Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008185.1 Hibiscus syriacus cultivar Beakdansim tig00110788_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3563405
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 16
Found at i:3347904 original size:21 final size:20
Alignment explanation
Indices: 3347880--3347922 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
3347870 AACAAGTAAT
3347880 ATTGATAGTATAAAAAACA-AA
1 ATTGAT-GT-TAAAAAACATAA
*
3347901 ATTGATGTTAAGAAACATAA
1 ATTGATGTTAAAAAACATAA
3347921 AT
1 AT
3347923 AGACTAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 6 0.30
21 6 0.30
ACGTcount: A:0.56, C:0.05, G:0.12, T:0.28
Consensus pattern (20 bp):
ATTGATGTTAAAAAACATAA
Found at i:3350775 original size:40 final size:40
Alignment explanation
Indices: 3350727--3350870 Score: 119
Period size: 41 Copynumber: 3.5 Consensus size: 40
3350717 CGTGTTTTTA
*
3350727 GCGGCGTTTGCACAAAAACGCCATTATATATTTGGATATC
1 GCGGCGTTTGCACAAAAACGCCACTATATATTTGGATATC
** * * * *** ** * *
3350767 GCGGCGTTTTTTACATAAATGCCACTAAAGTACACGTTTTTA
1 GCGGCG-TTTGCACAAAAACGCCACTATA-TATTTGGATATC
*
3350809 GCGGCGTTTGCACAAAAATGCCACTATATATTTGGATATC
1 GCGGCGTTTGCACAAAAACGCCACTATATATTTGGATATC
*
3350849 GCGACGTTTGTCA-AAAAACGCC
1 GCGGCGTTTG-CACAAAAACGCC
3350871 GCTACATGTA
Statistics
Matches: 75, Mismatches: 26, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
40 28 0.37
41 36 0.48
42 11 0.15
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (40 bp):
GCGGCGTTTGCACAAAAACGCCACTATATATTTGGATATC
Found at i:3350782 original size:82 final size:82
Alignment explanation
Indices: 3350561--3350857 Score: 383
Period size: 82 Copynumber: 3.7 Consensus size: 82
3350551 TATTGCATAA
* ** * * * *
3350561 GTTTATAGCGGCGTTTTTACAAAAACGCCACTATATATCTGGGCTATTGCGGCGTTTTATACATA
1 GTTTTTAGCGGCGTTTGCACAAAAACGCCACTATATAT-TTGGATATCGCGGCGTTTTTTACATA
*
3350626 AACGCCACTAAAGTACAT
65 AATGCCACTAAAGTACAT
* * *
3350644 GTTTTTAGCGGCGTTT----AAACACTG---CTATATATTCGGATATTGCGGCGTTTTTTACATA
1 GTTTTTAGCGGCGTTTGCACAAAAAC-GCCACTATATATTTGGATATCGCGGCGTTTTTTACATA
*
3350702 AATGCCACTAAAGTACGT
65 AATGCCACTAAAGTACAT
*
3350720 GTTTTTAGCGGCGTTTGCACAAAAACGCCATTATATATTTGGATATCGCGGCGTTTTTTACATAA
1 GTTTTTAGCGGCGTTTGCACAAAAACGCCACTATATATTTGGATATCGCGGCGTTTTTTACATAA
*
3350785 ATGCCACTAAAGTACAC
66 ATGCCACTAAAGTACAT
* *
3350802 GTTTTTAGCGGCGTTTGCACAAAAATGCCACTATATATTTGGATATCGCGACGTTT
1 GTTTTTAGCGGCGTTTGCACAAAAACGCCACTATATATTTGGATATCGCGGCGTTT
3350858 GTCAAAAAAC
Statistics
Matches: 190, Mismatches: 16, Indels: 17
0.85 0.07 0.08
Matches are distributed among these distances:
76 55 0.29
77 8 0.04
79 6 0.03
80 6 0.03
82 100 0.53
83 15 0.08
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (82 bp):
GTTTTTAGCGGCGTTTGCACAAAAACGCCACTATATATTTGGATATCGCGGCGTTTTTTACATAA
ATGCCACTAAAGTACAT
Found at i:3350832 original size:41 final size:41
Alignment explanation
Indices: 3350701--3350834 Score: 126
Period size: 41 Copynumber: 3.3 Consensus size: 41
3350691 TTTTTTACAT
*
3350701 AAATGCCACTAAAGTACGTGTTTTTAGCGGCGTTTGCACAA
1 AAATGCCACTAAAGTACATGTTTTTAGCGGCGTTTGCACAA
* * * ** ** * * ** *
3350742 AAACGCCATTATA-TATTTGGATATCGCGGCGTTTTTTACAT
1 AAATGCCACTAAAGTACATGTTTTTAGCGGCG-TTTGCACAA
*
3350783 AAATGCCACTAAAGTACACGTTTTTAGCGGCGTTTGCACAA
1 AAATGCCACTAAAGTACATGTTTTTAGCGGCGTTTGCACAA
3350824 AAATGCCACTA
1 AAATGCCACTA
3350835 TATATTTGGA
Statistics
Matches: 66, Mismatches: 25, Indels: 4
0.69 0.26 0.04
Matches are distributed among these distances:
40 12 0.18
41 43 0.65
42 11 0.17
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (41 bp):
AAATGCCACTAAAGTACATGTTTTTAGCGGCGTTTGCACAA
Found at i:3353488 original size:12 final size:12
Alignment explanation
Indices: 3353471--3353497 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3353461 GGTTCTGGAT
3353471 CTTGCTCTTGCC
1 CTTGCTCTTGCC
3353483 CTTGCTCTTGCC
1 CTTGCTCTTGCC
3353495 CTT
1 CTT
3353498 CGGTGCCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.41, G:0.15, T:0.44
Consensus pattern (12 bp):
CTTGCTCTTGCC
Found at i:3355617 original size:147 final size:147
Alignment explanation
Indices: 3355347--3355617 Score: 323
Period size: 147 Copynumber: 1.8 Consensus size: 147
3355337 CTGTCCGGGG
* * *
3355347 TGCATGTTTTTCGCAAATATTTGCCTGAATCTCGAAGATTCTCATCAACTTTCTGGTCCTGGAGT
1 TGCATGTTTTTCGCAAATATTTGCCTGAACCTCGAAGATTCTCATCAACTTTCTGATCCTGGAGC
* ** * **
3355412 GGTGGGGTATTCCCCAACTCACCATTTTCGGGCCAAGTTGAACTGTTAAAAGGATTTTCAATAGC
66 GATGGGGTATTCCCCAACTCACCATTCCCGGGCCAAATTGAACTACTAAAAGGATTTTCAATAGC
3355477 TTGCTCCACCATTTCCA
131 TTGCTCCACCATTTCCA
* * * * * * *
3355494 TGCATGTTTTTCGCAAATCTTTTCCTGAACCTTGAGGATTCTCATCGAGTTTCTGATCCTTGAGC
1 TGCATGTTTTTCGCAAATATTTGCCTGAACCTCGAAGATTCTCATCAACTTTCTGATCCTGGAGC
* * *
3355559 GATGGGGTATTCTCCAA-TCCACCATTCCCGTG-CAGAATTGAAAC-ACTAAAAGGCTTTTC
66 GATGGGGTATTCCCCAACT-CACCATTCCCGGGCCA-AATTG-AACTACTAAAAGGATTTTC
3355618 TGTCGCTTGA
Statistics
Matches: 102, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
146 3 0.03
147 96 0.94
148 3 0.03
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (147 bp):
TGCATGTTTTTCGCAAATATTTGCCTGAACCTCGAAGATTCTCATCAACTTTCTGATCCTGGAGC
GATGGGGTATTCCCCAACTCACCATTCCCGGGCCAAATTGAACTACTAAAAGGATTTTCAATAGC
TTGCTCCACCATTTCCA
Found at i:3359376 original size:23 final size:23
Alignment explanation
Indices: 3359350--3359394 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3359340 CACCACAGCT
*
3359350 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
3359373 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
3359395 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:3359559 original size:150 final size:149
Alignment explanation
Indices: 3359362--3359677 Score: 553
Period size: 150 Copynumber: 2.1 Consensus size: 149
3359352 TATAATTGCA
*
3359362 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
* *
3359426 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTCACACATGT
65 TTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTT-CAAGACCTCACACATGT
* *
3359491 TCCACAGAATATATATATATC
129 TCCAAAGAATATACATATATC
3359512 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
3359577 TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACCTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACCTCACACATGTTC
*
3359642 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
3359661 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
3359678 CCCTCTACCC
Statistics
Matches: 159, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
149 52 0.33
150 107 0.67
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACCTCACACATGTTC
CAAAGAATATACATATATC
Found at i:3360552 original size:11 final size:11
Alignment explanation
Indices: 3360536--3360565 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
3360526 ACTCATCCAT
3360536 ATCAAAATTCC
1 ATCAAAATTCC
3360547 ATCAAAATTCC
1 ATCAAAATTCC
3360558 ATCTAAAA
1 ATC-AAAA
3360566 AAAAACTGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (11 bp):
ATCAAAATTCC
Found at i:3368280 original size:25 final size:25
Alignment explanation
Indices: 3368251--3368301 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
3368241 TTAATTACAC
3368251 AAAGATTGTATTGCCATCTAATTGT
1 AAAGATTGTATTGCCATCTAATTGT
3368276 AAAGATTGTATTGCCATCTAATTGT
1 AAAGATTGTATTGCCATCTAATTGT
3368301 A
1 A
3368302 CAATCTAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (25 bp):
AAAGATTGTATTGCCATCTAATTGT
Found at i:3370846 original size:119 final size:119
Alignment explanation
Indices: 3370626--3370855 Score: 290
Period size: 119 Copynumber: 1.9 Consensus size: 119
3370616 TAAACTTCTA
*
3370626 ATGGGGAAATTAAGGTTTAAGAATTGAAATTTACGAGAAAACAAAAAAGAAATTCGTACCTTTGT
1 ATGGGGAAATTAAGGTTTAAGAATTGAAAATTACGAGAAAACAAAAAAGAAATTCGTACCTTTGT
* **
3370691 CTTGTCTGTGAGTCATTGTTTGTTACAGTCGGGTCATCGAAAGAAATTAAGTAC
66 CGTGTCTGTGAGTCATTCATTGTTACAGTCGGGTCATCGAAAGAAATTAAGTAC
* *
3370745 ATGGGGAAATTAGGGTTTAAGAATTGAAAATTACGATG-AAAC-AAAAAGATATTCGATACCTTT
1 ATGGGGAAATTAAGGTTTAAGAATTGAAAATTACGA-GAAAACAAAAAAGAAATTCG-TACCTTT
* * * *
3370808 TTCGTGTCTTTGAAG-CA-TCATTGCTTATAGT-GGCGTCATCGGAAGAAA
64 GTCGTGTCTGTG-AGTCATTCATTG-TTACAGTCGG-GTCATCGAAAGAAA
3370856 CCCTAGAGCC
Statistics
Matches: 96, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
118 18 0.19
119 75 0.78
120 3 0.03
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (119 bp):
ATGGGGAAATTAAGGTTTAAGAATTGAAAATTACGAGAAAACAAAAAAGAAATTCGTACCTTTGT
CGTGTCTGTGAGTCATTCATTGTTACAGTCGGGTCATCGAAAGAAATTAAGTAC
Found at i:3379544 original size:20 final size:21
Alignment explanation
Indices: 3379496--3379750 Score: 153
Period size: 20 Copynumber: 12.5 Consensus size: 21
3379486 TGACCAATAA
* *
3379496 AATCGCAACGCGATAT-CAA-
1 AATCGCAACGCGATTTAGAAG
*
3379515 AATCGTAACGCGATTTAGAAG
1 AATCGCAACGCGATTTAGAAG
** ***
3379536 -ATCGCAACGTTAAAAAGAA-
1 AATCGCAACGCGATTTAGAAG
* *
3379555 AATCGCAACG-G--TCAAAAG
1 AATCGCAACGCGATTTAGAAG
3379573 AAAATCGCAACGCGATTTAGAAG
1 --AATCGCAACGCGATTTAGAAG
*
3379596 AAAATCGCAATGCGA-TT-GATAG
1 --AATCGCAACGCGATTTAGA-AG
* *
3379618 AATCGCAATGCGATTGAG-AG
1 AATCGCAACGCGATTTAGAAG
*
3379638 AGTCGCAACGCGATTTAGAAGAG
1 AATCGCAACGCGATTTAG-A-AG
* *
3379661 AATCGCAATGCGA-CT-GATAG
1 AATCGCAACGCGATTTAGA-AG
* *
3379681 AATCGCAATGCGATTTA-TAG
1 AATCGCAACGCGATTTAGAAG
* *
3379701 AATCGCAATGCGATTGAG-AG
1 AATCGCAACGCGATTTAGAAG
3379721 AATCGCAACGCGATTTAGAA-
1 AATCGCAACGCGATTTAGAAG
3379741 AATCGCAACG
1 AATCGCAACG
3379751 TTAAAAAGAA
Statistics
Matches: 188, Mismatches: 29, Indels: 37
0.74 0.11 0.15
Matches are distributed among these distances:
17 3 0.02
19 14 0.07
20 126 0.67
21 7 0.04
22 6 0.03
23 32 0.17
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (21 bp):
AATCGCAACGCGATTTAGAAG
Found at i:3379644 original size:63 final size:63
Alignment explanation
Indices: 3379575--3379735 Score: 238
Period size: 63 Copynumber: 2.6 Consensus size: 63
3379565 GTCAAAAGAA
*
3379575 AATCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAG
1 AATCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAG
* * * *
3379638 AGTCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGATAGAATCGCAATGCGATTTATAG
1 AATCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAG
* *
3379701 AATCGCAATGCGA-TT-G-AGAGAATCGCAACGCGATT
1 AATCGCAACGCGATTTAGAAGAGAATCGCAATGCGATT
3379736 TAGAAAATCG
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
60 17 0.19
61 1 0.01
62 2 0.02
63 69 0.78
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.21
Consensus pattern (63 bp):
AATCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAG
Found at i:3379644 original size:83 final size:82
Alignment explanation
Indices: 3379555--3379750 Score: 231
Period size: 83 Copynumber: 2.4 Consensus size: 82
