 Consensus size: 104
1070951 TGCTATGTGT
* * *
1070961 AAGAAGGGGATGGTTTCCAAAGCTGAATATATAGTTGACACAATGAGAAAGCAAGGCATTAAGCT
1 AAGAAGGGGATGGTTTCCAAAGCTGAAGATATA-TTGACACAATGAGAAAGCAAGGCATTGAGCC
* * *** * *
1071026 TGACGTTGTCTTGTATAGCATATTGATCGATGCACTTTGC
65 TAATGTTGTCACATATAGCATATAGATCGATGCACATTGC
*
1071066 AAGAAGGGGATGGTTTCCAAAGCTGAAGATGTCATTGACACAATGAGAAAGCAAGGCATTGAGCC
1 AAGAAGGGGATGGTTTCCAAAGCTGAAGATAT-ATTGACACAATGAGAAAGCAAGGCATTGAGCC
* *
1071131 TAATGTTGTCACATATA-CTATACTAG-TGGATGCCCATTGC
65 TAATGTTGTCACATATAGC-ATA-TAGATCGATGCACATTGC
* ** * * * * * *
1071171 AAGGA-GGGA-GCAGTTTATAAAGCTAAAGGTATTGTTCACACAATGATAAATCAAGGCATTGAG
1 AAGAAGGGGATG--GTTTCCAAAGCTGAAGATA-TATTGACACAATGAGAAAGCAAGGCATTGAG
*
1071234 CCTAATGTTGTCACATACAGCA
63 CCTAATGTTGTCACATATAGCA
1071256 CTCTTATGCG
Statistics
Matches: 159, Mismatches: 24, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
103 1 0.01
104 5 0.03
105 148 0.93
106 5 0.03
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (104 bp):
AAGAAGGGGATGGTTTCCAAAGCTGAAGATATATTGACACAATGAGAAAGCAAGGCATTGAGCCT
AATGTTGTCACATATAGCATATAGATCGATGCACATTGC
Found at i:1075532 original size:40 final size:40
Alignment explanation
Indices: 1075484--1075607 Score: 239
Period size: 40 Copynumber: 3.1 Consensus size: 40
1075474 ATGAATAGTG
1075484 GATTCTTAATAAAGAAGTCTTTTTGTTGTTTCAATGAAAT
1 GATTCTTAATAAAGAAGTCTTTTTGTTGTTTCAATGAAAT
1075524 GATTCTTAATAAAGAAGTCTTTTTGTTGTTTCAATGAAAT
1 GATTCTTAATAAAGAAGTCTTTTTGTTGTTTCAATGAAAT
*
1075564 GATTCTTAATAAAGAAGTCTTTTTGTTGTTTCAATCAAAT
1 GATTCTTAATAAAGAAGTCTTTTTGTTGTTTCAATGAAAT
1075604 GATT
1 GATT
1075608 GGTCAACTGT
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 83 1.00
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (40 bp):
GATTCTTAATAAAGAAGTCTTTTTGTTGTTTCAATGAAAT
Found at i:1082766 original size:28 final size:29
Alignment explanation
Indices: 1082722--1082777 Score: 87
Period size: 28 Copynumber: 1.9 Consensus size: 29
1082712 TATATATTTA
*
1082722 TTAATTTTTAAATAAA-TTTTTAAAAATT
1 TTAATTTTTAAAAAAACTTTTTAAAAATT
1082750 TTAATTTTTAAAAAAATCTTTTTAAAAA
1 TTAATTTTTAAAAAAA-CTTTTTAAAAA
1082778 ATCTATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 15 0.60
30 10 0.40
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (29 bp):
TTAATTTTTAAAAAAACTTTTTAAAAATT
Found at i:1086163 original size:27 final size:27
Alignment explanation
Indices: 1086144--1086216 Score: 128
Period size: 27 Copynumber: 2.7 Consensus size: 27
1086134 TCGGGCTCTA
1086144 AAATGACTGAAATACCCTCGAGTTTTG
1 AAATGACTGAAATACCCTCGAGTTTTG
*
1086171 AAATGACTTAAATACCCTCGAGTTTTG
1 AAATGACTGAAATACCCTCGAGTTTTG
*
1086198 AAATGACTTAAATACCCTC
1 AAATGACTGAAATACCCTC
1086217 ATGGCTTGGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.30
Consensus pattern (27 bp):
AAATGACTGAAATACCCTCGAGTTTTG
Found at i:1102647 original size:16 final size:17
Alignment explanation
Indices: 1102613--1102647 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1102603 AATTTAATAT
*
1102613 AATAATATTTTTTTAAA
1 AATAATATGTTTTTAAA
1102630 AATAATATGTTTTTAAA
1 AATAATATGTTTTTAAA
1102647 A
1 A
1102648 GAATATCGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
AATAATATGTTTTTAAA
Found at i:1102652 original size:16 final size:17
Alignment explanation
Indices: 1102616--1102653 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1102606 TTAATATAAT
* *
1102616 AATATTTTTTTAAAAAT
1 AATATGTTTTTAAAAAG
1102633 AATATGTTTTT-AAAAG
1 AATATGTTTTTAAAAAG
1102649 AATAT
1 AATAT
1102654 CGGTGCCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (17 bp):
AATATGTTTTTAAAAAG
Found at i:1104405 original size:14 final size:14
Alignment explanation
Indices: 1104382--1104433 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
1104372 CGTTAAATTA
1104382 ATTTAATCAAAAAT
1 ATTTAATCAAAAAT
* **
1104396 ATTTATTCAACTCA-
1 ATTTAATCAA-AAAT
1104410 ATTTAATCAAAAAT
1 ATTTAATCAAAAAT
*
1104424 ATTTATTCAA
1 ATTTAATCAA
1104434 CTCAATTCAA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
13 1 0.03
14 27 0.93
15 1 0.03
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (14 bp):
ATTTAATCAAAAAT
Found at i:1104414 original size:28 final size:28
Alignment explanation
Indices: 1104381--1104448 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
1104371 TCGTTAAATT
1104381 AATTTAATCAAAAATATTTATTCAACTC
1 AATTTAATCAAAAATATTTATTCAACTC
1104409 AATTTAATCAAAAATATTTATTCAACTC
1 AATTTAATCAAAAATATTTATTCAACTC
*
1104437 AATTCAATCAAA
1 AATTTAATCAAA
1104449 TGATATCAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.37
Consensus pattern (28 bp):
AATTTAATCAAAAATATTTATTCAACTC
Found at i:1111072 original size:19 final size:19
Alignment explanation
Indices: 1111034--1111072 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1111024 GTCGTAAAAG
* *
1111034 ACTACACATTTTCACTGAT
1 ACTACACATTTCCACAGAT
1111053 ACTACACATTTCCACAGAT
1 ACTACACATTTCCACAGAT
1111072 A
1 A
1111073 TAAAAGTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.31
Consensus pattern (19 bp):
ACTACACATTTCCACAGAT
Found at i:1116022 original size:30 final size:29
Alignment explanation
Indices: 1115960--1116019 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
1115950 AAAAAAATTT
*
1115960 AATATTTTATGTACCAATTTTGATCAAAA
1 AATATTTTATGTACCAATTTTGACCAAAA
* *
1115989 AATATTTTATGTATCTATTTTGACCAAAA
1 AATATTTTATGTACCAATTTTGACCAAAA
1116018 AA
1 AA
1116020 ATAAATTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.42
Consensus pattern (29 bp):
AATATTTTATGTACCAATTTTGACCAAAA
Found at i:1117402 original size:24 final size:24
Alignment explanation
Indices: 1117375--1117429 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
1117365 AAACGGAGAT
* *
1117375 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATCCAA
* *
1117399 ATCAGATATCATAACAGAATCCAA
1 ATCAGAAATCAAAACAGAATCCAA
1117423 ATCAGAA
1 ATCAGAA
1117430 TAGAATTCAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.53, C:0.18, G:0.11, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATCCAA
Found at i:1121653 original size:9 final size:9
Alignment explanation
Indices: 1121636--1121880 Score: 111
Period size: 9 Copynumber: 26.9 Consensus size: 9
1121626 CTATTTTCTT
1121636 TTTTATTTA
1 TTTTATTTA
*
1121645 TTTTGTTTA
1 TTTTATTTA
* *
1121654 TTAT-TTTC
1 TTTTATTTA
*
1121662 TTTATATTCA
1 TTT-TATTTA
1121672 TTATT-TTTA
1 TT-TTATTTA
1121681 TTTTATTT-
1 TTTTATTTA
*
1121689 TATTTATCTA
1 T-TTTATTTA
1121699 TTTTTATTT-
1 -TTTTATTTA
**
1121708 TTTCCTTTA
1 TTTTATTTA
1121717 TCTTTATCTTTA
1 T-TTTA--TTTA
1121729 TCTTTATTTA
1 T-TTTATTTA
1121739 TTTTATTTA
1 TTTTATTTA
*
1121748 TTTTCTTTTA
1 TTTT-ATTTA
*
1121758 CTTTATTT-
1 TTTTATTTA
1121766 TTATT-TTT-
1 TT-TTATTTA
1121774 TTTCTATTTA
1 TTT-TATTTA
1121784 TTTTATTTA
1 TTTTATTTA
1121793 -TTTATTTTA
1 TTTTA-TTTA
1121802 TCTTTATTT-
1 T-TTTATTTA
1121811 TATTTATTT-
1 T-TTTATTTA
** *
1121820 TTTGGTTTC
1 TTTTATTTA
*
1121829 TTTATCTTTA
1 TTT-TATTTA
1121839 TTTTA-TT-
1 TTTTATTTA
1121846 TTTT-TTTA
1 TTTTATTTA
*
1121854 CTTTATCTTA
1 TTTTAT-TTA
*
1121864 TTTTCTTTA
1 TTTTATTTA
*
1121873 TTTCATTT
1 TTTTATTT
1121881 TTTCCTTCAT
Statistics
Matches: 182, Mismatches: 29, Indels: 50
0.70 0.11 0.19
Matches are distributed among these distances:
7 7 0.04
8 35 0.19
9 80 0.44
10 44 0.24
11 6 0.03
12 10 0.05
ACGTcount: A:0.17, C:0.07, G:0.01, T:0.75
Consensus pattern (9 bp):
TTTTATTTA
Found at i:1121683 original size:6 final size:6
Alignment explanation
Indices: 1121672--1121852 Score: 66
Period size: 6 Copynumber: 30.2 Consensus size: 6
1121662 TTTATATTCA
* *
