Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007841.1 Hibiscus syriacus cultivar Beakdansim tig00110195_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1873963
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1473045 original size:32 final size:31
Alignment explanation
Indices: 1472955--1473055 Score: 105
Period size: 31 Copynumber: 3.2 Consensus size: 31
1472945 CTTTGATAAA
* ** * *
1472955 TTTATAATAATTGAATAAGCTTGATAAACAT
1 TTTATAATAATTCAATAAATTTAATAATCAT
* *
1472986 TTTATAATAATTCGATAAATTTGATAATCAT
1 TTTATAATAATTCAATAAATTTAATAATCAT
*
1473017 TTTATAA-AATTTTAATATAATTTAATAATCAT
1 TTTATAATAA-TTCAATA-AATTTAATAATCAT
1473049 TTTATAA
1 TTTATAA
1473056 CCATCATTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
30 2 0.03
31 38 0.63
32 20 0.33
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.46
Consensus pattern (31 bp):
TTTATAATAATTCAATAAATTTAATAATCAT
Found at i:1477749 original size:30 final size:30
Alignment explanation
Indices: 1477713--1477770 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1477703 GTAGGACACA
*
1477713 CCCATCACAGTATTCCTCCATGAGATTGGC
1 CCCATCACAATATTCCTCCATGAGATTGGC
* *
1477743 CCCATCACAATGTTCCTCCATGGGATTG
1 CCCATCACAATATTCCTCCATGAGATTG
1477771 ACCTTTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.22, C:0.33, G:0.17, T:0.28
Consensus pattern (30 bp):
CCCATCACAATATTCCTCCATGAGATTGGC
Found at i:1479891 original size:3 final size:3
Alignment explanation
Indices: 1479885--1480024 Score: 181
Period size: 3 Copynumber: 46.7 Consensus size: 3
1479875 TTTTTATCCA
* ** *
1479885 TAT TAT TAT TAT TAA TAT TAT TAT TAT CCT TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
** * ** *
1479933 TAT TAT CCT TAT TAT TAT TAA TAT TAT TAT TAT CCT TAT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1479981 TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1480025 ATTTATATTA
Statistics
Matches: 115, Mismatches: 22, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 115 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1479917 original size:27 final size:27
Alignment explanation
Indices: 1479887--1480019 Score: 248
Period size: 27 Copynumber: 4.9 Consensus size: 27
1479877 TTTATCCATA
1479887 TTATTATTATTAATATTATTATTATCC
1 TTATTATTATTAATATTATTATTATCC
1479914 TTATTATTATTAATATTATTATTATCC
1 TTATTATTATTAATATTATTATTATCC
1479941 TTATTATTATTAATATTATTATTATCC
1 TTATTATTATTAATATTATTATTATCC
*
1479968 TTATTATTATTAATATTATTATTATCA
1 TTATTATTATTAATATTATTATTATCC
*
1479995 TTATTATTATTATTATTATTATTAT
1 TTATTATTATTAATATTATTATTAT
1480020 TATTAATTTA
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 104 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (27 bp):
TTATTATTATTAATATTATTATTATCC
Found at i:1492821 original size:5 final size:5
Alignment explanation
Indices: 1492805--1492888 Score: 66
Period size: 5 Copynumber: 16.2 Consensus size: 5
1492795 ATTATGCTTG
*
1492805 AAGAA AAAAA AAGAAA AAGAA AAG-A AAGAA AAGAAAA AAGAA AAGAA
1 AAGAA AAGAA AAG-AA AAGAA AAGAA AAGAA AAG--AA AAGAA AAGAA
* *
1492852 AAAAA ATAGAA AATG-A AA-AA AAGAG AAGAAA AAGAA A
1 AAGAA A-AGAA AA-GAA AAGAA AAGAA AAG-AA AAGAA A
1492889 GGGGGTCAAG
Statistics
Matches: 64, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
4 7 0.11
5 38 0.59
6 14 0.22
7 5 0.08
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (5 bp):
AAGAA
Found at i:1492832 original size:9 final size:9
Alignment explanation
Indices: 1492820--1492889 Score: 56
Period size: 9 Copynumber: 7.4 Consensus size: 9
1492810 AAAAAAAGAA
1492820 AAAGAAAAG
1 AAAGAAAAG
1492829 AAAGAAAAG
1 AAAGAAAAG
1492838 AAAAAAGAAAAG
1 ---AAAGAAAAG
1492850 AAA-AAAA-
1 AAAGAAAAG
*
1492857 ATAGAAAATG
1 AAAGAAAA-G
1492867 AAA-AAAAG
1 AAAGAAAAG
1492875 AGAAGAAAAAG
1 A-AAG-AAAAG
1492886 AAAG
1 AAAG
1492890 GGGGTCAAGG
Statistics
Matches: 50, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
7 2 0.04
8 10 0.20
9 18 0.36
10 5 0.10
11 6 0.12
12 9 0.18
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.03
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:1492847 original size:37 final size:37
Alignment explanation
Indices: 1492805--1492888 Score: 102
Period size: 37 Copynumber: 2.3 Consensus size: 37
1492795 ATTATGCTTG
1492805 AAGAAAA-AAAAAGAAAAAGAAAA-GAAAGAAAAGAAAA
1 AAGAAAAGAAAAA-AAAAAGAAAATGAAA-AAAAGAAAA
* *
1492842 AAGAAAAGAAAAAAAATAGAAAATGAAAAAAAGAGAA
1 AAGAAAAGAAAAAAAAAAGAAAATGAAAAAAAGAAAA
*
1492879 GA-AAAAGAAA
1 AAGAAAAGAAA
1492889 GGGGGTCAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
36 8 0.19
37 25 0.60
38 9 0.21
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (37 bp):
AAGAAAAGAAAAAAAAAAGAAAATGAAAAAAAGAAAA
Found at i:1492851 original size:42 final size:41
Alignment explanation
Indices: 1492805--1492888 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 41
1492795 ATTATGCTTG
1492805 AAGAAAAAAAA-AGAAAAAGAAAAGAAAGAAAAGAAAAAAGAA
1 AAGAAAAAAAATAGAAAAAGAAAA-AAAGAAAAG-AAAAAGAA
* *
1492847 AAGAAAAAAAATAGAAAATGAAAAAAAGAGAAGAAAAAGAA
1 AAGAAAAAAAATAGAAAAAGAAAAAAAGAAAAGAAAAAGAA
1492888 A
1 A
1492889 GGGGGTCAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
41 9 0.23
42 19 0.49
43 11 0.28
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (41 bp):
AAGAAAAAAAATAGAAAAAGAAAAAAAGAAAAGAAAAAGAA
Found at i:1494914 original size:113 final size:113
Alignment explanation
Indices: 1494716--1495376 Score: 1040
Period size: 113 Copynumber: 5.8 Consensus size: 113
1494706 TAGCAAAGAT
* *
1494716 TTGAATCCATCATTTGATGGAACAGA-TTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTG
1 TTGAATCCATCATTTGATGGATCA-ACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
1494780 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
** *
1494829 TTGAATCTGTCATTTGATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1494894 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
* *
1494942 TTGAATCCGTCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * * **
1495007 AGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
* * * * *
1495055 TTAAATTCATCATTTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
1495120 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTAC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
* * * *
1495168 CTGAATCCATCATTTGGTGAATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
1495233 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
* * *
1495281 TTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTG
1 TTGAATCCATCATTTGATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG
1495345 AAGAAGGAAG-AGAAAGTTCATAATGAGAAGAA
65 AAGAAGGAAGAAG-AAGTTCATAATGAGAAGAA
1495377 CTCATCAAGA
Statistics
Matches: 501, Mismatches: 44, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
112 4 0.01
113 497 0.99
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (113 bp):
TTGAATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
Found at i:1495635 original size:3 final size:3
Alignment explanation
Indices: 1495629--1495772 Score: 159
Period size: 3 Copynumber: 48.7 Consensus size: 3
1495619 TTTTTATCCA
* ** *
1495629 TAT TAT TAT TAT TAA TAT TAT TAT TAT CCT TAT TAT TAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
** * ** *
1495677 TAT CCT TAT TAT TAT TAA TAT TAT TAT CCT TAT TAT TAT TA- AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1495724 TAT TAT CAT TAT TAT TAT TAT TAT T-T TAT TAT TAT TAT TAAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT
1495768 TAT TA
1 TAT TA
1495773 AATATATTAA
Statistics
Matches: 115, Mismatches: 22, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
2 5 0.04
3 107 0.93
4 3 0.03
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:1500017 original size:21 final size:21
Alignment explanation
Indices: 1499991--1500030 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1499981 AATTGAACGT
*
1499991 TAAATGATGATAAATAAAAAA
1 TAAATGAAGATAAATAAAAAA
*
1500012 TAAATGAAGGTAAATAAAA
1 TAAATGAAGATAAATAAAA
1500031 TATGCATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (21 bp):
TAAATGAAGATAAATAAAAAA
Found at i:1503927 original size:63 final size:63
Alignment explanation
Indices: 1503852--1504045 Score: 159
Period size: 63 Copynumber: 3.2 Consensus size: 63
1503842 TTTAATTTGG
1503852 AAATATTTTCAACTTTGTTCTTAAATTTTGTATCCATAGACAATATTAGCCCATGAACTTATC
1 AAATATTTTCAACTTTGTTCTTAAATTTTGTATCCATAGACAATATTAGCCCATGAACTTATC
* * * * * **
1503915 AAAT-TTTCTCAACTTAGTCCTT---TTTT-T-T--TTTG--AA-ATCAGCTTATTTG-A-TTA-
1 AAATATTT-TCAACTTTGTTCTTAAATTTTGTATCCATAGACAATATTAGCCCA--TGAACTTAT
1503966 -
63 C
1503966 AAATGGATTTTCAACTTTGTTCTTAAATTTTGTATCCATAGACAATATTAGCCCATGAACTTATC
1 AAAT--ATTTTCAACTTTGTTCTTAAATTTTGTATCCATAGACAATATTAGCCCATGAACTTATC
1504031 AAAT-TTTCTCAACTT
1 AAATATTT-TCAACTT
1504046 AGTCCTTTTT
Statistics
Matches: 96, Mismatches: 14, Indels: 42
0.63 0.09 0.28
Matches are distributed among these distances:
51 4 0.04
53 21 0.22
54 6 0.06
55 2 0.02
56 6 0.06
57 1 0.01
58 2 0.02
59 1 0.01
60 6 0.06
61 2 0.02
62 9 0.09
63 32 0.33
65 4 0.04
ACGTcount: A:0.31, C:0.16, G:0.08, T:0.44
Consensus pattern (63 bp):
AAATATTTTCAACTTTGTTCTTAAATTTTGTATCCATAGACAATATTAGCCCATGAACTTATC
Found at i:1504006 original size:116 final size:115
Alignment explanation
Indices: 1503856--1504087 Score: 455
Period size: 116 Copynumber: 2.0 Consensus size: 115
1503846 ATTTGGAAAT
1503856 ATTTTCAACTTTGTTCTTAAATTTTGTATCCATAGACAATATTAGCCCATGAACTTATCAAATTT
1 ATTTTCAACTTTGTTCTTAAATTTTGTATCCATAGACAATATTAGCCCATGAACTTATCAAATTT
1503921 TCTCAACTTAGTCCTTTTTTTTTTTGAAATCAGCTTATTTGATTAAAATGG
66 TCTCAACTTAGTCC-TTTTTTTTTTGAAATCAGCTTATTTGATTAAAATGG
1503972 ATTTTCAACTTTGTTCTTAAATTTTGTATCCATAGACAATATTAGCCCATGAACTTATCAAATTT
1 ATTTTCAACTTTGTTCTTAAATTTTGTATCCATAGACAATATTAGCCCATGAACTTATCAAATTT
1504037 TCTCAACTTAGTCCTTTTTTTTTTGAAATCAGCTTATTTGATTAAAATGG
66 TCTCAACTTAGTCCTTTTTTTTTTGAAATCAGCTTATTTGATTAAAATGG
1504087 A
1 A
1504088 CTTGCACCAT
Statistics
Matches: 116, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
115 37 0.32
116 79 0.68
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.45
Consensus pattern (115 bp):
ATTTTCAACTTTGTTCTTAAATTTTGTATCCATAGACAATATTAGCCCATGAACTTATCAAATTT
TCTCAACTTAGTCCTTTTTTTTTTGAAATCAGCTTATTTGATTAAAATGG
Found at i:1505921 original size:17 final size:17
Alignment explanation
Indices: 1505895--1505927 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1505885 TTAAGCGAGT
1505895 TTTGTAAAAA-AAATAA
1 TTTGTAAAAAGAAATAA
1505911 TTTGATAAAAAGAAATA
1 TTTG-TAAAAAGAAATA
1505928 GGGTGAAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (17 bp):
TTTGTAAAAAGAAATAA
Found at i:1506157 original size:17 final size:17
Alignment explanation
Indices: 1506131--1506163 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1506121 TTAAGCGAGT
1506131 TTTGTAAAAA-AAATAA
1 TTTGTAAAAAGAAATAA
1506147 TTTGATAAAAAGAAATA
1 TTTG-TAAAAAGAAATA
1506164 GGGTGAAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (17 bp):
TTTGTAAAAAGAAATAA
Found at i:1506220 original size:236 final size:237
Alignment explanation
Indices: 1505806--1506278 Score: 939
Period size: 236 Copynumber: 2.0 Consensus size: 237
1505796 TAAGAATAAC
1505806 ATACTTAAAAAATTAGTCTCATCAGAATGCAGTCAGAGGAATCGAAGCATTTAAAACTTTAAATG
1 ATACTTAAAAAATTAGTCTCATCAGAATGCAGTCAGAGGAATCGAAGCATTTAAAACTTTAAATG
1505871 GATATTCGTCTATTTTAAGCGAGTTTTGTAAAAAAAATAATTTGATAAAAAGAAATAGGGTGAAA
66 GATATTCGTCTATTTTAAGCGAGTTTTGTAAAAAAAATAATTTGATAAAAAGAAATAGGGTGAAA
1505936 CGCGAATGTTTGCTATCGATTTGTAGGGAAATGAGGAAGAAAACGCAAAATAAAGTTCAGTACTA
131 CGCGAATGTTTGCTATCGATTTGTAGGGAAATGAGGAAGAAAACGCAAAATAAAGTTCAGTACTA
1506001 AAGTTGAAGAGTTTTAAAGTTCAATGGTAAAATCAACATATA
196 AAGTTGAAGAGTTTTAAAGTTCAATGGTAAAATCAACATATA
1506043 ATACTTAAAAAATTAGT-TCATCAGAATGCAGTCAGAGGAATCGAAGCATTTAAAACTTTAAATG
1 ATACTTAAAAAATTAGTCTCATCAGAATGCAGTCAGAGGAATCGAAGCATTTAAAACTTTAAATG
1506107 GATATTCGTCTATTTTAAGCGAGTTTTGTAAAAAAAATAATTTGATAAAAAGAAATAGGGTGAAA
66 GATATTCGTCTATTTTAAGCGAGTTTTGTAAAAAAAATAATTTGATAAAAAGAAATAGGGTGAAA
1506172 CGCGAATGTTTGCTATCGATTTGTAGGGAAATGAGGAAGAAAACGCAAAATAAAGTTCAGTACTA
131 CGCGAATGTTTGCTATCGATTTGTAGGGAAATGAGGAAGAAAACGCAAAATAAAGTTCAGTACTA
1506237 AAGTTGAAGAGTTTTAAAGTTCAATGGTAAAATCAACATATA
196 AAGTTGAAGAGTTTTAAAGTTCAATGGTAAAATCAACATATA
1506279 TTTAAAGTTT
Statistics
