Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008192.1 Hibiscus syriacus cultivar Beakdansim tig00110809_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: 1702141
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 9
Found at i:461142 original size:36 final size:36
Alignment explanation
Indices: 461087--461166 Score: 135
Period size: 36 Copynumber: 2.2 Consensus size: 36
461077 CCCATTCCTA
*
461087 TTTTC-AACAAACATCTACCAAACTTTGAAAAACAT
1 TTTTCAAAGAAACATCTACCAAACTTTGAAAAACAT
*
461122 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACAT
1 TTTTCAAAGAAACATCTACCAAACTTTGAAAAACAT
461158 TTTTCAAAG
1 TTTTCAAAG
461167 TTGGTTGCCA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
35 5 0.12
36 37 0.88
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (36 bp):
TTTTCAAAGAAACATCTACCAAACTTTGAAAAACAT
Found at i:465725 original size:21 final size:21
Alignment explanation
Indices: 465701--465757 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 21
465691 CAAACTTTAC
465701 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
**
465722 CAAA----G--AAACATTTAC
1 CAAACTTTGAAAAACATTTTT
465737 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
465758 AAAAGTTGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 12
0.62 0.10 0.29
Matches are distributed among these distances:
15 12 0.46
17 1 0.04
19 1 0.04
21 12 0.46
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.33
Consensus pattern (21 bp):
CAAACTTTGAAAAACATTTTT
Found at i:465737 original size:36 final size:35
Alignment explanation
Indices: 465692--465762 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 35
465682 AACATCTACC
*
465692 AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
1 AAACTTTACCAAACTTTGAAAAACATTTTTAAAAG
465727 AAACATTTACCAAACTTTGAAAAACATTTTTAAAAG
1 AAAC-TTTACCAAACTTTGAAAAACATTTTTAAAAG
465763 TTGGTTGCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 4 0.12
36 30 0.88
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (35 bp):
AAACTTTACCAAACTTTGAAAAACATTTTTAAAAG
Found at i:468640 original size:2 final size:2
Alignment explanation
Indices: 468633--468666 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
468623 TGCTATATCC
468633 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
468667 GATTATGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:469342 original size:28 final size:28
Alignment explanation
Indices: 469310--469397 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
469300 CAATGGATCA
469310 TTTTAATCTAAAGATTCAACTAAATAAC
1 TTTTAATCTAAAGATTCAACTAAATAAC
* * * ** *
469338 TTTTAATAGTCAATGGA-TC-ATTTTATGAC
1 TTTTAAT-CT-AA-AGATTCAACTAAATAAC
469367 TTTTAATCTAAAGATTCAACTAAATAAC
1 TTTTAATCTAAAGATTCAACTAAATAAC
469395 TTT
1 TTT
469398 GTATAATCCA
Statistics
Matches: 43, Mismatches: 12, Indels: 10
0.66 0.18 0.15
Matches are distributed among these distances:
26 2 0.05
27 4 0.09
28 17 0.40
29 14 0.33
30 4 0.09
31 2 0.05
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41
Consensus pattern (28 bp):
TTTTAATCTAAAGATTCAACTAAATAAC
Found at i:472416 original size:20 final size:20
Alignment explanation
Indices: 472388--472434 Score: 80
Period size: 18 Copynumber: 2.5 Consensus size: 20
472378 AATGAAGATC
472388 TCTCTATATATTGTAAAACT
1 TCTCTATATATTGTAAAACT
472408 TCTC-A-ATATTGTAAAACT
1 TCTCTATATATTGTAAAACT
472426 TCTCTATAT
1 TCTCTATAT
472435 TCTCTCTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 17 0.68
19 2 0.08
20 6 0.24
ACGTcount: A:0.34, C:0.17, G:0.04, T:0.45
Consensus pattern (20 bp):
TCTCTATATATTGTAAAACT
Found at i:474187 original size:20 final size:20
Alignment explanation
Indices: 474132--474187 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
474122 TTATATTATT
**
474132 TCTCTGTTTTTT-TTTCCGG
1 TCTCTGTTTTTTCTTTTTGG
*
474151 -CTCTGTGTTCTTC-TTTTGG
1 TCTCTGT-TTTTTCTTTTTGG
474170 TCTCTGTTTTTTCTTTTT
1 TCTCTGTTTTTTCTTTTT
474188 TTTTTCAGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
18 6 0.21
19 13 0.45
20 10 0.34
ACGTcount: A:0.00, C:0.20, G:0.14, T:0.66
Consensus pattern (20 bp):
TCTCTGTTTTTTCTTTTTGG
Found at i:474620 original size:3 final size:3
Alignment explanation
Indices: 474612--474701 Score: 162
Period size: 3 Copynumber: 30.0 Consensus size: 3
474602 TTAATATTTT
*
474612 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
474660 TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
474702 AATTAATATG
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 83 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:474989 original size:40 final size:40
Alignment explanation
Indices: 474945--475043 Score: 198
Period size: 40 Copynumber: 2.5 Consensus size: 40
474935 GTTGAACAAA
474945 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
474985 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
475025 TTCTTCTCATTATGAACTT
1 TTCTTCTCATTATGAACTT
475044 TCTCTGGAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.18, C:0.24, G:0.09, T:0.48
Consensus pattern (40 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
Found at i:475126 original size:153 final size:155
Alignment explanation
Indices: 474846--475156 Score: 475
Period size: 153 Copynumber: 2.0 Consensus size: 155
474836 ATTGAATAAA
* * * * *
474846 TTCTTCTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGCTGACCCA
1 TTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCT-GGGATAAAGATAACCCA
*
474911 TCAAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCT
65 TCAAATAATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCT
474976 TCAGATGAGTTCTTCTCATTATGAAC
130 TCAGATGAGTTCTTCTCATTATGAAC
*
475002 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT-CT-GGA-AAAGATAATCCA
1 TTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGATAAAGATAACCCA
* *** *
475064 TCAATTAATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCT
65 TCAAATAATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCT
475129 TCAGATGAGTTCTTCTCATTATGAAC
130 TCAGATGAGTTCTTCTCATTATGAAC
475155 TT
1 TT
475157 TCTCTGGAAA
Statistics
Matches: 142, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
153 94 0.66
154 3 0.02
156 8 0.06
157 37 0.26
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.40
Consensus pattern (155 bp):
TTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGATAAAGATAACCCAT
CAAATAATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTT
CAGATGAGTTCTTCTCATTATGAAC
Found at i:475192 original size:113 final size:113
Alignment explanation
Indices: 474985--475634 Score: 1203
Period size: 113 Copynumber: 5.8 Consensus size: 113
474975 TTCAGATGAG
474985 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * * *
475050 GAAAAGATAATCCATCAATTAATGAATTCAGGTAAAAGGTTGAACAAA
66 GAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAA
475098 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
475163 GAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAA
66 GAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAA
*
475211 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
475276 GAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAA
66 GAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAA
475324 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
475389 GAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAA
66 GAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAA
475437 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
475502 GAGATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAA
66 GAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAA
475550 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
475615 GAAATG-TCAATCCATCAAAT
66 GAAATGAT-GATCCATCAAAT
475635 AATAGATTTG
Statistics
Matches: 525, Mismatches: 11, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
112 1 0.00
113 524 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAA
Found at i:476583 original size:83 final size:83
Alignment explanation
Indices: 476442--477117 Score: 1053
Period size: 83 Copynumber: 8.2 Consensus size: 83
476432 TTTACTATGA
*
476442 GCAAATTCATCTTCCAAATTCAATGATTGG-TCTG-CCAAACCAGATCAGATAACTCAAAGAACA
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAAAGAACA
476505 CTTCCAGAAGATGCTATTG
65 CTTCCAGAAGATGCTATTG
* * *
476524 GCAAATTCCTCTTCTAAACTCCATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
476589 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
*
476607 GCAAATTCATCTTCTAAATTCAATGATTGGTTTTGTCCAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
476672 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
476690 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
*
476755 TTCCAGAAGATGTTATTG
66 TTCCAGAAGATGCTATTG
* *
476773 GCAAATTCATCTTCTAAACTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAAAAC
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
476838 TTCCAGAAGATGCTA-TG
66 TTCCAGAAGATGCTATTG
* *
476855 AGCAAATTTATCTT-TCAAATTCAATGGTTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAA
1 -GCAAATTCATCTTCT-AAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAAAGAA
*
476918 CACTTCCAGAAGATGCTATTA
63 CACTTCCAGAAGATGCTATTG
* * * *
476939 ACACATTCATCTTCTAAATTCAATGATTGGTTCTGTCAAACCAGATCAGACAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
477004 TTCCAGAAGATGCTA-TG
66 TTCCAGAAGATGCTATTG
* * * *
477021 AACACATTCATCTCCTAAATTCAATGATTGATTCTG-CCAAACCAGATCAGATAACTCAAAGAAC
1 -GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAAAGAAC
477085 ACTTCCAGAAGATGCTA-TG
64 ACTTCCAGAAGATGCTATTG
*
477104 AACAAATTCATCTT
1 -GCAAATTCATCTT
477118 TCAGTTAATG
Statistics
Matches: 553, Mismatches: 31, Indels: 19
0.92 0.05 0.03
Matches are distributed among these distances:
82 33 0.06
83 515 0.93
84 5 0.01
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATGCTATTG
Found at i:477918 original size:16 final size:18
Alignment explanation
Indices: 477879--477925 Score: 71
Period size: 16 Copynumber: 2.7 Consensus size: 18
477869 TCATATATAA
477879 AAATAAATTGAATTTCTAC
1 AAATAAATTGAA-TTCTAC
477898 AAATAAATTGAA-TCT-C
1 AAATAAATTGAATTCTAC
477914 AAATAAATTGAA
1 AAATAAATTGAA