1121672 TTATTT TTA-TT TTA-TT TTATTT ATCTATTT TTATTT TT-TCCT TTATCT
1 TTATTT TTATTT TTATTT TTATTT -T-TATTT TTATTT TTAT-TT TTATTT
* * *
1121720 TTATCT TTATCT TTATTT ATT-TTAT TTATTT TCTTTTACT TTATTT TTATTT
1 TTATTT TTATTT TTATTT -TTATT-T TTATTT T-TATT--T TTATTT TTATTT
* *
1121772 TT-TTT CTA--T TTA-TT TTATTT ATT-TATT TTATCT TTA-TT TTATTT
1 TTATTT TTATTT TTATTT TTATTT -TTAT-TT TTATTT TTATTT TTATTT
*
1121816 ATT-TTT TGGT-TTCT TTATCT TTA-TT TTATTT TT-TTT T
1 -TTATTT T--TATT-T TTATTT TTATTT TTATTT TTATTT T
1121853 ACTTTATCTT
Statistics
Matches: 141, Mismatches: 10, Indels: 49
0.70 0.05 0.25
Matches are distributed among these distances:
4 3 0.02
5 32 0.23
6 72 0.51
7 22 0.16
8 10 0.07
9 2 0.01
ACGTcount: A:0.16, C:0.07, G:0.01, T:0.76
Consensus pattern (6 bp):
TTATTT
Found at i:1121686 original size:5 final size:5
Alignment explanation
Indices: 1121636--1121881 Score: 129
Period size: 5 Copynumber: 47.8 Consensus size: 5
1121626 CTATTTTCTT
* *
1121636 TTTTA -TTTA TTTTGT TTATTA TTTTC TTTATA TTCATTA TTTTTA TTTTA
1 TTTTA TTTTA TTTT-A TT-TTA TTTTA TTT-TA TT--TTA -TTTTA TTTTA
* *
1121686 TTTTA -TTTA -TCTA TTTTTA TTTTT TCCTTTA TCTTTA TCTTTA TCTTTA
1 TTTTA TTTTA TTTTA -TTTTA TTTTA T--TTTA T-TTTA T-TTTA T-TTTA
* * *
1121735 -TTTA TTTTA -TTTA TTTTC TTTTA CTTTA TTTTTA TTTT- TTTTC TATTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA T-TTTA
1121784 TTTTA -TTTA -TTTA TTTTA TCTTTA TTTTA -TTTA TTTT- TTGGTT-
1 TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA TT--TTA
* * * * *
1121827 TCTTTA TCTTTA TTTTA TTTTT TTTTA CTTTA TCTTA TTTT- CTTTA TTTCA
1 T-TTTA T-TTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1121878 TTTT
1 TTTT
1121882 TTCCTTCATT
Statistics
Matches: 194, Mismatches: 23, Indels: 48
0.73 0.09 0.18
Matches are distributed among these distances:
4 40 0.21
5 89 0.46
6 53 0.27
7 9 0.05
8 3 0.02
ACGTcount: A:0.17, C:0.07, G:0.01, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:1121700 original size:24 final size:23
Alignment explanation
Indices: 1121636--1121881 Score: 127
Period size: 24 Copynumber: 10.2 Consensus size: 23
1121626 CTATTTTCTT
*
1121636 TTTTATTTATT-TTGTTTATTATTT
1 TTTTATTTATTATT-TTTATT-TTA
1121660 TCTTTATATTCATTATTTTTATTTTA
1 T-TTTAT-TT-ATTATTTTTATTTTA
*
1121686 TTTTATTTATCTATTTTTATTTTT
1 TTTTATTTAT-TATTTTTATTTTA
*
1121710 TCCTTTATCTTTATCTTTATCTTTA-TTTA
1 T--TTTA--TTTA---TTATTTTTATTTTA
* *
1121739 TTTTATTTATTTTCTTTTACTTTA
1 TTTTATTTATTAT-TTTTATTTTA
*
1121763 TTTTTATTT-TT-TTTCTA-TTTA
1 -TTTTATTTATTATTTTTATTTTA
1121784 TTTTATTTATT-TATTTTATCTTTA
1 TTTTATTTATTAT-TTTTAT-TTTA
*
1121808 TTTTATTTATT-TTTTGGTTTCTTTA
1 TTTTATTTATTATTTT--TAT-TTTA
1121833 TCTTTA-TT-TTATTTTT-TTTTA
1 T-TTTATTTATTATTTTTATTTTA
* *
1121854 CTTTATCTTATT-TTCTTTATTTCA
1 TTTTAT-TTATTATT-TTTATTTTA
1121878 TTTT
1 TTTT
1121882 TTCCTTCATT
Statistics
Matches: 182, Mismatches: 12, Indels: 56
0.73 0.05 0.22
Matches are distributed among these distances:
20 12 0.07
21 11 0.06
22 16 0.09
23 16 0.09
24 47 0.26
25 36 0.20
26 13 0.07
27 13 0.07
28 6 0.03
29 4 0.02
30 7 0.04
31 1 0.01
ACGTcount: A:0.17, C:0.07, G:0.01, T:0.75
Consensus pattern (23 bp):
TTTTATTTATTATTTTTATTTTA
Found at i:1121784 original size:45 final size:44
Alignment explanation
Indices: 1121629--1121881 Score: 180
Period size: 45 Copynumber: 5.5 Consensus size: 44
1121619 TTTACTACTA
* *
1121629 TTTTCTTTTTTATTTATTT-TGTTTA-TTATTTTCTTTATATTCATTAT
1 TTTTATTTTTT-TTTATTTAT-TTTATTTATTTTCTTT-TA--CTTTAT
* * *
1121676 TTTTATTTTATTTTATTTA-TCTATTT-TTATT-TTTTCCTTTAT
1 TTTTATTTTTTTTTATTTATTTTATTTATT-TTCTTTTACTTTAT
* *
1121718 CTTTATCTTTATCTTTATTTATTTTATTTATTTTCTTTTACTTTAT
1 TTTTAT-TTT-TTTTTATTTATTTTATTTATTTTCTTTTACTTTAT
*
1121764 TTTTATTTTTTTTCTATTTATTTTATTTA-TTTATTTTATCTTTATTT
1 TTTTATTTTTTTT-TATTTATTTTATTTATTTTCTTTTA-CTTTA--T
* *
1121811 TATTTATTTTTTGGTTTCTTTATCTTTATTTTATTTTTTTTTACTTTA-
1 T-TTTATTTTTT--TTTATTTAT-TTTA-TTTATTTTCTTTTACTTTAT
* *
1121859 TCTTA-TTTTCTTTATTTCATTTT
1 TTTTATTTTTTTTTATTT-ATTTT
1121882 TTCCTTCATT
Statistics
Matches: 169, Mismatches: 18, Indels: 41
0.74 0.08 0.18
Matches are distributed among these distances:
42 10 0.06
43 3 0.02
44 29 0.17
45 41 0.24
46 32 0.19
47 14 0.08
48 11 0.07
49 6 0.04
50 6 0.04
51 9 0.05
52 8 0.05
ACGTcount: A:0.16, C:0.08, G:0.01, T:0.75
Consensus pattern (44 bp):
TTTTATTTTTTTTTATTTATTTTATTTATTTTCTTTTACTTTAT
Found at i:1121805 original size:85 final size:81
Alignment explanation
Indices: 1121641--1121905 Score: 234
Period size: 81 Copynumber: 3.1 Consensus size: 81
1121631 TTCTTTTTTA
*
1121641 TTTATTTTGTTTA-TTATTTTCTTTATATTCATTATTTTTATTTTATTTTATTTATCTATTTTTA
1 TTTATTTT-TTTATTTATTTTCTTT-TA--CTTTATTTTTATTTTATTTTATTTAT-T-TTTTTA
*
1121705 TTTTTTCCTTTATCTTTATCTTTATC
60 -TTTAT--TTTATCTTTAT-TTTATC
*
1121731 TTTATTTATTTTATTTATTTTCTTTTACTTTATTTTTATTTTTTTTCTATTTATTTTATTTATTT
1 TTTATTT-TTTTATTTATTTTCTTTTACTTTATTTTTATTTTATTT-TATTTATTTT-TTTATTT
1121796 ATTTTATCTTTATTTTA--
63 ATTTTATCTTTATTTTATC
** * * *
1121813 TTTATTTTTTGGTTTCTTTATC-TTTATTTTATTTTT-TTTTACTTTATCTTATTTTCTTTATTT
1 TTTATTTTTTTATTTATTT-TCTTTTACTTTATTTTTATTTTATTTTAT-TTATTTT-TTTATTT
* * *
1121876 CATTTTTTCCTTCATTTTTTC
63 -ATTTTAT-CTTTATTTTATC
1121897 TTTATTTTT
1 TTTATTTTT
1121906 GTTTTCATTA
Statistics
Matches: 152, Mismatches: 13, Indels: 26
0.80 0.07 0.14
Matches are distributed among these distances:
79 3 0.02
80 20 0.13
81 28 0.18
82 17 0.11
84 13 0.09
85 11 0.07
87 6 0.04
88 22 0.14
89 7 0.05
90 13 0.09
91 12 0.08
ACGTcount: A:0.16, C:0.08, G:0.01, T:0.75
Consensus pattern (81 bp):
TTTATTTTTTTATTTATTTTCTTTTACTTTATTTTTATTTTATTTTATTTATTTTTTTATTTATT
TTATCTTTATTTTATC
Found at i:1121882 original size:31 final size:29
Alignment explanation
Indices: 1121765--1121927 Score: 81
Period size: 31 Copynumber: 5.5 Consensus size: 29
1121755 TTACTTTATT
* * *
1121765 TTTATTTTTTTTCTATTTATTTTATTTATTTAT
1 TTTATCTTTTTTC--TTTA-TTT-TTTGTTTAC
*
1121798 TTTATCTTTATTTTATTTATTTTTTGGTTT-C
1 TTTATC-TT-TTTTCTTTATTTTTT-GTTTAC
*
1121829 TTTATC-TTTAT-TTTATTTTTT-TTTAC
1 TTTATCTTTTTTCTTTATTTTTTGTTTAC
*
1121855 TTTATCTTATTTTCTTTATTTCATTT-TTTCC
1 TTTATCTT-TTTTCTTTATTT--TTTGTTTAC
* *
1121886 TTCA--TTTTTTCTTTA-TTTTTGTTTTC
1 TTTATCTTTTTTCTTTATTTTTTGTTTAC
*
1121912 ATTATATGTTTTTTCT
1 -TT-TATCTTTTTTCT
1121928 ATCTAACACG
Statistics
Matches: 106, Mismatches: 10, Indels: 31
0.72 0.07 0.21
Matches are distributed among these distances:
25 6 0.06
26 11 0.10
27 15 0.14
28 16 0.15
29 10 0.09
30 8 0.08
31 19 0.18
32 6 0.06
33 9 0.08
34 2 0.02
35 4 0.04
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.75
Consensus pattern (29 bp):
TTTATCTTTTTTCTTTATTTTTTGTTTAC
Found at i:1128180 original size:21 final size:22
Alignment explanation
Indices: 1128140--1128180 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1128130 CTAAAGGTTT
* *
1128140 TGTAAAGATATCCGCTAATTGG
1 TGTAAAGATATCCACAAATTGG
1128162 TGTAAAG-TATCCACAAATT
1 TGTAAAGATATCCACAAATT
1128181 CTAGAACTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (22 bp):
TGTAAAGATATCCACAAATTGG
Found at i:1131919 original size:12 final size:12
Alignment explanation
Indices: 1131902--1131929 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1131892 GAAGATCATT
1131902 TTTAGAAATAAA
1 TTTAGAAATAAA
1131914 TTTAGAAATAAA
1 TTTAGAAATAAA
1131926 TTTA
1 TTTA
1131930 TTATATTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (12 bp):
TTTAGAAATAAA
Found at i:1135158 original size:95 final size:96
Alignment explanation
Indices: 1135051--1135250 Score: 278
Period size: 95 Copynumber: 2.1 Consensus size: 96
