Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007840.1 Hibiscus syriacus cultivar Beakdansim tig00110194_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: 1104544
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:204665 original size:24 final size:24
Alignment explanation
Indices: 204633--204682 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
204623 ACCTTGAATT
204633 TACCGCACAAGAAGTTCATCCACC
1 TACCGCACAAGAAGTTCATCCACC
204657 TACCGCACAAGAAGTTCATCCACC
1 TACCGCACAAGAAGTTCATCCACC
204681 TA
1 TA
204683 AAACATTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.36, G:0.12, T:0.18
Consensus pattern (24 bp):
TACCGCACAAGAAGTTCATCCACC
Found at i:207552 original size:16 final size:16
Alignment explanation
Indices: 207531--207564 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
207521 TATCTAACAC
207531 ATTTATGAACACGAGT
1 ATTTATGAACACGAGT
207547 ATTTATGAACACGAGT
1 ATTTATGAACACGAGT
207563 AT
1 AT
207565 ATGATATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (16 bp):
ATTTATGAACACGAGT
Found at i:208688 original size:17 final size:17
Alignment explanation
Indices: 208668--208700 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
208658 TAAAATATTA
208668 TTAAATATAAA-AATAAT
1 TTAAA-ATAAATAATAAT
208685 TTAAAATAAATAATAA
1 TTAAAATAAATAATAA
208701 ATAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAAATAAATAATAAT
Found at i:212311 original size:19 final size:19
Alignment explanation
Indices: 212287--212325 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
212277 AAAAACTCAA
212287 TAAAATAGTAATTTATAAT
1 TAAAATAGTAATTTATAAT
* *
212306 TAAAATATTATTTTATAAT
1 TAAAATAGTAATTTATAAT
212325 T
1 T
212326 TTTAATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
TAAAATAGTAATTTATAAT
Found at i:216262 original size:12 final size:12
Alignment explanation
Indices: 216245--216271 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
216235 AGGTCATTGC
216245 TGATAATGTTGG
1 TGATAATGTTGG
216257 TGATAATGTTGG
1 TGATAATGTTGG
216269 TGA
1 TGA
216272 CATTGCTGGT
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:0.26, C:0.00, G:0.33, T:0.41
Consensus pattern (12 bp):
TGATAATGTTGG
Found at i:219838 original size:16 final size:15
Alignment explanation
Indices: 219803--219850 Score: 87
Period size: 15 Copynumber: 3.2 Consensus size: 15
219793 GTTAATATTA
219803 TAAAAAAATTAATTT
1 TAAAAAAATTAATTT
*
219818 TAAAAAATTTAATTT
1 TAAAAAAATTAATTT
219833 TAAAAAAATTAATTT
1 TAAAAAAATTAATTT
219848 TAA
1 TAA
219851 TATATTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAAAAAATTAATTT
Found at i:219839 original size:30 final size:33
Alignment explanation
Indices: 219789--219850 Score: 103
Period size: 30 Copynumber: 2.0 Consensus size: 33
219779 AAAAACATAT
219789 AAATGTTAATATTATAAAAAAATTAATTTTAAA
1 AAATGTTAATATTATAAAAAAATTAATTTTAAA
219822 AAAT-TTAAT-TT-TAAAAAAATTAATTTTAA
1 AAATGTTAATATTATAAAAAAATTAATTTTAA
219851 TATATTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 18 0.62
31 2 0.07
32 5 0.17
33 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (33 bp):
AAATGTTAATATTATAAAAAAATTAATTTTAAA
Found at i:220144 original size:2 final size:2
Alignment explanation
Indices: 220139--220166 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
220129 GGTTTAATCA
220139 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
220167 TCGTAAAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:222242 original size:6 final size:6
Alignment explanation
Indices: 222233--222287 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
222223 TGATCGTGGC
** * ** *
222233 CATGAT CATGAT TGTGGT CATGAT CATGAT TGTGGT CATGAT CATGAT
1 CATGAT CATGAT CATGAT CATGAT CATGAT CATGAT CATGAT CATGAT
222281 CATGAT C
1 CATGAT C
222288 TTTTGCACCT
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (6 bp):
CATGAT
Found at i:222243 original size:18 final size:18
Alignment explanation
Indices: 222222--222281 Score: 93
Period size: 18 Copynumber: 3.3 Consensus size: 18
222212 GATGATGGTG
*
222222 ATGATCGTGGCCATGATC
1 ATGATCGTGGTCATGATC
*
222240 ATGATTGTGGTCATGATC
1 ATGATCGTGGTCATGATC
*
222258 ATGATTGTGGTCATGATC
1 ATGATCGTGGTCATGATC
222276 ATGATC
1 ATGATC
222282 ATGATCTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (18 bp):
ATGATCGTGGTCATGATC
Found at i:234183 original size:16 final size:16
Alignment explanation
Indices: 234162--234194 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
234152 TTGTGGGCAG
234162 TCTTTCCCTCTTCCTC
1 TCTTTCCCTCTTCCTC
*
234178 TCTTTCCCTCTTTCTC
1 TCTTTCCCTCTTCCTC
234194 T
1 T
234195 GTGTCGGGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (16 bp):
TCTTTCCCTCTTCCTC
Found at i:249685 original size:17 final size:17
Alignment explanation
Indices: 249663--249701 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
249653 AACGGTCAAC
249663 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
249680 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
249697 GGTCA
1 GGTCA
249702 GACCGGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.13, C:0.23, G:0.46, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:249721 original size:19 final size:19
Alignment explanation
Indices: 249699--249803 Score: 115
Period size: 19 Copynumber: 5.5 Consensus size: 19
249689 TCGGGTCGGG
*
249699 TCAGACCGGTCAACCCGGT
1 TCAGACCGGTCAAACCGGT
*
249718 TCAGACCGGTTAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
249737 TCAGAACGGTCAAACCGG-
1 TCAGACCGGTCAAACCGGT
* *
249755 TCAAACCGGTTCGAACCGGT
1 TCAGACCGG-TCAAACCGGT
* *
249775 TGAAACCGGTCAAACCGG-
1 TCAGACCGGTCAAACCGGT
249793 TCAGAACCGGT
1 TCAG-ACCGGT
249804 TGCCACTCGC
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
18 9 0.12
19 55 0.76
20 8 0.11
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:249734 original size:9 final size:9
Alignment explanation
Indices: 249703--249804 Score: 71
Period size: 9 Copynumber: 10.8 Consensus size: 9
249693 GTCGGGTCAG
*
249703 ACCGGTCAA
1 ACCGGTTAA
* *
249712 CCCGGTTCAG
1 ACCGGTT-AA
249722 ACCGGTTAA
1 ACCGGTTAA
249731 ACCGGTTCAGA
1 ACCGGTT-A-A
*
249742 A-CGGTCAA
1 ACCGGTTAA
*
249750 ACCGGTCAA
1 ACCGGTTAA
*
249759 ACCGGTTCGA
1 ACCGGTT-AA
249769 ACCGGTTGAA
1 ACCGGTT-AA
*
249779 ACCGGTCAA
1 ACCGGTTAA
*
249788 ACCGGTCAGA
1 ACCGGTTA-A
249798 ACCGGTT
1 ACCGGTT
249805 GCCACTCGCC
Statistics
Matches: 75, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
8 2 0.03
9 37 0.49
10 34 0.45
11 2 0.03
ACGTcount: A:0.27, C:0.29, G:0.26, T:0.17
Consensus pattern (9 bp):
ACCGGTTAA
Found at i:249741 original size:38 final size:38
Alignment explanation
Indices: 249699--249804 Score: 133
Period size: 38 Copynumber: 2.8 Consensus size: 38
249689 TCGGGTCGGG
*
249699 TCAGACCGGTCAACCCGGTTCAGACCGGTT-AAACCGGT
1 TCAGACCGGTCAAACCGG-TCAGACCGGTTCAAACCGGT
* * *
249737 TCAGAACGGTCAAACCGGTCAAACCGGTTCGAACCGGT
1 TCAGACCGGTCAAACCGGTCAGACCGGTTCAAACCGGT
* *
249775 TGAAACCGGTCAAACCGGTCAGAACCGGTT
1 TCAGACCGGTCAAACCGGTCAG-ACCGGTT
249805 GCCACTCGCC
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
37 10 0.17
38 41 0.71
39 7 0.12
ACGTcount: A:0.27, C:0.29, G:0.26, T:0.17
Consensus pattern (38 bp):
TCAGACCGGTCAAACCGGTCAGACCGGTTCAAACCGGT
Found at i:250807 original size:21 final size:20
Alignment explanation
Indices: 250721--250878 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
250711 AAATGACCAA
**
250721 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
250740 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
250760 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
250780 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
250801 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
250822 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
250842 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
250863 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
250879 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:250888 original size:20 final size:20
Alignment explanation
Indices: 250845--251038 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
250835 CGATTTTCCA
* ** *
250845 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
250865 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
250885 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
250905 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
250925 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
250945 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
250965 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
250985 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
251005 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
251026 AAATCGCAACGCG
1 AAATCGCAACGCG
251039 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:250929 original size:60 final size:60
Alignment explanation
Indices: 250847--251038 Score: 249
Period size: 60 Copynumber: 3.2 Consensus size: 60
250837 ATTTTCCAAA
* ** * * *
250847 ATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGTGTATCCGTAT
1 ATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAT
* *** *
250907 ATCGCAACGCGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTAT
1 ATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAT
** *
250967 ATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTAT
251028 ATCGCAACGCG
1 ATCGCAACGCG
251039 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 19, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (60 bp):
ATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAT
Found at i:251457 original size:33 final size:33
Alignment explanation
Indices: 251418--251488 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
251408 TTCACTTAGA
* *
251418 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
251451 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
251484 TTTCA
1 TTTCA
251489 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:251594 original size:21 final size:20
Alignment explanation
Indices: 251568--251671 Score: 87