477926 CTTGAAATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.46
17 3 0.11
19 12 0.43
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (18 bp):
AAATAAATTGAATTCTAC
Found at i:478281 original size:20 final size:20
Alignment explanation
Indices: 478256--478303 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
478246 TTGACCCCCC
478256 TTTTTCTTTT-TACTCTTTTT
1 TTTTTCTTTTCT-CTCTTTTT
*
478276 TTTTTCTTTTCTTTCTTTTT
1 TTTTTCTTTTCTCTCTTTTT
478296 TTTTTCTT
1 TTTTTCTT
478304 CAAGCATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTTCTTTTCTCTCTTTTT
Found at i:488937 original size:15 final size:13
Alignment explanation
Indices: 488905--488950 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 13
488895 TTTGACAGTA
488905 AAAT-AAATAATG
1 AAATAAAATAATG
488917 AAATAAAATAATTG
1 AAATAAAATAA-TG
488931 CAAATAAAATAA--
1 -AAATAAAATAATG
488943 AAATAAAA
1 AAATAAAA
488951 CATATAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 8 0.26
12 4 0.13
13 6 0.19
14 2 0.06
15 11 0.35
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.22
Consensus pattern (13 bp):
AAATAAAATAATG
Found at i:490682 original size:19 final size:18
Alignment explanation
Indices: 490659--490714 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 18
490649 TTATATTATT
490659 TCTCTGTTTTTTTTTTCCGG
1 TCTCTGTTTTTTTTTT--GG
*
490679 -CTCTGTGTTCTTCTTTTGG
1 TCTCTGT-TT-TTTTTTTGG
490698 TCTCTGTTTTTTCTTTT
1 TCTCTGTTTTTT-TTTT
490715 TTTTTTCAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
18 2 0.07
19 14 0.47
20 8 0.27
21 6 0.20
ACGTcount: A:0.00, C:0.20, G:0.14, T:0.66
Consensus pattern (18 bp):
TCTCTGTTTTTTTTTTGG
Found at i:491129 original size:3 final size:3
Alignment explanation
Indices: 491121--491204 Score: 150
Period size: 3 Copynumber: 28.0 Consensus size: 3
491111 TTAATATTTT
*
491121 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
491169 TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
491205 AATTAATATG
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:494791 original size:23 final size:23
Alignment explanation
Indices: 494773--494828 Score: 96
Period size: 23 Copynumber: 2.4 Consensus size: 23
494763 CATTTTTATT
494773 TGTCTTTAT-GACATGTTTTCTTC
1 TGTCTTT-TGGACATGTTTTCTTC
494796 TGTCTTTTGGACATGTTTTCTTC
1 TGTCTTTTGGACATGTTTTCTTC
494819 TGTCTTTTGG
1 TGTCTTTTGG
494829 TACGCTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.09, C:0.16, G:0.18, T:0.57
Consensus pattern (23 bp):
TGTCTTTTGGACATGTTTTCTTC
Found at i:508718 original size:21 final size:23
Alignment explanation
Indices: 508683--508743 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
508673 TTGGTGCAGA
*
508683 GGGAATCGA-TCCCCCCATG-A-
1 GGGAACCGATTCCCCCCATGAAG
* **
508703 GGGAACTGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCATGAAG
508726 GGGAACCGATTCCCCCCA
1 GGGAACCGATTCCCCCCA
508744 CAGGGGAATC
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 7 0.23
21 8 0.26
22 1 0.03
23 15 0.48
ACGTcount: A:0.23, C:0.34, G:0.25, T:0.18
Consensus pattern (23 bp):
GGGAACCGATTCCCCCCATGAAG
Found at i:514082 original size:20 final size:19
Alignment explanation
Indices: 514057--514094 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
514047 GATCAATGTT
*
514057 CTGGTCAACAGTGGTCAACG
1 CTGGTCAAC-GGGGTCAACG
514077 CTGGTCAACGGGGTCAAC
1 CTGGTCAACGGGGTCAAC
514095 AGTCGACCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.24, C:0.26, G:0.32, T:0.18
Consensus pattern (19 bp):
CTGGTCAACGGGGTCAACG
Found at i:519531 original size:148 final size:148
Alignment explanation
Indices: 519257--519549 Score: 480
Period size: 148 Copynumber: 2.0 Consensus size: 148
519247 AAATACTCAA
*
519257 TTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC
1 TTCAGTTTATAAAATAGTTGACTCAAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC
* * * * *
519322 AAATTGAATTGAATTTTTGAGTTTCTGTTTAAATTTAATTACAAATATTTATCATATTATAATAT
66 AAATTGAATTGAATTTTCGAGTTTATGTTTAAATTTAATTACAAATACTTATAATACTATAATAT
*
519387 TATTTGATTTTAATTCAG
131 TATTTGATTCTAATTCAG
* *
519405 TTCAGTTTATAAAATAGTTGACTCAAAATATTTTT-TATTTGAGTTTATAAAATTTAATTCAAGT
1 TTCAGTTTATAAAATAGTTGACTCAAAAT-TTTTTCGATTTGAGTTTATAAAATTTAAATCAAGT
*
519469 CAAATTGAATTGAATTTTCGAGTTTATGTTTAAATTTAATTATAAATACTTATAATACTATAATA
65 CAAATTGAATTGAATTTTCGAGTTTATGTTTAAATTTAATTACAAATACTTATAATACTATAATA
519534 TTATTTGATTCTAATT
130 TTATTTGATTCTAATT
519550 TAAATAGTTT
Statistics
Matches: 134, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
148 129 0.96
149 5 0.04
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.47
Consensus pattern (148 bp):
TTCAGTTTATAAAATAGTTGACTCAAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC
AAATTGAATTGAATTTTCGAGTTTATGTTTAAATTTAATTACAAATACTTATAATACTATAATAT
TATTTGATTCTAATTCAG
Found at i:520089 original size:36 final size:35
Alignment explanation
Indices: 520049--520129 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
520039 GGGGTTGGGC
* * *
520049 ATGTAATTGAAGTATTTTTGGAATTTGAGGTTTAGA
1 ATGTAATTGAAG-AATTTTGAAATTTGAGGTTTAAA
* *
520085 ATGTAATTAAAGAATTTTGAAATTTGGGGTTTAAA
1 ATGTAATTGAAGAATTTTGAAATTTGAGGTTTAAA
520120 ATGTAATTGA
1 ATGTAATTGA
520130 TGACTCTGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
35 28 0.72
36 11 0.28
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (35 bp):
ATGTAATTGAAGAATTTTGAAATTTGAGGTTTAAA
Found at i:526813 original size:13 final size:13
Alignment explanation
Indices: 526777--526811 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
526767 TTTATAAAAG
526777 TTTTCTCTTTCTC
1 TTTTCTCTTTCTC
526790 TTTTCTCTTTCTC
1 TTTTCTCTTTCTC
526803 TTTTC-CTTT
1 TTTTCTCTTT
526812 TCCAGTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTCTCTTTCTC
Found at i:531742 original size:23 final size:25
Alignment explanation
Indices: 531701--531752 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 25
531691 AAAAAATGTT
531701 GAAAAAAAAATAGCAGTTCGAAAAA
1 GAAAAAAAAATAGCAGTTCGAAAAA
*
531726 GAAAAAAAAA-A-CTGTTCGAAAAA
1 GAAAAAAAAATAGCAGTTCGAAAAA
531749 -AAAA
1 GAAAA
531753 GACATGAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 4 0.15
23 11 0.42
24 1 0.04
25 10 0.38
ACGTcount: A:0.67, C:0.08, G:0.13, T:0.12
Consensus pattern (25 bp):
GAAAAAAAAATAGCAGTTCGAAAAA
Found at i:534207 original size:24 final size:24
Alignment explanation
Indices: 534175--534223 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
534165 AGTCTTCCTG
534175 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
534199 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
534223 A
1 A
534224 GTGTCATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:547432 original size:20 final size:21
Alignment explanation
Indices: 547380--547440 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
547370 AAGACGGAGA
*
547380 AAAACATGCCACAAAGACATAT
1 AAAACATGTCACAAAGACA-AT
* *
547402 ATAAACGTGTCATAAAGAC-AT
1 A-AAACATGTCACAAAGACAAT
547423 AAAACATGTCACAAAGAC
1 AAAACATGTCACAAAGAC
547441 GTAATTAGTC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
20 15 0.45
21 3 0.09
22 1 0.03
23 14 0.42
ACGTcount: A:0.52, C:0.20, G:0.11, T:0.16
Consensus pattern (21 bp):
AAAACATGTCACAAAGACAAT
Found at i:549337 original size:25 final size:23
Alignment explanation
Indices: 549309--549379 Score: 83
Period size: 25 Copynumber: 3.0 Consensus size: 23
549299 TTAAATTCAT
549309 AATATTATATATATATTAACTTAAA
1 AATATT-T-TATATATTAACTTAAA
549334 AATATTTT-TATATTAACTTATTAA
1 AATATTTTATATATTAACTTA--AA
549358 ATATATTTTAT-TATTAACTTAA
1 A-ATATTTTATATATTAACTTAA
549380 TTTAAAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
22 12 0.29
23 2 0.05
24 4 0.10
25 23 0.55
26 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
AATATTTTATATATTAACTTAAA
Found at i:549348 original size:22 final size:23
Alignment explanation
Indices: 549320--549379 Score: 86
Period size: 22 Copynumber: 2.6 Consensus size: 23
549310 ATATTATATA
549320 TATATTAACTTAAAAATAT-TTT
1 TATATTAACTTAAAAATATATTT
*
549342 TATATTAACTTATTAAATATATTT
1 TATATTAACTTA-AAAATATATTT
549366 TATTATTAACTTAA
1 TA-TATTAACTTAA
549380 TTTAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 12 0.36
23 6 0.18
24 5 0.15
25 10 0.30
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (23 bp):
TATATTAACTTAAAAATATATTT
Found at i:549590 original size:31 final size:31
Alignment explanation
Indices: 549552--549626 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
549542 TAACCTGTGA
*
549552 TGACCACATCTTAATTAAATAAAAACGAAAG
1 TGACCACATCTTAAGTAAATAAAAACGAAAG
549583 TGACCACATCTTAAGTAAATAAAAACGAAAG
1 TGACCACATCTTAAGTAAATAAAAACGAAAG
* *
549614 TGATCATATCTTA
1 TGACCACATCTTA
549627 TGTTTTTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (31 bp):
TGACCACATCTTAAGTAAATAAAAACGAAAG
Found at i:554201 original size:23 final size:23
Alignment explanation
Indices: 554167--554231 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
554157 CACCATAACT
*
554167 CGTATAAATGCACCAAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
* * *
554190 CGTAGAATTGCACCTAAGTGCCG
1 CGTAGAAATGCACCAAAGTGCCA
*
554213 CGTAGAAATGCACCGAAGT
1 CGTAGAAATGCACCAAAGT
554232 TCCATATAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCAAAGTGCCA
Found at i:554518 original size:30 final size:29
Alignment explanation
Indices: 554465--554523 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
554455 TGTAAACATA
* *
554465 TCACATATTCATATAAACTCGTAGCTTCAT
1 TCACATATACATATAAACACGTAG-TTCAT
* *
554495 TCACATATACATTTAATCACGTAGTTCAT
1 TCACATATACATATAAACACGTAGTTCAT
554524 GTAAATTCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (29 bp):
TCACATATACATATAAACACGTAGTTCAT
Found at i:557885 original size:46 final size:46
Alignment explanation
Indices: 557815--557982 Score: 227
Period size: 46 Copynumber: 3.7 Consensus size: 46
557805 TAAAATAATT
*
557815 ATTTTTAACATTTTTACTACAAATACTAAATCAATATTATTTTAAC
1 ATTTTTAACATTTTTACTAGAAATACTAAATCAATATTATTTTAAC
*
557861 ATTTTTAACTTTTTTACTAGAAATACTAAATCAATATTATTTTAAC
1 ATTTTTAACATTTTTACTAGAAATACTAAATCAATATTATTTTAAC
* *
557907 ATTTTTAACAGTTTTACAAGAAATACT-AATCAA-ATT-TTGATCTAA-
1 ATTTTTAACATTTTTACTAGAAATACTAAATCAATATTATT--T-TAAC
*
557952 TTATTTTAACATTTTTACTAGAAATACTAAA
