Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_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: 6984689
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 29
Found at i:4039183 original size:20 final size:20
Alignment explanation
Indices: 4039158--4039209 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
4039148 AATAACATGT
4039158 AGTATCGATACTACTATGAG
1 AGTATCGATACTACTATGAG
*
4039178 AGTATCAATACTACTATGAG
1 AGTATCGATACTACTATGAG
4039198 AGTATCGATACT
1 AGTATCGATACT
4039210 TCTCTTACCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (20 bp):
AGTATCGATACTACTATGAG
Found at i:4039904 original size:11 final size:11
Alignment explanation
Indices: 4039890--4039933 Score: 79
Period size: 11 Copynumber: 4.0 Consensus size: 11
4039880 TTATTTATAT
*
4039890 TTATTATACCC
1 TTATTATACTC
4039901 TTATTATACTC
1 TTATTATACTC
4039912 TTATTATACTC
1 TTATTATACTC
4039923 TTATTATACTC
1 TTATTATACTC
4039934 ATACTTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.52
Consensus pattern (11 bp):
TTATTATACTC
Found at i:4043003 original size:2 final size:2
Alignment explanation
Indices: 4042998--4043027 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4042988 TCTATTTTTT
4042998 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4043028 TTTTACTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:4043031 original size:34 final size:33
Alignment explanation
Indices: 4042945--4043031 Score: 97
Period size: 32 Copynumber: 2.6 Consensus size: 33
4042935 TTTTTTCTTA
* *
4042945 ATATTATATTTTATACGTTTTTATATATATATT
1 ATATTATATATTATACTTTTTTATATATATATT
* * *
4042978 TTATTA-ATATTCTATTTTTTTATATATATATAT
1 ATATTATATATTATACTTTTTTATATATATAT-T
4043011 ATATATATATATTATA-TTTTT
1 ATAT-TATATATTATACTTTTT
4043032 ACTTTATTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
32 21 0.48
33 9 0.20
34 7 0.16
35 7 0.16
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (33 bp):
ATATTATATATTATACTTTTTTATATATATATT
Found at i:4043046 original size:17 final size:18
Alignment explanation
Indices: 4043026--4043059 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4043016 TATATATTAT
4043026 ATTTTTACT-TTATTTTA
1 ATTTTTACTATTATTTTA
*
4043043 ATTTTTTCTATTATTTT
1 ATTTTTACTATTATTTT
4043060 TTTCTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (18 bp):
ATTTTTACTATTATTTTA
Found at i:4043253 original size:20 final size:20
Alignment explanation
Indices: 4043230--4043275 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
4043220 TGCGTCTTTG
4043230 TTTTTTTAACATTTTATTCA
1 TTTTTTTAACATTTTATTCA
* **
4043250 TTTTTTTTATTTTTTATTCA
1 TTTTTTTAACATTTTATTCA
4043270 TTTTTT
1 TTTTTT
4043276 ATTATTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTTTAACATTTTATTCA
Found at i:4043254 original size:10 final size:11
Alignment explanation
Indices: 4043241--4043284 Score: 67
Period size: 11 Copynumber: 4.3 Consensus size: 11
4043231 TTTTTTAACA
4043241 TTTTATTCATT
1 TTTTATTCATT
4043252 TTTT-TT-ATT
1 TTTTATTCATT
4043261 TTTTATTCATT
1 TTTTATTCATT
4043272 TTTTATT-ATT
1 TTTTATTCATT
4043282 TTT
1 TTT
4043285 ACGTGTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 7 0.23
10 10 0.32
11 14 0.45
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTATTCATT
Found at i:4043261 original size:18 final size:19
Alignment explanation
Indices: 4043240--4043321 Score: 64
Period size: 20 Copynumber: 4.4 Consensus size: 19
4043230 TTTTTTTAAC
4043240 ATTTTATTCATTTTTT-TT
1 ATTTTATTCATTTTTTATT
4043258 ATTTTTTATTCATTTTTTATT
1 A--TTTTATTCATTTTTTATT
* * * *
4043279 ATTTT-TACGTGTTTTGTT
1 ATTTTATTCATTTTTTATT
*
4043297 A-TTT-TTCATTTTTTCTT
1 ATTTTATTCATTTTTTATT
*
4043314 GTTTTATT
1 ATTTTATT
4043322 TATTATTCTC
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
17 12 0.24
18 14 0.28
19 6 0.12
20 15 0.30
21 3 0.06
ACGTcount: A:0.15, C:0.06, G:0.05, T:0.74
Consensus pattern (19 bp):
ATTTTATTCATTTTTTATT
Found at i:4043285 original size:20 final size:20
Alignment explanation
Indices: 4043241--4043284 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 20
4043231 TTTTTTAACA
4043241 TTTTATTCATTTTTTTTATT
1 TTTTATTCATTTTTTTTATT
4043261 TTTTATTCATTTTTTATTATT
1 TTTTATTCATTTTTT-TTATT
4043282 TTT
1 TTT
4043285 ACGTGTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTATTCATTTTTTTTATT
Found at i:4046438 original size:45 final size:45
Alignment explanation
Indices: 4046382--4046541 Score: 230
Period size: 45 Copynumber: 3.6 Consensus size: 45
4046372 GAAAAGTTGT
* * * *
4046382 ATATGGTTACATTATCAACTGAAAATTATACTATAGTTGAAATGT
1 ATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGC
*
4046427 ATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATAC
1 ATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGC
* * *
4046472 ATATAGGTGCATTATCAACAGAAAAGTATACTATAGTTTAAATGC
1 ATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGC
* *
4046517 ATATGGGTGCATTATCAACAAAAAA
1 ATATGGGTACATTATCAACAGAAAA
4046542 TATGATAAAG
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 104 1.00
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (45 bp):
ATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGC
Found at i:4048156 original size:94 final size:94
Alignment explanation
Indices: 4047985--4048161 Score: 234
Period size: 94 Copynumber: 1.9 Consensus size: 94
4047975 GTTACAGGAA
* * * **
