Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold412
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: 4645160
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 25 of 32
Found at i:3568899 original size:43 final size:44
Alignment explanation
Indices: 3568795--3568925 Score: 156
Period size: 43 Copynumber: 2.9 Consensus size: 44
3568785 ACAAAGGCGT
*
3568795 CAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-GAAGGTGC
* * * * *
3568844 TAATGTGTTGATTCAAGGCCAGCAACATTGGACTTA-AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGAAGGTGC
3568887 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGAA
3568926 TGCCACCAAC
Statistics
Matches: 70, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
43 38 0.54
44 2 0.03
45 1 0.01
49 29 0.41
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (44 bp):
CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGAAGGTGC
Found at i:3568967 original size:31 final size:27
Alignment explanation
Indices: 3568929--3569174 Score: 86
Period size: 28 Copynumber: 8.7 Consensus size: 27
3568919 CTTAGAATGC
3568929 CACCAACTTGTGTGGGCTTTTGAAAGGGTTG
1 CACCAACTTGTGT--GCTTTT-AAA-GGTTG
3568960 CACCAACTTGTGTGCTTTTAAAGGTTG
1 CACCAACTTGTGTGCTTTTAAAGGTTG
** * *
3568987 C-CCTTGCCTTGTGGGC-TTTGAAGGTTG
1 CACC--AACTTGTGTGCTTTTAAAGGTTG
* * * *
3569014 CCACTAACTTGTGGGCTTTTGAAAAGATG
1 -CACCAACTTGTGTGCTTTT-AAAGGTTG
** * *
3569043 TCACTGACTTGTGGGC-TTTGAAGGTTG
1 -CACCAACTTGTGTGCTTTTAAAGGTTG
** * * *
3569070 TCACTGACTTGTGGGCTTTGAAAGGGGTG
1 -CACCAACTTGTGTGCTTTTAAA-GGTTG
* * * *
3569099 CCACCGACTTGTGGGCTTCTGAAGGTTG
1 -CACCAACTTGTGTGCTTTTAAAGGTTG
** * *
3569127 CCACTGACTTGTGGGCTTTGAAAAGG-TG
1 -CACCAACTTGTGTGCTTT-TAAAGGTTG
* *
3569155 CCACTAACTTGTGAGCTTTT
1 -CACCAACTTGTGTGCTTTT
3569175 GAAAAGATGC
Statistics
Matches: 175, Mismatches: 31, Indels: 22
0.77 0.14 0.10
Matches are distributed among these distances:
26 2 0.01
27 46 0.26
28 62 0.35
29 52 0.30
31 13 0.07
ACGTcount: A:0.18, C:0.19, G:0.30, T:0.33
Consensus pattern (27 bp):
CACCAACTTGTGTGCTTTTAAAGGTTG
Found at i:3569010 original size:27 final size:27
Alignment explanation
Indices: 3568939--3569266 Score: 268
Period size: 29 Copynumber: 11.6 Consensus size: 27
3568929 CACCAACTTG
**
3568939 TGTGGGCTTTTGAAAGGGTTG-CACCAACT
1 TGTGGGC-TTTG-AA-GGTTGCCACTGACT
* * *
3568968 TGTGTGCTTTTAAAGGTTGCC-CTTGCCT
1 TGTGGGC-TTTGAAGGTTGCCAC-TGACT
*
3568996 TGTGGGCTTTGAAGGTTGCCACTAACT
1 TGTGGGCTTTGAAGGTTGCCACTGACT
* * *
3569023 TGTGGGCTTTTGAAAAGATGTCACTGACT
1 TGTGGGC-TTTG-AAGGTTGCCACTGACT
*
3569052 TGTGGGCTTTGAAGGTTGTCACTGACT
1 TGTGGGCTTTGAAGGTTGCCACTGACT
* *
3569079 TGTGGGCTTTGAAAGGGGTGCCACCGACT
1 TGTGGGCTTTG-AA-GGTTGCCACTGACT
3569108 TGTGGGCTTCTGAAGGTTGCCACTGACT
1 TGTGGGCTT-TGAAGGTTGCCACTGACT
*
3569136 TGTGGGCTTTGAAAAGG-TGCCACTAACT
1 TGTGGGCTTTG--AAGGTTGCCACTGACT
* * *
3569164 TGTGAGCTTTTGAAAAGATGCCACTGACT
1 TGTGGGC-TTTG-AAGGTTGCCACTGACT
* * *
3569193 TATGGGCTTTGAAAAGG-TACCATTGACT
1 TGTGGGCTTTG--AAGGTTGCCACTGACT
* *
3569221 TGTGGGCTTTTGAAAAGATGCCACTGACT
1 TGTGGGC-TTTG-AAGGTTGCCACTGACT
3569250 TGTGGGCTTTGGAAGGT
1 TGTGGGCTTT-GAAGGT
3569267 GAGGAATGTC
Statistics
Matches: 248, Mismatches: 35, Indels: 33
0.78 0.11 0.10
Matches are distributed among these distances:
27 55 0.22
28 92 0.37
29 99 0.40
30 2 0.01
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (27 bp):
TGTGGGCTTTGAAGGTTGCCACTGACT
Found at i:3569056 original size:29 final size:28
Alignment explanation
Indices: 3568994--3569260 Score: 297
Period size: 29 Copynumber: 9.5 Consensus size: 28
3568984 TTGCCCTTGC
* * *
3568994 CTTGTGGGCTTTG-AAGGTTGCCACTAA
1 CTTGTGGGCTTTGAAAAGATGCCACTGA
*
3569021 CTTGTGGGCTTTTGAAAAGATGTCACTGA
1 CTTGTGGGC-TTTGAAAAGATGCCACTGA
* * *
3569050 CTTGTGGGCTTTG-AAGGTTGTCACTGA
1 CTTGTGGGCTTTGAAAAGATGCCACTGA
* * *
3569077 CTTGTGGGCTTTGAAAGGGGTGCCACCGA
1 CTTGTGGGCTTTGAAA-AGATGCCACTGA
* *
3569106 CTTGTGGGCTTCTG-AAGGTTGCCACTGA
1 CTTGTGGGCTT-TGAAAAGATGCCACTGA
* *
3569134 CTTGTGGGCTTTGAAAAGGTGCCACTAA
1 CTTGTGGGCTTTGAAAAGATGCCACTGA
*
3569162 CTTGTGAGCTTTTGAAAAGATGCCACTGA
1 CTTGTGGGC-TTTGAAAAGATGCCACTGA
* * * *
3569191 CTTATGGGCTTTGAAAAGGTACCATTGA
1 CTTGTGGGCTTTGAAAAGATGCCACTGA
3569219 CTTGTGGGCTTTTGAAAAGATGCCACTGA
1 CTTGTGGGC-TTTGAAAAGATGCCACTGA
3569248 CTTGTGGGCTTTG
1 CTTGTGGGCTTTG
3569261 GAAGGTGAGG
Statistics
Matches: 206, Mismatches: 26, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
27 36 0.17
28 78 0.38
29 90 0.44
30 2 0.01
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (28 bp):
CTTGTGGGCTTTGAAAAGATGCCACTGA
Found at i:3569144 original size:57 final size:55
Alignment explanation
Indices: 3568994--3569260 Score: 336
Period size: 57 Copynumber: 4.7 Consensus size: 55
3568984 TTGCCCTTGC
* * *
3568994 CTTGTGGGCTTTGAAGGTTGCCACTAACTTGTGGGCTTTTGAAAAGATGTCACTGA
1 CTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGC-TTTGAAAAGGTGCCACTGA
* * *
3569050 CTTGTGGGCTTTGAAGGTTGTCACTGACTTGTGGGCTTTGAAAGGGGTGCCACCGA
1 CTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAA-AGGTGCCACTGA
*
3569106 CTTGTGGGCTTCTGAAGGTTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTAA
1 CTTGTGGGCTT-TGAAGGTTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGA
* * * * * *
3569162 CTTGTGAGCTTTTGAAAAGATGCCACTGACTTATGGGCTTTGAAAAGGTACCATTGA
1 CTTGTGGGC-TTTG-AAGGTTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGA
* *
3569219 CTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTG
1 CTTGTGGGC-TTTG-AAGGTTGCCACTGACTTGTGGGCTTTG
3569261 GAAGGTGAGG
Statistics
Matches: 188, Mismatches: 19, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
55 7 0.04
56 72 0.38
57 109 0.58
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (55 bp):
CTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGA
Found at i:3582870 original size:22 final size:23
Alignment explanation
Indices: 3582845--3582888 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
3582835 TAAAACAAAT
*
3582845 TAAGAATTTATATTA-TAACTTA
1 TAAGAATTAATATTATTAACTTA
* *
3582867 TAAGTATTAATTTTATTAACTT
1 TAAGAATTAATATTATTAACTT
3582889 GATGTTTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (23 bp):
TAAGAATTAATATTATTAACTTA
Found at i:3582964 original size:32 final size:32
Alignment explanation
Indices: 3582923--3582985 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
3582913 TTAATTTAAG
*
3582923 TTCAAGTCATTTTAGATTCGGGTCATTTCGGA
1 TTCAAGTCATTTTAGATTCAGGTCATTTCGGA
* *
3582955 TTCAAGTCATTTTGGGTTCAGGTCATTTCGG
1 TTCAAGTCATTTTAGATTCAGGTCATTTCGG
3582986 GTTTTGGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.19, C:0.16, G:0.24, T:0.41
Consensus pattern (32 bp):
TTCAAGTCATTTTAGATTCAGGTCATTTCGGA
Found at i:3583079 original size:16 final size:16
Alignment explanation
Indices: 3582928--3583079 Score: 78
Period size: 16 Copynumber: 9.4 Consensus size: 16
3582918 TTAAGTTCAA
* *
3582928 GTCATTTTAGATTCGG
1 GTCATTTCAGGTTCGG
**
3582944 GTCATTTC-GGATTCAA
1 GTCATTTCAGG-TTCGG
** *
3582960 GTCATTTTGGGTTCAG
1 GTCATTTCAGGTTCGG
* *
3582976 GTCATTTCGGGTTTTGG
1 GTCATTTCAGG-TTCGG
* * *
3582993 GTTATTTCAAGTTTGG
1 GTCATTTCAGGTTCGG
*
3583009 GTCATTTC-GAGTTTGG
1 GTCATTTCAG-GTTCGG
*
3583025 GTCAATTCAGGTGTC-G
1 GTCATTTCAGGT-TCGG
* *
3583041 GTCA-TTCTAGATTCGA
1 GTCATTTC-AGGTTCGG
*
3583057 GTTATTTCAGGTTCGG
1 GTCATTTCAGGTTCGG
3583073 GTCATTT
1 GTCATTT
3583080 TCGGTTTGAA
Statistics
Matches: 105, Mismatches: 22, Indels: 18
0.72 0.15 0.12
Matches are distributed among these distances:
15 6 0.06
16 81 0.77
17 18 0.17
ACGTcount: A:0.16, C:0.14, G:0.27, T:0.43
Consensus pattern (16 bp):
GTCATTTCAGGTTCGG
Found at i:3585029 original size:17 final size:17
Alignment explanation
Indices: 3585007--3585040 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3584997 CCATCGATTT
3585007 AATTCTATAAATTAATA
1 AATTCTATAAATTAATA
3585024 AATTCTATAAATTAATA
1 AATTCTATAAATTAATA
3585041 CTTCCTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTCTATAAATTAATA
Found at i:3587838 original size:2 final size:2
Alignment explanation
Indices: 3587831--3587857 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3587821 TAGTAAATTA
3587831 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3587858 AAATATGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3589952 original size:26 final size:24
Alignment explanation
Indices: 3589902--3589954 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
3589892 TAATTTTAGA
* **
3589902 AAATCAAAAAAATCAACAATCAAG
1 AAATCAAAAAAATCAAAAAAAAAG
3589926 AAATACAAAAAAATTCAAAAAAAAAG
1 AAAT-CAAAAAAA-TCAAAAAAAAAG
3589952 AAA
1 AAA
3589955 CAAGTTGGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.17
25 8 0.33
26 12 0.50
ACGTcount: A:0.74, C:0.11, G:0.04, T:0.11
Consensus pattern (24 bp):
AAATCAAAAAAATCAAAAAAAAAG
Found at i:3595198 original size:13 final size:13
Alignment explanation
Indices: 3595180--3595205 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3595170 CAGGGTAGTT
3595180 TTGTATCGATACA
1 TTGTATCGATACA
3595193 TTGTATCGATACA
1 TTGTATCGATACA
3595206 AAACTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3595936 original size:61 final size:61
Alignment explanation
Indices: 3595852--3595978 Score: 155
Period size: 61 Copynumber: 2.1 Consensus size: 61
3595842 AAAGATGATG
* * * * **
3595852 AAGATGCGAAGAATAATAAAGGTGTAAATATGCTGATTCCGAGCCAACGATATTAGGCTTA
1 AAGATGAGAAAAATAATAAAGGTGCAAACATGCTGATTCAAAGCCAACGATATTAGGCTTA
* * * * *
3595913 AAGATGAGAAAAATGATAAAGGTGCCAACATGCTGATTCAAATCCAGCGATATTGGGCTTA
1 AAGATGAGAAAAATAATAAAGGTGCAAACATGCTGATTCAAAGCCAACGATATTAGGCTTA
3595974 AAGAT
1 AAGAT
3595979 ACGAAGAATG
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (61 bp):
AAGATGAGAAAAATAATAAAGGTGCAAACATGCTGATTCAAAGCCAACGATATTAGGCTTA
Found at i:3596030 original size:52 final size:52
Alignment explanation
Indices: 3595981--3596194 Score: 157
Period size: 52 Copynumber: 4.1 Consensus size: 52
3595971 TTAAAGATAC
* * *
3595981 GAAGAATGCCAATATGCTGATTCACGGCTACCGACATTAGACTTGAAGATGA
1 GAAGAATGCCAATATACTGATTCAAGGCCACCGACATTAGACTTGAAGATGA
* * *
3596033 GAAGAATGCCAATATACTGATTCAAGGCCAGCGACATTAGGCTTAGGAATG-TTA
1 GAAGAATGCCAATATACTGATTCAAGGCCACCGACATTAGACTT--GAA-GATGA
* * ** * * *
3596087 -AAG-ATGCTAATATACTGATTCAAGGCCAGCGGTATTGGGCTTAAAGATGA
1 GAAGAATGCCAATATACTGATTCAAGGCCACCGACATTAGACTTGAAGATGA
* * * * * * * * * *
3596137 CAA-AGGTGACAATATGCTAATTCAAGGCCAGCAACATTTGACTTAAAGATTA
1 GAAGA-ATGCCAATATACTGATTCAAGGCCACCGACATTAGACTTGAAGATGA
3596189 GAAGAA
1 GAAGAA
3596195 GGATAAAGGT
Statistics
Matches: 129, Mismatches: 25, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
49 1 0.01
50 4 0.03
51 2 0.02
52 112 0.87
53 4 0.03
54 5 0.04
55 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (52 bp):
GAAGAATGCCAATATACTGATTCAAGGCCACCGACATTAGACTTGAAGATGA
Found at i:3596277 original size:52 final size:52
Alignment explanation
Indices: 3596214--3596340 Score: 137
Period size: 52 Copynumber: 2.4 Consensus size: 52
3596204 TGCCGGTATA
* * * **
3596214 CTGATTCAAGGCCGGTGATATTGAACTTAAAGATGAAAAAGGTGCCAATAAG