1 AT-TTTTAACATTTTTACTAGAAATACTAAA
557983 GGAATAATAA
Statistics
Matches: 109, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
43 2 0.02
44 3 0.03
45 8 0.07
46 94 0.86
47 2 0.02
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.45
Consensus pattern (46 bp):
ATTTTTAACATTTTTACTAGAAATACTAAATCAATATTATTTTAAC
Found at i:559869 original size:113 final size:111
Alignment explanation
Indices: 559567--560372 Score: 659
Period size: 113 Copynumber: 7.4 Consensus size: 111
559557 TCATTTTTAA
*
559567 TTTTT-ATTTGAAATATAAATTAATTAGATTATTTATTTTGAATTTT-CAGATTAAATTGTATTT
1 TTTTTAATTT-AAATAT-AATT-ATTAGACTATTTATTTT-AATTTTACAGATTAAATTGTATTT
* * *
559630 GAATGGATTGATAA-TTTAAATTTAAATTTTCGTGTAATTTTTAGTATAATTTTT
62 GAGTGGTTTGGTAAGTTT-AATTTAAATTTT-GTGTAATTTTTAGTATAA---TT
* * * *
559684 GTTTTTAATTTAAATTATAATGATTAGACTATTTATTTTGATTTTACAGATTAAACTGTATTCGA
1 -TTTTTAATTTAAA-TATAATTATTAGACTATTTATTTTAATTTTACAGATTAAATTGTATTTGA
*
559749 GTGGTTTGGTAAGTTAAATTTAAATTTTCGTGTAATTTTTAGTATAATT
64 GTGGTTTGGTAAGTTTAATTTAAATTTT-GTGTAATTTTTAGTATAATT
* * * *
559798 TTTTTAATTTAAACTATAATTATTATACTATTTATTTTAATTTTACATAATAAGTTGTATTTGAG
1 TTTTTAATTTAAA-TATAATTATTAGACTATTTATTTTAATTTTACAGATTAAATTGTATTTGAG
* * * *
559863 TAGTTTGGTAAGTTCAGTTTAAA-----T-T-ATTATTA-T-T--TT
65 TGGTTTGGTAAGTTTAATTTAAATTTTGTGTAATTTTTAGTATAATT
* * * * * *
559899 TTATTGA-GTAATATA-AATTATTAGACTAATTATTTTTATTTTACAGATTAAATCGTATTTGAG
1 TTTTTAATTTAA-ATATAATTATTAGACTATTTATTTTAATTTTACAGATTAAATTGTATTTGAG
* * *
559962 TGGTTTGGTAAGTTTAGTTTAAA--TT-T-T-ATTGTTTCGT-T-TTT
65 TGGTTTGGTAAGTTTAATTTAAATTTTGTGTAATT-TTTAGTATAATT
* * *
560003 TGTTTTTATTGTAAATATAAATTAATTAGACTATTTTATTTTGATTTTATAGATTAAATTGTATT
1 T-TTTTAATT-TAAATAT-AATT-ATTAGACTA-TTTATTTTAATTTTACAGATTAAATTGTATT
*
560068 TGAGTGGTTTGGTAAGTTTAATTTAAATTTTAGTGTAAATTTTAGTATAATT
61 TGAGTGGTTTGGTAAGTTTAATTTAAATTTT-GTGTAATTTTTAGTATAATT
* *
560120 TTTTTAATTTAAATTATAATTATTAGACTATTTATTTTAATTTTACACATTAAGTTGTATTTGAG
1 TTTTTAATTTAAA-TATAATTATTAGACTATTTATTTTAATTTTACAGATTAAATTGTATTTGAG
* * *
560185 TGGTTTGGTAGGTTTAGTTTAAA---T-TAT-ATTTTTA-T-T--TT
65 TGGTTTGGTAAGTTTAATTTAAATTTTGTGTAATTTTTAGTATAATT
* * * * * *
560223 TCTATTGA-GTAATATA-AATTATTAGACTAATTATTTTTATTTTATAGATTAAATTGTATTTGA
1 T-TTTTAATTTAA-ATATAATTATTAGACTATTTATTTTAATTTTACAGATTAAATTGTATTTGA
* * * *
560286 GTAGTTTGGTAAGTTTAGTTTAAATTTTAT-T--GTTTTA-T-T-ATT
64 GTGGTTTGGTAAGTTTAATTTAAATTTTGTGTAATTTTTAGTATAATT
*
560328 TTTTGT-ATTGTAAATATAAATTAATTAGACTATTTATTTTGATTT
1 TTTT-TAATT-TAAATAT-AATT-ATTAGACTATTTATTTTAATTT
560373 AACATATTTT
Statistics
Matches: 578, Mismatches: 71, Indels: 88
0.78 0.10 0.12
Matches are distributed among these distances:
99 62 0.11
100 5 0.01
101 13 0.02
102 66 0.11
103 11 0.02
104 19 0.03
105 20 0.03
106 9 0.02
107 14 0.02
108 26 0.04
109 9 0.02
110 54 0.09
112 2 0.00
113 128 0.22
114 12 0.02
115 14 0.02
116 18 0.03
117 76 0.13
118 13 0.02
119 7 0.01
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.54
Consensus pattern (111 bp):
TTTTTAATTTAAATATAATTATTAGACTATTTATTTTAATTTTACAGATTAAATTGTATTTGAGT
GGTTTGGTAAGTTTAATTTAAATTTTGTGTAATTTTTAGTATAATT
Found at i:559918 original size:99 final size:98
Alignment explanation
Indices: 559815--560372 Score: 495
Period size: 99 Copynumber: 5.3 Consensus size: 98
559805 TTTAAACTAT
* * * * * *
559815 AATTATTATACTATTTATTTTAATTTTACATAATAAGTTGTATTTGAGTAGTTTGGTAAGTTCAG
1 AATTATTAGACTATTTATTTTAATTTTACAGATTAAATTGTATTTGAGTGGTTTGGTAAGTTTAG
559880 TTTAAATTATTATTATTTTTTATTGAGTAATATA
66 TTTAAATT-TTATTATTTTTTATTGAGTAATATA
* * *
559914 AATTATTAGACTAATTATTTTTATTTTACAGATTAAATCGTATTTGAGTGGTTTGGTAAGTTTAG
1 AATTATTAGACTATTTATTTTAATTTTACAGATTAAATTGTATTTGAGTGGTTTGGTAAGTTTAG
* *
559979 TTTAAATTTTATTGTTTCGTTTTTTGTTTTTATTGTAAATATA
66 TTTAAATTTTATTATTT--TTTATTG-----A--GT-AATATA
* *
560022 AATTAATTAGACTATTTTATTTTGATTTTATAGATTAAATTGTATTTGAGTGGTTTGGTAAGTTT
1 AATT-ATTAGACTA-TTTATTTTAATTTTACAGATTAAATTGTATTTGAGTGGTTTGGTAAGTTT
* ***
560087 AATTTAAATTTTAGTGTAAATTTTAGTATAATTTTTTTAATTTAAATTA
64 AGTTTAAATTTTA-T-T--ATTTT--T-T-A-TTGAGTAA--T--A-TA
* * *
560136 TAATTATTAGACTATTTATTTTAATTTTACACATTAAGTTGTATTTGAGTGGTTTGGTAGGTTTA
1 -AATTATTAGACTATTTATTTTAATTTTACAGATTAAATTGTATTTGAGTGGTTTGGTAAGTTTA
*
560201 GTTTAAATTATATTTTTATTTTTCTATTGAGTAATATA
65 GTTTAAA-T-T-TTATTATTTTT-TATTGAGTAATATA
* * * *
560239 AATTATTAGACTAATTATTTTTATTTTATAGATTAAATTGTATTTGAGTAGTTTGGTAAGTTTAG
1 AATTATTAGACTATTTATTTTAATTTTACAGATTAAATTGTATTTGAGTGGTTTGGTAAGTTTAG
*
560304 TTTAAATTTTATTGTTTTATTATTTTTTGTATTGTAAATATA
66 TTTAAATTTTATTATTTT-TTA----TTG-A--GT-AATATA
*
560346 AATTAATTAGACTATTTATTTTGATTT
1 AATT-ATTAGACTATTTATTTTAATTT
560373 AACATATTTT
Statistics
Matches: 376, Mismatches: 43, Indels: 71
0.77 0.09 0.14
Matches are distributed among these distances:
98 8 0.02
99 74 0.20
100 8 0.02
101 1 0.00
102 64 0.17
103 5 0.01
104 2 0.01
105 1 0.00
106 3 0.01
107 12 0.03
108 35 0.09
109 12 0.03
110 61 0.16
111 2 0.01
112 7 0.02
113 53 0.14
114 17 0.05
115 7 0.02
116 2 0.01
117 2 0.01
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.54
Consensus pattern (98 bp):
AATTATTAGACTATTTATTTTAATTTTACAGATTAAATTGTATTTGAGTGGTTTGGTAAGTTTAG
TTTAAATTTTATTATTTTTTATTGAGTAATATA
Found at i:560159 original size:322 final size:324
Alignment explanation
Indices: 559679--560372 Score: 1114
Period size: 322 Copynumber: 2.2 Consensus size: 324
559669 TTTAGTATAA
*
559679 TTTTTGTTTTTAATT-TAAAT-TATAA-TGATTAGACTATTTATTTTGATTTTACAGATTAAACT
1 TTTTTGTTTTT-ATTGTAAATATA-AATTAATTAGACTATTTATTTTGATTTTACAGATTAAACT
* *
559741 GTATTCGAGTGGTTTGGTAAGTTAAATTTAAATTTTCGTGTAATTTTTAGTATAATTTTTTTAAT
64 GTATTCGAGTGGTTTGGTAAGTTAAATTTAAATTTTAGTGTAAATTTTAGTATAATTTTTTTAAT
* *
559806 TTAAACTATAATTATTATACTATTTATTTTAATTTTACATAATAAGTTGTATTTGAGTAGTTTGG
129 TTAAACTATAATTATTAGACTATTTATTTTAATTTTACACAATAAGTTGTATTTGAGTAGTTTGG
559871 TAAGTTCAGTTTAAA-T-TATTATTATTTTT-TATTGAGTAATATAAATTATTAGACTAATTATT
194 TAAGTTCAGTTTAAATTATATTATTATTTTTCTATTGAGTAATATAAATTATTAGACTAATTATT
* *
559933 TTTATTTTACAGATTAAATCGTATTTGAGTGGTTTGGTAAGTTTAGTTTAAATTTTATTGTTTCG
259 TTTATTTTACAGATTAAATCGTATTTGAGTAGTTTGGTAAGTTTAGTTTAAATTTTATTGTTTCA
559998 T
324 T
* *
559999 TTTTTGTTTTTATTGTAAATATAAATTAATTAGACTATTTTATTTTGATTTTATAGATTAAATTG
1 TTTTTGTTTTTATTGTAAATATAAATTAATTAGACTA-TTTATTTTGATTTTACAGATTAAACTG
* *
560064 TATTTGAGTGGTTTGGTAAGTTTAATTTAAATTTTAGTGTAAATTTTAGTATAATTTTTTTAATT
65 TATTCGAGTGGTTTGGTAAGTTAAATTTAAATTTTAGTGTAAATTTTAGTATAATTTTTTTAATT
* * *
560129 TAAATTATAATTATTAGACTATTTATTTTAATTTTACACATTAAGTTGTATTTGAGTGGTTTGGT
130 TAAACTATAATTATTAGACTATTTATTTTAATTTTACACAATAAGTTGTATTTGAGTAGTTTGGT
* * *
560194 AGGTTTAGTTTAAATTATATTTTTATTTTTCTATTGAGTAATATAAATTATTAGACTAATTATTT
195 AAGTTCAGTTTAAATTATATTATTATTTTTCTATTGAGTAATATAAATTATTAGACTAATTATTT
* * *
560259 TTATTTTATAGATTAAATTGTATTTGAGTAGTTTGGTAAGTTTAGTTTAAATTTTATTGTTTTAT
260 TTATTTTACAGATTAAATCGTATTTGAGTAGTTTGGTAAGTTTAGTTTAAATTTTATTGTTTCAT
* *
560324 TATTT-TTTGTATTGTAAATATAAATTAATTAGACTATTTATTTTGATTT
1 TTTTTGTTTTTATTGTAAATATAAATTAATTAGACTATTTATTTTGATTT
560373 AACATATTTT
Statistics
Matches: 345, Mismatches: 22, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
319 3 0.01
320 18 0.05
321 12 0.03
322 158 0.46
323 14 0.04
324 42 0.12
325 98 0.28
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.54
Consensus pattern (324 bp):
TTTTTGTTTTTATTGTAAATATAAATTAATTAGACTATTTATTTTGATTTTACAGATTAAACTGT
ATTCGAGTGGTTTGGTAAGTTAAATTTAAATTTTAGTGTAAATTTTAGTATAATTTTTTTAATTT
AAACTATAATTATTAGACTATTTATTTTAATTTTACACAATAAGTTGTATTTGAGTAGTTTGGTA
AGTTCAGTTTAAATTATATTATTATTTTTCTATTGAGTAATATAAATTATTAGACTAATTATTTT
TATTTTACAGATTAAATCGTATTTGAGTAGTTTGGTAAGTTTAGTTTAAATTTTATTGTTTCAT
Found at i:562523 original size:23 final size:23
Alignment explanation
Indices: 562496--562539 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
562486 ATATTAAATA
*
562496 AAATATTGATATTATTCACATAG
1 AAATATTGATATTAATCACATAG
562519 AAATATTGATATTAATCACAT
1 AAATATTGATATTAATCACAT
562540 TCATTCAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (23 bp):
AAATATTGATATTAATCACATAG
Found at i:562599 original size:27 final size:27
Alignment explanation
Indices: 562569--562668 Score: 200
Period size: 27 Copynumber: 3.7 Consensus size: 27
562559 ACAAATATCC
562569 ATCACATTCATTCAAATATTGATATTA
1 ATCACATTCATTCAAATATTGATATTA
562596 ATCACATTCATTCAAATATTGATATTA
1 ATCACATTCATTCAAATATTGATATTA
562623 ATCACATTCATTCAAATATTGATATTA
1 ATCACATTCATTCAAATATTGATATTA
562650 ATCACATTCATTCAAATAT
1 ATCACATTCATTCAAATAT
562669 AACATTAACA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 73 1.00
ACGTcount: A:0.41, C:0.16, G:0.03, T:0.40
Consensus pattern (27 bp):
ATCACATTCATTCAAATATTGATATTA
Found at i:565436 original size:16 final size:16
Alignment explanation
Indices: 565415--565453 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
565405 AACAATTTGC
565415 ATATTAGATTAAAATT
1 ATATTAGATTAAAATT
*
565431 ATATTAGATTAAAGTT
1 ATATTAGATTAAAATT
565447 ACTATTA
1 A-TATTA
565454 TTAATAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (16 bp):
ATATTAGATTAAAATT
Found at i:570756 original size:12 final size:11
Alignment explanation
Indices: 570726--570759 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
570716 GCCGTCCGTC
570726 TCGGGTCG-GG
1 TCGGGTCGTGG
570736 TCGGGTCGTGG
1 TCGGGTCGTGG
570747 TCGTGGTCGTGG
1 TCG-GGTCGTGG
570759 T
1 T
570760 AATACGTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 5 0.23
12 9 0.41
ACGTcount: A:0.00, C:0.18, G:0.53, T:0.29
Consensus pattern (11 bp):
TCGGGTCGTGG
Found at i:570868 original size:19 final size:19
Alignment explanation
Indices: 570844--570890 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
570834 TAACGAATTT
570844 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
570863 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
570882 TCGCAACGA
1 TCGCAACGA
570891 CAACTTTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:570911 original size:41 final size:40
Alignment explanation
Indices: 570862--571125 Score: 159
Period size: 41 Copynumber: 6.7 Consensus size: 40
570852 AATTTGGAAA
570862 ATCGCAACGAATTTGGAAAATCGCAACGACAACTTTAGACT
1 ATCGCAACGAATTTGGAAAATCGCAACGACAAC-TTAGACT