Matches: 236, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
236 219 0.93
237 17 0.07
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (237 bp):
ATACTTAAAAAATTAGTCTCATCAGAATGCAGTCAGAGGAATCGAAGCATTTAAAACTTTAAATG
GATATTCGTCTATTTTAAGCGAGTTTTGTAAAAAAAATAATTTGATAAAAAGAAATAGGGTGAAA
CGCGAATGTTTGCTATCGATTTGTAGGGAAATGAGGAAGAAAACGCAAAATAAAGTTCAGTACTA
AAGTTGAAGAGTTTTAAAGTTCAATGGTAAAATCAACATATA
Found at i:1512054 original size:50 final size:50
Alignment explanation
Indices: 1511943--1512060 Score: 139
Period size: 50 Copynumber: 2.4 Consensus size: 50
1511933 CGCGTGCGCT
* *
1511943 CAAACAAACACACACACAATCGACCTAACCCAATCCGACACGCGCGCAAA
1 CAAACAAACACACACACAATCGACCTAACCCAATCCGACACGCACACAAA
* * * * * **
1511993 CAAA-AACACACACATACAATCGGCCTGATCTAATCCGACACGCACACATG
1 CAAACAA-ACACACACACAATCGACCTAACCCAATCCGACACGCACACAAA
1512043 CAAACAAACACACACACA
1 CAAACAAACACACACACA
1512061 CACACATATA
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
49 2 0.04
50 52 0.93
51 2 0.04
ACGTcount: A:0.45, C:0.37, G:0.09, T:0.08
Consensus pattern (50 bp):
CAAACAAACACACACACAATCGACCTAACCCAATCCGACACGCACACAAA
Found at i:1512071 original size:2 final size:2
Alignment explanation
Indices: 1512066--1512091 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1512056 ACACACACAC
1512066 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
1512092 GACTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1522599 original size:59 final size:60
Alignment explanation
Indices: 1522477--1522602 Score: 173
Period size: 59 Copynumber: 2.1 Consensus size: 60
1522467 TAGTATGATG
*
1522477 ACCATTTTATAACTTTTAATAGTCAATGAATTCAACAAAGCAACATCATATAGCCAGAGA
1 ACCATTTTATAACTTTTAATAGTCAATGAACTCAACAAAGCAACATCATATAGCCAGAGA
* * ** * * *
1522537 ACCATTTTGTAACTTTTAATAGTCAGTG-ACTCAACAAAGCAGTATCCTATAGCCGGTGA
1 ACCATTTTATAACTTTTAATAGTCAATGAACTCAACAAAGCAACATCATATAGCCAGAGA
1522596 ACCATTT
1 ACCATTT
1522603 GTGTGCTTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
59 32 0.55
60 26 0.45
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (60 bp):
ACCATTTTATAACTTTTAATAGTCAATGAACTCAACAAAGCAACATCATATAGCCAGAGA
Found at i:1524476 original size:7 final size:7
Alignment explanation
Indices: 1524464--1524488 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1524454 ATATTAAAAT
1524464 TTCATAA
1 TTCATAA
1524471 TTCATAA
1 TTCATAA
1524478 TTCATAA
1 TTCATAA
1524485 TTCA
1 TTCA
1524489 CTCACATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (7 bp):
TTCATAA
Found at i:1528617 original size:2 final size:2
Alignment explanation
Indices: 1528610--1528666 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
1528600 ATATGAAGAA
1528610 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1528652 AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT
1528667 GGTTAGAGAA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1530908 original size:17 final size:18
Alignment explanation
Indices: 1530880--1530913 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1530870 AATATATTTA
1530880 AAAACAATAAAATAAATT
1 AAAACAATAAAATAAATT
1530898 AAAAC-ATAAAATAAAT
1 AAAACAATAAAATAAAT
1530914 GACTAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAACAATAAAATAAATT
Found at i:1532156 original size:3 final size:3
Alignment explanation
Indices: 1532148--1532271 Score: 185
Period size: 3 Copynumber: 40.7 Consensus size: 3
1532138 TTATTTATTA
*
1532148 AAT AAT AAT AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT
* **
1532195 ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GCT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1532243 AAT ACT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1532272 AATGGATAAA
Statistics
Matches: 109, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
3 103 0.94
4 6 0.06
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1532763 original size:61 final size:62
Alignment explanation
Indices: 1532676--1532794 Score: 213
Period size: 61 Copynumber: 1.9 Consensus size: 62
1532666 TGATGAATTT
*
1532676 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATATC
1 AAACAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATATC
*
1532738 AAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
1 AAACAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
1532795 GTTCTTCTCA
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
61 51 0.93
62 4 0.07
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (62 bp):
AAACAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATATC
Found at i:1532809 original size:175 final size:175
Alignment explanation
Indices: 1532518--1532908 Score: 748
Period size: 175 Copynumber: 2.2 Consensus size: 175
1532508 ACTCTTGATG
*
1532518 AGTTCTTCTCATTATGAACTT-TCTCTTCTTTCTTCAGATGATATCAAACAAAGGTTGAACAAGC
1 AGTTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGATATCAAACAAAGGTTGAACAAGC
1532582 TCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTCATGAACTTTCTTTG
65 TCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTCATGAACTTTCTTTG
1532647 GCCATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
130 GCCATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
1532693 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATATCAAACAAAGGTTGAACAAGCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATATCAAACAAAGGTTGAACAAGCT
*
1532758 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTCATGAACTTTCTTTGG
66 CTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTCATGAACTTTCTTTGG
1532823 CCATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
131 CCATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
1532868 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
1532909 GTTCTTCTCA
Statistics
Matches: 213, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
175 212 1.00
176 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (175 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATATCAAACAAAGGTTGAACAAGCT
CTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTCATGAACTTTCTTTGG
CCATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
Found at i:1532996 original size:113 final size:113
Alignment explanation
Indices: 1532742--1533454 Score: 1246
Period size: 113 Copynumber: 6.3 Consensus size: 113
1532732 GATATCAAAC
*
1532742 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* ** * * * * * *
1532807 CATGAACTTTCTTTGGCCATGTTGATCCATCAAATGATGAATTTAAACA
66 -ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
*
1532856 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
1532921 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
*
1532969 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1533034 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
1533082 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1533147 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
1533195 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1533260 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
1533308 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* ** * *
1533373 ATGAACTTTCTCTGGAAAAGTTGATCCATTAAGTGATGAATTCAAGCA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
1533421 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
1533455 CTCTGGTAAT
Statistics
Matches: 576, Mismatches: 23, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
113 513 0.89
114 63 0.11
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (113 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
Found at i:1534123 original size:52 final size:52
Alignment explanation
Indices: 1534045--1534503 Score: 740
Period size: 52 Copynumber: 8.7 Consensus size: 52
1534035 CACTTCTTCG
* * * *
1534045 GATCAAATAACTCAAAGAACACTTCCAGAAAATGCTATGTTCTGTCCCATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
1534097 GATCAGATAACTCAAAGAACACTTCCAGAAGAAGATGCTATATTCTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCC---AGAAGATGCTATGTTCTGTCCAACCA
* *
1534152 GATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
1534204 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACCA
*
1534256 GATCAGATAACTCAAAGAAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
1534309 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
1534361 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
* *
1534413 GATCAGATAACTCAAAGAAACACTTCCCGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
1534466 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1534504 TGAGTCTTCT
Statistics
Matches: 380, Mismatches: 20, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
52 234 0.62
53 99 0.26
55 47 0.12
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (52 bp):
GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
Found at i:1534314 original size:105 final size:104
Alignment explanation
Indices: 1534045--1534503 Score: 740
Period size: 105 Copynumber: 4.4 Consensus size: 104
1534035 CACTTCTTCG
* * * *
1534045 GATCAAATAACTCAAAGAACACTTCCAGAAAATGCTATGTTCTGTCCCATCAGATCAGATAACTC
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTC
*
1534110 AAAGAACACTTCCAGAAGAAGATGCTATATTCTGTCCAACCA
66 AAAGAACACTTCC---AGAAGATGCTATGTTCTGTCCAACCA
* *
1534152 GATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTC
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTC
*
1534217 AAAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACCA
66 AAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACCA
*
1534256 GATCAGATAACTCAAAGAAACACTTCCAGAAGATGCTATGTTCTGTTCAACCAGATCAGATAACT
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACT
*
1534321 CAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
65 CAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
1534361 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCAGATCAGATAACTC
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTC
* *
1534426 AAAGAAACACTTCCCGAAGATGCTATGTTCTGTCCAATCA
66 AAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
1534466 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1534504 TGAGTCTTCT
Statistics
Matches: 336, Mismatches: 12, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
104 91 0.27
105 171 0.51
107 74 0.22
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (104 bp):
GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTC
AAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
Found at i:1534345 original size:157 final size:156
Alignment explanation
Indices: 1534045--1534503 Score: 767
Period size: 157 Copynumber: 2.9 Consensus size: 156
1534035 CACTTCTTCG
* * * *
1534045 GATCAAATAACTCAAAGAACACTTCCAGAAAATGCTATGTTCTGTCCCATCAGATCAGATAACTC
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGT-CAACCAGATCAGATAACTC
* *
1534110 AAAG-AACACTTCCAGAAGAAGATGCTATATTCTGTCCAACCAGATTAGATAACTCAAAGAACAC
65 AAAGAAACACTTCC---AGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1534174 TTCCAGAAGATGCTATGTTCTGTCCAATCA
127 TTCCAGAAGATGCTATGTTCTGTCCAATCA
*
1534204 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGATCAACCAGATCAGATAACTC
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCAACCAGATCAGATAACTC
*
1534269 AAAGAAACACTTCCAGAAGATGCTATGTTCTGTTCAACCAGATCAGATAACTCAAAGAACACTTC
65 AAAGAAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTC
1534334 CAGAAGATGCTATGTTCTGTCCAATCA
130 CAGAAGATGCTATGTTCTGTCCAATCA
1534361 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCAGATCAGATAACTC
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCAACCAGATCAGATAACTC
* *
1534426 AAAGAAACACTTCCCGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
65 AAAGAAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTC
1534491 CAGAAGATGCTAT
130 CAGAAGATGCTAT
1534504 TGAGTCTTCT
Statistics
Matches: 285, Mismatches: 13, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
157 213 0.75
159 62 0.22
160 10 0.04
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (156 bp):
GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCAACCAGATCAGATAACTCA
AAGAAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCC
AGAAGATGCTATGTTCTGTCCAATCA
Found at i:1535623 original size:1 final size:1
Alignment explanation
Indices: 1535617--1535668 Score: 68
Period size: 1 Copynumber: 52.0 Consensus size: 1
1535607 CTTGACCCTC
* * * *