1135041 AGATTATAAT
* * *
1135051 ATTATATATATACAATGAAGCTTGAGTTGTCCCTCT-AGAGCAATTAGTTAAATGCCCCGACTTT
1 ATTATATATATACAATAAAGCTTGAGCTGTCCCTCTAAG-GCAATTAGTTAAACGCCCCGACTTT
* *
1135115 ATGGATAATATTCGGCTAACCAGATAAAGGTG
65 ATGGATAAGATTCAGCTAACCAGATAAAGGTG
* *
1135147 ATTATA-ATATACAATAAAGCTTGAGCTGTCCCTCTAAGGCAATTGGTTAAACGCCCCGGCTTTA
1 ATTATATATATACAATAAAGCTTGAGCTGTCCCTCTAAGGCAATTAGTTAAACGCCCCGACTTTA
* *
1135211 TGGATAAGATTCAGTTAACCTGATAAAGGTG
66 TGGATAAGATTCAGCTAACCAGATAAAGGTG
* *
1135242 TTTACATAT
1 ATTATATAT
1135251 TGAGTTATCC
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
95 81 0.89
96 10 0.11
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (96 bp):
ATTATATATATACAATAAAGCTTGAGCTGTCCCTCTAAGGCAATTAGTTAAACGCCCCGACTTTA
TGGATAAGATTCAGCTAACCAGATAAAGGTG
Found at i:1136594 original size:106 final size:106
Alignment explanation
Indices: 1136409--1136772 Score: 459
Period size: 106 Copynumber: 3.4 Consensus size: 106
1136399 AAGGGGCTTT
* * * * *
1136409 CCAGTTTTAGAGCCAATTTTAACTTCACAGCGAATGATATTGGACTCAAGACAGCACAAGTTCAA
1 CCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTTGACTCAAGACAGCACAAGCTCAA
*
1136474 CTTCACAACGAAGGGGCGGATGACT-ACAAGCAAACAACTTC
66 CTTCACAACGAAGGGGCGGATGACTGTCAA-CAAACAACTTC
*
1136515 CCAGTTTCAGAGCCAATTTCAACTTCAC-GACGAAGGATATTTGACTCAATACAGCACAAGCTCA
1 CCAGTTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTTGACTCAAGACAGCACAAGCTCA
* *
1136579 AATTCACAACAAAGGGGCGGATGACTGTCAACAAACAACTTC
65 ACTTCACAACGAAGGGGCGGATGACTGTCAACAAACAACTTC
* * *
1136621 CCAGTTTTAGAGCCAATTTCAACTTCACAGCGAAGGATA-TTGAACTCGAGACAGTACAAGCTCA
1 CCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTTG-ACTCAAGACAGCACAAGCTCA
* * * * *
1136685 ACTTCACAGCGAAGGGGCAGCTGACTGTCAACAAGCAATTTC
65 ACTTCACAACGAAGGGGCGGATGACTGTCAACAAACAACTTC
* * * *
1136727 CCAG-TTCTATAGTCAATTTCAACTTCACGGC-AGAGGATATTAGACT
1 CCAGTTTC-AGAGCCAATTTCAACTTCACAGCGA-AGGATATTTGACT
1136773 TGGAACAATA
Statistics
Matches: 226, Mismatches: 25, Indels: 14
0.85 0.09 0.05
Matches are distributed among these distances:
105 7 0.03
106 213 0.94
107 6 0.03
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.23
Consensus pattern (106 bp):
CCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTTGACTCAAGACAGCACAAGCTCAA
CTTCACAACGAAGGGGCGGATGACTGTCAACAAACAACTTC
Found at i:1136938 original size:36 final size:36
Alignment explanation
Indices: 1136898--1136973 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
1136888 AGACAATTTC
* *
1136898 CAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAA
1 CAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAA
* *
1136934 CAAATTTTGTCTCTCTTGAGACGGTTTCCCTTGAAA
1 CAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAA
1136970 CAAA
1 CAAA
1136974 AAACTTTGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (36 bp):
CAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAA
Found at i:1137050 original size:36 final size:36
Alignment explanation
Indices: 1136992--1137146 Score: 93
Period size: 37 Copynumber: 4.1 Consensus size: 36
1136982 AATTTTTTTT
* *
1136992 CCTTGAAACAAAATTTTGTCTCTCTTGAGACATTTTC
1 CCTTAAAAC-AAATTTTGTCTCTCTTGAGACAGTTTC
* *
1137029 TCTTAAAACAAAATTTT-TCTCTCTTGAGACGGTTTC
1 CCTTAAAAC-AAATTTTGTCTCTCTTGAGACAGTTTC
* *
1137065 CCTTGAAATAAAAACTTTGAATTTGTCTTTCTTGAGACAGTTTC
1 CCTT-AAA-ACAAA---T---TTTGTCTCTCTTGAGACAGTTTC
* * * *
1137109 TCTTTAAAA-AAA--ATGTCTCTCTTGAGATAATTTC
1 -CCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTC
1137143 CCTT
1 CCTT
1137147 GGAACAAAAT
Statistics
Matches: 94, Mismatches: 14, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
33 3 0.03
34 18 0.19
36 20 0.21
37 21 0.22
38 1 0.01
40 1 0.01
42 3 0.03
43 4 0.04
44 20 0.21
45 3 0.03
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (36 bp):
CCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTC
Found at i:1137078 original size:103 final size:102
Alignment explanation
Indices: 1136899--1137088 Score: 346
Period size: 103 Copynumber: 1.9 Consensus size: 102
1136889 GACAATTTCC
1136899 AAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACGGTTTCCC
1 AAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACGGTTTCCC
1136964 TTGAAACAAAAAACTTTGAATTTTTTTTCCTTGAAACA
66 TTGAAAC-AAAAACTTTGAATTTTTTTTCCTTGAAACA
1137002 AAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAACAAAATTTT-TCTCTCTTGAGACGGTTTCC
1 AAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAAC-AAATTTTGTCTCTCTTGAGACGGTTTCC
*
1137066 CTTGAAATAAAAACTTTGAATTT
65 CTTGAAACAAAAACTTTGAATTT
1137089 GTCTTTCTTG
Statistics
Matches: 85, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
102 15 0.18
103 63 0.74
104 7 0.08
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (102 bp):
AAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACGGTTTCCC
TTGAAACAAAAACTTTGAATTTTTTTTCCTTGAAACA
Found at i:1137226 original size:83 final size:82
Alignment explanation
Indices: 1137025--1137265 Score: 248
Period size: 83 Copynumber: 3.0 Consensus size: 82
1137015 CTTGAGACAT
* * *
1137025 TTTCTCTTAAAACAAAATTTT-TCTCTCTTGAGACGGTTTCCCTTGAAATAAAAACTTTGAATTT
1 TTTCTCTTAAAAC-AAATTTTGTCTCTCTTGAGACGGTTTCCCTTGGAATAAAATCTTTGAATAT
* *
1137089 GTCTTT-CTT-GA-GACAG
65 GT-TTTCCTTAAACAACAG
* *** * *
1137105 TTTCTCTTTAAAA-AAA--ATGTCTCTCTTGAGATAATTTCCCTTGGAACAAAATCTTTGAATCT
1 TTTCTC-TTAAAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTTGGAATAAAATCTTTGAATAT
1137167 GTTTTCCTTAAAACAACAG
65 GTTTTCCTT-AAACAACAG
*
1137186 TTTCT-TTCAAAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTT-GAAGTTAAATCTTTGAATA
1 TTTCTCTT-AAAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTTGGAA-TAAAATCTTTGAATA
1137249 TGTTTTCCTTTAAACAA
64 TGTTTTCC-TTAAACAA
1137266 ATTATTTCTC
Statistics
Matches: 132, Mismatches: 17, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
77 4 0.03
78 41 0.31
79 5 0.04
80 11 0.08
81 18 0.14
82 3 0.02
83 48 0.36
84 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (82 bp):
TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTTGGAATAAAATCTTTGAATATG
TTTTCCTTAAACAACAG
Found at i:1139215 original size:4 final size:4
Alignment explanation
Indices: 1139206--1139312 Score: 58
Period size: 4 Copynumber: 25.0 Consensus size: 4
1139196 GATCATTTAC
* *
1139206 ATTT ATTT ATTT ATTT ATTC ATTGT ATAT ACTATT -TTT ACTATT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATT-T ATTT A-T-TT ATTT A-T-TT ATTT
* *
1139254 -TCTT TTTT ATTT ATTT ATTT A-TT ATTTT CTTT ATATT CATTTT ATTT
1 AT-TT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT AT-TT -A-TTT ATTT
*
1139301 ATTT ATCT ATTT
1 ATTT ATTT ATTT
1139313 TTATTTTTAT
Statistics
Matches: 81, Mismatches: 9, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
3 6 0.07
4 56 0.69
5 11 0.14
6 7 0.09
7 1 0.01
ACGTcount: A:0.23, C:0.07, G:0.01, T:0.69
Consensus pattern (4 bp):
ATTT
Found at i:1139319 original size:5 final size:5
Alignment explanation
Indices: 1139248--1139488 Score: 94
Period size: 5 Copynumber: 47.4 Consensus size: 5
1139238 ATTTTTACTA
* * * *
1139248 TTATT TTCTT TTTTAT TTA-T TTATTT ATTATT TT-CT TTATAT TCATT
1 TTATT TTATT TTAT-T TTATT TTA-TT -TTATT TTATT TTAT-T TTATT
*
1139295 TTA-T TTA-T TTA-T CTATTT TTATTT TTATCT TTATCT TTATCT TTA-T
1 TTATT TTATT TTATT TTA-TT TTA-TT TTAT-T TTAT-T TTAT-T TTATT
* * * * *
1139341 TTATT TTCTT TTCTT TTCTT TTACT TTATTT TTATAT TT-TT GTA-T TTATT
1 TTATT TTATT TTATT TTATT TTATT TTA-TT TTAT-T TTATT TTATT TTATT
1139391 TTA-T TTATT TTATCT TTATCT TTATT TTATT GATT-TCT TTATCT TTATT