3379545 TTAAAAAGAA
*
3379555 AATCGCAACG-G-TCAAAAGAAAATCGCAACGCGATTTAGA-AGAAAATCGCAATGCGATTGATA
1 AATCGCAACGCGATCAAAAGAAAATCGCAACGCGA-CT-GATAG--AATCGCAATGCGATTGATA
3379617 GAATCGCAATGCGATTGAGAG
62 GAATCGCAATGCGATTGAGAG
* * * * * *
3379638 AGTCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGATAGAATCGCAATGCGATTTATAGAA
1 AATCGCAACGCGA-TCAAAAGAAAATCGCAACGCGACTGATAGAATCGCAATGCGATTGATAGAA
3379703 TCGCAATGCGATTGAGAG
65 TCGCAATGCGATTGAGAG
**
3379721 AATCGCAACGCGAT--TTAGAAAATCGCAACG
1 AATCGCAACGCGATCAAAAGAAAATCGCAACG
3379751 TTAAAAAGAA
Statistics
Matches: 97, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
80 12 0.12
82 1 0.01
83 60 0.62
84 3 0.03
85 3 0.03
86 18 0.19
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.19
Consensus pattern (82 bp):
AATCGCAACGCGATCAAAAGAAAATCGCAACGCGACTGATAGAATCGCAATGCGATTGATAGAAT
CGCAATGCGATTGAGAG
Found at i:3379760 original size:20 final size:20
Alignment explanation
Indices: 3379737--3379780 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
3379727 AACGCGATTT
*
3379737 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
3379757 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
3379777 AGAA
1 AGAA
3379781 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.16, G:0.18, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:3379873 original size:6 final size:6
Alignment explanation
Indices: 3379858--3379959 Score: 132
Period size: 6 Copynumber: 18.5 Consensus size: 6
3379848 GACACGTATT
*
3379858 ACCACG ACCACT ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
3379906 ACCACG ACCA-G ACC-CG ACC-CG ACC-CG ACC-CG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
3379947 ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACC
3379960 CGAGACGAGA
Statistics
Matches: 93, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
5 43 0.46
6 50 0.54
ACGTcount: A:0.28, C:0.54, G:0.17, T:0.01
Consensus pattern (6 bp):
ACCACG
Found at i:3379924 original size:5 final size:5
Alignment explanation
Indices: 3379874--3379962 Score: 115
Period size: 5 Copynumber: 16.6 Consensus size: 5
3379864 ACCACTACCA
*
3379874 CGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC AGACC CGACC
1 CGACC -CGACC -CGACC -CGACC -CGACC -CGACC -CGACC CGACC CGACC
3379925 CGACC CGACC CGACC CGACC CGACC CGACC CGACC CGA
1 CGACC CGACC CGACC CGACC CGACC CGACC CGACC CGA
3379963 GACGAGACGG
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
5 46 0.57
6 35 0.43
ACGTcount: A:0.27, C:0.54, G:0.19, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:3380800 original size:6 final size:6
Alignment explanation
Indices: 3380653--3380798 Score: 161
Period size: 6 Copynumber: 24.7 Consensus size: 6
3380643 TCTCGGGTCG
* * * * * * * *
3380653 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCTT GGTCTT GGTCTT GGTCTT GGTCTT GGTCTT GGTCTT GGTCTT
*
3380701 GGTCGT GGTCTT GG--TT GGTCTT GGTCTT GGTCTT GGTCTT GGTCTT
1 GGTCTT GGTCTT GGTCTT GGTCTT GGTCTT GGTCTT GGTCTT GGTCTT
* * * *
3380747 GGTCTT GGTCTT GGTCAT GGTCTT GGTCTT GGTCAT GGTCAT GGTCAT
1 GGTCTT GGTCTT GGTCTT GGTCTT GGTCTT GGTCTT GGTCTT GGTCTT
3380795 GGTC
1 GGTC
3380799 ATACGTGTCT
Statistics
Matches: 134, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
4 4 0.03
6 130 0.97
ACGTcount: A:0.03, C:0.16, G:0.40, T:0.40
Consensus pattern (6 bp):
GGTCTT
Found at i:3380908 original size:20 final size:20
Alignment explanation
Indices: 3380870--3381020 Score: 160
Period size: 20 Copynumber: 7.4 Consensus size: 20
3380860 ATTTTCAACG
* *
3380870 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTATCAATCGCA
* * *
3380890 TTGCAATTTTATAAATCGCA
1 TTGCGATTCTATCAATCGCA
* *
3380910 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTATCAATCGCA
* *
3380930 TTGCGCTTTTCT-TCTAAATCGCG
1 TTGCG--ATTCTATC--AATCGCA
* *
3380953 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTATCAATCGCA
3380973 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
3380993 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
3381013 TTGCGATT
1 TTGCGATT
3381021 TTCTTCTAAA
Statistics
Matches: 108, Mismatches: 18, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
20 87 0.81
21 5 0.05
22 6 0.06
23 10 0.09
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.37
Consensus pattern (20 bp):
TTGCGATTCTATCAATCGCA
Found at i:3380914 original size:40 final size:40
Alignment explanation
Indices: 3380870--3381022 Score: 189
Period size: 40 Copynumber: 3.8 Consensus size: 40
3380860 ATTTTCAACG
* *
3380870 TTGCGATTCTCTCAGTCGCATTGCAATTTTATAAATCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTTTATAAATCGCA
* * * *
3380910 TTGCGATTCTCTCAGTCGCATTGCGCTTTTCTTCTAAATCGCG
1 TTGCGATTCTCTCAATCGCATTGCG--ATT-TTATAAATCGCA
* * *
3380953 TTGCGACTCTCTCAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTTTATAAATCGCA
*
3380993 TTGCGATTCTATCAATCGCATTGCGATTTT
1 TTGCGATTCTCTCAATCGCATTGCGATTTT
3381023 CTTCTAAATC
Statistics
Matches: 96, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
40 59 0.61
41 2 0.02
42 2 0.02
43 33 0.34
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.38
Consensus pattern (40 bp):
TTGCGATTCTCTCAATCGCATTGCGATTTTATAAATCGCA
Found at i:3381012 original size:83 final size:83
Alignment explanation
Indices: 3380868--3381039 Score: 272
Period size: 83 Copynumber: 2.1 Consensus size: 83
3380858 TTATTTTCAA
* * * * *
3380868 CGTTGCGATTCTCTCAGTCGCATTGCAATTTTATAAATCGCATTGCGATTCTCTCAGTCGCATTG
1 CGTTGCGACTCTCTCAATCGCATTGCAATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
*
3380933 CGCTTTTCTTCTAAATCG
66 CGATTTTCTTCTAAATCG
* *
3380951 CGTTGCGACTCTCTCAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCATTG
1 CGTTGCGACTCTCTCAATCGCATTGCAATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
3381016 CGATTTTCTTCTAAATCG
66 CGATTTTCTTCTAAATCG
3381034 CGTTGC
1 CGTTGC
3381040 AAACTTGGAA
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (83 bp):
CGTTGCGACTCTCTCAATCGCATTGCAATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
CGATTTTCTTCTAAATCG
Found at i:3381098 original size:20 final size:20
Alignment explanation
Indices: 3380868--3381125 Score: 108
Period size: 20 Copynumber: 12.6 Consensus size: 20
3380858 TTATTTTCAA
* * *
3380868 CGTTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * *
3380888 CATTGCAATTTTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
3380908 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* *
3380928 CATTGCGCTTTTCTTCTAAATCG
1 CGTTGCG--ATT-TTCTAAATCG
* * *
3380951 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
3380971 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
3380991 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
3381011 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* ** ** *
3381034 CGTTGCAAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
3381055 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
3381073 ACCGTTGCGATTTTCTAAATCG
1 --CGTTGCGATTTTCTAAATCG
* *
3381095 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
3381114 CGTTGCGATTTT
1 CGTTGCGATTTT
3381126 ATTGGTCATT
Statistics
Matches: 183, Mismatches: 44, Indels: 23
0.73 0.18 0.09
Matches are distributed among these distances:
18 2 0.01
19 17 0.09
20 119 0.65
21 13 0.07
22 6 0.03
23 26 0.14
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:3381115 original size:19 final size:20
Alignment explanation
Indices: 3381075--3381125 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
3381065 TTCTTTTGAC
*
3381075 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
3381095 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
3381114 CGTTGCGATTTT
1 CGTTGCGATTTT
3381126 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:3382910 original size:300 final size:300
Alignment explanation
Indices: 3382368--3383580 Score: 2309
Period size: 300 Copynumber: 4.0 Consensus size: 300
3382358 TTGTCAAATC
3382368 CCAAATAGGAGCTAATATAGTGTTCCTTGTTATAATTGCAGATAGCTGAAAGTTCAATAATGAGT
1 CCAAATAGGAGCTAATATAGTGTTCCTTGTTATAATTGCAGATAGCTGAAAGTTCAATAATGAGT
*
3382433 AGTTGTGTAAAACCACTAGTACAAAGTGATGCAAATCCATTAGTTCTTCTCCATTGCTTTGACAG
66 AGTTGTGTACAACCACTAGTACAAAGTGATGCAAATCCATTAGTTCTTCTCCATTGCTTTGACAG
3382498 GTTAGTTCTTAGAAACATATAGATGTACACTAATTTACAAGCTTCCTCCCTAACCTCTTTCATTC
131 GTTAGTTCTTAGAAACATATAGATGTACACTAATTTACAAGCTTCCTCCCTAACCTCTTTCATTC
3382563 TGTTGTTGTCCATTAGTTCCTGTTTAGAATAGAGGTGTGCTTACCCGTTGTCTTATCATCCCATC
196 TGTTGTTGTCCATTAGTTCCTGTTTAGAATAGAGGTGTGCTTACCCGTTGTCTTATCATCCCATC
3382628 TTTTTAACTCTACTTTCACTGGAGTTTTCATGTACATCTA
261 TTTTTAACTCTACTTTCACTGGAGTTTTCATGTACATCTA
3382668 CCAAATAGGAGCTAATATAGTGTTCCTTGTTATAATTGCAGATAGCTGAAAGTTCAATAATGAGT
1 CCAAATAGGAGCTAATATAGTGTTCCTTGTTATAATTGCAGATAGCTGAAAGTTCAATAATGAGT
3382733 AGTTGTGTACAACCACTAGTACAAAGTGATGCAAATCCATTAGTTCTTCTCCATTGCTTTGACAG
66 AGTTGTGTACAACCACTAGTACAAAGTGATGCAAATCCATTAGTTCTTCTCCATTGCTTTGACAG
3382798 GTTAGTTCTTAGAAACATATAGATGTACACTAATTTACAAGCTTCCTCCCTAACCTCTTTCATTC
131 GTTAGTTCTTAGAAACATATAGATGTACACTAATTTACAAGCTTCCTCCCTAACCTCTTTCATTC
3382863 TGTTGTTGTCCATTAGTTCCTGTTTAGAATAGAGGTGTGCTTACCCGTTGTCTTATCATCCCATC
196 TGTTGTTGTCCATTAGTTCCTGTTTAGAATAGAGGTGTGCTTACCCGTTGTCTTATCATCCCATC
3382928 TTTTTAACTCTACTTTCACTGGAGTTTTCATGTACATCTA
261 TTTTTAACTCTACTTTCACTGGAGTTTTCATGTACATCTA
3382968 CCAAATAGGAGCTAATATAGTGTTCCTTGTTATAATTGCAGATAGCTGAAAGTTCAATAATGAGT
1 CCAAATAGGAGCTAATATAGTGTTCCTTGTTATAATTGCAGATAGCTGAAAGTTCAATAATGAGT
3383033 AGTTGTGTACAACCACTAGTACAAAGTGATGCAAATCCATTAGTTCTTCTCCATTGCTTTGACAG
66 AGTTGTGTACAACCACTAGTACAAAGTGATGCAAATCCATTAGTTCTTCTCCATTGCTTTGACAG
3383098 GTTAGTTCTTAGAAACATATAGATGTACACTAATTTACAAGCTTCCTCCCTAACCTCTTTCATTC
131 GTTAGTTCTTAGAAACATATAGATGTACACTAATTTACAAGCTTCCTCCCTAACCTCTTTCATTC
3383163 TGTTGTTGTCCATTAGTTCCTGTTTAGAATAGAGGTGTGCTTACCCGTTGTCTTATCATCCCATC
196 TGTTGTTGTCCATTAGTTCCTGTTTAGAATAGAGGTGTGCTTACCCGTTGTCTTATCATCCCATC
3383228 TTTTTAACTCTACTTTCACTGGAGTTTTCATGTACATCTA
261 TTTTTAACTCTACTTTCACTGGAGTTTTCATGTACATCTA
3383268 CCAAATAGGAGCTAATATAGTGTTCCTTGTTATAATTGCAGATAGCTGAAAGTTCAATAATGAGT
1 CCAAATAGGAGCTAATATAGTGTTCCTTGTTATAATTGCAGATAGCTGAAAGTTCAATAATGAGT
3383333 AGTTGTGTACAACCACTAGTACAAAGTGATGCAAATCCATTAGTTCTTCTCCATTGCTTTGACAG
66 AGTTGTGTACAACCACTAGTACAAAGTGATGCAAATCCATTAGTTCTTCTCCATTGCTTTGACAG
3383398 GTTAGTTCTTAGAAACATATAGATGTACACTAATTTACAAGCTTCCTCCCTAACCTCTTTCATTC
131 GTTAGTTCTTAGAAACATATAGATGTACACTAATTTACAAGCTTCCTCCCTAACCTCTTTCATTC
3383463 TGTTGTTGTCCATTAGTTCCTGTTTAGAATAGAGGTGTGCTTACCCGTTGTCTCCGATTTGGGTT
196 TGTTGTTGTCCATTAGTTCCTGTTTAGAATAGAGGTGTGCTTACCCGTTG--T-C--------TT
3383528 CATCATCCCATCTTTTTAACTCTACTTTCACTGGAGTTTTCATGTACATCTA
250 -ATCATCCCATCTTTTTAACTCTACTTTCACTGGAGTTTTCATGTACATCTA
3383580 C
1 C