1535617 TTTTTTTTCTTTTTCTTTTTTTTTCTTTTATTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1535669 CTTTCTTTCT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.02, C:0.06, G:0.00, T:0.92
Consensus pattern (1 bp):
T
Found at i:1535629 original size:9 final size:9
Alignment explanation
Indices: 1535615--1535707 Score: 93
Period size: 9 Copynumber: 10.4 Consensus size: 9
1535605 ACCTTGACCC
1535615 TCTTTTTTT
1 TCTTTTTTT
*
1535624 TC-TTTTTC
1 TCTTTTTTT
1535632 T-TTTTTTT
1 TCTTTTTTT
1535640 TCTTTTATTT
1 TCTTTT-TTT
*
1535650 TTTTTTTTT
1 TCTTTTTTT
*
1535659 TTTTTTTTT
1 TCTTTTTTT
*
1535668 TC-TTTCTT
1 TCTTTTTTT
*
1535676 TCTTTCTTT
1 TCTTTTTTT
1535685 TCTTTCTTTT
1 TCTTT-TTTT
*
1535695 TCTTTCTTT
1 TCTTTTTTT
1535704 TCTT
1 TCTT
1535708 CAAGCATAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
8 19 0.27
9 35 0.50
10 16 0.23
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.85
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:1535650 original size:27 final size:28
Alignment explanation
Indices: 1535618--1535704 Score: 115
Period size: 28 Copynumber: 3.1 Consensus size: 28
1535608 TTGACCCTCT
1535618 TTTTTTTCTTTTTCTTTTTTTTTCTTT-
1 TTTTTTTCTTTTTCTTTTTTTTTCTTTC
* *
1535645 TATTTTTTTTTTTTTTTTTTTTTTCTTTC
1 T-TTTTTTCTTTTTCTTTTTTTTTCTTTC
* *
1535674 TTTCTTTC-TTTTCTTTCTTTTTCTTTC
1 TTTTTTTCTTTTTCTTTTTTTTTCTTTC
1535701 TTTT
1 TTTT
1535705 CTTCAAGCAT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
27 21 0.41
28 29 0.57
29 1 0.02
ACGTcount: A:0.01, C:0.13, G:0.00, T:0.86
Consensus pattern (28 bp):
TTTTTTTCTTTTTCTTTTTTTTTCTTTC
Found at i:1535673 original size:4 final size:4
Alignment explanation
Indices: 1535628--1535703 Score: 54
Period size: 4 Copynumber: 19.8 Consensus size: 4
1535618 TTTTTTTCTT
* * * * *
1535628 TTTC TTT- TTT- TTTC TTT- TATTT TTTT TTTT TTTT TTTT TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTTC TTTC TTTC TTTC TTTC
1535674 TTTC TTTC TTTTC TTTC -TT- TTTC TTTC TTT
1 TTTC TTTC -TTTC TTTC TTTC TTTC TTTC TTT
1535704 TCTTCAAGCA
Statistics
Matches: 65, Mismatches: 1, Indels: 12
0.83 0.01 0.15
Matches are distributed among these distances:
3 11 0.17
4 49 0.75
5 5 0.08
ACGTcount: A:0.01, C:0.13, G:0.00, T:0.86
Consensus pattern (4 bp):
TTTC
Found at i:1546266 original size:12 final size:14
Alignment explanation
Indices: 1546249--1546281 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
1546239 TTTGACATAA
1546249 AAATAAATAC-TG-
1 AAATAAATACTTGC
1546261 AAATAAATACTTGC
1 AAATAAATACTTGC
1546275 AAATAAA
1 AAATAAA
1546282 CATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
13 2 0.11
14 7 0.37
ACGTcount: A:0.61, C:0.09, G:0.06, T:0.24
Consensus pattern (14 bp):
AAATAAATACTTGC
Found at i:1547085 original size:19 final size:19
Alignment explanation
Indices: 1547064--1547099 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1547054 AATATATTTA
1547064 AAAACA-ATAAAATAAATT
1 AAAACATATAAAATAAATT
1547082 AAAACATATAAAATAAAT
1 AAAACATATAAAATAAAT
1547100 GACTAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAACATATAAAATAAATT
Found at i:1547955 original size:32 final size:31
Alignment explanation
Indices: 1547910--1547971 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
1547900 TCGTTGGTAG
* *
1547910 TTTGTTTGTTTTCTTTTCTCTGTTTTTTTTTT
1 TTTGTTTGTTTTC-TGTCTCTGTCTTTTTTTT
1547942 TTTGTTCTG-TTTCTGTCTCTGTCTTTTTTT
1 TTTGTT-TGTTTTCTGTCTCTGTCTTTTTTT
1547972 CTGTCTCGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 15 0.56
32 10 0.37
33 2 0.07
ACGTcount: A:0.00, C:0.13, G:0.11, T:0.76
Consensus pattern (31 bp):
TTTGTTTGTTTTCTGTCTCTGTCTTTTTTTT
Found at i:1548349 original size:3 final size:3
Alignment explanation
Indices: 1548341--1548470 Score: 197
Period size: 3 Copynumber: 42.7 Consensus size: 3
1548331 TTATTTATTA
*
1548341 AAT AAT AAT AAT AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
* **
1548387 AAAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GCT AAT AAT
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1548433 AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1548471 AATGGATAAA
Statistics
Matches: 115, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
3 109 0.95
4 6 0.05
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1549842 original size:15 final size:15
Alignment explanation
Indices: 1549822--1549852 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1549812 TTAAGTCACA
1549822 AGTTCTATACCTATT
1 AGTTCTATACCTATT
1549837 AGTTCTATACCTATT
1 AGTTCTATACCTATT
1549852 A
1 A
1549853 AGAATACTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.45
Consensus pattern (15 bp):
AGTTCTATACCTATT
Found at i:1551948 original size:14 final size:14
Alignment explanation
Indices: 1551912--1551951 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1551902 AGATTTTAAG
* *
1551912 TTAGAGCTTAAGGT
1 TTAGAGGTTATGGT
1551926 TTA-AGGTTATGGT
1 TTAGAGGTTATGGT
1551939 TTAGAGGTTATGG
1 TTAGAGGTTATGG
1551952 GTTATGGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.25, C:0.03, G:0.33, T:0.40
Consensus pattern (14 bp):
TTAGAGGTTATGGT
Found at i:1551954 original size:21 final size:20
Alignment explanation
Indices: 1551930--1551969 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
1551920 TAAGGTTTAA
1551930 GGTTATGGTTTAGAGGTTATG
1 GGTTATGGTTTAG-GGTTATG
1551951 GGTTATGGTTTAGGGTTAT
1 GGTTATGGTTTAGGGTTAT
1551970 CACTTTAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.17, C:0.00, G:0.38, T:0.45
Consensus pattern (20 bp):
GGTTATGGTTTAGGGTTATG
Found at i:1555434 original size:31 final size:31
Alignment explanation
Indices: 1555396--1555467 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
1555386 AAAGAGGAGT
1555396 TTGGTGACTAAAGTAGAAAAATAGCAATAAG
1 TTGGTGACTAAAGTAGAAAAATAGCAATAAG
* * * *
1555427 TTGGTGACTAAAGTATACAAATATCAATAAT
1 TTGGTGACTAAAGTAGAAAAATAGCAATAAG
*
1555458 TTGCTGACTA
1 TTGGTGACTA
1555468 GTGATGTGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.43, C:0.10, G:0.18, T:0.29
Consensus pattern (31 bp):
TTGGTGACTAAAGTAGAAAAATAGCAATAAG
Found at i:1556909 original size:60 final size:60
Alignment explanation
Indices: 1556759--1556910 Score: 180
Period size: 60 Copynumber: 2.5 Consensus size: 60
1556749 TTTAAACCGA
* * * *
1556759 TCCCTATA-TTTTTAATATTCTAATTTCATCCATAGACTATGGCTCTCATTCTAAATTAG
1 TCCCTATACTTTTGAATATTCTAATTTCATCCCTAAACTATGACTCTCATTCTAAATTAG
* * ** * * *
1556818 TCCTTAAACTTTTGAACGTTCTAATTGCATCCCTAAACTATGACTCTCTTTCTAAATTGG
1 TCCCTATACTTTTGAATATTCTAATTTCATCCCTAAACTATGACTCTCATTCTAAATTAG
* *
1556878 TCCCCATACTTTTGAATATTCCAATTTCATCCC
1 TCCCTATACTTTTGAATATTCTAATTTCATCCC
1556911 CAAATTCATG
Statistics
Matches: 74, Mismatches: 18, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
59 6 0.08
60 68 0.92
ACGTcount: A:0.27, C:0.24, G:0.07, T:0.41
Consensus pattern (60 bp):
TCCCTATACTTTTGAATATTCTAATTTCATCCCTAAACTATGACTCTCATTCTAAATTAG
Found at i:1557135 original size:60 final size:59
Alignment explanation
Indices: 1557034--1557173 Score: 155
Period size: 60 Copynumber: 2.3 Consensus size: 59
1557024 ATTAGTATAT
* *
1557034 ATGT-ATAGTTTGAGATGAAATTTGAATGTTCATAAAGTTTGAGGAC-AAGTTTAGAATG
1 ATGTCATAGTTTGGGATGAAATTTGAATATTCATAAAGTTTGAGGACTAA-TTTAGAATG
1557092 AATGTCATAGTTTGGGGATGAAA-TTGAAATATTCGA-AAA-TTTGAGGACTAATTTAGAATG
1 -ATGTCATAGTTT-GGGATGAAATTTG-AATATTC-ATAAAGTTTGAGGACTAATTTAGAATG
*
1557152 ATAGTCATAGTTTAAGGATGAA
1 AT-GTCATAGTTT-GGGATGAA
1557174 TTAGAACATT
Statistics
Matches: 71, Mismatches: 4, Indels: 11
0.83 0.05 0.13
Matches are distributed among these distances:
59 6 0.08
60 45 0.63
61 19 0.27
62 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (59 bp):
ATGTCATAGTTTGGGATGAAATTTGAATATTCATAAAGTTTGAGGACTAATTTAGAATG
Found at i:1558911 original size:7 final size:7
Alignment explanation
Indices: 1558899--1558932 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
1558889 TCGAGTTTAT
1558899 AATATAA
1 AATATAA
1558906 AATATAA
1 AATATAA
1558913 AATATAA
1 AATATAA
*
1558920 AATACAA
1 AATATAA
1558927 AATATA
1 AATATA
1558933 TTTATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (7 bp):
AATATAA
Found at i:1560251 original size:16 final size:16
Alignment explanation
Indices: 1560230--1560273 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
1560220 AAAAATATCC
1560230 GAAATCGATTTTGAGA
1 GAAATCGATTTTGAGA
* *
1560246 GAAATCGATTTGGGGA
1 GAAATCGATTTTGAGA
*
1560262 GAAATCGGTTTT
1 GAAATCGATTTT
1560274 TTTTAAACCG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.32, C:0.07, G:0.30, T:0.32
Consensus pattern (16 bp):
GAAATCGATTTTGAGA
Found at i:1562694 original size:21 final size:21
Alignment explanation
Indices: 1562670--1562711 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1562660 AGTTTATTTT
*
1562670 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAAATATCG
*
1562691 TAAACTTTGTTTCAAATATCG
1 TAAACTTTATTTCAAATATCG
1562712 AACTTGGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.45
Consensus pattern (21 bp):
TAAACTTTATTTCAAATATCG
Found at i:1563003 original size:22 final size:21
Alignment explanation
Indices: 1562964--1563004 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1562954 GGTGAAAAAA
**
1562964 CCGGATCGATTTTTATCCGAT
1 CCGGATCGATTTAAATCCGAT
1562985 CCGGATCGGATTTAAATCCG
1 CCGGATC-GATTTAAATCCG
1563005 GCTATGTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (21 bp):
CCGGATCGATTTAAATCCGAT
Found at i:1564322 original size:66 final size:66
Alignment explanation
Indices: 1564244--1564589 Score: 241
Period size: 66 Copynumber: 5.2 Consensus size: 66
1564234 CATGAGTAGT
* * * *
1564244 ATCTCTTGCCATTAAAGCAGCATAGATAAATAATATTTCGTCACTATGATCGCATAGGTAAATAA
1 ATCTCTCGCCATTAAAGCCGCATAGATAAATAATATTTCGTCACTAAGATCGCATAGATAAATAA
1564309 C
66 C
* * * ** * * * *
1564310 ATCTCTCACCATTAAGGCCGCATAGATAAATAATATCTCACCATTAAGGTCACATATAAATAAAT
1 ATCTCTCGCCATTAAAGCCGCATAGATAAATAATATTTCGTCACTAAGATCGC--ATAGATAAAT
1564375 AAC
64 AAC
* ** * * *
1564378 ATCTATCGTTATT-AAGTTCGCATGGATAAATAATATTTTGTCACTAAGA-CTGCATAGATAAAT
1 ATCTCTCGCCATTAAAG-CCGCATAGATAAATAATATTTCGTCACTAAGATC-GCATAGATAAAT
1564441 AAC
64 AAC
* * * ** * ** *
1564444 ATCTCTCGCCATTAAGGCCGCATAGATAAATGATGTTTCACCGCTAAGGCCACATAGATAAATAA
1 ATCTCTCGCCATTAAAGCCGCATAGATAAATAATATTTCGTCACTAAGATCGCATAGATAAATAA
1564509 C
66 C
* ** * * * ** ** * *
1564510 A-CATTTTACCATTAAGGCCACATAAATAAATAATATCACACCACTAAGACCGTATAGATAAATA
1 ATC-TCTCGCCATTAAAGCCGCATAGATAAATAATATTTCGTCACTAAGATCGCATAGATAAATA
1564574 A-
65 AC
* *
1564575 ATATCTCACCATTAA
1 ATCTCTCGCCATTAA
1564590 GATCTGTTAA
Statistics
Matches: 214, Mismatches: 58, Indels: 17
0.74 0.20 0.06
Matches are distributed among these distances:
65 12 0.06
66 151 0.71
67 6 0.03
68 45 0.21
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (66 bp):
ATCTCTCGCCATTAAAGCCGCATAGATAAATAATATTTCGTCACTAAGATCGCATAGATAAATAA
C
Found at i:1564334 original size:34 final size:34
Alignment explanation
Indices: 1564294--1564590 Score: 175
Period size: 32 Copynumber: 8.9 Consensus size: 34
1564284 TCACTATGAT
*
1564294 CGCATAGGTAAATAACATCTCTCACCATTAAGGC
1 CGCATAGATAAATAACATCTCTCACCATTAAGGC
*
1564328 CGCATAGATAAAT-A-ATATCTCACCATTAAGGTC
1 CGCATAGATAAATAACATCTCTCACCATTAAGG-C
** * * *** **
1564361 ACATATAAATAAATAACATCTATCGTTATTAAGTT
1 -CGCATAGATAAATAACATCTCTCACCATTAAGGC
* * * * *
1564396 CGCATGGATAAATAATATTTTGTCA-C--TAAGAC
1 CGCATAGATAAATAACA-TCTCTCACCATTAAGGC
* *
1564428 TGCATAGATAAATAACATCTCTCGCCATTAAGGC
1 CGCATAGATAAATAACATCTCTCACCATTAAGGC
* * * **
1564462 CGCATAGATAAAT--GATGTTTCACCGCTAAGGC
1 CGCATAGATAAATAACATCTCTCACCATTAAGGC
* * *
1564494 CACATAGATAAATAACA-CATTTTACCATTAAGGC
1 CGCATAGATAAATAACATC-TCTCACCATTAAGGC
* * * * * *
1564528 CACATAAATAAAT-A-ATATCACACCACTAAGAC
1 CGCATAGATAAATAACATCTCTCACCATTAAGGC
* *
1564560 CGTATAGATAAATAA-ATATCTCACCATTAAG
1 CGCATAGATAAATAACATCTCTCACCATTAAG
1564591 ATCTGTTAAC
Statistics
Matches: 195, Mismatches: 55, Indels: 27
0.70 0.20 0.10
Matches are distributed among these distances:
31 4 0.02
32 81 0.42
33 18 0.09
34 76 0.39
35 5 0.03
36 11 0.06
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (34 bp):
CGCATAGATAAATAACATCTCTCACCATTAAGGC
Found at i:1564354 original size:32 final size:32
Alignment explanation
Indices: 1564252--1564590 Score: 176
Period size: 34 Copynumber: 10.2 Consensus size: 32
1564242 GTATCTCTTG
* * * *
1564252 CCATTAAAGCAGCATAGATAAATAATATTTCG