Period size: 21 Copynumber: 5.5 Consensus size: 20
251558 TGCAGAAGAG
251568 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
251589 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
251609 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
251630 GCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
251644 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
251663 TCGCAACGA
1 TCGCAACGA
251672 CAGAATCGCA
Statistics
Matches: 65, Mismatches: 12, Indels: 14
0.71 0.13 0.15
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 10 0.15
20 16 0.25
21 25 0.38
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.11
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:251612 original size:20 final size:21
Alignment explanation
Indices: 251566--251644 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
251556 TTTGCAGAAG
*
251566 AGTCGCAACGAGATAAATGAAA
1 AGTCGCAACGAGA-GAATGAAA
*
251588 A-TCGCAACGAGAGAATG-AC
1 AGTCGCAACGAGAGAATGAAA
*
251607 TGTCGCAACGAGAGAAATGAAA
1 AGTCGCAACGAGAG-AATGAAA
251629 AG-CGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
251645 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 19 0.39
21 26 0.53
22 3 0.06
ACGTcount: A:0.46, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
AGTCGCAACGAGAGAATGAAA
Found at i:251625 original size:41 final size:41
Alignment explanation
Indices: 251567--251644 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
251557 TTGCAGAAGA
* *
251567 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAAGCGCAACGAGAGAATGACT
251608 GTCGCAACGAGAGAAATGAAAAGCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAAGCGCAACGAGAGAAT
251645 CGCAACGCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.45, C:0.17, G:0.27, T:0.12
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAAGCGCAACGAGAGAATGACT
Found at i:251660 original size:33 final size:33
Alignment explanation
Indices: 251620--251689 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
251610 CGCAACGAGA
*
251620 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGACAGAATCGCAACGC
*
251653 GAAATGAAAATCGCAACGACAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGACAGAATCGCAACGC
251686 GAAA
1 GAAA
251690 CCAAAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.47, C:0.21, G:0.24, T:0.07
Consensus pattern (33 bp):
GAAATGAAAAGCGCAACGACAGAATCGCAACGC
Found at i:251696 original size:33 final size:33
Alignment explanation
Indices: 251626--251700 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
251616 GAGAGAAATG
* * **
251626 AAAAGCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGACAGAATCGCAACGCGAAACC
251659 AAAATCGCAACGACAGAATCGCAACGCGAAACC
1 AAAATCGCAACGACAGAATCGCAACGCGAAACC
251692 AAAATCGCA
1 AAAATCGCA
251701 TTGCGATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.47, C:0.25, G:0.21, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGACAGAATCGCAACGCGAAACC
Found at i:251699 original size:19 final size:18
Alignment explanation
Indices: 251642--251700 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
251632 GCAACGAGAG
*
251642 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-CAA
*
251661 AATCGCAA--CG--ACAG
1 AATCGCAACGCGAAACAA
251675 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-CAA
251694 AATCGCA
1 AATCGCA
251701 TTGCGATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 9 0.28
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.53
ACGTcount: A:0.46, C:0.27, G:0.19, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAACAA
Found at i:251718 original size:19 final size:19
Alignment explanation
Indices: 251696--251793 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
251686 GAAACCAAAA
*
251696 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
251715 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
251729 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
251748 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
251762 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
251781 TCGCGTTGCGATT
1 TCGCGTTGCGATT
251794 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:251737 original size:14 final size:14
Alignment explanation
Indices: 251718--251807 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
251708 TTTCATTTCG
251718 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
251732 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
251751 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
251765 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
251784 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
251798 CGTTGCGATT
1 CGTTGCGATT
251808 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:251743 original size:33 final size:33
Alignment explanation
Indices: 251701--251815 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
251691 CAAAATCGCA
251701 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
251734 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
251767 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
251800 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
251816 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:253671 original size:93 final size:93
Alignment explanation
Indices: 253512--253892 Score: 735
Period size: 93 Copynumber: 4.1 Consensus size: 93
253502 TAGATTGCTT
*
253512 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
253577 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
253605 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
253670 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
253698 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
253763 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
253791 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACATTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
253856 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
253884 AGTAAATTT
1 AGTAAATTT
253893 ATCCATTCAA
Statistics
Matches: 284, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 284 1.00
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:253976 original size:19 final size:19
Alignment explanation
Indices: 253936--254064 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
253926 TAGTTTACTT
* *
253936 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
253956 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
253975 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
253994 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
254008 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
* *
254027 TCGCAA--CG--A-TAAGA
1 TCGCAACGCGAAACCAAAA
254041 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
254060 TCGCA
1 TCGCA
254065 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 18 0.20
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 45 0.51
20 13 0.15
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:254015 original size:33 final size:32
Alignment explanation
Indices: 253972--254064 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
253962 CGCGAAACCA
**
253972 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
*
254004 AGAATCGCAACGCGAAACCAAAATCGCAACGAT
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
254037 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
254065 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.04
33 54 0.96
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:254062 original size:52 final size:52
Alignment explanation
Indices: 253936--254064 Score: 138
Period size: 52 Copynumber: 2.5 Consensus size: 52
253926 TAGTTTACTT
** *
253936 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGAGAAA
* * * *
253988 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGATAAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACGAGAA-A
*
254041 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
254065 TTGCGATTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.69
53 2 0.03
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGAGAAA
Found at i:254104 original size:14 final size:14
Alignment explanation
Indices: 254081--254137 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
254071 TTTTCATTCG
*
254081 CGTTGTGATTCTTT
1 CGTTGCGATTCTTT
254095 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
254112 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
254128 CGTTGCGATT
1 CGTTGCGATT
254138 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 15 0.42
16 7 0.19
17 8 0.22
19 6 0.17
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:254121 original size:19 final size:19
Alignment explanation
Indices: 254060--254212 Score: 130
Period size: 19 Copynumber: 8.6 Consensus size: 19
254050 GAAACCAAAA
*
254060 TCGCATTGCGATTTTCA-T
1 TCGCGTTGCGATTTTCATT
*
254078 TCGCGTTGTGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
254094 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
254111 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
254127 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
254144 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
254163 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
254182 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
254202 TCGTGTTGCGA
1 TCGCGTTGCGA
254213 AAGTAAACTA
Statistics
Matches: 111, Mismatches: 12, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
14 14 0.13
16 13 0.12
17 8 0.07
18 9 0.08
19 55 0.50
20 12 0.11
ACGTcount: A:0.10, C:0.18, G:0.25, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:254124 original size:33 final size:33
Alignment explanation
Indices: 254065--254194 Score: 154
Period size: 33 Copynumber: 3.8 Consensus size: 33
254055 CAAAATCGCA
* *
254065 TTGCGATTTTCA-TTCGCGTTGTGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
254097 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
254130 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCT-G--T--CG
**
254168 TTGCGATTTTGGTTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