3383581 TTCTTACAGT
Statistics
Matches: 900, Mismatches: 1, Indels: 12
0.99 0.00 0.01
Matches are distributed among these distances:
300 844 0.94
302 1 0.00
303 1 0.00
311 2 0.00
312 52 0.06
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (300 bp):
CCAAATAGGAGCTAATATAGTGTTCCTTGTTATAATTGCAGATAGCTGAAAGTTCAATAATGAGT
AGTTGTGTACAACCACTAGTACAAAGTGATGCAAATCCATTAGTTCTTCTCCATTGCTTTGACAG
GTTAGTTCTTAGAAACATATAGATGTACACTAATTTACAAGCTTCCTCCCTAACCTCTTTCATTC
TGTTGTTGTCCATTAGTTCCTGTTTAGAATAGAGGTGTGCTTACCCGTTGTCTTATCATCCCATC
TTTTTAACTCTACTTTCACTGGAGTTTTCATGTACATCTA
Found at i:3385406 original size:20 final size:20
Alignment explanation
Indices: 3385369--3385406 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3385359 TTAATGGGGA
*
3385369 TTTTGTTTTGTCTTCAATAC
1 TTTTGTTTTGTCTACAATAC
3385389 TTTTGTTTCTGT-TACAAT
1 TTTTGTTT-TGTCTACAAT
3385407 TGGTTAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.16, C:0.13, G:0.11, T:0.61
Consensus pattern (20 bp):
TTTTGTTTTGTCTACAATAC
Found at i:3385594 original size:8 final size:8
Alignment explanation
Indices: 3385581--3385610 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
3385571 TTGTCTCTTT
3385581 TTTTTTTC
1 TTTTTTTC
3385589 TTTTTTTC
1 TTTTTTTC
*
3385597 TTTTTTAC
1 TTTTTTTC
3385605 TTTTTT
1 TTTTTT
3385611 GTTGTTCTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTC
Found at i:3387017 original size:17 final size:17
Alignment explanation
Indices: 3386992--3387024 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3386982 TTTATTGGAG
*
3386992 AGAATAAAGAAAGAAGC
1 AGAAGAAAGAAAGAAGC
3387009 AGAAGAAAGAAAGAAG
1 AGAAGAAAGAAAGAAG
3387025 GCTTTGTCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.03, G:0.27, T:0.03
Consensus pattern (17 bp):
AGAAGAAAGAAAGAAGC
Found at i:3393298 original size:2 final size:2
Alignment explanation
Indices: 3393291--3393329 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3393281 TCAAAATTAT
3393291 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3393330 TTAACATATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3395274 original size:32 final size:32
Alignment explanation
Indices: 3395229--3395328 Score: 112
Period size: 32 Copynumber: 3.1 Consensus size: 32
3395219 TAACATATAA
* * * *
3395229 CACAACACACAAAATATTAATGTAATATATGT
1 CACATCACTCAAAATAATAATATAATATATGT
*
3395261 CACATCACTCAAAATAATAATATAATATATCT
1 CACATCACTCAAAATAATAATATAATATATGT
* * *
3395293 CACATAACAT-AAAATAATAACATGATATATGT
1 CACATCAC-TCAAAATAATAATATAATATATGT
3395325 CACA
1 CACA
3395329 CCATCTGAAG
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
32 57 0.98
33 1 0.02
ACGTcount: A:0.51, C:0.17, G:0.04, T:0.28
Consensus pattern (32 bp):
CACATCACTCAAAATAATAATATAATATATGT
Found at i:3395403 original size:33 final size:33
Alignment explanation
Indices: 3395349--3395418 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
3395339 TGATGACGTA
* *
3395349 ATATGAATACATCATTCAAAATGATGATATAAT
1 ATATAAATACATCATTCAAAATGATGAAATAAT
* * *
3395382 ATATAAATATATCATTTAAAATGATGAAATGAT
1 ATATAAATACATCATTCAAAATGATGAAATAAT
3395415 ATAT
1 ATAT
3395419 GTTACTTCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.36
Consensus pattern (33 bp):
ATATAAATACATCATTCAAAATGATGAAATAAT
Found at i:3395554 original size:23 final size:24
Alignment explanation
Indices: 3395515--3395560 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3395505 AATATTTTGA
* *
3395515 TAAAAAAATGTTAAGATATAATAT
1 TAAAAAAATATTAAGATAAAATAT
3395539 TAAAAAAATATT-AGATAAAATA
1 TAAAAAAATATTAAGATAAAATA
3395561 ATCATGGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (24 bp):
TAAAAAAATATTAAGATAAAATAT
Found at i:3396090 original size:17 final size:18
Alignment explanation
Indices: 3396063--3396100 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
3396053 TGAAAATATA
3396063 TTAATTATGTAGTTT-AAT
1 TTAATTATGTA-TTTAAAT
3396081 TTAATT-TGTATTTAAAT
1 TTAATTATGTATTTAAAT
3396098 TTA
1 TTA
3396101 TAACATGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.16
17 10 0.53
18 6 0.32
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (18 bp):
TTAATTATGTATTTAAAT
Found at i:3403780 original size:6 final size:6
Alignment explanation
Indices: 3403769--3403800 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
3403759 TCCAGTCGAT
3403769 TGGTAC TGGTAC TGGTAC TGGTAC TGGTAC TG
1 TGGTAC TGGTAC TGGTAC TGGTAC TGGTAC TG
3403801 TAGATGCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.16, G:0.34, T:0.34
Consensus pattern (6 bp):
TGGTAC
Found at i:3405824 original size:36 final size:36
Alignment explanation
Indices: 3405777--3406165 Score: 528
Period size: 36 Copynumber: 10.8 Consensus size: 36
3405767 GAGTTTGATC
3405777 CTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
1 CTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
3405813 CTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
1 CTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
* *
3405849 CTGAACCTCAGTCTGAGCCTCAACCTGAATCAGCTA
1 CTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
*
3405885 CTGAACCTCAGGCTGAGCCTCATCATGAATCAGCTA
1 CTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
*
3405921 CTGAACCCCAGGCTGAGCCTCAACATGAATCAGCTA
1 CTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
* *
3405957 CTGAACCTCAGGCTGAGCCTCAATATGAATTAGCTA
1 CTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
* * * * * **
3405993 CTGAACCTCGGGATAAGCTTCGACATGAATTTGCTA
1 CTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
* * * *
3406029 CTGAACCTCAGGCAGTGCCTCAACATGAATTAGCAA
1 CTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
* * * *
3406065 CCGAACCTCAGG-TAGTGCCTCAACATGAATTAGCAA
1 CTGAACCTCAGGCT-GAGCCTCAACATGAATCAGCTA
* * * *
3406101 CTGAACCTCAGGCAGTGCCTCAACATGAATTAGCAA
1 CTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
*
3406137 CTGAACCTCAGGCTGAGCCTCAACGTGAA
1 CTGAACCTCAGGCTGAGCCTCAACATGAA
3406166 CTGGCTTCTA
Statistics
Matches: 318, Mismatches: 33, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
36 318 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (36 bp):
CTGAACCTCAGGCTGAGCCTCAACATGAATCAGCTA
Found at i:3405891 original size:18 final size:18
Alignment explanation
Indices: 3405838--3405892 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
3405828 AGCCTCAACA
3405838 TGAATCAGCTACTGAACC
1 TGAATCAGCTACTGAACC
* * *
3405856 TCAGTCTGAGC--CTCAACC
1 TGAATC--AGCTACTGAACC
3405874 TGAATCAGCTACTGAACC
1 TGAATCAGCTACTGAACC
3405892 T
1 T
3405893 CAGGCTGAGC
Statistics
Matches: 27, Mismatches: 6, Indels: 8
0.66 0.15 0.20
Matches are distributed among these distances:
16 3 0.11
18 21 0.78
20 3 0.11
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (18 bp):
TGAATCAGCTACTGAACC
Found at i:3444183 original size:41 final size:41
Alignment explanation
Indices: 3444137--3444222 Score: 156
Period size: 41 Copynumber: 2.1 Consensus size: 41
3444127 GATCATGATA
3444137 GTCTGACTCTTCTATTATACTAACTG-TCTAGTGGAAGGACG
1 GTCTGACTCTTCTATTATACTAACTGCT-TAGTGGAAGGACG
3444178 GTCTGACTCTTCTATTATACTAACTGCTTAGTGGAAGGACG
1 GTCTGACTCTTCTATTATACTAACTGCTTAGTGGAAGGACG
3444219 GTCT
1 GTCT
3444223 CTCCGGAACA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
41 43 0.98
42 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (41 bp):
GTCTGACTCTTCTATTATACTAACTGCTTAGTGGAAGGACG
Found at i:3445603 original size:2 final size:2
Alignment explanation
Indices: 3445596--3445622 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3445586 TGTATCAGTA
3445596 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
3445623 AAAAATTATC
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:3446697 original size:59 final size:59
Alignment explanation
Indices: 3446579--3446713 Score: 164
Period size: 59 Copynumber: 2.3 Consensus size: 59
3446569 TCGGATTGTC
* * * * *
3446579 ATTTTATAATTTTTAATAGTTGAGGGATTTAACAAAACAACACCCTATCATTAAAAGACT
1 ATTTTATAACTTTTAATAGTTGA-GGATTCAACAAAACAACACCATATAATCAAAAGACT
* * * *
3446639 ATTTTGTAACTTTTAATAGTATGA-GATTCAACAAAATAACACCATATAATCGATAGACT
1 ATTTTATAACTTTTAATAGT-TGAGGATTCAACAAAACAACACCATATAATCAAAAGACT
3446698 ATTTTATAACTTTTAA
1 ATTTTATAACTTTTAA
3446714 ATTAATAAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
59 43 0.67
60 18 0.28
61 3 0.05
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (59 bp):
ATTTTATAACTTTTAATAGTTGAGGATTCAACAAAACAACACCATATAATCAAAAGACT
Found at i:3452532 original size:16 final size:18
Alignment explanation
Indices: 3452513--3452549 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
3452503 AAAATACCTT
3452513 GTAAA-GAAAA-AAGAAG
1 GTAAATGAAAACAAGAAG
3452529 GTAAATGAAAAGCAAGAAG
1 GTAAATGAAAA-CAAGAAG
3452548 GT
1 GT
3452550 TGAAGATGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.28
17 5 0.28
19 8 0.44
ACGTcount: A:0.59, C:0.03, G:0.27, T:0.11
Consensus pattern (18 bp):
GTAAATGAAAACAAGAAG
Found at i:3456992 original size:3 final size:3
Alignment explanation
Indices: 3456986--3457076 Score: 101
Period size: 3 Copynumber: 29.7 Consensus size: 3
3456976 TTCATTTAAA
* * * *
3456986 TAT TAT TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT AAT TAT AAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
3457034 TAA TAT TAT TATT TAT TAC TAA TAT TAT TAT TAAT TAT TAT TA
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
3457077 CAAACGGGCC
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
3 68 0.92
4 6 0.08
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:3457621 original size:19 final size:18
Alignment explanation
Indices: 3457584--3457618 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3457574 ACTGAACCGG
3457584 AGAGAAAGAAAAAAAAAC
1 AGAGAAAGAAAAAAAAAC
3457602 AGAGAAAGAAAAAAAAA
1 AGAGAAAGAAAAAAAAA
3457619 ACAACTAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (18 bp):
AGAGAAAGAAAAAAAAAC
Found at i:3460919 original size:14 final size:14
Alignment explanation
Indices: 3460881--3460934 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
3460871 ATTTTAAATA
*
3460881 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
3460895 TTTTACATTTGCAT
1 ATTTACATTTGCAT
3460909 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
3460924 CTTTGCATTTG
1 ATTTACATTTG
3460935 TATTGCACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:3466440 original size:83 final size:83
Alignment explanation
Indices: 3466336--3466682 Score: 590
Period size: 83 Copynumber: 4.2 Consensus size: 83
3466326 ATATCCTAGT
3466336 CCAATCATTGAATTT-GAAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTAG-AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
3466400 CTGATCTGGTTTAGCAGAA
65 CTGATCTGGTTTAGCAGAA
** *
3466419 CCAATCATTGAATTGGGAAGATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTAGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