* ** * * **
570903 ATCGCAACGCGATTTTCAACTATCGCAAC-ACGAAC-TGGAAA
1 ATCGCAACG-AATTTGGAA-AATCGCAACGAC-AACTTAGACT
* * *
570944 ATCGCAACGCGAA-ATGGAAAATCGCAACG-CGA-TTATCAACT
1 ATCGCAA--CGAATTTGGAAAATCGCAACGACAACTTA--GACT
*
570985 ATCGCAACGCGAA-CTGGAAAATCGCAACG----C---G---
1 ATCGCAA--CGAATTTGGAAAATCGCAACGACAACTTAGACT
571016 A-CGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACT
1 ATCGCAACGAATTTGGAAAATCGCAACGACAACT-TAGACT
*
571056 ATCGCAACGAATTTGGAAAATAGCAACGACAACTGTAGACT
1 ATCGCAACGAATTTGGAAAATCGCAACGACAACT-TAGACT
*
571097 ATCGCAACGCGAA-CTGGAAAATCGCAACG
1 ATCGCAA--CGAATTTGGAAAATCGCAACG
571126 CGAAATGGAA
Statistics
Matches: 175, Mismatches: 23, Indels: 49
0.71 0.09 0.20
Matches are distributed among these distances:
28 4 0.02
29 15 0.09
30 5 0.03
31 1 0.01
33 1 0.01
37 1 0.01
39 2 0.01
40 10 0.06
41 96 0.55
42 23 0.13
43 17 0.10
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (40 bp):
ATCGCAACGAATTTGGAAAATCGCAACGACAACTTAGACT
Found at i:570926 original size:21 final size:21
Alignment explanation
Indices: 570900--571016 Score: 80
Period size: 20 Copynumber: 5.7 Consensus size: 21
570890 ACAACTTTAG
* *
570900 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAATTGCA
* * *
570921 ACTATCGCAACACGAACTGGA
1 ACTATCGCAACGCGAATTGCA
* * *
570942 A-AATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAATTGCA
* *
570962 A-AATCGCAACGCG-ATTATCA
1 ACTATCGCAACGCGAATT-GCA
* *
570982 ACTATCGCAACGCGAACTGGA
1 ACTATCGCAACGCGAATTGCA
*
571003 A-AATCGCAACGCGA
1 ACTATCGCAACGCGA
571017 CGCAACGAAT
Statistics
Matches: 77, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
19 2 0.03
20 43 0.56
21 30 0.39
22 2 0.03
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.16
Consensus pattern (21 bp):
ACTATCGCAACGCGAATTGCA
Found at i:571041 original size:19 final size:19
Alignment explanation
Indices: 571017--571084 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
571007 CGCAACGCGA
571017 CGCAACGAATTTGGAAAAT
1 CGCAACGAATTTGGAAAAT
* * **
571036 CGCAACGACAACTGTAGACTAT
1 CGCAACG--AA-TTTGGAAAAT
571058 CGCAACGAATTTGGAAAAT
1 CGCAACGAATTTGGAAAAT
*
571077 AGCAACGA
1 CGCAACGA
571085 CAACTGTAGA
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 20 0.54
20 2 0.05
21 2 0.05
22 13 0.35
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.18
Consensus pattern (19 bp):
CGCAACGAATTTGGAAAAT
Found at i:571062 original size:22 final size:22
Alignment explanation
Indices: 571034--571105 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
571024 AATTTGGAAA
571034 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
571056 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
571075 ATAGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
571097 ATCGCAACG
1 ATCGCAACG
571106 CGAACTGGAA
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 12 0.32
20 2 0.05
21 2 0.05
22 21 0.57
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:571148 original size:20 final size:20
Alignment explanation
Indices: 570924--571148 Score: 109
Period size: 20 Copynumber: 10.6 Consensus size: 20
570914 ATTTTCAACT
* *
570924 ATCGCAACACGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
570944 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * *
570964 ATCGCAACGCGATTAT-CAACT
1 ATCGCAACGCGA-AATGGAA-A
*
570985 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
571005 ATCGCAACGCGACGCAACGAATTTGGAAA
1 ATCGCAA--CG-CG--A--AA--TGGAAA
* **
571034 ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAAATG--GAAA
*
571056 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAA-ATGGAAA
* * **
571075 ATAGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAAATG--GAAA
*
571097 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
571117 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
571137 ATCGCAATGCGA
1 ATCGCAACGCGA
571149 TTTTCAACTA
Statistics
Matches: 158, Mismatches: 25, Indels: 44
0.70 0.11 0.19
Matches are distributed among these distances:
19 9 0.06
20 78 0.49
21 21 0.13
22 28 0.18
23 2 0.01
24 1 0.01
25 1 0.01
27 5 0.03
29 13 0.08
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:571163 original size:21 final size:21
Alignment explanation
Indices: 571137--571186 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
571127 GAAATGGAAA
*
571137 ATCGCAATGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
571158 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
571179 ATCGCAAC
1 ATCGCAAC
571187 ACGAAATGCA
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:0.26, G:0.14, T:0.30
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:585556 original size:36 final size:36
Alignment explanation
Indices: 585509--585647 Score: 199
Period size: 36 Copynumber: 3.9 Consensus size: 36
585499 TGAATAAGAA
* * *
585509 GAACGAAAGGAAGCATCGACACTTTTGATTCAAATC
1 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGTC
585545 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGTC
1 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGTC
* *
585581 GAACGGAAGGAAGCATCGGCACTTTCGATTTAAGTC
1 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGTC
* * *
585617 GAACGGAATGAGGCGTCG-CACTTTCGATTCA
1 GAACGGAAGGAAGCATCGACACTTTCGATTCA
585648 GGTGTTCATC
Statistics
Matches: 94, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 12 0.13
36 82 0.87
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (36 bp):
GAACGGAAGGAAGCATCGACACTTTCGATTCAAGTC
Found at i:593690 original size:15 final size:16
Alignment explanation
Indices: 593665--593694 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
593655 CATGGTCTGT
593665 TAAGTTCGGGTACCCG
1 TAAGTTCGGGTACCCG
593681 TAAG-TCGGGTACCC
1 TAAGTTCGGGTACCC
593695 ATAAAACCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.20, C:0.27, G:0.30, T:0.23
Consensus pattern (16 bp):
TAAGTTCGGGTACCCG
Found at i:597244 original size:26 final size:25
Alignment explanation
Indices: 597205--597254 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
597195 CCTCCCTTTT
597205 TTTTAAACAAAAACTCTA-CCAATTC
1 TTTTAAACAAAAACTC-ACCCAATTC
*
597230 TTTTAAATCACAAACTCACCCAATT
1 TTTTAAA-CAAAAACTCACCCAATT
597255 AAATTCCCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.42, C:0.26, G:0.00, T:0.32
Consensus pattern (25 bp):
TTTTAAACAAAAACTCACCCAATTC
Found at i:601517 original size:21 final size:19
Alignment explanation
Indices: 601479--601534 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
601469 TGGTTTTATA
601479 AAGTTATTCTTTTCTTTATTTT
1 AAGTT-TTC-TTT-TTTATTTT
*
601501 CAGGTTTTCATTTTTTATTTT
1 -AAGTTTTC-TTTTTTATTTT
601522 AAGTTTTCTTTTT
1 AAGTTTTCTTTTT
601535 AAATATGTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 5 0.17
20 7 0.23
21 8 0.27
22 6 0.20
23 4 0.13
ACGTcount: A:0.16, C:0.09, G:0.07, T:0.68
Consensus pattern (19 bp):
AAGTTTTCTTTTTTATTTT
Found at i:603192 original size:31 final size:31
Alignment explanation
Indices: 603157--603219 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
603147 TATTCGGTGA
603157 ATTCAATATGTCCTTCTCACTAGAAACTCTC
1 ATTCAATATGTCCTTCTCACTAGAAACTCTC
*
603188 ATTCAATATGTCCTTCTCACTAGGAACTCTC
1 ATTCAATATGTCCTTCTCACTAGAAACTCTC
603219 A
1 A
603220 AACTCTTGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.35
Consensus pattern (31 bp):
ATTCAATATGTCCTTCTCACTAGAAACTCTC
Found at i:605863 original size:13 final size:13
Alignment explanation
Indices: 605845--605873 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
605835 ACATATTAAA
605845 TCATGTTTGCAAT
1 TCATGTTTGCAAT
605858 TCATGTTTGCAAT
1 TCATGTTTGCAAT
605871 TCA
1 TCA
605874 AATACCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (13 bp):
TCATGTTTGCAAT
Found at i:609428 original size:18 final size:18
Alignment explanation
Indices: 609405--609440 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
609395 CGTTTACACC
609405 ATTGAAATATAGATTCTA
1 ATTGAAATATAGATTCTA
609423 ATTGAAATATAGATTCTA
1 ATTGAAATATAGATTCTA
609441 CTACGAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (18 bp):
ATTGAAATATAGATTCTA
Found at i:609608 original size:70 final size:70
Alignment explanation
Indices: 609495--609634 Score: 271
Period size: 70 Copynumber: 2.0 Consensus size: 70
609485 ACAATTTATA
*
609495 GTGAATTTTTAAAGTTGACCTACATAAGCTGTTTGAACAGAATCTGCTGCCATTTTTTCTAACCT
1 GTGAATTTTTAAAGTTGACCTACATAAGATGTTTGAACAGAATCTGCTGCCATTTTTTCTAACCT
609560 ATCAT
66 ATCAT
609565 GTGAATTTTTAAAGTTGACCTACATAAGATGTTTGAACAGAATCTGCTGCCATTTTTTCTAACCT
1 GTGAATTTTTAAAGTTGACCTACATAAGATGTTTGAACAGAATCTGCTGCCATTTTTTCTAACCT
609630 ATCAT
66 ATCAT
609635 CGGTTAAAAA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (70 bp):
GTGAATTTTTAAAGTTGACCTACATAAGATGTTTGAACAGAATCTGCTGCCATTTTTTCTAACCT
ATCAT
Found at i:612296 original size:18 final size:21
Alignment explanation
Indices: 612254--612297 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 21
612244 TAAAGGTGAG
*
612254 AATAAATAAATAAAGTTTCAA
1 AATAAATAAATAAACTTTCAA
612275 AATAAAT-AA-AAACTTT-AA
1 AATAAATAAATAAACTTTCAA
612293 AATAA
1 AATAA
612298 TTCAGATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 6 0.27
20 2 0.09
21 7 0.32
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (21 bp):
AATAAATAAATAAACTTTCAA
Found at i:613711 original size:19 final size:19
Alignment explanation
Indices: 613687--613724 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
613677 GGTTCCAAAC
613687 AACTTTCCAATCTTAATTT
1 AACTTTCCAATCTTAATTT
613706 AACTTTCCAATCTTAATTT
1 AACTTTCCAATCTTAATTT
613725 TATTGCATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (19 bp):
AACTTTCCAATCTTAATTT
Found at i:616196 original size:3 final size:3
Alignment explanation
Indices: 616188--616225 Score: 58
Period size: 3 Copynumber: 12.0 Consensus size: 3
616178 AATATTAAAG
616188 ATA ATA ATA ATA ATA ATA ATA ATA ATA TATA ATTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA A-TA ATA
616226 TTTATAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 27 0.82
4 6 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:616510 original size:51 final size:51
Alignment explanation
Indices: 616452--616800 Score: 405
Period size: 55 Copynumber: 6.6 Consensus size: 51