254195 TTAAGTTTCG
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
32 12 0.14
33 44 0.52
34 1 0.01
36 1 0.01
38 27 0.32
ACGTcount: A:0.09, C:0.18, G:0.25, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:254184 original size:38 final size:39
Alignment explanation
Indices: 254095--254212 Score: 133
Period size: 33 Copynumber: 3.2 Consensus size: 39
254085 GTGATTCTTT
* *
254095 CGTTGCGATTTTCATTTCGCATTGCGATTCT--G--T--
1 CGTTGCGATTTTCATTTCGCGTTGCGATTTTAAGTTTCG
*
254128 CGTTGCGATTTTCATTTCGCGTTGCGATTTT-GGTTTCG
1 CGTTGCGATTTTCATTTCGCGTTGCGATTTTAAGTTTCG
**
254166 CGTTGCGATTTTGGTTTCGCGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCATTTCGCGTTGCGATTTTAAGTTTCG
*
254205 TGTTGCGA
1 CGTTGCGA
254213 AAGTAAACTA
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
33 29 0.40
34 1 0.01
36 1 0.01
38 29 0.40
39 13 0.18
ACGTcount: A:0.10, C:0.18, G:0.26, T:0.46
Consensus pattern (39 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTTTAAGTTTCG
Found at i:256153 original size:14 final size:14
Alignment explanation
Indices: 256134--256169 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
256124 ATTGTTTAAT
256134 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
256148 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
256162 TGATTTGT
1 TGATTTGT
256170 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:256300 original size:19 final size:19
Alignment explanation
Indices: 256276--256375 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
256266 AAAATTGACT
256276 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
256295 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
256314 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
256328 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
256347 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
256367 ATCGCAATG
1 ATCGCAATG
256376 GAATAATCGC
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.53
20 18 0.25
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:256434 original size:33 final size:33
Alignment explanation
Indices: 256397--256548 Score: 148
Period size: 33 Copynumber: 4.4 Consensus size: 33
256387 ATTCGAAAAG
256397 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
256430 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
256470 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
256501 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
256534 ATTTCCGCATTGCGA
1 ATTT-CGCATTGCGA
256549 AATGTAATGG
Statistics
Matches: 95, Mismatches: 12, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
31 9 0.09
32 5 0.05
33 40 0.42
34 10 0.11
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.09
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:256443 original size:19 final size:19
Alignment explanation
Indices: 256419--256548 Score: 163
Period size: 19 Copynumber: 7.3 Consensus size: 19
256409 GATTCTCTCG
256419 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
256438 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
256457 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
256471 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
256490 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
256509 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
256523 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
256543 TTGCGA
1 TTGCGA
256549 AATGTAATGG
Statistics
Matches: 96, Mismatches: 4, Indels: 21
0.79 0.03 0.17
Matches are distributed among these distances:
14 12 0.12
16 14 0.15
17 12 0.12
18 2 0.02
19 50 0.52
20 6 0.06
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:256454 original size:52 final size:52
Alignment explanation
Indices: 256397--256548 Score: 295
Period size: 52 Copynumber: 2.9 Consensus size: 52
256387 ATTCGAAAAG
256397 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
256449 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
256501 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGA
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGA
256549 AATGTAATGG
Statistics
Matches: 99, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 89 0.90
53 10 0.10
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:256631 original size:19 final size:19
Alignment explanation
Indices: 256607--256704 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
256597 AAAATTGACT
256607 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
256626 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
256645 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
256659 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
256678 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
256698 ATCGCAA
1 ATCGCAA
256705 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:256736 original size:53 final size:53
Alignment explanation
Indices: 256607--256723 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
256597 AAAATTGACT
256607 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
256659 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
256712 ATCGCAATGCGA
1 ATCGCAATGCGA
256724 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:259047 original size:12 final size:12
Alignment explanation
Indices: 259030--259054 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
259020 TCTTCGGGGA
259030 CTTTTTCTTCTT
1 CTTTTTCTTCTT
259042 CTTTTTCTTCTT
1 CTTTTTCTTCTT
259054 C
1 C
259055 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:259282 original size:24 final size:24
Alignment explanation
Indices: 259245--259296 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
259235 ATCCGTGTAT
* * *
259245 TGACCAATATCAAAGTCCGGATAC
1 TGACCAAGACCAAAGTCCGAATAC
* *
259269 TGACCAAGACCAAATTTCGAATAC
1 TGACCAAGACCAAAGTCCGAATAC
259293 TGAC
1 TGAC
259297 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.21
Consensus pattern (24 bp):
TGACCAAGACCAAAGTCCGAATAC
Found at i:259986 original size:20 final size:20
Alignment explanation
Indices: 259958--260167 Score: 208
Period size: 20 Copynumber: 10.5 Consensus size: 20
259948 AAATTTCAGT
* * * *
259958 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
259978 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
259998 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
260018 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
260038 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
260058 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
260078 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
260098 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATACGC
* *
260118 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
260138 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
260158 GTTGCGATTT
1 GTTGCGATTT
260168 TGGAAAATCG
Statistics
Matches: 160, Mismatches: 26, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
19 1 0.01
20 157 0.98
21 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:260184 original size:21 final size:21
Alignment explanation
Indices: 260154--260236 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
260144 ATTTTCATAT
*
260154 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
260175 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
260196 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
260217 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
260237 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:260227 original size:42 final size:43
Alignment explanation
Indices: 260134--260232 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
260124 ATTTATGTGT
* *
260134 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
260175 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
260217 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
260233 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:266702 original size:16 final size:16
Alignment explanation
Indices: 266681--266712 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
266671 CCTTTTCATG
266681 TGTTTCAAGGAACCAT
1 TGTTTCAAGGAACCAT
266697 TGTTTCAAGGAACCAT
1 TGTTTCAAGGAACCAT
266713 AGCGAGTCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (16 bp):
TGTTTCAAGGAACCAT
Found at i:269228 original size:35 final size:35
Alignment explanation
Indices: 269181--269292 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
269171 AAAACAGTCC
* *
269181 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* *
269216 TCAATTTTATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* * **
269251 TCAATTACATTCTAAACCCCAAATTCTAAAATTCT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
269286 TCAATTT
1 TCAATTT
269293 AAGGTTTAGA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.39, C:0.23, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:271135 original size:35 final size:34
Alignment explanation
Indices: 271061--271171 Score: 159
Period size: 35 Copynumber: 3.2 Consensus size: 34
271051 TCTAAACCTT
* * *
271061 AAATTGAAGTATTTTAGAATTTGGGTTTAGAATT
1 AAATTGAATTATTTTGGAATTTGGGTTTAGAATG
*
271095 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
*
271130 AAATTGAATTATTTTGGAAATTGGGGTTTAGAATG
1 AAATTGAATTATTTTGG-AATTTGGGTTTAGAATG
271165 AAATTGA
1 AAATTGA
271172 GGACTGTTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
34 19 0.28
35 46 0.67
36 4 0.06
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (34 bp):
AAATTGAATTATTTTGGAATTTGGGTTTAGAATG
Found at i:276030 original size:30 final size:30
Alignment explanation
Indices: 275996--276064 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
275986 TTTTTTAGTT
* *
275996 TAAGTACCTGAGGTATTTTTTTTGTCAAAA
1 TAAGTACCTAAAGTATTTTTTTTGTCAAAA
* *
276026 TAAGTATCTAAAGTTTTTTTTTTGTCAAAA
1 TAAGTACCTAAAGTATTTTTTTTGTCAAAA
*
276056 TAGGTACCT
1 TAAGTACCT
276065 TTCTATTAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.45
Consensus pattern (30 bp):
TAAGTACCTAAAGTATTTTTTTTGTCAAAA
Found at i:276185 original size:33 final size:31
Alignment explanation