4047985 GTATTGATACCATGGATCCAGAATGTCAAAATGGTATTGATACTGAAAAGGAGTATGGGTACCAT
1 GTATTGATACCATGCAACCAGAATATCAAAATGGTATCAATACTGAAAAGGAGTATGGGTACCAT
*
4048050 ATTATAATAGTATCGATAATGGGAGAAAT
66 AGTATAATAGTATCGATAATGGGAGAAAT
* *
4048079 GTATTGATACCATGCAACACAGAATAT-AGAAATGGTATCAATACT-AAAAGGGGTATTGGTACC
1 GTATTGATACCATGCAAC-CAGAATATCA-AAATGGTATCAATACTGAAAAGGAGTATGGGTACC
4048142 ATAGTATAGA-AGTATCGATA
64 ATAGTATA-ATAGTATCGATA
4048162 CCAATGTAGT
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
94 50 0.69
95 22 0.31
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.28
Consensus pattern (94 bp):
GTATTGATACCATGCAACCAGAATATCAAAATGGTATCAATACTGAAAAGGAGTATGGGTACCAT
AGTATAATAGTATCGATAATGGGAGAAAT
Found at i:4048650 original size:46 final size:46
Alignment explanation
Indices: 4048583--4048720 Score: 222
Period size: 46 Copynumber: 3.0 Consensus size: 46
4048573 AAAATAAATT
* *
4048583 CATAACTAAAATGCATGAAATGATACATTAAGGCATGAAAGGATGC
1 CATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAAGATGC
* *
4048629 CATAACTAAAATTCATGAAATGATGCATTAAGGAATGAAAAGATGC
1 CATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAAGATGC
* *
4048675 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGC
1 CATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAAGATGC
4048721 ATTAAGGCAT
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 84 1.00
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.22
Consensus pattern (46 bp):
CATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAAGATGC
Found at i:4048668 original size:20 final size:20
Alignment explanation
Indices: 4048595--4048740 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
4048585 TAACTAAAAT
*
4048595 GCATGAAATGATACATTAAG
1 GCATGAAATGATGCATTAAG
* *
4048615 GCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAATGATG-CAT---T--AAG
*
4048641 TCATGAAATGATGCATTAAG
1 GCATGAAATGATGCATTAAG
* * *
4048661 GAATGAAAAGATGCCATAACTAAAAT
1 GCATGAAATGATG-CAT---T--AAG
*
4048687 GCATGAAAGGATGCATTAAG
1 GCATGAAATGATGCATTAAG
4048707 GCATGAAATGATGCATTAAG
1 GCATGAAATGATGCATTAAG
4048727 GCATGAAATGATGC
1 GCATGAAATGATGC
4048741 CATAACTAAA
Statistics
Matches: 100, Mismatches: 14, Indels: 24
0.72 0.10 0.17
Matches are distributed among these distances:
20 58 0.58
21 6 0.06
22 2 0.02
24 2 0.02
25 6 0.06
26 26 0.26
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.23
Consensus pattern (20 bp):
GCATGAAATGATGCATTAAG
Found at i:4048718 original size:66 final size:66
Alignment explanation
Indices: 4048642--4048786 Score: 245
Period size: 66 Copynumber: 2.2 Consensus size: 66
4048632 AACTAAAATT
*
4048642 CATGAAATGATGCATTAAGGAATGAAAAGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
1 CATGAAATGATGCATTAAGGAATGAAAAGATGCCATAACTAAAATGCATGAAAGGATACATTAAG
4048707 G
66 G
* *
4048708 CATGAAATGATGCATTAAGGCATGAAATGATGCCATAACTAAAATGCATGAAAGGATACATTAAG
1 CATGAAATGATGCATTAAGGAATGAAAAGATGCCATAACTAAAATGCATGAAAGGATACATTAAG
4048773 G
66 G
* *
4048774 TATGAAAGGATGC
1 CATGAAATGATGC
4048787 TATAACTAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 74 1.00
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.22
Consensus pattern (66 bp):
CATGAAATGATGCATTAAGGAATGAAAAGATGCCATAACTAAAATGCATGAAAGGATACATTAAG
G
Found at i:4048757 original size:46 final size:46
Alignment explanation
Indices: 4048707--4048837 Score: 190
Period size: 46 Copynumber: 2.8 Consensus size: 46
4048697 ATGCATTAAG
* *
4048707 GCATGAAATGATGCATTAAGGCATGAAATGATGCCATAACTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
* * *
4048753 GCATGAAAGGATACATTAAGGTATGAAAGGATGCTATAACTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
* * *
4048799 GCATGAGAGGATGTATTAAGGCATAAAAGGATGCCATAA
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAA
4048838 ATGAAATTAA
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 74 1.00
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.23
Consensus pattern (46 bp):
GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
Found at i:4048792 original size:112 final size:112
Alignment explanation
Indices: 4048595--4048832 Score: 368
Period size: 112 Copynumber: 2.1 Consensus size: 112
4048585 TAACTAAAAT
* * * *
4048595 GCATGAAATGATACATTAAGGCATGAAAGGATGCCATAACTAAAATTCATGAAATGATGCATTAA
1 GCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATACATTAA
4048660 GGAATGAAAAGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
66 GGAATGAAAAGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
*
4048707 GCATGAAATGATGCATTAAGGCATGAAATGATGCCATAACTAAAATGCATGAAAGGATACATTAA
1 GCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATACATTAA
* * * * *
4048772 GGTATGAAAGGATGCTATAACTAAAATGCATGAGAGGATGTATTAAG
66 GGAATGAAAAGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
* *
4048819 GCATAAAAGGATGC
1 GCATGAAATGATGC
4048833 CATAAATGAA
Statistics
Matches: 114, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
112 114 1.00
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.23
Consensus pattern (112 bp):
GCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATACATTAA
GGAATGAAAAGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
Found at i:4055673 original size:46 final size:46
Alignment explanation
Indices: 4055598--4055713 Score: 160
Period size: 46 Copynumber: 2.5 Consensus size: 46
4055588 AAAACTATTT
* * *