1 CTGATTCAAGGCCAGCGACATTGAACTTAAAGAAAAAAAAGGTGCCAATAAG
* * * **
3596266 CTGATTCAAGGCCAGCGGCATTGGACTTGAAGAAAAAAAAGGTGCCAATTTG
1 CTGATTCAAGGCCAGCGACATTGAACTTAAAGAAAAAAAAGGTGCCAATAAG
* * *
3596318 TTGAATCAAGGCCAACGACATTG
1 CTGATTCAAGGCCAGCGACATTG
3596341 GGCTTAAAAG
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (52 bp):
CTGATTCAAGGCCAGCGACATTGAACTTAAAGAAAAAAAAGGTGCCAATAAG
Found at i:3597391 original size:20 final size:20
Alignment explanation
Indices: 3597368--3597440 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
3597358 ACAATTCAAA
3597368 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
3597388 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
3597409 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
*
3597429 GTATCAATACAT
1 GTATCGATACAT
3597441 AAAAAAGATG
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3597412 original size:21 final size:21
Alignment explanation
Indices: 3597386--3597461 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
3597376 ACATGTTGCA
3597386 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
3597407 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
* *
3597427 ATGTATCAATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
3597448 ATGTATCGATACAT
1 ATGTATCGATACAT
3597462 TTCTTGGCAG
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 14 0.33
21 29 0.67
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:3597419 original size:41 final size:41
Alignment explanation
Indices: 3597368--3597461 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
3597358 ACAATTCAAA
* *
3597368 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCAATACATAAAAAAGAT
3597409 GTATCGATACATGTTGCAATGTATCAATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCAATACATAAAAAAGAT
3597450 GTATCGATACAT
1 GTATCGATACAT
3597462 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCAATACATAAAAAAGAT
Found at i:3597518 original size:13 final size:13
Alignment explanation
Indices: 3597500--3597525 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3597490 TACAGCAAGT
3597500 ATGTATCGATACA
1 ATGTATCGATACA
3597513 ATGTATCGATACA
1 ATGTATCGATACA
3597526 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3601607 original size:15 final size:15
Alignment explanation
Indices: 3601587--3601617 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3601577 TAAAAATGTC
*
3601587 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
3601602 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
3601617 C
1 C
3601618 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:3603711 original size:20 final size:21
Alignment explanation
Indices: 3603633--3603710 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 21
3603623 ATGTCCAAAA
*
3603633 TGTATCGATACATGTTTTTG-
1 TGTATCGATACATCTTTTTGT
** *
3603653 TGTATCGATACATCTGGAAATTCT
1 TGTATCGATACATCT---TTTTGT
3603677 ATGTATCGATACAT-TTTTTGT
1 -TGTATCGATACATCTTTTTGT
3603698 TGTATCGATACAT
1 TGTATCGATACAT
3603711 TGTATCGATA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 27 0.59
21 3 0.07
23 2 0.04
24 1 0.02
25 13 0.28
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.45
Consensus pattern (21 bp):
TGTATCGATACATCTTTTTGT
Found at i:3603715 original size:13 final size:13
Alignment explanation
Indices: 3603697--3603735 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3603687 ACATTTTTTG
3603697 TTGTATCGATACA
1 TTGTATCGATACA
3603710 TTGTATCGATACA
1 TTGTATCGATACA
*
3603723 CTGTATCGATACA
1 TTGTATCGATACA
3603736 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3605603 original size:36 final size:36
Alignment explanation
Indices: 3605556--3605628 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
3605546 GGGGAGATTT
3605556 ATTAATAAACGGGGGAGATAAAGGAGAGAATGCGTG
1 ATTAATAAACGGGGGAGATAAAGGAGAGAATGCGTG
3605592 ATTAATAAACGGGGGAGATAAAGGAGAGAATGCGTG
1 ATTAATAAACGGGGGAGATAAAGGAGAGAATGCGTG
3605628 A
1 A
3605629 ATTACCTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.42, C:0.05, G:0.36, T:0.16
Consensus pattern (36 bp):
ATTAATAAACGGGGGAGATAAAGGAGAGAATGCGTG
Found at i:3606237 original size:20 final size:20
Alignment explanation
Indices: 3606214--3606286 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3606204 ACAATTCAAA
3606214 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
3606234 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
3606255 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3606275 GTATCGATACAT
1 GTATCGATACAT
3606287 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3606258 original size:21 final size:21
Alignment explanation
Indices: 3606232--3606307 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
3606222 ACATGTTGCA
3606232 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
3606253 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
3606273 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
3606294 ATGTATCGATACAT
1 ATGTATCGATACAT
3606308 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:3606265 original size:41 final size:41
Alignment explanation
Indices: 3606214--3606307 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
3606204 ACAATTCAAA
*
3606214 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3606255 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3606296 GTATCGATACAT
1 GTATCGATACAT
3606308 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:3606364 original size:13 final size:13
Alignment explanation
Indices: 3606346--3606371 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3606336 TACAGCAAGT
3606346 ATGTATCGATACA
1 ATGTATCGATACA
3606359 ATGTATCGATACA
1 ATGTATCGATACA
3606372 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3608039 original size:14 final size:13
Alignment explanation
Indices: 3608023--3608093 Score: 72
Period size: 13 Copynumber: 5.4 Consensus size: 13
3608013 TCTGGACCTT
*
3608023 TTTTTGTTGTTTG
1 TTTTTGTTTTTTG
3608036 TTTTTTGTTTTTTTG
1 -TTTTTG-TTTTTTG
3608051 TTTTTGTTTTTTG
1 TTTTTGTTTTTTG
* *
3608064 TTTTT-TTTTCTA
1 TTTTTGTTTTTTG
* *
3608076 TTTTTCTATTTTG
1 TTTTTGTTTTTTG
3608089 TTTTT
1 TTTTT
3608094 TTGTTGATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
12 10 0.20
13 21 0.43
14 12 0.24
15 6 0.12
ACGTcount: A:0.03, C:0.03, G:0.11, T:0.83
Consensus pattern (13 bp):
TTTTTGTTTTTTG
Found at i:3608048 original size:21 final size:21
Alignment explanation
Indices: 3608021--3608098 Score: 93
Period size: 21 Copynumber: 3.5 Consensus size: 21
3608011 CATCTGGACC
3608021 TTTTTTTGTTGTTTGTTTTTTG
1 TTTTTTTGTT-TTTGTTTTTTG
3608043 TTTTTTTGTTTTTGTTTTTTG
1 TTTTTTTGTTTTTGTTTTTTG
* *
3608064 TTTTTTTTTCTATTTTTCTATTTTG
1 TTTTTTTGT-T-TTTGT-T-TTTTG
3608089 TTTTTTTGTT
1 TTTTTTTGTT
3608099 GATTTTTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
21 19 0.39
22 11 0.22
23 4 0.08
24 2 0.04
25 13 0.27
ACGTcount: A:0.03, C:0.03, G:0.12, T:0.83
Consensus pattern (21 bp):
TTTTTTTGTTTTTGTTTTTTG
Found at i:3608049 original size:8 final size:8
Alignment explanation
Indices: 3608021--3608098 Score: 62
Period size: 8 Copynumber: 10.2 Consensus size: 8
3608011 CATCTGGACC
3608021 TTTTTTTG
1 TTTTTTTG
*
3608029 -TTGTTTG
1 TTTTTTTG
3608036 -TTTTTTG
1 TTTTTTTG
3608043 TTTTTTTG
1 TTTTTTTG
3608051 --TTTTTG
1 TTTTTTTG
3608057 -TTTTTTG
1 TTTTTTTG
3608064 TTTTTTT-
1 TTTTTTTG
3608071 TTCTATTTT-
1 TT-T-TTTTG
*
3608080 TCTATTTTG
1 T-TTTTTTG
3608089 TTTTTTTG
1 TTTTTTTG
3608097 TT
1 TT
3608099 GATTTTTTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
6 6 0.10
7 20 0.34
8 26 0.44
9 6 0.10
10 1 0.02
ACGTcount: A:0.03, C:0.03, G:0.12, T:0.83
Consensus pattern (8 bp):
TTTTTTTG
Found at i:3608049 original size:25 final size:24
Alignment explanation
Indices: 3608021--3608105 Score: 86
Period size: 25 Copynumber: 3.5 Consensus size: 24
3608011 CATCTGGACC
3608021 TTTTTTTGTTGTTTGTTTTTTG---
1 TTTTTTTGTT-TTTGTTTTTTGTTT
3608043 TTTTTTTGTTTTTGTTTTTTGTTT
1 TTTTTTTGTTTTTGTTTTTTGTTT
* * *
3608067 TTTTTTCTATTTTTCTATTTTGTTT
1 TTTTTT-TGTTTTTGTTTTTTGTTT
*
3608092 TTTTGTTGATTTTT
1 TTTTTTTG-TTTTT
3608106 TTTGTGAAGG
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
21 11 0.21
22 10 0.19
24 7 0.13
25 25 0.47
ACGTcount: A:0.04, C:0.02, G:0.12, T:0.82
Consensus pattern (24 bp):
TTTTTTTGTTTTTGTTTTTTGTTT
Found at i:3608094 original size:7 final size:7
Alignment explanation
Indices: 3608022--3608069 Score: 71
Period size: 7 Copynumber: 6.9 Consensus size: 7
3608012 ATCTGGACCT
3608022 TTTTTTG
1 TTTTTTG
*
3608029 TTGTTTG
1 TTTTTTG
3608036 TTTTTTG
1 TTTTTTG
3608043 TTTTTT-
1 TTTTTTG
3608049 TGTTTTTG
1 T-TTTTTG
3608057 TTTTTTG
1 TTTTTTG
3608064 TTTTTT
1 TTTTTT
3608070 TTTCTATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 1 0.03
7 35 0.95
8 1 0.03
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (7 bp):
TTTTTTG
Found at i:3610228 original size:101 final size:101
Alignment explanation
Indices: 3610098--3610299 Score: 404
Period size: 101 Copynumber: 2.0 Consensus size: 101
3610088 ACTTGATAAG
3610098 GTCAAGCCTTGCAATCAACCATGTAGTATAATATAACATGGACTACCTAAGTCTTTTAGCCGTCC
1 GTCAAGCCTTGCAATCAACCATGTAGTATAATATAACATGGACTACCTAAGTCTTTTAGCCGTCC
3610163 AAACCAAGGTACAGCATAACTTCTTGACTGTGGGAT
66 AAACCAAGGTACAGCATAACTTCTTGACTGTGGGAT
3610199 GTCAAGCCTTGCAATCAACCATGTAGTATAATATAACATGGACTACCTAAGTCTTTTAGCCGTCC
1 GTCAAGCCTTGCAATCAACCATGTAGTATAATATAACATGGACTACCTAAGTCTTTTAGCCGTCC
3610264 AAACCAAGGTACAGCATAACTTCTTGACTGTGGGAT
66 AAACCAAGGTACAGCATAACTTCTTGACTGTGGGAT
3610300 AGTTACACTC
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.28
Consensus pattern (101 bp):
GTCAAGCCTTGCAATCAACCATGTAGTATAATATAACATGGACTACCTAAGTCTTTTAGCCGTCC
AAACCAAGGTACAGCATAACTTCTTGACTGTGGGAT
Found at i:3617459 original size:13 final size:13
Alignment explanation
Indices: 3617441--3617466 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3617431 CATTTTGGGA
3617441 TGTATCGATACAT
1 TGTATCGATACAT
3617454 TGTATCGATACAT
1 TGTATCGATACAT
3617467 CTTGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3617463 original size:33 final size:32
Alignment explanation
Indices: 3617421--3617484 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
3617411 TACAAGCTAA
* *
3617421 TGTATCGATACATTTTGGGATGTATCGATACAT
1 TGTATCGATACATCTTGGG-TGTATCAATACAT
*
3617454 TGTATCGATACATCTTGTGTGTATCAATACA
1 TGTATCGATACATCTTGGGTGTATCAATACA
3617485 AATAGTTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCAATACAT
Found at i:3617585 original size:13 final size:13
Alignment explanation
Indices: 3617567--3617591 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3617557 TATTTGGTCA
3617567 TGTATCGATACTT
1 TGTATCGATACTT
3617580 TGTATCGATACT
1 TGTATCGATACT
3617592 GTGCAATATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (13 bp):
TGTATCGATACTT
Found at i:3617623 original size:20 final size:20
Alignment explanation
Indices: 3617600--3617640 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3617590 CTGTGCAATA
*
3617600 TGTATCGATACATTTGAAGG
1 TGTATCGATACATTTCAAGG