Indices: 276148--276216 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
276138 TATATAGAAA
* * *
276148 AAAAATCAAATACTTTAGGTACCTATTTTGATC
1 AAAAAT-AAA-ACTTTAGATAACTATTTTGACC
* *
276181 AAAAATATAACTTTAGATAATTATTTTGACC
1 AAAAATAAAACTTTAGATAACTATTTTGACC
276212 AAAAA
1 AAAAA
276217 ACACTTTAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 23 0.74
32 2 0.06
33 6 0.19
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (31 bp):
AAAAATAAAACTTTAGATAACTATTTTGACC
Found at i:277056 original size:18 final size:18
Alignment explanation
Indices: 277033--277088 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
277023 TCACTACGTT
277033 TTTTTTGTTTATTTGTAC
1 TTTTTTGTTTATTTGTAC
***
277051 TTTTTTCACTA--TGT--
1 TTTTTTGTTTATTTGTAC
277065 TTTTTTGTTTATTTGTAC
1 TTTTTTGTTTATTTGTAC
277083 TTTTTT
1 TTTTTT
277089 CACCATGTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
14 8 0.29
16 6 0.21
18 14 0.50
ACGTcount: A:0.11, C:0.07, G:0.09, T:0.73
Consensus pattern (18 bp):
TTTTTTGTTTATTTGTAC
Found at i:277073 original size:32 final size:32
Alignment explanation
Indices: 277006--277098 Score: 132
Period size: 32 Copynumber: 2.8 Consensus size: 32
276996 TTCTTCTGTT
* * *
277006 TTTAGTTTGTACTCTTATCACTACGTTTTTTTTG
1 TTTA-TTTGTACTTTTTTCACTATG-TTTTTTTG
277040 TTTATTTGTACTTTTTTCACTATGTTTTTTTG
1 TTTATTTGTACTTTTTTCACTATGTTTTTTTG
*
277072 TTTATTTGTACTTTTTTCACCATGTTT
1 TTTATTTGTACTTTTTTCACTATGTTT
277099 ATGAGTGTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 34 0.62
33 17 0.31
34 4 0.07
ACGTcount: A:0.14, C:0.13, G:0.10, T:0.63
Consensus pattern (32 bp):
TTTATTTGTACTTTTTTCACTATGTTTTTTTG
Found at i:278695 original size:60 final size:62
Alignment explanation
Indices: 278592--278734 Score: 147
Period size: 60 Copynumber: 2.4 Consensus size: 62
278582 AATTGGACTG
* * *
278592 TTCAAAAGTTTGGGGACCAATTTAGAATGCATGCCATATTTTAGGGAT-AAAGTTGAA-ATT
1 TTCAAAAGTTTAGGGACCAATTTAGAATGCATACCATAATTTAGGGATGAAAGTTGAACATT
* * *
278652 TTCAAAAGTTTAAGGG-CTAATTTAGAATG-ATAATCATAATTTAGGGATGAAATTTGAACA-T
1 TTCAAAAGTTT-AGGGACCAATTTAGAATGCAT-ACCATAATTTAGGGATGAAAGTTGAACATT
* *
278713 TT-AAAA-TTTATGGATCAATTTA
1 TTCAAAAGTTTAGGGACCAATTTA
278735 AAATAAGGAT
Statistics
Matches: 69, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
58 3 0.04
59 11 0.16
60 40 0.58
61 14 0.20
62 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (62 bp):
TTCAAAAGTTTAGGGACCAATTTAGAATGCATACCATAATTTAGGGATGAAAGTTGAACATT
Found at i:283958 original size:42 final size:42
Alignment explanation
Indices: 283899--284134 Score: 454
Period size: 42 Copynumber: 5.6 Consensus size: 42
283889 TGGATTTCAC
*
283899 CCTTAGGATCTCCTTGGTATGCACCACCAGTGGTCACCACCT
1 CCTTAGGATCTCCTTGGTATGCACCACCAGTGGTCACCGCCT
*
283941 CCTTAGGATCTCCTTGGTATGCACCACCAGTGGTCACCACCT
1 CCTTAGGATCTCCTTGGTATGCACCACCAGTGGTCACCGCCT
283983 CCTTAGGATCTCCTTGGTATGCACCACCAGTGGTCACCGCCT
1 CCTTAGGATCTCCTTGGTATGCACCACCAGTGGTCACCGCCT
284025 CCTTAGGATCTCCTTGGTATGCACCACCAGTGGTCACCGCCT
1 CCTTAGGATCTCCTTGGTATGCACCACCAGTGGTCACCGCCT
284067 CCTTAGGATCTCCTTGGTATGCACCACCAGTGGTCACCGCCT
1 CCTTAGGATCTCCTTGGTATGCACCACCAGTGGTCACCGCCT
284109 CCTTAGGATCTCCTTGGTATGCACCA
1 CCTTAGGATCTCCTTGGTATGCACCA
284135 GTAAGGTTTG
Statistics
Matches: 193, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 193 1.00
ACGTcount: A:0.18, C:0.35, G:0.20, T:0.27
Consensus pattern (42 bp):
CCTTAGGATCTCCTTGGTATGCACCACCAGTGGTCACCGCCT
Found at i:290636 original size:15 final size:15
Alignment explanation
Indices: 290616--290645 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
290606 TTAGGTTGAT
290616 ACCTAATTTGATGTG
1 ACCTAATTTGATGTG
290631 ACCTAATTTGATGTG
1 ACCTAATTTGATGTG
290646 GTTTAAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (15 bp):
ACCTAATTTGATGTG
Found at i:313386 original size:23 final size:21
Alignment explanation
Indices: 313347--313388 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
313337 GCAATTCCTT
*
313347 ATCTTTTTCTATCTTGTTTTA
1 ATCTTTTTCTACCTTGTTTTA
313368 ATCTTGTTTCTTACCTTGTTT
1 ATCTT-TTTC-TACCTTGTTT
313389 CCATCACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 4 0.22
23 9 0.50
ACGTcount: A:0.12, C:0.17, G:0.07, T:0.64
Consensus pattern (21 bp):
ATCTTTTTCTACCTTGTTTTA
Found at i:314414 original size:183 final size:189
Alignment explanation
Indices: 314106--314479 Score: 706
Period size: 183 Copynumber: 2.0 Consensus size: 189
314096 ACTAATGAAG
314106 GTATTTGGTTCTGAAATTTTACAGGTGGTTTCTTGAGGCATCGAAAGACATTCAAGAATTTTTCC
1 GTATTTGGTTCTGAAATTTTACAGGTGGTTTCTTGAGGCATCGAAAGACATTCAAGAATTTTTCC
314171 AGAATTTTTGGACACCGGTAACCCCCTCAAAAACGTTGCTCAAGTTGATCCAGCGTTTTCTAGGT
66 AGAATTTTTGGACACCGGTAACCCCCTCAAAAACGTTGCTCAAGTTGATCCAGCGTTTTCTAGGT
314236 TTTCTGG-TTGG-CCC-TTTT-TTTGACT-TTAGTGCTTTAGGTTC-TTTGTTTTTCCT
131 TTTCTGGTTTGGTCCCTTTTTCTTTGACTCTTAGTGCTTTAGGTTCTTTTGTTTTTCCT
314289 GTATTTGGTTCTGAAATTTTACAGGTGGTTTCTTGAGGCATCGAAAGACATTCAAGAATTTTTCC
1 GTATTTGGTTCTGAAATTTTACAGGTGGTTTCTTGAGGCATCGAAAGACATTCAAGAATTTTTCC
314354 AGAATTTTTGGACACCGGTAACCCCCTCAAAAACGTTGCTCAAGTTGATCCAGCGTTTTCTAGGT
66 AGAATTTTTGGACACCGGTAACCCCCTCAAAAACGTTGCTCAAGTTGATCCAGCGTTTTCTAGGT
314419 TTTCTGGTTTGGTCCCTTTTTCTTTGACTCTTAGTGCTTTAGGTTCTTTTGTTTTTCCT
131 TTTCTGGTTTGGTCCCTTTTTCTTTGACTCTTAGTGCTTTAGGTTCTTTTGTTTTTCCT
314478 GT
1 GT
314480 TATTGTTCTT
Statistics
Matches: 185, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
183 137 0.74
184 4 0.02
185 3 0.02
186 4 0.02
187 7 0.04
188 16 0.09
189 14 0.08
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (189 bp):
GTATTTGGTTCTGAAATTTTACAGGTGGTTTCTTGAGGCATCGAAAGACATTCAAGAATTTTTCC
AGAATTTTTGGACACCGGTAACCCCCTCAAAAACGTTGCTCAAGTTGATCCAGCGTTTTCTAGGT
TTTCTGGTTTGGTCCCTTTTTCTTTGACTCTTAGTGCTTTAGGTTCTTTTGTTTTTCCT
Found at i:318435 original size:21 final size:21
Alignment explanation
Indices: 318410--318551 Score: 157
Period size: 21 Copynumber: 6.7 Consensus size: 21
318400 GTAATTTGCA
*
318410 CCGAAGTGCCACATAATTGTC
1 CCGAAGTGCCACATATTTGTC
318431 CCGAAGTGCCACA-ATTTGTC
1 CCGAAGTGCCACATATTTGTC
* *
318451 TCGAAGTACCACATATTTGTC
1 CCGAAGTGCCACATATTTGTC
*
318472 CCGAAGTACCACATATTTGTC
1 CCGAAGTGCCACATATTTGTC
* *
318493 CCAAAG-GACCATATAATTT-TGC
1 CCGAAGTG-CCACAT-ATTTGT-C
318515 ACCGAAGTGCCACATATTTGTC
1 -CCGAAGTGCCACATATTTGTC
318537 CCGAAG-GACCACATA
1 CCGAAGTG-CCACATA
318552 AAACCCTTGA
Statistics
Matches: 104, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
20 18 0.17
21 64 0.62
22 10 0.10
23 11 0.11
24 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.25
Consensus pattern (21 bp):
CCGAAGTGCCACATATTTGTC
Found at i:318522 original size:44 final size:43
Alignment explanation
Indices: 318410--318552 Score: 179
Period size: 44 Copynumber: 3.4 Consensus size: 43
318400 GTAATTTGCA
318410 CCGAAGTG-CCACATAA-TTGTCCCGAAGTGCCACA-ATTTGTC
1 CCGAAG-GACCACATAATTTGTCCCGAAGTGCCACATATTTGTC
* * *
318451 TCGAAGTACCACAT-ATTTGTCCCGAAGTACCACATATTTGTC
1 CCGAAGGACCACATAATTTGTCCCGAAGTGCCACATATTTGTC
* *
318493 CCAAAGGACCATATAATTT-TGCACCGAAGTGCCACATATTTGTC
1 CCGAAGGACCACATAATTTGT-C-CCGAAGTGCCACATATTTGTC
318537 CCGAAGGACCACATAA
1 CCGAAGGACCACATAA
318553 AACCCTTGAC
Statistics
Matches: 86, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
40 1 0.01
41 28 0.33
42 18 0.21
43 5 0.06
44 34 0.40
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (43 bp):
CCGAAGGACCACATAATTTGTCCCGAAGTGCCACATATTTGTC
Found at i:318712 original size:21 final size:21
Alignment explanation
Indices: 318686--318735 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
318676 ATAGAGTATG
318686 TTCACATTCACTGGTTCAAAA
1 TTCACATTCACTGGTTCAAAA
* *
318707 TTCACATTCACTTGTTCAAAG
1 TTCACATTCACTGGTTCAAAA
318728 TTCACATT
1 TTCACATT
318736 TCCATAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.38
Consensus pattern (21 bp):
TTCACATTCACTGGTTCAAAA
Found at i:319266 original size:22 final size:22
Alignment explanation
Indices: 319238--319293 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
319228 CTACCCTCTC
319238 AGTATCGATACTCTCCTCAACG
1 AGTATCGATACTCTCCTCAACG
*
319260 AGTATCGATACCCTCCTCAACG
1 AGTATCGATACTCTCCTCAACG
*
319282 GGTATCGATACT
1 AGTATCGATACT
319294 ACCCTTAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (22 bp):
AGTATCGATACTCTCCTCAACG
Found at i:320410 original size:18 final size:18
Alignment explanation
Indices: 320365--320403 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
320355 AAAAAAACAG
320365 TACAGACAAATTTGAAAA
1 TACAGACAAATTTGAAAA
*
320383 TACAGACAAATTTGACAA
1 TACAGACAAATTTGAAAA
320401 TAC
1 TAC
320404 TGTCAAACGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.15, G:0.10, T:0.23
Consensus pattern (18 bp):
TACAGACAAATTTGAAAA
Found at i:336943 original size:200 final size:202
Alignment explanation
Indices: 336599--337003 Score: 742
Period size: 200 Copynumber: 2.0 Consensus size: 202
336589 TGAAACGAAT
336599 AAACCAAAGAACAAATCCTCCACATTCGCCTTTGTGCGGTTTGGTAATGAGACAGGTCTGAGAAA
1 AAACCAAAGAACAAATCCTCCACATTCGCCTTTGTGCGGTTTGGTAATGAGACAGGTCTGAGAAA
336664 GGCAATCGAGAATATAAACGGATCGTGGATAGATGGGAGGAAAGTATCAATAGGAGTCGCAAAAT
66 GGCAATCGAGAATATAAACGGATCGTGGATAGATGGGAGGAAAGTATCAATAGGAGTCGCAAAAT
*
336729 ATCAGAAAGATCGATCTAGGATAGTGGAGACAAATCGATCACTGACTG-TGCTTCAAGGTCAGTT
131 ATCAGAAAGATCGATCTAGGATAGTGGAGACAAATCGATCACTGACTGATGCTTCAAGGTCAATT
336793 ACAGAAG
196 ACAGAAG
* **
336800 AAACCAAAGTACAAATCCTCCACATTCG-CTTTGTGCGGTTTGGTAATGAGGTAGGTCTGAGAAA
1 AAACCAAAGAACAAATCCTCCACATTCGCCTTTGTGCGGTTTGGTAATGAGACAGGTCTGAGAAA
*
336864 GGCAATCGAGAATATAAACGGGTCGTGGATAGATGGGAGGAAAGTATCAATAGGAGTCGCAAAAT
66 GGCAATCGAGAATATAAACGGATCGTGGATAGATGGGAGGAAAGTATCAATAGGAGTCGCAAAAT
*
336929 ATCATAAAGATCGATCTAGGATAGTGGAGACAAATCGATCACTGACTGATGCTTCAAGGTCAATT
131 ATCAGAAAGATCGATCTAGGATAGTGGAGACAAATCGATCACTGACTGATGCTTCAAGGTCAATT
336994 ACAGAAG
196 ACAGAAG
337001 AAA
1 AAA
337004 TATCAAACCT
Statistics
Matches: 197, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
200 145 0.74
201 52 0.26
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.22
Consensus pattern (202 bp):