4055598 CATAACTAAAATGCTTGAAATGATACATTAAGGCATGACAGGATGC
1 CATAACTAAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGC
* * *
4055644 CATAACTAAAATTCATGAAAGGGTGCATTAAGGCATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGC
* *
4055690 CATAACTATAAGGCATGAAAGGAT
1 CATAACTAAAATGCATGAAAGGAT
4055714 GCCATAAATG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.22
Consensus pattern (46 bp):
CATAACTAAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGC
Found at i:4055708 original size:26 final size:26
Alignment explanation
Indices: 4055626--4055720 Score: 103
Period size: 26 Copynumber: 3.9 Consensus size: 26
4055616 AATGATACAT
*
4055626 TAAGGCATGACAGGATGCCATAACTA
1 TAAGGCATGAAAGGATGCCATAACTA
* ** *
4055652 AAATTCATGAAAGGGTG-C---A-T-
1 TAAGGCATGAAAGGATGCCATAACTA
4055672 TAAGGCATGAAAGGATGCCATAACTA
1 TAAGGCATGAAAGGATGCCATAACTA
4055698 TAAGGCATGAAAGGATGCCATAA
1 TAAGGCATGAAAGGATGCCATAA
4055721 ATGAAATTAA
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
20 13 0.24
21 2 0.04
22 1 0.02
24 1 0.02
25 2 0.04
26 35 0.65
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (26 bp):
TAAGGCATGAAAGGATGCCATAACTA
Found at i:4057085 original size:38 final size:38
Alignment explanation
Indices: 4057034--4057111 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
4057024 TATCTTCAGG
4057034 TAATGGTTCTAGTTTCAAAAGTTGACTCAATATAAATT
1 TAATGGTTCTAGTTTCAAAAGTTGACTCAATATAAATT
4057072 TAATGGTTCTAGTTTCAAAAGTTGACTCAATATAAATT
1 TAATGGTTCTAGTTTCAAAAGTTGACTCAATATAAATT
4057110 TA
1 TA
4057112 CTTGATGTGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (38 bp):
TAATGGTTCTAGTTTCAAAAGTTGACTCAATATAAATT
Found at i:4067689 original size:20 final size:21
Alignment explanation
Indices: 4067652--4067691 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4067642 ACTGTAGGAA
4067652 TTCATGGCCTCGAAAAAAGAT
1 TTCATGGCCTCGAAAAAAGAT
*
4067673 TTCATGGCTTC-AAAAAAGA
1 TTCATGGCCTCGAAAAAAGA
4067692 CTCTGATGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.25
Consensus pattern (21 bp):
TTCATGGCCTCGAAAAAAGAT
Found at i:4079611 original size:34 final size:33
Alignment explanation
Indices: 4079551--4079615 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
4079541 ATGTGGCATA
* ***
4079551 GTAACAATTGAAAATGCTATGGCAAATTAAAAT
1 GTAACAATTCAAAATGCTAAAACAAATTAAAAT
4079584 GTAACAATTCAAGAATGCTAAAACAAATTAAA
1 GTAACAATTCAA-AATGCTAAAACAAATTAAA
4079616 TTGAGAATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 11 0.41
34 16 0.59
ACGTcount: A:0.52, C:0.11, G:0.12, T:0.25
Consensus pattern (33 bp):
GTAACAATTCAAAATGCTAAAACAAATTAAAAT
Found at i:4092353 original size:15 final size:15
Alignment explanation
Indices: 4092333--4092361 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4092323 ACTTTATAAT
4092333 TAAGTGATCATAAAA
1 TAAGTGATCATAAAA
4092348 TAAGTGATCATAAA
1 TAAGTGATCATAAA
4092362 TAGTTGGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (15 bp):
TAAGTGATCATAAAA
Found at i:4092362 original size:14 final size:14
Alignment explanation
Indices: 4092328--4092363 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
4092318 AAATCACTTT
*
4092328 ATAATTAAGTGATC
1 ATAAATAAGTGATC
4092342 ATAAAATAAGTGATC
1 AT-AAATAAGTGATC
4092357 ATAAATA
1 ATAAATA
4092364 GTTGGTATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.53, C:0.06, G:0.11, T:0.31
Consensus pattern (14 bp):
ATAAATAAGTGATC
Found at i:4094455 original size:14 final size:15
Alignment explanation
Indices: 4094421--4094455 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4094411 ACCGTAAAAT
4094421 ATTTTTCAAAAATTA
1 ATTTTTCAAAAATTA
* *
4094436 ATTTTTCAATAATTC
1 ATTTTTCAAAAATTA
4094451 ATTTT
1 ATTTT
4094456 ACGTAAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTTTCAAAAATTA
Found at i:4095697 original size:3 final size:3
Alignment explanation
Indices: 4095689--4095791 Score: 140
Period size: 3 Copynumber: 34.7 Consensus size: 3
4095679 TTTTTATCCA
4095689 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
* *
4095735 TAT TAT TAT TAT TAT CA- TAT TAAT TAT TA- TAA TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
*
4095778 TAT TTT TAT TAT TA
1 TAT TAT TAT TAT TA
4095792 AATATATTAA
Statistics
Matches: 90, Mismatches: 5, Indels: 10
0.86 0.05 0.10
Matches are distributed among these distances:
2 5 0.06
3 79 0.88
4 6 0.07
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:4096594 original size:13 final size:13
Alignment explanation
Indices: 4096576--4096604 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
4096566 ACCACCGTTA
4096576 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
4096589 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
4096602 CGG
1 CGG
4096605 AGTACGGTGG
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:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:4097063 original size:13 final size:13
Alignment explanation
Indices: 4097045--4097069 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4097035 TTTTAGTCAC
4097045 TAAAAAATAAAAA
1 TAAAAAATAAAAA
4097058 TAAAAAATAAAA
1 TAAAAAATAAAA
4097070 TATTTAATCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
TAAAAAATAAAAA
Found at i:4097160 original size:17 final size:17
Alignment explanation
Indices: 4097138--4097171 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4097128 ATTTAGTCAT
4097138 TTATTTTATAGTTTTAA
