Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020854.1 Corchorus olitorius cultivar O-4 contig20887, 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: 256735
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:77 original size:10 final size:10
Alignment explanation
Indices: 62--86 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
52 TTAATTAAAA
62 TTTTTTTTCT
1 TTTTTTTTCT
72 TTTTTTTTCT
1 TTTTTTTTCT
82 TTTTT
1 TTTTT
87 CTTTTAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:2755 original size:19 final size:19
Alignment explanation
Indices: 2704--2758 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 19
2694 AATTACTTGC
*
2704 TGCATTAGGATTTACAAA-
1 TGCATTAGGATATACAAAT
* * *
2722 T-CCTTTGGGTATACAAAT
1 TGCATTAGGATATACAAAT
2740 TGCATTAGGATATACAAAT
1 TGCATTAGGATATACAAAT
2759 CCAAACAGAG
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
17 12 0.43
18 2 0.07
19 14 0.50
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (19 bp):
TGCATTAGGATATACAAAT
Found at i:3133 original size:53 final size:53
Alignment explanation
Indices: 3071--3173 Score: 145
Period size: 53 Copynumber: 1.9 Consensus size: 53
3061 GCATTATATT
* * * *
3071 AACAAAGCATATAAT-ATACTATACTATGATGATAAAATTACAAAATTAGATCA
1 AACAAAGCATATAATCATA-TAAACCATAATGATAAAAATACAAAATTAGATCA
*
3124 AACAAAGCATATACTCATATAAACCATAATGATAAAAATACAAAATTAGA
1 AACAAAGCATATAATCATATAAACCATAATGATAAAAATACAAAATTAGA
3174 CCAGCGCTGG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
53 41 0.93
54 3 0.07
ACGTcount: A:0.55, C:0.13, G:0.07, T:0.25
Consensus pattern (53 bp):
AACAAAGCATATAATCATATAAACCATAATGATAAAAATACAAAATTAGATCA
Found at i:8540 original size:109 final size:107
Alignment explanation
Indices: 8335--8554 Score: 311
Period size: 109 Copynumber: 2.0 Consensus size: 107
8325 TATGCAGCTG
*
8335 TTTATGTTGGGAGACTCATCCACTATAATCAGGTATGCGACATGGATAGAATTCAAATTAATCAG
1 TTTATGTTGGGAGACTCATCCACTATAATCAGGTATGCGACACGGATAGAATTCAAATTAATCAG
* * *
8400 AACAAAGCCCTAGATATCAGATGGGATAAAAAAAAACCGTCAAA
66 AACAAAACCCTAAATACCAGATGGGAT-AAAAAAAA-CGTCAAA
* * *
8444 TTTATGTTGGGAGACTCATCCACTATAA-CGAGGTATGCGATACGGATAGAATTCGAATTAGTCA
1 TTTATGTTGGGAGACTCATCCACTATAATC-AGGTATGCGACACGGATAGAATTCAAATTAATCA
*
8508 -AGACAAAACCCTAAATACCATAT-GGATAAAAAAAACGTCAAA
65 GA-ACAAAACCCTAAATACCAGATGGGATAAAAAAAACGTCAAA
8550 TTTAT
1 TTTAT
8555 TTTTATTCTT
Statistics
Matches: 101, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
106 12 0.12
107 8 0.08
108 6 0.06
109 75 0.74
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (107 bp):
TTTATGTTGGGAGACTCATCCACTATAATCAGGTATGCGACACGGATAGAATTCAAATTAATCAG
AACAAAACCCTAAATACCAGATGGGATAAAAAAAACGTCAAA
Found at i:34430 original size:33 final size:33
Alignment explanation
Indices: 34382--34464 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
34372 ACGGAGTCTC
*
34382 CAGCACCAGCACCAGCACCAGGGTCACCA-AATT
1 CAGCACCAGCACCAGCACAAGGGTCACCAGAA-T
* *
34415 CAGCCCCAGCGCCAGCACAAGGGTCACCAGAAT
1 CAGCACCAGCACCAGCACAAGGGTCACCAGAAT
*
34448 CAGCACCAACACCAGCA
1 CAGCACCAGCACCAGCA
34465 ACACCCCCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 41 0.95
34 2 0.05
ACGTcount: A:0.34, C:0.41, G:0.19, T:0.06
Consensus pattern (33 bp):
CAGCACCAGCACCAGCACAAGGGTCACCAGAAT
Found at i:61721 original size:20 final size:20
Alignment explanation
Indices: 61693--61735 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
61683 ATAAATCAGA
61693 TTTGCATTTT-ATTACACCCT
1 TTTGCATTTTGA-TACACCCT
* *
61713 TTTGTATTTTGATATACCCT
1 TTTGCATTTTGATACACCCT
61733 TTT
1 TTT
61736 TGCGTTCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.56
Consensus pattern (20 bp):
TTTGCATTTTGATACACCCT
Found at i:75863 original size:3 final size:3
Alignment explanation
Indices: 75855--75903 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
75845 GAAGCCCAAC
* * * *
75855 GAT GAT GAT GAT GAA GAT GGT GAG GAT TAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
75903 G
1 G
75904 GGGATTAATA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:96659 original size:67 final size:67
Alignment explanation
Indices: 96543--96679 Score: 220
Period size: 67 Copynumber: 2.0 Consensus size: 67
96533 TAGGTTGGGT
*
96543 CCATCATCAATGTCATAATGCCATATTAATCTATTGGGCTTGCTCATCATCAATGTTTGGGTCGG
1 CCATCATCAATGTCATAATGCCATATTAATCTATTGGGCTTACTCATCATCAATGTTTGGGTCGG
96608 GC
66 GC
* * * * *
96610 CCATTATCAATTTCATAATGCCATATTAATCTATTGGGCTTATTTATCATCAATGTTTGGGTTGG
1 CCATCATCAATGTCATAATGCCATATTAATCTATTGGGCTTACTCATCATCAATGTTTGGGTCGG
96675 GC
66 GC
96677 CCA
1 CCA
96680 AAAATTATTT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (67 bp):
CCATCATCAATGTCATAATGCCATATTAATCTATTGGGCTTACTCATCATCAATGTTTGGGTCGG
GC
Found at i:119131 original size:3 final size:3
Alignment explanation
Indices: 119123--119184 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
119113 TTAGTATAAA
119123 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
119171 ATT ATT ATT ATT AT
1 ATT ATT ATT ATT AT
119185 GTATATAATA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:125810 original size:2 final size:2
Alignment explanation
Indices: 125803--125827 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
125793 CTAGGGATTC
125803 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
125828 AAAAACTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:130205 original size:2 final size:2
Alignment explanation
Indices: 130198--130225 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
130188 GCTTCCAAAA
130198 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
130226 TGGCTTCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:149835 original size:21 final size:21
Alignment explanation
Indices: 149811--149863 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
149801 ACGACAACTC
* *
149811 CAACACCAACACCAGCAACAG
1 CAACAACAACACCAGCAACAA
* * *
149832 CAACAGCAACATCAGTAACAA
1 CAACAACAACACCAGCAACAA
149853 CAACAACAACA
1 CAACAACAACA
149864 ACAACATTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.53, C:0.36, G:0.08, T:0.04
Consensus pattern (21 bp):
CAACAACAACACCAGCAACAA
Found at i:156592 original size:18 final size:17
Alignment explanation
Indices: 156568--156611 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
156558 TTTATATAAT
156568 TTTAAAAAAACTATCCA
1 TTTAAAAAAACTATCCA
*
156585 TTTAAAAAAGCTATCCA
1 TTTAAAAAAACTATCCA
*
156602 ATTAAAAAAA
1 TTTAAAAAAA
156612 ACTGTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (17 bp):
TTTAAAAAAACTATCCA
Found at i:161525 original size:85 final size:81
Alignment explanation
Indices: 161386--161550 Score: 276
Period size: 85 Copynumber: 2.0 Consensus size: 81
161376 AACTTCATGC
161386 ATTAGTCCTAACAAATTGACCCATATAGAACAAATTAAACCAATTGGTTTATTAATATTTTTTCT
1 ATTAGTCCTAACAAATTGACCCATATAGAACAAATTAAACCAATTGGTTTATTAATATTTTTTCT
161451 ATGAACGAAACATACT
66 ATGAACGAAACATACT
*
161467 ATTAGTCCTAACAAATTGACCCATATATATAGAACAAATTAAACCAATTGGTTTATTAATCTTTT
1 ATTAGTCCTAACAAATTGACCC----ATATAGAACAAATTAAACCAATTGGTTTATTAATATTTT
*
161532 TTCTATGAACGGAACATAC
62 TTCTATGAACGAAACATAC
161551 CATCAATGCG
Statistics
Matches: 78, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
81 22 0.28
85 56 0.72
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (81 bp):
ATTAGTCCTAACAAATTGACCCATATAGAACAAATTAAACCAATTGGTTTATTAATATTTTTTCT
ATGAACGAAACATACT
Found at i:166281 original size:33 final size:33
Alignment explanation
Indices: 166235--166298 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
166225 AATTCCGTAA
*
166235 TGATTGTTCTCTTCCTTTCGGGCATGGTAGCTG
1 TGATTATTCTCTTCCTTTCGGGCATGGTAGCTG
* * * *
166268 TGATTATTTTCTTCTTTTCTGGCATGTTAGC
1 TGATTATTCTCTTCCTTTCGGGCATGGTAGC
166299 AGTCATTCTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (33 bp):
TGATTATTCTCTTCCTTTCGGGCATGGTAGCTG
Found at i:168259 original size:14 final size:14
Alignment explanation
Indices: 168240--168269 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
168230 TACCTCTGTC
168240 CTGATCGTCTAAAG
1 CTGATCGTCTAAAG
168254 CTGATCGTCTAAAG
1 CTGATCGTCTAAAG
168268 CT
1 CT
168270 TCCCCAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (14 bp):
CTGATCGTCTAAAG
Found at i:168942 original size:48 final size:48
Alignment explanation
Indices: 168889--170330 Score: 1289
Period size: 48 Copynumber: 30.3 Consensus size: 48
168879 AAATTAGTAA
* * * *
168889 TTAAAAAAATTTAAAAAAGTGACTGATGAGAGTTGTCTCTCCTAACAA
1 TTAAAAAAATTTAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
*** * *
168937 TTAAAATTTTTTTAAAAAGTTACCGATGAGAGCTGTCTCTCCAAACAC
1 TTAAAAAAATTTAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
*** * * *
168985 TTAAAATTTTTTCAAAAAGCGACCGGTGAGAGC--TCTCTCCAAACAC
1 TTAAAAAAATTTAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
* *
169031 -TAAAAAATTTTATTAAAAAGTGACCGATGAGAGTTGTCTCTCCAAACAC
1 TTAAAAAAATTTA--AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
* *
169080 TTAAAAATA-TT--AAAAGTGACCGATGAGAGCTGTCTCTCCAAGCAC
1 TTAAAAAAATTTAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
*
169125 TT---AAAATTTTAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
1 TTAAAAAAATTTAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
* *
169170 TTAAAACTCTCCAAATACTTAAAAAAATTTATAGAAAGTGATCGATGAGAGTTGTCTCTCCAAAC
1 TTAAAA------AAAT--TT------A---A-A-AAAGTGACCGATGAGAGCTGTCTCTCCAAAC
*
169235 AA
47 AC
* * *
169237 TT-AAAAAGTTTATAAAAAGTGACCGATGAGAGCTGTCTCTCCCAACAA
1 TTAAAAAAATTTA-AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
*** * *
169285 TTAAAATTTTTTTAAAAAGTGACCGATGAGAGCTGTCTCTCCAAATAC
1 TTAAAAAAATTTAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
*
169333 TT-AAAAAATTT-AAAAAGTAACCGATGAGAGCTGTCTCTCCAAACA-
1 TTAAAAAAATTTAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
* * *
169378 --AAAAAAACTT-AAAAAGTGACCGATGAAAGCTGTCTCTCCAAACAT
1 TTAAAAAAATTTAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
* * * *
169423 TTAAAAAAGTTACTAATAAAA--G--C--T----GC-CTCTC-CAAACAC-T
1 TTAAAAAAATT--TAA-AAAAGTGACCGATGAGAGCTGTCTCTCCAA-ACAC
* * *
169462 TAAAAAAATTTAT-AAAAAGTGACCGATGAGAGCTGTCTTTCCAAACAC
1 TTAAAAAAATT-TAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
* * *
169510 TTAAAATAAATTTATAAAAAGTGATCGATGAGAGCTGTCTCTCCGAACGC
1 TTAAAA-AAATTTA-AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
*
169560 TTAAAAAAATTTATAAAAAGTGACCGATGAGAGTTGTCTCTCCAAACAC
1 TTAAAAAAATTTA-AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
** ** * *
169609 TT-AAAATTTTTTGAAAAGGGACCGATGAGAGCTGTCTCTCTAAACAC
1 TTAAAAAAATTTAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
* * *
169656 TT--AAAATTTTATTAAAAAGTGACCGATGAGAGCTATCTCTCCAAAGAC
1 TTAAAAAAATTTA--AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
* * *
169704 TT-GACAAATTT-AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAA
1 TTAAAAAAATTTAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
* *
169750 TT-AAAAATTTTAAAAAAGTTACCGATGAGAGCTGTCTCTCCAAACAC
1 TTAAAAAAATTTAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
** * * * * *
169797 TT-AAAATTTTTTAAAAAGCGATCGATGATAGCTGTCTTTCCAAACAC
1 TTAAAAAAATTTAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
* *
169844 -T-AAAAATTTTATTAAAATGTGACCGATGAGAGCTGTCTCTCCAAACAC
1 TTAAAAAAATTTA--AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
* *
169892 TTAAAAATA-TT--AAAAGTGACTGATGAGAGCTG--TCT-CAAACAC
1 TTAAAAAAATTTAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
* * *
169934 TT-AAAAAATTT-AAAAAGTGACCGATGAGAGCTATCTCTCCTAACAA
1 TTAAAAAAATTTAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
** * *
169980 TTAAAAATTTTTTAAAGAGTGACCGATGAGAGC--TCTCTCCAAACAC
1 TTAAAAAAATTTAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
* *
170026 TTAAAAAAATTTATAGAAAGTGACCGATGAGAGCTGTCTCTCTC-AACAA
1 TTAAAAAAATTTA-AAAAAGTGACCGATGAGAGCTGTCTCTC-CAAACAC
*** *
170075 TTAAAATTTTTTTAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
1 TTAAAAAAATTTAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
* * * *
170123 TTAAAAAAAATATATAAAAAGTGACCGATGAGAGCTGTTTCTCCCAACGC
1 TT-AAAAAAATTTA-AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
* *
170173 TTAAAAAAATTTATAAAAAGTGACCGATGAGAGC--TCTCTCCCAACAA
1 TTAAAAAAATTTA-AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
** **
170220 TT-AAAACTTTTTTAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