AAACCAAAGAACAAATCCTCCACATTCGCCTTTGTGCGGTTTGGTAATGAGACAGGTCTGAGAAA
GGCAATCGAGAATATAAACGGATCGTGGATAGATGGGAGGAAAGTATCAATAGGAGTCGCAAAAT
ATCAGAAAGATCGATCTAGGATAGTGGAGACAAATCGATCACTGACTGATGCTTCAAGGTCAATT
ACAGAAG
Found at i:339042 original size:39 final size:39
Alignment explanation
Indices: 338991--339070 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
338981 TTCTGCAAGA
338991 AACCAAAGTTGAGAATTTTCCAAGTTCATTCTTTAAAAG
1 AACCAAAGTTGAGAATTTTCCAAGTTCATTCTTTAAAAG
* *
339030 AACCCAAGTTGAGAATTTTCCAAGTTCATTCTTTAGAAG
1 AACCAAAGTTGAGAATTTTCCAAGTTCATTCTTTAAAAG
339069 AA
1 AA
339071 GTGGGTTGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33
Consensus pattern (39 bp):
AACCAAAGTTGAGAATTTTCCAAGTTCATTCTTTAAAAG
Found at i:355223 original size:23 final size:23
Alignment explanation
Indices: 355193--355236 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
355183 GCCCTAACAT
355193 GGCTTAATATCACTAAATGACTA
1 GGCTTAATATCACTAAATGACTA
355216 GGCTTAATATCACTAAATGAC
1 GGCTTAATATCACTAAATGAC
355237 ATGCCAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (23 bp):
GGCTTAATATCACTAAATGACTA
Found at i:359304 original size:29 final size:29
Alignment explanation
Indices: 359262--359321 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
359252 AACATGATTT
359262 CAAAAACAATTACTAATACTAACTTAGAG
1 CAAAAACAATTACTAATACTAACTTAGAG
* *
359291 CAAAAATAATTACTAATCCTAACTTAGAG
1 CAAAAACAATTACTAATACTAACTTAGAG
359320 CA
1 CA
359322 GATGATGAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.50, C:0.18, G:0.07, T:0.25
Consensus pattern (29 bp):
CAAAAACAATTACTAATACTAACTTAGAG
Found at i:368479 original size:24 final size:22
Alignment explanation
Indices: 368439--368515 Score: 67
Period size: 24 Copynumber: 3.6 Consensus size: 22
368429 ATGCAATTAA
368439 TGCATCGATGCA---TAAGGAG
1 TGCATCGATGCACTGTAAGGAG
368458 TGCATCGATGCACATGTTAAGG-G
1 TGCATCGATGCAC-TG-TAAGGAG
* *
368481 ATGCATCGATACACTGT-A-GAA
1 -TGCATCGATGCACTGTAAGGAG
368502 TGCATCGATGCACT
1 TGCATCGATGCACT
368516 TCAAGGGAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
19 12 0.25
20 14 0.29
21 1 0.02
22 1 0.02
23 3 0.06
24 17 0.35
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACTGTAAGGAG
Found at i:370111 original size:23 final size:23
Alignment explanation
Indices: 370080--370129 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
370070 CCTTATATGA
* *
370080 CACTTCGGTGCATTTCTACGCGG
1 CACTACGGTGCAATTCTACGCGG
*
370103 CACTACGGTGCAATTCTACGTGG
1 CACTACGGTGCAATTCTACGCGG
370126 CACT
1 CACT
370130 TTAGTGCATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.18, C:0.30, G:0.24, T:0.28
Consensus pattern (23 bp):
CACTACGGTGCAATTCTACGCGG
Found at i:370145 original size:23 final size:23
Alignment explanation
Indices: 370087--370145 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
370077 TGACACTTCG
*
370087 GTGCATTTCTACGCGGCACTACG
1 GTGCATTTCTACGCGGCACTACA
* * **
370110 GTGCAATTCTACGTGGCACTTTA
1 GTGCATTTCTACGCGGCACTACA
*
370133 GTGCATTTATACG
1 GTGCATTTCTACG
370146 AGCTGTGGTG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (23 bp):
GTGCATTTCTACGCGGCACTACA
Found at i:377826 original size:15 final size:15
Alignment explanation
Indices: 377808--377838 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
377798 AAATTCTAAA
377808 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
377823 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
377838 T
1 T
377839 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:382778 original size:19 final size:21
Alignment explanation
Indices: 382751--382792 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
382741 TGTTTGTCAT
*
382751 CACAGTAAAAAT-A-ATTAAA
1 CACAATAAAAATGATATTAAA
382770 CACAATAAAAATGATATTAAA
1 CACAATAAAAATGATATTAAA
382791 CA
1 CA
382793 GATAAAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 11 0.55
20 1 0.05
21 8 0.40
ACGTcount: A:0.62, C:0.12, G:0.05, T:0.21
Consensus pattern (21 bp):
CACAATAAAAATGATATTAAA
Found at i:382797 original size:20 final size:20
Alignment explanation
Indices: 382752--382812 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 20
382742 GTTTGTCATC
382752 ACAG-TAAAAAT-A-ATTAA
1 ACAGATAAAAATGATATTAA
*
382769 ACACAATAAAAATGATATTAA
1 ACA-GATAAAAATGATATTAA
382790 ACAGAT-AAAATGACTATTGAA
1 ACAGATAAAAATGA-TATT-AA
382811 AC
1 AC
382813 GTGAATATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
17 3 0.08
19 14 0.39
20 7 0.19
21 12 0.33
ACGTcount: A:0.59, C:0.10, G:0.08, T:0.23
Consensus pattern (20 bp):
ACAGATAAAAATGATATTAA
Found at i:383569 original size:412 final size:412
Alignment explanation
Indices: 382803--383611 Score: 1469
Period size: 412 Copynumber: 2.0 Consensus size: 412
382793 GATAAAATGA
*
382803 CTATTGAAACGTGAATATTTTAATGACTATTCTTAAGACGAAATCAGGGAGAAATTAAATATCTT
1 CTATTGAAACGTGAATATTTTAATGACTATTCTTAAGACGAAATCAAGGAGAAATTAAATATCTT
382868 ACAAAATATGTTTACGGATAAAATGCAATCTTATAACGTAACTTTTCATGATTTAGCCTTCCATA
66 ACAAAATATGTTTACGGATAAAATGCAATCTTATAACGTAACTTTTCATGATTTAGCCTTCCATA
*
382933 AAGATGCCAGACTGAAACTTTCAACTGACCATTAGAACTACAAAAAATCCTCACATCTTATCTGT
131 AAGATGCCAGACTGAAACTTTCAACTGACCATTAGAACTACAAAAAATCCTCACATCCTATCTGT
* *
382998 GTTACCTGGACTCTTCATTTACCTAAAGCACCTAAGTGATCTCTTATATTAAATATATGTAGAAA
196 GTTACCTGGACTCTTCATTTACCTAAAGCACCTAAGTGATCTCTTAAATGAAATATATGTAGAAA
*
383063 CTTAGAAAATATTGAAAACCCATGTTAGATTAATACCAATGAGTAGCACTTGACCCAGAGTTACA
261 CTTAGAAAATATTGAAAACCCATGTTAGATTAATACCAATGAGTAACACTTGACCCAGAGTTACA
383128 GGACCCTACCCCCAACAGTTGTTACTG-AAAAATAGTTTAAT-GAGTTACTAGCCTTGGCAGGTC
326 GGACCCTACCCCCAACAGTTGTTACTGAAAAAATAG-TTAATGGAGTTACTAGCCTTGGCAGGTC
383191 ACTTGATTCTTTTCATCTACAAC
390 ACTTGATTCTTTTCATCTACAAC
* * *
383214 CTATTGAAATGTGAATATTTTAATGACTATTCTTAAGACGAAATCAAGGAGAAATTGAATGTCTT
1 CTATTGAAACGTGAATATTTTAATGACTATTCTTAAGACGAAATCAAGGAGAAATTAAATATCTT
383279 ACAAAATATGTTTACGGATAAAATGCAATCTTATAACGTAACTTTTCATGATTTAGCCTTCCATA
66 ACAAAATATGTTTACGGATAAAATGCAATCTTATAACGTAACTTTTCATGATTTAGCCTTCCATA
*
383344 AAGATGCCAGACTGAAACTTTCAACTGACCATTAGAACTGCAAAAAAATCCTCACATCCTATCTG
131 AAGATGCCAGACTGAAACTTTCAACTGACCATTAGAACTAC-AAAAAATCCTCACATCCTATCTG
383409 TGTTACCTGGACTCTTCATTTACCTAAAGCACCTAAGTGATCTCTTAAATGAAATATATGTAGAA
195 TGTTACCTGGACTCTTCATTTACCTAAAGCACCTAAGTGATCTCTTAAATGAAATATATGTAGAA
* *
383474 ACTTCGAAAATCTTGAAAACCCATGTTAGATTAATACCAATGAGTAACACTTGACCCAGAGTTAC
260 ACTTAGAAAATATTGAAAACCCATGTTAGATTAATACCAATGAGTAACACTTGACCCAGAGTTAC
* *
383539 AGGACCTTACCCCCAACAGTTGTTACTGAAAAAATAGTTCATGGAGTTACTAGCCTTGGCAGGTC
325 AGGACCCTACCCCCAACAGTTGTTACTGAAAAAATAGTTAATGGAGTTACTAGCCTTGGCAGGTC
383604 ACTTGATT
390 ACTTGATT
383612 ATGCATAGCA
Statistics
Matches: 382, Mismatches: 13, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
411 166 0.43
412 178 0.47
413 38 0.10
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (412 bp):
CTATTGAAACGTGAATATTTTAATGACTATTCTTAAGACGAAATCAAGGAGAAATTAAATATCTT
ACAAAATATGTTTACGGATAAAATGCAATCTTATAACGTAACTTTTCATGATTTAGCCTTCCATA
AAGATGCCAGACTGAAACTTTCAACTGACCATTAGAACTACAAAAAATCCTCACATCCTATCTGT
GTTACCTGGACTCTTCATTTACCTAAAGCACCTAAGTGATCTCTTAAATGAAATATATGTAGAAA
CTTAGAAAATATTGAAAACCCATGTTAGATTAATACCAATGAGTAACACTTGACCCAGAGTTACA
GGACCCTACCCCCAACAGTTGTTACTGAAAAAATAGTTAATGGAGTTACTAGCCTTGGCAGGTCA
CTTGATTCTTTTCATCTACAAC
Found at i:386379 original size:24 final size:24
Alignment explanation
Indices: 386345--386449 Score: 97
Period size: 24 Copynumber: 4.4 Consensus size: 24
386335 AAACGAAGAT
386345 ATCAGAAATCAAAACAGAATTCAGA
1 ATCAGAAATCAAAACAGAATTCA-A
* *
386370 AT-AGATATCAAAACAGAATCCAA
1 ATCAGAAATCAAAACAGAATTCAA
* * *
386393 ATCAGAAATCAAAACAAAATTTAG
1 ATCAGAAATCAAAACAGAATTCAA
* * *
386417 GTCATG-TATCAGAACAGAATTCAA
1 ATCA-GAAATCAAAACAGAATTCAA
*
386441 GTCAGAAAT
1 ATCAGAAAT
386450 TAGACAAAGT
Statistics
Matches: 63, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
23 4 0.06
24 56 0.89
25 3 0.05
ACGTcount: A:0.52, C:0.15, G:0.12, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAA
Found at i:386405 original size:12 final size:12
Alignment explanation
Indices: 386345--386405 Score: 54
Period size: 12 Copynumber: 5.1 Consensus size: 12
386335 AAACGAAGAT
386345 ATCAGAAATCAA
1 ATCAGAAATCAA
* *
386357 AACAGAATTCAGA
1 ATCAGAAATCA-A
*
386370 AT-AGATATCAA
1 ATCAGAAATCAA
*
386381 AACAG-AATCCAA
1 ATCAGAAAT-CAA
386393 ATCAGAAATCAA
1 ATCAGAAATCAA
386405 A
1 A
386406 ACAAAATTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
11 4 0.11
12 28 0.76
13 5 0.14
ACGTcount: A:0.57, C:0.16, G:0.10, T:0.16
Consensus pattern (12 bp):
ATCAGAAATCAA
Found at i:395706 original size:2 final size:2
Alignment explanation
Indices: 395699--395726 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
395689 TCAAAAAGAC
395699 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
395727 TTTTTACTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:398050 original size:18 final size:17
Alignment explanation
Indices: 398018--398051 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
398008 TTTGATAATT
398018 AATAAAAAAATTATTAA
1 AATAAAAAAATTATTAA
*
398035 AATAAAATATATTATTA
1 AATAAAA-AAATTATTA
398052 TTAAATTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AATAAAAAAATTATTAA
Found at i:400708 original size:18 final size:18
Alignment explanation
Indices: 400681--400717 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
400671 AAAAACAACG
* *
400681 AAACAGAAGCAGAGTACA
1 AAACACAAGCAGAGAACA
400699 AAACACAAGCAGAGAACA
1 AAACACAAGCAGAGAACA
400717 A
1 A
400718 GTCAATACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.59, C:0.19, G:0.19, T:0.03
Consensus pattern (18 bp):
AAACACAAGCAGAGAACA
Found at i:408745 original size:49 final size:50
Alignment explanation
Indices: 408648--408746 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 50
408638 TACAAATATT
*
408648 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATTATTTTA
1 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
* * * *
408698 AAATATTA-AAATAAT-TTATTTATTATTAAATA-TTATTTTTATAATTTTA
1 AAATATAATAAATAATATTATTTATCA-TAAA-ACTTAATATTATAATTTTA