1 TTATT TTATT TTAT-T TTAT-T TTATT TTATT --TTAT-T TTAT-T TTATT
* * * * * *
1139440 TTA-T TTGTT TTATT TT-TT GTACT TTATC TTATT TT-CT TTATT TCATT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT
1139487 TT
1 TT
1139489 TTCCTTCATT
Statistics
Matches: 186, Mismatches: 27, Indels: 46
0.72 0.10 0.18
Matches are distributed among these distances:
4 40 0.22
5 79 0.42
6 61 0.33
7 6 0.03
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.73
Consensus pattern (5 bp):
TTATT
Found at i:1139346 original size:34 final size:33
Alignment explanation
Indices: 1139310--1139512 Score: 141
Period size: 35 Copynumber: 6.1 Consensus size: 33
1139300 TATTTATCTA
*
1139310 TTTTTATTTTTATCTTTATCTTTATCTTTATTT
1 TTTTTATTTTTTTCTTTATCTTTATCTTTATTT
*
1139343 ATTTTCT-TTTCTTTTCTTT-TACTTTATTTTTATATT
1 -TTTT-TATTT-TTTTCTTTAT-CTTTATCTTTAT-TT
* *
1139379 TTTGTATTTATTTTATTTAT-TTTATCTTTATCTT
1 TTTTTATTT-TTTTCTTTATCTTTATCTTTAT-TT
**
1139413 TATTTTATTGATTTCTTTATCTTTAT-TTTATTT
1 T-TTTTATTTTTTTCTTTATCTTTATCTTTATTT
* *
1139446 GTTTTATTTTTTGTACTTTATC-TTAT-TTTCTTT
1 TTTTTATTTTTT-T-CTTTATCTTTATCTTTATTT
* * * * * *
1139479 ATTTCATTTTTTCCTTCAT-TTTTTCTTCATTT
1 TTTTTATTTTTTTCTTTATCTTTATCTTTATTT
1139511 TT
1 TT
1139513 GTTTTCATTA
Statistics
Matches: 134, Mismatches: 23, Indels: 26
0.73 0.13 0.14
Matches are distributed among these distances:
31 8 0.06
32 15 0.11
33 23 0.17
34 42 0.31
35 43 0.32
36 3 0.02
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.73
Consensus pattern (33 bp):
TTTTTATTTTTTTCTTTATCTTTATCTTTATTT
Found at i:1139437 original size:6 final size:6
Alignment explanation
Indices: 1139312--1139443 Score: 70
Period size: 6 Copynumber: 22.8 Consensus size: 6
1139302 TTTATCTATT
* * *
1139312 TTTATT TTTATC TTTATC TTTATC TTTATT TATTTTC TTT-TC TTT-TC
1 TTTATC TTTATC TTTATC TTTATC TTTATC T-TTATC TTTATC TTTATC
* * * *
1139359 TTT-TAC TTTATTT TTATATT TTTGTA TTTAT- TTTA-- TTTAT- TTTATC
1 TTTAT-C TTTA-TC TT-TATC TTTATC TTTATC TTTATC TTTATC TTTATC
1139405 TTTATC TTTAT- TTTAT- TGATT-TC TTTATC TTTAT- TTTAT
1 TTTATC TTTATC TTTATC T--TTATC TTTATC TTTATC TTTAT
1139444 TTGTTTTATT
Statistics
Matches: 107, Mismatches: 8, Indels: 23
0.78 0.06 0.17
Matches are distributed among these distances:
4 4 0.04
5 33 0.31
6 54 0.50
7 13 0.12
8 3 0.03
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.73
Consensus pattern (6 bp):
TTTATC
Found at i:1139466 original size:122 final size:121
Alignment explanation
Indices: 1139256--1139478 Score: 265
Period size: 122 Copynumber: 1.8 Consensus size: 121
1139246 TATTATTTTC
* * *
1139256 TTTTTTATTTATTTATTTATTATTTTCTTTATATTCATTTTATTTATTTATCTATTTTTATTTTT
1 TTTTTTATTTATTTATTTATTATTATCTTTATATTCATTTTATTGATTTATCTATCTTTATTTTT
* * *
1139321 ATCTTTATCTTTATCTTTATTTATTTTCTTTTCTTTTCTTTTACTTTATTTTTATA
66 ATCTTTATCTTTATCTGTATTTATCTTATTTTCTTTTCTTTTACTTTATTTTTATA
* * * *
1139377 TTTTTGTATTTATTTTATTTATT-TTATCTTTATCTTTATTTTATTGATTTCTTTATCTTTATTT
1 TTTTT-TATTTA-TTTATTTATTATTATCTTTATATTCATTTTATTGATTTATCTATCTTTATTT
* *
1139441 TATTTGTTTTAT-TTT-T-TGTACTTTATCTTATTTTCTTT
64 T-TAT-CTTTATCTTTATCTGTA-TTTATCTTATTTTCTTT
1139479 ATTTCATTTT
Statistics
Matches: 85, Mismatches: 12, Indels: 9
0.80 0.11 0.08
Matches are distributed among these distances:
121 8 0.09
122 57 0.67
123 15 0.18
124 5 0.06
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.74
Consensus pattern (121 bp):
TTTTTTATTTATTTATTTATTATTATCTTTATATTCATTTTATTGATTTATCTATCTTTATTTTT
ATCTTTATCTTTATCTGTATTTATCTTATTTTCTTTTCTTTTACTTTATTTTTATA
Found at i:1139506 original size:11 final size:12
Alignment explanation
Indices: 1139481--1139512 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
1139471 TTTTCTTTAT
1139481 TTCATTTTTTCC
1 TTCATTTTTTCC
1139493 TTCATTTTTT-C
1 TTCATTTTTTCC
1139504 TTCATTTTT
1 TTCATTTTT
1139513 GTTTTCATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (12 bp):
TTCATTTTTTCC
Found at i:1142945 original size:14 final size:14
Alignment explanation
Indices: 1142888--1142946 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
1142878 AGTTAGTAAA
* *
1142888 AAAAGAAAATAATGA
1 AAAATAAAATAA-GT
*
1142903 AAAATAATA-AAG-
1 AAAATAAAATAAGT
1142915 AAAATAAAATTAA-T
1 AAAATAAAA-TAAGT
1142929 AAAATAAAATAAGT
1 AAAATAAAATAAGT
1142943 AAAA
1 AAAA
1142947 GGGTTAGTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
12 8 0.22
13 4 0.11
14 18 0.49
15 7 0.19
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.19
Consensus pattern (14 bp):
AAAATAAAATAAGT
Found at i:1144818 original size:165 final size:163
Alignment explanation
Indices: 1144566--1145491 Score: 749
Period size: 165 Copynumber: 5.6 Consensus size: 163
1144556 AATTTATTGA
* * * ** **
1144566 CAGATAGCCCTTCTAGCCTTGAGCTATGCTATAAATCTGAT-TCGCCTCTGAGCTGAGTATAATC
1 CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAA--TGATGT-GCCT-TGAGCTGAGCGTAATC
*
1144630 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGC
62 GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-
* * * * **
1144695 CCTCAAAGTTGAGTGTAATCGAACTTGGGGGTCTTTGG
126 CCTCAGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGG
* * *
1144733 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAATCGAA
* * * * ** * * * *
1144798 CTCAAAGGTTTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTCGTGCTACAAATGATATGTCTT
65 CTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTC
* *
1144863 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTG
130 AGAGCTGAGTGTAGTCGAACTCGAAGGTCTTT-G-G
* * * * ** * * * *
1144899 ACAGATAACCCTTCTAGCCTTGAGTTATGTTGTGAATGATATGCCCTCGAAGATGAGTGTAATCG
1 -CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTG-CCTTG-AGCTGAGCGTAATCG
* ** * *
1144964 AACTTGGGGGTC---T-TTCGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC
63 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC
** *
1145025 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTG
128 TCAGAGCTGAGTGTAGTCGAACTCGAAGGTC-TTTG--G
* * * * *
1145064 CCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 -CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTG-CCTTG-AGCTGAGCGTAATCG
** *
1145129 AACTCGGGGGTC---T-TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTC
63 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-C
* * *
1145190 GT-TGAGCTGAGTGTAGTCGAACTCAAAGGTCTTTTGTTGG
127 CTCAGAGCTGAGTGTAGTCGAACTCGAAGGTC---T-TTGG
* * * * * *
1145230 CAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTTGAA
1 CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAATCGAA
* * * * * * * ** *
1145295 CTCGAAGGT-ATTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATCCTGTGAATGATATGCCCT
65 CTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCT
* * * * **
1145359 CAAAGTTGAGTGTAATCGGACTCGGGGGTCTTTGG
129 CAGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGG
* * * * *
1145394 CAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATGATGTGCATTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAATCGAA
* * * *
1145459 CTTGAAGGTCTTTGGTTGGCAAATAGCCCTTCT
65 CTCGAAGGTCTTTTGTTGGCAGATAACCCTTCT
1145492 TGTCTTGAGC
Statistics
Matches: 622, Mismatches: 117, Indels: 42
0.80 0.15 0.05
Matches are distributed among these distances:
164 189 0.30
165 276 0.44
166 7 0.01
167 105 0.17
168 45 0.07
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (163 bp):
CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGAGCTGAGCGTAATCGAAC
TCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTCA
GAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGG
Found at i:1145388 original size:413 final size:413
Alignment explanation