3617620 TGTATCGATACATTTCAAGG
1 TGTATCGATACATTTCAAGG
3617640 T
1 T
3617641 TTTGACCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATTTCAAGG
Found at i:3618173 original size:22 final size:22
Alignment explanation
Indices: 3618146--3618190 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
3618136 TTTTCTTTTC
3618146 TCTCCCCCTTAATCAAAA-AATT
1 TCTCCCCCTTAAT-AAAATAATT
3618168 TCTCCCCCTTAATAAAATAATT
1 TCTCCCCCTTAATAAAATAATT
3618190 T
1 T
3618191 AACAATTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.36, C:0.29, G:0.00, T:0.36
Consensus pattern (22 bp):
TCTCCCCCTTAATAAAATAATT
Found at i:3619063 original size:37 final size:37
Alignment explanation
Indices: 3619013--3619088 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
3619003 AAGGTGAAGG
3619013 TACCGATCATGGGAATGAAGGTGGGTGGCTTTGTTGT
1 TACCGATCATGGGAATGAAGGTGGGTGGCTTTGTTGT
3619050 TACCGATCATGGGAATGAAGGTGGGTGGCTTTGTTGT
1 TACCGATCATGGGAATGAAGGTGGGTGGCTTTGTTGT
3619087 TA
1 TA
3619089 GGAACTCGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.20, C:0.11, G:0.37, T:0.33
Consensus pattern (37 bp):
TACCGATCATGGGAATGAAGGTGGGTGGCTTTGTTGT
Found at i:3620318 original size:8 final size:8
Alignment explanation
Indices: 3620305--3620330 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
3620295 AACATCATTC
3620305 ATCACAAA
1 ATCACAAA
3620313 ATCACAAA
1 ATCACAAA
3620321 ATCACAAA
1 ATCACAAA
3620329 AT
1 AT
3620331 TTAATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (8 bp):
ATCACAAA
Found at i:3622105 original size:13 final size:13
Alignment explanation
Indices: 3622087--3622112 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3622077 CTATTTATGA
3622087 TGTATCGATACAC
1 TGTATCGATACAC
3622100 TGTATCGATACAC
1 TGTATCGATACAC
3622113 ATAAATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:3622197 original size:21 final size:22
Alignment explanation
Indices: 3622159--3622216 Score: 109
Period size: 21 Copynumber: 2.7 Consensus size: 22
3622149 TGATTTTTAA
3622159 CGATACATGAACAGTGATGTAT
1 CGATACATGAACAGTGATGTAT
3622181 CGATACATGAA-AGTGATGTAT
1 CGATACATGAACAGTGATGTAT
3622202 CGATACATGAACAGT
1 CGATACATGAACAGT
3622217 ATGAATAGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 21 0.60
22 14 0.40
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (22 bp):
CGATACATGAACAGTGATGTAT
Found at i:3622325 original size:53 final size:53
Alignment explanation
Indices: 3622261--3622397 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
3622251 CTACTTCCAA
3622261 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
3622314 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
3622367 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
3622398 TATGCAATTT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 67 0.84
54 13 0.16
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:3622430 original size:20 final size:20
Alignment explanation
Indices: 3622367--3622437 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
3622357 GCCAATGTCC
**
3622367 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
3622387 TGTATCGATAC-TATGCAATT
1 TGTATCGATACATAT-TAATG
3622407 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
3622427 TGTATCGATAC
1 TGTATCGATAC
3622438 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:3622503 original size:21 final size:21
Alignment explanation
Indices: 3622477--3622517 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3622467 GTCAACCTTG
3622477 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
3622498 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
3622518 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:3627725 original size:19 final size:20
Alignment explanation
Indices: 3627680--3627731 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
3627670 TTACAAGCCA
* *
3627680 ATGTATCGATACTTTTTGGG
1 ATGTATCGATACATCTTGGG
*
3627700 ATGTATCGATACATCTTGTG
1 ATGTATCGATACATCTTGGG
3627720 -TGTATCGATACA
1 ATGTATCGATACA
3627732 AACAATTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATCTTGGG
Found at i:3627820 original size:20 final size:21
Alignment explanation
Indices: 3627773--3627828 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
3627763 GCCAATGACC
*
3627773 TGTATCGATACATTCT-TTACA
1 TGTATCGATACATT-TGGTACA
*
3627794 AGTATCGATACATTTGGT-CA
1 TGTATCGATACATTTGGTACA
3627814 TGTATCGATAC-TTTG
1 TGTATCGATACATTTG
3627829 TATCGATACT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 4 0.13
20 13 0.42
21 14 0.45
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (21 bp):
TGTATCGATACATTTGGTACA
Found at i:3627832 original size:13 final size:13
Alignment explanation
Indices: 3627814--3627838 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3627804 CATTTGGTCA
3627814 TGTATCGATACTT
1 TGTATCGATACTT
3627827 TGTATCGATACT
1 TGTATCGATACT
3627839 GTGCAATATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (13 bp):
TGTATCGATACTT
Found at i:3630682 original size:51 final size:51
Alignment explanation
Indices: 3630627--3630740 Score: 167
Period size: 51 Copynumber: 2.2 Consensus size: 51
3630617 ATAGCGGGGT
* * *
3630627 TGGAGTATCCCCGATTGTGAGAAATTGGTGTTTTGGAAATAAAATC-GGAGC
1 TGGAGTATCCCCGATTGTGAAAAATTGGTATTTTAGAAATAAAATCAGGA-C
* *
3630678 TGGAGTATCACCGATTGTGAAAAATTGGTATTTTAGAAATAAAATCAGGAT
1 TGGAGTATCCCCGATTGTGAAAAATTGGTATTTTAGAAATAAAATCAGGAC
3630729 TGGAGTATCCCC
1 TGGAGTATCCCC
3630741 TCGAAAATAA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 53 0.95
52 3 0.05
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.30
Consensus pattern (51 bp):
TGGAGTATCCCCGATTGTGAAAAATTGGTATTTTAGAAATAAAATCAGGAC
Found at i:3630776 original size:28 final size:30
Alignment explanation
Indices: 3630723--3630799 Score: 92
Period size: 28 Copynumber: 2.7 Consensus size: 30
3630713 GAAATAAAAT
3630723 CAGGATTGGAGTATCCCC--TCGAAAATAA
1 CAGGATTGGAGTATCCCCGATCGAAAATAA
3630751 C-GAGATTGGAGTATCCCCGAT-G-AAATAA
1 CAG-GATTGGAGTATCCCCGATCGAAAATAA
* *
3630779 CAGGGTTGGAGTACCCCCGAT
1 CAGGATTGGAGTATCCCCGAT
3630800 TATGAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
27 1 0.02
28 39 0.91
29 2 0.05
30 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (30 bp):
CAGGATTGGAGTATCCCCGATCGAAAATAA
Found at i:3630918 original size:76 final size:76
Alignment explanation
Indices: 3630756--3630999 Score: 253
Period size: 76 Copynumber: 3.2 Consensus size: 76
3630746 AATAACGAGA
* * * *
3630756 TTGGAGTATCCC--CGATGAAATAAC-AGGGTTGGAGTACCCCCGATTATGAAAAAATAATATTT
1 TTGGAGTATCCCTTCGA--AAATAACGA-GGTTGGAGTATCCCC-A--ATGAAAAATTGAT-GTT
* *
3630818 TTAGATATAAAGCCGGGG
59 TTAGAAATAAAACCGGGG
* *
3630836 TTGGAGTAT-CCTCTCGGAAATAATGAGGTTGGAGTATCCCCAATGAAAAATTGATGTTTTAGAA
1 TTGGAGTATCCCT-TCGAAAATAACGAGGTTGGAGTATCCCCAATGAAAAATTGATGTTTTAGAA
*
3630900 ATAAAACCTGGG
65 ATAAAACCGGGG
* * * * *
3630912 TTGGAGTGTCCCTTTGAAAATAACGGGGTTGGAGTATCCCCGATGAAAAATTGATGTTTTATAAA
1 TTGGAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCCAATGAAAAATTGATGTTTTAGAAA
3630977 TAAAACCGGGG
66 TAAAACCGGGG
*
3630988 TTAGAGTATCCC
1 TTGGAGTATCCC
3631000 CGAGATGAAA
Statistics
Matches: 140, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
76 91 0.65
77 14 0.10
79 3 0.02
80 29 0.21
81 1 0.01
82 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.28
Consensus pattern (76 bp):
TTGGAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCCAATGAAAAATTGATGTTTTAGAAA
TAAAACCGGGG
Found at i:3631133 original size:102 final size:103
Alignment explanation
Indices: 3630954--3631218 Score: 324
Period size: 102 Copynumber: 2.6 Consensus size: 103
3630944 AGTATCCCCG
* * *
3630954 ATGAAAAATTGATGTTTTATAAATAAAACCGGGGTTAGAGTATCCCCGA--GATGAAAAATTGGT
1 ATGAAAAATTGGTGTTTTAGAAATAAAACCGGGGTTAGAGTATCCCCGATTG-TGAAAAATTAGT
*
3631017 GTTTTTGGAAATAAAATCAAAGTTAGAGTGTCCACGATT
65 GTTTTTGGAAATAAAATCAAAGTTAGAGTATCCACGATT
* *
3631056 AT-AGAAAATTGGTGTTTT-GAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAATTAG
1 ATGA-AAAATTGGTGTTTTAG-AAATAAAACCGGGGTTAGAGTATCCCCGATTGTGAAAAATTAG
* ** * *
3631119 TG-TTTTGGTAATAAAATCGGAGTTGGAGTATCCCCGATT
64 TGTTTTTGGAAATAAAATCAAAGTTAGAGTATCCACGATT
* * * * *
3631158 GTGAAAAATTAGTGTTTTAGGAATAAAACCGGGGTTAGAGTACCCCCGATTATGAAAAATT
1 ATGAAAAATTGGTGTTTTAGAAATAAAACCGGGGTTAGAGTATCCCCGATTGTGAAAAATT
3631219 GAGAAACTTA
Statistics
Matches: 139, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
101 1 0.01
102 124 0.89
103 13 0.09
104 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (103 bp):
ATGAAAAATTGGTGTTTTAGAAATAAAACCGGGGTTAGAGTATCCCCGATTGTGAAAAATTAGTG
TTTTTGGAAATAAAATCAAAGTTAGAGTATCCACGATT
Found at i:3631216 original size:51 final size:50
Alignment explanation
Indices: 3630935--3631218 Score: 265
Period size: 51 Copynumber: 5.6 Consensus size: 50
3630925 TTGAAAATAA
* **
3630935 CGGGGTTGGAGTATCCCCG---ATGAAAAATT-GATGTTTTATAAATAAAAC
1 CGGGGTTAGAGTATCCCCGATTATGAAAAATTAG-TGTTTT-GGAATAAAAC
* * *
3630983 CGGGGTTAGAGTATCCCCGA-GATGAAAAATTGGTGTTTTTGGAAATAAAAT
1 CGGGGTTAGAGTATCCCCGATTATGAAAAATTAGTG-TTTTGG-AATAAAAC
*** * * * *
3631034 CAAAGTTAGAGTGTCCACGATTAT-AGAAAATTGGTGTTTTGAAAATAAAAC
1 CGGGGTTAGAGTATCCCCGATTATGA-AAAATTAGTGTTTTG-GAATAAAAC
* * * *
3631085 CGGGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTGGTAATAAAAT
1 CGGGGTTAGAGTATCCCCGATTATGAAAAATTAGTGTTTTGG-AATAAAAC
* * *
3631136 CGGAGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGGAATAAAAC
1 CGGGGTTAGAGTATCCCCGATTATGAAAAATTAGTGTTTT-GGAATAAAAC
*
3631187 CGGGGTTAGAGTACCCCCGATTATGAAAAATT
1 CGGGGTTAGAGTATCCCCGATTATGAAAAATT
3631219 GAGAAACTTA
Statistics
Matches: 195, Mismatches: 30, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
48 18 0.09
50 12 0.06
51 151 0.77
52 14 0.07
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.30
Consensus pattern (50 bp):
CGGGGTTAGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAATAAAAC
Found at i:3631219 original size:153 final size:147
Alignment explanation
Indices: 3630924--3631215 Score: 333
Period size: 153 Copynumber: 2.0 Consensus size: 147
3630914 GGAGTGTCCC
*
3630924 TTTGAAAATAACGGGGTTGGAGTATCCCCGATGAAAAATTGATGTTTTATAAATAAAACCGGGGT
1 TTTGAAAATAACGGGGTTGGAGTATCCCCGATGAAAAATTGATGTTTTATAAATAAAACCGGAGT
* * * **
3630989 TAGAGTATCCCCGAGATGAAAAATTGGTGTTTTTGGAAATAAAATCAAAGTTAGAGTGTCCACGA
66 TAGAGTATCCCCGAGATGAAAAATTAGTGTTTTAGGAAATAAAACCAAAGTTAGAGTACCCACGA
3631054 TTATAGAAAATTGGTGT
131 TTATAGAAAATTGGTGT
* *
3631071 TTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAATT-AGTGTTTTGGT-AATAAA
1 TTTGAAAAT--AA-CGGGGTTGGAGTATCCCCGA---TGAAAAATTGA-TGTTTT-ATAAATAAA
* * ***
3631134 ATCGGAGTTGGAGTATCCCCGATTG-TGAAAAATTAGTGTTTTAGG-AATAAAACCGGGGTTAGA
58 ACCGGAGTTAGAGTATCCCCGA--GATGAAAAATTAGTGTTTTAGGAAATAAAACCAAAGTTAGA
*
3631197 GTACCCCCGATTAT-GAAAA
121 GTACCCACGATTATAGAAAA
3631216 ATTGAGAAAC
Statistics
Matches: 121, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
147 9 0.07
149 2 0.02
150 20 0.17
152 6 0.05
153 64 0.53
154 19 0.16
155 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (147 bp):