1 TTAAAAAAATTTAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
170267 TTAAAAAGAATTTATAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
1 TTAAAAA-AATTTA-AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
170317 TTAAAAAGAATTTA
1 TTAAAAA-AATTTA
170331 TAAACTTAAA
Statistics
Matches: 1156, Mismatches: 155, Indels: 164
0.78 0.11 0.11
Matches are distributed among these distances:
36 4 0.00
37 1 0.00
38 2 0.00
39 13 0.01
40 7 0.01
41 7 0.01
42 15 0.01
43 24 0.02
44 40 0.03
45 120 0.10
46 138 0.12
47 193 0.17
48 269 0.23
49 137 0.12
50 133 0.12
51 4 0.00
52 1 0.00
54 4 0.00
56 2 0.00
58 2 0.00
60 3 0.00
65 1 0.00
66 4 0.00
67 32 0.03
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (48 bp):
TTAAAAAAATTTAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAC
Found at i:169040 original size:47 final size:46
Alignment explanation
Indices: 168902--170323 Score: 877
Period size: 47 Copynumber: 29.9 Consensus size: 46
168892 AAAAAATTTA
* * * * *
168902 AAAAAGTGACTGATGAGAGTTGTCTCTCCTAACAATTAAAATTTTTTT
1 AAAAAGTGACCGATGAGAG-CGTCTCTCCAAAC-ACTAAAAATTTTTT
* *
168950 AAAAAGTTACCGATGAGAGCTGTCTCTCCAAACACTTAAAATTTTTT
1 AAAAAGTGACCGATGAGAGC-GTCTCTCCAAACACTAAAAATTTTTT
* *
168997 CAAAAAGCGACCGGTGAGAGC-TCTCTCCAAACACTAAAAAATTTTATT
1 -AAAAAGTGACCGATGAGAGCGTCTCTCCAAACACT-AAAAATTTT-TT
* *
169045 AAAAAGTGACCGATGAGAGTTGTCTCTCCAAACACTTAAAAA--TATT
1 AAAAAGTGACCGATGAGAG-CGTCTCTCCAAACAC-TAAAAATTTTTT
* *
169091 -AAAAGTGACCGATGAGAGCTGTCTCTCCAAGCACTTAAAA--TTTT
1 AAAAAGTGACCGATGAGAGC-GTCTCTCCAAACACTAAAAATTTTTT
* *
169135 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACACTTAAAACTCTCCAAATACTT
1 AAAAAGTGACCGATGAGAGC-GTCTCTCCAAACAC-TAAAAAT-T-----T-TTT
* *** * * ** * * * * *** **
169190 AAAAA--AATTTATAGAAAGTGATCGAT-GAGAGTTGTCTCTCCAAACAATTAA
1 AAAAAGTGACCGAT-GAGAGCG-TCTCTCCA-A----ACACT-AAAAATTTTTT
* * *
169241 AAAGTTTATAAAAAGTGACCGATGAGAGCTGTCTCTCCCAACAATTAAAATTTTTTT
1 AA---------AAAGTGACCGATGAGAGC-GTCTCTCCAAAC-ACTAAAAATTTTTT
* *
169298 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAATACTTAAAAA--ATTT
1 AAAAAGTGACCGATGAGAGC-GTCTCTCCAAACAC-TAAAAATTTTTT
* ***
169344 AAAAAGTAACCGATGAGAGCTGTCTCTCCAAACA--AAAAA-AACTT
1 AAAAAGTGACCGATGAGAGC-GTCTCTCCAAACACTAAAAATTTTTT
* *
169388 AAAAAGTGACCGATGAAAGCTGTCTCTCC-AA-AC-----A--TTTA
1 AAAAAGTGACCGATGAGAGC-GTCTCTCCAAACACTAAAAATTTTTT
* ** * * * * *
169426 AAAAAGTTACTAATAAAAGCTGCCTCTCCAAACACTTAAAAAAATTTAT
1 AAAAAGTGACCGATGAGAGC-GTCTCTCCAAACAC-T-AAAAATTTTTT
* * *
169475 AAAAAGTGACCGATGAGAGCTGTCTTTCCAAACACTTAAAATAAATTTAT
1 AAAAAGTGACCGATGAGAGC-GTCTCTCCAAACAC-T-AAA-AATTTTTT
* * * * *
169525 AAAAAGTGATCGATGAGAGCTGTCTCTCCGAACGCTTAAAAAAATTTAT
1 AAAAAGTGACCGATGAGAGC-GTCTCTCCAAACAC-T-AAAAATTTTTT
* *
169574 AAAAAGTGACCGATGAGAGTTGTCTCTCCAAACACTTAAAATTTTTT
1 AAAAAGTGACCGATGAGAG-CGTCTCTCCAAACACTAAAAATTTTTT
* * * *
169621 GAAAAGGGACCGATGAGAGCTGTCTCTCTAAACACTTAAAATTTTATT
1 AAAAAGTGACCGATGAGAGC-GTCTCTCCAAACACTAAAAATTTT-TT
* * *
169669 AAAAAGTGACCGATGAGAGCTATCTCTCCAAAGACTTGACAAA---TTT
1 AAAAAGTGACCGATGAGAGC-GTCTCTCCAAACAC-T-AAAAATTTTTT
* *
169715 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAATTAAAAA-TTTTA
1 AAAAAGTGACCGATGAGAGC-GTCTCTCCAAAC-ACTAAAAATTTTTT
* *
169762 AAAAAGTTACCGATGAGAGCTGTCTCTCCAAACACTTAAAATTTTTT
1 AAAAAGTGACCGATGAGAGC-GTCTCTCCAAACACTAAAAATTTTTT
* * * *
169809 AAAAAGCGATCGATGATAGCTGTCTTTCCAAACACTAAAAATTTTATT
1 AAAAAGTGACCGATGAGAGC-GTCTCTCCAAACACTAAAAATTTT-TT
* *
169857 AAAATGTGACCGATGAGAGCTGTCTCTCCAAACACTTAAAAA--TATT
1 AAAAAGTGACCGATGAGAGC-GTCTCTCCAAACAC-TAAAAATTTTTT
* * *
169903 -AAAAGTGACTGATGAGAGC-TGTCT-CAAACACTTAAAAA--ATTT
1 AAAAAGTGACCGATGAGAGCGTCTCTCCAAACAC-TAAAAATTTTTT
* * *
169945 AAAAAGTGACCGATGAGAGCTATCTCTCCTAACAATTAAAAATTTTTT
1 AAAAAGTGACCGATGAGAGC-GTCTCTCCAAAC-ACTAAAAATTTTTT
* * *
169993 AAAGAGTGACCGATGAGAGC-TCTCTCCAAACACTTAAAAAAATTTAT
1 AAAAAGTGACCGATGAGAGCGTCTCTCCAAACAC-T-AAAAATTTTTT
* * *
170040 AGAAAGTGACCGATGAGAGCTGTCTCTCTC-AACAATTAAAATTTTTTT
1 AAAAAGTGACCGATGAGAGC-GTCTCTC-CAAAC-ACTAAAAATTTTTT
* * *
170088 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACACTTAAAAAAAATATAT
1 AAAAAGTGACCGATGAGAGC-GTCTCTCCAAACAC-T--AAAAATTTTTT
* * * * *
170138 AAAAAGTGACCGATGAGAGCTGTTTCTCCCAACGCTTAAAAAAATTTAT
1 AAAAAGTGACCGATGAGAGC-GTCTCTCCAAACAC-T-AAAAATTTTTT
* * *
170187 AAAAAGTGACCGATGAGAGC-TCTCTCCCAACAATTAAAACTTTTTT
1 AAAAAGTGACCGATGAGAGCGTCTCTCCAAAC-ACTAAAAATTTTTT
* *
170233 -AAAAGTGACCGATGAGAGCTGTCTCTCCAAACACTTAAAAAGAATTTAT
1 AAAAAGTGACCGATGAGAGC-GTCTCTCCAAACAC-T-AAAA-ATTTTTT
170282 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACACTTAAAAA
1 AAAAAGTGACCGATGAGAGC-GTCTCTCCAAACAC-TAAAAA
170324 GAATTTATAA
Statistics
Matches: 1112, Mismatches: 171, Indels: 182
0.76 0.12 0.12
Matches are distributed among these distances:
38 25 0.02
39 3 0.00
40 2 0.00
42 17 0.02
43 29 0.03
44 38 0.03
45 109 0.10
46 127 0.11
47 219 0.20
48 212 0.19
49 148 0.13
50 128 0.12
51 2 0.00
52 1 0.00
53 5 0.00
54 9 0.01
55 7 0.01
57 9 0.01
58 7 0.01
60 3 0.00
61 8 0.01
62 4 0.00
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (46 bp):
AAAAAGTGACCGATGAGAGCGTCTCTCCAAACACTAAAAATTTTTT
Found at i:169057 original size:95 final size:93
Alignment explanation
Indices: 168902--170322 Score: 1029
Period size: 95 Copynumber: 14.9 Consensus size: 93
168892 AAAAAATTTA
* * * * * * *
168902 AAAAAGTGACTGATGAGAGTTGTCTCTCCTAACAATTAAAATTTTTTTAAAAAGTTACCGATGAG
1 AAAAAGTGACCGATGAGAGCT-TCTCTCCAAAC-ACTAAAAATTTATTAAAAAGTGACCGATGAG
168967 AGCTGTCTCTCCAAACACTTAAAATTTTTT
64 AGCTGTCTCTCCAAACACTTAAAATTTTTT
* *
168997 CAAAAAGCGACCGGTGAGAGC-TCTCTCCAAACACTAAAAAATTTTATTAAAAAGTGACCGATGA
1 -AAAAAGTGACCGATGAGAGCTTCTCTCCAAACACT-AAAAA-TTTATTAAAAAGTGACCGATGA
* * *
169061 GAGTTGTCTCTCCAAACACTTAAAA-ATATT
63 GAGCTGTCTCTCCAAACACTTAAAATTTTTT
* *
169091 -AAAAGTGACCGATGAGAGCTGTCTCTCCAAGCACTTAAAA-TT-TTAAAAAGTGACCGATGAGA
1 AAAAAGTGACCGATGAGAGCT-TCTCTCCAAACACTAAAAATTTATTAAAAAGTGACCGATGAGA
*
169153 GCTGTCTCTCCAAACACTTAAAACTCTCCAAATACTT
65 GCTGTCTCTCCAAACACTTAAAA-T-T-----T-TTT
* *** * ** * * * * * *
169190 AAAAA--AATTTATAGAAAG-TGATCGAT-GAGAGTTGTCTCTCCAAACAATTA-AAAAGTTTAT
1 AAAAAGTGACCGAT-GAGAGCT--TCTCTCCA-A----ACACT--AAAAATTTATTAAA------
* *
169250 AAAAAGTGACCGATGAGAGCTGTCTCTCCCAACAATTAAAATTTTTTT
50 ---AAGTGACCGATGAGAGCTGTCTCTCCAAACACTTAAAA-TTTTTT
* * *
169298 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAATACTTAAAAA-AT-TTAAAAAGTAACCGATGAG
1 AAAAAGTGACCGATGAGAGCT-TCTCTCCAAACAC-TAAAAATTTATTAAAAAGTGACCGATGAG
****
169361 AGCTGTCTCTCCAAACA---AAAAAAACTT
64 AGCTGTCTCTCCAAACACTTAAAATTTTTT
* * ** * *
169388 AAAAAGTGACCGATGAAAGCTGTCTCTCC-AA-AC-----ATTTA--AAAAAGTTACTAATAAAA
1 AAAAAGTGACCGATGAGAGCT-TCTCTCCAAACACTAAAAATTTATTAAAAAGTGACCGATGAGA
* * *
169444 GCTGCCTCTCCAAACACTTAAAAAAATTTAT
65 GCTGTCTCTCCAAACACTT--AAAATTTTTT
* *
169475 AAAAAGTGACCGATGAGAGCTGTCTTTCCAAACACTTAAAATAAATTTA-TAAAAAGTGATCGAT
1 AAAAAGTGACCGATGAGAGCT-TCTCTCCAAACAC-T--AA-AAATTTATTAAAAAGTGACCGAT
* * * *
169539 GAGAGCTGTCTCTCCGAACGCTTAAAAAAATTTAT
61 GAGAGCTGTCTCTCCAAACACTT--AAAATTTTTT
* * * * *
169574 AAAAAGTGACCGATGAGAGTTGTCTCTCCAAACACTTAAAATTTTTTGAAAAGGGACCGATGAGA
1 AAAAAGTGACCGATGAGAGCT-TCTCTCCAAACACTAAAAATTTATTAAAAAGTGACCGATGAGA
*
169639 GCTGTCTCTCTAAACACTTAAAATTTTATT
65 GCTGTCTCTCCAAACACTTAAAATTTT-TT
* *
169669 AAAAAGTGACCGATGAGAGCTATCTCTCCAAAGACTTGACAAA--T-TTAAAAAGTGACCGATGA
1 AAAAAGTGACCGATGAGAGCT-TCTCTCCAAACAC-T-AAAAATTTATTAAAAAGTGACCGATGA
* * *
169731 GAGCTGTCTCTCCAAACAATTAAAAATTTTA
63 GAGCTGTCTCTCCAAACACTTAAAATTTTTT
* * * * * *
169762 AAAAAGTTACCGATGAGAGCTGTCTCTCCAAACACTTAAAATTTTTTAAAAAGCGATCGATGATA
1 AAAAAGTGACCGATGAGAGCT-TCTCTCCAAACACTAAAAATTTATTAAAAAGTGACCGATGAGA
* *
169827 GCTGTCTTTCCAAACACTAAAAATTTTATT
65 GCTGTCTCTCCAAACACTTAAAATTTT-TT
* *
169857 AAAATGTGACCGATGAGAGCTGTCTCTCCAAACACTTAAAAA--TATT-AAAAGTGACTGATGAG
1 AAAAAGTGACCGATGAGAGCT-TCTCTCCAAACAC-TAAAAATTTATTAAAAAGTGACCGATGAG
**
169919 AGCTG--TCT-CAAACACTTAAAA-AATTT
64 AGCTGTCTCTCCAAACACTTAAAATTTTTT
* * * *
169945 AAAAAGTGACCGATGAGAGCTATCTCTCCTAACAATTAAAAATTTTTTAAAGAGTGACCGATGAG
1 AAAAAGTGACCGATGAGAGCT-TCTCTCCAAAC-ACTAAAAATTTATTAAAAAGTGACCGATGAG
* *
170010 AGC--TCTCTCCAAACACTTAAAAAAATTTAT
64 AGCTGTCTCTCCAAACACTT--AAAATTTTTT
* * * *
170040 AGAAAGTGACCGATGAGAGCTGTCTCTCTC-AACAATTAAAATTTTTTTAAAAAGTGACCGATGA
1 AAAAAGTGACCGATGAGAGCT-TCTCTC-CAAAC-ACTAAAAATTTATTAAAAAGTGACCGATGA
* * *
170104 GAGCTGTCTCTCCAAACACTTAAAAAAAATATAT
63 GAGCTGTCTCTCCAAACACTT---AAAATTTTTT
* * *
170138 AAAAAGTGACCGATGAGAGCTGTTTCTCCCAACGCTTAAAAAAATTTA-TAAAAAGTGACCGATG
1 AAAAAGTGACCGATGAGAGCT-TCTCTCCAAACAC-T--AAAAATTTATTAAAAAGTGACCGATG
* *
170202 AGAGC--TCTCTCCCAACAATTAAAACTTTTTT
62 AGAGCTGTCTCTCCAAACACTTAAAA-TTTTTT
170233 -AAAAGTGACCGATGAGAGCTGTCTCTCCAAACACTTAAAAAGAATTTA-TAAAAAGTGACCGAT
1 AAAAAGTGACCGATGAGAGCT-TCTCTCCAAACAC-T--AAA-AATTTATTAAAAAGTGACCGAT
170296 GAGAGCTGTCTCTCCAAACACTTAAAA
61 GAGAGCTGTCTCTCCAAACACTTAAAA
170323 AGAATTTATA
Statistics
Matches: 1075, Mismatches: 160, Indels: 179
0.76 0.11 0.13
Matches are distributed among these distances:
82 29 0.03
83 1 0.00
87 33 0.03
88 42 0.04
89 6 0.01
90 87 0.08
91 31 0.03
92 27 0.03
93 57 0.05
94 197 0.18
95 212 0.20
96 56 0.05
97 49 0.05
98 53 0.05
99 104 0.10
100 11 0.01
103 7 0.01
104 4 0.00
105 4 0.00
106 6 0.01
108 7 0.01
109 9 0.01
110 5 0.00
114 1 0.00
115 37 0.03
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (93 bp):
AAAAAGTGACCGATGAGAGCTTCTCTCCAAACACTAAAAATTTATTAAAAAGTGACCGATGAGAG
CTGTCTCTCCAAACACTTAAAATTTTTT
Found at i:169181 original size:18 final size:18
Alignment explanation
Indices: 169158--169193 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
169148 TGAGAGCTGT
169158 CTCTCCAAACACTTAAAA
1 CTCTCCAAACACTTAAAA
*
169176 CTCTCCAAATACTTAAAA
1 CTCTCCAAACACTTAAAA
169194 AAATTTATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (18 bp):
CTCTCCAAACACTTAAAA
Found at i:169184 original size:157 final size:159
Alignment explanation
Indices: 169019--169338 Score: 486
Period size: 157 Copynumber: 2.0 Consensus size: 159
169009 GGTGAGAGCT
* *
169019 CTCTCCAAACAC-TAAAAAATTTTATTAAAAAGTGACCGATGAGAGTTGTCTCTCCAAACACTTA
1 CTCTCCAAACACTTAAAAAAATTTA-TAAAAAGTGACCGATGAGAGTTGTCTCTCCAAACAATTA
* *
169083 AAAA-TATTAAAAGTGACCGATGAGAGCTGTCTCT-CCAAGCACTTAAAA-TTTTAAAAAGTGAC
65 AAAATTATAAAAAGTGACCGATGAGAGCTGTCTCTCCCAA-CAATTAAAATTTTTAAAAAGTGAC
169145 CGATGAGAGCTGTCTCTCCAAACACTTAAAA
129 CGATGAGAGCTGTCTCTCCAAACACTTAAAA
* * *
169176 CTCTCCAAATACTTAAAAAAATTTATAGAAAGTGATCGATGAGAGTTGTCTCTCCAAACAATTAA
1 CTCTCCAAACACTTAAAAAAATTTATAAAAAGTGACCGATGAGAGTTGTCTCTCCAAACAATTAA
169241 AAAGTTTATAAAAAGTGACCGATGAGAGCTGTCTCTCCCAACAATTAAAATTTTTTTAAAAAGTG
66 AAA--TTATAAAAAGTGACCGATGAGAGCTGTCTCTCCCAACAATTAAAA--TTTTTAAAAAGTG
*
169306 ACCGATGAGAGCTGTCTCTCCAAATACTTAAAA
127 ACCGATGAGAGCTGTCTCTCCAAACACTTAAAA
169339 AATTTAAAAA
Statistics
Matches: 147, Mismatches: 8, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
157 51 0.35
158 11 0.07
160 37 0.25
161 4 0.03
163 44 0.30
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.28
Consensus pattern (159 bp):
CTCTCCAAACACTTAAAAAAATTTATAAAAAGTGACCGATGAGAGTTGTCTCTCCAAACAATTAA
AAATTATAAAAAGTGACCGATGAGAGCTGTCTCTCCCAACAATTAAAATTTTTAAAAAGTGACCG
ATGAGAGCTGTCTCTCCAAACACTTAAAA
Found at i:169289 original size:115 final size:108
Alignment explanation
Indices: 169068--169290 Score: 311
Period size: 115 Copynumber: 2.0 Consensus size: 108
169058 TGAGAGTTGT
* *
169068 CTCTCCAAACACTTAAAAATATTAAAAGTGACCGATGAGAGCTGTCTCTCCAAGCACTTAAAATT
1 CTCTCCAAACACTTAAAAATATTAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAATTAAAATT
*
169133 TTAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACACTTAAAA
66 TTAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAATTAAAA
* * * *
169176 CTCTCCAAATACTTAAAAAAATTTATAGAAAGTGATCGATGAGAGTTGTCTCTCCAAACAATTAA
1 CTCTCCAAACACTT--AAAAATAT-TA-AAAGTGACCGATGAGAGCTGTCTCTCCAAACAATT-A
*
169241 AAAGTTTATAAAAAGTGACCGATGAGAGCTGTCTCTCCCAACAATTAAAA
61 AAA-TTT-TAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAATTAAAA
169291 TTTTTTTAAA
Statistics
Matches: 100, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
108 13 0.13
110 7 0.07
111 2 0.02
112 31 0.31
113 4 0.04
114 3 0.03
115 40 0.40
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (108 bp):
CTCTCCAAACACTTAAAAATATTAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAATTAAAATT
TTAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACAATTAAAA
Found at i:169478 original size:50 final size:49
Alignment explanation
Indices: 169443--170334 Score: 1056
Period size: 47 Copynumber: 18.7 Consensus size: 49
169433 TACTAATAAA
*
169443 AGCTGCCTCTCCAAACACTTAAAAAAATTTATAAAAAGTGACCGATGAG
1 AGCTGTCTCTCCAAACACTTAAAAAAATTTATAAAAAGTGACCGATGAG
* *
169492 AGCTGTCTTTCCAAACACTTAAAATAAATTTATAAAAAGTGATCGATGAG
1 AGCTGTCTCTCCAAACACTTAAAA-AAATTTATAAAAAGTGACCGATGAG
* *
169542 AGCTGTCTCTCCGAACGCTTAAAAAAATTTATAAAAAGTGACCGATGAG
1 AGCTGTCTCTCCAAACACTTAAAAAAATTTATAAAAAGTGACCGATGAG
* * * * *
169591 AGTTGTCTCTCCAAACACTT--AAAATTTTTTGAAAAGGGACCGATGAG
1 AGCTGTCTCTCCAAACACTTAAAAAAATTTATAAAAAGTGACCGATGAG
* *
169638 AGCTGTCTCTCTAAACACTT--AAAATTTTATTAAAAAGTGACCGATGAG
1 AGCTGTCTCTCCAAACACTTAAAAAAATTTA-TAAAAAGTGACCGATGAG
* * * *
169686 AGCTATCTCTCCAAAGACTT-GACAAA-TT-TAAAAAGTGACCGATGAG
1 AGCTGTCTCTCCAAACACTTAAAAAAATTTATAAAAAGTGACCGATGAG
* * *
169732 AGCTGTCTCTCCAAACAATT-AAAAATTTTA-AAAAAGTTACCGATGAG
1 AGCTGTCTCTCCAAACACTTAAAAAAATTTATAAAAAGTGACCGATGAG
* * * * *
169779 AGCTGTCTCTCCAAACACTT--AAAATTTTTTAAAAAGCGATCGATGAT
1 AGCTGTCTCTCCAAACACTTAAAAAAATTTATAAAAAGTGACCGATGAG
* * *
169826 AGCTGTCTTTCCAAACAC-T-AAAAATTTTATTAAAATGTGACCGATGAG
1 AGCTGTCTCTCCAAACACTTAAAAAAATTTA-TAAAAAGTGACCGATGAG
* *
169874 AGCTGTCTCTCCAAACACTT--AAAAA--TATTAAAAGTGACTGATGAG
1 AGCTGTCTCTCCAAACACTTAAAAAAATTTATAAAAAGTGACCGATGAG
169919 AGCTG--TCT-CAAACACTT-AAAAAA-TT-TAAAAAGTGACCGATGAG
1 AGCTGTCTCTCCAAACACTTAAAAAAATTTATAAAAAGTGACCGATGAG
* * * * * *
169962 AGCTATCTCTCCTAACAATT-AAAAATTTTTTAAAGAGTGACCGATGAG
1 AGCTGTCTCTCCAAACACTTAAAAAAATTTATAAAAAGTGACCGATGAG
*
170010 AGC--TCTCTCCAAACACTTAAAAAAATTTATAGAAAGTGACCGATGAG
1 AGCTGTCTCTCCAAACACTTAAAAAAATTTATAAAAAGTGACCGATGAG
* ** *
170057 AGCTGTCTCTCTC-AACAATT-AAAATTTTTTTAAAAAGTGACCGATGAG
1 AGCTGTCTCTC-CAAACACTTAAAAAAATTTATAAAAAGTGACCGATGAG
*
170105 AGCTGTCTCTCCAAACACTTAAAAAAAATATATAAAAAGTGACCGATGAG
1 AGCTGTCTCTCCAAACACTT-AAAAAAATTTATAAAAAGTGACCGATGAG
* * *
170155 AGCTGTTTCTCCCAACGCTTAAAAAAATTTATAAAAAGTGACCGATGAG
1 AGCTGTCTCTCCAAACACTTAAAAAAATTTATAAAAAGTGACCGATGAG
* * * * *
170204 AGC--TCTCTCCCAACAATT--AAAACTTTTTTAAAAGTGACCGATGAG
1 AGCTGTCTCTCCAAACACTTAAAAAAATTTATAAAAAGTGACCGATGAG
170249 AGCTGTCTCTCCAAACACTTAAAAAGAATTTATAAAAAGTGACCGATGAG
1 AGCTGTCTCTCCAAACACTTAAAAA-AATTTATAAAAAGTGACCGATGAG
170299 AGCTGTCTCTCCAAACACTTAAAAAGAATTTATAAA
1 AGCTGTCTCTCCAAACACTTAAAAA-AATTTATAAA
170335 CTTAAAAAAT
Statistics
Matches: 729, Mismatches: 86, Indels: 55
0.84 0.10 0.06
Matches are distributed among these distances:
42 9 0.01
43 28 0.04
44 1 0.00
45 50 0.07
46 74 0.10
47 179 0.25
48 131 0.18
49 113 0.16
50 144 0.20
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (49 bp):
AGCTGTCTCTCCAAACACTTAAAAAAATTTATAAAAAGTGACCGATGAG
Found at i:170347 original size:17 final size:19
Alignment explanation
Indices: 170315--170350 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
170305 CTCTCCAAAC
170315 ACTTAAAAAGAATTTATAA
1 ACTTAAAAAGAATTTATAA
170334 ACTT-AAAA-AATTTATAA
1 ACTTAAAAAGAATTTATAA
170351 CAGTGACCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (19 bp):
ACTTAAAAAGAATTTATAA
Found at i:170374 original size:66 final size:67
Alignment explanation
Indices: 170265--170398 Score: 193
Period size: 66 Copynumber: 2.0 Consensus size: 67
170255 CTCTCCAAAC
170265 ACTTAAAAAGAATTTATAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACACTTAAAAAGAATTT
1 ACTTAAAAAGAATTTATAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACACTTAAAAA-AATTT
170330 ATAA
65 -TAA
* * * *
170334 ACTT-AAAA-AATTTAT-AACAGTGACCGATGAGATCTGTCTCTCGAAACACTTTAAAAAATTTT
1 ACTTAAAAAGAATTTATAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACACTTAAAAAAATTTT
170396 AA
66 AA
170398 A
1 A
170399 AAATTGACGC
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
64 4 0.07
65 5 0.08
66 37 0.61
67 7 0.11
68 4 0.07
69 4 0.07
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (67 bp):
ACTTAAAAAGAATTTATAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACACTTAAAAAAATTTT
AA
Found at i:171213 original size:293 final size:295
Alignment explanation
Indices: 170682--171249 Score: 809
Period size: 293 Copynumber: 1.9 Consensus size: 295
170672 TTTAACCATC
* *** * *
170682 ACGGTTTCTAGCTGAAAATGTGTTCCGGGCCCCGACTCAATTTTGCATGATTTTTGGCACCGAGA
1 ACGGTTTCTAGCTGAAAACGCACTCCGGGCCCCGACTCAATTTTACAAGATTTTTGGCACCGAGA
* * * * *
170747 CTCCTTGTAATATCTATATTCATCAAATCATGTCTCATCCACATTGGATTTAAGGATATGTTTTT
66 CTCCTTGAAATATCTATAATCATCAAATCAAGTCTCAGCCACATTGGATTTAAGGATATGGTTTT
** * *
170812 ACGAGCTTTTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATATCAAAAACCAT
131 ACGAGCTTCAGAATCTTGTTTCGATTTAATCAGAAATTAATTGGGAAAAAAATAGCAAAAACCAT
* * *
170877 AAGTGAAGCATAAAAAGCCGTTAAACCTTTTTTGTGGTGAATTATAAATTTTT-ATGAGTACTAT
196 AAGTGAAGCATAAAAAGCCCTTAAACCTTTTTGGCGGTGAATTATAAATTTTTCATGAGTACTAT
**
170941 GGTGAAAAATTGAGTAATTTAGCCGAAATCGTGTG
261 GGCCAAAAATTGAGTAATTTAGCCGAAATCGTGTG
* * * * *
170976 ACGGTTTCTGGCTGAAAACGCACTCCGGGCCCCGGCTCAGTTTTACAAGATTTTTGGCGCGGAGA
1 ACGGTTTCTAGCTGAAAACGCACTCCGGGCCCCGACTCAATTTTACAAGATTTTTGGCACCGAGA
*
171041 CTCCTTGAAATATCTATAATCATCTAATCAAGTCTCAGCCACA-TGGATTTAAGGATATGGTTTT
66 CTCCTTGAAATATCTATAATCATCAAATCAAGTCTCAGCCACATTGGATTTAAGGATATGGTTTT
*
171105 ACGAGCTTCAGAATCTTGTTTCGATTTAATCAGAAATTAATTGGGAAAAAAATAGGAAAAACCA-
131 ACGAGCTTCAGAATCTTGTTTCGATTTAATCAGAAATTAATTGGGAAAAAAATAGCAAAAACCAT
** * * * *
171169 AATGTGAAGCATGTAAAGCCCTTAAATCTTTTTGGCGTTGAATTATATATTTTTCATGAGTACTT
196 AA-GTGAAGCATAAAAAGCCCTTAAACCTTTTTGGCGGTGAATTATAAATTTTTCATGAGTACTA
171234 TGGCCAAAAATTGAGT
260 TGGCCAAAAATTGAGT
171250 GAAAATTTTT
Statistics
Matches: 239, Mismatches: 33, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
292 2 0.01
293 122 0.51
294 115 0.48
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Consensus pattern (295 bp):
ACGGTTTCTAGCTGAAAACGCACTCCGGGCCCCGACTCAATTTTACAAGATTTTTGGCACCGAGA
CTCCTTGAAATATCTATAATCATCAAATCAAGTCTCAGCCACATTGGATTTAAGGATATGGTTTT
ACGAGCTTCAGAATCTTGTTTCGATTTAATCAGAAATTAATTGGGAAAAAAATAGCAAAAACCAT
AAGTGAAGCATAAAAAGCCCTTAAACCTTTTTGGCGGTGAATTATAAATTTTTCATGAGTACTAT
GGCCAAAAATTGAGTAATTTAGCCGAAATCGTGTG
Found at i:172307 original size:332 final size:332
Alignment explanation
Indices: 170976--172633 Score: 2392
Period size: 334 Copynumber: 5.0 Consensus size: 332
170966 AAATCGTGTG
** *
170976 ACGGTTTCTGGCTGAAAACGCACTCCGG-GCCCCGGCTCAGTTTTACAAGATTTTTGGCGCGGAG
1 ACGGTTTCTGGCTGAAAACGCGTTCCGGCGCCCCGGCTCAGTTTTGCAAGATTTTTGGCGCGGAG
* *
171040 ACTCCTTGAAATATCTATAATCATCTAATCAAGTCTCAGCCACA-TGGATTTAAGGATATGGTTT
66 ACTCCTTGAAGTATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGGTTT
* * *
171104 TACGAGCTTCAGAATCTTGTTTCGATTTAATCAGAAATTAATTGGGAAAAAAATAGGAAAAACCA
131 TACGAGATTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAAACCA
* *
171169 AATGTGAAGCATGTAAAGCCCTTAAATCTTTTTGGCGTTGAATTATATATTTTTCATGAGTACTT
196 AATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGCGTTGAATTATATATTTTTCATGAGTACTA
*
171234 TGGCCAAAAATTGAGTGAAAATTTTTCGATTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC
261 TGGCCAAAAATTGAG-GAAAATTTTTCGATTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTA-
171299 GTTAACCATC
324 -TTAACCATC
* * *
171309 ACGGTTTCTGGCTGAAAACGCGTTCCAGCGCCCCGGCTCAGTTTTGCAAGATTTTTGGCGCGAAA
1 ACGGTTTCTGGCTGAAAACGCGTTCCGGCGCCCCGGCTCAGTTTTGCAAGATTTTTGGCGCGGAG
* *
171374 ACTCCTTGAAGTATCTATATTCATC-AGATCAAGTCTCAGCCACATTGGATTTAAGGATAAGTTT
66 ACTCCTTGAAGTATCTATATTCATCTA-ATCAAGTCTCAGCCACATTGGATTTAAGGATATGGTT
* * *
171438 TTATGAGATTCTGAATCTTCTTTCGATTTAATCA-AATTTAATTTGGAAAAAAATAGGAAAAACC
130 TTACGAGATTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAAACC
* * * * *
171502 ATATGCGAATCATGAAAAGCCCTTAAATCATTTTTGGCGTTGAATTATATATTTTTTTATAATGT
195 AAATGTGAAGCATGAAAAGCCCTTAAATC-TTTTTGGCGTTGAATTATATA-TTTTTCATGA-GT
* * *
171567 ACTATGGCCAACAATTGAGGAAAATTTTTCGTTTCAGTTTTTACAAAATTTTAGCCGAAATCGTG
257 ACTATGGCCAAAAATTGAGGAAAATTTTTCGATTCAGTTTTTGCAAAATTTTAGCCGAAATCGTG
171632 TATTAACCATC
322 TATTAACCATC
* * *
171643 ACGGTTTCTGGCTGAAAACACGTTCCGGGGCACCC-GCTCAGTTTTGCATGATTTTTGGCGTCGG
1 ACGGTTTCTGGCTGAAAACGCGTTCCGGCGC-CCCGGCTCAGTTTTGCAAGATTTTTGGCG-CGG
* *
171707 -GAC-CCTTAGTAA-TATCTATATTTATCTAATCAAGTCTCAGCCACATTGGATTTACGGATATG
64 AGACTCCTT-G-AAGTATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATG
* * * *
171769 TTTTTACGAGTTTCTAAATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAAATAGGAAA
127 GTTTTACGAGATTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGG-AAAAAAATAGGAAA
* * * * * *
171834 AACCATAA-GTGAAGCATAAAAAGCCCTTAAACCTTTTTTGTGTTGAATTATA-AATTTTAATGA
191 AACCA-AATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGCGTTGAATTATATATTTTTCATGA
* * **
171897 GTACTATGGCGAAAAATTGAGGAAAAATTTGTCCCTTCTAGTTTTTGCAAAATTTTAGCCGAAAT
255 GTACTATGGCCAAAAATTGAGG-AAAATTTTTCGATTC-AGTTTTTGCAAAATTTTAGCCGAAAT
*
171962 CGTGTACTAACCATC
318 CGTGTATTAACCATC
* * * * *
171977 ACGGTTTCTGGCTGAAAACACTTTCCGGCGCCCCGACTCAGTTTTGTAAGATTTTTGGCGTGGAG
1 ACGGTTTCTGGCTGAAAACGCGTTCCGGCGCCCCGGCTCAGTTTTGCAAGATTTTTGGCGCGGAG
*
172042 ACTCCTTGAAGTATCTATAATCATCTAATCAAGTCTCAGCCACA-TGGATTTAAGGATATGGTTT
66 ACTCCTTGAAGTATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGGTTT
*
172106 TACGAGATTCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATAGGAAAAACCA
131 TACGAGATTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAAACCA
* *
172171 AATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATATATTTTTCATGAGTACTG
196 AATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGCGTTGAATTATATATTTTTCATGAGTACTA
*
172236 TGGCCAAAAATTAAGGAAAAATTTTTCGATTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTAT
261 TGGCCAAAAATTGAGG-AAAATTTTTCGATTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTAT
172301 TAACCATC
325 TAACCATC
* *
172309 ACGGTTTCTGGCTGAAAACGCGTTCCGGCGCCCCGGCTCAGTTTAGCAAGATTTTTGGCGCGGTG
1 ACGGTTTCTGGCTGAAAACGCGTTCCGGCGCCCCGGCTCAGTTTTGCAAGATTTTTGGCGCGGAG
* *
172374 ACTCCTTGAAGTATCTATATTCATCAAATCAAGTCTCAGCCACATTGGATTTAAGGATA-AGTTT
66 ACTCCTTGAAGTATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGGTTT
* * * *
172438 TTCGAGCTTCAGAATCTTCTTTCGATTTAATCA-AAATTAATTTGG-AAAAAATA-GAAAAACCA
131 TACGAGATTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAAACCA
* * * *
172500 TATGTGAATCATGAAAAGCCCTTAAATCTTTTTGGCGTTGAATTATATATTTTTTTATAATGTAC
196 AATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGCGTTGAATTATATA-TTTTTCATGA-GTAC
* * * *
172565 TATGGCCAACAATTGAGGAAAATTTTTCGTTTCAGTTTTTACAAAATTTTAGCTGAAATCGTGTA
259 TATGGCCAAAAATTGAGGAAAATTTTTCGATTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTA
172630 TTAA
324 TTAA
172634 TCGTGCATGA
Statistics
Matches: 1191, Mismatches: 109, Indels: 53
0.88 0.08 0.04
Matches are distributed among these distances:
329 55 0.05
330 64 0.05
331 33 0.03
332 252 0.21
333 173 0.15
334 393 0.33
335 108 0.09
336 93 0.08
337 20 0.02
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Consensus pattern (332 bp):
ACGGTTTCTGGCTGAAAACGCGTTCCGGCGCCCCGGCTCAGTTTTGCAAGATTTTTGGCGCGGAG
ACTCCTTGAAGTATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGGTTT
TACGAGATTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAAACCA
AATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGCGTTGAATTATATATTTTTCATGAGTACTA
TGGCCAAAAATTGAGGAAAATTTTTCGATTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTATT
AACCATC
Found at i:173731 original size:332 final size:333
Alignment explanation
Indices: 172855--177579 Score: 6061
Period size: 334 Copynumber: 14.3 Consensus size: 333
172845 AATGAGTACT
172855 AAAAATTTTTCGCCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTT
1 AAAAATTTTTCG-CTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTT
* * *
172920 ATGGCTGAAAACGCGTTCC-GGGCCCCCGGCTCAGTTTTGCAAGATTTTTGGCGT-GGAGATTCC
65 CTGGCTGAAAACGCGTTCCGGGGCACCC-GCTCAGTTTTGCAAGATTTTTGGCGTCGGAGACTCC
*
172983 TTGAAGTATCTATAATCATCTAATCAAGTCTCAGCCACA-TGGATTTAAGGATATAG-TTTTACG
129 TTGAAGTATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATAT-GTTTTTACG
* * *
173046 AGCTTCTGAATCTTGTTTCGATTTAATTAGAAATTAATTGGGAAAAAAATAGGAAAAACCAAATG
193 AGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAAACCATATG
* * *
173111 TGAAGCATGAAAAGCCCTTAAATCTTTTTGGCGTTGAATTATATATTTTTCATGAGTACTTTGGC