Indices: 1144628--1145491 Score: 1476
Period size: 413 Copynumber: 2.1 Consensus size: 413
1144618 CTGAGTATAA
1144628 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * *
1144693 GCCCTCAAAGTTGAGTGTAATCGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
66 GCCCTCAAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCT
*
1144758 ATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTTTTTTGTTGGCAGACA
131 ATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACA
*
1144823 ACCCTTCTAGACTTAAGTCGTGCTACAAATGATATGTCTTGGAGCTGAGCGTAGTCGAACTCGAA
196 ACCCTTCTAGACTTAAGTCGTGCTACAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
* ** *
1144888 GGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTGAATGATATGCCCTCGAAGAT
261 GGTATTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATCCTGTGAATGATATGCCCTCAAAGAT
* *
1144953 GAGTGTAATCGAACTTGGGGGTCTTTCGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATG
326 GAGTGTAATCGAACTCGGGGGTCTTTCGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATG
*
1145018 ATGTGCCTTGGAGCTGAGCGTAG
391 ATGTGCATTGGAGCTGAGCGTAG
* * *
1145041 TCGAACTCGAAGGTCTTTTGTTGCCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
*
1145106 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCT
66 GCCCTCAAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCT
* *
1145171 ATGCTGCAAATGATGTGTCGTTGAGCTGAGTGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACA
131 ATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACA
* * *
1145236 ACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTTGAACTCGAA
196 ACCCTTCTAGACTTAAGTCGTGCTACAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
*
1145301 GGTATTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATCCTGTGAATGATATGCCCTCAAAGTT
261 GGTATTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATCCTGTGAATGATATGCCCTCAAAGAT
* * *
1145366 GAGTGTAATCGGACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATG
326 GAGTGTAATCGAACTCGGGGGTCTTTCGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATG
1145431 ATGTGCATTGGAGCTGAGCGTAG
391 ATGTGCATTGGAGCTGAGCGTAG
* * *
1145454 TCGAACTTGAAGGTCTTTGGTTGGCAAATAGCCCTTCT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
1145492 TGTCTTGAGC
Statistics
Matches: 421, Mismatches: 30, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
413 421 1.00
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.31
Consensus pattern (413 bp):
TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
GCCCTCAAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCT
ATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACA
ACCCTTCTAGACTTAAGTCGTGCTACAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
GGTATTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATCCTGTGAATGATATGCCCTCAAAGAT
GAGTGTAATCGAACTCGGGGGTCTTTCGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATG
ATGTGCATTGGAGCTGAGCGTAG
Found at i:1145491 original size:248 final size:245
Alignment explanation
Indices: 1144562--1145473 Score: 974
Period size: 248 Copynumber: 3.7 Consensus size: 245
1144552 GACAAATTTA
* * * * *
1144562 TTGACAGATAGCCCTTCTAGCCTTGAGCTATGCTATAAATCTGAT-T-CGCCTCTG-AGCTGAGT
1 TTGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAA--TGATATGC-CCTC-GAAGCTGAGT
* ** *
1144624 ATAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
62 GTAATCGAACTCGGGGGTC--T--TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
* * **
1144689 ATGTGCCCTCAAAGTTGAGTGTAATCGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTA
123 ATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTA
* *
1144754 AGCTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTTTTTTG
188 AGTTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGG-TTTTTG
* * ** ** * * * * *
1144813 TTGGCAGACAACCCTTCTAGACTTAAGTCGTGCTACAAATGATATG-TCTTGGAGCTGAGCGTAG
1 TTGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAA
** * * * * * ** *
1144877 TCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTGAATGATATG
66 TCGAACTCGGGGGTCTTT-G-G-CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* ** *
1144942 CCCTCGAAGATGAGTGTAATCGAACTTGGGGGTCTTTCGCAGATAGCCCTTCTCGACTTAAGTTA
128 CCCTCGAAGCTGAGTGTAATCGAACTTGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTA
1145007 TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
193 TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT-TTTTG
* * *
1145061 TTGCCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAA
* *
1145126 TCGAACTCGGGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCG
66 TCGAACTCGGGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCC
* * ** * * *
1145191 TTG-AGCTGAGTGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTT
131 TCGAAGCTGAGTGTAATCGAACTTGAAGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGTT
* * * *
1145255 GTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTTGAACTCGAAGGTATTTG
192 ATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTG
* * * * * * *
1145309 GTGACAGATAACCCTTCTAGCCTTGAGTTATCCTGTGAATGATATGCCCTCAAAGTTGAGTGTAA
1 TTGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAA
* * * *
1145374 TCGGACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATGATGTG-CA
66 TCGAACTCGGGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCC
* * * *
1145438 TTGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTGG
131 TCGAAGCTGAGTGTAATCGAACTTGAAGGTCTTTGG
1145474 TTGGCAAATA
Statistics
Matches: 564, Mismatches: 83, Indels: 35
0.83 0.12 0.05
Matches are distributed among these distances:
244 4 0.01
245 24 0.04
246 38 0.07
247 10 0.02
248 327 0.58
249 130 0.23
250 1 0.00
251 30 0.05
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.31
Consensus pattern (245 bp):
TTGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAA
TCGAACTCGGGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCC
TCGAAGCTGAGTGTAATCGAACTTGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGC
TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTG
Found at i:1149340 original size:17 final size:16
Alignment explanation
Indices: 1149320--1149376 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 16
1149310 AAAAGTTAGT
1149320 AAAAAAGAAAATAATGA
1 AAAAAAGAAAATAAT-A
1149337 AAAATAATGAAAAATAATA
1 AAAA-AA-G-AAAATAATA
*
1149356 AAGAAAATAAAATAA-A
1 AA-AAAAGAAAATAATA
1149372 AAAAA
1 AAAAA
1149377 TAAAAAAAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
15 3 0.09
16 3 0.09
17 11 0.31
18 2 0.06
19 6 0.17
20 10 0.29
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (16 bp):
AAAAAAGAAAATAATA
Found at i:1149349 original size:9 final size:10
Alignment explanation
Indices: 1149327--1149354 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1149317 AGTAAAAAAG
1149327 AAAATAATGA
1 AAAATAATGA
1149337 AAAATAATGA
1 AAAATAATGA
1149347 AAAATAAT
1 AAAATAAT
1149355 AAAGAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (10 bp):
AAAATAATGA
Found at i:1149361 original size:23 final size:23
Alignment explanation
Indices: 1149322--1149390 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
1149312 AAGTTAGTAA
* *
1149322 AAAAGAAAATAATGAAAA-ATAAT
1 AAAA-AAAATAAAGAAAATAAAAT
*
1149345 GAAAAATAATAAAGAAAATAAAAT
1 -AAAAAAAATAAAGAAAATAAAAT
1149369 AAAAAAAATAAA-AAAAGTAAAA
1 AAAAAAAATAAAGAAAA-TAAAA
1149391 GGGTTAGTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
22 4 0.10
23 27 0.69
24 8 0.21
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.14
Consensus pattern (23 bp):
AAAAAAAATAAAGAAAATAAAAT
Found at i:1149369 original size:5 final size:5
Alignment explanation