1 TTATTTTATAGTTTTAA
*
4097155 TTATTTTATTGTTTTAA
1 TTATTTTATAGTTTTAA
4097172 ATATATTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (17 bp):
TTATTTTATAGTTTTAA
Found at i:4108418 original size:21 final size:21
Alignment explanation
Indices: 4108392--4108488 Score: 99
Period size: 21 Copynumber: 4.6 Consensus size: 21
4108382 ATTATGCTTG
4108392 AAAAAAAAAAAGAAAGAAGAA
1 AAAAAAAAAAAGAAAGAAGAA
*
4108413 AAAAAAAAAAAAAAAGAAGAGA
1 AAAAAAAAAAAGAAAGAAGA-A
* *
4108435 AAGAAAAGAAAAGAAAAAAG-A
1 AA-AAAAAAAAAGAAAGAAGAA
** *
4108456 AAGGAAAAGAAGAAA-AAGAA
1 AAAAAAAAAAAGAAAGAAGAA
4108476 AAAGAAAAAAAAG
1 AAA-AAAAAAAAG
4108489 GGGTCAAGGT
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
19 3 0.05
20 12 0.20
21 29 0.48
22 3 0.05
23 14 0.23
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAAGAAAGAAGAA
Found at i:4108421 original size:26 final size:26
Alignment explanation
Indices: 4108392--4108488 Score: 106
Period size: 30 Copynumber: 3.5 Consensus size: 26
4108382 ATTATGCTTG
4108392 AAAAAAAAAAAGAAAGAAG-AAAAAA
1 AAAAAAAAAAAGAAAGAAGAAAAAAA
4108417 AAAAAAAAAAAGAAGAGAAAGAAAAGAAA
1 AAAAAAAAAAAGAA-AG-AAGAAAA-AAA
*
4108446 AGAAAAAAGAAAGGAAAAGAAGAAAAAGAA
1 A-AAAAAA-AAAAG-AAAGAAGAAAAA-AA
4108476 AAAGAAAAAAAAG
1 AAA-AAAAAAAAG
4108489 GGGTCAAGGT
Statistics
Matches: 61, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
25 14 0.23
26 2 0.03
27 3 0.05
28 3 0.05
29 11 0.18
30 20 0.33
31 6 0.10
32 2 0.03
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (26 bp):
AAAAAAAAAAAGAAAGAAGAAAAAAA
Found at i:4108464 original size:36 final size:33
Alignment explanation
Indices: 4108398--4108487 Score: 119
Period size: 36 Copynumber: 2.6 Consensus size: 33
4108388 CTTGAAAAAA
4108398 AAAAAGAAAGAAGAAAAAAAAAAAAAAAAAGAAG
1 AAAAAGAAA-AAGAAAAAAAAAAAAAAAAAGAAG
*
4108432 AGAAAG-AAAAGAAAAGAAAAAAGAAAGGAAAAGAAG
1 AAAAAGAAAAAGAAAA-AAAAAA-AAA--AAAAGAAG
4108468 AAAAAGAAAAAGAAAAAAAA
1 AAAAAGAAAAAGAAAAAAAA
4108488 GGGGTCAAGG
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
32 7 0.14
33 8 0.16
34 8 0.16
36 17 0.35
37 9 0.18
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (33 bp):
AAAAAGAAAAAGAAAAAAAAAAAAAAAAAGAAG
Found at i:4109597 original size:51 final size:51
Alignment explanation
Indices: 4109422--4109872 Score: 857
Period size: 51 Copynumber: 8.8 Consensus size: 51
4109412 TATGTGCTCA
4109422 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAAC
4109474 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAAC
4109526 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
4109577 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
*
4109628 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
*
4109679 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
4109730 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
4109781 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGAAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTAGAAGAAC
4109833 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
4109873 ATTGGACAGA
Statistics
Matches: 396, Mismatches: 2, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
51 248 0.63
52 148 0.37
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (51 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
Found at i:4111048 original size:331 final size:334
Alignment explanation
Indices: 4110294--4111795 Score: 2088
Period size: 328 Copynumber: 4.6 Consensus size: 334
4110284 TCAAAGATTT
*
4110294 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAGTTCATAATGAGAAGAACTTG
1 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAATTCATAATGAGAAGAACTTG
* * * * *
4110359 TTCAACC-TTTGCCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAG-AAGTT-ATAATGAGA
66 TTCAACCTTTTGCTTAAATTCATCATTTGATGGATCA-C-ATTCCAGAGAAAGTTCATAATGAGA
* *
4110421 AG-ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAA
129 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAA
4110485 ATTCATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCGTCATCTGAA
194 ATT-ATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAA--C-TCATCTGAA
* *
4110550 GAAGGAAGAAGAATTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATCATCATTTGGTG
255 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGAATCATCATTTGGTG
4110615 GATCATC-TTTCCAG
320 GATCATCTTTTCCAG
*
4110629 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-ATAAGAAGTTCATAATGAGAAGAAC-T
1 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA-TTCATAATGAGAAGAACTT
* *
4110692 GTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCACATTCCAGAGAAAGTTCATAATGAGAA
65 GTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCACATTCCAGAGAAAGTTCATAATGAGAA
* * *
4110757 GAACTCGTCATTGAAGAAGG-A-AAGAATTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
130 GAACTCATC--TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTA
* *
4110820 AATT-TCATTTG-GGGATC-A-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
193 AATTATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
* ** * *
4110881 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGA
258 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGAA-TCATCATTTGGTGGA
* *
4110946 TCAACATTTCCAG
322 TCATCTTTTCCAG
4110959 AGAAAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAG-AGAATTCATAATGAGAAGAAC