408747 TTAATAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
48 9 0.21
49 25 0.60
50 8 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (50 bp):
AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
Found at i:408791 original size:32 final size:30
Alignment explanation
Indices: 408725--408793 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 30
408715 ATTTATTATT
*
408725 AAATATT-ATTTTTATAATTTTATTAATAA
1 AAATATTAATTTTTATAATTTTATAAATAA
*
408754 AAATATTAATTTTTGTATATTTTAGTGAAAT-A
1 AAATATTAATTTTTATA-ATTTTA-T-AAATAA
408786 AAATATTA
1 AAATATTA
408794 TAAATTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 7 0.21
30 8 0.24
31 6 0.18
32 10 0.29
33 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (30 bp):
AAATATTAATTTTTATAATTTTATAAATAA
Found at i:408884 original size:23 final size:23
Alignment explanation
Indices: 408835--408897 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
408825 GTATTATATT
* **
408835 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
408858 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
408881 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
408898 AAATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:408935 original size:26 final size:27
Alignment explanation
Indices: 408882--408944 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 27
408872 TTTATTAAAA
408882 TATTATTTAAATATATAAATAATATTAT
1 TATTA-TTAAATATATAAATAATATTAT
*
408910 TCATTATTAAATATA-AAA-AATTTTAT
1 T-ATTATTAAATATATAAATAATATTAT
408936 TATATATTA
1 TAT-TATTA
408945 TTAAAATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 2 0.06
26 13 0.41
27 3 0.09
28 10 0.31
29 4 0.12
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
TATTATTAAATATATAAATAATATTAT
Found at i:408945 original size:29 final size:30
Alignment explanation
Indices: 408912--408984 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
408902 AATATTATTC
**
408912 ATTATTAAATATAAAAA-ATTTTAT-TATAT
1 ATTATTAAATATAAAAATATAATATCT-TAT
408941 ATTATTAAA-ATAAAAATATAATATCTTAT
1 ATTATTAAATATAAAAATATAATATCTTAT
408970 ATTATTATAATATAA
1 ATTATTA-AATATAA
408985 TTGATTATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 7 0.18
29 24 0.63
30 3 0.08
31 4 0.11
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (30 bp):
ATTATTAAATATAAAAATATAATATCTTAT
Found at i:408962 original size:58 final size:58
Alignment explanation
Indices: 408872--409041 Score: 142
Period size: 58 Copynumber: 3.0 Consensus size: 58
408862 TTTAAATATC
* * *
408872 TTTATTAAAATATTATTTAAATATATAA-ATAATATTATTCATTATTAAATATAA-AAAA
1 TTTATT-ATATATTATTAAAATA-AAAATATAATATTATTCATTATTAAATATAATAAAA
* * *
408930 TTTTATTATATATTATTAAAATAAAAATATAATA-TCTT-A-TATT-ATTATAATATAA
1 -TTTATTATATATTATTAAAATAAAAATATAATATTATTCATTATTAAATATAATAAAA
* * *
408985 TTGATTAT-T-TTATCTAATATAAAAATATAATATAATATCATTA-TAAATATTAATAAA
1 TTTATTATATATTAT-TAAAATAAAAATATAATATTAT-TCATTATTAAATA-TAATAAA
409042 TAAATAAATA
Statistics
Matches: 90, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
52 4 0.04
53 18 0.20
54 14 0.16
55 8 0.09
56 3 0.03
57 11 0.12
58 26 0.29
59 6 0.07
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (58 bp):
TTTATTATATATTATTAAAATAAAAATATAATATTATTCATTATTAAATATAATAAAA
Found at i:409278 original size:42 final size:42
Alignment explanation
Indices: 409230--409341 Score: 152
Period size: 42 Copynumber: 2.7 Consensus size: 42
409220 ATGAATTACA
* * *
409230 TTCCGGAAAACCAATTACGTGAAATAAAAATGAGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAAAACGAGAAAACATT
* * *
409272 TTCCGGAAAACGAATTAAGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAAAACGAGAAAACATT
* *
409314 TTCCGAAAAATGAATTACGTGAAACAAA
1 TTCCGGAAAACGAATTACGTGAAACAAA
409342 TACGGGAATT
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.49, C:0.15, G:0.16, T:0.20
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAAAACGAGAAAACATT
Found at i:410516 original size:34 final size:35
Alignment explanation
Indices: 410462--410530 Score: 122
Period size: 34 Copynumber: 2.0 Consensus size: 35
410452 TCAAAAGATG
*
410462 TCCTCAATGGACAAATGGTGTTAGGTCAGCTAGTT
1 TCCTCAATGGACAAATGGTGTTAGGTCAACTAGTT
410497 TCCTCAATGG-CAAATGGTGTTAGGTCAACTAGTT
1 TCCTCAATGGACAAATGGTGTTAGGTCAACTAGTT
410531 GAACATGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 23 0.70
35 10 0.30
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (35 bp):
TCCTCAATGGACAAATGGTGTTAGGTCAACTAGTT
Found at i:412585 original size:13 final size:13
Alignment explanation
Indices: 412567--412593 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
412557 AACCAATAAA
412567 ATTAAATAATTAT
1 ATTAAATAATTAT
412580 ATTAAATAATTAT
1 ATTAAATAATTAT
412593 A
1 A
412594 ATGATAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTAAATAATTAT
Found at i:414124 original size:36 final size:36
Alignment explanation
Indices: 414081--414161 Score: 155
Period size: 36 Copynumber: 2.3 Consensus size: 36
414071 AACTAATTTT
414081 TTTTAAATCTTAAAGAAAAACTTCAACCTAAGCTAA
1 TTTTAAATCTTAAAGAAAAACTTCAACCTAAGCTAA
414117 TTTTAAATCTTAAAGAAAAACTTCAACCTAAGCTAA
1 TTTTAAATCTTAAAGAAAAACTTCAACCTAAGCTAA
414153 -TTTAAATCT
1 TTTTAAATCT
414162 CGCAGCAGTA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 9 0.20
36 36 0.80
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.33
Consensus pattern (36 bp):
TTTTAAATCTTAAAGAAAAACTTCAACCTAAGCTAA
Found at i:416497 original size:190 final size:190
Alignment explanation
Indices: 416260--416640 Score: 735
Period size: 190 Copynumber: 2.0 Consensus size: 190
416250 AGTCCCTGGA
416260 GGATGATATCGAGGATGAGTCAATAAAAGAAAAGGCAGTGCTTTCAGCTGCAAAGCACTCACTTT
1 GGATGATATCGAGGATGAGTCAATAAAAGAAAAGGCAGTGCTTTCAGCTGCAAAGCACTCACTTT
416325 CTGTTGAGGTAAAGTTAAATTGTTAAACATGTCAAAATTCTCTTGCCTTTTCTAATGCACATTAC
66 CTGTTGAGGTAAAGTTAAATTGTTAAACATGTCAAAATTCTCTTGCCTTTTCTAATGCACATTAC
*
416390 AGTCGTTGGTCCTTGCCCGTGAAGAGGATTTAACTATTAAGACCTTTCCTTATCTCAGTT
131 AGTCGTTGGTCCTTGCCCGTGAAGAGGATTTAACTATTAAGACCTTTACTTATCTCAGTT
* *
416450 GGATGATATTGAGGATGAGTCAGTAAAAGAAAAGGCAGTGCTTTCAGCTGCAAAGCACTCACTTT
1 GGATGATATCGAGGATGAGTCAATAAAAGAAAAGGCAGTGCTTTCAGCTGCAAAGCACTCACTTT
416515 CTGTTGAGGTAAAGTTAAATTGTTAAACATGTCAAAATTCTCTTGCCTTTTCTAATGCACATTAC
66 CTGTTGAGGTAAAGTTAAATTGTTAAACATGTCAAAATTCTCTTGCCTTTTCTAATGCACATTAC
416580 AGTCGTTGGTCCTTGCCCGTGAAGAGGATTTAACTATTAAGACCTTTACTTATCTCAGTT
131 AGTCGTTGGTCCTTGCCCGTGAAGAGGATTTAACTATTAAGACCTTTACTTATCTCAGTT
416640 G
1 G
416641 AATTTCTATG
Statistics
Matches: 188, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
190 188 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (190 bp):
GGATGATATCGAGGATGAGTCAATAAAAGAAAAGGCAGTGCTTTCAGCTGCAAAGCACTCACTTT
CTGTTGAGGTAAAGTTAAATTGTTAAACATGTCAAAATTCTCTTGCCTTTTCTAATGCACATTAC
AGTCGTTGGTCCTTGCCCGTGAAGAGGATTTAACTATTAAGACCTTTACTTATCTCAGTT
Found at i:421005 original size:15 final size:15
Alignment explanation
Indices: 420987--421039 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
420977 CCGGTTTCGG
420987 TTTTAAAAAAACCGA
1 TTTTAAAAAAACCGA
* *
421002 TTTTTTTAAAAAACCGG
1 --TTTTAAAAAAACCGA
*
421019 TTATAAAAAAACCGA
1 TTTTAAAAAAACCGA
421034 TTTTAA
1 TTTTAA
421040 TATTATTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
15 17 0.57
17 13 0.43
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (15 bp):
TTTTAAAAAAACCGA
Found at i:421292 original size:11 final size:12
Alignment explanation
Indices: 421271--421316 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
421261 CCCGGATAAA
421271 AACCGGTTTTTT
1 AACCGGTTTTTT
421283 AACCGGTTTTTTT
1 AACCGG-TTTTTT
421296 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
421310 ATCCGGT
1 AACCGGT
421317 AAAAAAACCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:421301 original size:15 final size:14
Alignment explanation
Indices: 421270--421309 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
421260 TCCCGGATAA
421270 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
421283 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
421296 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
421310 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:433356 original size:11 final size:11
Alignment explanation
Indices: 433332--433365 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
433322 AATTTTCATC
433332 CATATATAATAT
1 CATATAT-ATAT
433344 CATATATATAT
1 CATATATATAT
*
433355 CACATATATAT
1 CATATATATAT
433366 ATTACTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (11 bp):
CATATATATAT
Found at i:436834 original size:105 final size:105
Alignment explanation
Indices: 436691--438025 Score: 2333
Period size: 105 Copynumber: 12.7 Consensus size: 105
436681 CAAGAAAAGT
* * *
436691 TGGTTGTCAATAAACAACTTC-CTAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1 TGGTTGTCAACAAAC-ATTTCTC-AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
436755 ACTCCAGACAGCGCAAGTTCAACTTCACGACGAAGGGACCGC
64 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
436797 TGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
1 TGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
*
436862 TCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
66 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
436902 TGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
1 TGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
436967 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
66 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
437007 TGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
1 TGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
*
437072 TCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
66 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
437112 TGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
1 TGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
437177 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
66 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
*