258 TGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATA-ATTTTTTATGAGTACTATGGC
*
173176 CAAAAATTGAGT
322 CAAAAATTGAGG
*
173188 AAAAATTTTTCGATTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACGT---CATCACGGTTT
1 AAAAATTTTTCGCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTAC-TAACCATCACGGTTT
*
173250 CTGGCTGAAAACGCGTTCCGGCGC-CCCGGCTCAGTTTTGCAAGATTTTTGGCG-CGGAGACTCC
65 CTGGCTGAAAACGCGTTCCGGGGCACCC-GCTCAGTTTTGCAAGATTTTTGGCGTCGGAGACTCC
* *
173313 TTGAAGTATCTATATTCATC-AGATCAAGTCTCAGCCACATTGGATTTAAGGATAAGTTTTTATG
129 TTGAAGTATCTATATTCATCTA-ATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTACG
* *
173377 AGCTTCTGAATCTTCTTTCGATTTAATCA-AATTTAATTTGGAAAAAAATAGGAAAAACCATATG
193 AGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAAACCATATG
* * * *
173441 TGAATCATGAAAAGCCCTTAAATCATTTTGGCGTTGAATTATATATTTTTTTATAATGTACTATG
258 TGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATA-A-TTTTTTATGA-GTACTATG
*
173506 GCCAACAATTGAGG
320 GCCAAAAATTGAGG
* * * * *
173520 -AAAATTTTTCGTTTCAGTTTTTACAAAATTTTAGTCGAAATCGTGTATTAACCAGCACGGTTTC
1 AAAAATTTTTCGCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTC
*
173584 TGGCTGAAAACACGTTCCGGGGCACCCGCTCAGTTTTGCATA-ATTTTTGGCGTC-G-GAC-CCT
66 TGGCTGAAAACGCGTTCCGGGGCACCCGCTCAGTTTTGCA-AGATTTTTGGCGTCGGAGACTCCT
* * *
173645 TAGTAA-TATATATATTCATCTAATCAAGTCTCAGCCACATCGGATTTACGGATATGTTTTTACG
130 T-G-AAGTATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTACG
* ** *
173709 AGCTTCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGCTAAACCATAAG
193 AGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAAACCATATG
* * * * *
173774 TGAAGCATAAAAAGCCCTTAAACCTTTTTTGTGTTGAATTATAAATTTTTATGAGTACTATGGCG
258 TGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATAATTTTTTATGAGTACTATGGCC
173839 AAAAATTGAGG
323 AAAAATTGAGG
173850 AAAAATTTTTCGCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTC
1 AAAAATTTTTCGCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTC
*
173915 TGGCTGAAAACGCGTTCC-GGGCCCCCGGCTCAGTTTTGCAAGATTTTT-G-GTACGGAGACTCC
66 TGGCTGAAAACGCGTTCCGGGGCACCC-GCTCAGTTTTGCAAGATTTTTGGCGT-CGGAGACTCC
* * *
173977 TTGAAGTATCTATATTCATCTAATAAAGTCTCAGACAAATTGGATTTAAGGATATGTTTTTACGA
129 TTGAAGTATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTACGA
* *
174042 GCTTCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAA-ATGGAAAAACCATAAG
194 GCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATA-GGAAAAACCATATG
* * * * *
174106 TGAAGCATAAAAAGCCCTTAAACCTTTTTTGTGTTGAATTATAAATTTTTATGAGTACTATGGCG
258 TGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATAATTTTTTATGAGTACTATGGCC
174171 AAAAATT---G
323 AAAAATTGAGG
* * *
174179 --AAATTTTTCGCTTCAGTTTTTGTAAAATTTTAGCGGAAATCGTGTACTAACTATCACGGTTTC
1 AAAAATTTTTCGCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTC
* * *
174242 TGGCTGAAAACGCGTTCC-GGGCCCCCGGCTTAGTTTTGCAAGATTTTTGGCGT-GGAGATTCCT
66 TGGCTGAAAACGCGTTCCGGGGCACCC-GCTCAGTTTTGCAAGATTTTTGGCGTCGGAGACTCCT
* *
174305 TGAAGTATCTATAATCATCTAATCAAGTCTCAGCCACA-TGGATTTAAGGATATGGTTTTACGAG
130 TGAAGTATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTACGAG
* *
174369 CTTCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TTGGAAAAAAATAGGAAAAACCCAAATGT
195 CTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAAA-CCATATGT
** * * *
174433 GAAGCATGAAAAGCCCTTAAATCTTTTTCGACGTTGAATTATATATGTTTCATGAGTACTGTGGC
259 GAAGCATGAAAAGCCCTTAAATCTTTTT-GGTGTTGAATTATA-ATTTTTTATGAGTACTATGGC
174498 CAAAAATTGAGG
322 CAAAAATTGAGG
* * * *
174510 AAAAATTGTTCGATTCAGTTTTTCGCAAAATTTTAGCCGAAATCGTATACTAACCATCATGGTTT
1 AAAAATTTTTCGCTTCAGTTTTT-GCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTT
* *
174575 TTGGCTGAAAACGCGTTCC--GGCACCCCGGCGCAGTTTTGCAAGATTTTTGGCG-CGGAGACTC
65 CTGGCTGAAAACGCGTTCCGGGGCA-CCC-GCTCAGTTTTGCAAGATTTTTGGCGTCGGAGACTC
* *
174637 CTTGAAGTATCTATATTCATC-AGATCAAGTCTCAGCCACATTGGATTTAAGGATAAGTTTTTAT
128 CTTGAAGTATCTATATTCATCTA-ATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTAC
* *
174701 GAGCTTCTGAATCTTCTTTCGATTTAATCA-AATTTAATTTGGAAAAAAATAGGAAAAACCATAT
192 GAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAAACCATAT
* ** *
174765 GTGAATCATGAAAAGCCCTTAAATCTTTTTGGCATTGAATTATATTATTTTTTTATAATGTACTA
257 GTGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATA--A-TTTTTTATGA-GTACTA
*
174830 TGGCCAACAATTGAGG
318 TGGCCAAAAATTGAGG
* * *
174846 -AAAATTTTTCGTTTCAGTTTTTACAAAATTTTAGCCGAAATCGTGTATTAACCATCACGGTTTC
1 AAAAATTTTTCGCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTC
* * *
174910 TGGCTGAAATCACGTTCCGGGGCACCCGCTCAGTTTTGCATGATTTTTGGCGTCGG-GAC-CCTT
66 TGGCTGAAAACGCGTTCCGGGGCACCCGCTCAGTTTTGCAAGATTTTTGGCGTCGGAGACTCCTT
* *
174973 AGTAA-TATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTACGGATATGTTTTTATGA
131 -G-AAGTATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTACGA
* * *
175037 GCTTCTAAATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAAATAGGAAAAACCATAAG
194 GCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGG-AAAAAAATAGGAAAAACCATATG
* * * * * *
175102 TGAAGCATAAAAAGCCCTTAAACCTTTTTTGTGTTGAATTATAAATTTTCATGAGTACTATGGCG
258 TGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATAATTTTTTATGAGTACTATGGCC
175167 AAAAATTGAGG
323 AAAAATTGAGG
*
175178 AAAAATTTTTCGCCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTATACTAACCATCACGCGTT
1 AAAAATTTTTCG-CTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACG-GTT
* *
175243 TCTGGCTGAAAACGCGTTCC-GGGC-CCTCGACTCAGTTTTGCAAGATTTTTGGTG-CGAAGACT
64 TCTGGCTGAAAACGCGTTCCGGGGCACC-CG-CTCAGTTTTGCAAGATTTTTGGCGTCGGAGACT
* *
175305 CCGTGAAGTATCTATAATCATCTAATCAAGTCTCAGCCACA-TGGATTTAAGGATATGTTTTTAC
127 CCTTGAAGTATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTAC
* * *
175369 AAGCTTCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTGTG-AAAAAATAGGAAAAACCAAA
192 GAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTG-GAAAAAAATAGGAAAAACCATA
* * *
175433 TGTGAAGCATGAAAAACCCTTAAATCTTTATAGTGTTGAATTATATATTTTTTATGAGTACTATG
256 TGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATA-ATTTTTTATGAGTACTATG
175498 GCC-AAAATTGAGG
320 GCCAAAAATTGAGG
* * * *
175511 AAAAA-TTTT-GTTTCAATTGTTGCAAAATTTTAGCCGAAATCAG-GTACTAATTCATCACGGTT
1 AAAAATTTTTCGCTTCAGTTTTTGCAAAATTTTAGCCGAAATC-GTGTACTAA-CCATCACGGTT
* * ** *
175573 TCTCGCTGAAAACGCGTTCCAGGGC-CCCGGCTCAGTTTTATAAGATTTTTGGC-ACGGAGACTC
64 TCTGGCTGAAAACGCGTTCCGGGGCACCC-GCTCAGTTTTGCAAGATTTTTGGCGTCGGAGACTC
* * * * *
175636 CTTGAAGTATCTATATTCATCTAATCAAATCTCAGACAAATTCGATTTAAGGATATGTTTTTAGG
128 CTTGAAGTATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTACG
* * *
175701 AGCTTCTGAATCTTCTTTCGATTTAATCA-AAATTAATTTGGAAAAAAAGAGAAAAAGAAAAAGC
193 AGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAG-----GAAAAACC
* *
175765 ATATGTGAAGCATGAAAAGCCCTTAAATCGTTTTGGTGTTGAATTATATATCTTTTTATAATGTA
253 ATATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATA-AT-TTTTTATGA-GTA
* *
175830 CTATGGCCAACAATTGATG
315 CTATGGCCAAAAATTGAGG
** *
175849 -AAAATTTTTCATTTCAGCTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTC
1 AAAAATTTTTCGCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTC
* * * *
175913 TGGCTGAAAACACGTTCCGAGGCACCGGCTCAGTTTTGCATGATTTTTGGCGTCGG-GACT-CTT
66 TGGCTGAAAACGCGTTCCGGGGCACCCGCTCAGTTTTGCAAGATTTTTGGCGTCGGAGACTCCTT
* * *
175976 TATAATATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTGAAGGATATGTTTTTACGAG
131 GA-AGTATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTACGAG
* * * * * * *
176041 TTTCTGAATCTTGTTTTGATTTTATTAGAAATTTATTTGGAAAAAAA-AGGGAAAACCAAATGTG
195 CTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAAACCATATGTG
*
176105 AAGCATGAAAAGCCCTTAAATCTTTTT-G-GTT--A-TA-AATTTTTTATGAGTACTGTGGCCAA
260 AAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATAATTTTTTATGAGTACTATGGCCAA
176164 AAATTGAGG
325 AAATTGAGG
* * *
176173 AAAAATTTTTCAG-TTCAGTTTTTTGCAAAATTTTAGCCGAGATCGT-TCAATGACCATCACGGT
1 AAAAATTTTTC-GCTTCAG-TTTTTGCAAAATTTTAGCCGAAATCGTGT-ACTAACCATCACGGT
* * * * * * *
176236 TTCTGGCTGAAAAAGCGTTTCGGGGTATCGGCTCAGTTTTGCAAGATTTTAGGTG-CGGAGACTC
63 TTCTGGCTGAAAACGCGTTCCGGGGCACCCGCTCAGTTTTGCAAGATTTTTGGCGTCGGAGACTC
* * *
176300 TTTGAGGTATCTATATTCATCTAATCAAGTCTCAGCCAC-------------AT-TGTTTTTATG
128 CTTGAAGTATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTACG
*
176351 AGCTTCT-ATATCTTGTTTCGATTTAATCAGAAATTAATTTGGGAAAAAAAATAGGAAAAACCAA
193 AGCTTCTGA-ATCTTGTTTCGATTTAATCAGAAATTAATTT-GG-AAAAAAATAGGAAAAACCAT
* * * *
176415 ATGTGAAGCATGAAAAGCCCTTGAATCTTTTTGGTGTTGAATTATAAATATTTTATGAATACTGT
255 ATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTAT-AATTTTTTATGAGTACTAT
176480 GGCCAAAAATTGAGG
319 GGCCAAAAATTGAGG
* * * * *
176495 AAAAAATTTTCGATTAAGTTTTTGCAAAATTTTAGCCAAAATCATGTACTATAACCATCACGGTT
1 AAAAATTTTTCGCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTAC--TAACCATCACGGTT
* * **
176560 TCTGGCTGAAAATGCGTT-CGGGG-ACCCCGACTCAGTTTTGCATGATTTTTGGCAAC-GAGACT
64 TCTGGCTGAAAACGCGTTCCGGGGCA-CCCG-CTCAGTTTTGCAAGATTTTTGGCGTCGGAGACT
* * * * *
176622 CCTTGTAA-TATCTATATTCATCTAATCAAGTCTTATCCATATTGGATTTAAGGATATATTCTTA
127 CCTTG-AAGTATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTA
* * * * *
176686 CGAGCTTTTGAATCTTTTTTCTATTTAAACAGAAATTAATTTGGAAATAAATAGGAAAAACCATA
191 CGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAAACCATA
* * * ** *
176751 TATGAAGCATGAAAAG-CCTTAAATCTTTTTGGCGTTGAATTTTAATTTTTTTATGAGTGTTGTG
256 TGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATAA-TTTTTTATGAGTACTATG
*
176815 GCCAAAAATCGAGG
320 GCCAAAAATTGAGG
* *
176829 AAAATTTTTTCGCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTAGTAACCATCACGGTTTC
1 AAAAATTTTTCGCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTC
* * * * * *
176894 -GGCTGAAAACACGTTCCGGGACACCGGCTCAGTTTTGCATGATTTTTGGAGTCGG-GACTCTTT
66 TGGCTGAAAACGCGTTCCGGGGCACCCGCTCAGTTTTGCAAGATTTTTGGCGTCGGAGACTCCTT
* * * *
176957 GTAA-TATCTATATTCATCTAATCAAGTCTCAGCCGCATTGAATTTAAGGATATGTTTTTAGGAT
131 G-AAGTATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTACGAG
177021 CTTCTGAATCTT-TTTCGATTTAATCAGAAATTAATTTGG-AAAAAATAGGAAAAACCATATGTG
195 CTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAAACCATATGTG
* ** *
177084 ATGCATGAAAAGCCCTTAAATCTTTTTGGCATTGAATTATATATTTTTTTATAATGTACTATGGC
260 AAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATA-A-TTTTTTATGA-GTACTATGGC
* *
177149 TAACAATTGAGG
322 CAAAAATTGAGG
* * *
177161 AAAAATTGTTCGTTTCAGTTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTC
1 AAAAATTTTTCGCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTC
* * * * * * * * *
177226 TGGCTTAAAACACGTTCTGGGGCACCGGTTCAGTTTTGCATGACTTTTGGCGTC-GAGGAGTCTT
66 TGGCTGAAAACGCGTTCCGGGGCACCCGCTCAGTTTTGCAAGATTTTTGGCGTCGGA-GACTCCT
* * *
177290 TCTAA-TATCTATATTCATGTAATGAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTACGA
130 T-GAAGTATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTACGA
* *
177354 GCTTCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAAACCATAAGT
194 GCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAAACCATATGT
* * **
177419 GAAGCCT-AAAATGCCCTTAAACCTTTTTGTGTGTTGAATTATAAAATTTTATGAGTACTATGGC
259 GAAGCATGAAAA-GCCCTTAAATCTTTTTG-GTGTTGAATTATAATTTTTTATGAGTACTATGGC
* *
177483 GAACAATTGAGG
322 CAAAAATTGAGG
*
177495 AAAAATTTTTCGCTTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTC
1 AAAAATTTTTCGCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTC
*
177560 TGGCTGAAAACACGTTCCGG
66 TGGCTGAAAACGCGTTCCGG
177580 ACCCCTGAAG
Statistics
Matches: 3876, Mismatches: 374, Indels: 283
0.86 0.08 0.06
Matches are distributed among these distances:
311 1 0.00
312 42 0.01
313 4 0.00
314 7 0.00
315 42 0.01
316 1 0.00
317 3 0.00
319 1 0.00
320 2 0.00
321 27 0.01
322 54 0.01
323 89 0.02
324 21 0.01
325 45 0.01
326 213 0.05
327 165 0.04
328 27 0.01
329 41 0.01
330 399 0.10
331 401 0.10
332 453 0.12
333 364 0.09
334 734 0.19
335 320 0.08
336 142 0.04
337 71 0.02
338 149 0.04
339 58 0.01
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (333 bp):
AAAAATTTTTCGCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTC
TGGCTGAAAACGCGTTCCGGGGCACCCGCTCAGTTTTGCAAGATTTTTGGCGTCGGAGACTCCTT
GAAGTATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTACGAGC
TTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAAACCATATGTGA
AGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATAATTTTTTATGAGTACTATGGCCAAA
AATTGAGG
Found at i:177276 original size:664 final size:663
Alignment explanation
Indices: 172669--178093 Score: 6395
Period size: 668 Copynumber: 8.3 Consensus size: 663
172659 CCCTTAATAA
* *
172669 TATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTATGGATATATTTTTACGAGCTTCT
1 TATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTACGAGCTTCT
* * * *
172734 AAATCTTGATTCGATTTAATTAGAAATTAATTTGGAAAAAAAATAGGAAAAACCATAAGTGAAGC
66 GAATCTTGTTTCGATTTAATCAGAAATTAATTTGG--AAAAAATAGGAAAAACCATATGTGAAGC
* * * * * *
172799 ATAAAAAGCCCTTAAACCTTTTTTGTGTTGAATTATAAAATATTTTAATGAG---TA----C---
129 ATGAAAAGCCCTTAAATCTTTTTGGCGTTGAATTAT--AATTTTTTTATGAGTACTATGGCCAAA
172854 ---T-A--AAAATTTTTCGCCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATC
192 AATTGAGGAAAATTTTTCG-CTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATC
* * * *
172913 ACGGTTTATGGCTGAAAACGCGTTCCGGGCCCCCGGCTCAGTTTTGCAAGATTTTTGGCGT-GGA
256 ACGGTTTCTGGCTGAAAACACGTTCCGGGGCACCGGCTCAGTTTTGCAAGATTTTTGGCGTCGGA
* * *
172977 GATTCCTTGAAGTATCTATAATCATCTAATCAAGTCTCAGCCACA-TGGATTTAAGGATATAG-T
321 GACTCTTTGAA-TATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATAT-GTT
* *
173040 TTTACGAGCTTCTGAATCTTGTTTCGATTTAATTAGAAATTAATTGGGAAAAAAATAGGAAAAAC
384 TTTACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAAAC
* * *
173105 CAAATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGCGTTGAATTATATATTTTTCATGAGTAC
449 CATATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTAC
* *
173170 TTTGGCCAAAAATTGAGTAAAAATTTTTCGATTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGT
514 TATGGCCAAAAATTGAGGAAAAATTTTTCGATTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGT
*
173235 ACGT---CATCACGGTTTCTGGCTGAAAACGCGTTCCGGCGCCCCGGCTCAGTTTTGCAAGATTT
579 AC-TAACCATCACGGTTTCTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCAAGATTT
173297 TTGGCGCGGAGACTCCTTGAAG
643 TTGGCGC-GAGACTCCTTGAAG
* *
173319 TATCTATATTCATC-AGATCAAGTCTCAGCCACATTGGATTTAAGGATAAGTTTTTATGAGCTTC
1 TATCTATATTCATCTA-ATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTACGAGCTTC
* * *
173383 TGAATCTTCTTTCGATTTAATCA-AATTTAATTTGGAAAAAAATAGGAAAAACCATATGTGAATC
65 TGAATCTTGTTTCGATTTAATCAGAAATTAATTTGG-AAAAAATAGGAAAAACCATATGTGAAGC
* * *
173447 ATGAAAAGCCCTTAAATCATTTTGGCGTTGAATTATATATTTTTTTATAATGTACTATGGCCAAC
129 ATGAAAAGCCCTTAAATCTTTTTGGCGTTGAATTATA-ATTTTTTTATGA-GTACTATGGCCAAA
* * * * *
173512 AATTGAGGAAAATTTTTCGTTTCAGTTTTTACAAAATTTTAGTCGAAATCGTGTATTAACCAGCA
192 AATTGAGGAAAATTTTTCGCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCA
*
173577 CGGTTTCTGGCTGAAAACACGTTCCGGGGCACCCGCTCAGTTTTGCATA-ATTTTTGGCGTC-G-
257 CGGTTTCTGGCTGAAAACACGTTCCGGGGCACCGGCTCAGTTTTGCA-AGATTTTTGGCGTCGGA
* * * * *
173639 GACCCTTAGTAATATATATATTCATCTAATCAAGTCTCAGCCACATCGGATTTACGGATATGTTT
321 GACTCTTTG-AATATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTT
* **
173704 TTACGAGCTTCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGCTAAACC
385 TTACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAAACC
* * * * *
173769 ATAAGTGAAGCATAAAAAGCCCTTAAACCTTTTTTGTGTTGAATTATA-AATTTTTATGAGTACT
450 ATATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTACT
* *
173833 ATGGCGAAAAATTGAGGAAAAATTTTTCGCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTA
515 ATGGCCAAAAATTGAGGAAAAATTTTTCGATTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTA
*
173898 CTAACCATCACGGTTTCTGGCTGAAAACGCGTTCCGGGCCCCCGGCTCAGTTTTGCAAGATTTTT
580 CTAACCATCACGGTTTCTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCAAGATTTTT
173963 GGTACG-GAGACTCCTTGAAG
645 GG--CGCGAGACTCCTTGAAG
* * *
173983 TATCTATATTCATCTAATAAAGTCTCAGACAAATTGGATTTAAGGATATGTTTTTACGAGCTTCT
1 TATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTACGAGCTTCT
* * *
174048 AAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAAATGGAAAAACCATAAGTGAAGCA
66 GAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAATA-GGAAAAACCATATGTGAAGCA
* * * * * *
174113 TAAAAAGCCCTTAAACCTTTTTTGTGTTGAATTATAA-ATTTTTATGAGTACTATGGCGAAAAAT
130 TGAAAAGCCCTTAAATCTTTTTGGCGTTGAATTATAATTTTTTTATGAGTACTATGGCCAAAAAT
* * *
174177 T---G-AAATTTTTCGCTTCAGTTTTTGTAAAATTTTAGCGGAAATCGTGTACTAACTATCACGG
195 TGAGGAAAATTTTTCGCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGG
* * * * *
174238 TTTCTGGCTGAAAACGCGTTCCGGGCCCCCGGCTTAGTTTTGCAAGATTTTTGGCGT-GGAGATT
260 TTTCTGGCTGAAAACACGTTCCGGGGCACCGGCTCAGTTTTGCAAGATTTTTGGCGTCGGAGACT
* * *
174302 CCTTGAAGTATCTATAATCATCTAATCAAGTCTCAGCCACA-TGGATTTAAGGATATGGTTTTAC
325 CTTTGAA-TATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTAC
* *
174366 GAGCTTCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TTGGAAAAAAATAGGAAAAACCCAAA
389 GAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAAA-CCATA
** * * *
174430 TGTGAAGCATGAAAAGCCCTTAAATCTTTTTCGACGTTGAATTATATATGTTTCATGAGTACTGT
453 TGTGAAGCATGAAAAGCCCTTAAATCTTTTT-GGTGTTGAATTATATATTTTTTATGAGTACTAT
* *
174495 GGCCAAAAATTGAGGAAAAATTGTTCGATTCAGTTTTTCGCAAAATTTTAGCCGAAATCGTATAC
517 GGCCAAAAATTGAGGAAAAATTTTTCGATTCAGTTTTT-GCAAAATTTTAGCCGAAATCGTGTAC
* * ** *
174560 TAACCATCATGGTTTTTGGCTGAAAACGCGTTCCGGCACCCCGGCGCAGTTTTGCAAGATTTTTG
581 TAACCATCACGGTTTCTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCAAGATTTTTG
174625 GCGCGGAGACTCCTTGAAG
646 GCGC-GAGACTCCTTGAAG
* *
174644 TATCTATATTCATC-AGATCAAGTCTCAGCCACATTGGATTTAAGGATAAGTTTTTATGAGCTTC
1 TATCTATATTCATCTA-ATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTACGAGCTTC
* * *
174708 TGAATCTTCTTTCGATTTAATCA-AATTTAATTTGGAAAAAAATAGGAAAAACCATATGTGAATC
65 TGAATCTTGTTTCGATTTAATCAGAAATTAATTTGG-AAAAAATAGGAAAAACCATATGTGAAGC
* *
174772 ATGAAAAGCCCTTAAATCTTTTTGGCATTGAATTATATTATTTTTTTATAATGTACTATGGCCAA
129 ATGAAAAGCCCTTAAATCTTTTTGGCGTTGAATTATA--ATTTTTTTATGA-GTACTATGGCCAA
* * * *
174837 CAATTGAGGAAAATTTTTCGTTTCAGTTTTTACAAAATTTTAGCCGAAATCGTGTATTAACCATC
191 AAATTGAGGAAAATTTTTCGCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATC
* * *
174902 ACGGTTTCTGGCTGAAATCACGTTCCGGGGCACCCGCTCAGTTTTGCATGATTTTTGGCGTCGG-
256 ACGGTTTCTGGCTGAAAACACGTTCCGGGGCACCGGCTCAGTTTTGCAAGATTTTTGGCGTCGGA
* * *
174966 GACCCTTAGTAATATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTACGGATATGTTT
321 GACTCTTTG-AATATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTT
* * *
175031 TTATGAGCTTCTAAATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAAATAGGAAAAAC
385 TTACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGG-AAAAAAATAGGAAAAAC
* * * * * *
175096 CATAAGTGAAGCATAAAAAGCCCTTAAACCTTTTTTGTGTTGAATTATA-AATTTTCATGAGTAC
449 CATATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTAC
* * *
175160 TATGGCGAAAAATTGAGGAAAAATTTTTCGCCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTA
514 TATGGCCAAAAATTGAGGAAAAATTTTTCG-ATTCAGTTTTTGCAAAATTTTAGCCGAAATCGTG
*
175225 TACTAACCATCACGCGTTTCTGGCTGAAAACGCGTTCC-GGGCCCTCGACTCAGTTTTGCAAGAT
578 TACTAACCATCACG-GTTTCTGGCTGAAAACGCGTTCCGGGGCCC-CGGCTCAGTTTTGCAAGAT
* *
175289 TTTTGGTGCGAAGACTCCGTGAAG
641 TTTTGGCGCG-AGACTCCTTGAAG
* *
175313 TATCTATAATCATCTAATCAAGTCTCAGCCACA-TGGATTTAAGGATATGTTTTTACAAGCTTCT
1 TATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTACGAGCTTCT
* *
175377 GAATCTTGTTTCGATTTAATTAGAAATTAATTTGTGAAAAAATAGGAAAAACCAAATGTGAAGCA
66 GAATCTTGTTTCGATTTAATCAGAAATTAATTTG-GAAAAAATAGGAAAAACCATATGTGAAGCA
* * * *
175442 TGAAAAACCCTTAAATCTTTATAGTGTTGAATTAT-ATATTTTTTATGAGTACTATGGCC-AAAA
130 TGAAAAGCCCTTAAATCTTTTTGGCGTTGAATTATAAT-TTTTTTATGAGTACTATGGCCAAAAA
* * * * *
175505 TTGAGGAAAAATTTT-GTTTCAATTGTTGCAAAATTTTAGCCGAAATCAG-GTACTAATTCATCA
194 TTGAGGAAAATTTTTCGCTTCAGTTTTTGCAAAATTTTAGCCGAAATC-GTGTACTAA-CCATCA
* * * * ** *
175568 CGGTTTCTCGCTGAAAACGCGTTCCAGGGCCCCGGCTCAGTTTTATAAGATTTTTGGC-ACGGAG
257 CGGTTTCTGGCTGAAAACACGTTCCGGGGCACCGGCTCAGTTTTGCAAGATTTTTGGCGTCGGAG
* * * * *
175632 ACTCCTTGAAGTATCTATATTCATCTAATCAAATCTCAGACAAATTCGATTTAAGGATATGTTTT
322 ACTCTTTGAA-TATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTT
* * *
175697 TAGGAGCTTCTGAATCTTCTTTCGATTTAATCA-AAATTAATTTGGAAAAAAAGAGAAAAAGAAA
386 TACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAG-----GAAA
* * *
175761 AAGCATATGTGAAGCATGAAAAGCCCTTAAATCGTTTTGGTGTTGAATTATATATCTTTTTATAA
446 AACCATATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATATAT-TTTTTATGA
* * *
175826 TGTACTATGGCCAACAATTGATG-AAAATTTTTC-ATTTCAGCTTTTGCAAAATTTTAGCCGAAA
510 -GTACTATGGCCAAAAATTGAGGAAAAATTTTTCGA-TTCAGTTTTTGCAAAATTTTAGCCGAAA
* * * *
175889 TCGTGTACTAACCATCACGGTTTCTGGCTGAAAACACGTTCCGAGGCACCGGCTCAGTTTTGCAT
573 TCGTGTACTAACCATCACGGTTTCTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCAA
* * *
175954 GATTTTTGGCGTCGGGACT-CTTTATAA
638 GATTTTTGGCG-CGAGACTCCTTGA-AG
* *
175981 TATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTGAAGGATATGTTTTTACGAGTTTCT
1 TATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTACGAGCTTCT
* * * * * * *
176046 GAATCTTGTTTTGATTTTATTAGAAATTTATTTGGAAAAAAAAGGGAAAACCAAATGTGAAGCAT
66 GAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAATAGGAAAAACCATATGTGAAGCAT
*
176111 GAAAAGCCCTTAAATCTTTTT-G-GTT--A-TA-AA-TTTTTTATGAGTACTGTGGCCAAAAATT
131 GAAAAGCCCTTAAATCTTTTTGGCGTTGAATTATAATTTTTTTATGAGTACTATGGCCAAAAATT
* * *
176169 GAGGAAAAATTTTTCAG-TTCAGTTTTTTGCAAAATTTTAGCCGAGATCGT-TCAATGACCATCA
196 GAGG-AAAATTTTTC-GCTTCAG-TTTTTGCAAAATTTTAGCCGAAATCGTGT-ACTAACCATCA
* * * * *
176232 CGGTTTCTGGCTGAAAA-AGCGTTTCGGGGTATCGGCTCAGTTTTGCAAGATTTTAGGTG-CGGA
257 CGGTTTCTGGCTGAAAACA-CGTTCCGGGGCACCGGCTCAGTTTTGCAAGATTTTTGGCGTCGGA
*
176295 GACTCTTTGAGGTATCTATATTCATCTAATCAAGTCTCAGCCAC-------------AT-TGTTT
321 GACTCTTTGA-ATATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTT
*
176346 TTATGAGCTTCT-ATATCTTGTTTCGATTTAATCAGAAATTAATTTGGGAAAAAAAATAGGAAAA
385 TTACGAGCTTCTGA-ATCTTGTTTCGATTTAATCAGAAATTAATTT-GG-AAAAAAATAGGAAAA
* * * * *
176410 ACCAAATGTGAAGCATGAAAAGCCCTTGAATCTTTTTGGTGTTGAATTATAAATATTTTATGAAT
447 ACCATATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATATATTTTTTATGAGT
* * * * *
176475 ACTGTGGCCAAAAATTGAGGAAAAAATTTTCGATTAAGTTTTTGCAAAATTTTAGCCAAAATCAT
512 ACTATGGCCAAAAATTGAGGAAAAATTTTTCGATTCAGTTTTTGCAAAATTTTAGCCGAAATCGT
* * *
176540 GTACTATAACCATCACGGTTTCTGGCTGAAAATGCGTT-CGGGGACCCCGACTCAGTTTTGCATG
577 GTAC--TAACCATCACGGTTTCTGGCTGAAAACGCGTTCCGGGG-CCCCGGCTCAGTTTTGCAAG
*
176604 ATTTTTGGCAACGAGACTCCTTGTAA-
639 ATTTTTGGC-GCGAGACTCCTTG-AAG
* * * * * *
176630 TATCTATATTCATCTAATCAAGTCTTATCCATATTGGATTTAAGGATATATTCTTACGAGCTTTT
1 TATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTACGAGCTTCT
* * * *
176695 GAATCTTTTTTCTATTTAAACAGAAATTAATTTGGAAATAAATAGGAAAAACCATATATGAAGCA
66 GAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAA-AAATAGGAAAAACCATATGTGAAGCA
* ** *
176760 TGAAAAG-CCTTAAATCTTTTTGGCGTTGAATTTTAATTTTTTTATGAGTGTTGTGGCCAAAAAT
130 TGAAAAGCCCTTAAATCTTTTTGGCGTTGAATTATAATTTTTTTATGAGTACTATGGCCAAAAAT
* *
176824 CGAGGAAAATTTTTTCGCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTAGTAACCATCACG
195 TGAGGAAAA-TTTTTCGCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACG
* * *
176889 GTTTC-GGCTGAAAACACGTTCCGGGACACCGGCTCAGTTTTGCATGATTTTTGGAGTCGG-GAC
259 GTTTCTGGCTGAAAACACGTTCCGGGGCACCGGCTCAGTTTTGCAAGATTTTTGGCGTCGGAGAC
* *
176952 TCTTTGTAATATCTATATTCATCTAATCAAGTCTCAGCCGCATTGAATTTAAGGATATGTTTTTA
324 TCTTTG-AATATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTA
* *
177017 GGATCTTCTGAATCTT-TTTCGATTTAATCAGAAATTAATTTGG-AAAAAATAGGAAAAACCATA
388 CGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAAACCATA
* ** *
177080 TGTGATGCATGAAAAGCCCTTAAATCTTTTTGGCATTGAATTATATATTTTTTTATAATGTACTA
453 TGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATATA-TTTTTTATGA-GTACTA
* * * * *
177145 TGGCTAACAATTGAGGAAAAATTGTTCGTTTCAGTTTTTACAAAATTTTAGCCGAAATCGTGTAC
516 TGGCCAAAAATTGAGGAAAAATTTTTCGATTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTAC
* * * * * * *
177210 TAACCATCACGGTTTCTGGCTTAAAACACGTTCTGGGGCACCGGTTCAGTTTTGCATGACTTTTG
581 TAACCATCACGGTTTCTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCAAGATTTTTG
* * *
177275 GCGTCGAGGAGTCTTTCTAA-
646 GCG-CGA-GACTCCTT-GAAG
* *
177295 TATCTATATTCATGTAATGAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTACGAGCTTCT
1 TATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTACGAGCTTCT
* * *
177360 AAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAAACCATAAGTGAAGCC
66 GAATCTTGTTTCGATTTAATCAGAAATTAATTTGG-AAAAAATAGGAAAAACCATATGTGAAGCA
* * ** * *
177425 T-AAAATGCCCTTAAACCTTTTTGTGTGTTGAATTATAA-AATTTTATGAGTACTATGGCGAACA
130 TGAAAA-GCCCTTAAATCTTTTTG-GCGTTGAATTATAATTTTTTTATGAGTACTATGGCCAAAA
*
177488 ATTGAGGAAAAATTTTTCGCTTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCA
193 ATTGAGG-AAAATTTTTCGCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCA
* *
177553 CGGTTTCTGGCTGAAAACACGTTCC--GG-ACC--C-C-----TG-AAG---TAT--C-T---AT
257 CGGTTTCTGGCTGAAAACACGTTCCGGGGCACCGGCTCAGTTTTGCAAGATTTTTGGCGTCGGAG
* * * ** * * * * * * **
177597 AATCATCT--A-ATC-A-AGTCTCATCCACATGGA-TTTAAG-GATA-TGG-TTTTACGAGCT-T
322 ACTC-TTTGAATATCTATA-T-TCATCTA-ATCAAGTCTCAGCCACATTGGATTTAAGGATATGT
** ** * ** * ** * * * *
177652 TTGAATCTTGTTTC-G-AT-TTAG-TTAAAATTAATTGGGAAA-AAAATAGG----AAA-A--AC
383 TTTTA-CGAGCTTCTGAATCTT-GTTTCGATTTAA-TCAGAAATTAATTTGGAAAAAAATAGGAA
* ** ** * *
177705 ----CAAATGTGAAGTTTGAAAAGCCCTTAAATCTTTTTGACGTTGAATTATATATGTTTCATGA
445 AAACCATATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATATATTTTTTATGA
* *
177766 GTACTGTGGCCAAAAATTGAGGAAAAATTGTTCGATTCAGTTTTTGCAAAATTTTAGCCGAAATC
510 GTACTATGGCCAAAAATTGAGGAAAAATTTTTCGATTCAGTTTTTGCAAAATTTTAGCCGAAATC
*
177831 GTGTACTAACCATCACGGTTTCTGGCTGAAAACGCGTTCCGGCGCCCCGGCTCAGTTTTGCAAGA
575 GTGTACTAACCATCACGGTTTCTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCAAGA
*
177896 TTTTTGGCGCGGAGACTCCTTAAAG
640 TTTTTGGCGC-GAGACTCCTTGAAG
* * * *
177921 CATCTATAATCATCAAATCAAGTCTCATCCACATTGGATTTAAGGATATGTTTTTACGAGCTTCT
1 TATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTACGAGCTTCT
* * * * **
177986 GAATCTTGTTTCGATTTAATTAAAAATTAATTGGGAAAAAAATAGGAAAAACCAAATGTGAAGTT
66 GAATCTTGTTTCGATTTAATCAGAAATTAATTTGG-AAAAAATAGGAAAAACCATATGTGAAGCA
178051 TGAAAAGCCCTTAAATCTTTTTGGCGTTGAATTATATATTTTT
130 TGAAAAGCCCTTAAATCTTTTTGGCGTTGAATTATA-ATTTTT
178094 CGCTTCACTT
Statistics
Matches: 4123, Mismatches: 492, Indels: 343
0.83 0.10 0.07
Matches are distributed among these distances:
625 14 0.00
626 141 0.03
627 134 0.03
628 7 0.00
629 45 0.01
633 1 0.00
635 1 0.00
636 3 0.00
638 2 0.00
639 14 0.00
640 10 0.00
641 10 0.00
642 3 0.00
643 3 0.00
644 13 0.00
645 4 0.00
646 19 0.00
647 60 0.01
648 120 0.03
649 179 0.04
650 146 0.04
651 18 0.00
652 4 0.00
653 10 0.00
654 83 0.02
655 57 0.01
656 43 0.01
657 19 0.00
658 192 0.05
659 50 0.01
660 111 0.03
661 208 0.05
662 142 0.03
663 250 0.06
664 465 0.11
665 379 0.09
666 179 0.04
667 74 0.02
668 470 0.11
669 350 0.08
670 55 0.01
671 35 0.01
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (663 bp):
TATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTACGAGCTTCT
GAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAATAGGAAAAACCATATGTGAAGCAT
GAAAAGCCCTTAAATCTTTTTGGCGTTGAATTATAATTTTTTTATGAGTACTATGGCCAAAAATT
GAGGAAAATTTTTCGCTTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGT
TTCTGGCTGAAAACACGTTCCGGGGCACCGGCTCAGTTTTGCAAGATTTTTGGCGTCGGAGACTC
TTTGAATATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTACGA
GCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAAACCATATGT
GAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTACTATGGCC
AAAAATTGAGGAAAAATTTTTCGATTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACC
ATCACGGTTTCTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCAAGATTTTTGGCGCG
AGACTCCTTGAAG
Found at i:179683 original size:333 final size:332
Alignment explanation
Indices: 178705--179978 Score: 1546
Period size: 333 Copynumber: 3.8 Consensus size: 332
178695 ATTTTTGGCG
* * * * * * * * *
178705 TTTACCCGAAATCGTGTACTAACCATCACAGTTTCTGGCTGAAAACACGTTCCGGGGCACCCGCT
1 TTTAGCCGAAATCATTTACAAACCATCACGGTTTCTAGCTGAAAACGCATTCCGGGGC-CCGGCT
* * * ** *
178770 CAGTTTTGCATGATTTTTGGCGTCGGGACTTTTTGTAATATCTATATTCATCTAATCAAATCTCA
65 CAGTTTTGCAAGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCA
* *
178835 GCCACATTGGATTTAAGGATATGTTTTTACGAGCTTCTGAATCTTGTTTTGATTTAATTAGAAAT
130 GCCACATTGGATTTAAGGATATGTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAAT
* *
178900 TTATTTGGAAAAAAAATAGGAAAAACCAAATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGTG
195 TAATTTGGAAAAAATA-AGGAAAAACCAAATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGTG
* * * *
178965 TTAAATTATAAATTTTTCATGAGTATTGTGACCAAAAATTGAGGAAAAATTTTTCGGTTCAGTTC
259 TTGAATTATAAATTTTTTATGAGTATTGTGACCAAAAATTGAGGAAAAATTTTTCGGTTTAGTTT
179030 TTGCAAAAT
324 TTGCAAAAT
* * * * * * * *
179039 TTTAGCCGAAATCGTTTACTAACAATCACGATTTCTGGCTGAAAAAGCGTTCCGGGATCCCGGCT
1 TTTAGCCGAAATCATTTACAAACCATCACGGTTTCTAGCTGAAAACGCATTCCGGG-GCCCGGCT
* * * * *
179104 CAGTTTTGCAAGATTTTAGGC-ACGTAGACTCTTTGAAGTATCTATATTCATCTAATCAAGTCTC
65 CAGTTTTGCAAGATTTTTGGCGCCG-AGACTCCTTGAAATATCTATATTCATCTAATCAAATCTC
* * *
179168 AGCCACA-TGAATTTCAA-TATATGTTTTTATGAGCTTCT-ATATCTTGTTTCGATTTAATCAGA
129 AGCCACATTGGATTT-AAGGATATGTTTTTACGAGCTTCTGA-ATCTTGTTTCGATTTAATCAGA
179230 AATTAATTTGGAAAAAA-AAGG-AAAACCAAATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGG
192 AATTAATTTGGAAAAAATAAGGAAAAACCAAATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGG
* * * * *
179293 TGTTGAATCATAAATTTTTTATGAGTATTGTGGCAAAAAATTGAGGAAAATTTTTTCGGTTTGGT
257 TGTTGAATTATAAATTTTTTATGAGTATTGTGACCAAAAATTGAGGAAAAATTTTTCGGTTTAGT
179358 TTTTGCAAAAT
322 TTTTGCAAAAT
* *
179369 TTTAGCCGAACTCATTTACAAACCATCACGGTTTCTAGCTGAAAACGCATTACGGGGCCTCGGCT
1 TTTAGCCGAAATCATTTACAAACCATCACGGTTTCTAGCTGAAAACGCATTCCGGGGCC-CGGCT
* * * * *
179434 CATTTTTTCAAGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAAACAAGTCTTA
65 CAGTTTTGCAAGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCA
* * *
179499 ACCACATTGGATTTAAGGATATGTTTTTACGAGTTTCTGAATCTTGTTTCGATTTAATTAGAAAT
130 GCCACATTGGATTTAAGGATATGTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAAT
* * * *
179564 TAATTTGGAAAAAATAAGGAAAAACCATATGTGGAGCATGAAAAGCTCTTAAATCTTTTTGTTGT
195 TAATTTGGAAAAAATAAGGAAAAACCAAATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGT
* * *
179629 TGAATTATATATTTTTTATGAGTACTATGACCAAAAATTGAGGAAAAATTTTTC-GTTTCAGTTT
260 TGAATTATAAATTTTTTATGAGTATTGTGACCAAAAATTGAGGAAAAATTTTTCGGTTT-AGTTT
179693 TTGCAAAAT
324 TTGCAAAAT
* ** *
179702 TTTAGCC-ATAATAATGTTTTAAA-CATCACGGTTTCTAGCTGAAAACGCATTCCGGGGATCCGG
1 TTTAGCCGA-AATCAT-TTACAAACCATCACGGTTTCTAGCTGAAAACGCATTCCGGGG-CCCGG
* * * *
179765 CTCAGTTTTGCATGATTTTTGGCTCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCT
63 CTCAGTTTTGCAAGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCT
** * * * * * *
179830 CAGCCTTATTGGATTTATGGATTTGTTTTTACGTGCGTCTGAATCATGTTTCGATTTAATCATAA
128 CAGCCACATTGGATTTAAGGATATGTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAA
** * * * * * * * *
179895 ATTAATTCAGATAAAAT-TGGAAAAA-C-AATGTTAGAAGCGTGAAAAACTCTTCATTCTTTTTT
193 ATTAATTTGGAAAAAATAAGGAAAAACCAAATG-T-GAAGCATGAAAAGCCCTTAAATCTTTTTG
* *
179957 GTGTTGAATTATATACTTTTTA
256 GTGTTGAATTATAAATTTTTTA
179979 ATGGGTAAAT
Statistics
Matches: 817, Mismatches: 106, Indels: 36
0.85 0.11 0.04
Matches are distributed among these distances:
329 2 0.00
330 225 0.28
331 69 0.08
332 62 0.08
333 336 0.41
334 122 0.15
335 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (332 bp):
TTTAGCCGAAATCATTTACAAACCATCACGGTTTCTAGCTGAAAACGCATTCCGGGGCCCGGCTC
AGTTTTGCAAGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAG
CCACATTGGATTTAAGGATATGTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATT
AATTTGGAAAAAATAAGGAAAAACCAAATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTT
GAATTATAAATTTTTTATGAGTATTGTGACCAAAAATTGAGGAAAAATTTTTCGGTTTAGTTTTT
GCAAAAT
Found at i:181302 original size:49 final size:49
Alignment explanation
Indices: 181221--181341 Score: 179
Period size: 49 Copynumber: 2.5 Consensus size: 49
181211 CAACACGCGA
* * *
181221 AGACACGAAGATACACAAGAAGACATAGCCTCCACAGTGAGGCGAGGCC
1 AGACACGAAGATACACGAGAAGAAATAACCTCCACAGTGAGGCGAGGCC
* * *
181270 AGACACGAAGATACATGAGAAGAAATAACCTCCGCAGTGGGGCGAGGCC
1 AGACACGAAGATACACGAGAAGAAATAACCTCCACAGTGAGGCGAGGCC
*
181319 AGACACGAAGGTACACGAGAAGA
1 AGACACGAAGATACACGAGAAGA
181342 CACACAACAC
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 64 1.00
ACGTcount: A:0.40, C:0.23, G:0.29, T:0.08
Consensus pattern (49 bp):
AGACACGAAGATACACGAGAAGAAATAACCTCCACAGTGAGGCGAGGCC
Found at i:181416 original size:49 final size:49
Alignment explanation
Indices: 181360--181460 Score: 166
Period size: 49 Copynumber: 2.1 Consensus size: 49
181350 ACACACAAAT
* *
181360 ACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGATACACGAGAAG
1 ACATAGCCTCCGCAGTGAGGCGAGGCAAGACACGAAGATACACAAGAAG
* *
181409 ACATAGCCTCCGCGGTGAGGCGAGGCAAGACACGAAGGTACACAAGAAG
1 ACATAGCCTCCGCAGTGAGGCGAGGCAAGACACGAAGATACACAAGAAG
181458 ACA
1 ACA
181461 CAACACACAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.36, C:0.26, G:0.31, T:0.08
Consensus pattern (49 bp):
ACATAGCCTCCGCAGTGAGGCGAGGCAAGACACGAAGATACACAAGAAG
Found at i:181440 original size:117 final size:115
Alignment explanation
Indices: 181233--181526 Score: 437
Period size: 117 Copynumber: 2.5 Consensus size: 115
181223 ACACGAAGAT
* * * * *
181233 ACACAAGAAGACATAGCCTCCACAGTGAGGCGAGGCCAGACACGAAGATACATGAGAAGAAATAA
1 ACACACGAAAACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGATACACGAGAAGACATAA
* * *
181298 CCTCCGCAGTGGGGCGAGGCCAGACACGAAGGTACACGAGAAGACACACAAC
66 CCTCCGCAGTGAGGCGAGGCAAGACACGAAGGTACACAAGAAG--ACACAAC
181350 ACACAC-AAATACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGATACACGAGAAGACATA
1 ACACACGAAA-ACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGATACACGAGAAGACATA
* *
181414 GCCTCCGCGGTGAGGCGAGGCAAGACACGAAGGTACACAAGAAGACACAAC
65 ACCTCCGCAGTGAGGCGAGGCAAGACACGAAGGTACACAAGAAGACACAAC
* * *
181465 ACACACGAAAATATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGACGACA
1 ACACACGAAAACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGATACACGAGAAGACA
181527 CAAGACACAC
Statistics
Matches: 162, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
115 62 0.38
116 5 0.03
117 95 0.59
ACGTcount: A:0.38, C:0.27, G:0.27, T:0.08
Consensus pattern (115 bp):
ACACACGAAAACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGATACACGAGAAGACATAA
CCTCCGCAGTGAGGCGAGGCAAGACACGAAGGTACACAAGAAGACACAAC
Found at i:181494 original size:66 final size:66
Alignment explanation
Indices: 181405--181647 Score: 378
Period size: 68 Copynumber: 3.6 Consensus size: 66
181395 AGATACACGA
* * *
181405 GAAGACATAGCCTCCGCGGTGAGGCGAGGCAAGACACGAAGGTACACAAGAAGACACAACACACA
1 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACAACACACA
181470 C
66 C
* * *
181471 GAAAATATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGACGACACAAGACACA
1 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACAC-A-ACACA
181536 CAC
64 CAC
181539 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACACAACACA
1 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAG--ACACAACACA
*
181604 CAT
64 CAC
*
181607 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACATGAAG
1 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAG
181648 ATAGAGATGG
Statistics
Matches: 162, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
66 51 0.31
67 1 0.01
68 105 0.65
69 1 0.01
70 4 0.02
ACGTcount: A:0.37, C:0.27, G:0.28, T:0.07
Consensus pattern (66 bp):
GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACAACACACA
C
Found at i:181574 original size:134 final size:136
Alignment explanation
Indices: 181388--181647 Score: 409
Period size: 134 Copynumber: 1.9 Consensus size: 136
181378 GGCGAGGCCA
* *
181388 GACACGAAGATACACGAGAAGACATAGCCTCCGCGGTGAGGCGAGGCAAGACACGAAGGTACACA
1 GACACGAAGACACACGAGAAGACATAGCCTCCGCAGTGAGGCGAGGCAAGACACGAAGGTACACA
*
181453 AGAAG-ACACAACACACACGAAAATATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACA
66 AGAAGAACACAACACACACGAAAACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACA
181517 CGAGAC
131 CGAGAC
*
181523 GACAC-AAGACACAC-ACGAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACAC
1 GACACGAAGACACACGA-GAAGACATAGCCTCCGCAGTGAGGCGAGGCAAGACACGAAGGTACAC
* * * *
181586 GAGAAGACACACAACACACATGAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACATGAAG
65 AAGAAGA-ACACAACACACACGAAAACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAG
181648 ATAGAGATGG
Statistics
Matches: 114, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
133 1 0.01
134 58 0.51