616442 ACAGGTTCGT
616452 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACGTGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACGTGTCCGC
616503 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACGTGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACGTGTCCGC
* *
616554 TCCCTATTTCTTCAGAGAGTATATGACTCAATCTTCAACAAACGTGTCCGC
1 TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACGTGTCCGC
* * * **
616605 TCCCTATTCCTTCAGAGAGTATAGGAATTTAACAATCTTCAACAAACATATCTAC
1 TCCCTATTCCTTCAGAGAGTATAGG-A-CT--CAATCTTCAACAAACGTGTCCGC
* * * *
616660 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAAGCTTCAACAATCGTGTCTGC
1 TCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACAAACGTGTCCGC
* * * **
616715 TCCCTATTCCTTCAG-GAAGTATAGAACTCGAACAAGCTTCAACAATCGTGTATGC
1 TCCCTATTCCTTCAGAG-AGTATAGGACT----CAATCTTCAACAAACGTGTCCGC
*
616770 TCCCTATTCCTTCAG-GAAGTATAGAACTCAA
1 TCCCTATTCCTTCAGAG-AGTATAGGACTCAA
616801 ATACATTCTG
Statistics
Matches: 272, Mismatches: 19, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
51 126 0.46
52 1 0.00
53 2 0.01
54 2 0.01
55 141 0.52
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (51 bp):
TCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACGTGTCCGC
Found at i:616850 original size:54 final size:53
Alignment explanation
Indices: 616787--616970 Score: 253
Period size: 54 Copynumber: 3.4 Consensus size: 53
616777 TCCTTCAGGA
* * *
616787 AGTATAGAACTCAA-ATACATTCTGCAAACGAGTTCGCTCCCTCTTTCTCTAAGG
1 AGTATAGAACTCAACAT-C-TTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGG
*
616841 AGTATAGAACTCAGACATCTTCTTCAAACGGGTTTGCTCCCTCTTTCTCTAGGG
1 AGTATAGAACTCA-ACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGG
* *
616895 AGTATGGAACTCGAACATCTTCTTCAAACGGGCTCGCTCCCTCTTTCTCTAGGG
1 AGTATAGAACTC-AACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGG
*
616949 AGTATGGAACTCGAACATCTTC
1 AGTATAGAACTC-AACATCTTC
616971 ATATGCTCCA
Statistics
Matches: 120, Mismatches: 7, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
54 115 0.96
55 3 0.03
56 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (53 bp):
AGTATAGAACTCAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGG
Found at i:618137 original size:18 final size:19
Alignment explanation
Indices: 618115--618190 Score: 68
Period size: 19 Copynumber: 3.9 Consensus size: 19
618105 GAACCCTCCC
618115 TTTTTCTTCCTTTTTTTT-G
1 TTTTT-TTCCTTTTTTTTAG
** *
618134 TTTTTTTTATTTTTTTTAT
1 TTTTTTTCCTTTTTTTTAG
618153 TTTTTTTCCTTTTTTTCT--
1 TTTTTTTCCTTTTTTT-TAG
618171 TTTTTTTCCCCTTTTTTTTA
1 TTTTTTT--CCTTTTTTTTA
618191 AGCAAAATAC
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 17 0.36
19 20 0.43
20 10 0.21
ACGTcount: A:0.04, C:0.13, G:0.01, T:0.82
Consensus pattern (19 bp):
TTTTTTTCCTTTTTTTTAG
Found at i:618178 original size:9 final size:9
Alignment explanation
Indices: 618114--618178 Score: 76
Period size: 9 Copynumber: 7.1 Consensus size: 9
618104 TGAACCCTCC
*
618114 CTTTTTCTTC
1 CTTTTT-TTT
618124 CTTTTTTTT
1 CTTTTTTTT
*
618133 GTTTTTTTT
1 CTTTTTTTT
*
618142 ATTTTTTTT
1 CTTTTTTTT
*
618151 ATTTTTTTT
1 CTTTTTTTT
*
618160 CCTTTTTTT
1 CTTTTTTTT
618169 CTTTTTTTT
1 CTTTTTTTT
618178 C
1 C
618179 CCCTTTTTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
9 43 0.88
10 6 0.12
ACGTcount: A:0.03, C:0.12, G:0.02, T:0.83
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:618189 original size:1 final size:1
Alignment explanation
Indices: 618125--618177 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
618115 TTTTTCTTCC
* * * ** *
618125 TTTTTTTTGTTTTTTTTATTTTTTTTATTTTTTTTCCTTTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
618178 CCCCTTTTTT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.04, C:0.06, G:0.02, T:0.89
Consensus pattern (1 bp):
T
Found at i:632538 original size:4 final size:4
Alignment explanation
Indices: 632529--632553 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
632519 AGATGAAAAT
632529 TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA T
632554 TAGGATAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:633253 original size:19 final size:19
Alignment explanation
Indices: 633229--633265 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
633219 AATAATATCC
*
633229 TAAAACTTAATTAAAATAT
1 TAAAACCTAATTAAAATAT
*
633248 TAAAACCTAGTTAAAATA
1 TAAAACCTAATTAAAATA
633266 AAATACCTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.32
Consensus pattern (19 bp):
TAAAACCTAATTAAAATAT
Found at i:638035 original size:20 final size:20
Alignment explanation
Indices: 637994--638043 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
637984 AAAATAGTCC
* * *
637994 AATTTC-ACATTCTAACATA
1 AATTTCAACACTCAAACAGA
638013 AATTTCAACACTCAAACAGA
1 AATTTCAACACTCAAACAGA
638033 AATTTCCAACA
1 AATTT-CAACA
638044 TAGTACAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 6 0.23
20 15 0.58
21 5 0.19
ACGTcount: A:0.46, C:0.24, G:0.02, T:0.28
Consensus pattern (20 bp):
AATTTCAACACTCAAACAGA
Found at i:640411 original size:87 final size:87
Alignment explanation
Indices: 640262--640435 Score: 305
Period size: 87 Copynumber: 2.0 Consensus size: 87
640252 ATATACAAAC
*
640262 AAATAACATGTCGGGATAATGTTGTTTTAGATTTTTTTACCAAATTTCAAAATGATTCCCATCTG
1 AAATAACATGTAGGGATAATGTTGTTTTAGATTTTTTTACCAAATTTCAAAATGATTCCCATCTG
640327 AAAGGACT-GCTGACCAACTCAA
66 AAAGGA-TAGCTGACCAACTCAA
* *
640349 AAATAACATGTAGGGATAATGTTGTTTTAGATTTTTTTACTAAATTTCAAAATGATTTCCATCTG
1 AAATAACATGTAGGGATAATGTTGTTTTAGATTTTTTTACCAAATTTCAAAATGATTCCCATCTG
640414 AAAGGATAGCTGACCAACTCAA
66 AAAGGATAGCTGACCAACTCAA
640436 TTATACTATG
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
86 1 0.01
87 82 0.99
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (87 bp):
AAATAACATGTAGGGATAATGTTGTTTTAGATTTTTTTACCAAATTTCAAAATGATTCCCATCTG
AAAGGATAGCTGACCAACTCAA
Found at i:641397 original size:14 final size:14
Alignment explanation
Indices: 641378--641410 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
641368 TATTTTTAAA
641378 TAAAAAACTGTTAT
1 TAAAAAACTGTTAT
*
641392 TAAAAAATTGTTAT
1 TAAAAAACTGTTAT
641406 TAAAA
1 TAAAA
641411 TAAATAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (14 bp):
TAAAAAACTGTTAT
Found at i:641845 original size:21 final size:21
Alignment explanation
Indices: 641816--641865 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
641806 CGTTATAATC
* *
641816 CATCATAAATCGTCACAGT-AA
1 CATCGTAAACCGTCACA-TCAA
641837 CATCGTAAACCGTCACATCAA
1 CATCGTAAACCGTCACATCAA
641858 CATCGTAA
1 CATCGTAA
641866 TGGTTAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.40, C:0.28, G:0.10, T:0.22
Consensus pattern (21 bp):
CATCGTAAACCGTCACATCAA
Found at i:642358 original size:20 final size:20
Alignment explanation
Indices: 642333--642370 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
642323 CCAAATTCGC
642333 AACGCGAATCTGTAAATCAT
1 AACGCGAATCTGTAAATCAT
*
642353 AACGCGAATTTGTAAATC
1 AACGCGAATCTGTAAATC
642371 GCAACACAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.26
Consensus pattern (20 bp):
AACGCGAATCTGTAAATCAT
Found at i:642448 original size:20 final size:20
Alignment explanation
Indices: 642414--642488 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
642404 ACAATGCGAT
**
642414 AGTCAAATTTACAACACAAA
1 AGTCAAATTCGCAACACAAA
* *
642434 AGTCAAATTCGCAACGCGAATC
1 AGTCAAATTCGCAACAC-AA-A
* *
642456 TGT-AAA-TCGCAACACAGA
1 AGTCAAATTCGCAACACAAA
642474 AGTCAAATTCGCAAC
1 AGTCAAATTCGCAAC
642489 TGAATTTCAA
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
18 2 0.05
19 4 0.10
20 29 0.69
21 5 0.12
22 2 0.05
ACGTcount: A:0.44, C:0.24, G:0.13, T:0.19
Consensus pattern (20 bp):
AGTCAAATTCGCAACACAAA
Found at i:642527 original size:38 final size:40
Alignment explanation
Indices: 642476--642565 Score: 114
Period size: 39 Copynumber: 2.3 Consensus size: 40
642466 AACACAGAAG
*
642476 TCAAATTCGCAAC-TGAATTTCAAATTCCCAAC-TGAATT
1 TCAAATTCGCAACTTGAATTTCAAATTCCCAACACGAATT
* * *
642514 TCAAATTCGCAACTTGATTTTCGAATTCGCAACACGAATT
1 TCAAATTCGCAACTTGAATTTCAAATTCCCAACACGAATT
*
642554 T-AATTTCGCAAC
1 TCAAATTCGCAAC
642566 AGGTTTTAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 13 0.29
39 26 0.58
40 6 0.13
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.32
Consensus pattern (40 bp):
TCAAATTCGCAACTTGAATTTCAAATTCCCAACACGAATT
Found at i:642540 original size:20 final size:19
Alignment explanation
Indices: 642476--642565 Score: 110
Period size: 19 Copynumber: 4.7 Consensus size: 19
642466 AACACAGAAG
642476 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
642495 TCAAATTCCCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
642514 TCAAATTCGCAACTTGATTT
1 TCAAATTCGCAAC-TGAATT
* *
642534 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAAC-TGAATT
*
642554 T-AATTTCGCAAC
1 TCAAATTCGCAAC
642566 AGGTTTTAGT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
19 39 0.64
20 22 0.36
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.32
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:642562 original size:39 final size:38
Alignment explanation
Indices: 642462--642565 Score: 111
Period size: 39 Copynumber: 2.7 Consensus size: 38
642452 AATCTGTAAA
* *
642462 TCGCAACACAGAAGTCAAATTCGCAACTGAATTTCAAAT
1 TCGCAACAC-GAATTTAAATTCGCAACTGAATTTCAAAT
* * * *
642501 TCCCAAC-TGAATTTCAAATTCGCAACTTGATTTTCGAAT
1 TCGCAACACGAATTT-AAATTCGCAAC-TGAATTTCAAAT
*
642540 TCGCAACACGAATTTAATTTCGCAAC
1 TCGCAACACGAATTTAAATTCGCAAC
642566 AGGTTTTAGT
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
37 4 0.08
38 11 0.21
39 32 0.60
40 6 0.11
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.29
Consensus pattern (38 bp):
TCGCAACACGAATTTAAATTCGCAACTGAATTTCAAAT
Found at i:642741 original size:14 final size:15
Alignment explanation
Indices: 642722--642759 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
642712 TCCCCAACTC
642722 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
642736 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
642752 TAATTTTT
1 TAATTTTT
642760 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:643528 original size:24 final size:24
Alignment explanation