3466483 CTGATCTGGTTTAGCAGAA
65 CTGATCTGGTTTAGCAGAA
**
3466502 CCAATCATTGAATTTAGAAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
3466567 TGATCTGGTTTAGCAGAA
66 TGATCTGGTTTAGCAGAA
**
3466585 CCAATCATTGAATTTAGAAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
*
3466650 TGATCTGGTTTGGCAGAA
66 TGATCTGGTTTAGCAGAA
3466668 CCAATCATTGAATTT
1 CCAATCATTGAATTT
3466683 GAGTTATCTG
Statistics
Matches: 253, Mismatches: 8, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
83 251 0.99
84 2 0.01
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (83 bp):
CCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGGTTTAGCAGAA
Found at i:3466696 original size:41 final size:41
Alignment explanation
Indices: 3466639--3466785 Score: 278
Period size: 41 Copynumber: 3.6 Consensus size: 41
3466629 GGAAGTGTTC
3466639 TTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
1 TTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
3466680 TTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
1 TTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
3466721 TTTGAGTTATCTGATCTGG-TTGGACAGAACCAATCATTGAA
1 TTTGAGTTATCTGATCTGGTTTGG-CAGAACCAATCATTGAA
3466762 TTTGAGTTATCTGATCTGGTTTGG
1 TTTGAGTTATCTGATCTGGTTTGG
3466786 TAAGAACTAC
Statistics
Matches: 104, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
40 4 0.04
41 96 0.92
42 4 0.04
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (41 bp):
TTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
Found at i:3468914 original size:40 final size:40
Alignment explanation
Indices: 3468869--3468944 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
3468859 TGAGCAGAGT
*
3468869 CCACAGCAAAGGATGAATGCGTTGTCAAATGTTTTATGTC
1 CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTATGTC
* *
3468909 CCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTA
1 CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTA
3468945 CATCTAAGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (40 bp):
CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTATGTC
Found at i:3469365 original size:22 final size:22
Alignment explanation
Indices: 3469336--3469390 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
3469326 ATCTACACTC
*
3469336 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
3469358 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
3469380 TTCAAAGATGA
1 TTCAAAGATGA
3469391 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:3470046 original size:113 final size:113
Alignment explanation
Indices: 3469792--3470563 Score: 1085
Period size: 113 Copynumber: 6.9 Consensus size: 113
3469782 AGCAAAGATA
*
3469792 TGAATTCATCATTCGATGATTCAGCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATTCATCATTCGATGATTCAGCATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
3469857 G--AAAA-AAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCT
66 GAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCT
*
3469902 TGAATTCATCATTCGATGATTCAGCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATTCATCATTCGATGATTCAGCATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
*
3469967 GAAAAAATAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCT
66 GAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCT
*
3470015 TGAATTCATCATTCGATGATTCAGCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATTCATCATTCGATGATTCAGCATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
3470080 GAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCT
66 GAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCT
* ****
3470128 TGAATTCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATTCATCATTCGATGATTCAGCATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
** * *
3470193 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT-GCT
66 GAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCT
** * * * ****
3470241 CAAATCCATC-TCTTGATGGA-TCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
1 TGAATTCATCAT-TCGAT-GATTCAGCATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTG
3470304 AAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCT
64 AAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCT
*
3470354 TGAATTCATCATTCGATGATTCAGTATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATTCATCATTCGATGATTCAGCATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
** * *
3470419 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT-GCT
66 GAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCT
** * * * ****
3470467 CAAATCCATC-TCTTGATGGA-TCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
1 TGAATTCATCAT-TCGAT-GATTCAGCATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTG
**
3470530 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
64 AAGAAAAAAGAAGAAGTTCATAATGAGAAGAACT
3470564 CATCTGAAGA
Statistics
Matches: 602, Mismatches: 48, Indels: 21
0.90 0.07 0.03
Matches are distributed among these distances:
110 66 0.11
112 13 0.02
113 508 0.84
114 15 0.02
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (113 bp):
TGAATTCATCATTCGATGATTCAGCATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
GAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCT
Found at i:3470558 original size:40 final size:40
Alignment explanation
Indices: 3470503--3470603 Score: 184
Period size: 40 Copynumber: 2.5 Consensus size: 40
3470493 TTTCCAGAGA
**
3470503 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAG
3470543 AAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAG
3470583 AAGTTCATAATGAGAAGAACT
1 AAGTTCATAATGAGAAGAACT
3470604 TGTTCAACTT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.50, C:0.10, G:0.22, T:0.19
Consensus pattern (40 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAG
Found at i:3470573 original size:153 final size:153
Alignment explanation
Indices: 3470391--3470714 Score: 467
Period size: 153 Copynumber: 2.1 Consensus size: 153
3470381 TTCCAGTTCG
** *
3470391 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAATTCATAATGAGAAGAACTTGTTC
*
3470456 AACCTTTT-GCTCAAATCCATC-TCTTGATGGA-TCAGCT-TTTCCAGAGAAAGTTCATAATGAG
66 AA-CTTTTCGCTCAAATCCATCAT-TCGAT-GATTCAG-TATTTCCAGAGAAAGTTCATAATGAG
3470517 AAGAACTCATCTGAAGAAGGAAGAAGA
127 AAGAACTCATCTGAAGAAGGAAGAAGA
*
3470544 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAATTCATAATGAGAAGAACTTGTTC
** * ****
3470609 AACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGTTCGAGTTCATAATGAGAAGA
66 AACTTTTCGCTCAAATCCATCATTCGATGATTCAGTATTTCCAGAGAAAGTTCATAATGAGAAGA
3470674 ACTCATCTGAAGAAGGAAGAAGA
131 ACTCATCTGAAGAAGGAAGAAGA
*
3470697 AATTCATAATGAGAAGAA
1 AGTTCATAATGAGAAGAA
3470715 TTTGTTCAAC
Statistics
Matches: 154, Mismatches: 13, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
152 8 0.05
153 145 0.94
154 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (153 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAATTCATAATGAGAAGAACTTGTTC
AACTTTTCGCTCAAATCCATCATTCGATGATTCAGTATTTCCAGAGAAAGTTCATAATGAGAAGA
ACTCATCTGAAGAAGGAAGAAGA
Found at i:3470589 original size:266 final size:266
Alignment explanation
Indices: 3470277--3470827 Score: 1084
Period size: 266 Copynumber: 2.1 Consensus size: 266
3470267 TTTCCAGAGA
3470277 AAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTT
3470342 CAACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGTTCGAGTTCATAATGAGAAG
66 CAACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGTTCGAGTTCATAATGAGAAG
3470407 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAAT
131 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAAT
* *
3470472 CCATCTCTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
196 CCATCTCTTGATGGATAAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
3470537 AAGAAG
261 AAGAAG
3470543 AAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTT
3470608 CAACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGTTCGAGTTCATAATGAGAAG
66 CAACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGTTCGAGTTCATAATGAGAAG
3470673 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAAT
131 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAAT
3470738 CCATCTCTTGATGGATAAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
196 CCATCTCTTGATGGATAAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
3470803 AAGAAG
261 AAGAAG
3470809 AAGTTCATAATGAGAAGAA
1 AAGTTCATAATGAGAAGAA
3470828 TTTGTTCAAC
Statistics
Matches: 283, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
266 283 1.00
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (266 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGTTCGAGTTCATAATGAGAAG
AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAAT
CCATCTCTTGATGGATAAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
AAGAAG
Found at i:3470827 original size:226 final size:226
Alignment explanation
Indices: 3469829--3470563 Score: 1194
Period size: 226 Copynumber: 3.3 Consensus size: 226
3469819 TACCAGTTCG
3469829 AGTTCATAATGAGAAGAACTCATCTGAAG--AAAA-AAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
3469891 AACTTTTCGCTTGAATTCATCATTCGATGATTCAGCATTACCAGTTCGAGTTCATAATGAGAAGA
66 AACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGTTCGAGTTCATAATGAGAAGA
** * * * **
3469956 ACTCATCTGAAGAAAAAATAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTTGAAT
131 ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT-GCTCAAAT
* * * * ****
3470020 TCATCAT-TCGAT-GATTCAGCATTACCAGTTCG
195 CCATC-TCTTGATGGA-TCAGCTTTTCCAGAGAA
3470052 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
****
3470117 AACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATGAGAAGA
66 AACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGTTCGAGTTCATAATGAGAAGA
3470182 ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
131 ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
3470247 CATCTCTTGATGGATCAGCTTTTCCAGAGAA
196 CATCTCTTGATGGATCAGCTTTTCCAGAGAA
3470278 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
3470343 AACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGTTCGAGTTCATAATGAGAAGA
66 AACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGTTCGAGTTCATAATGAGAAGA
3470408 ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
131 ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
3470473 CATCTCTTGATGGATCAGCTTTTCCAGAGAA
196 CATCTCTTGATGGATCAGCTTTTCCAGAGAA
**
3470504 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACT
3470564 CATCTGAAGA
Statistics
Matches: 479, Mismatches: 27, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
223 29 0.06
225 5 0.01
226 438 0.91
227 7 0.01