Indices: 1149359--1149440 Score: 55
Period size: 5 Copynumber: 16.2 Consensus size: 5
1149349 AATAATAAAG
* * **
1149359 AAAAT AAAAT AAAA- AAAAT AAAA- AAAGT AAAAGGGT TAGTT AAAA-
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA---T AAAAT AAAAT
1149404 A-AAT AAAAT AAGAAT AAAAT AAAAAT AAAAT AAAAT A
1 AAAAT AAAAT AA-AAT AAAAT -AAAAT AAAAT AAAAT A
1149441 TTTAAACTTA
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
3 2 0.03
4 9 0.15
5 37 0.62
6 10 0.17
8 2 0.03
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:1149372 original size:22 final size:21
Alignment explanation
Indices: 1149322--1149440 Score: 66
Period size: 22 Copynumber: 5.5 Consensus size: 21
1149312 AAGTTAGTAA
* *
1149322 AAAAGAAAATAAT-GAAAAAT
1 AAAATAAAATAATAAAAAAAT
*
1149342 AATGA-AAAATAATAAAGAAAAT
1 AA-AATAAAATAATAAA-AAAAT
*
1149364 AAAATAAAAAAAATAAAAAAAGT
1 AAAAT-AAAATAATAAAAAAA-T
**** *
1149387 AAAA-GGGTTAGTTAAAAAAAT
1 AAAATAAAATA-ATAAAAAAAT
1149408 AAAATAAGAATAA-AATAAAAAT
1 AAAATAA-AATAATAA-AAAAAT
1149430 AAAATAAAATA
1 AAAATAAAATA
1149441 TTTAAACTTA
Statistics
Matches: 74, Mismatches: 15, Indels: 19
0.69 0.14 0.18
Matches are distributed among these distances:
20 10 0.14
21 15 0.20
22 32 0.43
23 17 0.23
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (21 bp):
AAAATAAAATAATAAAAAAAT
Found at i:1149390 original size:9 final size:9
Alignment explanation
Indices: 1149322--1149390 Score: 50
Period size: 9 Copynumber: 7.4 Consensus size: 9
1149312 AAGTTAGTAA
1149322 AAAAGAAAAT
1 AAAA-AAAAT
*
1149332 AATGAAAAAT
1 AA-AAAAAAT
*
1149342 AATGAAAAAT
1 AA-AAAAAAT
* *
1149352 AATAAAGA-
1 AAAAAAAAT
*
1149360 AAATAAAAT
1 AAAAAAAAT
1149369 AAAAAAAAT
1 AAAAAAAAT
*
1149378 AAAAAAAGT
1 AAAAAAAAT
1149387 AAAA
1 AAAA
1149391 GGGTTAGTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
8 5 0.10
9 24 0.49
10 19 0.39
11 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.14
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:1149421 original size:11 final size:10
Alignment explanation
Indices: 1149403--1149440 Score: 58
Period size: 11 Copynumber: 3.6 Consensus size: 10
1149393 GTTAGTTAAA
1149403 AAAATAAAAT
1 AAAATAAAAT
1149413 AAGAATAAAAT
1 AA-AATAAAAT
1149424 AAAAATAAAAT
1 -AAAATAAAAT
1149435 AAAATA
1 AAAATA
1149441 TTTAAACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.31
11 16 0.62
12 2 0.08
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:1149422 original size:16 final size:15
Alignment explanation
Indices: 1149403--1149440 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 15
1149393 GTTAGTTAAA
1149403 AAAATAAAATAAGAAT
1 AAAATAAAATAA-AAT
1149419 AAAATAAAAATAAAAT
1 AAAAT-AAAATAAAAT
1149435 AAAATA
1 AAAATA
1149441 TTTAAACTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.05
16 13 0.62
17 7 0.33
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (15 bp):
AAAATAAAATAAAAT
Found at i:1149487 original size:18 final size:19
Alignment explanation
Indices: 1149464--1149499 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1149454 CGTGAAAGAA
1149464 AAAAAT-AATAAATTAAAC
1 AAAAATGAATAAATTAAAC
*
1149482 AAAAATGACTAAATTAAA
1 AAAAATGAATAAATTAAA
1149500 ATAAAAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.22
Consensus pattern (19 bp):
AAAAATGAATAAATTAAAC
Found at i:1154873 original size:283 final size:281
Alignment explanation
Indices: 1154313--1154878 Score: 1114
Period size: 283 Copynumber: 2.0 Consensus size: 281
1154303 CTTCGGCCTA
1154313 AAATTCTGAAGAAAGAAAAAGAAAAAAAACGGCGACAAAGCAAGAGGCTAATCAAATGGTTGAAT
1 AAATTCTGAAGAAAGAAAAAGAAAAAAAACGGCGACAAAGCAAGAGGCTAATCAAATGGTTGAAT
1154378 GAGTCGATAATCACCGCTGTGAAGCATTGCAGTCTCTTCGGAACATCCTCTTTGGAACATCGGTG
66 GAGTCGATAATCACCGCTGTGAAGCATTGCAGTCTCTTCGGAACATCCTCTTTGGAACATCGGTG
1154443 CAGGGAATGGTGCCCACAAGAATGGGAATCCAAAGCAAAAACACCTCTCCTAGATACATTTATCT
131 CAGGGAATGGTGCCCACAAGAATGGGAATCCAAAGCAAAAACACCTCTCCTAGATACATTTATCT
1154508 CCAATTACTTCGAACTAATCAAGTAAGAACCTGAAAACATCAGTAAGTGAGACAATGCCTTCGAC
196 CCAATTACTTCGAACTAATCAAGTAAGAACCTGAAAACATCAGTAAGTGAGACAATGCCTTCGAC
1154573 ACGGTTACTGTCAGCTTCCAC
261 ACGGTTACTGTCAGCTTCCAC
1154594 AAATTCTGAAGAAAGAAAAAGAAAAAAAACGGCGACAAAGCAAGAGGCTAATCAAATGGTTGAAT
1 AAATTCTGAAGAAAGAAAAAGAAAAAAAACGGCGACAAAGCAAGAGGCTAATCAAATGGTTGAAT
1154659 GAGTCGATAATCACCGCTGTGAAGCATTGCAGTCTCTTCGGAACATCCTCTTTGGAACATCGGGT
66 GAGTCGATAATCACCGCTGTGAAGCATTGCAGTCTCTTCGGAACATCCTCTTTGGAACATC-GGT
1154724 GCAGGGAATGGTGCCCACAAGAAATGGGAATCCAAAGCAAAAACACCTCTCCTAGATACATTTAT
130 GCAGGGAATGGTGCCCACAAG-AATGGGAATCCAAAGCAAAAACACCTCTCCTAGATACATTTAT
1154789 CTCCAATTACTTCGAACTAATCAAGTAAGAACCTGAAAACATCAGTAAGTGAGACAATGCCTTCG
194 CTCCAATTACTTCGAACTAATCAAGTAAGAACCTGAAAACATCAGTAAGTGAGACAATGCCTTCG
1154854 ACACGGTTACTGTCAGCTTCCAC
259 ACACGGTTACTGTCAGCTTCCAC
1154877 AA
1 AA
1154879 TGACAAGCCG
Statistics
Matches: 283, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
281 126 0.45
282 24 0.08
283 133 0.47
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (281 bp):
AAATTCTGAAGAAAGAAAAAGAAAAAAAACGGCGACAAAGCAAGAGGCTAATCAAATGGTTGAAT
GAGTCGATAATCACCGCTGTGAAGCATTGCAGTCTCTTCGGAACATCCTCTTTGGAACATCGGTG
CAGGGAATGGTGCCCACAAGAATGGGAATCCAAAGCAAAAACACCTCTCCTAGATACATTTATCT
CCAATTACTTCGAACTAATCAAGTAAGAACCTGAAAACATCAGTAAGTGAGACAATGCCTTCGAC
ACGGTTACTGTCAGCTTCCAC
Found at i:1156369 original size:72 final size:72
Alignment explanation
Indices: 1156252--1156393 Score: 266
Period size: 72 Copynumber: 2.0 Consensus size: 72
1156242 AGGGTAAATG
*
1156252 GCACCACTCATAAACACAACTATCAAAAGACATGCTGCCATTACCAAATGGCAAGGAACAAAGGA
1 GCACCACTCATAAACACAACTATCAAAAGACATGCTGCCATTACCAAAGGGCAAGGAACAAAGGA
1156317 AACAATA
66 AACAATA
*
1156324 GCACCACTCATAAACACAACTGTCAAAAGACATGCTGCCATTACCAAAGGGCAAGGAACAAAGGA
1 GCACCACTCATAAACACAACTATCAAAAGACATGCTGCCATTACCAAAGGGCAAGGAACAAAGGA
1156389 AACAA
66 AACAA
1156394 AAGATAAAGC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.46, C:0.25, G:0.15, T:0.13
Consensus pattern (72 bp):
GCACCACTCATAAACACAACTATCAAAAGACATGCTGCCATTACCAAAGGGCAAGGAACAAAGGA
AACAATA
Found at i:1156716 original size:54 final size:54
Alignment explanation
Indices: 1156658--1156829 Score: 124
Period size: 54 Copynumber: 3.1 Consensus size: 54
1156648 AGGAGCATGA
1156658 TTATTGATTCTTTCTCATTGCCATCATTACATAGAATCATCATTACTCAAATGG
1 TTATTGATTCTTTCTCATTGCCATCATTACATAGAATCATCATTACTCAAATGG
* * * * * *** * *
1156712 TTATTGATGC--ACTGA-T---ATCATTATATGGAA-CAAGGTTTGCCTCAAGAGGAG
1 TTATTGATTCTTTCTCATTGCCATCATTACATAGAATC-ATCATT-ACTCAA-ATG-G
1156763 CATGATTATTGATTCTTTCTCATTGCCATCATTACATAGAATCATCATTACTCAAATGG
1 --T---TATTGATTCTTTCTCATTGCCATCATTACATAGAATCATCATTACTCAAATGG
1156822 TTATTGAT
1 TTATTGAT
1156830 GCACTGATAT
Statistics
Matches: 82, Mismatches: 20, Indels: 32
0.61 0.15 0.24
Matches are distributed among these distances:
47 1 0.01
48 15 0.18
49 5 0.06
50 2 0.02
51 2 0.02
52 3 0.04
53 1 0.01
54 16 0.20
56 8 0.10
57 1 0.01
58 3 0.04
59 2 0.02
60 2 0.02
61 5 0.06
62 15 0.18
63 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.38
Consensus pattern (54 bp):
TTATTGATTCTTTCTCATTGCCATCATTACATAGAATCATCATTACTCAAATGG
Found at i:1156841 original size:110 final size:110
Alignment explanation
Indices: 1156648--1156875 Score: 447
Period size: 110 Copynumber: 2.1 Consensus size: 110
1156638 TTGTCTCATT
1156648 AGGAGCATGATTATTGATTCTTTCTCATTGCCATCATTACATAGAATCATCATTACTCAAATGGT
1 AGGAGCATGATTATTGATTCTTTCTCATTGCCATCATTACATAGAATCATCATTACTCAAATGGT
*
1156713 TATTGATGCACTGATATCATTATATGGAACAAGGTTTGCCTCAAG
66 TATTGATGCACTGATATCATTATATAGAACAAGGTTTGCCTCAAG