Indices: 643501--643554 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
643491 GTATTCGAAA
643501 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
643525 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
643549 TTTGAT
1 TTTGAT
643555 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:646174 original size:20 final size:20
Alignment explanation
Indices: 646151--646198 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
646141 ATTCACATTC
646151 CGAATTTGACTATCGCAATG
1 CGAATTTGACTATCGCAATG
* * **
646171 CGAATTTGATTTTCGCGTTG
1 CGAATTTGACTATCGCAATG
646191 CGAATTTG
1 CGAATTTG
646199 TACCTTCAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.38
Consensus pattern (20 bp):
CGAATTTGACTATCGCAATG
Found at i:646393 original size:64 final size:65
Alignment explanation
Indices: 646253--646395 Score: 225
Period size: 65 Copynumber: 2.2 Consensus size: 65
646243 ATTTTAAAAC
646253 AACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAATAATTCTTATTTACACATAAAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAATAATTCTTATTTACACATAAAATTA
* * * * *
646318 AACAAATCAACTTTTACGAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCAT-CAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAATAATTCTTATTTACACATAAAATTA
*
646382 AATAAATCAACTTT
1 AACAAATCAACTTT
646396 CAATGTAAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
64 18 0.25
65 54 0.75
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.31
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAATAATTCTTATTTACACATAAAATTA
Found at i:647805 original size:21 final size:20
Alignment explanation
Indices: 647781--647854 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 20
647771 GAAGGACCCA
*
647781 TTGAACGATGATATGGGCCTC
1 TTGAACGATGAGA-GGGCCTC
* *
647802 TTGAACGGTGGGAGTGGCCTC
1 TTGAACGATGAGAG-GGCCTC
*
647823 TTGAACGATAAGAGGAGCCTC
1 TTGAACGATGAGAGG-GCCTC
647844 TTGAACGATGA
1 TTGAACGATGA
647855 CAGGTGAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 2 0.05
21 42 0.95
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.24
Consensus pattern (20 bp):
TTGAACGATGAGAGGGCCTC
Found at i:648148 original size:21 final size:21
Alignment explanation
Indices: 648124--648173 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
648114 TAAAACAATC
* *
648124 TCACATAGAGCGGCTACCTCA
1 TCACATAGAGCAGATACCTCA
* * *
648145 TCACGTAAAGTAGATACCTCA
1 TCACATAGAGCAGATACCTCA
648166 TCACATAG
1 TCACATAG
648174 CGCACCATTG
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (21 bp):
TCACATAGAGCAGATACCTCA
Found at i:648269 original size:63 final size:63
Alignment explanation
Indices: 648175--648296 Score: 149
Period size: 63 Copynumber: 1.9 Consensus size: 63
648165 ATCACATAGC
* *
648175 GCACCATTGTCATCGCGTAAAACATCCACCTCACCACGTAAAG-ACCGTACCTCATCACGCCAT
1 GCACCATTGTCATCACGTAAAACATCCACCTCACCACGCAAAGCACCG-ACCTCATCACGCCAT
* ** **
648238 GCACCATTGTCTTCACGTAAAGTA-CCGACCTCATGACGCAAAGCACCGACCTCATCACG
1 GCACCATTGTCATCACGTAAAACATCC-ACCTCACCACGCAAAGCACCGACCTCATCACG
648297 TAACTCCCCT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
62 2 0.04
63 44 0.88
64 4 0.08
ACGTcount: A:0.30, C:0.37, G:0.15, T:0.19
Consensus pattern (63 bp):
GCACCATTGTCATCACGTAAAACATCCACCTCACCACGCAAAGCACCGACCTCATCACGCCAT
Found at i:648296 original size:42 final size:41
Alignment explanation
Indices: 648200--648299 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 41
648190 CGTAAAACAT
* * *
648200 CCACCTCACCACGTAAAGACCGTACCTCATCACGCCATGCA
1 CCACCTCATCACGTAAAGACCGTACCTCATCACGCAAAGCA
** * *
648241 CCATTGTCTTCACGTAAAGTACCG-ACCTCATGACGCAAAGCA
1 CCA-CCTCATCACGTAAAG-ACCGTACCTCATCACGCAAAGCA
648283 CCGACCTCATCACGTAA
1 CC-ACCTCATCACGTAA
648300 CTCCCCTAAC
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
41 3 0.07
42 38 0.83
43 5 0.11
ACGTcount: A:0.30, C:0.38, G:0.14, T:0.18
Consensus pattern (41 bp):
CCACCTCATCACGTAAAGACCGTACCTCATCACGCAAAGCA
Found at i:650529 original size:22 final size:22
Alignment explanation
Indices: 650497--650554 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
650487 GATGGAGATA
*
650497 GACGAATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
650519 GATGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
650541 GACGGATGTCGCCG
1 GACGGATTTCGCCG
650555 TAGAGAGTGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.19, C:0.17, G:0.43, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:650731 original size:20 final size:20
Alignment explanation
Indices: 650706--651053 Score: 173
Period size: 20 Copynumber: 17.4 Consensus size: 20
650696 CGGGCTTTGT
650706 GAATTTAACTTTCGCGTTGC
1 GAATTTAACTTTCGCGTTGC
* * *
650726 GAATTTGACTTTTGTGTTGC
1 GAATTTAACTTTCGCGTTGC
* *
650746 GAATTTGAA-ATTCAGTGTTGC
1 GAATTT-AACTTTC-GCGTTGC
*
650767 GAATTTAACTATCGCGTTGC
1 GAATTTAACTTTCGCGTTGC
*
650787 GAATTTGACTTAT-GCGTTGC
1 GAATTTAACTT-TCGCGTTGC
* *
650807 GAATTTGAC-TTCTGTGTTGC
1 GAATTTAACTTTC-GCGTTGC
** *
650827 -AATTTATAGATTCACGTTGC
1 GAATTTA-ACTTTCGCGTTGC
* * *
650847 GAATTTGACTTTTGTGTTGC
1 GAATTTAACTTTCGCGTTGC
* *
650867 GAATTTGACTATCGCGTTGC
1 GAATTTAACTTTCGCGTTGC
* * *
650887 GAATTTGACTATCGCGTTAC
1 GAATTTAACTTTCGCGTTGC
* * *
650907 GAATTTGAC-TTCTGTGTTAC
1 GAATTTAACTTTC-GCGTTGC
* *
650927 GAATTTGACTTAT-GTGTTGC
1 GAATTTAACTT-TCGCGTTGC
*
650947 G-ATTTACAAATTT-GCGTTGC
1 GAATTT--AACTTTCGCGTTGC
** *
650967 G-ATTTACAAATTCGCGTTAC
1 GAATTTA-ACTTTCGCGTTGC
**
650987 G-ATTTATAGATTCGCGTTGC
1 GAATTTA-ACTTTCGCGTTGC
** *
651007 G-ATTTACAGATTCGCGTTTC
1 GAATTTA-ACTTTCGCGTTGC
651027 G-ATTT-ACTGATTCGCGTTGC
1 GAATTTAACT--TTCGCGTTGC
651047 GAATTTA
1 GAATTTA
651054 GAAACTAGGT
Statistics
Matches: 266, Mismatches: 42, Indels: 38
0.77 0.12 0.11
Matches are distributed among these distances:
18 3 0.01
19 16 0.06
20 213 0.80
21 33 0.12
22 1 0.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.41
Consensus pattern (20 bp):
GAATTTAACTTTCGCGTTGC
Found at i:650826 original size:40 final size:40
Alignment explanation
Indices: 650706--650948 Score: 216
Period size: 40 Copynumber: 6.0 Consensus size: 40
650696 CGGGCTTTGT
* *
650706 GAATTTAACTT-TCGCGTTGCGAATTTGACTTTTGTGTTGC
1 GAATTTGACTTAT-GCGTTGCGAATTTGACTTCTGTGTTGC
* * * *
650746 GAATTTGAAATTCA-GTGTTGCGAATTTAACTATC-GCGTTGC
1 GAATTTG-ACTT-ATGCGTTGCGAATTTGACT-TCTGTGTTGC
650787 GAATTTGACTTATGCGTTGCGAATTTGACTTCTGTGTTGC
1 GAATTTGACTTATGCGTTGCGAATTTGACTTCTGTGTTGC
*
650827 -AATTTATAGA-TTCA--CGTTGCGAATTTGACTTTTGTGTTGC
1 GAA-TT-T-GACTT-ATGCGTTGCGAATTTGACTTCTGTGTTGC
* *
650867 GAATTTGAC-TATCGCGTTGCGAATTTGACTATC-GCGTTAC
1 GAATTTGACTTAT-GCGTTGCGAATTTGACT-TCTGTGTTGC
* * * *
650907 GAATTTGACTTCTGTGTTACGAATTTGACTTATGTGTTGC
1 GAATTTGACTTATGCGTTGCGAATTTGACTTCTGTGTTGC
650947 GA
1 GA
650949 TTTACAAATT
Statistics
Matches: 165, Mismatches: 20, Indels: 36
0.75 0.09 0.16
Matches are distributed among these distances:
37 1 0.01
38 3 0.02
39 7 0.04
40 111 0.67
41 39 0.24
42 4 0.02
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (40 bp):
GAATTTGACTTATGCGTTGCGAATTTGACTTCTGTGTTGC
Found at i:650853 original size:60 final size:62
Alignment explanation
Indices: 650717--650952 Score: 283
Period size: 60 Copynumber: 3.9 Consensus size: 62
650707 AATTTAACTT
* * *
650717 TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGAAATTCAGTGTTGCGAATTTA-A-CTA
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTG-ACTTCTGTGTTGCGAATTTATAGATA
* *
650778 TCGCGTTGCGAATTTGACTTATGCGTTGCGAATTTGACTTCTGTGTTGC-AATTTATAGAT-
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTCTGTGTTGCGAATTTATAGATA
* *
650838 TCACGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATC-GCGTTGCGAA-TT-T-GACTA
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACT-TCTGTGTTGCGAATTTATAGA-TA
* * * *
650898 TCGCGTTACGAATTTGACTTCTGTGTTACGAATTTGACTTATGTGTTGCG-ATTTA
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTCTGTGTTGCGAATTTA
650953 CAAATTTGCG
Statistics
Matches: 151, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
58 2 0.01
59 10 0.07
60 100 0.66
61 39 0.26
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.42
Consensus pattern (62 bp):
TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTCTGTGTTGCGAATTTATAGATA
Found at i:650876 original size:80 final size:82
Alignment explanation
Indices: 650706--650914 Score: 261
Period size: 80 Copynumber: 2.6 Consensus size: 82
650696 CGGGCTTTGT
* * *
650706 GAATTTAACTT-TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGAAATTCAGTGTTGCGAA
1 GAATTTGACTTATCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGAAATTCAGCGTTGCGAA
650770 TTTAACTATCGCGTTGC
66 TTTAACTATCGCGTTGC
650787 GAATTTGACTTAT-GCGTTGCGAATTTGACTTCTGTGTTGC-AATTT-ATAGATTCA-CGTTGCG
1 GAATTTGACTTATCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGA-A-ATTCAGCGTTGCG
* * * *
650848 AATTTGACTTTTGTGTTGC
64 AATTTAACTATCGCGTTGC
* *
650867 GAATTTGAC-TATCGCGTTGCGAATTTGACTATC-GCGTTACGAATTTGA
1 GAATTTGACTTATCGCGTTGCGAATTTGACT-TCTGTGTTGCGAATTTGA
650915 CTTCTGTGTT
Statistics
Matches: 112, Mismatches: 9, Indels: 13
0.84 0.07 0.10
Matches are distributed among these distances:
79 4 0.04
80 58 0.52
81 48 0.43
82 2 0.02
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (82 bp):
GAATTTGACTTATCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGAAATTCAGCGTTGCGAA
TTTAACTATCGCGTTGC
Found at i:651066 original size:60 final size:60
Alignment explanation
Indices: 650942--651068 Score: 148
Period size: 60 Copynumber: 2.1 Consensus size: 60
650932 TGACTTATGT
* * * * *
650942 GTTGCGATTTACAAATTTGCGTTGCGATTTACAAATTCGCGTTACGATTTATAGATTCGC
1 GTTGCGATTTACAAATTCGCGTTGCGATTTACAAATTCGCGTTACGATTTAGAAACTAGC
* * ** *
651002 GTTGCGATTTACAGATTCGCGTTTCGATTTACTGATTCGCGTTGCGAATTTAGAAACTAG-
1 GTTGCGATTTACAAATTCGCGTTGCGATTTACAAATTCGCGTTACG-ATTTAGAAACTAGC
651062 GTTGCGA
1 GTTGCGA
651069 AATTGGAGTT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 47 0.84
61 9 0.16
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.37
Consensus pattern (60 bp):
GTTGCGATTTACAAATTCGCGTTGCGATTTACAAATTCGCGTTACGATTTAGAAACTAGC
Found at i:661906 original size:23 final size:23
Alignment explanation
Indices: 661880--661948 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