1 AGAAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAATTCATAATGAGAAGAAC
* *
4111023 -TGTTC-ACCTTTTGCTTGAATTCATCA-TTG-TGGATCATCTTTTCCAGAGAAAGTTCATAATG
63 TTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCA-C-ATTCCAGAGAAAGTTCATAATG
*
4111084 AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT--GAAGAACTTGTTCAA-CTTTTGTT
126 AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCT
*
4111146 TAAATTCATCATTTGATGGATCAACATTTCCAGAG-AAGTTCAT-A--AGAAGAACTCGTCTGAA
191 TAAATT-ATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
4111207 GAAGGAAGAAGAAGTTCATAATGAG-AGAACTTGTTCAACCTTTTG-CTGAAT--TCATTTGGTG
255 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGAATCATCATTTGGTG
4111268 GATCATCTTTTCC--
320 GATCATCTTTTCCAG
*
4111281 AGAAAG-TCATAATGAGAAGAACTCATCTG-AGAAGGAAGAAGAAGTCATAATGAGAAGAACTTG
1 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAATTCATAATGAGAAGAACTTG
* *
4111344 TTCAACTTTTTGTTTAAA-TCATCA-TTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGA
66 TTCAACCTTTTGCTTAAATTCATCATTTGATGGATC-ACA-TTCCAGAGAAAGTTCATAATGAGA
4111407 AGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCT
129 AGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCT
* *
4111472 TGAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAA-TCAT-TGAA
191 TAAATT-ATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
*
4111535 GAAGGAAGAAGAAGTTCATAATGAGAAGAA-TTTTTCAACC-TTTGCCTGAATC--CATATTGGT
255 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGAATCATCAT-TTGGT
4111596 GGATCATCTTTTCCAG
319 GGATCATCTTTTCCAG
*
4111612 AG-AAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTCATAATGAGAAGAACTTG
1 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAATTCATAATGAGAAGAACTTG
* * *
4111675 TTC-A-C-TTTGTTTAAATTCATCATTTGATGGATCAACATGGCCAAAGAAAGTTCATGAATGAG
66 TTCAACCTTTTGCTTAAATTCATCATTTGATGGATC-ACAT-TCCAGAGAAAGTTCAT-AATGAG
*
4111737 AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
128 AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
4111796 GTTTGATATC
Statistics
Matches: 1063, Mismatches: 54, Indels: 107
0.87 0.04 0.09
Matches are distributed among these distances:
317 9 0.01
318 27 0.03
319 15 0.01
320 46 0.04
321 16 0.02
322 7 0.01
323 31 0.03
324 20 0.02
325 15 0.01
326 41 0.04
327 15 0.01
328 198 0.19
329 125 0.12
330 80 0.08
331 167 0.16
332 37 0.03
333 40 0.04
334 27 0.03
335 89 0.08
336 48 0.05
337 1 0.00
338 9 0.01
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (334 bp):
AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAATTCATAATGAGAAGAACTTG
TTCAACCTTTTGCTTAAATTCATCATTTGATGGATCACATTCCAGAGAAAGTTCATAATGAGAAG
AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAAT
TATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGAATCATCATTTGGTGGATCAT
CTTTTCCAG
Found at i:4111322 original size:22 final size:23
Alignment explanation
Indices: 4111295--4111337 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
4111285 AGTCATAATG
*
4111295 AGAAGAACTCAT-CTGAGAAGGA
1 AGAAGAACTCATAATGAGAAGGA
*
4111317 AGAAGAAGTCATAATGAGAAG
1 AGAAGAACTCATAATGAGAAG
4111338 AACTTGTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.49, C:0.09, G:0.28, T:0.14
Consensus pattern (23 bp):
AGAAGAACTCATAATGAGAAGGA
Found at i:4112085 original size:3 final size:3
Alignment explanation
Indices: 4112077--4112184 Score: 168
Period size: 3 Copynumber: 37.0 Consensus size: 3
4112067 TTTTTATCCA
4112077 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
4112124 TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAA TAT TAT TAA TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4112171 TAT TAT T-T TAT TAT
1 TAT TAT TAT TAT TAT
4112185 AAATATTAAA
Statistics
Matches: 97, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
2 6 0.06
3 91 0.94
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:4112967 original size:13 final size:13
Alignment explanation
Indices: 4112949--4112977 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
4112939 ACCACCGTTA
4112949 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
4112962 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
4112975 CGG
1 CGG
4112978 AGTACGGTGG
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:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:4113560 original size:19 final size:19
Alignment explanation
Indices: 4113522--4113557 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4113512 CAATTTAGTC
4113522 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
4113541 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
4113558 TAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:4113622 original size:19 final size:20
Alignment explanation
Indices: 4113586--4113625 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
4113576 AGAATTATTC
**
4113586 TTTTATTATATTGTTAAATA
1 TTTTATTATATTCATAAATA
4113606 TTTTA-TATATTCATAAATA
1 TTTTATTATATTCATAAATA
4113625 T
1 T
4113626 ATATAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTTATTATATTCATAAATA
Found at i:4125467 original size:2 final size:2
Alignment explanation
Indices: 4125460--4125484 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4125450 TTGTTTTGTT
4125460 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 T
4125485 TGCAGGTTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4129206 original size:18 final size:17
Alignment explanation