1 CCATTAAGGCCGCATAGATAAATAATATCTCA
* * * ** * *
1564284 TCACTATGATCGCATAGGTAAATAACATCTCTCA
1 CCATTAAGGCCGCATAGATAAAT-A-ATATCTCA
1564318 CCATTAAGGCCGCATAGATAAATAATATCTCA
1 CCATTAAGGCCGCATAGATAAATAATATCTCA
** * *
1564350 CCATTAAGGTCACATATAAATAAATAACATCT-A
1 CCATTAAGG-C-CGCATAGATAAATAATATCTCA
* ** * * **
1564383 TCGTTATTAAGTTCGCATGGATAAATAATATTTTG
1 -C--CATTAAGGCCGCATAGATAAATAATATCTCA
* * * * * *
1564418 TCACTAAGACTGCATAGATAAATAACATCTCTCG
1 CCATTAAGGCCGCATAGATAAAT-A-ATATCTCA
* * *
1564452 CCATTAAGGCCGCATAGATAAATGATGTTTCA
1 CCATTAAGGCCGCATAGATAAATAATATCTCA
** * * * *
1564484 CCGCTAAGGCCACATAGATAAATAACACATTTTA
1 CCATTAAGGCCGCATAGATAAAT-A-ATATCTCA
* * *
1564518 CCATTAAGGCCACATAAATAAATAATATCACA
1 CCATTAAGGCCGCATAGATAAATAATATCTCA
* * *
1564550 CCACTAAGACCGTATAGATAAATAAATATCTCA
1 CCATTAAGGCCGCATAGATAAAT-AATATCTCA
1564583 CCATTAAG
1 CCATTAAG
1564591 ATCTGTTAAC
Statistics
Matches: 223, Mismatches: 71, Indels: 25
0.70 0.22 0.08
Matches are distributed among these distances:
32 94 0.42
33 21 0.09
34 102 0.46
36 6 0.03
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.28
Consensus pattern (32 bp):
CCATTAAGGCCGCATAGATAAATAATATCTCA
Found at i:1564498 original size:134 final size:135
Alignment explanation
Indices: 1564263--1564508 Score: 361
Period size: 134 Copynumber: 1.8 Consensus size: 135
1564253 CATTAAAGCA
* *
1564263 GCATAGATAAATAATATTTCGTCACTATGATCGCATAGGTAAATAACATCTCTCACCATTAAGGC
1 GCATAGATAAATAATATTTCGTCACTAAGATCGCATAGATAAATAACATCTCTCACCATTAAGGC
* *
1564328 CGCATAGATAAATAATATCTCACCATTAAGGTCACAT-ATAAATAAATAACATCTATCGTTATTA
66 CGCATAGATAAATAATATCTCACCACTAAGGCCACATAATAAATAAATAACATCTATCGTTATTA
1564392 AGTTC
131 AGTTC
* * *
1564397 GCATGGATAAATAATATTTTGTCACTAAGA-CTGCATAGATAAATAACATCTCTCGCCATTAAGG
1 GCATAGATAAATAATATTTCGTCACTAAGATC-GCATAGATAAATAACATCTCTCACCATTAAGG
* * * *
1564461 CCGCATAGATAAATGATGTTTCACCGCTAAGGCCACATAGATAAATAA
65 CCGCATAGATAAATAATATCTCACCACTAAGGCCACATA-ATAAATAA
1564509 CACATTTTAC
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
133 1 0.01
134 89 0.91
136 8 0.08
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (135 bp):
GCATAGATAAATAATATTTCGTCACTAAGATCGCATAGATAAATAACATCTCTCACCATTAAGGC
CGCATAGATAAATAATATCTCACCACTAAGGCCACATAATAAATAAATAACATCTATCGTTATTA
AGTTC
Found at i:1565679 original size:146 final size:150
Alignment explanation
Indices: 1565502--1565791 Score: 457
Period size: 146 Copynumber: 2.0 Consensus size: 150
1565492 TGCAAATGGA
* * *
1565502 TTTTATAAAATATATTTGAAAACATTTATATATTATATAGTTTTTTAAAACGTTTGTGAAAAT-A
1 TTTTATAAAACATATTTGAAAACATTTATATATTATATAATTTTTTAAAACGTTTGTAAAAATAA
*
1565566 AATATAATATATAGTTTTTAAAACATTTTTGAAAACATGTATATTATATAG-TTTAAAAACATTT
66 AATATAATATATAGTTTTTAAAACATTTTTG-AAA-ATATATATTATATAGTTTTAAAAACATTT
1565630 T-GAAAA-TATATAATATATAG
129 TAGAAAACTATATAATATATAG
*
1565650 TTTT-TAAAACAT-TTTGAAAACATTTATATATTATATAATTTTTTAAAACGTTTTTAAAAATAA
1 TTTTATAAAACATATTTGAAAACATTTATATATTATATAATTTTTTAAAACGTTTGTAAAAATAA
* *
1565713 AATATAATATATAGTTTTTAAAATATTTTTGAAAATATATATTATATAGTTTTTAAAACATTTTA
66 AATATAATATATAGTTTTTAAAACATTTTTGAAAATATATATTATATAGTTTTAAAAACATTTTA
1565778 GAAAACTATATAAT
131 GAAAACTATATAAT
1565792 TTTGAAAATA
Statistics
Matches: 131, Mismatches: 7, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
145 14 0.11
146 62 0.47
147 43 0.33
148 12 0.09
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (150 bp):
TTTTATAAAACATATTTGAAAACATTTATATATTATATAATTTTTTAAAACGTTTGTAAAAATAA
AATATAATATATAGTTTTTAAAACATTTTTGAAAATATATATTATATAGTTTTAAAAACATTTTA
GAAAACTATATAATATATAG
Found at i:1565852 original size:64 final size:63
Alignment explanation
Indices: 1565718--1565853 Score: 150
Period size: 66 Copynumber: 2.1 Consensus size: 63
1565708 AATAAAATAT
* * * * * *
1565718 AATATATAGTTTTTAAAATATTTTTGAAAATATATATTATATAGTTTTTAAAACATTTTAGAA
1 AATATATAATTTTGAAAATATTTTTAAAAATATATAATATATAGATATTAAAACATTTTAGAA
**
1565781 AACTATATAATTTTGAAAATATTTTTTTAAAAATATATAATATATA-ATATTAAAATGTTTGTA-
1 AA-TATATAATTTTGAAAATA--TTTTTAAAAATATATAATATATAGATATTAAAACATTT-TAG
1565844 AA
62 AA
1565846 AATATATA
1 AATATATA
1565854 TTATATAGAT
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
63 2 0.03
64 22 0.36
65 14 0.23
66 23 0.38
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.46
Consensus pattern (63 bp):
AATATATAATTTTGAAAATATTTTTAAAAATATATAATATATAGATATTAAAACATTTTAGAA
Found at i:1569069 original size:18 final size:19
Alignment explanation
Indices: 1569048--1569092 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1569038 ATTTAGACAT
1569048 TTTGCATTTT-TTATTTCC
1 TTTGCATTTTATTATTTCC
*
1569066 TTTGCATTTTATTATTTTC
1 TTTGCATTTTATTATTTCC
*
1569085 TCTGCATT
1 TTTGCATT
1569093 CACATTAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.13, C:0.16, G:0.07, T:0.64
Consensus pattern (19 bp):
TTTGCATTTTATTATTTCC
Found at i:1572696 original size:85 final size:82
Alignment explanation
Indices: 1572465--1573309 Score: 925
Period size: 85 Copynumber: 10.2 Consensus size: 82
1572455 GCTCAAGGCC
* * *
1572465 AGAAGGGCTATCTGCCCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTG-CCA-CAAAGACCCTTGAGTTCGACTACGCTCAGCTTCAAGGCACATCATT
* * *
1572530 TGCAGAATAGCTTAAGTCG
64 TGCAGCATAACTTAAGTCA
* * *
1572549 AGAAGGGCTATCTG-C-CAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATTT
1 AGAAGGGTTATCTGCCACAAAGACCCTTGAGTTCGACTACGCTCAGCTTC-AAGGCACATCATTT
*
1572612 GCAGTATAACTTAAGTCA
65 GCAGCATAACTTAAGTCA
* * * *
1572630 AGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCAT
1 AGAAGGGTTATCTGCC-AC-AAAGACCCTTGAGTTCGACTACGCTCAGCTTCAA-GGCACATCAT
* * * *
1572695 TTACAGCATAACTCAAGGCT
63 TTGCAGCATAACTTAAGTCA
* * *
1572715 AGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
1 AGAAGGGTTATCTGCCA-CAAAGACCCTTGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTT
* * *
1572780 GCAGAATAGCTTAAGTCG
65 GCAGCATAACTTAAGTCA
* * *
1572798 AGAAGGGCTATCTG-C-CAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATTT
1 AGAAGGGTTATCTGCCACAAAGACCCTTGAGTTCGACTACGCTCAGCTTC-AAGGCACATCATTT
*
1572861 GCAGTATAACTTAAGTCA
65 GCAGCATAACTTAAGTCA
* * * *
1572879 AGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCAT
1 AGAAGGGTTATCTGCC-AC-AAAGACCCTTGAGTTCGACTACGCTCAGCTTCAA-GGCACATCAT
* * * *
1572944 TTACAGCATAACTCAAGGCT
63 TTGCAGCATAACTTAAGTCA
* * *
1572964 AGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
1 AGAAGGGTTATCTGCCA-CAAAGACCCTTGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTT
* * *
1573029 GCAGAATAGCTTAAGTCG
65 GCAGCATAACTTAAGTCA
* * * *
1573047 AGAAGGGCTATCTG-C-CAAAGACCCTCGAGTTCGACTACGTTCGGCTTCGAAGGCACATCATTT
1 AGAAGGGTTATCTGCCACAAAGACCCTTGAGTTCGACTACGCTCAGCTTC-AAGGCACATCATTT
*
1573110 GCAGTATAACTTAAGTCA
65 GCAGCATAACTTAAGTCA
* * * * *
1573128 AGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTTAAGGGCATATCAT
1 AGAAGGGTTATCTGCC-AC-AAAGACCCTTGAGTTCGACTACGCTCAGCTTCAA-GGCACATCAT
* * *
1573193 TTACAGCATAACTCAAGGCTA
63 TTGCAGCATAACTTAAGTC-A
* *
1573214 A-AAGGGTTATCTGTGACCA-AAAGA-CCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCACATCA
1 AGAAGGGTTATC--TG-CCACAAAGACCCTT-GAGTTCGACTACGCTCAGCTTCAAGGCACATCA
1573276 TTTGCAGCATAACTTAAGTCA
62 TTTGCAGCATAACTTAAGTCA
1573297 AGAAGGGTTATCT
1 AGAAGGGTTATCT
1573310 ACTAAAGACT
Statistics
Matches: 638, Mismatches: 97, Indels: 54
0.81 0.12 0.07
Matches are distributed among these distances:
80 86 0.13
81 126 0.20
82 7 0.01
83 74 0.12
84 122 0.19
85 216 0.34
86 2 0.00
87 3 0.00
88 2 0.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (82 bp):
AGAAGGGTTATCTGCCACAAAGACCCTTGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTG
CAGCATAACTTAAGTCA
Found at i:1573414 original size:498 final size:499
Alignment explanation
Indices: 1572456--1573426 Score: 1545
Period size: 498 Copynumber: 1.9 Consensus size: 499
1572446 TGCAGCTTAG
1572456 CTCAAGGCCAGAAGGGCTATCTGCCCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCCAGAAGGGCTATCTGCCCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
1572521 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTA
66 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTA
1572586 CGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTA
131 CGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTA
1572651 AAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCTA
196 AAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCTA
* *
1572716 GAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
261 AAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
* * * * * *
1572781 CAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACGTTCAGCTTC
326 CAGAATAACTTAAGTCAAGAAGGGCTATCTACCAAAGACCCTCGAGTTCGACTACATTCAACTTA
* * * * * * *
1572846 GAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAAAGACCCTTAA
391 GAAGGCAAATCACTTACAGAATAACTCAAGGCAAGAAGGGTTATCTGCCAACTAAAGACCCTCAA
*
1572911 GTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAA
456 GTTCGATTACAATCAGCTTCAAGGGCATATCATTTACAGCATAA
* * *
1572955 CTCAAGGCTAGAAGGGTTATCTG-TCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCCAGAAGGGCTATCTGCCCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
1573019 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTA
66 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTA
*
1573084 CGTTCGGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTA
131 CGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTA
*
1573149 AAGACCCTTAAGTTCGATTACACTCAGCTTTAAGGGCATATCATTTACAGCATAACTCAAGGCTA
196 AAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCTA
* *
1573214 AAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCACATCATTT
261 AAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* * * ** * * *
1573279 GCAGCATAACTTAAGTCAAGAAGGGTTATCTACTAAAGACTTTTGAGTTCGATTATATTCAACTT
325 GCAGAATAACTTAAGTCAAGAAGGGCTATCTACCAAAGACCCTCGAGTTCGACTACATTCAACTT
* * ***
1573344 AG-AGGCAAATCAAGCTTACAGAATAGCTCAAGGCAAGAAGGGTTATCTGTCAA-TAAA-ATTGT
390 AGAAGGCAAATC-A-CTTACAGAATAACTCAAGGCAAGAAGGGTTATCTGCCAACTAAAGACCCT
* *
1573406 CGAGTTCGATTCCAATCAGCT
453 CAAGTTCGATTACAATCAGCT
1573427 CGATGACACC
Statistics
Matches: 431, Mismatches: 38, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
498 276 0.64
499 123 0.29
500 32 0.07
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (499 bp):
CTCAAGGCCAGAAGGGCTATCTGCCCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTA
CGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTA
AAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCTA
AAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
CAGAATAACTTAAGTCAAGAAGGGCTATCTACCAAAGACCCTCGAGTTCGACTACATTCAACTTA
GAAGGCAAATCACTTACAGAATAACTCAAGGCAAGAAGGGTTATCTGCCAACTAAAGACCCTCAA
GTTCGATTACAATCAGCTTCAAGGGCATATCATTTACAGCATAA
Found at i:1573416 original size:249 final size:249
Alignment explanation
Indices: 1572456--1573318 Score: 1573
Period size: 249 Copynumber: 3.5 Consensus size: 249
1572446 TGCAGCTTAG
* * *
1572456 CTCAAGGCCAGAAGGGCTATCTGCCCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCTAGAAGGGTTATCTG-TCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
1572521 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTA
65 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTA
1572586 CGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTA
130 CGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTA
1572651 AAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAA
195 AAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAA
1572706 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
1572771 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTAC
66 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTAC
1572836 GTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAA
131 GTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAA
1572901 AGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAA
196 AGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAA
1572955 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
1573020 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTAC
66 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTAC
*
1573085 GTTCGGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAA
131 GTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAA
*