437217 TGGTTGTCAACAAACATTT-TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA-TGGAC
1 TGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
437280 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
66 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
*
437320 TGGTTGTCAACAAACATTTTTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
1 TGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* *
437385 TCAAAACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
66 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
*
437425 TGGTTGTCAACAAATATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
1 TGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
437490 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
66 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
* *
437530 TGGTTGTCAACAAACATTTTTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
1 TGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
437595 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA-CGC
66 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
437634 TGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
1 TGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* *
437699 TCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCAC
66 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
* *
437739 TGGTTGTCAAC-AACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
1 TGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
*
437803 CTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
65 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
*
437844 TGGTTGTCAACAAACAATTTC-CTAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1 TGGTTGTCAACAAAC-ATTTCTC-AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
437908 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGAC
64 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-C
* *
437950 TGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGA
1 TGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
*
438015 CTCGAGACAAC
65 CTCCAGACAAC
438026 ATAACTTTCA
Statistics
Matches: 1187, Mismatches: 33, Indels: 18
0.96 0.03 0.01
Matches are distributed among these distances:
103 64 0.05
104 180 0.15
105 771 0.65
106 171 0.14
107 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
TGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
Found at i:437766 original size:523 final size:525
Alignment explanation
Indices: 436691--438025 Score: 2365
Period size: 523 Copynumber: 2.5 Consensus size: 525
436681 CAAGAAAAGT
* *
436691 TGGTTGTCAATAAACAACTTCCTAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
1 TGGTTGTCAA-CAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
* *
436756 CTCCAGACAGCGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAA
65 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTTTCAA
436821 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTC
130 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTC
*
436886 ACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACA
195 ACGACGAAGGGACCGCTGGTTGTCAACAAAAATTTCTCAATTTCAGAGCCAATTTCAACTTCACA
436951 GCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
260 GCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
*
437016 ACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAA
325 ACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAA
437081 CGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCC
390 CGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCC
*
437146 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
455 AATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGG
*
437211 GACCGC
520 GACCAC
**
437217 TGGTTGTCAAC-A-AACATTTTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA-TGGA
1 TGGTTGTCAACAACAAC-TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
437279 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTTTCAA
65 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTTTCAA
*
437344 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAAACAACGCAAGTTCAACTTC
130 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTC
*
437409 ACGACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCAATTTCAGAGCCAATTTCAACTTCACA
195 ACGACGAAGGGACCGCTGGTTGTCAACAAAAATTTCTCAATTTCAGAGCCAATTTCAACTTCACA
437474 GCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
260 GCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* *
437539 ACAAACATTTTTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAA
325 ACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAA
437604 CGCAAGTTCAACTTCACGACGAAGGGA-CGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCC
390 CGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCC
437668 AATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGG
455 AATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGG
437733 GACCAC
520 GACCAC
*
437739 TGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
1 TGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
* * *
437804 TCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCTAA
66 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTTTC-AA
* * *
437869 TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTC
130 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTC
* * *
437934 ACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTTAACTTCA
195 ACGACGAAGGGACCG-CTGGTTGTCAACAAA-AATTTCTCAATTTCAGAGCCAATTTCAACTTCA
*
437998 CAGCGAAGGATATTGGACTCGAGACAAC
258 CAGCGAAGGATATTGGACTCCAGACAAC
438026 ATAACTTTCA
Statistics
Matches: 774, Mismatches: 28, Indels: 14
0.95 0.03 0.02
Matches are distributed among these distances:
522 117 0.15
523 392 0.51
524 109 0.14
525 89 0.11
526 67 0.09
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (525 bp):
TGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTTTCAAT
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCA
CGACGAAGGGACCGCTGGTTGTCAACAAAAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAG
CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
CAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAAC
GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCA
ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCAC
Found at i:438624 original size:11 final size:11
Alignment explanation
Indices: 438600--438633 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
438590 AATTTTCATC
438600 CATATATAATAT
1 CATATAT-ATAT
438612 CATATATATAT
1 CATATATATAT
*
438623 CACATATATAT
1 CATATATATAT
438634 TACTTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (11 bp):
CATATATATAT
Found at i:443189 original size:16 final size:17
Alignment explanation
Indices: 443160--443193 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
443150 TTATTTTAGG
*
443160 TATCCGAAATTTTCGGA
1 TATCCGAAAATTTCGGA
443177 TATCC-AAAATTTCGGA
1 TATCCGAAAATTTCGGA
443193 T
1 T
443194 TGAATAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (17 bp):
TATCCGAAAATTTCGGA
Found at i:443938 original size:32 final size:33
Alignment explanation
Indices: 443875--443939 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
443865 TGAGTAATGG
*
443875 TTTTCAATTATGATTTTTTTTTTATTATTTTAAT
1 TTTTCAATTATGA-TTTTTTTTAATTATTTTAAT
* *
443909 TTTTCAATTTTGA-TTTTTTTAATTGTTTTAA
1 TTTTCAATTATGATTTTTTTTAATTATTTTAA
443940 AGCGTTGGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 16 0.57
34 12 0.43
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (33 bp):
TTTTCAATTATGATTTTTTTTAATTATTTTAAT
Found at i:447780 original size:3 final size:3
Alignment explanation
Indices: 447772--447808 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
447762 TAGTACAAAC
447772 ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
447809 GGAAATTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:447795 original size:17 final size:17
Alignment explanation
Indices: 447775--447808 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
447765 TACAAACATA
447775 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
447792 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
447809 GGAAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:452601 original size:36 final size:34
Alignment explanation
Indices: 452542--452608 Score: 98
Period size: 36 Copynumber: 1.9 Consensus size: 34
452532 CCAAACACCA
452542 ATATATTATATTATAAAAATATTTTAGTTTTGTT
1 ATATATTATATTATAAAAATATTTTAGTTTTGTT
* *
452576 ATATATTTATTTTATAAATAATATTTTATTTTT
1 ATATA-TTATATTATAAA-AATATTTTAGTTTT
452609 AAAAGTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 5 0.17
35 11 0.38
36 13 0.45
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (34 bp):
ATATATTATATTATAAAAATATTTTAGTTTTGTT
Found at i:455426 original size:22 final size:22
Alignment explanation
Indices: 455395--455756 Score: 541
Period size: 22 Copynumber: 16.5 Consensus size: 22
455385 AATAATAAAT
455395 TTTTCAAAATAAATCAATCCATA
1 TTTT-AAAATAAATCAATCCATA
*
455418 TTTTAAAAT-AATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
* *
455439 TTTTAAAATTAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
** *
455461 TTTTAAAATAAAAT-TTTTCATA
1 TTTTAAAAT-AAATCAATCCATA
455483 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
455505 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
455527 TTTTAAAATAAATCTATCCATA
1 TTTTAAAATAAATCAATCCATA
*
455549 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
455571 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
455593 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
455615 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
455637 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
* *
455659 TTTTAAAATTAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
455681 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
455703 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
* *
455725 ATTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
455747 TTTTAAAATA
1 TTTTAAAATA
455757 GATTTAAATA
Statistics
Matches: 306, Mismatches: 28, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