Indices: 4129174--4129219 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
4129164 CAATCTAATA
* *
4129174 ATTTTAAAAATTATTTT
1 ATTTAAAAAATTATTAT
4129191 ATTTAAAAATATTATTAT
1 ATTTAAAAA-ATTATTAT
4129209 ATTTATAAAAA
1 ATTTA-AAAAA
4129220 AACCATAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.32
18 13 0.52
19 4 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAAAAAATTATTAT
Found at i:4129237 original size:213 final size:219
Alignment explanation
Indices: 4128869--4129289 Score: 622
Period size: 227 Copynumber: 1.9 Consensus size: 219
4128859 CTAAAGTTAT
* *
4128869 AAACGTTTGTATTTTAGGTGCCCGGGTCGTCAACAGTGTTAGTTTTTCCCGTTAAGTGACACATT
1 AAACATTTGTATTTTAGGTGCCCGGGTCGTCAACAGTGTTAGTTTTTCCCGTTAAGTGACACATA
* *
4128934 TTACAACCTGATAATTTTAAAAATTATTTTGCTTAAAATTATTAAAAATATTATTATATTTATGA
66 TCACAACCTAATAATTTTAAAAATTA-TTT-CTT--AATTATTAAAAATATTATTATATTTAT--
* *
4128999 AAAAAAAAAACCCTAACTTTTTCTTATATTACAAAATATCCTCAAAATCCCAAATCCTAACCTTA
125 --AAAAAAAACCATAACTTTTTCTTATATTACAAAATAGCCTCAAAATCCCAAATCCTAACCTTA
*
4129064 ATCCGTCGTCGTCGCCGACATAGTCCTTGCAC
188 ATCCATCGTCGTCGCCGACATAGTCCTTGCAC
*
4129096 AAACATTTGTATTTTAGGTGCCCGGGTCGTCAACAGTGTTAG-TTTTCCTCGTTAAGTGACACGT
1 AAACATTTGTATTTTAGGTGCCCGGGTCGTCAACAGTGTTAGTTTTTCC-CGTTAAGTGACACAT
*
4129160 ATCACAATCTAATAATTTTAAAAATTA-TT-TT-A-T-TTAAAAATATTATTATATTTAT-AAAA
65 ATCACAACCTAATAATTTTAAAAATTATTTCTTAATTATTAAAAATATTATTATATTTATAAAAA
*
4129219 AAACCATAACTTTTTCTTATATTACAAAATAGCCTCAAAATCCCAAATCCTAACCTTAATTCATC
130 AAACCATAACTTTTTCTTATATTACAAAATAGCCTCAAAATCCCAAATCCTAACCTTAATCCATC
4129284 GTCGTC
195 GTCGTC
4129290 ACCCTATTCG
Statistics
Matches: 183, Mismatches: 10, Indels: 16
0.88 0.05 0.08
Matches are distributed among these distances:
213 71 0.39
218 22 0.12
219 1 0.01
220 1 0.01
223 2 0.01
225 2 0.01
226 6 0.03
227 78 0.43
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.37
Consensus pattern (219 bp):
AAACATTTGTATTTTAGGTGCCCGGGTCGTCAACAGTGTTAGTTTTTCCCGTTAAGTGACACATA
TCACAACCTAATAATTTTAAAAATTATTTCTTAATTATTAAAAATATTATTATATTTATAAAAAA
AACCATAACTTTTTCTTATATTACAAAATAGCCTCAAAATCCCAAATCCTAACCTTAATCCATCG
TCGTCGCCGACATAGTCCTTGCAC
Found at i:4130428 original size:18 final size:19
Alignment explanation
Indices: 4130405--4130444 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
4130395 AAACTGATTG
*
4130405 TAATATTAAAT-TATTTTT
1 TAATATTAAATATAATTTT
4130423 TAATATTAAATATAATTTT
1 TAATATTAAATATAATTTT
4130442 TAA
1 TAA
4130445 AGTTGTCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TAATATTAAATATAATTTT
Found at i:4130875 original size:2 final size:2
Alignment explanation
Indices: 4130868--4130937 Score: 73
Period size: 2 Copynumber: 38.5 Consensus size: 2
4130858 CCATCCCGAT
* *
4130868 TA TA TA TA TA TA TA -A TA T- TT TA TA TA T- TT TA TA T- TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4130905 T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4130938 TTTATATTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
1 7 0.12
2 52 0.88
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:4131016 original size:5 final size:6
Alignment explanation
Indices: 4130973--4130997 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4130963 ATAAAATATT
4130973 TTCGGG TTCGGG TTCGGG TTCGGG T
1 TTCGGG TTCGGG TTCGGG TTCGGG T
4130998 ATAATATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TTCGGG
Found at i:4135628 original size:17 final size:16
Alignment explanation
Indices: 4135601--4135632 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
4135591 GTTTTCAATT
4135601 GAATTAAATTTAAGAA
1 GAATTAAATTTAAGAA
4135617 GAATTCAAATTTAAGA
1 GAATT-AAATTTAAGA
4135633 TTTTTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.31
Consensus pattern (16 bp):
GAATTAAATTTAAGAA
Found at i:4142995 original size:34 final size:34
Alignment explanation
Indices: 4142957--4143025 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
4142947 GTATCTTATA
4142957 AGAGCATCACAACATATCTAAGTACATGCCAACT
1 AGAGCATCACAACATATCTAAGTACATGCCAACT
4142991 AGAGCATCACAACATATCTAAGTACATGCCAACT
1 AGAGCATCACAACATATCTAAGTACATGCCAACT
4143025 A
1 A
4143026 CTAATATCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.42, C:0.26, G:0.12, T:0.20
Consensus pattern (34 bp):
AGAGCATCACAACATATCTAAGTACATGCCAACT
Found at i:4151032 original size:4 final size:4
Alignment explanation
Indices: 4151023--4151062 Score: 55
Period size: 4 Copynumber: 9.8 Consensus size: 4
4151013 AGAAAAAAAG
4151023 AAAT AAAT -AAT AAAT AAAT AAAT AAAT ATGAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A--AAT AAAT AAA
4151063 ACGAAGATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 3 0.09
4 26 0.79
6 4 0.12
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:4151058 original size:18 final size:19
Alignment explanation
Indices: 4151023--4151062 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
4151013 AGAAAAAAAG
4151023 AAATAAATAATAAATAAAT
1 AAATAAATAATAAATAAAT
*
4151042 AAATAAAT-ATGAATAAAT
1 AAATAAATAATAAATAAAT
4151060 AAA
1 AAA
4151063 ACGAAGATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (19 bp):
AAATAAATAATAAATAAAT
Found at i:4151094 original size:25 final size:24
Alignment explanation
Indices: 4151056--4151102 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
4151046 AAATATGAAT
*
4151056 AAATAAAACGAAGATAAAGAAAATA