1573150 AGACCCTTAAGTTCGATTACACTCAGCTTTAAGGGCATATCATTTACAGCATAA
196 AGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAA
* * * *
1573204 CTCAAGGCTAAAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGG
1 CTCAAGGCTAGAAGGGTTATCTGTCACC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
* * * * * *
1573269 CACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTACTAAAGAC
65 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
1573319 TTTTGAGTTC
Statistics
Matches: 597, Mismatches: 15, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
249 498 0.83
250 99 0.17
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (249 bp):
CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTAC
GTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAA
AGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAA
Found at i:1574085 original size:34 final size:35
Alignment explanation
Indices: 1573978--1574250 Score: 253
Period size: 34 Copynumber: 7.8 Consensus size: 35
1573968 TGCAAATGGA
*
1573978 TTTTATAAAATATATTTGAAAACATTTATATATTATATAG
1 TTTT-TAAAACAT-TTTGAAAACA--TATATA-TATATAG
* *
1574018 TTTTTTAAAACGTTTGTGAAAATA-ATATAATATATAG
1 -TTTTTAAAACATTT-TGAAAACATATAT-ATATATAG
*
1574055 TTTTT-AAACATTTTGAAAACATGTATATATATAG
1 TTTTTAAAACATTTTGAAAACATATATATATATAG
*
1574089 -TTTAAAAACATTTTG---A-A-ATATATATATAG
1 TTTTTAAAACATTTTGAAAACATATATATATATAG
* *
1574118 TTTTTAAAACATTTTGAAAACATTTATATTATATAA
1 TTTTTAAAACATTTTGAAAACATATATA-TATATAG
* * * *
1574154 TTTTTTAAACGTTTTTAAAA-ATAAATATATATAG
1 TTTTTAAAACATTTTGAAAACATATATATATATAG
* *
1574188 TTTTTAAAATATTTTTGAAAATATATAT-TATATAG
1 TTTTTAAAACA-TTTTGAAAACATATATATATATAG
1574223 TTTTTAAAACATTTTAGAAAAC-TATATA
1 TTTTTAAAACATTTT-GAAAACATATATA
1574251 ATTTGAAAAT
Statistics
Matches: 193, Mismatches: 24, Indels: 36
0.76 0.09 0.14
Matches are distributed among these distances:
29 11 0.06
30 15 0.08
31 1 0.01
33 4 0.02
34 49 0.25
35 49 0.25
36 33 0.17
37 11 0.06
38 1 0.01
39 2 0.01
40 13 0.07
41 4 0.02
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (35 bp):
TTTTTAAAACATTTTGAAAACATATATATATATAG
Found at i:1576615 original size:35 final size:35
Alignment explanation
Indices: 1576576--1576689 Score: 131
Period size: 35 Copynumber: 3.2 Consensus size: 35
1576566 GAAAGCATCG
* *
1576576 CACTTTCAATTCAAATCGAACGGAAGGAGGTTCGA
1 CACTTTCGATTCAAATCGAACGGAAGGACGTTCGA
** *
1576611 CACTTTCGATTCAAATCGAACGGAAGGAACCATCGG
1 CACTTTCGATTCAAATCGAACGGAAGG-ACGTTCGA
* * *
1576647 CACTTCCGATTCAAATCGAACGGAAAGATGTATC-A
1 CACTTTCGATTCAAATCGAACGGAAGGACGT-TCGA
1576682 CACTTTCG
1 CACTTTCG
1576690 TTTCGGGTGT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
35 34 0.52
36 31 0.48
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (35 bp):
CACTTTCGATTCAAATCGAACGGAAGGACGTTCGA
Found at i:1576658 original size:36 final size:35
Alignment explanation
Indices: 1576571--1576671 Score: 132
Period size: 36 Copynumber: 2.9 Consensus size: 35
1576561 CGAAAGAAAG
* *
1576571 CATC-GCACTTTCAATTCAAATCGAACGGAAGGAG
1 CATCGGCACTTTCGATTCAAATCGAACGGAAGGAC
** *
1576605 GTTCGACACTTTCGATTCAAATCGAACGGAAGGAAC
1 CATCGGCACTTTCGATTCAAATCGAACGGAAGG-AC
*
1576641 CATCGGCACTTCCGATTCAAATCGAACGGAA
1 CATCGGCACTTTCGATTCAAATCGAACGGAA
1576672 AGATGTATCA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
34 2 0.04
35 26 0.46
36 28 0.50
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.21
Consensus pattern (35 bp):
CATCGGCACTTTCGATTCAAATCGAACGGAAGGAC
Found at i:1580271 original size:102 final size:102
Alignment explanation
Indices: 1580156--1580643 Score: 818
Period size: 102 Copynumber: 4.8 Consensus size: 102
1580146 CTCATACACT
*
1580156 GGAGGCTTCTTTGGAGTCTCATGGACTGGTGGTTTGGGTTCTGGCTTCTCTTTCTTTGGTGGTGT
1 GGAGGCTTCTTTGGAGTCTCATAGACTGGTGGTTTGGGTTCTGGCTTCTCTTTCTTTGGTGGTGT
1580221 ATAAACTGGTGGCTTTGGTGGCTTAGGCTCATACGTC
66 ATAAACTGGTGGCTTTGGTGGCTTAGGCTCATACGTC
* *
1580258 GGAGGCTTCTTTGGAGTCCCATAGACTGGTGGTTTGGGTTCTGGTTTCTCTTTCTTTGGTGGTGT
1 GGAGGCTTCTTTGGAGTCTCATAGACTGGTGGTTTGGGTTCTGGCTTCTCTTTCTTTGGTGGTGT
1580323 ATAAACTGGTGGCTTTGGTGGCTTAGGCTCATACGTC
66 ATAAACTGGTGGCTTTGGTGGCTTAGGCTCATACGTC
1580360 GGAGGCTTCTTTGGAGTCTCATAGACTGGTGGTTTGGGTTCTGGCTTCTCTTTCTTTGGTGGTGT
1 GGAGGCTTCTTTGGAGTCTCATAGACTGGTGGTTTGGGTTCTGGCTTCTCTTTCTTTGGTGGTGT
*
1580425 ATAAACTGGTGGCTTTGGTGGCTTAGGCTCATACGTT
66 ATAAACTGGTGGCTTTGGTGGCTTAGGCTCATACGTC
* * * *
1580462 GGAGGCTTCTTTGGAGGCTCATAGACCGGAGGTTTGGGTTCAGGCTTCTCTTTCTTTGGTGGTGT
1 GGAGGCTTCTTTGGAGTCTCATAGACTGGTGGTTTGGGTTCTGGCTTCTCTTTCTTTGGTGGTGT
* *
1580527 ATAAACCGGTGGCTTTGGTGGCTTAGGCTCATAC-AC
66 ATAAACTGGTGGCTTTGGTGGCTTAGGCTCATACGTC
* * * *
1580563 TGGTGGCTTCTTTGGAGGT-TCATAGACTGGTGGTTTAGGTTCAGGCTTCTCTTTCTTTGGAGGT
1 -GGAGGCTTCTTTGGA-GTCTCATAGACTGGTGGTTTGGGTTCTGGCTTCTCTTTCTTTGGTGGT
1580627 GTATAAACTGGTGGCTT
64 GTATAAACTGGTGGCTT
1580644 AGGTTCAGGT
Statistics
Matches: 364, Mismatches: 20, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
102 363 1.00
103 1 0.00
ACGTcount: A:0.12, C:0.16, G:0.33, T:0.39
Consensus pattern (102 bp):
GGAGGCTTCTTTGGAGTCTCATAGACTGGTGGTTTGGGTTCTGGCTTCTCTTTCTTTGGTGGTGT
ATAAACTGGTGGCTTTGGTGGCTTAGGCTCATACGTC
Found at i:1580286 original size:57 final size:56
Alignment explanation
Indices: 1580225--1580396 Score: 145
Period size: 57 Copynumber: 3.2 Consensus size: 56
1580215 TGGTGTATAA
1580225 ACTGGTGGCTTTGGTGGCTTAGGCTCATACGTCGGAGGCTTCTTTGGAGTCCCATAG
1 ACTGGTGG-TTTGGTGGCTTAGGCTCATACGTCGGAGGCTTCTTTGGAGTCCCATAG
* * * * ** *
1580282 ACTGGTGGTTT-G-GG-TTCTGG-T--TTC-TC-----TTTCTTTGGTGGT-GTATAA
1 ACTGGTGGTTTGGTGGCTT-AGGCTCATACGTCGGAGGCTTCTTTGG-AGTCCCATAG
*
1580327 ACTGGTGGCTTTGGTGGCTTAGGCTCATACGTCGGAGGCTTCTTTGGAGTCTCATAG
1 ACTGGTGG-TTTGGTGGCTTAGGCTCATACGTCGGAGGCTTCTTTGGAGTCCCATAG
1580384 ACTGGTGGTTTGG
1 ACTGGTGGTTTGG
1580397 GTTCTGGCTT
Statistics
Matches: 85, Mismatches: 14, Indels: 33
0.64 0.11 0.25
Matches are distributed among these distances:
45 19 0.22
46 5 0.06
47 1 0.01
48 4 0.05
49 3 0.04
50 2 0.02
51 4 0.05
52 2 0.02
53 3 0.04
54 4 0.05
55 1 0.01
56 10 0.12
57 27 0.32
ACGTcount: A:0.12, C:0.17, G:0.34, T:0.37
Consensus pattern (56 bp):
ACTGGTGGTTTGGTGGCTTAGGCTCATACGTCGGAGGCTTCTTTGGAGTCCCATAG
Found at i:1580716 original size:45 final size:45
Alignment explanation
Indices: 1580570--1580785 Score: 220
Period size: 45 Copynumber: 4.8 Consensus size: 45
1580560 CACTGGTGGC
* * * * *
1580570 TTCTTTGGAGGTTCATAGACTGGTGGTTTAGGTTCAGGCTTCTCT
1 TTCTTTGGTGGCTCGTAGACTGGTGGCTTAGGTTCAGGTTTCTCT
* *
1580615 TTCTTTGGAGG-T-GTATAAACTGGTGGCTTAGGTTCAGGTTTCTCT
1 TTCTTTGGTGGCTCG--TAGACTGGTGGCTTAGGTTCAGGTTTCTCT
* * * *
1580660 TTCTTCGGTGGCTCGTAGACTGGTGGTTTGGGTTCTGGTTTCTCT
1 TTCTTTGGTGGCTCGTAGACTGGTGGCTTAGGTTCAGGTTTCTCT
* * * * *
1580705 TTCTTTGGTGGCTCGTAGACAGGGGGCTTGGGTTTAGGTTTGTCT
1 TTCTTTGGTGGCTCGTAGACTGGTGGCTTAGGTTCAGGTTTCTCT
* * * *
1580750 TTCTTTGGTGGTTCATAGACAGGGGGCTTAGGTTCA
1 TTCTTTGGTGGCTCGTAGACTGGTGGCTTAGGTTCA
1580786 TAAGTTGGTG
Statistics
Matches: 146, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.01
45 143 0.98
46 1 0.01
47 1 0.01
ACGTcount: A:0.12, C:0.15, G:0.32, T:0.41
Consensus pattern (45 bp):
TTCTTTGGTGGCTCGTAGACTGGTGGCTTAGGTTCAGGTTTCTCT
Found at i:1581326 original size:172 final size:172
Alignment explanation
Indices: 1581040--1581386 Score: 678
Period size: 172 Copynumber: 2.0 Consensus size: 172
1581030 TCCATTGGAA
1581040 ATAATCAGCTAGGTGTTATTAAATCTTCTCAGTAATTCATAAATGTAATTTGGTCCATTCATGTC
1 ATAATCAGCTAGGTGTTATTAAATCTTCTCAGTAATTCATAAATGTAATTTGGTCCATTCATGTC
1581105 CCACTTGGTTGAAATTCTGTACCATGTGGATACAAGGCCTCAGTCATGATTGAAGAAAACTACAA
66 CCACTTGGTTGAAATTCTGTACCATGTGGATACAAGGCCTCAGTCATGATTGAAGAAAACTACAA
1581170 GAGCGTTATTGCAGAGTTAGAGGGGAAACACAAAAGAAAATT
131 GAGCGTTATTGCAGAGTTAGAGGGGAAACACAAAAGAAAATT
1581212 ATAATCAGCTAGGTGTTATTAAATCTTCTCAGTAATTCATAAATGTAATTTTGGTCCATTCATGT
1 ATAATCAGCTAGGTGTTATTAAATCTTCTCAGTAATTCATAAATGTAA-TTTGGTCCATTCATGT
1581277 CCCACTTGGTTGAAATTC-GTACCATGTGGATACAAGGCCTCAGTCATGATTGAAGAAAACTACA
65 CCCACTTGGTTGAAATTCTGTACCATGTGGATACAAGGCCTCAGTCATGATTGAAGAAAACTACA
1581341 AGAGCGTTATTGCAGAGTTAGAGGGGAAACACAAAAGAAAATT
130 AGAGCGTTATTGCAGAGTTAGAGGGGAAACACAAAAGAAAATT
1581384 ATA
1 ATA
1581387 GAGGTTGATG
Statistics
Matches: 174, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
172 140 0.80
173 34 0.20
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.30
Consensus pattern (172 bp):
ATAATCAGCTAGGTGTTATTAAATCTTCTCAGTAATTCATAAATGTAATTTGGTCCATTCATGTC
CCACTTGGTTGAAATTCTGTACCATGTGGATACAAGGCCTCAGTCATGATTGAAGAAAACTACAA
GAGCGTTATTGCAGAGTTAGAGGGGAAACACAAAAGAAAATT
Found at i:1581880 original size:61 final size:62
Alignment explanation
Indices: 1581809--1581931 Score: 176
Period size: 62 Copynumber: 2.0 Consensus size: 62
1581799 AATCCTTTAA
* *
1581809 ATATCTATTTAAATAATAAATTTTCTCT-ATTTTCGTTTAACATATCATAATTTAGTATAAT
1 ATATCCATTTAAATAATAAATTTCCTCTAATTTTCGTTTAACATATCATAATTTAGTATAAT
* * * * *
1581870 ATATCCATTTAAATAATAAATTTCCTCTAATTTTTGTTTAATATGTTATAATTTGGTATAAT
1 ATATCCATTTAAATAATAAATTTCCTCTAATTTTCGTTTAACATATCATAATTTAGTATAAT
1581932 TTGATTGTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
61 26 0.48
62 28 0.52
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.50
Consensus pattern (62 bp):
ATATCCATTTAAATAATAAATTTCCTCTAATTTTCGTTTAACATATCATAATTTAGTATAAT
Found at i:1583809 original size:52 final size:52
Alignment explanation
Indices: 1583726--1583882 Score: 278
Period size: 52 Copynumber: 3.0 Consensus size: 52
1583716 TTATGTTAAA
* * *
1583726 TCATATGAACTTTTAAGAAATATTACGCATTCCACGTATGTTACTGCATGCC
1 TCATATGAACTTTTAAGAAATATTACACATTCCACGTATGTAAGTGCATGCC
*
1583778 TCATATAAACTTTTAAGAAATATTACACATTCCACGTATGTAAGTGCATGCC
1 TCATATGAACTTTTAAGAAATATTACACATTCCACGTATGTAAGTGCATGCC
1583830 TCATATGAACTTTTAAGAAATATTACACATTCCACGTATGTAAGTGCATGCC
1 TCATATGAACTTTTAAGAAATATTACACATTCCACGTATGTAAGTGCATGCC
1583882 T
1 T
1583883 AACATTTCCA
Statistics
Matches: 100, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 100 1.00
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.34
Consensus pattern (52 bp):
TCATATGAACTTTTAAGAAATATTACACATTCCACGTATGTAAGTGCATGCC
Found at i:1599446 original size:23 final size:23
Alignment explanation
Indices: 1599420--1599467 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1599410 ATAAAGTACA
*
1599420 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
1599443 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1599466 AT
1 AT
1599468 TGACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1599854 original size:23 final size:23
Alignment explanation
Indices: 1599804--1599863 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
1599794 TAAGCACTAA
*
1599804 CTATTACATTATATAAACGCTAC
1 CTATTACATTATATAAACGATAC
* **
1599827 TTATTACATTATATAAGTGATAC
1 CTATTACATTATATAAACGATAC
*
1599850 CTATTACATCATAT
1 CTATTACATTATAT
1599864 TTTTACCTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (23 bp):
CTATTACATTATATAAACGATAC
Found at i:1600316 original size:23 final size:23
Alignment explanation
Indices: 1600281--1600352 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
1600271 ATACTTTACA
*
1600281 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
1600304 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
1600327 ATATAAGCGCTA-CTATTACATC
1 ATATAAGCGCTACCTATTACATT
1600349 ATAT
1 ATAT
1600353 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 13 0.29
23 32 0.71
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.35
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:1600527 original size:490 final size:490
Alignment explanation
Indices: 1599596--1600700 Score: 1933
Period size: 490 Copynumber: 2.3 Consensus size: 490
1599586 TAAAGTTATG
* * * *
1599596 TAATATATATTTAATATATATGTTTATTGTTTTTAATTTAATGATAATATATACCGTAACATAAA
1 TAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAA
** * * *
1599661 AAATAAATCATTAGATACATATAATTACTAAATTGATATATTAAAACTCACTCAAAAAATAACCT
66 AAATAAATCATTAGACGCATATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCT
* *
1599726 TAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAATGATATATACTTTACA
131 TAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGATAGATACTTTACA
* *
1599791 ATATAAGCACTAACTATTACATTATATAAACGCTACTTATTACATTATATAAGTGATACCTATTA
196 ATATAAGCACTAACTATTACATTATATAAACGCTACCTATTACATTATATAAGCGATACCTATTA