135 5 0.04
136 50 0.44
ACGTcount: A:0.38, C:0.27, G:0.28, T:0.07
Consensus pattern (136 bp):
GACACGAAGACACACGAGAAGACATAGCCTCCGCAGTGAGGCGAGGCAAGACACGAAGGTACACA
AGAAGAACACAACACACACGAAAACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACA
CGAGAC
Found at i:182380 original size:48 final size:49
Alignment explanation
Indices: 182270--182389 Score: 188
Period size: 48 Copynumber: 2.5 Consensus size: 49
182260 TGCCATCTCT
* * *
182270 ACACAAAGATACATGAGAAGACATAGCCTCCGCAGTGAGGCGAGGCCAG
1 ACACGAAGATACACGAGAAGACATAGCCTCCGCAGCGAGGCGAGGCCAG
*
182319 ACACGAAGATACACGAGAAGGCATAGCCTCCG-AGCGAGGCGAGGCCAG
1 ACACGAAGATACACGAGAAGACATAGCCTCCGCAGCGAGGCGAGGCCAG
*
182367 ACACGAAGGTACACGAGAAGACA
1 ACACGAAGATACACGAGAAGACA
182390 CACAACACAC
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
48 36 0.55
49 29 0.45
ACGTcount: A:0.38, C:0.25, G:0.30, T:0.07
Consensus pattern (49 bp):
ACACGAAGATACACGAGAAGACATAGCCTCCGCAGCGAGGCGAGGCCAG
Found at i:182431 original size:68 final size:68
Alignment explanation
Indices: 182335--182603 Score: 387
Period size: 68 Copynumber: 4.1 Consensus size: 68
182325 AGATACACGA
* *
182335 GAAGGCATAGCCTCCG-AGCGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACACAACACA
1 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACACAACACA
182399 CAC
66 CAC
* *
182402 GAAGACATAGCCTCCGCAGTGAGGTGAGGCCAGACACGAAGGTACACGAGAAG---------GCA
1 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACACAACACA
182458 CAC
66 CAC
*
182461 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACACGACACA
1 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACACAACACA
182526 CAC
66 CAC
* * *
182529 GAAGACATAGCCTCCGCAGTGAGGTGAGGCCAGAAACGAAGGTACACGAGAAGACACACAACATA
1 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACACAACACA
*
182594 GAC
66 CAC
182597 GAAGACA
1 GAAGACA
182604 GACACAAAGG
Statistics
Matches: 181, Mismatches: 11, Indels: 19
0.86 0.05 0.09
Matches are distributed among these distances:
59 57 0.31
67 15 0.08
68 109 0.60
ACGTcount: A:0.38, C:0.27, G:0.29, T:0.07
Consensus pattern (68 bp):
GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACACAACACA
CAC
Found at i:182468 original size:59 final size:59
Alignment explanation
Indices: 182397--182587 Score: 274
Period size: 59 Copynumber: 3.1 Consensus size: 59
182387 ACACACAACA
182397 CACACGAAGACATAGCCTCCGCAGTGAGGTGAGGCCAGACACGAAGGTACACGAGAAGG
1 CACACGAAGACATAGCCTCCGCAGTGAGGTGAGGCCAGACACGAAGGTACACGAGAAGG
*
182456 CACACGAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACACG
1 CACACGAAGACATAGCCTCCGCAGTGAGGTGAGGCCAGACACGAAGGTACACGAGAAG------G
* *
182521 ACACACACGAAGACATAGCCTCCGCAGTGAGGTGAGGCCAGAAACGAAGGTACACGAGAAGA
1 ---CACACGAAGACATAGCCTCCGCAGTGAGGTGAGGCCAGACACGAAGGTACACGAGAAGG
182583 CACAC
1 CACAC
182588 AACATAGACG
Statistics
Matches: 119, Mismatches: 4, Indels: 18
0.84 0.03 0.13
Matches are distributed among these distances:
59 62 0.52
65 1 0.01
68 56 0.47
ACGTcount: A:0.36, C:0.27, G:0.29, T:0.07
Consensus pattern (59 bp):
CACACGAAGACATAGCCTCCGCAGTGAGGTGAGGCCAGACACGAAGGTACACGAGAAGG
Found at i:182502 original size:127 final size:126
Alignment explanation
Indices: 182335--182587 Score: 452
Period size: 127 Copynumber: 2.0 Consensus size: 126
182325 AGATACACGA
*
182335 GAAGGCATAGCCTCCGAGCGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACACAACACAC
1 GAAGACATAGCCTCCGAGCGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACACAACACAC
* *
182400 ACGAAGACATAGCCTCCGCAGTGAGGTGAGGCCAGACACGAAGGTACACGAGAAGGCACAC
66 ACGAAGACATAGCCTCCGCAGTGAGGTGAGGCCAGAAACGAAGGTACACGAGAAGACACAC
* *
182461 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACACGACACA
1 GAAGACATAGCCTCCG-AGCGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACACAACACA
182526 CACGAAGACATAGCCTCCGCAGTGAGGTGAGGCCAGAAACGAAGGTACACGAGAAGACACAC
65 CACGAAGACATAGCCTCCGCAGTGAGGTGAGGCCAGAAACGAAGGTACACGAGAAGACACAC
182588 AACATAGACG
Statistics
Matches: 121, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
126 15 0.12
127 106 0.88
ACGTcount: A:0.36, C:0.27, G:0.30, T:0.07
Consensus pattern (126 bp):
GAAGACATAGCCTCCGAGCGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACACACAACACAC
ACGAAGACATAGCCTCCGCAGTGAGGTGAGGCCAGAAACGAAGGTACACGAGAAGACACAC
Found at i:185265 original size:12 final size:12
Alignment explanation
Indices: 185248--185272 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
185238 GCAACAAGAA
185248 TGAGAAAACCTT
1 TGAGAAAACCTT
185260 TGAGAAAACCTT
1 TGAGAAAACCTT
185272 T
1 T
185273 AATGTAAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (12 bp):
TGAGAAAACCTT
Found at i:186991 original size:30 final size:30
Alignment explanation
Indices: 186955--187011 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
186945 ATGCTTAGCA
186955 ATGAATATTAGATGGCAAGATA-TACAAAAG
1 ATGAATATTAGATGGCAAG-TAGTACAAAAG
186985 ATGAATATTAGATGGCAAGTAGTACAA
1 ATGAATATTAGATGGCAAGTAGTACAA
187012 TTTGTTTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.25
Consensus pattern (30 bp):
ATGAATATTAGATGGCAAGTAGTACAAAAG
Found at i:197155 original size:9 final size:9
Alignment explanation
Indices: 197141--197166 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
197131 CTTGAGAGAA
197141 AAAAAAAAC
1 AAAAAAAAC
197150 AAAAAAAAC
1 AAAAAAAAC
197159 AAAAAAAA
1 AAAAAAAA
197167 ACCCCAGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:197155 original size:10 final size:10
Alignment explanation
Indices: 197140--197168 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
197130 CCTTGAGAGA
197140 AAAAAAAAAC
1 AAAAAAAAAC
197150 -AAAAAAAAC
1 AAAAAAAAAC
197159 AAAAAAAAAC
1 AAAAAAAAAC
197169 CCCAGATGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:213803 original size:48 final size:48
Alignment explanation
Indices: 213772--213873 Score: 159
Period size: 48 Copynumber: 2.1 Consensus size: 48
213762 TTGGTGGAGG
*
213772 AACTGGTGGCTTAACTGGTGGCTGAGTTGGTGGCTTGGTTGGAGGGTA
1 AACTGGTGGCTTAACTGGTGCCTGAGTTGGTGGCTTGGTTGGAGGGTA
*** *
213820 AACTGGTGGCTTGGGTGGTGCCTGAGTTGGTGGCTTGGTCGGAGGGTA
1 AACTGGTGGCTTAACTGGTGCCTGAGTTGGTGGCTTGGTTGGAGGGTA
213868 AACTGG
1 AACTGG
213874 GTGCGGTGGT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.14, C:0.12, G:0.45, T:0.29
Consensus pattern (48 bp):
AACTGGTGGCTTAACTGGTGCCTGAGTTGGTGGCTTGGTTGGAGGGTA
Found at i:213826 original size:24 final size:24
Alignment explanation
Indices: 213799--213873 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
213789 GTGGCTGAGT
213799 TGGTGGCTTGGTTGGAGGGTAAAC
1 TGGTGGCTTGGTTGGAGGGTAAAC
* * ** * **
213823 TGGTGGCTTGGGTGGTGCCTGAGT
1 TGGTGGCTTGGTTGGAGGGTAAAC
*
213847 TGGTGGCTTGGTCGGAGGGTAAAC
1 TGGTGGCTTGGTTGGAGGGTAAAC
213871 TGG
1 TGG
213874 GTGCGGTGGT
Statistics
Matches: 36, Mismatches: 15, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.12, C:0.11, G:0.48, T:0.29
Consensus pattern (24 bp):
TGGTGGCTTGGTTGGAGGGTAAAC
Found at i:213993 original size:18 final size:18
Alignment explanation
Indices: 213952--213993 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
213942 TTGGGGCAGG
*
213952 GGTGG-GAGGATGAGGGT
1 GGTGGTGAGGATGAGGAT
213969 -GTGGGTGAGGATGAGGAT
1 GGT-GGTGAGGATGAGGAT
213987 GGTGGTG
1 GGTGGTG
213994 GTGGTGGTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
16 2 0.10
17 2 0.10
18 15 0.71
19 2 0.10
ACGTcount: A:0.17, C:0.00, G:0.62, T:0.21
Consensus pattern (18 bp):
GGTGGTGAGGATGAGGAT
Found at i:221121 original size:14 final size:14
Alignment explanation
Indices: 221102--221138 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
221092 ACTTACGTGG
221102 ATGTTTTCTGATCT
1 ATGTTTTCTGATCT
*
221116 ATGTTTTCTGATTT
1 ATGTTTTCTGATCT
221130 ATGTTTTCT
1 ATGTTTTCT
221139 AAAGAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.14, C:0.11, G:0.14, T:0.62
Consensus pattern (14 bp):
ATGTTTTCTGATCT
Found at i:221726 original size:2 final size:2
Alignment explanation
Indices: 221719--221752 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
221709 TTTCTTCATC
221719 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
221753 TTTGTCCACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:224340 original size:6 final size:6
Alignment explanation
Indices: 224307--224339 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
224297 ATCTGAAATG
*
224307 AAAGGC AAAGGC AAAGGC AAAGGC AAAAGC AAA
1 AAAGGC AAAGGC AAAGGC AAAGGC AAAGGC AAA
224340 ATATATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.58, C:0.15, G:0.27, T:0.00
Consensus pattern (6 bp):
AAAGGC
Found at i:225816 original size:16 final size:16
Alignment explanation
Indices: 225795--225829 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
225785 TATTGAATCA
225795 TTTATATTTCATATTC
1 TTTATATTTCATATTC
225811 TTTATATTTCATATTC
1 TTTATATTTCATATTC
225827 TTT
1 TTT
225830 GTATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTATATTTCATATTC
Found at i:237669 original size:1 final size:1
Alignment explanation
Indices: 237658--237693 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
237648 TCCCCTGCAT
* *
237658 AAAATAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
237694 TGTTAGATGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.94, C:0.00, G:0.03, T:0.03
Consensus pattern (1 bp):
A
Found at i:249647 original size:16 final size:16
Alignment explanation
Indices: 249626--249657 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
249616 ATTCTTATGC
*
249626 AAGCTCAAAGTATGAA
1 AAGCTCAAAATATGAA
249642 AAGCTCAAAATATGAA
1 AAGCTCAAAATATGAA
249658 TTAAGCAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.12, G:0.16, T:0.19
Consensus pattern (16 bp):
AAGCTCAAAATATGAA
Found at i:252224 original size:3 final size:3
Alignment explanation
Indices: 252216--252240 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
252206 CTAAAGAGAT
252216 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
252241 CCAAAAGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:254993 original size:342 final size:334
Alignment explanation
Indices: 253299--255333 Score: 2779
Period size: 334 Copynumber: 6.1 Consensus size: 334
253289 AACAATTATT
* *
253299 AGGGTTTTTCACGCTTCGAATATCGTTTTT-CTTATGCTTTTCCGAATTAATTTCTAATTAAATC
1 AGGGTTTTTCACGCTTCGAATATCGTTTTTCCTAATGCTTTTCCGAATTAATTTCCAATTAAATC
* * * * *
253363 GAAACTGGATTCTAATGCTCGTAAAAACAAATATTTAAATCTCATGTGGCTGAGATTTTGGTAGA
66 GAAACTGGATTCTGATGTTCGTAAAAACAAATCTTTAAATCTTATGTGGCTGAGATTTGGGTAGA
* * * * *
253428 TGAATATAGATATTCCAAGGAGTCTTGGAGTCAAAAATCATACGAAACAGAGCC-GGGCCTCGGA
131 TGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAACTGAGCCGGGGCCCCGGA
* * *
253492 ACGTGTTTTTAGTCGAAAACTGTGAT-GTAACGCACACGATTTCGGTAAAGATTTTACAAAAATT
196 ACGCGTTTTTAGTCGAAAACTGTGATGGTTA-GCACACGATTTCGGTCAAGATTTTACAAAAATT
*
253556 GACCCGAATGATTTTTCCTCAAATTTTGGCCAAAATACTCATAAAAAACATATAAATCATCGCCA
260 GACCCGAATGATTTTTCCTCAAATTTTGGCCAAAATACTCATAAAAAATATATAAATCATCGCCA
*
253621 AAAATATTGA
325 AAAAGATTGA
*
253631 AGGGGTTTTCACGCTTCGAA-AGTCGTTTTTCCT-ATGCTTTTCCGAATTAATTTCCAATTAAAT
1 AGGGTTTTTCACGCTTCGAATA-TCGTTTTTCCTAATGCTTTTCCGAATTAATTTCCAATTAAAT
* *
253694 CGAAACAGGATTCTGATGTTCGTAAAAACAAATCTTTAAATATTATGTGGCTGAGATTTGGGTAG
65 CGAAACTGGATTCTGATGTTCGTAAAAACAAATCTTTAAATCTTATGTGGCTGAGATTTGGGTAG
* * * * *
253759 ATCAATATATATAATCCAAGGAGTCTTGGCGCCAAAAATCATATAAAACTGAACCGGGGCCCCGG
130 ATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAACTGAGCCGGGGCCCCGG
*
253824 AACGCGCTTTTAGTCGAAAACTGTGATGGTTAGCACACGATTTCGGTCAAGATTTTACAAAAATT
195 AACGCGTTTTTAGTCGAAAACTGTGATGGTTAGCACACGATTTCGGTCAAGATTTTACAAAAATT
* * * *
253889 GACCCGAATGATTTTTCCTCAATTTTTTGCAAAAAAATACTCAT-AAAAATATATAAATCATCTC
260 GACCCGAATGATTTTTCCTCAAATTTTGGC--CAAAATACTCATAAAAAATATATAAATCATCGC
*
253953 CAAAAAGAATGA
323 CAAAAAGATTGA
* *
253965 AGGGTTTTTCACGCTTCGAAGATCGTTTTTCCTAA-GCCTTTCCGAATTAATTTCCAATTAAATC
1 AGGGTTTTTCACGCTTCGAATATCGTTTTTCCTAATGCTTTTCCGAATTAATTTCCAATTAAATC
* * *
254029 GAAACTGGATTCTGATGGTCGTAAAAACTAATCTTTAAATCTTATGTGGCTGAGATTTGGGTACA
66 GAAACTGGATTCTGATGTTCGTAAAAACAAATCTTTAAATCTTATGTGGCTGAGATTTGGGTAGA
* *
254094 TGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATTATACAAAATCTGAGCTGGGGCCCCGG
131 TGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAA-CTGAGCCGGGGCCCCGG
* *
254159 AACGCGATTTTAGTCGAAAACTGTGATGGTTAGCACACGATTTCGGTCAAGATTTTGCAAAAATT