661870 CACCACAGCT
*
661880 CGTATAAATACACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
* * * *
661903 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATACACCGAAGTGCCA
*
661926 TGTAGAAATACACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
661949 TATAAGGTTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCA
Found at i:662381 original size:2 final size:2
Alignment explanation
Indices: 662374--662409 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
662364 ATTCATCTTC
662374 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
662410 CATTTTTCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:665514 original size:24 final size:24
Alignment explanation
Indices: 665487--665532 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
665477 TTTCCTTTAC
*
665487 TATACCACATTA-CTATGATCCAAA
1 TATACAACATTATCTA-GATCCAAA
*
665511 TATACAACTTTATCTAGATCCA
1 TATACAACATTATCTAGATCCA
665533 TTTCATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.33
Consensus pattern (24 bp):
TATACAACATTATCTAGATCCAAA
Found at i:667033 original size:23 final size:23
Alignment explanation
Indices: 666996--667059 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
666986 CAACTTGTAT
*
666996 AAATGCACCGAAGTGCCACGTAG
1 AAATACACCGAAGTGCCACGTAG
* * **
667019 AATTACACCGTAGTGCTGCGTAG
1 AAATACACCGAAGTGCCACGTAG
*
667042 AAATGCACCGAAGTGCCA
1 AAATACACCGAAGTGCCA
667060 TATAAGGTTG
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (23 bp):
AAATACACCGAAGTGCCACGTAG
Found at i:667457 original size:2 final size:2
Alignment explanation
Indices: 667450--667487 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
667440 ATGTCTTATC
667450 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
667488 TCACATGTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:668280 original size:22 final size:20
Alignment explanation
Indices: 668235--668280 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
668225 CTTCTATATT
* *
668235 CATATAATTTCTTATTATAT
1 CATATAATTTCTCATTATAA
668255 CATATAATTTACATCATTATAA
1 CATATAATTT-C-TCATTATAA
668277 CATA
1 CATA
668281 GCATATATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
21 1 0.05
22 11 0.50
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (20 bp):
CATATAATTTCTCATTATAA
Found at i:671622 original size:30 final size:31
Alignment explanation
Indices: 671578--671642 Score: 107
Period size: 29 Copynumber: 2.1 Consensus size: 31
671568 AACCTGAATC
671578 AAATCTTTTCTTTAATGATAATAAAAAATTGT
1 AAATCTTTTCTTTAATGATAAT-AAAAATTGT
671610 AAATC-TTT-TTTAATGATAATAAAAATTGT
1 AAATCTTTTCTTTAATGATAATAAAAATTGT
671639 AAAT
1 AAAT
671643 ATTAAATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
29 13 0.39
30 12 0.36
31 3 0.09
32 5 0.15
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (31 bp):
AAATCTTTTCTTTAATGATAATAAAAATTGT
Found at i:675226 original size:2 final size:2
Alignment explanation
Indices: 675221--675255 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
675211 CATCTAACAT
675221 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 T
675256 TGATTGGAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:678386 original size:21 final size:21
Alignment explanation
Indices: 678360--678399 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
678350 GTCGAGGGTT
678360 TCATAGGTCATTCGGGACAAC
1 TCATAGGTCATTCGGGACAAC
* *
678381 TCATAGGTCCTTTGGGACA
1 TCATAGGTCATTCGGGACA
678400 TATTCACAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (21 bp):
TCATAGGTCATTCGGGACAAC
Found at i:678414 original size:21 final size:20
Alignment explanation
Indices: 678359--678414 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
678349 AGTCGAGGGT
*
678359 TTCATAGGTCATTCGGGACAA
1 TTCATAGGTC-TTTGGGACAA
*
678380 CTCATAGGTCCTTTGGGACATA
1 TTCATAGGT-CTTTGGGACA-A
*
678402 TTCACAGGTCTTT
1 TTCATAGGTCTTT
678415 CGAGATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 20 0.69
22 9 0.31
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (20 bp):
TTCATAGGTCTTTGGGACAA
Found at i:683939 original size:26 final size:26
Alignment explanation
Indices: 683910--683962 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
683900 CAACCATGAG
* *
683910 TGACATTCATTGAAATACACCACTAA
1 TGACATGCATTAAAATACACCACTAA
**
683936 TGACATGCATTAAAATGTACCACTAA
1 TGACATGCATTAAAATACACCACTAA
683962 T
1 T
683963 ATAAAATAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (26 bp):
TGACATGCATTAAAATACACCACTAA
Found at i:684485 original size:20 final size:19
Alignment explanation
Indices: 684460--684500 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
684450 TGATTTAAGC
* *
684460 ATTTAAATTTTATTTAACAA
1 ATTTAAATGTAATTTAA-AA
684480 ATTTAAATGTAATTTAAAA
1 ATTTAAATGTAATTTAAAA
684499 AT
1 AT
684501 CATACATCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (19 bp):
ATTTAAATGTAATTTAAAA
Found at i:685875 original size:16 final size:18
Alignment explanation
Indices: 685843--685877 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
685833 ATATAAAAAC
685843 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
685861 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
685877 A
1 A
685878 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:686002 original size:2 final size:2
Alignment explanation
Indices: 685995--686019 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
685985 AAAATAGGAA
685995 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 A
686020 AATAACACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:686479 original size:37 final size:36
Alignment explanation
Indices: 686429--686566 Score: 172
Period size: 37 Copynumber: 3.8 Consensus size: 36
686419 GTGCTTGTGG
* * * * *
686429 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA-AAATCT
* *
686466 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAAT-CT
*
686503 ATCCTATTTTTAGGAGTTTGAATCCTA--AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
686537 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
686567 GGACGAAAAG
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
34 28 0.31
35 4 0.04
36 4 0.04
37 53 0.60
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
Found at i:686540 original size:34 final size:35
Alignment explanation
Indices: 686463--686563 Score: 161
Period size: 34 Copynumber: 2.9 Consensus size: 35
686453 TTAGTAGAAC
686463 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATG
1 TCTATCCTATTTTTAGGAGTTTGAATCCT---AAAATG
686501 T-TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
686534 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
686564 GTAGGACGAA
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
33 1 0.02
34 33 0.53
37 27 0.44
38 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
Found at i:687398 original size:105 final size:104
Alignment explanation
Indices: 687111--687969 Score: 1201
Period size: 105 Copynumber: 8.3 Consensus size: 104
687101 CATTGTTCCA
* * ** *
687111 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGG-ATTGGGAAATTG-TTGTTGACAAG
* * *
687176 CAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** *
687217 AGTCC-ATATCCTTCGTTGTGAAGTTGAAATTGAATCT-GAAT--GAAATT-TTGTTGACAAGCA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGGAAATTGTTGTTGACAAGCA
687277 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
687316 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GGATTGGGAAATTGTTGTTGACAAGC
*
687381 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
687421 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAT--GAAATT-TTGTTGACAAGCA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGGAAATTGTTGTTGACAAGCA
687482 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
687521 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGGTT-GGAAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-GATTGGGAAA-TTGTTGTTGACAAG
*
687585 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
687626 AGTCCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCT-GAAT--GAAATT-TTGTTGACAAGCA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGGAAATTGTTGTTGACAAGCA
687687 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
687726 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GGAAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-GATTGGGAAA-TTGTTGTTGACAAG
*
687790 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
687831 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-GATTGGGAAATTGTTGTTGACAAGC
* * * *
687896 AGCGGTCCCTTCATCGTGAAATTGAACTTGTGTTGTCTCG
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
687936 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
687970 CGCGGATGGC
Statistics
Matches: 684, Mismatches: 48, Indels: 40
0.89 0.06 0.05
Matches are distributed among these distances:
98 1 0.00
99 51 0.07
100 203 0.30
101 13 0.02
102 12 0.02
103 14 0.02
104 10 0.01
105 347 0.51
106 12 0.02
108 21 0.03
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (104 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGGAAATTGTTGTTGACAAGCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:687435 original size:205 final size:205
Alignment explanation
Indices: 687111--687969 Score: 1321
Period size: 205 Copynumber: 4.2 Consensus size: 205
687101 CATTGTTCCA
* * * **
687111 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAA-TTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGGA-TTGGAAAGTTG-TTGTTGACAA
* * ** * *
687175 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCC-ATATCCTTCGTTGTGA
64 GCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGA
**
687238 AGTTGAAATTGAATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
128 AGTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
687303 TTGCGTTGTCTGG
193 TTGCGTTGTCTGG
* * *
687316 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGAAAGTTGTTGTTGACAAGC
687381 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
687446 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
131 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
687511 CGTTGTCTGG
196 CGTTGTCTGG