TTTGAAAATAACGGGGTTGGAGTATCCCCGATGAAAAATTGATGTTTTATAAATAAAACCGGAGT
TAGAGTATCCCCGAGATGAAAAATTAGTGTTTTAGGAAATAAAACCAAAGTTAGAGTACCCACGA
TTATAGAAAATTGGTGT
Found at i:3633528 original size:20 final size:20
Alignment explanation
Indices: 3633503--3633557 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
3633493 AAAATACCTG
*
3633503 AATGTATCGATACATTGTAA
1 AATGTATCGATACATTGCAA
*
3633523 AATGTATCGATACAATGCAA
1 AATGTATCGATACATTGCAA
3633543 AATGTATCGATACAT
1 AATGTATCGATACAT
3633558 CTGGGTAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATTGCAA
Found at i:3634782 original size:60 final size:61
Alignment explanation
Indices: 3634553--3634788 Score: 266
Period size: 61 Copynumber: 3.9 Consensus size: 61
3634543 AAGGAAGTAT
* *
3634553 GTCCTACTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGC
1 GTCCTACTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGC
* * * * * * *
3634614 GTCCT-GTCCTTTGAGGACTGGAAGGTGCCAGCAACTTATGTGGGTTTTGCAAAAAGAAA-GC
1 GTCCTACT-CTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTG-AAAAGGAAAGGC
* * *
3634675 ATCCTACCCTTTGAGGACTGAAAAGTGCCGCCAACTTGTGTGGGCTTT-AAAAGGATAAGGC
1 GTCCTACTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGGA-AAGGC
* * * *
3634736 GTCCTGCTCTTTGAGGACTG-AAGGAGCCACCAGCTTGTGTGGGCTTT-AAAAGG
1 GTCCTACTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGG
3634789 CATCCTGCTT
Statistics
Matches: 144, Mismatches: 26, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
59 6 0.04
60 32 0.22
61 99 0.69
62 7 0.05
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (61 bp):
GTCCTACTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGC
Found at i:3634990 original size:215 final size:214
Alignment explanation
Indices: 3634612--3635008 Score: 529
Period size: 215 Copynumber: 1.8 Consensus size: 214
3634602 AAAAGAAAAG
* *
3634612 GCGTCCTGTCCTTTGAGGACTGGAAGGTGCCAGCAACTTATGTGGGTTTTGCAAAAAGAAAGCAT
1 GCGTCCTGTCCTTTGAGGACTGGAAGGTGCCACCAACTTATGTGGGCTTT-CAAAAAGAAAGCAT
* * * * *
3634677 CCTACCCTTTGAGGACTGAAAAGTGCCGCCAACTTGTGTGGGCTTTAAAAGGATAAGGCGTCCTG
65 CCTACCCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAAGCATCCTG
* *
3634742 CTCTTTGAGGACTGAAGGAGCCACCAGCTTGTGTGGGCTTT-AAAAGGCATCCTGCTTTTTGAAG
130 CTCTTTGAGGACTGAAGAAGCCACCAACTTGTGTGGGCTTTGAAAA-GCATCCTGCTTTTTGAAG
3634806 ACAAAAAGGTGAAAGGAGAGA
194 ACAAAAAGGTGAAAGGAGAGA
* *
3634827 GCGTCCTG-CTCTTTGAGGACTAGGAA-GTGCCACCAACTTGTGTGGGCTTT-AAAAGGAGAAGG
1 GCGTCCTGTC-CTTTGAGGACT-GGAAGGTGCCACCAACTTATGTGGGCTTTCAAAA--AGAAAG
* * *
3634889 CATCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTAGGCTTTGAAAA-GAAAAAGCAT
62 CATCCTACCCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTAGGCTTT-AAAAGGAAAAAGCAT
*
3634952 CCTGGTCTTTGAGGACTAGAA-AATGCCACCAACTTGTGTGGGCTTTGAAAAGCATCC
126 CCTGCTCTTTGAGGACT-GAAGAA-GCCACCAACTTGTGTGGGCTTTGAAAAGCATCC
3635009 AGATCTTTGA
Statistics
Matches: 159, Mismatches: 15, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
213 4 0.03
214 49 0.31
215 98 0.62
216 8 0.05
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (214 bp):
GCGTCCTGTCCTTTGAGGACTGGAAGGTGCCACCAACTTATGTGGGCTTTCAAAAAGAAAGCATC
CTACCCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAAGCATCCTGC
TCTTTGAGGACTGAAGAAGCCACCAACTTGTGTGGGCTTTGAAAAGCATCCTGCTTTTTGAAGAC
AAAAAGGTGAAAGGAGAGA
Found at i:3635001 original size:28 final size:27
Alignment explanation
Indices: 3634970--3635057 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 27
3634960 TTGAGGACTA
3634970 GAAAATGCCACCAACTTGTGTGGGCTTT
1 GAAAATGCCACCAACTT-TGTGGGCTTT
* * *
3634998 GAAAA-G-CATCCAGATCTTTGAGGAC-TG
1 GAAAATGCCA-CCA-A-CTTTGTGGGCTTT
3635025 GAAAATGCCACCAACTTATGTGGGCTTT
1 GAAAATGCCACCAACTT-TGTGGGCTTT
3635053 GAAAA
1 GAAAA
3635058 GAAAAAGCAT
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
26 5 0.11
27 16 0.34
28 21 0.45
29 5 0.11
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (27 bp):
GAAAATGCCACCAACTTTGTGGGCTTT
Found at i:3635756 original size:27 final size:27
Alignment explanation
Indices: 3635616--3635756 Score: 70
Period size: 27 Copynumber: 5.1 Consensus size: 27
3635606 TGAGGACTGG
3635616 AAAATGCCACCAACTTGTGTGGGCTTT
1 AAAATGCCACCAACTTGTGTGGGCTTT
* * ** * * * **
3635643 GAAA-GGCATCCTGCTCTTTGAGGACTGG
1 AAAATGCCA-CCAACT-TGTGTGGGCTTT
*
3635671 AAAATGCCACCCACTTGTGTGGGCTTT
1 AAAATGCCACCAACTTGTGTGGGCTTT
* ** * * * **
3635698 AAAA-GGCATCCTGCTCTTTGAGGACTGG
1 AAAATGCCA-CCAACT-TGTGTGGGCTTT
3635726 AAAATGCCACCAACTTGTGTGGGCTTT
1 AAAATGCCACCAACTTGTGTGGGCTTT
3635753 AAAA
1 AAAA
3635757 GACGTCCTGC
Statistics
Matches: 74, Mismatches: 34, Indels: 12
0.62 0.28 0.10
Matches are distributed among these distances:
26 6 0.08
27 33 0.45
28 29 0.39
29 6 0.08
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (27 bp):
AAAATGCCACCAACTTGTGTGGGCTTT
Found at i:3636032 original size:55 final size:55
Alignment explanation
Indices: 3634830--3636033 Score: 1346
Period size: 55 Copynumber: 21.0 Consensus size: 55
3634820 GGAGAGAGCG
*
3634830 TCCTGCTCTTTGAGGACTAGG-AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCA
1 TCCTGCTCTTTGAGGACT-GGAAAATGCCACCAACTTGTGTGGGCTTT-----GA-AAGGCA
** *
3634891 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTAGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCA
* * *
3634951 TCCTGGTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
* * *
3635006 TCCAGATCTTTGAGGACTGGAAAATGCCACCAACTTATGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCA
3635067 TCCTGCTCTTTG-GGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
* *
3635121 TCCTGCTCTTTAAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
* * * * **
3635176 TCCTACTCTTTGAAGACTGGAAAAAGCCACCAACTTGTGTGGGCATTAAAAAGAGAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGC-TT----TGA-AAGGCA
* ** * *
3635237 TCATGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-----GAAAGGCA
3635296 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCA
* ** *
3635357 TCTTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGCA
** *
3635416 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGCA
*
3635475 TCCTGCTCTTTGAGGACTGGAAGATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCA
* * *
3635536 TCCTACTTTTTGAGGACTGGAAAATGCCACCAACGTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCA
3635597 T-CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
* *
3635651 TCCTGCTCTTTGAGGACTGGAAAATGCCACCCACTTGTGTGGGCTTTAAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
* * *
3635706 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGACG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
*
3635761 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
* * *
3635816 TCATGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGACTTTGAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
* * * *
3635871 TCCTGCTCTTTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGACG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
* *
3635926 TCTTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
* *
3635981 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCGACTTGTGTGGGCTTTGAAAGG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGG
3636034 AAAAGGCGTC
Statistics
Matches: 1016, Mismatches: 79, Indels: 102
0.85 0.07 0.09
Matches are distributed among these distances:
54 26 0.03
55 473 0.47
56 20 0.02
59 110 0.11
60 227 0.22
61 154 0.15
64 6 0.01
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
Found at i:3637029 original size:1 final size:1
Alignment explanation
Indices: 3637023--3637094 Score: 63
Period size: 1 Copynumber: 72.0 Consensus size: 1
3637013 GCAGATTCTC
* * * * * * * * *
3637023 TTTTTTTTTTCTCTTTTTTCTTTGTTTTTTTTTATTTTTTTTTATTTTTTTGTTGTTTTTTGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3637088 TTTTTTT
1 TTTTTTT
3637095 GAAAAAAAGA
Statistics
Matches: 53, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.03, C:0.04, G:0.06, T:0.88
Consensus pattern (1 bp):
T
Found at i:3637036 original size:13 final size:13
Alignment explanation
Indices: 3637018--3637055 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
3637008 CATAAGCAGA
3637018 TTCTCTTTTTTTT
1 TTCTCTTTTTTTT
*
3637031 TTCTCTTTTTTCT
1 TTCTCTTTTTTTT
*
3637044 TTGT-TTTTTTTT
1 TTCTCTTTTTTTT
3637056 ATTTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 7 0.32
13 15 0.68
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.84
Consensus pattern (13 bp):
TTCTCTTTTTTTT
Found at i:3637041 original size:10 final size:10
Alignment explanation
Indices: 3637025--3637094 Score: 70
Period size: 10 Copynumber: 6.7 Consensus size: 10
3637015 AGATTCTCTT
*
3637025 TTTTTTTTCTC
1 TTTTTTTT-TA
*
3637036 TTTTTTCTTTG
1 TTTTTT-TTTA
3637047 TTTTTTTTTA
1 TTTTTTTTTA
3637057 TTTTTTTTTA
1 TTTTTTTTTA
*
3637067 TTTTTTTGTTG
1 TTTTTTT-TTA
3637078 TTTTTTGTTT-
1 TTTTTT-TTTA
3637088 TTTTTTT
1 TTTTTTT
3637095 GAAAAAAAGA
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
9 1 0.02
10 26 0.49
11 23 0.43
12 3 0.06
ACGTcount: A:0.03, C:0.04, G:0.06, T:0.87
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:3637071 original size:31 final size:31
Alignment explanation
Indices: 3637023--3637094 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 31
3637013 GCAGATTCTC
*
3637023 TTTTTTTTTTCTCTTTTTTCT-TTGTTTTTT-
1 TTTTTTTTTTCTATTTTTT-TGTTGTTTTTTG
*
3637053 TTTATTTTTTTTTATTTTTTTGTTGTTTTTTG
1 TTT-TTTTTTTCTATTTTTTTGTTGTTTTTTG
3637085 TTTTTTTTTT
1 TTTTTTTTTT
3637095 GAAAAAAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
30 4 0.11
31 30 0.81
32 3 0.08
ACGTcount: A:0.03, C:0.04, G:0.06, T:0.88
Consensus pattern (31 bp):
TTTTTTTTTTCTATTTTTTTGTTGTTTTTTG
Found at i:3638771 original size:84 final size:84
Alignment explanation
Indices: 3638630--3638799 Score: 304
Period size: 84 Copynumber: 2.0 Consensus size: 84
3638620 CATCACGCGT
* *
3638630 TTGCCATTCTCTCTTCAATTGATAAACGACGAGGGCTGAATCTCCAAATACTTGCAACACCCAGA
1 TTGCCATTATCCCTTCAATTGATAAACGACGAGGGCTGAATCTCCAAATACTTGCAACACCCAGA
3638695 TGCCGCTTTCGATGGCTGC
66 TGCCGCTTTCGATGGCTGC
*
3638714 TTGCCATTATCCCTTCAATTGATAAACGACGAGGGCTGAATCTCCAAATACTTGCAACACCCGGA
1 TTGCCATTATCCCTTCAATTGATAAACGACGAGGGCTGAATCTCCAAATACTTGCAACACCCAGA
*
3638779 TGCCTCTTTCGATGGCTGC
66 TGCCGCTTTCGATGGCTGC
3638798 TT
1 TT
3638800 AGAGTCCCAG
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (84 bp):
TTGCCATTATCCCTTCAATTGATAAACGACGAGGGCTGAATCTCCAAATACTTGCAACACCCAGA
TGCCGCTTTCGATGGCTGC
Found at i:3644693 original size:13 final size:13
Alignment explanation
Indices: 3644675--3644705 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3644665 GCATTGCTTC
3644675 ATGTATCGATACA
1 ATGTATCGATACA
3644688 ATGTATCGATACA
1 ATGTATCGATACA
*
3644701 TTGTA
1 ATGTA
3644706 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3644693 original size:33 final size:33
Alignment explanation
Indices: 3644655--3644721 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
3644645 ATTACAAGCT
* *
3644655 ATGTATCGATGCATTGCT-TCATGTATCGATACA
1 ATGTATCGATACATTG-TACCATGTATCGATACA