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (226 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGTTCGAGTTCATAATGAGAAGA
ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
CATCTCTTGATGGATCAGCTTTTCCAGAGAA
Found at i:3470835 original size:226 final size:228
Alignment explanation
Indices: 3470538--3470959 Score: 609
Period size: 226 Copynumber: 1.9 Consensus size: 228
3470528 TGAAGAAGGA
*
3470538 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAAC
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAAC
* ** * ***
3470603 TTGTTCAA-CTTTTCGCTTGAATTCATCATTCGAT-GATTCAGTATTTCCAGTTCGAGTTCATAA
66 TTGTTCAACCTTTT-GCTTAAATTCATCATTCGATGGA-TCAACATTGCCAGGAAGAGTTCATAA
** * * *
3470666 TGAGAAGAA-C-TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTT
129 TGAGAAGAACCGTCATCTGAAGAAAAAAGAAGAAATTCATAATAAGAAGAACTTATTCAACCTTT
3470729 TGCTCAAATCCATCTCTTGATGGATAAGCTTTTCC
194 TGCTCAAATCCATCTCTTGATGGATAAGCTTTTCC
** *
3470764 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAAC
* *
3470829 TTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATG
66 TTGTTCAACCTTTTGCTTAAATTCATCATTCGATGGATCAACATTGCCAGGAAGAGTTCATAATG
* *
3470894 AGAAGAACTCGTCATCTGAAGAAAAAAGAAGAAGTTCATAATAAGAAGAGCTTATTCAACCTTTT
131 AGAAGAAC-CGTCATCTGAAGAAAAAAGAAGAAATTCATAATAAGAAGAACTTATTCAACCTTTT
3470959 G
195 G
3470960 AATGACTCTA
Statistics
Matches: 171, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
226 115 0.67
227 7 0.04
228 1 0.01
229 48 0.28
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (228 bp):
AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAAC
TTGTTCAACCTTTTGCTTAAATTCATCATTCGATGGATCAACATTGCCAGGAAGAGTTCATAATG
AGAAGAACCGTCATCTGAAGAAAAAAGAAGAAATTCATAATAAGAAGAACTTATTCAACCTTTTG
CTCAAATCCATCTCTTGATGGATAAGCTTTTCC
Found at i:3470888 original size:492 final size:494
Alignment explanation
Indices: 3470052--3470959 Score: 1536
Period size: 492 Copynumber: 1.8 Consensus size: 494
3470042 TACCAGTTCG
3470052 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
3470117 AACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATGAGAAGA
66 AACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATGAGAAGA
3470182 ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
131 ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
* *
3470247 CATCTCTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAA
196 CATCTCTTGATGGATAAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAA
*
3470312 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGATTCA
261 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTAAATTCATCATTCGATGATTCA
** * *** **
3470377 GTATTTCCAGTTCGAGTTCATAATGAGAAGAA-C-TCATCTGAAGAAGGAAGAAGAAATTCATAA
326 ACATTGCCAGGAAGAGTTCATAATGAGAAGAACCGTCATCTGAAGAAAAAAGAAGAAATTCATAA
* * *
3470440 TGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCTCTTGATGGATCAGCTTTTCCAGAGAAA
391 TAAGAAGAACTTATTCAACCTTTTGCTCAAATCCATCTCTTGATGGATCAGCTTTTCCAGAGAAA
3470505 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
456 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
3470544 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
****
3470609 AACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGTTCGAGTTCATAATGAGAAGA
66 AACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATGAGAAGA
3470674 ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
131 ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
**
3470739 CATCTCTTGATGGATAAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
196 CATCTCTTGATGGATAAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAA
* * *
3470804 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GTTTAAATTCATCATTTGATGGA-T
261 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTTAAATTCATCATTCGAT-GATT
*
3470867 CAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAAAAAGAAGAAGTTCA
324 CAACATTGCCAGGAAGAGTTCATAATGAGAAGAAC-CGTCATCTGAAGAAAAAAGAAGAAATTCA
*
3470932 TAATAAGAAGAGCTTATTCAACCTTTTG
388 TAATAAGAAGAACTTATTCAACCTTTTG
3470960 AATGACTCTA
Statistics
Matches: 386, Mismatches: 25, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
492 330 0.85
493 7 0.02
494 1 0.00
495 48 0.12
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (494 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATGAGAAGA
ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
CATCTCTTGATGGATAAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTAAATTCATCATTCGATGATTCA
ACATTGCCAGGAAGAGTTCATAATGAGAAGAACCGTCATCTGAAGAAAAAAGAAGAAATTCATAA
TAAGAAGAACTTATTCAACCTTTTGCTCAAATCCATCTCTTGATGGATCAGCTTTTCCAGAGAAA
GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
Found at i:3470956 original size:116 final size:113
Alignment explanation
Indices: 3470539--3470959 Score: 526
Period size: 113 Copynumber: 3.7 Consensus size: 113
3470529 GAAGAAGGAA
3470539 GAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACT
1 GAAG-AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACT
* * **
3470604 TGTTCAA-CTTTTCGCTTGAATTCATCATTCGAT-GATTCAGTATTTCCAG
65 TGTTCAACCTTTT-GCTTAAATTCATCATTTGATGGA-TCAACATTTCCAG
*** ** * *
3470653 TTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTT
1 GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTT
* * *
3470718 GTTCAACCTTTTGCTCAAATCCATC-TCTTGATGGAT-AAGCTTTTCCAG
66 GTTCAACCTTTTGCTTAAATTCATCAT-TTGATGGATCAA-CATTTCCAG
* * ** *
3470766 AAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
1 GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTT
* *
3470831 GTTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAG
66 GTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAACATTTCCAG
* *
3470879 GAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAAAAAGAAGAAGTTCATAATAAGAAGAG
1 GAAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAA
*
3470944 CTTATTCAACCTTTTG
63 CTTGTTCAACCTTTTG
3470960 AATGACTCTA
Statistics
Matches: 266, Mismatches: 32, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
112 2 0.01
113 203 0.76
114 11 0.04
115 1 0.00
116 49 0.18
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTT
GTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAACATTTCCAG
Found at i:3471196 original size:3 final size:3
Alignment explanation
Indices: 3471182--3471275 Score: 98
Period size: 3 Copynumber: 30.7 Consensus size: 3
3471172 TTCATTTAAA
* * * *
3471182 TAT TAC TAT TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT AAT TAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
3471230 TAC TAA TAT TAT TATT TAT TAC TAA TAT TAT TAT TAAT TAT TAT TA
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
3471276 CAAACGGGCC
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
3 69 0.92
4 6 0.08
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:3471821 original size:20 final size:19
Alignment explanation
Indices: 3471782--3471818 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3471772 ACAGAACCGG
3471782 AGAGAAAGAAAAAAAAAAC
1 AGAGAAAGAAAAAAAAAAC
3471801 AGAGAAAGAAAAAAAAAA
1 AGAGAAAGAAAAAAAAAA
3471819 ACAACTAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (19 bp):
AGAGAAAGAAAAAAAAAAC
Found at i:3494624 original size:28 final size:28
Alignment explanation
Indices: 3494569--3494624 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
3494559 AATCTTTGTT
* * ** *
3494569 TATATTATGTTGTCGAGTTGATGTTTGA
1 TATATTATGTTGGCAAGTCAATGCTTGA
3494597 TATATTATGTTGGCAAGTCAATGCTTGA
1 TATATTATGTTGGCAAGTCAATGCTTGA
3494625 AAGAAACGAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.45
Consensus pattern (28 bp):
TATATTATGTTGGCAAGTCAATGCTTGA
Found at i:3499329 original size:2 final size:2
Alignment explanation
Indices: 3499322--3499347 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3499312 ACAACAAACC
3499322 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
3499348 ATGAAAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3506551 original size:22 final size:23
Alignment explanation
Indices: 3506526--3506572 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
3506516 ATTCATATTC
3506526 ATTCATTTAATATT-ATAAACAT
1 ATTCATTTAATATTCATAAACAT
* *
3506548 ATTCATTTAATGTTCGTAAACAT
1 ATTCATTTAATATTCATAAACAT
3506571 AT
1 AT
3506573 GTATTTACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.45
Consensus pattern (23 bp):
ATTCATTTAATATTCATAAACAT
Found at i:3508241 original size:21 final size:21
Alignment explanation
Indices: 3508190--3508242 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
3508180 ATTATGACTA
3508190 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
3508211 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
3508232 TCGCAATGCGA
1 TCGCAATGCGA
3508243 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:3508304 original size:20 final size:20
Alignment explanation
Indices: 3508275--3508359 Score: 116
Period size: 20 Copynumber: 4.2 Consensus size: 20
3508265 TTGGAAAATA
* *
3508275 GCAACGCGATACTGACTATC
1 GCAACTCGATACTGACTTTC
*
3508295 GCAACACGATACTGACTTTC
1 GCAACTCGATACTGACTTTC
* *
3508315 GCAACTCGATACTTAATTTC
1 GCAACTCGATACTGACTTTC
*
3508335 GCAACTCAATACTGACTTTC
1 GCAACTCGATACTGACTTTC
3508355 GCAAC
1 GCAAC
3508360 GAGATAATAC
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (20 bp):
GCAACTCGATACTGACTTTC
Found at i:3508581 original size:22 final size:22
Alignment explanation
Indices: 3508553--3508596 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3508543 CACTCTCTCA
*
3508553 CCCATCTCCGATGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
3508575 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
3508597 TATCTCTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:3508908 original size:20 final size:20
Alignment explanation
Indices: 3508859--3508917 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
3508849 TTTATTCTCT
* **
3508859 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
3508879 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
3508899 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
3508918 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:3509108 original size:25 final size:24
Alignment explanation
Indices: 3509054--3509108 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
3509044 TGTTTATTAT
* *
3509054 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
3509078 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
3509104 TGTTT
1 TGTTT
3509109 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:3510258 original size:18 final size:18
Alignment explanation
Indices: 3510237--3510284 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
3510227 TCCACTTCGG
3510237 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
3510255 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
3510273 GAGCCATCACCT
1 GAGCCATCACCT