195 AACGCGTTTTTAGTCGAAAACTGTGATGGTTAGCACACGATTTCGGTCAAGATTTTACAAAAATT
* *
254224 GACCCGAATGATTTTTCCTCAAATTTTGGCCCAAATAACTCATAAAAAAATATATAAATCTTCGC
260 GACCCGAATGATTTTTCCTCAAATTTTGGCCAAAAT-ACTCAT-AAAAAATATATAAATCATCGC
*
254289 C-AAAGGATTGA
323 CAAAAAGATTGA
* **
254300 AGGGTTTTTAACGCTAAGAATATCGTTTTTCC-AATGCTTTTCCGAATTAATTTCCAATTAAATC
1 AGGGTTTTTCACGCTTCGAATATCGTTTTTCCTAATGCTTTTCCGAATTAATTTCCAATTAAATC
* * * *
254364 GAAACTGGATT-TTATGCTCGTAAAAACAAATCTTTAAATCCTATGTGGCTGAGATTTGTGTAGA
66 GAAACTGGATTCTGATGTTCGTAAAAACAAATCTTTAAATCTTATGTGGCTGAGATTTGGGTAGA
** * * * * *
254428 TGAATATAGGCATTCAAAGGATTCTTGGCGCAAAAAATCACACAAAACTGAGCCGGGGCCGCGGA
131 TGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAACTGAGCCGGGGCCCCGGA
* * *
254493 ACGCGTTTTTAGCTGAAAAGTGAAAACTGTGATGGTTAGCACACGATTTGGGTCAAGATTTTGCA
196 ACGCGTTTTTAG-T------CGAAAACTGTGATGGTTAGCACACGATTTCGGTCAAGATTTTACA
* * *
254558 AAAATTAACCCTAATGATTTTTCCTCAAATTTTGGCCAAAATACTCATAAAAAATATATAAGTCA
254 AAAATTGACCCGAATGATTTTTCCTCAAATTTTGGCCAAAATACTCATAAAAAATATATAAATCA
*
254623 TCGCCAAAAAGTTTGA
319 TCGCCAAAAAGATTGA
* * * * * * *
254639 AGGATTTTTCACGCTTTGATTATCGTTTTT-CTAATGTTTTTACGAATTAATTTCCAATGAAATT
1 AGGGTTTTTCACGCTTCGAATATCGTTTTTCCTAATGCTTTTCCGAATTAATTTCCAATTAAATC
* * *
254703 GAAACTGGATTCTGATGTTCGTAAAAATAAATCTTTAAATCTTATGTGGTTGAGATTTGGGTTGA
66 GAAACTGGATTCTGATGTTCGTAAAAACAAATCTTTAAATCTTATGTGGCTGAGATTTGGGTAGA
* * * * *
254768 TGAATATAGATATTCCAAGGAGTCTCGGTGCCAAAAATCATACAAAACAGAGTCGGGGCCTCGGA
131 TGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAACTGAGCCGGGGCCCCGGA
* * * *
254833 ACGCGTTTTTAGCCGAAAACTGTGA-GGAAAAATCATACAAGAATACGATTTCGGTTAAGATTTT
196 ACGCGTTTTTAGTCGAAAACTGTGATGG-----T--T---AGCACACGATTTCGGTCAAGATTTT
* * * * *
254897 GCAAAACTTGACCCGATTGATTTTTCCTCAAATTTTGGCCAAAATACTAATAAAAGATATATAAA
251 ACAAAAATTGACCCGAATGATTTTTCCTCAAATTTTGGCCAAAATACTCATAAAAAATATATAAA
*
254962 TCATCGCCAAAAATATTGA
316 TCATCGCCAAAAAGATTGA
* * *
254981 AGGGGTTTTCACGCTTCGAA-AGTCGTTTTTCCT-ATGCTTTTTCGAATTAATTTTCAATTAAAT
1 AGGGTTTTTCACGCTTCGAATA-TCGTTTTTCCTAATGCTTTTCCGAATTAATTTCCAATTAAAT
* *
255044 CGAAACAGGATTCTGATGTTCGTAAAAACAAATCTTTAAATATTATGTGGCTGAGATTTGGGTAG
65 CGAAACTGGATTCTGATGTTCGTAAAAACAAATCTTTAAATCTTATGTGGCTGAGATTTGGGTAG
* * * * *
255109 ATCAATATATATATTCCAAGGAGTCTTGGCGCCAAGAATCATATAAAACTGAACCGGGGCCCCGG
130 ATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAACTGAGCCGGGGCCCCGG
* * *
255174 AATGCGCTTTTAGTCGAAAACTGTGATGGTTAGCACCCGATTTCGGTCAAGATTTTACAAAAATT
195 AACGCGTTTTTAGTCGAAAACTGTGATGGTTAGCACACGATTTCGGTCAAGATTTTACAAAAATT
* *
255239 GATCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAA-ATATAAATCATCGCCA
260 GACCCGAATGATTTTTCCTCAAATTTTGGCCAAAATACTCATAAAAAATATATAAATCATCGCCA
255303 AAAAGATTGA
325 AAAAGATTGA
* *
255313 A-GGTTTTTCACGATTTGAATA
1 AGGGTTTTTCACGCTTCGAATA
255334 ACGCGTTTTT
Statistics
Matches: 1498, Mismatches: 168, Indels: 74
0.86 0.10 0.04
Matches are distributed among these distances:
331 16 0.01
332 189 0.13
333 208 0.14
334 287 0.19
335 194 0.13
336 20 0.01
337 1 0.00
338 22 0.01
339 79 0.05
340 194 0.13
341 1 0.00
342 283 0.19
343 4 0.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Consensus pattern (334 bp):
AGGGTTTTTCACGCTTCGAATATCGTTTTTCCTAATGCTTTTCCGAATTAATTTCCAATTAAATC
GAAACTGGATTCTGATGTTCGTAAAAACAAATCTTTAAATCTTATGTGGCTGAGATTTGGGTAGA
TGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAACTGAGCCGGGGCCCCGGA
ACGCGTTTTTAGTCGAAAACTGTGATGGTTAGCACACGATTTCGGTCAAGATTTTACAAAAATTG
ACCCGAATGATTTTTCCTCAAATTTTGGCCAAAATACTCATAAAAAATATATAAATCATCGCCAA
AAAGATTGA
Found at i:255502 original size:159 final size:159
Alignment explanation
Indices: 255202--255494 Score: 478
Period size: 159 Copynumber: 1.8 Consensus size: 159
255192 AACTGTGATG
*
255202 GTTAGCACCCGATTTCGGTCAAGATTTTACAAAAATTGATCCGAATGATTTTTCCTCAATTTTTG
1 GTTAGCACACGATTTCGGTCAAGATTTTACAAAAATTGATCCGAATGATTTTTCCTCAATTTTTG
* *
255267 GCCAAAATACTCATAAAAAAATATAAATCATCGCCAAAAAGATTGAAGGTTTTTCACGATTTGAA
66 GCCAAAATACTCATAAAAAAATATAAATCATCGCCAAAAAGATTGAAGGTTTTTAACGATTCGAA
255332 TAACGCGTTTTTAGCCAAAAATTGCGATC
131 TAACGCGTTTTTAGCCAAAAATTGCGATC
* *
255361 GTTAGCACACGATTTCGGTCGAGATTTTGCAAAAATTGATCCGAATGATTTTTCCTCAATTTTTG
1 GTTAGCACACGATTTCGGTCAAGATTTTACAAAAATTGATCCGAATGATTTTTCCTCAATTTTTG
* ** * *
255426 GCCAAAATACTCATAAAAGATATATAAATCATTTCTAAAAAGATTGAAGGGTTTTTAACGCTTCG
66 GCCAAAATACTCATAAAA-AAATATAAATCATCGCCAAAAAGATTGAA-GGTTTTTAACGATTCG
255491 AATA
129 AATA
255495 TCGTTTTTCC
Statistics
Matches: 122, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
159 80 0.66
160 25 0.20
161 17 0.14
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (159 bp):
GTTAGCACACGATTTCGGTCAAGATTTTACAAAAATTGATCCGAATGATTTTTCCTCAATTTTTG
GCCAAAATACTCATAAAAAAATATAAATCATCGCCAAAAAGATTGAAGGTTTTTAACGATTCGAA
TAACGCGTTTTTAGCCAAAAATTGCGATC
Found at i:255801 original size:492 final size:493
Alignment explanation
Indices: 254877--255826 Score: 1636
Period size: 492 Copynumber: 1.9 Consensus size: 493
254867 ATACAAGAAT
* * *
254877 ACGATTTCGGTTAAGATTTTGCAAAACTTGACCCGATTGATTTTTCCTCAAATTTTGGCCAAAAT
1 ACGATTTCGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTCAAATTTTGGCCAAAAT
* *
254942 ACTAATAAAAGATATATAAATCATCGCCAAAAATATTGAAGGGGTTTTCACGCTTCGAAAGTCGT
66 ACTAATAAAAGATATATAAATCATCGCCAAAAAGATTGAAGGGGTTTTAACGCTTCGAAAGTCGT
* * *
255007 TTTTCCTATGCTTTTTCGAATTAATTTTCAATTAAATCGAAACAGGATTCTGATGTTCGTAAAAA
131 TTTTCCTATGCTTTTTCGAATTAATTTCCAATTAAATCGAAACAGGAATCTGATGCTCGTAAAAA
255072 CAAATCTTTAAATATTATGTGGCTGAGATTTGGGTAGATCAATATATATATTCCAAGGAGTCTTG
196 CAAATCTTTAAATATTATGTGGCTGAGATTTGGGTAGATCAATATATATATTCCAAGGAGTCTTG
* *
255137 GCGCCAAGAATCATATAAAACTGAACCGGGGCCCCGGAATGCGCTTTTAGTCGAAAACTGTGATG
261 GCGCCAAAAATCATATAAAACTGAACCGGGGCCCCGGAACGCGCTTTTAGTCGAAAACTGTGATG
* * *
255202 GTTAGCACCCGATTTCGGTCAAGATTTTACAAAAATTGATCCGAATGATTTTTCCTCAATTTTTG
326 GTTAGCACACGATATCGGTCAAGATTTTACAAAAATTGACCCGAATGATTTTTCCTCAATTTTTG
255267 GCCAAAATACTCATAAAAAAATATAAATCATCGCCAAAAAGATTGAA-GGTTTTTCACGATTTGA
391 GCCAAAATACTCATAAAAAAATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGATTTGA
255331 ATAACGCGTTTTTAGCCAAAAATTGCGATCGTTAGCAC
456 ATAACGCGTTTTTAGCCAAAAATTGCGATCGTTAGCAC
* * *
255369 ACGATTTCGGTCGAGATTTTGCAAAAATTGATCCGAATGATTTTTCCTCAATTTTTGGCCAAAAT
1 ACGATTTCGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTCAAATTTTGGCCAAAAT
* ** * *
255434 ACTCATAAAAGATATATAAATCATTTCTAAAAAGATTGAAGGGTTTTTAACGCTTCGAATA-TCG
66 ACTAATAAAAGATATATAAATCATCGCCAAAAAGATTGAAGGGGTTTTAACGCTTCGAA-AGTCG
* *
255498 TTTTTCCTATGC-TTTTCTGAATTAATTTCCAATTAAATCGACACTGGAATCTGATGCTCGTAAA
130 TTTTTCCTATGCTTTTTC-GAATTAATTTCCAATTAAATCGAAACAGGAATCTGATGCTCGTAAA
255562 AACAAATCTTTAAATATTATGTGGCTGAGATTTGGGTAGATCAATATATATATTCCAAGGAGTCT
194 AACAAATCTTTAAATATTATGTGGCTGAGATTTGGGTAGATCAATATATATATTCCAAGGAGTCT
255627 TGGCGCCAAAAATCATATAAAACTGAACCGGGGCCCCGGAACGCGCTTTTAGTCGAAAACTGTGA
259 TGGCGCCAAAAATCATATAAAACTGAACCGGGGCCCCGGAACGCGCTTTTAGTCGAAAACTGTGA
255692 TGGTTAGCACACGATATCGGTCAAGATTTTACAAAAATTGACCCGAATGATTTTTCCTCAATTTT
324 TGGTTAGCACACGATATCGGTCAAGATTTTACAAAAATTGACCCGAATGATTTTTCCTCAATTTT
* *
255757 TGGCCAAAATACTCATAAAAATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGCTTT
389 TGGCCAAAATACTCATAAAAAAATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGATTT
255822 GAATA
454 GAATA
255827 CCCATTTTCC
Statistics
Matches: 430, Mismatches: 25, Indels: 5
0.93 0.05 0.01
Matches are distributed among these distances:
491 5 0.01
492 405 0.94
493 20 0.05
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (493 bp):
ACGATTTCGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTCAAATTTTGGCCAAAAT
ACTAATAAAAGATATATAAATCATCGCCAAAAAGATTGAAGGGGTTTTAACGCTTCGAAAGTCGT
TTTTCCTATGCTTTTTCGAATTAATTTCCAATTAAATCGAAACAGGAATCTGATGCTCGTAAAAA
CAAATCTTTAAATATTATGTGGCTGAGATTTGGGTAGATCAATATATATATTCCAAGGAGTCTTG
GCGCCAAAAATCATATAAAACTGAACCGGGGCCCCGGAACGCGCTTTTAGTCGAAAACTGTGATG
GTTAGCACACGATATCGGTCAAGATTTTACAAAAATTGACCCGAATGATTTTTCCTCAATTTTTG
GCCAAAATACTCATAAAAAAATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGATTTGA
ATAACGCGTTTTTAGCCAAAAATTGCGATCGTTAGCAC
Found at i:255904 original size:332 final size:331
Alignment explanation
Indices: 255333--256114 Score: 1066
Period size: 332 Copynumber: 2.3 Consensus size: 331
255323 CGATTTGAAT
* * * *
255333 AACGCGTTTTTAGCCAAAAATTGCGATCGTTAGCACACGATTTCGGTCGAGATTTTGCAAAAATT
1 AACGCGTTTTTAGACAAAAAATGTGATCGTTAGCACACGA-TTCGGTCAAGATTTTGCAAAAATT
* ** *
255398 GATCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAGATATATAAATCATTTCTA
65 GACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAA-ATATATAAATCATCGCCA
* ** **
255463 AAAAGATTGAAGGGTTTTTAACGCTTCGAATATCGTTTTTCCTATGCTTTTCTGAATTAATTTCC
129 AAAAGATTGAAGGGTTTTTAACGCTTCGAATACCCATTTTCCTATGCTTTTCCAAATTAATTTCC
*
255528 AATTAAATCGACACTGGAATCTGATGCTCGTAAAAACAAATCTTTAAATATTATGTGGCTGAGAT
194 AATTAAATCGAAACTGGAATCTGATGCTCGTAAAAACAAATCTTTAAATATTATGTGGCTGAGAT
* * * *
255593 TTGGGTAGATCAATATATATATTCCAAGGAGTCTTGGCGCCAAAAATCATATAAAACTGAACC-G
259 TTGGGTAGATCAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAATCACACAAAACTG-ACCTG
255657 GGGCCCCGG
323 GGGCCCCGG
* * * * * *
255666 AACGCGCTTTTAGTCGAAAACTGTGATGGTTAGCACACGATATCGGTCAAGATTTTACAAAAATT
1 AACGCGTTTTTAGACAAAAAATGTGATCGTTAGCACACGAT-TCGGTCAAGATTTTGCAAAAATT
255731 GACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAATATATAAATCATCGCCAA
65 GACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAATATATAAATCATCGCCAA
* *
255796 AAAGATTGAAGGGTTTTTCACGCTTTGAATACCCATTTTCCTATGCTTTTCCAAATTAATTTCCA
130 AAAGATTGAAGGGTTTTTAACGCTTCGAATACCCATTTTCCTATGCTTTTCCAAATTAATTTCCA
* *
255861 ATTAAATCGAAA-TCGG-ATTTCGATGCTCGTAAAAACAAATCTTTAAATTTTATGTGGCTGAGA
195 ATTAAATCGAAACT-GGAATCT-GATGCTCGTAAAAACAAATCTTTAAATATTATGTGGCTGAGA
* * *
255924 TTTGGGTAGATGAATATAGATATTCAAAGGATTCTTGGTGCCAAAAATCACACAAAACTGACCTG
258 TTTGGGTAGATCAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAATCACACAAAACTGACCTG
*
255989 GGGCCTCGG
323 GGGCCCCGG
* * * * * * * *
255998 AACGTGTTTTTAGGAAAAAAAATCGTGATTGTTAGTAGACGACTCCGGTTAATATTTTGCAAAAA
1 AACGCGTTTTTA-GACAAAAAAT-GTGATCGTTAGCACACGA-TTCGGTCAAGATTTTGCAAAAA
* ** *
256063 CTGACCCGAAAAATTTTTCCTCAAATTTTGGCCAAAATACTCATAAAAATAT
63 TTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAATAT
256115 TTGCATATAG
Statistics
Matches: 395, Mismatches: 47, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
331 7 0.02
332 201 0.51
333 106 0.27
334 80 0.20
335 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (331 bp):
AACGCGTTTTTAGACAAAAAATGTGATCGTTAGCACACGATTCGGTCAAGATTTTGCAAAAATTG
ACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAATATATAAATCATCGCCAAA
AAGATTGAAGGGTTTTTAACGCTTCGAATACCCATTTTCCTATGCTTTTCCAAATTAATTTCCAA
TTAAATCGAAACTGGAATCTGATGCTCGTAAAAACAAATCTTTAAATATTATGTGGCTGAGATTT
GGGTAGATCAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAATCACACAAAACTGACCTGGGG
CCCCGG
Found at i:256261 original size:180 final size:182
Alignment explanation
Indices: 255937--256291 Score: 466
Period size: 180 Copynumber: 2.0 Consensus size: 182
255927 GGGTAGATGA
* * * *
255937 ATATAGATATTCAAAGGATTCTTGGTGCCAAAAATCACACAAAACTGACCTGGGGCCTCGGAACG
1 ATATAGATATTCAAAGGAGTCTTGGCGCCAAAAATCACACAAAACTAACCTGGGACCTCGGAACG
* * * * *
256002 TGTTTTTAGGAAAAAAAATCGTGATTGTTAGTAGACGACTCCGGTTAATATTTTGCAAAAACTGA
66 AGTTTTTAGGAAAAAAAATCGTGATTGTTAGCACACGACTCCGGTCAAGATTTTGCAAAAACTGA
256067 CCCGAAAAATTTTTCCTCAAATTTTGGCCAAAATACTCATAAAAATATTTGC
131 CCCGAAAAATTTTTCCTCAAATTTTGGCCAAAATACTCATAAAAATATTTGC
* * * *
256119 ATATAGATATTCCAAGTAGTCTTGGCGCCAAAAATCATACAAAACTAAGCC-GGGATCTCGGAAC
1 ATATAGATATTCAAAGGAGTCTTGGCGCCAAAAATCACACAAAACTAA-CCTGGGACCTCGGAAC
*** * * * *
256183 GCAG-TTTTA-GCTGAAAACT-GTGATTGTTAGCACACGATTTCGGTCAAGATTTTGCAAAAATT
65 G-AGTTTTTAGGAAAAAAAATCGTGATTGTTAGCACACGACTCCGGTCAAGATTTTGCAAAAACT
**
256245 GACCCGAATGATTTTTCCTCAAATTTTGGCCAAAATACTCATAAAAA
129 GACCCGAAAAATTTTTCCTCAAATTTTGGCCAAAATACTCATAAAAA
256292 ATATATAAAT
Statistics
Matches: 149, Mismatches: 22, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
180 81 0.54
181 6 0.04
182 59 0.40
183 3 0.02
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (182 bp):
ATATAGATATTCAAAGGAGTCTTGGCGCCAAAAATCACACAAAACTAACCTGGGACCTCGGAACG
AGTTTTTAGGAAAAAAAATCGTGATTGTTAGCACACGACTCCGGTCAAGATTTTGCAAAAACTGA
CCCGAAAAATTTTTCCTCAAATTTTGGCCAAAATACTCATAAAAATATTTGC
Done.