3644688 ATGTATCGATACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
3644721 A
1 A
3644722 ATAGTGATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 1 0.03
33 30 0.97
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:3644809 original size:13 final size:13
Alignment explanation
Indices: 3644791--3644817 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3644781 TACATTAAAC
3644791 ATGTATTGATACA
1 ATGTATTGATACA
3644804 ATGTATTGATACA
1 ATGTATTGATACA
3644817 A
1 A
3644818 GGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
ATGTATTGATACA
Found at i:3647182 original size:20 final size:19
Alignment explanation
Indices: 3647141--3647180 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 19
3647131 TTCTGTTGAT
3647141 GATTTTGATGAAAAATGAAA
1 GATTTTGATGAAAAAT-AAA
3647161 GATTTTGAAGTGAAAAATAA
1 GATTTTG-A-TGAAAAATAA
3647181 GAATTTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (19 bp):
GATTTTGATGAAAAATAAA
Found at i:3647325 original size:13 final size:13
Alignment explanation
Indices: 3647307--3647335 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3647297 AAATAGTACC
3647307 CAATGTATCGATA
1 CAATGTATCGATA
3647320 CAATGTATCGATA
1 CAATGTATCGATA
3647333 CAA
1 CAA
3647336 GGAATGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:3647486 original size:20 final size:18
Alignment explanation
Indices: 3647461--3647501 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
3647451 CTATAGACCC
3647461 TAATTCAAGTCAAACAAACA
1 TAATTCAA-TCAAAC-AACA
*
3647481 TAATTCAATCATACAACA
1 TAATTCAATCAAACAACA
3647499 TAA
1 TAA
3647502 CAAACATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 5 0.25
20 8 0.40
ACGTcount: A:0.54, C:0.20, G:0.02, T:0.24
Consensus pattern (18 bp):
TAATTCAATCAAACAACA
Found at i:3653489 original size:20 final size:20
Alignment explanation
Indices: 3653464--3653516 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
3653454 ATTACAAGCT
3653464 ATGTATCGATACATTTCTTC
1 ATGTATCGATACATTTCTTC
3653484 ATGTATCGATACATTTCTTC
1 ATGTATCGATACATTTCTTC
3653504 ATGTATCGATACA
1 ATGTATCGATACA
3653517 ATGTATCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTCTTC
Found at i:3653603 original size:19 final size:20
Alignment explanation
Indices: 3653579--3653632 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
3653569 CTGCCAATTT
*
3653579 CATGTATCGATACATTG-AA
1 CATGTATCGATACATGGCAA
* *
3653598 CATGTATCGATACAAGGCAG
1 CATGTATCGATACATGGCAA
3653618 CATGTATCGATACAT
1 CATGTATCGATACAT
3653633 CTGAGTGTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (20 bp):
CATGTATCGATACATGGCAA
Found at i:3657828 original size:29 final size:29
Alignment explanation
Indices: 3657786--3658617 Score: 941
Period size: 28 Copynumber: 29.0 Consensus size: 29
3657776 AACATTCATC
3657786 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
*
3657815 CTTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
*
3657844 CTTTT-AAAGCCCACAAGTCAGTGACACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
*
3657872 CTTTTCAAAGCCCATAAGTCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
*
3657901 CTTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
*
3657929 CCTTTC-AAGCCCACAAGTCAGTGGCA--
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
*
3657955 CTTTTCAAAGCCCACAAATCAGTGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
3657983 CCTTTCAAAGCCCACGCAAGTCAGTGGTACC
1 CTTTTCAAAGCCCA--CAAGTCAGTGGCACT
* * *
3658014 CTTTT-GAAGCCCACGCAAGTTAGTGGCACC
1 CTTTTCAAAGCCCA--CAAGTCAGTGGCACT
3658044 CTTTT-AAAGCCCACAAGTCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
3658072 CTTTTCAAAGCCCACAAGTTAGTGGTAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
3658100 CGTTTCAAAGCCCACGAGTCAGTAGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
**
3658129 C-TTTCAAAGCCCATGAGTCAGTGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
3658156 CCTTTCAAAGCCCACGAGTCAATGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
3658184 CTTTTCAAAGCCCACGAGTCAGTGGCACC
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
3658213 CTTTTCAAAGCCCACGAGTCAATGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
3658241 CCTTTCAAAGTCCACTAGTGAGTGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
*
3658269 CGTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
3658298 C-TTTCAAAACCCACAAATCAGTGGCA-T
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
3658325 CCTTTCAAAGCCCACGCAAGTCAGTGGCGCC
1 CTTTTCAAAGCCCA--CAAGTCAGTGGCACT
* * *
3658356 CTTTT-AAAGCCCACAAGTTAATGGTACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
3658384 CTTTTCAAAG-CCAGAAGTTAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
*
3658412 -TTTTCAAAGCCCACAAGTTAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
3658440 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
3658469 TTTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
3658497 CCTCTCAAAGCCCACAAGTCAGTGGCATT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
*
3658526 CTTTTCAAAGCCCACAAG-CTAGTGGTAACT
1 CTTTTCAAAGCCCACAAGTC-AGTGG-CACT
* *
3658556 TTTTTCAAAGCCCACACGAGTCGGTGGCAACT
1 CTTTTCAAAGCCCACA--AGTCAGTGGC-ACT
*
3658588 CTTTTCAAAGCCCACACAAGTTAGTGGCAC
1 CTTTTCAAAG-CC-CACAAGTCAGTGGCAC
3658618 CATTTTTTTT
Statistics
Matches: 698, Mismatches: 78, Indels: 52
0.84 0.09 0.06
Matches are distributed among these distances:
26 5 0.01
27 50 0.07
28 311 0.45
29 207 0.30
30 82 0.12
31 10 0.01
32 26 0.04
33 3 0.00
34 4 0.01
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (29 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:3657874 original size:57 final size:57
Alignment explanation
Indices: 3657785--3658623 Score: 907
Period size: 57 Copynumber: 14.6 Consensus size: 57
3657775 GAACATTCAT
3657785 CCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
3657843 CCTTTT-AAAGCCCACAAGTCAGTGACACTCTTTTCAAAGCCCATAAGTCAGTGGCAC
1 CCTTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
3657900 TCTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTC-AAGCCCACAAGTCAGTGGCA-
1 CCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
3657955 -CTTTTCAAAGCCCACAAATCAGTGGCACCCTTTCAAAGCCCACGCAAGTCAGTGGTAC
1 CCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCA--CAAGTCAGTGGCAC
* *
3658013 CCTTTT-GAAGCCCACGCAAGTTAGTGGCACCCTTTT-AAAGCCCACAAGTCAGTGGCAC
1 CCTTTTCAAAGCCCA--CAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCAC
* * * * * *
3658071 TCTTTTCAAAGCCCACAAGTTAGTGGTACCGTTTCAAAGCCCACGAGTCAGTAGCAC
1 CCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAC
* ** * * *
3658128 TC-TTTCAAAGCCCATGAGTCAGTGGCACCCTTTCAAAGCCCACGAGTCAATGGCA-
1 CCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
3658183 CCTTTTCAAAGCCCACGAGTCAGTGGCACCCTTTTCAAAGCCCACGAGTCAATGGCAC
1 CCTTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCAC
* * * *
3658241 CC-TTTCAAAGTCCACTAGTGAGTGGCACCGTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAC
* * * *
3658297 TC-TTTCAAAACCCACAAATCAGTGGCATCC-TTTCAAAGCCCACGCAAGTCAGTGGCGC
1 CCTTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCA--CAAGTCAGTGGCAC
* * * * *
3658355 CCTTTT-AAAGCCCACAAGTTAATGGTACTCTTTTCAAAG-CCAGAAGTTAGTGGCA-
1 CCTTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
3658410 CTTTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCAC
** * * * *
3658468 TTTTTTCAAAGCCCACAAGTTAGTGGCACCCTCTCAAAGCCCACAAGTCAGTGGCAT
1 CCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAC
* * * *
3658525 TCTTTTCAAAGCCCACAAG-CTAGTGGTAACTTTTTTCAAAGCCCACACGAGTCGGTGGCAAC
1 CCTTTTCAAAGCCCACAAGTC-AGTGG-CAC-CTTTTCAAAGCCCACA--AGTCAGTGGC-AC
* *
3658587 TCTTTTCAAAGCCCACACAAGTTAGTGGCACCATTTT
1 CCTTTTCAAAG-CC-CACAAGTCAGTGGCACC-TTTT
3658624 TTTTAAAAAA
Statistics
Matches: 675, Mismatches: 73, Indels: 61
0.83 0.09 0.08
Matches are distributed among these distances:
54 32 0.05
55 13 0.02
56 194 0.29
57 219 0.32
58 117 0.17
59 36 0.05
60 19 0.03
61 14 0.02
62 12 0.02
63 8 0.01
64 11 0.02
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (57 bp):
CCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAC
Found at i:3658791 original size:49 final size:45
Alignment explanation
Indices: 3658683--3658804 Score: 120
Period size: 49 Copynumber: 2.6 Consensus size: 45
3658673 TTGTCTGACA
* * *
3658683 TCGCTAGCATTGAATCAGCATATTGGCACTTTTATTAGCCCAATG
1 TCGCTGGCCTTGAATCAGCACATTGGCACTTTTATTAGCCCAATG
* * * *
3658728 TCGTTGGCCCTGAATCAGCACATTGGTCCACTTTTCCCTTAGTCCAATG
1 TCGCTGGCCTTGAATCAGCACATTGG--CACTTTT--ATTAGCCCAATG
*
3658777 TCGCTGGCCTTGAAT-TGACACATTGGCA
1 TCGCTGGCCTTGAATCAG-CACATTGGCA
3658805 ATCCTCTCAT
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
45 21 0.34
47 9 0.15
48 1 0.02
49 31 0.50
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (45 bp):
TCGCTGGCCTTGAATCAGCACATTGGCACTTTTATTAGCCCAATG
Found at i:3659204 original size:20 final size:20
Alignment explanation
Indices: 3659176--3659250 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
3659166 TTTTACCCAG
3659176 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
3659196 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
3659216 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
3659236 ATGTATCGATACATT
1 ATGTATCGATACATT
3659251 CTGTCTTTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:3663906 original size:79 final size:79
Alignment explanation
Indices: 3663794--3663944 Score: 205
Period size: 79 Copynumber: 1.9 Consensus size: 79
3663784 TACTCTTATC
* * **
3663794 GTTATTTTAGAGAGGATACTCCAACCCCGATTTTATTTTCAAAATGCCAATTTTCTATAATCAGG
1 GTTATTTTAGAGAGGATACTCCAACCCCAATTTTATTTCCAAAACACCAATTTTCTATAATCAGG
3663859 GATACTCCAACCCT
66 GATACTCCAACCCT
* * * * *
3663873 GTTATTTCT-GAGGGGATACTCCAACCTCAATTTTATTTCCAAAACATCGATTTTCTATAATCGG
1 GTTATTT-TAGAGAGGATACTCCAACCCCAATTTTATTTCCAAAACACCAATTTTCTATAATCAG
3663937 GGATACTC
65 GGATACTC
3663945 TAGCCCCATT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
79 61 0.98
80 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (79 bp):
GTTATTTTAGAGAGGATACTCCAACCCCAATTTTATTTCCAAAACACCAATTTTCTATAATCAGG
GATACTCCAACCCT
Found at i:3667931 original size:13 final size:13
Alignment explanation
Indices: 3667913--3667938 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3667903 CAGGGTAGCT
3667913 TTGTATCGATACA
1 TTGTATCGATACA
3667926 TTGTATCGATACA
1 TTGTATCGATACA
3667939 ACACTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3668887 original size:49 final size:49
Alignment explanation
Indices: 3668824--3669301 Score: 437
Period size: 49 Copynumber: 9.6 Consensus size: 49
3668814 ATGTTAAAGA
* *
3668824 TGCCAATATGCTGATTCAAGGCCAACGATATCAGATTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATCAGATTTAAAGATGAAGG
* * * * *
3668873 TGCCAATGTACTGATTCAAGGCTAACGATATCAGACTTAAAGATGGTTAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATCAGATTTAAAGAT-G--AAGG
* * * *
3668925 TGCCAATGTGTTGATTCAAGGCCAACGACATCAG-TCTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATCAGAT-TTAAAGATGAAGG
* * * *