3510285 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:3510844 original size:20 final size:20
Alignment explanation
Indices: 3510819--3510864 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3510809 TAGTTTACTT
3510819 TCGCAACACAAAAATGACTA
1 TCGCAACACAAAAATGACTA
** * *
3510839 TCGCAACGTAGAAATGGCTA
1 TCGCAACACAAAAATGACTA
3510859 TCGCAA
1 TCGCAA
3510865 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.17
Consensus pattern (20 bp):
TCGCAACACAAAAATGACTA
Found at i:3510880 original size:19 final size:19
Alignment explanation
Indices: 3510858--3510954 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
3510848 AGAAATGGCT
3510858 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3510877 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
3510891 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3510910 ATCGCAA--CG--AT-AAA
1 ATCGCAATGCGAAATGAAA
*
3510924 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3510943 ATCGCAATGCGA
1 ATCGCAATGCGA
3510955 TTTGTGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 20 0.32
15 3 0.05
16 3 0.05
17 3 0.05
18 3 0.05
19 31 0.49
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3510905 original size:33 final size:33
Alignment explanation
Indices: 3510858--3510949 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
3510848 AGAAATGGCT
3510858 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
3510891 ATCGCAATGTGAAATGAAAATCGCAACGATAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
3510924 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
3510950 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.48, C:0.20, G:0.18, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:3510926 original size:14 final size:14
Alignment explanation
Indices: 3510874--3510932 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
3510864 ATGCGAAATG
*
3510874 AAAATCGCAACGAC
1 AAAATCGCAACGAT
*
3510888 AAAATCGCAATGTGAAAT
1 AAAATCGCAA--CG--AT
3510906 GAAAATCGCAACGAT
1 -AAAATCGCAACGAT
3510921 AAAATCGCAACG
1 AAAATCGCAACG
3510933 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 22 0.59
15 2 0.05
16 1 0.03
17 1 0.03
18 1 0.03
19 10 0.27
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.14
Consensus pattern (14 bp):
AAAATCGCAACGAT
Found at i:3510983 original size:19 final size:19
Alignment explanation
Indices: 3510961--3511071 Score: 105
Period size: 20 Copynumber: 5.7 Consensus size: 19
3510951 GCGATTTGTG
**
3510961 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATAGTCA
**
3510980 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATAGTCA
* * *
3510999 CTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATAGTCA
3511018 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGATAGTCA
* *
3511038 TTTTCGCGTTGCGAAAGTAA
1 -TTTCGCGTTGCGATAGTCA
*
3511058 GTTTCGTGTTGCGA
1 -TTTCGCGTTGCGA
3511072 AAGTAAACTA
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
19 35 0.45
20 40 0.51
21 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTCA
Found at i:3511062 original size:20 final size:20
Alignment explanation
Indices: 3511022--3511077 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
3511012 TAGCCATTTC
* * *
3511022 CGCGTTGCGATAGTCATTTT
1 CGCGTTGCGAAAGTAAGTTT
3511042 CGCGTTGCGAAAGTAAGTTT
1 CGCGTTGCGAAAGTAAGTTT
*
3511062 CGTGTTGCGAAAGTAA
1 CGCGTTGCGAAAGTAA
3511078 ACTATTCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGAAAGTAAGTTT
Found at i:3511490 original size:42 final size:42
Alignment explanation
Indices: 3511419--3511526 Score: 119
Period size: 42 Copynumber: 2.5 Consensus size: 42
3511409 GACTCACCTG
* * *
3511419 TCATTCCTCAAGAGTCTCCT-CCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTC-CCTCCCAACCGTTCAAGAGGCCACTA
* *
3511461 TCATCCCTCAAGAGTCCCTCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCTCCCAACCGTTCAAGAGGCCACTA
** *
3511503 TCATCGTTGAAGAGGTCCCTCCCA
1 TCATCCCTCAAGA-GTCCCTCCCA
3511527 CCATTCCAGA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
41 3 0.05
42 43 0.78
43 9 0.16
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.23
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCTCCCAACCGTTCAAGAGGCCACTA
Found at i:3511510 original size:21 final size:20
Alignment explanation
Indices: 3511442--3511522 Score: 54
Period size: 21 Copynumber: 3.9 Consensus size: 20
3511432 GTCTCCTCCA
3511442 ATCGTTCAAGAGGCCCCTATC
1 ATCGTTCAAGAGG-CCCTATC
** * **
3511463 ATCCCTCAAGAGTCCCTCCCC
1 ATCGTTCAAGAGGCCCT-ATC
* *
3511484 ACCGTTCAAGAGGCCACTGTC
1 ATCGTTCAAGAGGCC-CTATC
*
3511505 ATCGTTGAAGAGGTCCCT
1 ATCGTTCAAGAGG-CCCT
3511523 CCCACCATTC
Statistics
Matches: 44, Mismatches: 13, Indels: 6
0.70 0.21 0.10
Matches are distributed among these distances:
20 4 0.09
21 36 0.82
22 4 0.09
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.22
Consensus pattern (20 bp):
ATCGTTCAAGAGGCCCTATC
Found at i:3513115 original size:19 final size:19
Alignment explanation
Indices: 3513091--3513163 Score: 146
Period size: 19 Copynumber: 3.8 Consensus size: 19
3513081 ATCGCAACGA
3513091 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
3513110 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
3513129 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
3513148 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
3513164 TTTTCTAGCT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 54 1.00
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:3513437 original size:20 final size:20
Alignment explanation
Indices: 3513412--3513482 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
3513402 TTGAAGATGA
3513412 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
3513432 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
* **
3513452 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
3513473 TTGCGATTTT
1 TTGCGATTTT
3513483 GTTAGTTACA
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
20 24 0.59
21 17 0.41
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:3515123 original size:19 final size:18
Alignment explanation
Indices: 3515101--3515231 Score: 97
Period size: 19 Copynumber: 7.7 Consensus size: 18
3515091 GGAAATTACT
3515101 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
3515120 ATCGCAA-C--AA-GATA
1 ATCGCAAGCGAAATGAAA
3515134 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
3515153 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
3515167 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
3515186 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
3515200 ATCGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
3515219 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
3515232 TTTAGTTTCG
Statistics
Matches: 88, Mismatches: 8, Indels: 32
0.69 0.06 0.25
Matches are distributed among these distances:
14 27 0.31
15 6 0.07
16 5 0.06
17 5 0.06
18 6 0.07
19 39 0.44
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:3515143 original size:33 final size:33
Alignment explanation
Indices: 3515101--3515227 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
3515091 GGAAATTACT
* *
3515101 ATCGCAATGCGAAATGAAAATCGCAACAAGATA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
3515134 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
3515167 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
3515200 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
3515228 CGAATTTAGT
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3515269 original size:19 final size:19
Alignment explanation
Indices: 3515227--3515303 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 19
3515217 AAATCGCAAC
* *
3515227 GCGAATTTAGTTTCGTGTT
1 GCGATTTTAGTTTCGCGTT
3515246 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
3515265 GCGATTTT-G--T--CGTT
1 GCGATTTTAGTTTCGCGTT
*
3515279 GCGATTTTCA-TTTCGCATT
1 GCGATTTT-AGTTTCGCGTT
3515298 GCGATT
1 GCGATT
3515304 ATATCGTTGC
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
14 12 0.24
16 1 0.02
17 1 0.02
18 1 0.02
19 34 0.69
ACGTcount: A:0.13, C:0.16, G:0.25, T:0.47
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:3515285 original size:33 final size:33
Alignment explanation
Indices: 3515243--3515335 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 33
3515233 TTAGTTTCGT
* * *
3515243 GTTGCGATTTT-AGTTTCGCGTTGCGATTTTGTC
1 GTTGCGATTTTCA-TTTCGCATTGCGATTATATC
3515276 GTTGCGATTTTCATTTCGCATTGCGATTATATC
1 GTTGCGATTTTCATTTCGCATTGCGATTATATC
* *
3515309 GTTGCGATTTTCATTTCGTATTACGAT
1 GTTGCGATTTTCATTTCGCATTGCGAT
3515336 AGTAATTTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 53 0.98
34 1 0.02
ACGTcount: A:0.15, C:0.16, G:0.22, T:0.47
Consensus pattern (33 bp):
GTTGCGATTTTCATTTCGCATTGCGATTATATC
Found at i:3515463 original size:14 final size:14
Alignment explanation
Indices: 3515444--3515478 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
3515434 TCAATTAAAG
3515444 AAATCAACTTTTAC
1 AAATCAACTTTTAC
*
3515458 AAATCACCTTTTAC
1 AAATCAACTTTTAC
3515472 AAATCAA
1 AAATCAA
3515479 TTAAGCAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAACTTTTAC
Found at i:3517342 original size:91 final size:90
Alignment explanation
Indices: 3517165--3517349 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 90
3517155 ATTTCAAACT
*
3517165 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
*
3517230 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAACAACCGAATAAATTTAC
3517258 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* *
3517322 GTATTGGCAACAACCTAATAAATTTAC
64 GAATTGGCAACAACCGAATAAATTTAC
3517349 T
1 T
3517350 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 40 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.48, C:0.19, G:0.11, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAACAACCGAATAAATTTAC
Found at i:3519051 original size:20 final size:19
Alignment explanation
Indices: 3519024--3519178 Score: 133
Period size: 19 Copynumber: 8.8 Consensus size: 19
3519014 TCTTTTAGTT
3519024 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
3519043 GATAATGAAAATCGCAACGCA
1 GA-AATGAAAATCGCAACG-A
**
3519064 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
3519083 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
3519097 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
3519116 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
3519130 GAAATGAAAATAGCAACGA
1 GAAATGAAAATCGCAACGA
*
3519149 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
3519163 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
3519179 TGCGATTTTG
Statistics
Matches: 109, Mismatches: 10, Indels: 34
0.71 0.07 0.22
Matches are distributed among these distances:
14 31 0.28
16 6 0.06
17 6 0.06
19 33 0.30
20 30 0.28
21 3 0.03