1 AAATAAAACAAAGA-AAAGAAAATA
* *
4151081 AAATAAAATAAAGAGAAGAAAA
1 AAATAAAACAAAGAAAAGAAAA
4151103 AGTAAATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.74, C:0.02, G:0.13, T:0.11
Consensus pattern (24 bp):
AAATAAAACAAAGAAAAGAAAATA
Found at i:4151162 original size:2 final size:2
Alignment explanation
Indices: 4151155--4151199 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
4151145 TAAAGAAATA
4151155 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4151197 AT A
1 AT A
4151200 GTCATCAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4151470 original size:135 final size:132
Alignment explanation
Indices: 4151183--4151470 Score: 375
Period size: 134 Copynumber: 2.1 Consensus size: 132
4151173 ATATATATAT
* * *
4151183 ATATATATATATATATAGTCATCAAAATATTAATAAAAAAAATATAATATATATATAATAAATGT
1 ATATA-ATATATATATA-T-ATCAAAATATTAATAAAAAAAATAGAATATATACATAATAAATAT
* *
4151248 TAAAAAACTACCCCTCACTTCACCGAAAGTGAGGGACTTTGGTTAGAGACAAAACAAAAAGAGGG
63 TAAAAAACTACCCCTCACTTCACCGAAAGTGAGGGACTTTGGTCAAAGACAAAACAAAAAGAGGG
*
4151313 GCTCC
128 GCCCC
* *
4151318 ATATGATATATAT-TATAT-AAAATATTAATAAAACAAATAGAATATATGTACATAATAAATATT
1 ATATAATATATATATATATCAAAATATTAATAAAAAAAATAGAATATA--TACATAATAAATATT
* * *
4151381 AAAAAACTTCCCCCATCACTTCACCGAAAGTGGGGGGACTTTGGTCAAAGACAAAATAAAAAGA-
64 AAAAAAC-TACCCC-TCACTTCACCGAAAGT-GAGGGACTTTGGTCAAAGACAAAACAAAAAGAG
4151445 GGGCCCC
126 GGGCCCC
*
4151452 ATGTAATATATATATATAT
1 ATATAATATATATATATAT
4151471 TTAATACACA
Statistics
Matches: 134, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
130 26 0.19
131 2 0.01
132 21 0.16
133 7 0.05
134 41 0.31
135 37 0.28
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.27
Consensus pattern (132 bp):
ATATAATATATATATATATCAAAATATTAATAAAAAAAATAGAATATATACATAATAAATATTAA
AAAACTACCCCTCACTTCACCGAAAGTGAGGGACTTTGGTCAAAGACAAAACAAAAAGAGGGGCC
CC
Found at i:4151508 original size:135 final size:129
Alignment explanation
Indices: 4151218--4151510 Score: 336
Period size: 135 Copynumber: 2.2 Consensus size: 129
4151208 AATATTAATA
* *
4151218 AAAAAAATATAATATATATATAATAAATGTTAAAAAACTACCCCTCACTTCACCGAAAGTGAGGG
1 AAAAAAATAAAATATATATATAATAAATATTAAAAAACTACCCCTCACTTCACCGAAAGTGAGGG
* * * * **
4151283 ACTTTGGTTAGAGACAAAACAAAAAGAGGGGCTCCATATGATATATATTATATAAAATATTAAT
66 ACTTTGGTCAAAGACAAAACAAAAAGAGGGGCCCCATATAATATATATTATATAAAATAACAAT
* * *
4151347 AAAACAAATAGAATATATGTACATAATAAATATTAAAAAACTTCCCCCATCACTTCACCGAAAGT
1 AAAA-AAATA-AA-ATATATATATAATAAATATTAAAAAAC-TACCCC-TCACTTCACCGAAAGT
* * * **
4151412 GGGGGGACTTTGGTCAAAGACAAAATAAAAAGA-GGGCCCCATGTAATATATATATATATTTAAT
61 -GAGGGACTTTGGTCAAAGACAAAACAAAAAGAGGGGCCCCATATAATATATAT-TATATAAAAT
4151476 ACACAAT
124 A-ACAAT
*
4151483 AATAATAATAAAATATATATGATAATAA
1 AA-AAAAATAAAATATATAT-ATAATAA
4151511 TAAAACGTAA
Statistics
Matches: 135, Mismatches: 19, Indels: 14
0.80 0.11 0.08
Matches are distributed among these distances:
129 4 0.03
130 5 0.04
131 1 0.01
132 24 0.18
133 5 0.04
134 39 0.29
135 46 0.34
136 9 0.07
137 2 0.01
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (129 bp):
AAAAAAATAAAATATATATATAATAAATATTAAAAAACTACCCCTCACTTCACCGAAAGTGAGGG
ACTTTGGTCAAAGACAAAACAAAAAGAGGGGCCCCATATAATATATATTATATAAAATAACAAT
Found at i:4153526 original size:34 final size:34
Alignment explanation
Indices: 4153442--4153527 Score: 145
Period size: 34 Copynumber: 2.5 Consensus size: 34
4153432 GTGGATGGCC
*
4153442 CCTTCGTCGTGAAGTTAAGCCTTGAATTAGATAT
1 CCTTCGTCGTGAAGTTGAGCCTTGAATTAGATAT
*
4153476 CCTTCGTCGTGAAGTTGAGCCTTGAATTGGATAT
1 CCTTCGTCGTGAAGTTGAGCCTTGAATTAGATAT
*
4153510 CCTTCATCGTGAAGTTGA
1 CCTTCGTCGTGAAGTTGA
4153528 AATCCAATGT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (34 bp):
CCTTCGTCGTGAAGTTGAGCCTTGAATTAGATAT
Found at i:4153755 original size:43 final size:43
Alignment explanation
Indices: 4153681--4153805 Score: 169
Period size: 43 Copynumber: 2.9 Consensus size: 43
4153671 ATCTAGAGTT
* * *
4153681 GGCATGATATCCTTCATCGTGAAGTTGAAATCGTGGATGTGTA
1 GGCACGATATCCTCCATCGTGGAGTTGAAATCGTGGATGTGTA
* * * * *
4153724 GGCACGATATCCTCCGTTGTGGAGTTAAAATCGTGGATTTGTG
1 GGCACGATATCCTCCATCGTGGAGTTGAAATCGTGGATGTGTA
*
4153767 GGTACGATATCCTCCATCGTGGAGTTGAAATCGTGGATG
1 GGCACGATATCCTCCATCGTGGAGTTGAAATCGTGGATG
4153806 GCCCATTCGT
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 69 1.00
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (43 bp):
GGCACGATATCCTCCATCGTGGAGTTGAAATCGTGGATGTGTA
Found at i:4156128 original size:21 final size:21
Alignment explanation
Indices: 4156102--4156157 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
4156092 GAGCGTTGGG
4156102 GGGTATCGGTACCCCTGTATA
1 GGGTATCGGTACCCCTGTATA
*
4156123 GGGTATCGATACCCCTGTATA
1 GGGTATCGGTACCCCTGTATA
4156144 GGGTATCGGTACCC
1 GGGTATCGGTACCC
4156158 TGCTGTGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.25, G:0.29, T:0.27
Consensus pattern (21 bp):
GGGTATCGGTACCCCTGTATA
Found at i:4157008 original size:23 final size:22
Alignment explanation
Indices: 4156962--4157042 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 22
4156952 ACCCCGTGGA
*
4156962 GGGTATCAGTACC--CTCAAGG
1 GGGTATCGGTACCTACTCAAGG
4156982 GGGTATCGGTACCTACTCAAAGG
1 GGGTATCGGTACCTACTC-AAGG
*
4157005 GGGTATCGGTACCCA-TGCAAGG
1 GGGTATCGGTACCTACT-CAAGG
*
4157027 AGGGTATCGATACCTA
1 -GGGTATCGGTACCTA
4157043 GCCCAGAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