3668974 TGCCAATATGCTGATTTAAGGCCAGCGATATCGGACTTAAAGATGAACG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATCAGATTTAAAGATGAAGG
* * * * *
3669023 TGCCAATGTGCTGATTCAAGGTCAGCGACAT-GGGTCTTAAAG--GCAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATCAGAT-TTAAAGATG-AAGG
* * * ** * *
3669071 TGCTAATATGCTGATTTAAGGCCAACGATATTGGACTTAAAGATGAACG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATCAGATTTAAAGATGAAGG
* * * ** * * *
3669120 TGCCAATGTGCTAATTCAAGGCCAGCGACATTGGGTTTTAAAAATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATA-TCAGATTTAAAGATGAAGG
* *
3669170 TGCCAATATGCTGATTCAAGGCCAGCGATATCAAACTTAAAGATGGTTAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATCAGATTTAAAGAT-G--AAGG
* * *
3669222 TGCCAATATGCTGATTGAAGGCCAGCGATAT-TGGTCTTAAAGAT-AATGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATCAGAT-TTAAAGATGAA-GG
*
3669271 TGCCAATATGCTGATTCAAGGCCAGCAATAT
1 TGCCAATATGCTGATTCAAGGCCAGCGATAT
3669302 TGGGCTTGTG
Statistics
Matches: 350, Mismatches: 63, Indels: 32
0.79 0.14 0.07
Matches are distributed among these distances:
47 1 0.00
48 38 0.11
49 185 0.53
50 42 0.12
51 1 0.00
52 83 0.24
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATCAGATTTAAAGATGAAGG
Found at i:3669295 original size:101 final size:97
Alignment explanation
Indices: 3668824--3669301 Score: 526
Period size: 101 Copynumber: 4.8 Consensus size: 97
3668814 ATGTTAAAGA
* * * * * * * *
3668824 TGCCAATATGCTGATTCAAGGCCAACGATATCAGAT-TTAAAGATGAAGATGCCAATGTACTGAT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACAT-TGGTCTTAAAGAT-AAGGTGCCAATATGCTGAT
* * *
3668888 TCAAGGCTAACGATATCAGACTTAAAGATGGTTAAGG
64 TCAAGGCCAGCGATATCAGACTTAAAGAT-G--AACG
* * **
3668925 TGCCAATGTGTTGATTCAAGGCCAACGACATCAGTCTTAAAGATGAAGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAT-AAGGTGCCAATATGCTGATT
* *
3668990 TAAGGCCAGCGATATCGGACTTAAAGATGAACG
65 CAAGGCCAGCGATATCAGACTTAAAGATGAACG
* * ** * *
3669023 TGCCAATGTGCTGATTCAAGGTCAGCGACATGGGTCTTAAAGGCAAGGTGCTAATATGCTGATTT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAGGTGCCAATATGCTGATTC
* **
3669088 AAGGCCAACGATATTGGACTTAAAGATGAACG
66 AAGGCCAGCGATATCAGACTTAAAGATGAACG
* * *
3669120 TGCCAATGTGCTAATTCAAGGCCAGCGACATTGGGTTTTAAAAATAAAGGTGCCAATATGCTGAT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATT-GGTCTTAAAGAT-AAGGTGCCAATATGCTGAT
* *
3669185 TCAAGGCCAGCGATATCAAACTTAAAGATGGTTAAGG
64 TCAAGGCCAGCGATATCAGACTTAAAGAT-G--AACG
* * *
3669222 TGCCAATATGCTGATTGAAGGCCAGCGATATTGGTCTTAAAGATAATGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAA-GGTGCCAATATGCTGATT
*
3669287 CAAGGCCAGCAATAT
65 CAAGGCCAGCGATAT
3669302 TGGGCTTGTG
Statistics
Matches: 325, Mismatches: 45, Indels: 14
0.85 0.12 0.04
Matches are distributed among these distances:
97 79 0.24
98 48 0.15
99 42 0.13
100 5 0.02
101 120 0.37
102 31 0.10
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (97 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAGGTGCCAATATGCTGATTC
AAGGCCAGCGATATCAGACTTAAAGATGAACG
Found at i:3669455 original size:28 final size:28
Alignment explanation
Indices: 3669370--3669702 Score: 348
Period size: 29 Copynumber: 11.6 Consensus size: 28
3669360 CACCAACTTC
* *
3669370 TGTGGGCTTTTGAGAAGATGCCACTGATT
1 TGTGGGC-TTTGAAAAGATGCCACTGACT
* * *
3669399 TGTGGGTTTTTTG-AAGGTTGCCACTGACT
1 TGTGGG--CTTTGAAAAGATGCCACTGACT
*
3669428 TGTGGGCTTTGAGAAGATGCCACTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
3669456 TGTGGGCTTTTGAAAAGATGCCACTGACT
1 TGTGGGC-TTTGAAAAGATGCCACTGACT
* * *
3669485 TGTGGGCTTTGAAAAAGGTGCCACCGATT
1 TGTGGGCTTTG-AAAAGATGCCACTGACT
* * * *
3669514 TGTGGGCTTTGAAGGAGGTGCCACCGATT
1 TGTGGGCTTTGAA-AAGATGCCACTGACT
* *
3669543 TGTGGGCTTCTG-AAGGTTGCCACTGACT
1 TGTGGGCTT-TGAAAAGATGCCACTGACT
* *
3669571 TGTGGGCTTTCG-AAGGTTGCCACTGACT
1 TGTGGGCTTT-GAAAAGATGCCACTGACT
3669599 TGTGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACT
*
3669627 TGTAGGCTTTTGAAAAAGATGCCACTGACT
1 TGTGGGC-TTTG-AAAAGATGCCACTGACT
*
3669657 TGTGGGCTTTTGAAAAAGATGCTACTGACT
1 TGTGGGC-TTTG-AAAAGATGCCACTGACT
* *
3669687 TATGGGCTTTGGAAAG
1 TGTGGGCTTTGAAAAG
3669703 TGAGGAATGC
Statistics
Matches: 267, Mismatches: 26, Indels: 23
0.84 0.08 0.07
Matches are distributed among these distances:
27 6 0.02
28 96 0.36
29 108 0.40
30 57 0.21
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.32
Consensus pattern (28 bp):
TGTGGGCTTTGAAAAGATGCCACTGACT
Found at i:3669467 original size:86 final size:86
Alignment explanation
Indices: 3669351--3669697 Score: 376
Period size: 86 Copynumber: 4.0 Consensus size: 86
3669341 TGGACTTAGA
* * * *
3669351 AGAAGATGCCACCAACTTCTGTGGGCTTTTGAGAAGATGCCACTGATTTGTGGGTTTTTTGAAGG
1 AGAAGATGCCACCGAC-T-TGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGTTTTTAGAAGG
3669416 TTGCCACTGACTTGTGGGCTTTG
64 TTGCCACTGACTTGTGGGCTTTG
* ** *
3669439 AGAAGATGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAAGG-
1 AGAAGATGCCACCGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGG-TTTTTAGAAGGT
* *
3669503 TGCCACCGATTTGTGGGCTTTG
65 TGCCACTGACTTGTGGGCTTTG
* * * * * * * *
3669525 AAGGAGGTGCCACCGATTTGTGGGCTTCTG-AAGGTTGCCACTGACTTGTGGG-CTTTCGAAGGT
1 -AGAAGATGCCACCGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGTTTTTAGAAGGT
3669588 TGCCACTGACTTGTGGGCTTTG
65 TGCCACTGACTTGTGGGCTTTG
* * * * * *
3669610 AAAAGATGCCACTGACTTGTAGGCTTTTGAAAAAGATGCCACTGACTTGTGGGCTTTTGAAAAAG
1 AGAAGATGCCACCGACTTGTGGGCTTTTG-AAAAGATGCCACTGACTTGTGGG-TTTTTAGAAGG
* * *
3669675 ATGCTACTGACTTATGGGCTTTG
64 TTGCCACTGACTTGTGGGCTTTG
3669698 GAAAGTGAGG
Statistics
Matches: 211, Mismatches: 41, Indels: 14
0.79 0.15 0.05
Matches are distributed among these distances:
84 27 0.13
85 20 0.09
86 93 0.44
87 32 0.15
88 39 0.18
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.31
Consensus pattern (86 bp):
AGAAGATGCCACCGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGTTTTTAGAAGGTT
GCCACTGACTTGTGGGCTTTG
Found at i:3670102 original size:37 final size:37
Alignment explanation
Indices: 3670052--3670136 Score: 170
Period size: 37 Copynumber: 2.3 Consensus size: 37
3670042 AAAAACGAAG
3670052 CACAAATGCATCATGCAAAATGAAATGTTATGAATGT
1 CACAAATGCATCATGCAAAATGAAATGTTATGAATGT
3670089 CACAAATGCATCATGCAAAATGAAATGTTATGAATGT
1 CACAAATGCATCATGCAAAATGAAATGTTATGAATGT
3670126 CACAAATGCAT
1 CACAAATGCAT
3670137 GATTGTGGCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (37 bp):
CACAAATGCATCATGCAAAATGAAATGTTATGAATGT
Found at i:3671613 original size:13 final size:13
Alignment explanation
Indices: 3671595--3671620 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3671585 CTATTTATTA
3671595 TGTATCGATACAC
1 TGTATCGATACAC
3671608 TGTATCGATACAC
1 TGTATCGATACAC
3671621 ACAAATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:3671705 original size:21 final size:22
Alignment explanation
Indices: 3671649--3671724 Score: 109
Period size: 21 Copynumber: 3.4 Consensus size: 22
3671639 ATGAATAGTG
* *
3671649 ATGAACAGTGATTTTTAACGATAC
1 ATGAACAGTGA--TGTATCGATAC
3671673 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
3671695 ATGAA-AGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
3671716 ATGAACAGT
1 ATGAACAGT
3671725 ATGAATAGTG
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
21 21 0.43
22 17 0.35
24 11 0.22
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:3671833 original size:53 final size:53
Alignment explanation
Indices: 3671769--3671905 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
3671759 CTACTTCCAA
3671769 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
3671822 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
3671875 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
3671906 TATGCAATTT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 67 0.84
54 13 0.16
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:3671938 original size:20 final size:20
Alignment explanation
Indices: 3671875--3671945 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
3671865 GCCAATGTCC
**
3671875 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
3671895 TGTATCGATAC-TATGCAATT
1 TGTATCGATACATAT-TAATG
3671915 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
3671935 TGTATCGATAC
1 TGTATCGATAC
3671946 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:3672323 original size:19 final size:17
Alignment explanation
Indices: 3672299--3672333 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
3672289 ACAACTTGGT
3672299 TTGACAAACAAGTGATTAG
1 TTGACAAA-AAG-GATTAG
3672318 TTGACAAAAAGGATTA
1 TTGACAAAAAGGATTA
3672334 ATTTTGGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.26
Consensus pattern (17 bp):
TTGACAAAAAGGATTAG
Found at i:3672609 original size:13 final size:13
Alignment explanation
Indices: 3672587--3672622 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
3672577 ATTCGGACCC
*
3672587 TTTTTATTGTTCG
1 TTTTTTTTGTTCG
*
3672600 TTTTTTTTGTTTG
1 TTTTTTTTGTTCG
3672613 TTTTTTTTGT
1 TTTTTTTTGT
3672623 GGAGGATGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.03, C:0.03, G:0.14, T:0.81
Consensus pattern (13 bp):
TTTTTTTTGTTCG
Found at i:3676365 original size:13 final size:13
Alignment explanation
Indices: 3676344--3676373 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3676334 CGATACTATT
3676344 TACAATGTATCGA
1 TACAATGTATCGA
*
3676357 TACACTGTATCGA
1 TACAATGTATCGA
3676370 TACA
1 TACA
3676374 TCAATAGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:3676496 original size:22 final size:22
Alignment explanation
Indices: 3676443--3676515 Score: 96
Period size: 22 Copynumber: 3.4 Consensus size: 22
3676433 AGCGAACAGG
* *
3676443 GAACAGTGAAGTATCGATACAT
1 GAACAGTGATGTATCGATAGAT
3676465 GAACAGTGATGTATCGATAGAT
1 GAACAGTGATGTATCGATAGAT
* *
3676487 GAACAGTGATGAATAG-T-GAT
1 GAACAGTGATGTATCGATAGAT
3676507 GAACAGTGA
1 GAACAGTGA
3676516 AAATGAAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
20 12 0.26
21 1 0.02
22 34 0.72
ACGTcount: A:0.40, C:0.10, G:0.27, T:0.23
Consensus pattern (22 bp):
GAACAGTGATGTATCGATAGAT
Found at i:3676499 original size:10 final size:10
Alignment explanation
Indices: 3676484--3676515 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
3676474 TGTATCGATA
3676484 GATGAACAGT
1 GATGAACAGT
*
3676494 GATGAATAGT
1 GATGAACAGT
3676504 GATGAACAGT
1 GATGAACAGT
3676514 GA
1 GA
3676516 AAATGAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.41, C:0.06, G:0.31, T:0.22
Consensus pattern (10 bp):
GATGAACAGT
Found at i:3676561 original size:13 final size:13
Alignment explanation
Indices: 3676543--3676567 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3676533 TGCCAATGCT
3676543 ATGTATCGATACA
1 ATGTATCGATACA
3676556 ATGTATCGATAC
1 ATGTATCGATAC
3676568 TTAGCAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3676687 original size:21 final size:21
Alignment explanation
Indices: 3676647--3676687 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3676637 GTCAACCTTG
*
3676647 TGTATTGATACCAATAGTATA
1 TGTATTGATACCAACAGTATA
3676668 TGTATTGATA-CAACACGTAT
1 TGTATTGATACCAACA-GTAT