1156758 AGGAGCATGATTATTGATTCTTTCTCATTGCCATCATTACATAGAATCATCATTACTCAAATGGT
1 AGGAGCATGATTATTGATTCTTTCTCATTGCCATCATTACATAGAATCATCATTACTCAAATGGT
1156823 TATTGATGCACTGATATCATTATATAGAACAAGGTTTGCCTCAAG
66 TATTGATGCACTGATATCATTATATAGAACAAGGTTTGCCTCAAG
1156868 AGGAGCAT
1 AGGAGCAT
1156876 AGCTGCATGG
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
110 117 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (110 bp):
AGGAGCATGATTATTGATTCTTTCTCATTGCCATCATTACATAGAATCATCATTACTCAAATGGT
TATTGATGCACTGATATCATTATATAGAACAAGGTTTGCCTCAAG
Found at i:1160552 original size:10 final size:10
Alignment explanation
Indices: 1160537--1160576 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
1160527 TTTATCACAC
1160537 CAAATTCTCT
1 CAAATTCTCT
1160547 CAAATTCTCT
1 CAAATTCTCT
1160557 -AAATTTCTCT
1 CAAA-TTCTCT
*
1160567 CAAATACTCT
1 CAAATTCTCT
1160577 ATCTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:1160895 original size:111 final size:111
Alignment explanation
Indices: 1160701--1161033 Score: 576
Period size: 111 Copynumber: 3.0 Consensus size: 111
1160691 TAGAAATCAT
* * *
1160701 ATATCTCTACACTTTGCTGATACAGTAACATTTTAATGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCAACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
1160766 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
1160812 ATATCTCAACACTTTGTTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCAACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
1160877 TAATTAGTTGATTTATTTAATGTATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* * *
1160923 ATATCTCGACACTTTGCTGATACGGTAATATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCAACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
1160988 TAATTAGTTGATTTATTTAATGCATGATTATTAGAGTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
1161034 TTTTTGTAAT
Statistics
Matches: 210, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 210 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.46
Consensus pattern (111 bp):
ATATCTCAACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:1166912 original size:49 final size:51
Alignment explanation
Indices: 1166808--1166921 Score: 137
Period size: 49 Copynumber: 2.3 Consensus size: 51
1166798 CCCCTACGTG
* * *
1166808 GCGTATAGCGCGG-AGCAGGGGGTGCGTTATACCTCACGTGTAACCCAGTCA
1 GCGTATAGCGCGGTAGCAGGGGGTGCG-TATACCTCACGTGGAACCAAATCA
**
1166859 GCGTATAGCGCGGTA-CAGGGGGGTGC-TATA-CTCACGTGGCGCCAAATCA
1 GCGTATAGCGCGGTAGCA-GGGGGTGCGTATACCTCACGTGGAACCAAATCA
1166908 GCGTATAGCGCGGT
1 GCGTATAGCGCGGT
1166922 TCAGAGGGCG
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
49 28 0.50
50 4 0.07
51 15 0.27
52 9 0.16
ACGTcount: A:0.21, C:0.25, G:0.35, T:0.19
Consensus pattern (51 bp):
GCGTATAGCGCGGTAGCAGGGGGTGCGTATACCTCACGTGGAACCAAATCA
Found at i:1173922 original size:18 final size:18
Alignment explanation
Indices: 1173883--1173924 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1173873 TTTTAGGGTT
* *
1173883 ATTTTAAAAAATAATAAT
1 ATTTTTAAAAATAATAAC
1173901 ATTTTTAAAAAT-ATAGAC
1 ATTTTTAAAAATAATA-AC
1173919 ATTTTT
1 ATTTTT
1173925 TTAACTATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTTTTAAAAATAATAAC
Found at i:1175723 original size:71 final size:71
Alignment explanation
Indices: 1175607--1175753 Score: 294
Period size: 71 Copynumber: 2.1 Consensus size: 71
1175597 TATCAAAAAA
1175607 AAAATATTGTTTTTATTAGACATAAGGTTTATGAAACTATTAACAAGAATAAGTTGTGCCTCATA
1 AAAATATTGTTTTTATTAGACATAAGGTTTATGAAACTATTAACAAGAATAAGTTGTGCCTCATA
1175672 TGAATT
66 TGAATT
1175678 AAAATATTGTTTTTATTAGACATAAGGTTTATGAAACTATTAACAAGAATAAGTTGTGCCTCATA
1 AAAATATTGTTTTTATTAGACATAAGGTTTATGAAACTATTAACAAGAATAAGTTGTGCCTCATA
1175743 TGAATT
66 TGAATT
1175749 AAAAT
1 AAAAT
1175754 CCTACTAGGC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 76 1.00
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (71 bp):
AAAATATTGTTTTTATTAGACATAAGGTTTATGAAACTATTAACAAGAATAAGTTGTGCCTCATA
TGAATT
Found at i:1186355 original size:205 final size:205
Alignment explanation
Indices: 1186107--1186517 Score: 822
Period size: 205 Copynumber: 2.0 Consensus size: 205
1186097 TGGATACATC
1186107 TATTTGCACTAGCATGAGTAGGACCATAGTTGGGCGCATTTTTACTAATGTGGCAATGGGTTCAG
1 TATTTGCACTAGCATGAGTAGGACCATAGTTGGGCGCATTTTTACTAATGTGGCAATGGGTTCAG
1186172 TCGGACTTTGTAGTGTTTTCCCTATTTAGAATCAATGTGAAAGAAAGGGAAAAAGGGATAAAATG
66 TCGGACTTTGTAGTGTTTTCCCTATTTAGAATCAATGTGAAAGAAAGGGAAAAAGGGATAAAATG
1186237 TAAAAAATTGTGGAAGGAAGAAACACGCGTGGTACGTATTAGAGCCGAGTTGGACAACGACCACT
131 TAAAAAATTGTGGAAGGAAGAAACACGCGTGGTACGTATTAGAGCCGAGTTGGACAACGACCACT
1186302 CTTAGCAGGG
196 CTTAGCAGGG
1186312 TATTTGCACTAGCATGAGTAGGACCATAGTTGGGCGCATTTTTACTAATGTGGCAATGGGTTCAG
1 TATTTGCACTAGCATGAGTAGGACCATAGTTGGGCGCATTTTTACTAATGTGGCAATGGGTTCAG
1186377 TCGGACTTTGTAGTGTTTTCCCTATTTAGAATCAATGTGAAAGAAAGGGAAAAAGGGATAAAATG
66 TCGGACTTTGTAGTGTTTTCCCTATTTAGAATCAATGTGAAAGAAAGGGAAAAAGGGATAAAATG
1186442 TAAAAAATTGTGGAAGGAAGAAACACGCGTGGTACGTATTAGAGCCGAGTTGGACAACGACCACT
131 TAAAAAATTGTGGAAGGAAGAAACACGCGTGGTACGTATTAGAGCCGAGTTGGACAACGACCACT
1186507 CTTAGCAGGG
196 CTTAGCAGGG
1186517 T
1 T
1186518 GCGCTTTGTT
Statistics
Matches: 206, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
205 206 1.00
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (205 bp):
TATTTGCACTAGCATGAGTAGGACCATAGTTGGGCGCATTTTTACTAATGTGGCAATGGGTTCAG
TCGGACTTTGTAGTGTTTTCCCTATTTAGAATCAATGTGAAAGAAAGGGAAAAAGGGATAAAATG
TAAAAAATTGTGGAAGGAAGAAACACGCGTGGTACGTATTAGAGCCGAGTTGGACAACGACCACT
CTTAGCAGGG
Found at i:1187823 original size:29 final size:29
Alignment explanation
Indices: 1187789--1187847 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1187779 CCTAAATTAA
*
1187789 TTTGATGTCATTGCTTACGTCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1187818 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1187847 T
1 T
1187848 AGGTGAAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1189315 original size:36 final size:36
Alignment explanation
Indices: 1189268--1189339 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
1189258 GATTGGATCG
1189268 TAGATTCTGGCTGCTCAAATCATATGACGGGTGACA
1 TAGATTCTGGCTGCTCAAATCATATGACGGGTGACA
1189304 TAGATTCTGGCTGCTCAAATCATATGACGGGTGACA
1 TAGATTCTGGCTGCTCAAATCATATGACGGGTGACA
1189340 AACAGAAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (36 bp):
TAGATTCTGGCTGCTCAAATCATATGACGGGTGACA
Found at i:1192504 original size:29 final size:29
Alignment explanation
Indices: 1192470--1192528 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1192460 CCTAAATTAA
1192470 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1192499 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1192528 T
1 T
1192529 AGATGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1194310 original size:2 final size:2
Alignment explanation
Indices: 1194303--1194329 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1194293 TTGTTAAAAC
1194303 AT 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 AT A
1194330 CATGTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1196078 original size:58 final size:58
Alignment explanation
Indices: 1196016--1196137 Score: 174
Period size: 58 Copynumber: 2.1 Consensus size: 58
1196006 GTTTGGGATC
** * *
1196016 AATTTAGAATGAGGGTTACTATTTGATATGAATTTAAAATTTTA-AAAGTTTACAAACT
1 AATTTAGAATGAGAATCACAATTTGATATGAATTTAAAATTTTAGAAA-TTTACAAACT
* *
1196074 AATTTAGAATGAGAATCACAATTTGATATGAATTTAAAATTTTAGAAATTTATAGACT
1 AATTTAGAATGAGAATCACAATTTGATATGAATTTAAAATTTTAGAAATTTACAAACT
1196132 AATTTA
1 AATTTA