*
1599856 CATCATATTTTTACCTATTATATTGAAAGTGTTCATACTTTTTATAAAAAGGATCGATACTTTTT
261 CATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTT
1599921 TTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGAGTTTCATGTTTTCCACCTACAATAT
326 TTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGAGTTTCATGTTTTCCACCTACAATAT
*
1599986 TAATTTAATAATTTTATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATT
391 TAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATT
1600051 TAGAATTTAAATTTAACAATATTAACCAAAGATAA
456 TAGAATTTAAATTTAACAATATTAACCAAAGATAA
* * *
1600086 TAATAAATATGTAATATATATGTTTTTTGTTGTTAATTTAATAATAATATATATCGTAACGTAAA
1 TAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAA
1600151 AAATAAATCATTAGACGCATATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCT
66 AAATAAATCATTAGACGCATATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCT
*
1600216 TAAATTAATGTTTTCCGCAGTGAAAAAAGTATGGACACTTTTATAAAAATGATAGATACTTTACA
131 TAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGATAGATACTTTACA
* *
1600281 ATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTA-CTATTA
196 ATATAAGCACTAACTATTACATTATATAAACGCTACCTATTACATTATATAAGCGATACCTATTA
* *
1600345 CATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTTTAAAAATGATCGATACTTTTT
261 CATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTT
*
1600410 TTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATA
325 TTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGAGTTTCATGTTTTCCACCTACAATA
*
1600475 TTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
390 TTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATAT
*
1600540 TTAGTATTTAAATTTAACAATATTAACCAAAGATAA
455 TTAGAATTTAAATTTAACAATATTAACCAAAGATAA
* *
1600576 TAATGAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCATAACGTAAA
1 TAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAA
*
1600641 AAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGAT
66 AAATAAATCATTAGACGCATATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGAT
1600701 GTACATACCT
Statistics
Matches: 582, Mismatches: 32, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
489 63 0.11
490 519 0.89
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (490 bp):
TAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAA
AAATAAATCATTAGACGCATATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCT
TAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGATAGATACTTTACA
ATATAAGCACTAACTATTACATTATATAAACGCTACCTATTACATTATATAAGCGATACCTATTA
CATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTT
TTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGAGTTTCATGTTTTCCACCTACAATAT
TAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATT
TAGAATTTAAATTTAACAATATTAACCAAAGATAA
Found at i:1603509 original size:183 final size:183
Alignment explanation
Indices: 1603201--1604138 Score: 1641
Period size: 183 Copynumber: 5.1 Consensus size: 183
1603191 TACTTAAAAT
*
1603201 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATG
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
* *
1603266 TTTATACCGATTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCTGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
1603331 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
1603384 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1603449 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
*
1603514 CGACACTTTTTGACAAGGTATCGACACACTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
1603567 TACTGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
*
1603632 TTTATACCGGTTATATTACAAAATAATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
* **
1603697 CGACACTTTTTGACAAGGTTTCGACACATTTTTCTTTTAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
* *
1603750 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACATATTCGCTCATAAAATCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1603815 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
*
1603880 CGACACTTTTTGACAAGGTATAGACACATTTTT-TTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
* *
1603932 TACCGACACAATATTAAAAAGTATCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGATATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
* *
1603997 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTTTTTCAA-
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATG--TGTAAAT
* * *
1604061 -TCGACACTTTTTGA-AATGGTATAGACACATTTTTCTTCTATTCTGGACATAAAG
129 GTCGACACTTTTTGACAA-GGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
1604115 TACAGACACAATATTAAAAAGTGT
1 TACCGACACAATATTAAAAAGTGT
1604139 GAAAACTTTG
Statistics
Matches: 723, Mismatches: 28, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
181 2 0.00
182 165 0.23
183 552 0.76
184 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (183 bp):
TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
Found at i:1605359 original size:6 final size:6
Alignment explanation
Indices: 1605348--1605434 Score: 84
Period size: 6 Copynumber: 14.5 Consensus size: 6
1605338 ACTTGTTTGG
* * * *
1605348 ATCATC ATCATC ATCATC ATCATC GTCATC ATCTTC ATCGTC ATCTTC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC
* * * * * *
1605396 ATCGTC AGCTTC ATCGTC ATCATC ATCGTC ATCTTC ATC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATC
1605435 GTCAGCTTCA
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.23, C:0.33, G:0.07, T:0.37
Consensus pattern (6 bp):
ATCATC
Found at i:1605365 original size:12 final size:12
Alignment explanation
Indices: 1605352--1605451 Score: 119
Period size: 12 Copynumber: 8.3 Consensus size: 12
1605342 GTTTGGATCA
* *
1605352 TCATCATCATCA
1 TCATCTTCATCG
* * *
1605364 TCATCATCGTCA
1 TCATCTTCATCG
1605376 TCATCTTCATCG
1 TCATCTTCATCG
1605388 TCATCTTCATCG
1 TCATCTTCATCG
*
1605400 TCAGCTTCATCG
1 TCATCTTCATCG
*
1605412 TCATCATCATCG
1 TCATCTTCATCG
1605424 TCATCTTCATCG
1 TCATCTTCATCG
* *
1605436 TCAGCTTCATCT
1 TCATCTTCATCG
1605448 TCAT
1 TCAT
1605452 TGACCGCTTG
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 77 1.00
ACGTcount: A:0.21, C:0.33, G:0.08, T:0.38
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:1605449 original size:6 final size:6
Alignment explanation
Indices: 1605352--1605451 Score: 83
Period size: 6 Copynumber: 16.7 Consensus size: 6
1605342 GTTTGGATCA
* * * * * * *
1605352 TCATCA TCATCA TCATCA TCGTCA TCATCT TCATCG TCATCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * * * *
1605400 TCAGCT TCATCG TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
1605448 TCAT
1 TCAT
1605452 TGACCGCTTG
Statistics
Matches: 77, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 77 1.00
ACGTcount: A:0.21, C:0.33, G:0.08, T:0.38
Consensus pattern (6 bp):
TCATCT
Found at i:1607572 original size:199 final size:200
Alignment explanation
Indices: 1606945--1607708 Score: 1316
Period size: 199 Copynumber: 3.8 Consensus size: 200
1606935 AACATTAAAC
* * * *
1606945 AGTGTCGATACA-TATTATATACCAATTCTCTCATAAAATCGGTATACTTGTACCGGTTAGATTG
1 AGTGTCGACACATTATT-TAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG
* *
1607009 AAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
65 AAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
* *
1607074 GGATCGACACTTTATTGTTACACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
130 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
*
1607139 TAAACAA
195 TACA-AA
* *
1607146 AGTGTCGACACATTATTTAGACCTATTATCTCATAAAACCGGTATACTTGTACTGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1607211 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
1607276 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
1607341 ACAAA
196 ACAAA
* *
1607346 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAATCGATATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
1607411 AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTATGGGATCGACAC-TTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* *
1607475 GATCGACACTTTATGGTTGCAGCCTGTTTGCCATTCATTCTGGACCAGAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
1607540 ACAAA
196 ACAAA
* *
1607545 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
1607610 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTTTGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
1607675 GATCGACACTTTATGGTTGCACCCTGTTTGCCAT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCAT
1607709 ATTGTAAATT
Statistics
Matches: 535, Mismatches: 26, Indels: 5
0.95 0.05 0.01
Matches are distributed among these distances:
199 190 0.36
200 159 0.30
201 182 0.34
202 4 0.01
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (200 bp):
AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
ACAAA
Found at i:1607832 original size:18 final size:18
Alignment explanation
Indices: 1607809--1607869 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
1607799 TCTCATTCAT
*
1607809 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
1607827 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
1607846 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
1607865 AATTA
1 AATTA
1607870 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:1607845 original size:19 final size:19
Alignment explanation
Indices: 1607821--1607869 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1607811 TTATATTCAC
1607821 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
1607840 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1607859 ATACAAAATTA
1 ATACAAAATTA
1607870 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1609699 original size:33 final size:33
Alignment explanation
Indices: 1609662--1609727 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1609652 CATCTTAATA
*
1609662 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
1609695 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
1609728 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:1609786 original size:21 final size:21
Alignment explanation
Indices: 1609761--1609825 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
1609751 CCCCTTATGC
* *
1609761 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1609782 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
1609803 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1609824 CT
1 CT
1609826 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:1611968 original size:20 final size:20
Alignment explanation
Indices: 1611941--1611987 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1611931 TCCGGTAACG
1611941 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
1611960 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
1611981 TTTTACC
1 TTTTACC
1611988 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:1612142 original size:182 final size:181
Alignment explanation
Indices: 1611728--1612199 Score: 703
Period size: 182 Copynumber: 2.6 Consensus size: 181
1611718 CGTACTTACA
* * *
1611728 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATATCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * *
1611793 TATCATATTTTTACATGTTATATCGTTGTGGATCGATA-TTTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* *
1611857 AGGCGCTAAAACTGCTTTTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
*
1611908 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
1611973 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
1612038 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * * **
1612090 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
1612155 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
1612200 AATTTGGATC
Statistics
Matches: 263, Mismatches: 27, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
180 96 0.37
181 68 0.26
182 99 0.38
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (181 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:1612201 original size:181 final size:180
Alignment explanation
Indices: 1611728--1612201 Score: 696
Period size: 180 Copynumber: 2.6 Consensus size: 180
1611718 CGTACTTACA
* * *
1611728 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATATCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * ** *
1611793 TATCATATTTTTACATGTTATATCGTTGTGGATCGATATTTTTTTTAAAGTATCGACACATTATA
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAAAAGTATCGACACATTATA
* *
1611858 GGCGCTAAAACTGCTTTTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
131 GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
*
1611908 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
1611973 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACA-TTTTTAAAAGTATCGACACATTAT
** *
1612038 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
130 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * * **
1612090 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
1612155 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTTAA
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAA
1612202 TTTGGATCGA
Statistics
Matches: 264, Mismatches: 28, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
180 96 0.36
181 74 0.28
182 94 0.36
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (180 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAAAAGTATCGACACATTATA
GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:1614433 original size:13 final size:13
Alignment explanation
Indices: 1614415--1614446 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1614405 ACAATATGGG
1614415 TCAAGCTCAATCA
1 TCAAGCTCAATCA
1614428 TCAAGCTCAATCA
1 TCAAGCTCAATCA
1614441 TCAAGC
1 TCAAGC
1614447 AATAGGTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.31, G:0.09, T:0.22
Consensus pattern (13 bp):
TCAAGCTCAATCA
Found at i:1617064 original size:7 final size:7
Alignment explanation
Indices: 1617052--1617078 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1617042 GGGTGATTTC
1617052 ATCATGA
1 ATCATGA
1617059 ATCATGA
1 ATCATGA
1617066 ATCATGA
1 ATCATGA
1617073 ATCATG
1 ATCATG
1617079 GTTTTGGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (7 bp):
ATCATGA
Found at i:1632905 original size:2 final size:2
Alignment explanation
Indices: 1632898--1632962 Score: 114
Period size: 2 Copynumber: 33.0 Consensus size: 2
1632888 GAATCAAAAC
1632898 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1632940 AT AT AT AT AT AT AT TT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
1632963 TATTAATGAT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1633190 original size:24 final size:23
Alignment explanation
Indices: 1633161--1633225 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 23
1633151 TAAAATGATA
1633161 AACGAATACAAACGAACGAACAT
1 AACGAATACAAACGAACGAACAT
* * *
1633184 GAACGAACACAAACGATCGAGCAT
1 -AACGAATACAAACGAACGAACAT
*
1633208 AAGCGAATATAAACGAAC
1 AA-CGAATACAAACGAAC
1633226 AAATATAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 2 0.06
24 32 0.94
ACGTcount: A:0.52, C:0.22, G:0.17, T:0.09
Consensus pattern (23 bp):
AACGAATACAAACGAACGAACAT
Found at i:1634206 original size:2 final size:2
Alignment explanation
Indices: 1634195--1634224 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1634185 CTCATATCCT
1634195 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1634225 TATTTATTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1637407 original size:20 final size:20
Alignment explanation
Indices: 1637382--1637431 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1637372 ATATATCATT
* *
1637382 TCTTTTCTTTGGCCTTCCTC
1 TCTTTTCCTTAGCCTTCCTC
* *
1637402 TCTTTTCCTTAGCTTTCCTT
1 TCTTTTCCTTAGCCTTCCTC
1637422 TCTTTTCCTT
1 TCTTTTCCTT
1637432 TATTATTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.02, C:0.32, G:0.06, T:0.60
Consensus pattern (20 bp):
TCTTTTCCTTAGCCTTCCTC
Found at i:1645210 original size:2 final size:2
Alignment explanation
Indices: 1645205--1645233 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1645195 ATAATTGATG
1645205 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1645234 TATTAGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1647727 original size:14 final size:14
Alignment explanation
Indices: 1647708--1647734 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1647698 TATTATTCAA
1647708 TATATAAATATATG
1 TATATAAATATATG
1647722 TATATAAATATAT
1 TATATAAATATAT
1647735 ATTGACAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (14 bp):
TATATAAATATATG
Found at i:1653944 original size:15 final size:15
Alignment explanation
Indices: 1653924--1653963 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
1653914 TGTTTTCCAG
1653924 TGGAGTCAATGGTAA
1 TGGAGTCAATGGTAA
1653939 TGGAGTCAATGGTAA
1 TGGAGTCAATGGTAA
1653954 TGGAGTCAAT
1 TGGAGTCAAT
1653964 TGCAGTGGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (15 bp):
TGGAGTCAATGGTAA
Found at i:1653972 original size:15 final size:15
Alignment explanation
Indices: 1653921--1653983 Score: 72
Period size: 15 Copynumber: 4.2 Consensus size: 15
1653911 GCTTGTTTTC
1653921 CAGTGGAGTCAATGG
1 CAGTGGAGTCAATGG
* *
1653936 TAATGGAGTCAATGG
1 CAGTGGAGTCAATGG
* * *
1653951 TAATGGAGTCAATTG
1 CAGTGGAGTCAATGG
*
1653966 CAGTGGACTCAATGG
1 CAGTGGAGTCAATGG
1653981 CAG
1 CAG
1653984 ATGATTTGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.30, C:0.13, G:0.33, T:0.24
Consensus pattern (15 bp):
CAGTGGAGTCAATGG
Found at i:1664167 original size:18 final size:18
Alignment explanation
Indices: 1664141--1664175 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1664131 TCGAAAGGAC
*
1664141 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1664159 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
1664176 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1667114 original size:132 final size:132
Alignment explanation
Indices: 1666862--1667229 Score: 440
Period size: 132 Copynumber: 2.8 Consensus size: 132
1666852 ATAATTTTAA
*
1666862 GAGAGAAAATGATAATATCTAATCATTTCCAATCGAGAAT-AATGATCTCTCATACCTTAAAA-C
1 GAGAGAAAATGATAATATCTAATCATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAAGC
* * * * *
1666925 AATCA-TTATTACTCCAATCGAAATGAAGAGATATCACTATTTCGTCTTAAAATTCAATATCGAT
66 AATCATTTATTACTCCAATCGAAATGAAGAGATATAACTATTCCATCTTAAAAATCAATATCAAT
1666989 TC
131 TC
* * * *
1666991 GAGTGAAAATGATAATATCTAATGATTTCCAATTGAGAATAAATGACCTCTCATATCTTAAAAGC
1 GAGAGAAAATGATAATATCTAATCATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAAGC
* * * *
1667056 AATCATTTATTGCTCCAATCGAAATGAATAGATATAA-TCATTCCATTTTAAAAATCAATATTAA
66 AATCATTTATTACTCCAATCGAAATGAAGAGATATAACT-ATTCCATCTTAAAAATCAATATCAA
1667120 TTC
130 TTC
* * ** * * * *
1667123 GAGAAAAAAAGGCAATATCGAATTATTTCCAATGGAGAATAAATGACCTCTCATGCCTT-AAAGC
1 GAGAGAAAATGATAATATCTAATCATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAAGC
* * * * * *
1667187 AGTAATTTATTACTCCAACCGAAATGAAAAAATATTACTATTC
66 AATCATTTATTACTCCAATCGAAATGAAGAGATATAACTATTC
1667230 GCAATATCGA
Statistics
Matches: 203, Mismatches: 31, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
129 37 0.18
130 20 0.10
131 46 0.23
132 100 0.49
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (132 bp):
GAGAGAAAATGATAATATCTAATCATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAAGC
AATCATTTATTACTCCAATCGAAATGAAGAGATATAACTATTCCATCTTAAAAATCAATATCAAT
TC
Found at i:1670769 original size:22 final size:22
Alignment explanation
Indices: 1670741--1670853 Score: 93
Period size: 22 Copynumber: 5.5 Consensus size: 22
1670731 TTATAATGTT
1670741 AAATATATTATTTAATTATTTA
1 AAATATATTATTTAATTATTTA
* *
1670763 AAATATA--A-TAAATGA-TTA
1 AAATATATTATTTAATTATTTA
1670781 TAAATATATTATTTAATTATTTA
1 -AAATATATTATTTAATTATTTA
* *
1670804 AAATATA--A-TAAATGA-TTA
1 AAATATATTATTTAATTATTTA
*
1670822 TAA-ATATTATTCTAATTATTTA
1 AAATATATTATT-TAATTATTTA
1670844 AAATAT-TTAT
1 AAATATATTAT
1670854 ATATTTAGGT
Statistics
Matches: 70, Mismatches: 10, Indels: 22
0.69 0.10 0.22
Matches are distributed among these distances:
17 3 0.04
18 8 0.11
19 18 0.26
20 3 0.04
21 5 0.07
22 28 0.40
23 5 0.07
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.48
Consensus pattern (22 bp):
AAATATATTATTTAATTATTTA
Found at i:1670787 original size:19 final size:19
Alignment explanation
Indices: 1670763--1670828 Score: 71
Period size: 19 Copynumber: 3.3 Consensus size: 19
1670753 TAATTATTTA
1670763 AAATATAATAAATGATTAT
1 AAATATAATAAATGATTAT
* *
1670782 AAATATATTATTTAATTATT-T
1 AAATATA--A-TAAATGATTAT
1670803 AAAATATAATAAATGATTAT
1 -AAATATAATAAATGATTAT
1670823 AAATAT
1 AAATAT
1670829 TATTCTAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
19 20 0.53
20 2 0.05
21 2 0.05
22 14 0.37
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
AAATATAATAAATGATTAT
Found at i:1670787 original size:41 final size:41
Alignment explanation
Indices: 1670740--1670849 Score: 197
Period size: 41 Copynumber: 2.7 Consensus size: 41
1670730 TTTATAATGT
1670740 TAAATATATTATTTAATTATTTAAAATATAATAAATGATTA
1 TAAATATATTATTTAATTATTTAAAATATAATAAATGATTA
1670781 TAAATATATTATTTAATTATTTAAAATATAATAAATGATTA
1 TAAATATATTATTTAATTATTTAAAATATAATAAATGATTA
1670822 T-AA-ATATTATTCTAATTATTTAAAATAT
1 TAAATATATTATT-TAATTATTTAAAATAT
1670850 TTATATATTT
Statistics
Matches: 68, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
39 8 0.12
40 18 0.26
41 42 0.62
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (41 bp):
TAAATATATTATTTAATTATTTAAAATATAATAAATGATTA
Found at i:1676091 original size:2 final size:2
Alignment explanation
Indices: 1676084--1676144 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1676074 AATTTTCAAG
1676084 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1676126 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1676145 ATTAATACTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1676363 original size:20 final size:20
Alignment explanation
Indices: 1676338--1676389 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
1676328 TAGTTGAAAA
1676338 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTTCATT
1676358 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTTCATT
1676378 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1676390 AGTCTACAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (20 bp):
TCGCGTTGCGATTTTTCATT
Found at i:1676409 original size:22 final size:22
Alignment explanation
Indices: 1676381--1676452 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
1676371 TTTCATTTCG
1676381 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
** *
1676403 CGTTGCGATTTTCTA-AATT-T
1 CGTTGCGATAGTCTACAGTTGT
*
1676423 -GTT--G-TAATCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
1676441 CGTTGCGATAGT
1 CGTTGCGATAGT
1676453 TAAAAAAAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 12
0.66 0.12 0.21
Matches are distributed among these distances:
16 5 0.14
17 4 0.11
18 1 0.03
19 6 0.16
20 1 0.03
21 4 0.11
22 16 0.43
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.42
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:1676540 original size:6 final size:6
Alignment explanation
Indices: 1676529--1676561 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1676519 GACACGTATT
1676529 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1676562 CGAGACGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1677117 original size:6 final size:6
Alignment explanation
Indices: 1677101--1677145 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
1677091 TCTCGTCTCG
1677101 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1677146 ATACGTGTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
5 5 0.13
6 34 0.87
ACGTcount: A:0.00, C:0.18, G:0.51, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:1678043 original size:13 final size:13
Alignment explanation
Indices: 1678025--1678105 Score: 57
Period size: 13 Copynumber: 6.3 Consensus size: 13
1678015 GTCACAACCC
1678025 GACCCGACCCGTT
1 GACCCGACCCGTT
1678038 GACCCGACCC---
1 GACCCGACCCGTT
1678048 GACCCGTTGACCC---
1 GACCC---GACCCGTT
1678061 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1678074 GACCTGACCCGTT
1 GACCCGACCCGTT
*
1678087 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
1678102 GACC
1 GACC
1678106 GGAGTTGACC
Statistics
Matches: 59, Mismatches: 1, Indels: 14
0.80 0.01 0.19
Matches are distributed among these distances:
10 10 0.17
13 36 0.61
15 13 0.22
ACGTcount: A:0.16, C:0.44, G:0.23, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1678044 original size:18 final size:18
Alignment explanation
Indices: 1678021--1678084 Score: 119
Period size: 18 Copynumber: 3.6 Consensus size: 18
1678011 ACCGGTCACA