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:3519092 original size:14 final size:14
Alignment explanation
Indices: 3519073--3519161 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
3519063 AGAAATGACT
3519073 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
3519087 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
3519106 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
3519120 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
*
3519139 ATAGCAACGAGAGA
1 ATCGCAACGAGAGA
3519153 ATCGCAACG
1 ATCGCAACG
3519162 CGAAATGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 28 0.47
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 19 0.32
ACGTcount: A:0.45, C:0.21, G:0.25, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:3519110 original size:33 final size:33
Alignment explanation
Indices: 3519024--3519178 Score: 220
Period size: 33 Copynumber: 4.5 Consensus size: 33
3519014 TCTTTTAGTT
3519024 GAAATGAAAATCGCAACGAGATAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAG---A-G--AATCGCAACGC
**
3519063 AGAAATGACTATCGCAACGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3519097 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
3519130 GAAATGAAAATAGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3519163 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
3519179 TGCGATTTTG
Statistics
Matches: 109, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
33 78 0.72
34 11 0.10
36 1 0.01
37 1 0.01
40 18 0.17
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3519799 original size:20 final size:20
Alignment explanation
Indices: 3519758--3520032 Score: 148
Period size: 20 Copynumber: 13.6 Consensus size: 20
3519748 GCTATGTAAA
* *
3519758 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
*
3519778 TCGTATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
3519798 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
* *
3519819 TCGCATTGCGATTTACTTAA
1 TCGCATTGCGATTTACGTAT
*
3519839 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* * * *
3519859 TCGCATTGCGAATTATGAAAA
1 TCGCATTGCGATTTACG-TAT
** * *
3519880 TCGCAACGCGA-ATACGTAAA
1 TCGCATTGCGATTTACGT-AT
** * *
3519900 TCGCAACGCGA-ATACGTAAA
1 TCGCATTGCGATTTACGT-AT
* * * *
3519920 TCGCAATGCGAATTAGGAAAAT
1 TCGCATTGCGATTTACG--TAT
*
3519942 T-GCATTGCGATAGT-CAGTA-
1 TCGCATTGCGAT-TTAC-GTAT
* **
3519961 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACGTAT
*
3519982 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACGTAT
*
3520002 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACGTAT
3520022 TCGCATTGCGA
1 TCGCATTGCGA
3520033 ATTGGGAAAA
Statistics
Matches: 204, Mismatches: 38, Indels: 26
0.76 0.14 0.10
Matches are distributed among these distances:
19 4 0.02
20 144 0.71
21 52 0.25
22 4 0.02
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:3519829 original size:41 final size:41
Alignment explanation
Indices: 3519776--3520032 Score: 150
Period size: 41 Copynumber: 6.3 Consensus size: 41
3519766 CGATAGTAAG
* *
3519776 ATTCGTATTGCGATTTACGTATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTA
* * * *
3519817 ATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGT-
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTA
* * * ** * * *
3519857 ATTCGCATTGCGAATTATGAAAATCGCAACGCGA-ATACGTA
1 ATTCGCATTGCGATTTACG-TAATCGCATTGCGATTTTCCTA
* ** * * *****
3519898 AATCGCAACGCGA-ATACGTAAATCGCAATGCGAATTAGGAAA
1 ATTCGCATTGCGATTTACGT-AATCGCATTGCG-ATTTTCCTA
* *
3519940 ATT-GCATTGCGATAGT-CAGT-ATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGAT-TTAC-GTAATCGCATTGCGATTTTCCTA
* * * *
3519980 ATTCGCATTGCGATTTACTTATTCGCATTGCGA-TTTACTT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTA
3520020 ATTCGCATTGCGA
1 ATTCGCATTGCGA
3520033 ATTGGGAAAA
Statistics
Matches: 163, Mismatches: 42, Indels: 23
0.71 0.18 0.10
Matches are distributed among these distances:
40 62 0.38
41 94 0.58
42 4 0.02
43 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (41 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTA
Found at i:3519902 original size:61 final size:61
Alignment explanation
Indices: 3519783--3519903 Score: 138
Period size: 61 Copynumber: 2.0 Consensus size: 61
3519773 AAGATTCGTA
* * * ** * *
3519783 TTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACTTAATCGCG
1 TTGCGATTTACGTATTCGCATTGCGATTATCCAAAATCGCAACGCGATATACTAAATCGCG
*
3519844 TTGCGATTTACGTATTCGCATTGCGAATTAT-GAAAATCGCAACGCGA-ATACGTAAATCGC
1 TTGCGATTTACGTATTCGCATTGCG-ATTATCCAAAATCGCAACGCGATATAC-TAAATCGC
3519904 AACGCGAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
60 3 0.06
61 43 0.86
62 4 0.08
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (61 bp):
TTGCGATTTACGTATTCGCATTGCGATTATCCAAAATCGCAACGCGATATACTAAATCGCG
Found at i:3520074 original size:21 final size:22
Alignment explanation
Indices: 3520022--3520074 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
3520012 ATTTACTTAT
3520022 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
3520043 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
3520064 TCGCATTGCGA
1 TCGCATTGCGA
3520075 TTATCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:3522092 original size:26 final size:27
Alignment explanation
Indices: 3522036--3522092 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 27
3522026 TCGAAAAATA
*
3522036 AAAATAAAAACTTATGAGATTTTTCAT
1 AAAATAAAAACTTACGAGATTTTTCAT
*
3522063 -AAAT-AAAA-TTACGAGATTATTTTAT
1 AAAATAAAAACTTACGAGATT-TTTCAT
3522088 AAAAT
1 AAAAT
3522093 TTTAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 9 0.35
25 9 0.35
26 8 0.31
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (27 bp):
AAAATAAAAACTTACGAGATTTTTCAT
Found at i:3525965 original size:42 final size:42
Alignment explanation
Indices: 3525919--3526010 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
3525909 TCCCGAAACC
** *
3525919 CCGTGTTTATTTCACGTAATTAGTTTTCCGGAAAATGTTTTT
1 CCGTGTTTATTTCACGTAATTAGTTTTCCAAAAAATGTTTTA
* * *
3525961 CCGTGTTTGTTTCATGTAATTCGTTTTCCAAAAAATGTTTTA
1 CCGTGTTTATTTCACGTAATTAGTTTTCCAAAAAATGTTTTA
*
3526003 CAGTGTTT
1 CCGTGTTT
3526011 GGTTGGAGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.48
Consensus pattern (42 bp):
CCGTGTTTATTTCACGTAATTAGTTTTCCAAAAAATGTTTTA
Found at i:3526396 original size:27 final size:27
Alignment explanation
Indices: 3526316--3526401 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
3526306 AATAAAATTT
* *
3526316 ATATTATTTAT-TAATTTCATAGAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
* *
3526343 ATATTA-TTAAAT-TATTAATAATGAATA
1 ATATTATTTATATAT-TTAAT-ATAAATA
3526370 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
3526399 ATA
1 ATA
3526402 ATCTAATAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
25 1 0.02
26 7 0.15
27 19 0.41
28 12 0.26
29 7 0.15
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:3526541 original size:91 final size:87
Alignment explanation
Indices: 3526429--3526598 Score: 202
Period size: 89 Copynumber: 1.9 Consensus size: 87
3526419 CAAAGATATT
* * * *
3526429 TAAAATATACTAATTAATATTTTTA-AAATATAA-TATAAAACTATTACTTTAATAA-ATAATTA
1 TAAAATATACAAATTAATATTTTTATAAATAAAATTATAAAAATAATA-TTTAATAATAT-A-TA
3526491 ATATAATTTATAATATTTTTATTTCAG
63 A-ATAATTT-TAATATTTTTATTTCAG
*
3526518 TAAAATATACCAATATTAATATTTTTATTAATAAAATTATAAAAATAATATTTAATAATATATAA
1 TAAAATATA-CAA-ATTAATATTTTTATAAATAAAATTATAAAAATAATATTTAATAATATATAA
*
3526583 ATTATTTTAATATTTT
64 ATAATTTTAATATTTT
3526599 AAAAAATAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
89 18 0.26
90 8 0.11
91 16 0.23
92 15 0.21
93 13 0.19
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (87 bp):
TAAAATATACAAATTAATATTTTTATAAATAAAATTATAAAAATAATATTTAATAATATATAAAT
AATTTTAATATTTTTATTTCAG
Found at i:3526584 original size:21 final size:20
Alignment explanation
Indices: 3526555--3526608 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
3526545 TTAATAAAAT
3526555 TATAAAAATAATATTTAATAA
1 TATAAAAATAAT-TTTAATAA
* * *
3526576 TATATAAATTATTTTAATAT
1 TATAAAAATAATTTTAATAA
*
3526596 TTTAAAAAATAAT
1 TAT-AAAAATAAT
3526609 AATATTAAGT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TATAAAAATAATTTTAATAA
Found at i:3526841 original size:15 final size:15
Alignment explanation
Indices: 3526795--3526841 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
3526785 CCGAAAAACG
3526795 TTTTCCAGAATTCAA
1 TTTTCCAGAATTCAA
* *
3526810 -ATTCCAGTAA-TCCA
1 TTTTCCAG-AATTCAA
3526824 TTTTCCAGAATTCAA
1 TTTTCCAGAATTCAA
3526839 TTT
1 TTT
3526842 CTAGAAAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.40
Consensus pattern (15 bp):
TTTTCCAGAATTCAA
Found at i:3526847 original size:14 final size:14
Alignment explanation
Indices: 3526796--3526847 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
3526786 CGAAAAACGT
3526796 TTTCCAGAATTCAA
1 TTTCCAGAATTCAA
* * *
3526810 ATTCCAGTAATCCAT
1 TTTCCAG-AATTCAA
3526825 TTTCCAGAATTCAA
1 TTTCCAGAATTCAA
*
3526839 TTTCTAGAA
1 TTTCCAGAA
3526848 AATCAATTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
14 19 0.63
15 11 0.37
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.37
Consensus pattern (14 bp):
TTTCCAGAATTCAA
Found at i:3530076 original size:31 final size:31
Alignment explanation
Indices: 3530041--3530107 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
3530031 AAATTTAGGC
*
3530041 ATCAAAGTAAACTTTAAAATTAAACTAAAAT
1 ATCAAACTAAACTTTAAAATTAAACTAAAAT
* * * *
3530072 ATCAAACTAAATTTTAAAATTCAATTCAAAT
1 ATCAAACTAAACTTTAAAATTAAACTAAAAT
3530103 ATCAA
1 ATCAA
3530108 TATATATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.31
Consensus pattern (31 bp):
ATCAAACTAAACTTTAAAATTAAACTAAAAT
Found at i:3531710 original size:59 final size:59
Alignment explanation
Indices: 3531635--3531751 Score: 189
Period size: 59 Copynumber: 2.0 Consensus size: 59
3531625 ATGCATGCAA
** *
3531635 TCCTAATCTATTGAATTGTTTATCATGGAAGGTGAAGTTTAGACCATAACTGTAAATAT
1 TCCTAATCTAAAGAATTATTTATCATGGAAGGTGAAGTTTAGACCATAACTGTAAATAT
* *
3531694 TCCTAATCTAAAGAATTATTTATCATGGAATGTGAAGTTTAGATCATAACTGTAAATA
1 TCCTAATCTAAAGAATTATTTATCATGGAAGGTGAAGTTTAGACCATAACTGTAAATA
3531752 CAACGTAATA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (59 bp):
TCCTAATCTAAAGAATTATTTATCATGGAAGGTGAAGTTTAGACCATAACTGTAAATAT
Found at i:3541190 original size:5 final size:5
Alignment explanation
Indices: 3541166--3541229 Score: 83
Period size: 5 Copynumber: 12.8 Consensus size: 5
3541156 GTCCGTCCGT
* * * * *
3541166 CTCGT CTCGG CTCGG CTCGG CTCGG CACGG CACGG CACGG CACGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
3541216 CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCG
3541230 TGGTCGTGGT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 56 1.00