21 27 0.09
22 268 0.88
23 11 0.04
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:461521 original size:33 final size:33
Alignment explanation
Indices: 461479--461546 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
461469 ATACATGTCG
*
461479 AAGACACACACGAGTTGACCAAACGACGATAGC
1 AAGACACACACGAGTTGACCAAACGAAGATAGC
*
461512 AAGACACACACGAGTTGACCAAACGAATATAGC
1 AAGACACACACGAGTTGACCAAACGAAGATAGC
461545 AA
1 AA
461547 CACGCATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.10
Consensus pattern (33 bp):
AAGACACACACGAGTTGACCAAACGAAGATAGC
Found at i:464970 original size:59 final size:60
Alignment explanation
Indices: 464907--465053 Score: 160
Period size: 60 Copynumber: 2.5 Consensus size: 60
464897 ATCTTTAAAT
* * * ** *
464907 TTTTGGATATTCTAATTCCATCTC-AAACTA-CGA-A-TCTTATTATAAATTAGTCCTTAAGC
1 TTTTGAATATTCTAATTTCATCCCTAAACTATC-ACATTCTT-TT-TAAATTAGTCCCCAAAC
*
464966 TTTTGAACAATT-TAATTTCATCCCTAAACTATCACATTCTTTTTAAATTAGTCCCCAAAC
1 TTTTGAA-TATTCTAATTTCATCCCTAAACTATCACATTCTTTTTAAATTAGTCCCCAAAC
465026 TTTTGAATATTCTAATTTCATCCCTAAA
1 TTTTGAATATTCTAATTTCATCCCTAAA
465054 TTCATTCAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
59 19 0.26
60 47 0.64
61 4 0.05
62 4 0.05
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.41
Consensus pattern (60 bp):
TTTTGAATATTCTAATTTCATCCCTAAACTATCACATTCTTTTTAAATTAGTCCCCAAAC
Found at i:468201 original size:30 final size:30
Alignment explanation
Indices: 468152--468223 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 30
468142 TCATTCTAAA
* * *
468152 TTCATCCTCAAAC-TTTTGAAAATTTTAGT
1 TTCATCCCCAAACTTTTTGAAAATTTCAAT
*
468181 TTCATCCCCAAACTTTTTGAACATTTCAAT
1 TTCATCCCCAAACTTTTTGAAAATTTCAAT
468211 TTCAT-CCCAAACT
1 TTCATCCCCAAACT
468224 ATATGTTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 20 0.53
30 18 0.47
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.40
Consensus pattern (30 bp):
TTCATCCCCAAACTTTTTGAAAATTTCAAT
Found at i:468450 original size:21 final size:21
Alignment explanation
Indices: 468422--468469 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
468412 ATTTTTTAAA
468422 AAAAAATTTAAAATAATA-ATT
1 AAAAAATTTAAAA-AATATATT
*
468443 ATAAAATTTAAAAAATATATT
1 AAAAAATTTAAAAAATATATT
468464 AAAAAA
1 AAAAAA
468470 GTTCCATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAAAATTTAAAAAATATATT
Found at i:476233 original size:179 final size:178
Alignment explanation
Indices: 475922--476278 Score: 680
Period size: 179 Copynumber: 2.0 Consensus size: 178
475912 TTCTACAACA
475922 ATTCAAATAAATGTCAAGTCTATCCCAAATTTCTTGAAAATATCCAAGTATCTGGTTAATATTTT
1 ATTCAAATAAATGTCAAGTCTATCCCAAATTTCTTGAAAATATCCAAGTATCTGGTTAATATTTT
*
475987 TTAAAATATTGCAAAGGTTCATATTATCTATAATTAAACCTAAATATATAGAAATAGATTATATA
66 TTAAAATATTGCAAAGGTTCATATTATCTATAATTAAACCTAAATATATAGAAATAGAATATATA
476052 AGTGCATACAATTTAAACCCTTTCCTACAAAGAACAGTTTTGTAAGTT
131 AGTGCATACAATTTAAACCCTTTCCTACAAAGAACAGTTTTGTAAGTT
476100 ATTCAAATAAATGTCAAGTCTATCCCAAATTTCTTGAAAATATCCAAGTTATCTGGTTAATATTT
1 ATTCAAATAAATGTCAAGTCTATCCCAAATTTCTTGAAAATATCCAAG-TATCTGGTTAATATTT
476165 TTTAAAATATTGCAAAGGTTCATATTATCTATAATTAAACCTAAAATATATAGAAATAGAAT-TA
65 TTTAAAATATTGCAAAGGTTCATATTATCTATAATTAAACCT-AAATATATAGAAATAGAATATA
476229 TAAGTGCATACAATTTAAACCCTTTCCTACAAAGAACAGTTTTGTAAGTT
129 TAAGTGCATACAATTTAAACCCTTTCCTACAAAGAACAGTTTTGTAAGTT
476279 TCTCCTCCCA
Statistics
Matches: 176, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
178 48 0.27
179 110 0.62
180 18 0.10
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (178 bp):
ATTCAAATAAATGTCAAGTCTATCCCAAATTTCTTGAAAATATCCAAGTATCTGGTTAATATTTT
TTAAAATATTGCAAAGGTTCATATTATCTATAATTAAACCTAAATATATAGAAATAGAATATATA
AGTGCATACAATTTAAACCCTTTCCTACAAAGAACAGTTTTGTAAGTT
Found at i:483337 original size:24 final size:25
Alignment explanation
Indices: 483310--483356 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
483300 ATTTCTATGT
*
483310 GGTCCTTCGGGACAAA-TTCTACAC
1 GGTCCTTCGAGACAAATTTCTACAC
483334 GGTCCTTCGAGACAAATTTCTAC
1 GGTCCTTCGAGACAAATTTCTAC
483357 GCGACACTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (25 bp):
GGTCCTTCGAGACAAATTTCTACAC
Found at i:500609 original size:235 final size:233
Alignment explanation
Indices: 500156--500619 Score: 784
Period size: 234 Copynumber: 2.0 Consensus size: 233
500146 CTAAAATTGG
* * *
500156 ACATGTATGCTCACCTGGGAAACTTAAAACCAAATATAAAGCAAAAAAAATTTGCCACATTCCGT
1 ACATGTATGCTCAACAGGGAAACTTAAAACCAAATATAAAGCAAAAAAAAATTGCCACATTCCGT
500221 CTCTATAATCACTCACTCACAATATCACTCAAGCACAATCAAAACAACATCAAGTTTGTTCAACA
66 CTCTATAATCACTCACTCACAATATCACTCAAGCACAATCAAAACAACATCAAGTTTGTTCAACA
*
500286 CATCAAACTAAAATAACTAGCATCCAGCCATCTCATGCATCAAAAGAAGGTAACATTTGATCAAT
131 CATCAAACTAAAATAACTAACATCCAGCCATCTCATGCATCAAAAGAAGGTAACATTTGATCAAT
500351 TTCAAACATACGTTCTTTAAATAAATTGGAAAAAATGA
196 TTCAAACATACGTTCTTTAAATAAATTGGAAAAAATGA
* *
500389 ACATGTATGCTCAACAGGGAAGCTTAAAACCAAATATAAAGCAAAAAAAAAATTGCCATATTCCG
1 ACATGTATGCTCAACAGGGAAACTTAAAACCAAATATAAAGC-AAAAAAAAATTGCCACATTCCG
* **
500454 TCTCTATAATCACTCACTCACAATATCACTCAAGCACACTGGAAACAACATCAAGTTTGTTCAAC
65 TCTCTATAATCACTCACTCACAATATCACTCAAGCACAATCAAAACAACATCAAGTTTGTTCAAC
* * * *
500519 ACATCAAACTAAAATAAAGTAACATCCAGCCATCTCGTTCATCAAACGAAGGTAACATTTGATCA
130 ACATCAAACTAAAAT-AACTAACATCCAGCCATCTCATGCATCAAAAGAAGGTAACATTTGATCA
*
500584 ATTTCAAACATATGTTCTTTAAATAAATTGGAAAAA
194 ATTTCAAACATACGTTCTTTAAATAAATTGGAAAAA
500620 TCACAGGCTT
Statistics
Matches: 215, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
233 39 0.18
234 97 0.45
235 79 0.37
ACGTcount: A:0.43, C:0.22, G:0.10, T:0.25
Consensus pattern (233 bp):
ACATGTATGCTCAACAGGGAAACTTAAAACCAAATATAAAGCAAAAAAAAATTGCCACATTCCGT
CTCTATAATCACTCACTCACAATATCACTCAAGCACAATCAAAACAACATCAAGTTTGTTCAACA
CATCAAACTAAAATAACTAACATCCAGCCATCTCATGCATCAAAAGAAGGTAACATTTGATCAAT
TTCAAACATACGTTCTTTAAATAAATTGGAAAAAATGA
Found at i:502719 original size:17 final size:18
Alignment explanation
Indices: 502683--502722 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
502673 TTTGTTTAAA
*
502683 AAAATTAAAATTATTATT
1 AAAATCAAAATTATTATT
*
502701 AAAATCAAAA-TATTTTT
1 AAAATCAAAATTATTATT
502718 AAAAT
1 AAAAT
502723 TCTTATAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATCAAAATTATTATT
Found at i:502935 original size:18 final size:19
Alignment explanation
Indices: 502900--502936 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
502890 CACAGAATGT
502900 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
502920 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
502937 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:505189 original size:81 final size:81
Alignment explanation
Indices: 505102--505265 Score: 301
Period size: 81 Copynumber: 2.0 Consensus size: 81
505092 TTGGGTGTAG
505102 TAAAATAATTATTATTAATTAATAAATTAGAATTTTTATTAGAATATTAATAGATTAGTCATTTG
1 TAAAATAATTATTATTAATTAATAAATTAGAATTTTTATTAGAATATTAATAGATTAGTCATTTG
505167 TCATCTATTAGTAAAT
66 TCATCTATTAGTAAAT
* * *
505183 TAAAATAATTATTATTAATTAATAATTTAGTATTTTTATTAGAATATTAATATATTAGTCATTTG
1 TAAAATAATTATTATTAATTAATAAATTAGAATTTTTATTAGAATATTAATAGATTAGTCATTTG
505248 TCATCTATTAGTAAAT
66 TCATCTATTAGTAAAT
505264 TA
1 TA
505266 GTAAATTTTA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.48
Consensus pattern (81 bp):
TAAAATAATTATTATTAATTAATAAATTAGAATTTTTATTAGAATATTAATAGATTAGTCATTTG
TCATCTATTAGTAAAT
Found at i:518010 original size:11 final size:11
Alignment explanation
Indices: 517994--518052 Score: 90
Period size: 11 Copynumber: 5.7 Consensus size: 11
517984 CTTTATTTAA
517994 AATTATCATAC
1 AATTATCATAC
518005 AATTATCA-A-
1 AATTATCATAC
518014 AATTATCATAC
1 AATTATCATAC
518025 AATTATCA-A-
1 AATTATCATAC
518034 AATTATCATAC
1 AATTATCATAC
518045 AATTATCA
1 AATTATCA
518053 AGAGGAGGAC
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
9 16 0.36
10 4 0.09
11 24 0.55
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (11 bp):
AATTATCATAC
Found at i:518017 original size:20 final size:20
Alignment explanation
Indices: 517992--518053 Score: 124
Period size: 20 Copynumber: 3.1 Consensus size: 20
517982 ATCTTTATTT
517992 AAAATTATCATACAATTATC
1 AAAATTATCATACAATTATC
518012 AAAATTATCATACAATTATC
1 AAAATTATCATACAATTATC
518032 AAAATTATCATACAATTATC
1 AAAATTATCATACAATTATC
518052 AA
1 AA
518054 GAGGAGGACA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATTATCATACAATTATC
Found at i:518426 original size:2 final size:2
Alignment explanation
Indices: 518419--518468 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
518409 ATCGGGTCGG
* * * *
518419 AT AT AT AT AT AT AT AT AT AT AT TT AA AT -T AA AT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
518460 AT -T AT AT AT
1 AT AT AT AT AT
518469 TTTTAATTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:518478 original size:5 final size:5
Alignment explanation
Indices: 518470--518538 Score: 52
Period size: 5 Copynumber: 12.8 Consensus size: 5
518460 ATTATATATT
*
518470 TTTAA TTTAA TTTAAA TATATAA -TTATA TATAA -TTAA TTTAA TTTAA
1 TTTAA TTTAA TTT-AA T-T-TAA TTTA-A TTTAA TTTAA TTTAA TTTAA
518517 TTTAAA TTTAAA TTTAAA TTTA
1 TTT-AA TTT-AA TTT-AA TTTA
518539 TTAATATTAT
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
4 5 0.09
5 24 0.44
6 22 0.40
7 3 0.05
8 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (5 bp):
TTTAA
Found at i:518496 original size:32 final size:34
Alignment explanation
Indices: 518419--518516 Score: 110
Period size: 32 Copynumber: 2.8 Consensus size: 34
518409 ATCGGGTCGG
*
518419 ATATATATATATATATATATATTTAAATTAAATATATAA
1 ATAT-TATATATA-AT-TA-ATTTAATTTAAATATAT-A
**
518458 ATATTATATATTTTTAATTTAATTTAAATATAT-
1 ATATTATATATAATTAATTTAATTTAAATATATA
518491 A-ATTATATATAATTAATTTAATTTAA
1 ATATTATATATAATTAATTTAATTTAA
518517 TTTAAATTTA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
32 23 0.43
33 1 0.02
35 16 0.30
36 2 0.04
37 1 0.02
38 7 0.13
39 4 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (34 bp):
ATATTATATATAATTAATTTAATTTAAATATATA
Done.