687521 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGG-TTGGAAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-GGATTGGAAAGTTGTTGTTGACAAG
*
687585 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTTGCTGTGAAG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
687650 TTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
130 TTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
687715 GCGTTGTCTGG
195 GCGTTGTCTGG
*
687726 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGAAAGTTGTTGTTGACAAGC
**
687791 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCATTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
* * * *
687856 TGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCATCGTGAAATTGA
131 TGAAATTGGCTCTGA-A-T--GAAATT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
* *
687921 ACTTGTGTTGTCTCG
191 ACTTGCGTTGTCTGG
* * *
687936 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
687970 CGCGGATGGC
Statistics
Matches: 609, Mismatches: 32, Indels: 18
0.92 0.05 0.03
Matches are distributed among these distances:
203 1 0.00
204 55 0.09
205 469 0.77
206 3 0.00
207 1 0.00
209 5 0.01
210 50 0.08
211 3 0.00
213 22 0.04
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (205 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGAAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
CGTTGTCTGG
Found at i:688872 original size:67 final size:67
Alignment explanation
Indices: 688800--688958 Score: 241
Period size: 67 Copynumber: 2.4 Consensus size: 67
688790 GAAACGAAAT
* *
688800 TTTGTTTTAAGGGAGATA-AAT-TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCATAGGAGAC
1 TTTGTTTCAAGGGA-A-ACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAAGGAGAC
688863 AAAA
64 AAAA
*
688867 TTTGTTTCGAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAAGGAGACAA
1 TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAAGGAGACAA
688932 AA
66 AA
**
688934 TTTGTTTCAAGGGAAATTATCTCAA
1 TTTGTTTCAAGGGAAACAATCTCAA
688959 GAAAGACGAA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 79 0.94
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.32
Consensus pattern (67 bp):
TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAAGGAGACAA
AA
Found at i:688883 original size:36 final size:35
Alignment explanation
Indices: 688833--689105 Score: 187
Period size: 36 Copynumber: 7.9 Consensus size: 35
688823 AAAGATTTTG
*
688833 TGTTTCAAGAGAAACTGTCTCATAGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCA-AGGAGACAAAATT
* ** **
688869 TGTTTCGAGGGAAACAATCTCAA--AG---ATTTT
1 TGTTTCAAGGGAAACTGTCTCAAGGAGACAAAATT
*
688899 GTGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATT
1 -TGTTTCAAGGGAAACTGTCTC-AAGGAGACAAAATT
* * * *
688936 TGTTTCAAGGGAAATTATCTCAAGAAAGACGAAATT
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGACAAAATT
** * * *
688972 CATTTCAAGGGAAA-TGTTTTCAA--TG-----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGGAGACAAAATT
689000 ATGTTTC-AGGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGG-GAAACTGTCTCAA-GGAGACAAAA-TT
* *
689038 TGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGACAAAATT
689074 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGACAA
689106 TGGTGAGCAC
Statistics
Matches: 183, Mismatches: 31, Indels: 46
0.70 0.12 0.18
Matches are distributed among these distances:
28 5 0.03
29 13 0.07
30 5 0.03
31 17 0.09
32 3 0.02
33 3 0.02
34 2 0.01
35 5 0.03
36 96 0.52
37 30 0.16
38 4 0.02
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.28
Consensus pattern (35 bp):
TGTTTCAAGGGAAACTGTCTCAAGGAGACAAAATT
Found at i:689575 original size:18 final size:18
Alignment explanation
Indices: 689548--689583 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
689538 TGATGAATCC
* *
689548 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
689566 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
689584 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:690076 original size:22 final size:22
Alignment explanation
Indices: 689999--690069 Score: 106
Period size: 22 Copynumber: 3.2 Consensus size: 22
689989 TTGTGTTTGG
*
689999 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
690021 TCAAAGGTTTAACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
* *
690043 TTAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTTGATGC
690065 TCAAA
1 TCAAA
690070 AGATTGATGG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:690738 original size:8 final size:7
Alignment explanation
Indices: 690726--690794 Score: 59
Period size: 8 Copynumber: 9.1 Consensus size: 7
690716 TGATTTTTGC
690726 TCTTTTT
1 TCTTTTT
690733 TCCTTTTGT
1 T-CTTTT-T
*
690742 TCTTGTT
1 TCTTTTT
690749 TCTCTTTT
1 TCT-TTTT
690757 TCTTTGTT
1 TCTTT-TT
690765 T-TTTTT
1 TCTTTTT
*
690771 GCTTTTT
1 TCTTTTT
690778 TGCTTCTTT
1 T-CTT-TTT
690787 TCTTTTT
1 TCTTTTT
690794 T
1 T
690795 GTTCTTGATT
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
6 2 0.04
7 19 0.37
8 24 0.47
9 6 0.12
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (7 bp):
TCTTTTT
Found at i:690739 original size:16 final size:17
Alignment explanation
Indices: 690720--690773 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
690710 TCTTTTTGAT
*
690720 TTTTGCTCTTTTTTC-C
1 TTTTGCTCTTGTTTCTC
*
690736 TTTTGTTCTTGTTTCTC
1 TTTTGCTCTTGTTTCTC
*
690753 TTTTTCT-TTGTTT-T-
1 TTTTGCTCTTGTTTCTC
690767 TTTTGCT
1 TTTTGCT
690774 TTTTTGCTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 6 0.19
15 1 0.03
16 19 0.59
17 6 0.19
ACGTcount: A:0.00, C:0.17, G:0.09, T:0.74
Consensus pattern (17 bp):
TTTTGCTCTTGTTTCTC
Found at i:690793 original size:16 final size:16
Alignment explanation
Indices: 690767--690800 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
690757 TCTTTGTTTT
690767 TTTTGCTTTTTTGCTTC
1 TTTTGCTTTTTTG-TTC
690784 TTTT-CTTTTTTGTTC
1 TTTTGCTTTTTTGTTC
690799 TT
1 TT
690801 GATTAGATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 8 0.47
17 4 0.24
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.76
Consensus pattern (16 bp):
TTTTGCTTTTTTGTTC
Found at i:691361 original size:26 final size:24
Alignment explanation
Indices: 691332--691380 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
691322 GTATCAAAAA
691332 AAATAAAGGTAATGTTCAAGAATTTC
1 AAATAAAGGTAATG-TCAA-AATTTC
**
691358 AAATGGAGGTAATGTCAAAATTT
1 AAATAAAGGTAATGTCAAAATTT
691381 GGTTTTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 4 0.19
26 12 0.57
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.31
Consensus pattern (24 bp):
AAATAAAGGTAATGTCAAAATTTC
Found at i:693982 original size:16 final size:18
Alignment explanation
Indices: 693950--693984 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
693940 ATATAAAAAC
693950 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
693968 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
693984 A
1 A
693985 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:694574 original size:37 final size:36
Alignment explanation
Indices: 694524--694661 Score: 172
Period size: 37 Copynumber: 3.8 Consensus size: 36
694514 GTGCTTGTGG
* * * * *
694524 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA-AAATCT
* *
694561 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAAT-CT
*
694598 ATCCTATTTTTAGGAGTTTGAATCCTA--AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
694632 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
694662 GGACGAAAAG
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
34 28 0.31
35 4 0.04
36 4 0.04
37 53 0.60
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
Found at i:694635 original size:34 final size:35
Alignment explanation
Indices: 694558--694658 Score: 161
Period size: 34 Copynumber: 2.9 Consensus size: 35
694548 TTAGTAGAAC
694558 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATG
1 TCTATCCTATTTTTAGGAGTTTGAATCCT---AAAATG
694596 T-TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
694629 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
694659 GTAGGACGAA
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
33 1 0.02
34 33 0.53
37 27 0.44
38 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
Found at i:697024 original size:24 final size:23
Alignment explanation
Indices: 696979--697026 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 23
696969 TACTCAACAC
696979 ATAAATTTAATGTATAATAATAT
1 ATAAATTTAATGTATAATAATAT
697002 ATAATATTATAATGTA-AATAATAT
1 ATAA-ATT-TAATGTATAATAATAT
697026 A
1 A
697027 CAACATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.17
24 12 0.52
25 7 0.30
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (23 bp):
ATAAATTTAATGTATAATAATAT
Found at i:702507 original size:45 final size:46
Alignment explanation
Indices: 702419--702509 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
702409 TTGAAAAAGC
* *
702419 CTGAGTGCATCGATGCATAGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATAGTCATGTGCATCGATGCATAAAATGCA
* *
702465 CTGAGTGCATTGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATAGTCATGTGCATCGATGCATAAAATGCA
702510 TTCGATGTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 22 0.54
46 19 0.46
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATAGTCATGTGCATCGATGCATAAAATGCA
Found at i:710116 original size:45 final size:46
Alignment explanation
Indices: 710028--710118 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 46
710018 TTGAAAAAGC
* *
710028 CTGAGTGCATCGATGCATAGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATAGTCATGTGCATCGATGCATAAAATGCA
*
710074 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATAGTCATGTGCATCGATGCATAAAATGCA
710119 TTCGATGTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 22 0.52
46 20 0.48
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATAGTCATGTGCATCGATGCATAAAATGCA
Found at i:710166 original size:20 final size:20
Alignment explanation
Indices: 710138--710176 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
710128 CAAGAAATTA
710138 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
710158 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
710177 CCCTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Done.