3676688 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (21 bp):
TGTATTGATACCAACAGTATA
Found at i:3681475 original size:34 final size:35
Alignment explanation
Indices: 3681437--3681503 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
3681427 CCTTACAACA
3681437 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
3681471 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
3681504 AATCGCTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:3682023 original size:22 final size:22
Alignment explanation
Indices: 3681994--3682073 Score: 126
Period size: 22 Copynumber: 3.6 Consensus size: 22
3681984 CATCAACAGT
3681994 GATGAACAGTGCA-GTATCGATA
1 GATGAACAGTG-ATGTATCGATA
*
3682016 CATGAACAGTGATGTATCGATA
1 GATGAACAGTGATGTATCGATA
*
3682038 GATTAACAGTGATGTATCGATA
1 GATGAACAGTGATGTATCGATA
3682060 GATGAACAGTGATG
1 GATGAACAGTGATG
3682074 AATAGTAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
21 1 0.02
22 52 0.98
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.26
Consensus pattern (22 bp):
GATGAACAGTGATGTATCGATA
Found at i:3682165 original size:20 final size:20
Alignment explanation
Indices: 3682142--3682214 Score: 146
Period size: 20 Copynumber: 3.6 Consensus size: 20
3682132 ACTTAGCAAA
3682142 ATGTATCGATACATCTGAGT
1 ATGTATCGATACATCTGAGT
3682162 ATGTATCGATACATCTGAGT
1 ATGTATCGATACATCTGAGT
3682182 ATGTATCGATACATCTGAGT
1 ATGTATCGATACATCTGAGT
3682202 ATGTATCGATACA
1 ATGTATCGATACA
3682215 ATCAAGGGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACATCTGAGT
Found at i:3682294 original size:21 final size:21
Alignment explanation
Indices: 3682254--3682294 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3682244 GTCAACCTTG
*
3682254 TGTATTGATACCAATAGTATA
1 TGTATTGATACCAACAGTATA
3682275 TGTATTGATA-CAACACGTAT
1 TGTATTGATACCAACA-GTAT
3682295 TTTTACTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (21 bp):
TGTATTGATACCAACAGTATA
Found at i:3684866 original size:20 final size:20
Alignment explanation
Indices: 3684841--3684895 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
3684831 AAAACCCTTA
3684841 AAAGTATCGATACATAATT-C
1 AAAGTATCGATACAT-ATTGC
*
3684861 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATATTGC
*
3684881 AATGTATCGATACAT
1 AAAGTATCGATACAT
3684896 CAAAAATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (20 bp):
AAAGTATCGATACATATTGC
Found at i:3684973 original size:20 final size:20
Alignment explanation
Indices: 3684947--3684999 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
3684937 GTAGCCAAAC
* *
3684947 TTGTATCGATACAC-CAAAG
1 TTGTATCGATACACAAAAAA
3684966 TATGTATCGATACACAAAAAA
1 T-TGTATCGATACACAAAAAA
3684987 TTGTATCGATACA
1 TTGTATCGATACA
3685000 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 1 0.03
20 25 0.83
21 4 0.13
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:3689110 original size:20 final size:21
Alignment explanation
Indices: 3689087--3689143 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
3689077 ACAATTCAAA
**
3689087 GTATCGATACATGTTGCA-AT
1 GTATCGATACATGTTAAAGAT
**
3689107 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTAAAGAT
3689128 GTATCGATACATGTTA
1 GTATCGATACATGTTA
3689144 TTGGGATTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (21 bp):
GTATCGATACATGTTAAAGAT
Found at i:3689208 original size:13 final size:13
Alignment explanation
Indices: 3689190--3689215 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3689180 ACACAAAAGT
3689190 ATGTATCGATACA
1 ATGTATCGATACA
3689203 ATGTATCGATACA
1 ATGTATCGATACA
3689216 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3689213 original size:33 final size:33
Alignment explanation
Indices: 3689171--3689235 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
3689161 TAGCCAAACT
*
3689171 TGTATCGATACAC-AAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAAT-TGTATCGATACAA
3689204 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
3689236 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 25 0.83
34 5 0.17
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:3695560 original size:20 final size:20
Alignment explanation
Indices: 3695517--3695562 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
3695507 AAATCTTTTG
3695517 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
3695538 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
3695558 CAAAA
1 CAAAA
3695563 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:3698013 original size:33 final size:32
Alignment explanation
Indices: 3697951--3698014 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
3697941 TAGCCAAACT
* ** *
3697951 TGTATCGATACACAAAGTATGTATTGATACAA
1 TGTATCGATACAAAAAAAATGTATCGATACAA
3697983 TGTATCGATACAAAAAAAATTGTATCGATACA
1 TGTATCGATACAAAAAAAA-TGTATCGATACA
3698015 TTGGCTTGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 16 0.59
33 11 0.41
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (32 bp):
TGTATCGATACAAAAAAAATGTATCGATACAA
Found at i:3703017 original size:20 final size:20
Alignment explanation
Indices: 3702992--3703046 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
3702982 AAAACCCTTA
3702992 AAAGTATCGATACATAATT-C
1 AAAGTATCGATACAT-ATTGC
* *
3703012 AAAGTATTGATACATGTTGC
1 AAAGTATCGATACATATTGC
*
3703032 AATGTATCGATACAT
1 AAAGTATCGATACAT
3703047 CAAAAATATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (20 bp):
AAAGTATCGATACATATTGC
Found at i:3703141 original size:33 final size:33
Alignment explanation
Indices: 3703099--3703163 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
3703089 TAGCCAAACT
* *
3703099 TGTATCGATACAC-CAAAGTATGTATTGATACAA
1 TGTATCGATACACAAAAAAT-TGTATTGATACAA
3703132 TGTATCGATACACAAAAAATTGTATTGATACA
1 TGTATCGATACACAAAAAATTGTATTGATACA
3703164 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATTGATACAA
Found at i:3711729 original size:24 final size:21
Alignment explanation
Indices: 3711681--3711730 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 21
3711671 GACATGTTGT
*
3711681 AAATGCATGAAACATAGCTCA
1 AAATGCATGAAACATAGCACA
*
3711702 AAATGCATGATGAACATGGCACA
1 AAATGCATGA--AACATAGCACA
3711725 CAAATG
1 -AAATG
3711731 ACCTCAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 10 0.42
23 9 0.38
24 5 0.21
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.18
Consensus pattern (21 bp):
AAATGCATGAAACATAGCACA
Found at i:3712336 original size:21 final size:21
Alignment explanation
Indices: 3712303--3712347 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3712293 TTGCAAGTTG
*
3712303 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
3712325 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
3712345 AAA
1 AAA
3712348 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:3715770 original size:20 final size:19
Alignment explanation
Indices: 3715723--3715797 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 19
3715713 AAAAAGATAT
*
3715723 AATGTATCGATACATTGAA
1 AATGTATCGATACATTCAA
*
3715742 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCA-A
* *
3715763 CATGTATCGATATA-TCGAAA
1 AATGTATCGATACATTC--AA
3715783 AATGTATCGATACAT
1 AATGTATCGATACAT
3715798 CTGGGTAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.05
20 40 0.91
21 2 0.05
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.32
Consensus pattern (19 bp):
AATGTATCGATACATTCAA
Found at i:3716726 original size:143 final size:143
Alignment explanation
Indices: 3716314--3718182 Score: 2509
Period size: 143 Copynumber: 13.0 Consensus size: 143
3716304 TGGTGATTTG
** * *
3716314 AAAAGG-GTTGCCACTGACTTGCATGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAG
1 AAAAGGAG-TGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTAAAAG
** * * *
3716378 AGTGCCACTGACTCATGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAAGGTGCCAC
65 AGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCAC
*
3716443 TGACTCGTGGGCTTT
129 TGACTTGTGGGCTTT
* * * * *
3716458 GAAAA-G-GTGCCACTGACTTGGGTAGGCTTTAAAAAGGTGCCACTAACTTGCGTGGGCTTTGAA
1 -AAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTT-AA
* * *
3716521 AAGA-TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCC
62 AAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCC
* *
3716585 ACTGACTCGTGGGTTTT
127 ACTGACTTGTGGGCTTT
3716602 AAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTAAAAGA
1 AAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTAAAAGA
* * * *
3716667 GTGCCACTAAATTGTGGGCTTCGCAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
66 GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
*
3716732 ACTTGTGGGTTTT
131 ACTTGTGGGCTTT
* * * *
3716745 GAAAGGA-TGCCACTGAC-T-TGTGGGTTTTGAAAGAGTGCCACTGACTCGTGGGCTTTAAAAGA
1 AAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTAAAAGA
* * ** * *
3716807 GTGCCATTGACTCGTGGGCTTTGAAAAAAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACT
66 GTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
3716872 GACTTGCGTGGGCTTT
130 GACTT--GTGGGCTTT
* * * * * *
3716888 AAAAAG-GTGCCACTAACTTGCGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGA
1 AAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTAAAAGA
* * * *
3716952 GTGCCATTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTCGTGGGC-TTGAAAGGGTGCCACTG
66 GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
*
3717016 ACTCGTGGGCTTT
131 ACTTGTGGGCTTT
3717029 AAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTAAAAGA
1 AAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTAAAAGA
* * * * *
3717094 GTGCCACTAAATTGTGGGCTTCGCAAGGGTGCCACTGACTTGTGGGCTTTGAACGGGTGCCACTG
66 GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
*
3717159 ACTTGTGGGCTCT
131 ACTTGTGGGCTTT
*
3717172 AAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGA
1 AAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTAAAAGA
* * *
3717237 GTGCCACTGAATTGTGGGCTTCGCAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
66 GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
*
3717302 ACTTGTGGGCTCT
131 ACTTGTGGGCTTT
*
3717315 AAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGA
1 AAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTAAAAGA
* * * * * *
3717380 GTGCCACTGAATTGTGGGCTTCGCAAGGGTGCCACTGACTTGTGGGTTTTGAAAGAGTGCCACTA
66 GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
*
3717445 ACTTGTGGGTTTT
131 ACTTGTGGGCTTT
* * *
3717458 GAAAGGAGTGCCACTAAC-T-TGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAG
1 AAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT-AAAAG
* * * *
3717521 AGTGCCACTGATTTGTGGGCTTTGAAAAGAGTTCCACTGACTTGTGGGCTTTGAAAAGAGTGCCA
65 AGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCA
3717586 CTGACTTGTGGGCTTT
128 CTGACTTGTGGGCTTT
* * * *
3717602 GAAAGGAGTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGAGTTGTGGGCTTTGAAAGG
1 AAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTAAAAGA
* *
3717665 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCAC
66 GTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCAC
3717730 TGACTTGTGGGCTTT