ACGTcount: A:0.06, C:0.41, G:0.38, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:3541238 original size:6 final size:6
Alignment explanation
Indices: 3541227--3541287 Score: 104
Period size: 6 Copynumber: 10.2 Consensus size: 6
3541217 TCGGCTCGGC
* *
3541227 TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
3541275 TCGTGG TCGTGG T
1 TCGTGG TCGTGG T
3541288 AATATGTGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.03, C:0.16, G:0.49, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:3541434 original size:22 final size:22
Alignment explanation
Indices: 3541409--3541463 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
3541399 TCAGGAGTTA
* *
3541409 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
3541431 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
3541453 CGGGAGTTATA
1 CAGGAGTTATA
3541464 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:3547011 original size:5 final size:5
Alignment explanation
Indices: 3546992--3547050 Score: 73
Period size: 5 Copynumber: 11.8 Consensus size: 5
3546982 GTCCGTCCGT
* * * * *
3546992 CTCGT CTCGG CTCGG CTCGG CACGG CACGG CACGG CACGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
3547042 CTCGG CTCG
1 CTCGG CTCG
3547051 TGGTCGTGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 51 1.00
ACGTcount: A:0.07, C:0.41, G:0.37, T:0.15
Consensus pattern (5 bp):
CTCGG
Found at i:3547059 original size:6 final size:6
Alignment explanation
Indices: 3547048--3547102 Score: 92
Period size: 6 Copynumber: 9.2 Consensus size: 6
3547038 TCGGCTCGGC
* *
3547048 TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
3547096 TCGTGG T
1 TCGTGG T
3547103 AATACGTGTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.04, C:0.16, G:0.49, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:3547402 original size:22 final size:22
Alignment explanation
Indices: 3547377--3547431 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
3547367 TCAGGAGTTA
* *
3547377 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
3547399 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
3547421 CGGGAGTTATA
1 CAGGAGTTATA
3547432 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:3551554 original size:27 final size:27
Alignment explanation
Indices: 3551516--3551597 Score: 146
Period size: 27 Copynumber: 3.0 Consensus size: 27
3551506 AAACTAAACT
* *
3551516 TGCTCTATATCCTCTCTTCCATGACCC
1 TGCTCTCTATCCCCTCTTCCATGACCC
3551543 TGCTCTCTATCCCCTCTTCCATGACCC
1 TGCTCTCTATCCCCTCTTCCATGACCC
3551570 TGCTCTCTATCCCCTCTTCCATGACCC
1 TGCTCTCTATCCCCTCTTCCATGACCC
3551597 T
1 T
3551598 CTCAACTTTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.12, C:0.45, G:0.07, T:0.35
Consensus pattern (27 bp):
TGCTCTCTATCCCCTCTTCCATGACCC
Found at i:3551599 original size:13 final size:13
Alignment explanation
Indices: 3551529--3551599 Score: 56
Period size: 13 Copynumber: 5.3 Consensus size: 13
3551519 TCTATATCCT
3551529 CTCTTCCATGACC
1 CTCTTCCATGACC
* *
3551542 CTGCTCTCTAT-CCC
1 CT-CT-TCCATGACC
3551556 CTCTTCCATGACC
1 CTCTTCCATGACC
* *
3551569 CTGCTCTCTAT-CCC
1 CT-CT-TCCATGACC
3551583 CTCTTCCATGACC
1 CTCTTCCATGACC
3551596 CTCT
1 CTCT
3551600 CAACTTTCGA
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
12 8 0.18
13 16 0.36
14 12 0.27
15 8 0.18
ACGTcount: A:0.11, C:0.48, G:0.07, T:0.34
Consensus pattern (13 bp):
CTCTTCCATGACC
Found at i:3554550 original size:20 final size:20
Alignment explanation
Indices: 3554525--3554573 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
3554515 CACGGAATAT
* *
3554525 AGATTATTAGTGTGAATAAA
1 AGATTATCAGTGGGAATAAA
3554545 AGATTATCAGTGGGAATAAA
1 AGATTATCAGTGGGAATAAA
3554565 AGATTATCA
1 AGATTATCA
3554574 TAGAATAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.31
Consensus pattern (20 bp):
AGATTATCAGTGGGAATAAA
Found at i:3554581 original size:18 final size:20
Alignment explanation
Indices: 3554525--3554581 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
3554515 CACGGAATAT
* *
3554525 AGATTATTAGTGTGAATAAA
1 AGATTATCAGTGAGAATAAA
*
3554545 AGATTATCAGTGGGAATAAA
1 AGATTATCAGTGAGAATAAA
3554565 AGATTATCA-T-AGAATAA
1 AGATTATCAGTGAGAATAA
3554582 GATTATTGGG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
18 6 0.18
19 1 0.03
20 27 0.79
ACGTcount: A:0.47, C:0.04, G:0.19, T:0.30
Consensus pattern (20 bp):
AGATTATCAGTGAGAATAAA
Found at i:3555810 original size:645 final size:640
Alignment explanation
Indices: 3554576--3555820 Score: 1628
Period size: 645 Copynumber: 1.9 Consensus size: 640
3554566 GATTATCATA
* * *
3554576 GAATAAGATTATTGGGAATATTGTATTTTATGTTTGGTTGGTTTAGCAGGAAGGTAAGATTACCG
1 GAATAAGATTAATGAGAATATTGTATTTTATGTTTGGTTGGTTTAGCAGGAAGGTAAGATTACAG
3554641 TGTTTGGTTAAAAGAAAAAAGATTATTAAATATATATTTGAACAAATTACCTTATTATATATTTA
66 TGTTTGGTTAAAAGAAAAAAGATTATTAAATATATATTTGAACAAATTACCTTATTATATATTTA
* * *
3554706 TTTTTTAACAAGTTAGAAAGTATTTATATATTTTCTTTAAAAAATTTAAATTCATAAATATATAT
131 TTTTTTAACAAATTAGAAAATATTTATATATTTTCTTTAAAAAAATTAAATTC----A-ATATAT
* *
3554771 ATATTTTTATAAAATTAAAATATAAAAGGTTTAATGAAAGGGTAAAATTTTATTTTAACCCCTGA
191 ATATTTTTACAAAATTAAAATATAAAAGGTTTAATGAAAGGGTAAAATTTTATTTTAACCCCTAA
3554836 ACTTCATATAAAATTTTAATTATAGATTTTTTTATAAATATAAAATAGTTTAAAGATAAATTTAT
256 ACTTCATATAAAATTTTAATTATAGATTTTTTTATAAATATAAAATAGTTTAAAGATAAATTTAT
* * * *
3554901 AATTTAACCTTCGTAAAATTTTTATTATTCAATGACAGAATAATATATTTTTAAAGAATTTTTTT
321 AATTTAACATTCGTAAAATTTTTATTATTCAATGACAAAAGAATATATTTTTAAAAAATTTTTTT
* * *
3554966 AAGGGCATTTTAGTCTAAAACACTGGTAATCCAACAATACCTAAAGAAATGGATGTAATGACATT
386 AAGGGCATTTTAGTCCAAAACACTGGTAATCCAACAATACATAAAGAAATGGAGGTAATGACATT
* * * ** * * **
3555031 CCCGGTAATATACCCAAAAAATCCACTATTGGTAAGGTAAGATTACCGGGAATGACATTCCCGGC
451 CACAGTAATATACCAAAAAAATCCACTATTGGTAAGAAAACATTACCGGAAATGACATTCCCAAC
* * **
3555096 CAACCAAACGGTGAATATGGATTTCATTCCCATGGGAATTTCACATTCCCCCAACCAAACACACC
516 CAACCAAACAGTGAATATGGATTCCATTCCCATGGGAATCCCACATTCCCCCAACCAAACACACC
3555161 CTAAGGGTGC-GTTTGGTTCACAAAATATAAGATTACCAGTGAGAATGTAAGATTACAAGG
581 CTAAGGG-GCTGTTTGGTTCACAAAATATAAGATTACCAGTGAGAATGTAAGATTACAAGG
* * * *
3555221 GAATAAGATTAATGAGAATGTTGTATTTTGTGTTTGGTTGGTTTAGCAGGAATGTAAGATTATAG
1 GAATAAGATTAATGAGAATATTGTATTTTATGTTTGGTTGGTTTAGCAGGAAGGTAAGATTACAG
* * * * * * * *
3555286 TGTTTTGTTAAATGAATAAAGATTATTGGAATGTATATTTGACCAAATTGTCTTTATTATATATT
66 TGTTTGGTTAAAAGAAAAAAGATTATT-AAATATATATTTGAACAAATT-ACCTTATTATATATT
*
3555351 TATTTTTTTAACAAATTGGAAAATATTTATATATTTTCTTTAAAAAAATTAAATTC-ATA-ATAT
129 TA-TTTTTTAACAAATTAGAAAATATTTATATATTTTCTTTAAAAAAATTAAATTCAATATATAT
3555414 -TTTTTACAAAATTTAAAATATAAAAAGGTTTAATGAAAGGGT-AAA-TTT-TTTTAACCCCTAA
193 ATTTTTACAAAA-TTAAAATAT-AAAAGGTTTAATGAAAGGGTAAAATTTTATTTTAACCCCTAA
* * * * *
3555475 ACTTCATATAAAATTTTAATTATAGATTTTTTTTGTAAATCTAAAATATTTTAAGGATAAATTTG
256 ACTTCATATAAAATTTTAATTATAGA-TTTTTTTATAAATATAAAATAGTTTAAAGATAAATTTA
* * *
3555540 TAATTTAATATTTGTAGAATTTTTATTATTCAATGACAAAAGAATGATATTTTTGAAGAAAATTT
320 TAATTTAACATTCGTAAAATTTTTATTATTCAATGACAAAAGAAT-ATATTTTT-AA-AAAATTT
* **** *
3555605 TTTTAAGGGCATTTTAGTCCAAAAC-GTCGGTAATGTTGCAATACATAAGGAAATGGAGGTAATG
382 TTTTAAGGGCATTTTAGTCCAAAACACT-GGTAATCCAACAATACATAAAGAAATGGAGGTAATG
* * * * *
3555669 ACATTTACATTAATATACTCAAAAAAAATCTACTATTGGTAATAAAACATTACCGGAAATGAGAT
446 ACATTCACAGTAATATAC-C-AAAAAAATCCACTATTGGTAAGAAAACATTACCGGAAATGACAT
* * * *** *
3555734 TCTCAACCAACCAAACA-TAGGAATGTGTATTCCATTCCCATGGGAATCCCACATTCCTTTATCC
509 TCCCAACCAACCAAACAGT--GAATATGGATTCCATTCCCATGGGAATCCCACATTCCCCCAACC
*
3555798 AAAC-CCCCCTAAGGGGCTGTTTG
572 AAACACACCCTAAGGGGCTGTTTG
3555821 ATTAAATCAA
Statistics
Matches: 517, Mismatches: 68, Indels: 30
0.84 0.11 0.05
Matches are distributed among these distances:
639 38 0.07
640 85 0.16
641 24 0.05
642 26 0.05
643 73 0.14
644 4 0.01
645 146 0.28
646 57 0.11
647 15 0.03
648 49 0.09
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.37
Consensus pattern (640 bp):
GAATAAGATTAATGAGAATATTGTATTTTATGTTTGGTTGGTTTAGCAGGAAGGTAAGATTACAG
TGTTTGGTTAAAAGAAAAAAGATTATTAAATATATATTTGAACAAATTACCTTATTATATATTTA
TTTTTTAACAAATTAGAAAATATTTATATATTTTCTTTAAAAAAATTAAATTCAATATATATATT
TTTACAAAATTAAAATATAAAAGGTTTAATGAAAGGGTAAAATTTTATTTTAACCCCTAAACTTC
ATATAAAATTTTAATTATAGATTTTTTTATAAATATAAAATAGTTTAAAGATAAATTTATAATTT
AACATTCGTAAAATTTTTATTATTCAATGACAAAAGAATATATTTTTAAAAAATTTTTTTAAGGG
CATTTTAGTCCAAAACACTGGTAATCCAACAATACATAAAGAAATGGAGGTAATGACATTCACAG
TAATATACCAAAAAAATCCACTATTGGTAAGAAAACATTACCGGAAATGACATTCCCAACCAACC
AAACAGTGAATATGGATTCCATTCCCATGGGAATCCCACATTCCCCCAACCAAACACACCCTAAG
GGGCTGTTTGGTTCACAAAATATAAGATTACCAGTGAGAATGTAAGATTACAAGG
Found at i:3555978 original size:23 final size:23
Alignment explanation
Indices: 3555948--3556010 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
3555938 TGTACTTTAA
3555948 TGCTGAATCATTCAACAGTGTTT
1 TGCTGAATCATTCAACAGTGTTT
*
3555971 TGCTGAATCATTCAGCAGTGTTT
1 TGCTGAATCATTCAACAGTGTTT
3555994 TGCTGAATCATTCAACA
1 TGCTGAATCATTCAACA
3556011 CAGTCTTCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (23 bp):
TGCTGAATCATTCAACAGTGTTT
Found at i:3557399 original size:143 final size:142
Alignment explanation
Indices: 3557227--3557512 Score: 563
Period size: 143 Copynumber: 2.0 Consensus size: 142
3557217 CATTTAGTAT
3557227 GAATTTGAAATTAGATGAGAATTTGAAATTTTCAATAACGATTGCCTCCCTCGATCCATCCTTAG
1 GAATTTGAAATTAGATGAGAATTTGAAATTTTCAATAACGATTGCCTCCCTCGATCCATCCTTAG
3557292 TTAAAAGTGATGATTGAATGATTTGTACATAATTATTTATAACTATATAGTTAATTATATTTTTT
66 TTAAAAGTGATGATTGAATGATTTGTACATAATTATTTATAACTATATAGTTAATTATATTTTTT
3557357 AAATTTGTTTGG
131 AAATTTGTTTGG
3557369 GAATTTGAAATTAGATGAAGAATTTGAAATTTTCAATAACGATTGCCTCCCTCGATCCATCCTTA
1 GAATTTGAAATTAGATG-AGAATTTGAAATTTTCAATAACGATTGCCTCCCTCGATCCATCCTTA
3557434 GTTAAAAGTGATGATTGAATGATTTGTACATAATTATTTATAACTATATAGTTAATTATATTTTT
65 GTTAAAAGTGATGATTGAATGATTTGTACATAATTATTTATAACTATATAGTTAATTATATTTTT
3557499 TAAATTTGTTTGG
130 TAAATTTGTTTGG
3557512 G
1 G
3557513 GTTTAACTAT
Statistics
Matches: 143, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
142 17 0.12
143 126 0.88
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (142 bp):
GAATTTGAAATTAGATGAGAATTTGAAATTTTCAATAACGATTGCCTCCCTCGATCCATCCTTAG
TTAAAAGTGATGATTGAATGATTTGTACATAATTATTTATAACTATATAGTTAATTATATTTTTT
AAATTTGTTTGG
Found at i:3558063 original size:24 final size:24
Alignment explanation
Indices: 3558031--3558086 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
3558021 GGATATGGTT
3558031 TCTTCATCCGAGCTTACTCGGAAA
1 TCTTCATCCGAGCTTACTCGGAAA
3558055 TCTTCATCCGAGCTTACTCGGAAA
1 TCTTCATCCGAGCTTACTCGGAAA
3558079 TCTTCATC
1 TCTTCATC
3558087 ATCTTTCTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.32
Consensus pattern (24 bp):
TCTTCATCCGAGCTTACTCGGAAA
Done.