1678021 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1678039 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1678057 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
1678075 ACCTGACCCG
1 ACCCGACCCG
1678085 TTGACCGTTG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.17, C:0.50, G:0.22, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1678077 original size:8 final size:8
Alignment explanation
Indices: 1678066--1678105 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
1678056 GACCCGACCC
1678066 GACCCGTT
1 GACCCGTT
1678074 GA-CC--T
1 GACCCGTT
1678079 GACCCGTT
1 GACCCGTT
1678087 GA-CCGTT
1 GACCCGTT
1678094 GACCCGTT
1 GACCCGTT
1678102 GACC
1 GACC
1678106 GGAGTTGACC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 3 0.11
6 2 0.07
7 9 0.32
8 14 0.50
ACGTcount: A:0.15, C:0.38, G:0.25, T:0.23
Consensus pattern (8 bp):
GACCCGTT
Found at i:1678098 original size:15 final size:14
Alignment explanation
Indices: 1678066--1678106 Score: 66
Period size: 15 Copynumber: 2.9 Consensus size: 14
1678056 GACCCGACCC
1678066 GACCCGTTGACC-T
1 GACCCGTTGACCGT
1678079 GACCCGTTGACCGTT
1 GACCCGTTGACCG-T
1678094 GACCCGTTGACCG
1 GACCCGTTGACCG
1678107 GAGTTGACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 12 0.46
15 14 0.54
ACGTcount: A:0.15, C:0.37, G:0.27, T:0.22
Consensus pattern (14 bp):
GACCCGTTGACCGT
Found at i:1679444 original size:18 final size:18
Alignment explanation
Indices: 1679418--1679453 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1679408 TCGAAAGGAC
*
1679418 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1679436 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1679454 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1680645 original size:24 final size:24
Alignment explanation
Indices: 1680550--1680651 Score: 111
Period size: 24 Copynumber: 4.2 Consensus size: 24
1680540 ATTTTCGATT
* *
1680550 TGATTTCTGATTTGATACTTGACA
1 TGATTTCTGATCTGATACTTGACC
*
1680574 TGGA-TTCTGATCTGATA-TCTGACT
1 T-GATTTCTGATCTGATACT-TGACC
*
1680598 TGGA-TTCTGATCTGTTACTTGACC
1 T-GATTTCTGATCTGATACTTGACC
*
1680622 TGATTTCTGATATGATACTTGACC
1 TGATTTCTGATCTGATACTTGACC
1680646 TGATTT
1 TGATTT
1680652 ATGTTTTGAT
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
23 3 0.04
24 62 0.91
25 3 0.04
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.44
Consensus pattern (24 bp):
TGATTTCTGATCTGATACTTGACC
Found at i:1682833 original size:13 final size:13
Alignment explanation
Indices: 1682833--1682862 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1682823 CCGTTGACCC
1682833 GACCCGACCCGTT
1 GACCCGACCCGTT
1682846 GACCCGACCCGTT
1 GACCCGACCCGTT
1682859 GACC
1 GACC
1682863 GGAGTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1682834 original size:18 final size:18
Alignment explanation
Indices: 1682811--1682856 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
1682801 ACCGGTCACA
1682811 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1682829 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1682847 ACCCGACCCG
1 ACCCGACCCG
1682857 TTGACCGGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.17, C:0.52, G:0.22, T:0.09
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1684197 original size:18 final size:18
Alignment explanation
Indices: 1684171--1684206 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1684161 TCGAAAGGAC
*
1684171 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1684189 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1684207 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1685399 original size:24 final size:24
Alignment explanation
Indices: 1685304--1685405 Score: 111
Period size: 24 Copynumber: 4.2 Consensus size: 24
1685294 ATTTTCGATT
* *
1685304 TGATTTCTGATTTGATACTTGACA
1 TGATTTCTGATCTGATACTTGACC
*
1685328 TGGA-TTCTGATCTGATA-TCTGACT
1 T-GATTTCTGATCTGATACT-TGACC
*
1685352 TGGA-TTCTGATCTGTTACTTGACC
1 T-GATTTCTGATCTGATACTTGACC
*
1685376 TGATTTCTGATATGATACTTGACC
1 TGATTTCTGATCTGATACTTGACC
1685400 TGATTT
1 TGATTT
1685406 ATGTTTTGAT
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
23 3 0.04
24 62 0.91
25 3 0.04
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.44
Consensus pattern (24 bp):
TGATTTCTGATCTGATACTTGACC
Found at i:1686244 original size:22 final size:22
Alignment explanation
Indices: 1686219--1686291 Score: 89
Period size: 22 Copynumber: 3.4 Consensus size: 22
1686209 AATTTGGAAA
1686219 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* **
1686241 ATCGCAACG-CGAAATG--GAAA
1 ATCGCAACGAC-AACTGTAGACT
1686261 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
1686283 ATCGCAACG
1 ATCGCAACG
1686292 CGAAATGGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
20 15 0.37
21 2 0.05
22 24 0.59
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:1686266 original size:20 final size:20
Alignment explanation
Indices: 1686241--1686396 Score: 129
Period size: 20 Copynumber: 7.6 Consensus size: 20
1686231 ACTGTAGACT
1686241 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
1686261 ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAAATG--GAAA
1686283 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * *
1686303 ATCGCAACGCG-ATTGTCAACT
1 ATCGCAACGCGAAATG-GAA-A
*
1686324 ATCACAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * *
1686344 ATCGCAACGCG-ATTGTCAACT
1 ATCGCAACGCGAAATG-GAA-A
*
1686365 ATCGCAACACGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
1686385 ATCGCAACGCGA
1 ATCGCAACGCGA
1686397 TTTTCAACTA
Statistics
Matches: 104, Mismatches: 22, Indels: 20
0.71 0.15 0.14
Matches are distributed among these distances:
19 6 0.06
20 51 0.49
21 26 0.25
22 21 0.20
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:1686333 original size:21 final size:21
Alignment explanation
Indices: 1686303--1686417 Score: 103
Period size: 21 Copynumber: 5.6 Consensus size: 21
1686293 GAAATGGAAA
1686303 ATCGCAACGCGATTGTCAACT
1 ATCGCAACGCGATTGTCAACT
* * * *
1686324 ATCACAACGCGAAATG-GAA-A
1 ATCGCAACGCG-ATTGTCAACT
1686344 ATCGCAACGCGATTGTCAACT
1 ATCGCAACGCGATTGTCAACT
* * * *
1686365 ATCGCAACACGAAATG-GAA-A
1 ATCGCAACGCG-ATTGTCAACT
*
1686385 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTGTCAACT
1686406 ATCGCAACGCGA
1 ATCGCAACGCGA
1686418 AATGCAACGC
Statistics
Matches: 71, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
19 5 0.07
20 24 0.34
21 36 0.51
22 6 0.08
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGATTGTCAACT
Found at i:1686337 original size:41 final size:41
Alignment explanation
Indices: 1686213--1686421 Score: 305
Period size: 41 Copynumber: 5.0 Consensus size: 41
1686203 GCAACAAATT
* *
1686213 TGGAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACG-CGATTGTCA-ACTATCGCAACGCGAAA
* *
1686255 TGGAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACG-CGATTGTCA-ACTATCGCAACGCGAAA
*
1686297 TGGAAAATCGCAACGCGATTGTCAACTATCACAACGCGAAA
1 TGGAAAATCGCAACGCGATTGTCAACTATCGCAACGCGAAA
*
1686338 TGGAAAATCGCAACGCGATTGTCAACTATCGCAACACGAAA
1 TGGAAAATCGCAACGCGATTGTCAACTATCGCAACGCGAAA
*
1686379 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTGTCAACTATCGCAACGCGAAA
1686420 TG
1 TG
1686422 CAACGCGAAT
Statistics
Matches: 159, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
41 101 0.64
42 58 0.36
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.17
Consensus pattern (41 bp):
TGGAAAATCGCAACGCGATTGTCAACTATCGCAACGCGAAA
Found at i:1687060 original size:23 final size:23
Alignment explanation
Indices: 1687015--1687061 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1687005 TTATTGAACG
* *
1687015 TGTTCACAAACGTTGAACGAACA
1 TGTTCACAAACGTTAAACAAACA
* *
1687038 TGTTCTCAAACTTTAAACAAACA
1 TGTTCACAAACGTTAAACAAACA
1687061 T
1 T
1687062 ATTTGTGAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (23 bp):
TGTTCACAAACGTTAAACAAACA
Found at i:1687873 original size:15 final size:15
Alignment explanation
Indices: 1687849--1687885 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1687839 TTTGAAGGAA
1687849 GATAGGGTTTCAGTT
1 GATAGGGTTTCAGTT
*
1687864 GATAGTGTTTCAGTT
1 GATAGGGTTTCAGTT
1687879 GATAGGG
1 GATAGGG
1687886 AAAAGAAGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.22, C:0.05, G:0.35, T:0.38
Consensus pattern (15 bp):
GATAGGGTTTCAGTT
Found at i:1694427 original size:218 final size:218
Alignment explanation
Indices: 1693600--1694890 Score: 2533
Period size: 218 Copynumber: 6.0 Consensus size: 218
1693590 TAACCGATCG
1693600 TATAGAAACCCAAGTGCACTACGAACTTAAACAACTAAAGTTTGACAGACAAACTTAAGAATAAA
1 TATAGAAACCCAAGTGCACTACGAACTTAAACAACTAAAGTTTGACAGACAAACTTAAGAATAAA
1693665 ACACTTTTATTAATAGAAAACACAATTACAATTTTACACCCTTACCTCACTACTTTTTTCTTTTC
66 ACACTTTTATTAATAGAAAACACAATTACAATTTTACACCCTTACCTCACTACTTTTTTCTTTTC
1693730 TATCTCTAAGCTCTCTTTCTCTAACTCACACTTTTGACACTTTCTAG--ATAATATTAAATATTA
131 TATCTCTAAGCTCTCTTTCTCTAACTCACACTTTTGACACTTTCTAGATATAATATTAAATATTA
1693793 AAAATATATAGACACTAAAAATA
196 AAAATATATAGACACTAAAAATA
1693816 TATAGAAACCCAAGTGCACTACGAACTTAAACAACTAAAGTTTGACAGACAAACTTAAGAATAAA
1 TATAGAAACCCAAGTGCACTACGAACTTAAACAACTAAAGTTTGACAGACAAACTTAAGAATAAA
1693881 ACACTTTTATTAATAGAAAACACAATTACAATTTTACACCCTTACCTCACTACTTTTTTCTTTTC
66 ACACTTTTATTAATAGAAAACACAATTACAATTTTACACCCTTACCTCACTACTTTTTTCTTTTC
1693946 TATCTCTAAGCTCTCTTTCTCTAACTCACACTTTTGACACTTTCTAGATATAATATTAAATATT-
131 TATCTCTAAGCTCTCTTTCTCTAACTCACACTTTTGACACTTTCTAGATATAATATTAAATATTA
1694010 AAAA-ATATAGACACTAAAAATA
196 AAAATATATAGACACTAAAAATA
1694032 TATAGAAACCCAAGTG--C-ACGAACTTAAACAACTAAAGTTTGACAGACAAACTTAAGAATAAA
1 TATAGAAACCCAAGTGCACTACGAACTTAAACAACTAAAGTTTGACAGACAAACTTAAGAATAAA
1694094 ACACTTTTATTAATAGAAAACACAATTACAATTTTACACCCTTACCTCACTACTTTTTTCTTTTC
66 ACACTTTTATTAATAGAAAACACAATTACAATTTTACACCCTTACCTCACTACTTTTTTCTTTTC
1694159 TATCTCTAAGCTCTCTTTCTCTAACTCACACTTTTGACACTTTCTAGATATAATATTAAATATTA
131 TATCTCTAAGCTCTCTTTCTCTAACTCACACTTTTGACACTTTCTAGATATAATATTAAATATTA
1694224 AAAATATATAGACACTAAAAATA
196 AAAATATATAGACACTAAAAATA
1694247 TATAGAAACCCAAGTGCACTACGAACTTAAACAACTAAAGTTTGACAGACAAACTTAAGAATAAA
1 TATAGAAACCCAAGTGCACTACGAACTTAAACAACTAAAGTTTGACAGACAAACTTAAGAATAAA
1694312 ACACTTTTATTAATAGAAAACACAATTACAATTTTACACCCTTACCTCACTACTTTTTTCTTTTC
66 ACACTTTTATTAATAGAAAACACAATTACAATTTTACACCCTTACCTCACTACTTTTTTCTTTTC
1694377 TATCTCTAAGCTCTCTTTCTCTAACTCACACTTTTGACACTTTCTAGATATAATATTAAATATTA
131 TATCTCTAAGCTCTCTTTCTCTAACTCACACTTTTGACACTTTCTAGATATAATATTAAATATTA
1694442 AAAATATATAGACACTAAAAATA
196 AAAATATATAGACACTAAAAATA
1694465 TATAGAAACCCAAGTGCACTACGAACTTAAACAACTAAAGTTTGACAGACAAACTTAAGAATAAA
1 TATAGAAACCCAAGTGCACTACGAACTTAAACAACTAAAGTTTGACAGACAAACTTAAGAATAAA
1694530 ACACTTTTATTAATAGAAAACACAATTACAATTTTACACCCTTACCTCACTACTTTTTTCTTTTC
66 ACACTTTTATTAATAGAAAACACAATTACAATTTTACACCCTTACCTCACTACTTTTTTCTTTTC
1694595 TATCTCTAAGCTCTCTTTCTCTAACTCACACTTTTGACACTTTCTAGATATAATATTAAATATTA
131 TATCTCTAAGCTCTCTTTCTCTAACTCACACTTTTGACACTTTCTAGATATAATATTAAATATTA
1694660 AAAATATATAGACACTAAAAATA
196 AAAATATATAGACACTAAAAATA
1694683 TATAGAAACCCAAGTGCACTACGAACTTAAACAACTAAAGTTTGACAGACAAACTTAAGAATAAA
1 TATAGAAACCCAAGTGCACTACGAACTTAAACAACTAAAGTTTGACAGACAAACTTAAGAATAAA
1694748 ACACTTTTATTAATAGAAAACACAATTACAATTTTACACCCTTACCTCACTACTTTTTTCTTTTC
66 ACACTTTTATTAATAGAAAACACAATTACAATTTTACACCCTTACCTCACTACTTTTTTCTTTTC
1694813 TATCTCTAAGCTCTCTTTCTCTAACTCACACTTTTGACACTTTCTAGATATAATATTAAATATTA
131 TATCTCTAAGCTCTCTTTCTCTAACTCACACTTTTGACACTTTCTAGATATAATATTAAATATTA
1694878 AAAATATATAGAC
196 AAAATATATAGAC
1694891 TATTTTATAG
Statistics
Matches: 1068, Mismatches: 0, Indels: 12
0.99 0.00 0.01
Matches are distributed among these distances:
213 174 0.16
214 5 0.00
215 34 0.03
216 211 0.20
217 5 0.00
218 639 0.60
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (218 bp):
TATAGAAACCCAAGTGCACTACGAACTTAAACAACTAAAGTTTGACAGACAAACTTAAGAATAAA
ACACTTTTATTAATAGAAAACACAATTACAATTTTACACCCTTACCTCACTACTTTTTTCTTTTC
TATCTCTAAGCTCTCTTTCTCTAACTCACACTTTTGACACTTTCTAGATATAATATTAAATATTA
AAAATATATAGACACTAAAAATA
Found at i:1699093 original size:2 final size:2
Alignment explanation
Indices: 1699088--1699113 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1699078 GTACACACTT
1699088 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1699114 AAGTATGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.