1196138 AAATAAGAGT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 54 0.95
59 3 0.05
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.39
Consensus pattern (58 bp):
AATTTAGAATGAGAATCACAATTTGATATGAATTTAAAATTTTAGAAATTTACAAACT
Found at i:1203846 original size:24 final size:26
Alignment explanation
Indices: 1203789--1203851 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 26
1203779 TTTCTTTTCA
* * *
1203789 TTTAAGTAAAATATTTTATATTATTT
1 TTTAATTAAAATATTTTATATAATAT
*
1203815 TTTCATTAAAATATTTT-TA-AATAT
1 TTTAATTAAAATATTTTATATAATAT
1203839 TTTAATTAAAATA
1 TTTAATTAAAATA
1203852 GATATTTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 15 0.47
25 2 0.06
26 15 0.47
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (26 bp):
TTTAATTAAAATATTTTATATAATAT
Found at i:1206065 original size:21 final size:21
Alignment explanation
Indices: 1206034--1206139 Score: 94
Period size: 21 Copynumber: 5.0 Consensus size: 21
1206024 CGATTTACAT
*
1206034 ATTCGCATTGCGATAGTCCAA
1 ATTCGCGTTGCGATAGTCCAA
* *
1206055 GTTCGCGTTGCGATTTATTCCAA
1 ATTCGCGTTGCGA--TAGTCCAA
*
1206078 ATT--CGTTGCGATAGTCGAA
1 ATTCGCGTTGCGATAGTCCAA
* *
1206097 GTTCGCGTTGCGATTTATTCCAA
1 ATTCGCGTTGCGA--TAGTCCAA
1206120 ATT--CGTTGCGATAGTCCAA
1 ATTCGCGTTGCGATAGTCCAA
1206139 A
1 A
1206140 ATCGTAACGA
Statistics
Matches: 68, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
19 16 0.24
21 35 0.51
23 17 0.25
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.34
Consensus pattern (21 bp):
ATTCGCGTTGCGATAGTCCAA
Found at i:1206092 original size:42 final size:42
Alignment explanation
Indices: 1206041--1206138 Score: 187
Period size: 42 Copynumber: 2.3 Consensus size: 42
1206031 CATATTCGCA
1206041 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
1206083 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
1206125 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
1206139 AATCGTAACG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:1206252 original size:5 final size:5
Alignment explanation
Indices: 1206232--1206266 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
1206222 CGTATTACCA
1206232 CGACC ACGACCC CGACC CGACC CGACC CGACC CGA
1 CGACC -CGA-CC CGACC CGACC CGACC CGACC CGA
1206267 GACAGACGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 20 0.71
6 6 0.21
7 2 0.07
ACGTcount: A:0.23, C:0.57, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:1206811 original size:22 final size:22
Alignment explanation
Indices: 1206783--1206832 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
1206773 GTTGAAGGCG
1206783 ATCACATGTAGGCAGCCTATCA
1 ATCACATGTAGGCAGCCTATCA
1206805 ATCACATGTAGGCAGCCTATCA
1 ATCACATGTAGGCAGCCTATCA
1206827 ATCACA
1 ATCACA
1206833 ACCATCCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (22 bp):
ATCACATGTAGGCAGCCTATCA
Found at i:1208504 original size:92 final size:92
Alignment explanation
Indices: 1208347--1208531 Score: 370
Period size: 92 Copynumber: 2.0 Consensus size: 92
1208337 TGTTTGAAAA
1208347 ACTGTGGGGAGTAGCCGTCAGGACCAGGAGCTTTGTTGTTGCCCTGGTCAAAAACGGCTTCTTTA
1 ACTGTGGGGAGTAGCCGTCAGGACCAGGAGCTTTGTTGTTGCCCTGGTCAAAAACGGCTTCTTTA
1208412 ATCTCTTCTGAGGTTACTGGCTTGGTC
66 ATCTCTTCTGAGGTTACTGGCTTGGTC
1208439 ACTGTGGGGAGTAGCCGTCAGGACCAGGAGCTTTGTTGTTGCCCTGGTCAAAAACGGCTTCTTTA
1 ACTGTGGGGAGTAGCCGTCAGGACCAGGAGCTTTGTTGTTGCCCTGGTCAAAAACGGCTTCTTTA
1208504 ATCTCTTCTGAGGTTACTGGCTTGGTC
66 ATCTCTTCTGAGGTTACTGGCTTGGTC
1208531 A
1 A
1208532 GAGAGGAATC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 93 1.00
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.31
Consensus pattern (92 bp):
ACTGTGGGGAGTAGCCGTCAGGACCAGGAGCTTTGTTGTTGCCCTGGTCAAAAACGGCTTCTTTA
ATCTCTTCTGAGGTTACTGGCTTGGTC
Found at i:1216506 original size:2 final size:2
Alignment explanation
Indices: 1216499--1216525 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1216489 AATATTTTAT
1216499 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1216526 TTATTTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1216562 original size:22 final size:24
Alignment explanation
Indices: 1216491--1216562 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 24
1216481 TCTACAAAAA
* *
1216491 TATT-TTATTATATATATATATA-
1 TATTATTATTATATATTTATTTAT
1216513 TA-TA-TA-TATATATTTATTTAT
1 TATTATTATTATATATTTATTTAT
*
1216534 TATTATTATTATATTTTTATTTTAT
1 TATTATTATTATATATTTA-TTTAT
1216559 TATT
1 TATT
1216563 TTTGCAAGCC
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
20 12 0.29
21 5 0.12
22 4 0.10
23 2 0.05
24 9 0.22
25 9 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TATTATTATTATATATTTATTTAT
Found at i:1216657 original size:33 final size:33
Alignment explanation
Indices: 1216620--1216682 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
1216610 ATAAATTAAT
1216620 GTATTTGAGTCATATTAAAACACTAAAACCAAC
1 GTATTTGAGTCATATTAAAACACTAAAACCAAC
* * *
1216653 GTATTTGAGTTATATTGAAACATTAAAACC
1 GTATTTGAGTCATATTAAAACACTAAAACC
1216683 GAAACATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (33 bp):
GTATTTGAGTCATATTAAAACACTAAAACCAAC
Found at i:1217118 original size:38 final size:37
Alignment explanation
Indices: 1217032--1217119 Score: 90
Period size: 38 Copynumber: 2.3 Consensus size: 37
1217022 TCTCCTAATT
**
1217032 TTAATATTTTTATTTCTTTTTACATTGTTATATATTTA
1 TTAATATTTTT-TTTCTTTTTACATTAATATATATTTA
* *
1217070 TTTATTTTTTTTTTCATTTTT-CATTAA-ATATTATTATA
1 TTAATATTTTTTTTC-TTTTTACATTAATATA-TATT-TA
1217108 TTAATATTTTTT
1 TTAATATTTTTT
1217120 ATTATTCTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
36 3 0.07
37 12 0.29
38 26 0.63
ACGTcount: A:0.26, C:0.05, G:0.01, T:0.68
Consensus pattern (37 bp):
TTAATATTTTTTTTCTTTTTACATTAATATATATTTA
Found at i:1218986 original size:27 final size:27
Alignment explanation
Indices: 1218934--1218986 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 27
1218924 ACGGAGAGCA
1218934 TTGCGCCCTGGTGATGGGATTGTTTTT
1 TTGCGCCCTGGTGATGGGATTGTTTTT
1218961 TTGCG-CCTGGTGATGGGATTGTTTTT
1 TTGCGCCCTGGTGATGGGATTGTTTTT
1218987 CCATGTCGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.08, C:0.13, G:0.34, T:0.45
Consensus pattern (27 bp):
TTGCGCCCTGGTGATGGGATTGTTTTT
Found at i:1221079 original size:2 final size:2
Alignment explanation
Indices: 1221074--1221177 Score: 208
Period size: 2 Copynumber: 52.0 Consensus size: 2
1221064 TACCCCCCTC
1221074 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1221116 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1221158 CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT
1221178 ATATATATAT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 102 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1222968 original size:21 final size:20
Alignment explanation
Indices: 1222882--1223038 Score: 93
Period size: 20 Copynumber: 7.8 Consensus size: 20
1222872 AAATGACCAA
**
1222882 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1222901 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1222921 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1222941 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
1222962 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
1222982 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1223002 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1223023 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1223039 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 9
0.73 0.20 0.06
Matches are distributed among these distances:
19 16 0.15
20 56 0.54
21 32 0.31
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Done.