129 TGACTTGTGGGCTTT
* * *
3717745 GAAAGGAGTGCCACTAAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGG
1 AAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT-AAAAG
* * *
3717808 AGTGCCACTGACTTGTGGTCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCAC
65 AGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCAC
*
3717873 TGATTTGTGGGCTTT
129 TGACTTGTGGGCTTT
3717888 GAAAA-GAGTGCCACTGAC-T-TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAA
1 -AAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTT-AAA
* * * * *
3717950 AGAGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGATTTGAAAAGAGTGC
63 AGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGC
3718015 CACTGACTTGTGGGCTTT
126 CACTGACTTGTGGGCTTT
* * *
3718033 GAAAGGAGTGTCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCCCTGACTTGTGGGCTTTGAAAAG
1 AAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT-AAAAG
* *
3718096 AGTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCA
65 AGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCA
*
3718161 CTAACTTGTGGGCTTT
128 CTGACTTGTGGGCTTT
*
3718177 GAAAGG
1 AAAAGG
3718183 GATGAACATT
Statistics
Matches: 1570, Mismatches: 128, Indels: 53
0.90 0.07 0.03
Matches are distributed among these distances:
140 59 0.04
141 93 0.06
142 139 0.09
143 721 0.46
144 314 0.20
145 239 0.15
146 5 0.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (143 bp):
AAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTAAAAGA
GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
ACTTGTGGGCTTT
Found at i:3718181 original size:29 final size:29
Alignment explanation
Indices: 3716322--3718182 Score: 2472
Period size: 28 Copynumber: 64.9 Consensus size: 29
3716312 TGAAAAGGGT
3716322 TGCCACTGACTTGCATGGGCTTTGAAAGGA-
1 TGCCACTGACTTG--TGGGCTTTGAAAGGAG
3716352 TGCCACTGACTTGTGGGCTTTGAAA-GAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
**
3716380 TGCCACTGACTCATGGGCTTTGAAA-GAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
3716408 TGCCACTGACTCGTGGGCTTTGAAA-AAGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGA-G
* *
3716437 TGCCACTGACTCGTGGGCTTTGAAAAG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * *
3716465 TGCCACTGACTTGGGTAGGCTTTAAAAAG-G
1 TGCCACTGACTT--GTGGGCTTTGAAAGGAG
* *
3716495 TGCCACTAACTTGCGTGGGCTTTGAAAAGA-
1 TGCCACTGACTT--GTGGGCTTTGAAAGGAG
3716525 TGCCACTGACTTGTGGGCTTTGAAA-GAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
3716553 TGCCACTGACTCGTGGGCTTTGAAAAG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * *
3716581 TGCCACTGACTCGTGGGTTTTAAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
3716610 TGCCACTGACTTGTGTGGGCTTTGAAAGG-G
1 TGCCACTGAC-T-TGTGGGCTTTGAAAGGAG
*
3716640 TGCCACTGACTTGTGGGCTTT-AAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * * *
3716668 TGCCACTAAATTGTGGGCTTCGCAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
3716696 TGCCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3716724 TGCCACTGACTTGTGGGTTTTGAAAGGA-
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3716752 TGCCACTGACTTGTGGGTTTTGAAA-GAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
3716780 TGCCACTGACTCGTGGGCTTT-AAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * **
3716808 TGCCATTGACTCGTGGGCTTTGAAAAAAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
3716837 TGCCACTGACTCGTGGGCTTTGAAAAG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
3716865 TGCCACTGACTTGCGTGGGCTTTAAAAAG-G
1 TGCCACTGACTT--GTGGGCTTTGAAAGGAG
* *
3716895 TGCCACTAACTTGCGTGGGCTTTGAAAAGA-
1 TGCCACTGACTT--GTGGGCTTTGAAAGGAG
3716925 TGCCACTGACTTGTGGGCTTTGAAA-GAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * *
3716953 TGCCATTGACTCGTGGGCTTTGAAAAG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3716981 TGCCACTGACTCGTGGGC-TTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
3717008 TGCCACTGACTCGTGGGCTTTAAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
3717037 TGCCACTGACTTGTGTGGGCTTTGAAAGG-G
1 TGCCACTGAC-T-TGTGGGCTTTGAAAGGAG
*
3717067 TGCCACTGACTTGTGGGCTTT-AAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * * *
3717095 TGCCACTAAATTGTGGGCTTCGCAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3717123 TGCCACTGACTTGTGGGCTTTGAACGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
3717151 TGCCACTGACTTGTGGGCTCTAAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
3717180 TGCCACTGACTTGTGTGGGCTTTGAAAGG-G
1 TGCCACTGAC-T-TGTGGGCTTTGAAAGGAG
3717210 TGCCACTGACTTGTGGGCTTTGAAA-GAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * *
3717238 TGCCACTGAATTGTGGGCTTCGCAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
3717266 TGCCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
3717294 TGCCACTGACTTGTGGGCTCTAAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
3717323 TGCCACTGACTTGTGTGGGCTTTGAAAGG-G
1 TGCCACTGAC-T-TGTGGGCTTTGAAAGGAG
3717353 TGCCACTGACTTGTGGGCTTTGAAA-GAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * *
3717381 TGCCACTGAATTGTGGGCTTCGCAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3717409 TGCCACTGACTTGTGGGTTTTGAAA-GAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
3717437 TGCCACTAACTTGTGGGTTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3717466 TGCCACTAACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
3717494 TGCCACTAACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
3717523 TGCCACTGATTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
3717552 TTCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
3717581 TGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
3717610 TGCCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3717638 TGCCACTGAGTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3717666 TGCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3717695 TGCCACTGATTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
3717724 TGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3717753 TGCCACTAACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
3717781 TGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3717810 TGCCACTGACTTGTGGTCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
3717838 TGCCACTAACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
3717867 TGCCACTGATTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
3717896 TGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3717925 TGCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
3717954 TGCCACTAACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * *
3717983 TGCCACTGATTTGTGGGATTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
3718012 TGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3718041 TGTCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
3718069 TGCCCCTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3718098 TGCCACTGATTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3718127 TGCCACTGATTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
3718156 TGCCACTAACTTGTGGGCTTTGAAAGG
1 TGCCACTGACTTGTGGGCTTTGAAAGG
3718183 GATGAACATT
Statistics
Matches: 1662, Mismatches: 124, Indels: 91
0.89 0.07 0.05
Matches are distributed among these distances:
27 48 0.03
28 763 0.46
29 632 0.38
30 164 0.10
31 55 0.03
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (29 bp):
TGCCACTGACTTGTGGGCTTTGAAAGGAG
Found at i:3719406 original size:1 final size:1
Alignment explanation
Indices: 3719402--3719464 Score: 63
Period size: 1 Copynumber: 63.0 Consensus size: 1
3719392 TTTTTTGCTA
* * * * * * *
3719402 TTTTTTTCTTTTTTTTTGTTTTTCTGTTTTGTTTTTTTTTTATTTTTTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3719465 GGGTGTAAAG
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.02, C:0.03, G:0.06, T:0.89
Consensus pattern (1 bp):
T
Found at i:3719417 original size:10 final size:10
Alignment explanation
Indices: 3719387--3719462 Score: 53
Period size: 10 Copynumber: 7.2 Consensus size: 10
3719377 ATCTAGACCC
*
3719387 TTCTATTTTT
1 TTCTTTTTTT
* *
3719397 TGCTATTTTT
1 TTCTTTTTTT
3719407 TTCTTTTTTT
1 TTCTTTTTTT
*
3719417 TTGTTTTTCTGTT
1 TT-CTTTT-T-TT
*
3719430 TTGTTTTTTTT
1 TT-CTTTTTTT
*
3719441 TTATTTTTTT
1 TTCTTTTTTT
*
3719451 TTGTTTTTTT
1 TTCTTTTTTT
3719461 TT
1 TT
3719463 TTGGGTGTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
10 37 0.65
11 8 0.14
12 2 0.04
13 10 0.18
ACGTcount: A:0.04, C:0.05, G:0.07, T:0.84
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:3719423 original size:16 final size:16
Alignment explanation
Indices: 3719404--3719464 Score: 79
Period size: 16 Copynumber: 3.8 Consensus size: 16
3719394 TTTTGCTATT
3719404 TTTTTCTTTTTTTTTG
1 TTTTTCTTTTTTTTTG
*
3719420 TTTTTCTGTTTTGTTTTT
1 TTTTTCT-TTTT-TTTTG
*
3719438 TTTTTATTTTTTTTTG
1 TTTTTCTTTTTTTTTG
3719454 TTTTT-TTTTTT
1 TTTTTCTTTTTT
3719465 GGGTGTAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
15 6 0.15
16 16 0.40
17 8 0.20
18 10 0.25
ACGTcount: A:0.02, C:0.03, G:0.07, T:0.89
Consensus pattern (16 bp):
TTTTTCTTTTTTTTTG
Found at i:3719432 original size:34 final size:34
Alignment explanation
Indices: 3719394--3719458 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
3719384 CCCTTCTATT
*
3719394 TTTTGCTATTTTTTTCTTTTTTTTTGTTTTTCTG
1 TTTTGCTATTTTTTTATTTTTTTTTGTTTTTCTG
* *
3719428 TTTTGTTTTTTTTTTATTTTTTTTTGTTTTT
1 TTTTGCTATTTTTTTATTTTTTTTTGTTTTT
3719459 TTTTTTGGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.03, C:0.05, G:0.08, T:0.85
Consensus pattern (34 bp):
TTTTGCTATTTTTTTATTTTTTTTTGTTTTTCTG
Found at i:3733504 original size:20 final size:20
Alignment explanation
Indices: 3733448--3733527 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
3733438 TAGGTAAAAA
3733448 GATATAATGTATCGATACATT
1 GATA-AATGTATCGATACATT
* *
3733469 GA-AGAATATATTGATACATT
1 GATA-AATGTATCGATACATT
* * * *
3733489 TATACATGTATCGATATATC
1 GATAAATGTATCGATACATT
*
3733509 GAAAAATGTATCGATACAT
1 GATAAATGTATCGATACAT
3733528 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 13, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
20 42 0.93
21 3 0.07
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (20 bp):
GATAAATGTATCGATACATT
Found at i:3733525 original size:40 final size:39
Alignment explanation
Indices: 3733450--3733527 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
3733440 GGTAAAAAGA
* * *
3733450 TATAATGTATCGATACATTGAAGAATATATTGATACATT
1 TATAATGTATCGATACATCGAAAAATATATCGATACATT
* *
3733489 TATACATGTATCGATATATCGAAAAATGTATCGATACAT
1 TATA-ATGTATCGATACATCGAAAAATATATCGATACAT
3733528 CTGGGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (39 bp):
TATAATGTATCGATACATCGAAAAATATATCGATACATT
Found at i:3735368 original size:15 final size:15
Alignment explanation
Indices: 3735348--3735378 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3735338 TAAAAATGTC
*
3735348 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
3735363 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
3735378 C
1 C
3735379 CAAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Done.