20 12 0.23
22 8 0.15
23 32 0.62
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21
Consensus pattern (22 bp):
GGGTATCGGTACCTACTCAAGG
Found at i:4160835 original size:22 final size:21
Alignment explanation
Indices: 4160793--4160832 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
4160783 AAGACTATTT
4160793 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
4160814 TCATTTTT-ATATTTTGAAA
1 TCATTTTTCA-ATTTTGAAA
4160833 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:4162812 original size:21 final size:21
Alignment explanation
Indices: 4162786--4162825 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
4162776 AATCTTACGT
4162786 GGGGGTATCGGTACCCTCTTG
1 GGGGGTATCGGTACCCTCTTG
4162807 GGGGGTATCGGTACCCTCT
1 GGGGGTATCGGTACCCTCT
4162826 GGACAATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.25, G:0.38, T:0.28
Consensus pattern (21 bp):
GGGGGTATCGGTACCCTCTTG
Found at i:4167023 original size:26 final size:26
Alignment explanation
Indices: 4166987--4167043 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
4166977 TACTCACTAT
4166987 GCTTCAAGAATTTGAGGAATTCTTTA
1 GCTTCAAGAATTTGAGGAATTCTTTA
4167013 GCTTCAAGAATTTGAGGAATTCTTTA
1 GCTTCAAGAATTTGAGGAATTCTTTA
4167039 GCTTC
1 GCTTC
4167044 TTCCTCCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (26 bp):
GCTTCAAGAATTTGAGGAATTCTTTA
Found at i:4172340 original size:4 final size:4
Alignment explanation
Indices: 4172331--4172466 Score: 91
Period size: 4 Copynumber: 32.2 Consensus size: 4
4172321 GAAAAAAAGG
*
4172331 AATA AATA AATA GA-A AA-A AAT- AATA AATA AATA AATA AATA TGAATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA --AATA
* * * *
4172378 AATAA AACGA AGATA AAGA AAAA AATA AAAA AATAA AATAA AATAA AATA
1 AAT-A AA-TA A-ATA AATA AATA AATA AATA AAT-A AAT-A AAT-A AATA
*
4172428 AAGA GAATA AA-A AATA AATA AATAA AATA AATA AGATA A
1 AATA -AATA AATA AATA AATA AAT-A AATA AATA A-ATA A
4172467 GAAAAAAATA
Statistics
Matches: 109, Mismatches: 11, Indels: 23
0.76 0.08 0.16
Matches are distributed among these distances:
3 11 0.10
4 61 0.56
5 32 0.29
6 5 0.05
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.18
Consensus pattern (4 bp):
AATA
Found at i:4172346 original size:22 final size:21
Alignment explanation
Indices: 4172320--4172451 Score: 83
Period size: 22 Copynumber: 6.0 Consensus size: 21
4172310 AAAAAGATAA
4172320 AGAAAAAAAGGAATAAATAAAT
1 AGAAAAAAA-GAATAAATAAAT
*
4172342 AGAAAAAAATAATAAATAAAT
1 AGAAAAAAAGAATAAATAAAT
*
4172363 A-AATAAATATGAATAAATAAA-
1 AGAA-AAA-AAGAATAAATAAAT
* *
4172384 ACGAAGATAAAGAAAAAAATAAA-
1 A-GAA-AAAAAG-AATAAATAAAT
* * *
4172407 AAAATAAAATAAAATAAAATAAAG
1 AGAA-AAAA-AGAAT-AAATAAAT
*
4172431 AGAATAAAA-AATAAATAAAT
1 AGAAAAAAAGAATAAATAAAT
4172451 A
1 A
4172452 AAATAAATAA
Statistics
Matches: 87, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
20 10 0.11
21 19 0.22
22 30 0.34
23 25 0.29
24 3 0.03
ACGTcount: A:0.75, C:0.01, G:0.08, T:0.17
Consensus pattern (21 bp):
AGAAAAAAAGAATAAATAAAT
Found at i:4172349 original size:21 final size:20
Alignment explanation
Indices: 4172316--4172477 Score: 95
Period size: 21 Copynumber: 8.0 Consensus size: 20
4172306 AGAGAAAAAG
* *
4172316 ATAAAGAAAAAAAGGAATAA
1 ATAAATAAAAAAAAGAATAA
*
4172336 ATAAATAGAAAAAAATAATAA
1 ATAAATA-AAAAAAAGAATAA
* * *
4172357 ATAAAT-AAATAAA-TATGA
1 ATAAATAAAAAAAAGAATAA
**
4172375 ATAAATAAAACGAAG-ATAA
1 ATAAATAAAAAAAAGAATAA
* *
4172394 AGAAA-AAAATAAAAAAATAAA
1 ATAAATAAAA-AAAAGAAT-AA
4172415 ATAAAATAAAATAAAGAGAATAA
1 AT-AAATAAAA-AAA-AGAATAA
4172438 A-AAATAAATAAATAA-AATAA
1 ATAAATAAA-AAA-AAGAATAA
*
4172458 ATAAGATAAGAAAAA-AATAA
1 ATAA-ATAAAAAAAAGAATAA
4172478 TAGTAAAGAA
Statistics
Matches: 113, Mismatches: 16, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
18 13 0.12
19 20 0.18
20 21 0.19
21 35 0.31
22 9 0.08
23 11 0.10
24 4 0.04
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.17
Consensus pattern (20 bp):
ATAAATAAAAAAAAGAATAA
Found at i:4172353 original size:14 final size:13
Alignment explanation
Indices: 4172334--4172473 Score: 81
Period size: 14 Copynumber: 10.2 Consensus size: 13
4172324 AAAAAGGAAT
4172334 AAATAAATAGAAAA
1 AAATAAATA-AAAA
*
4172348 AAAT-AAT-AAAT
1 AAATAAATAAAAA
*
4172359 AAATAAATAAATAT
1 AAATAAATAAA-AA
*
4172373 GAATAAATAAAACGA
1 AAATAAATAAAA--A
* *
4172388 AGATAAA-GAAAA
1 AAATAAATAAAAA
4172400 AAATAAA-AAAATA
1 AAATAAATAAAA-A
*
4172413 AAATAAAATAAAAT
1 AAAT-AAATAAAAA
*
4172427 AAAGAGAATAAAAAA
1 AAATA-AAT-AAAAA
*
4172442 TAAATAAATAAAAT
1 -AAATAAATAAAAA
4172456 AAATAAGATAAGAAA
1 AAATAA-ATAA-AAA
4172471 AAA
1 AAA
4172474 ATAATAGTAA
Statistics
Matches: 99, Mismatches: 14, Indels: 25
0.72 0.10 0.18
Matches are distributed among these distances:
11 7 0.07
12 13 0.13
13 18 0.18
14 36 0.36
15 21 0.21
16 4 0.04
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.17
Consensus pattern (13 bp):
AAATAAATAAAAA
Found at i:4172377 original size:25 final size:26
Alignment explanation
Indices: 4172331--4172466 Score: 88
Period size: 25 Copynumber: 5.2 Consensus size: 26
4172321 GAAAAAAAGG
4172331 AATAAATAAATAGAAAAAAAT-AATA
1 AATAAATAAATAGAAAAAAATAAATA
**
4172356 AATAAATAAATA-AATATGAATAAATA
1 AATAAATAAATAGAA-AAAAATAAATA
* *
4172382 AA-ACGAAGATAA-AGAAAAAAATAAAAA
1 AATA--AATA-AATAGAAAAAAATAAATA
* *
4172409 AATAAAATAAAATA-AAATAAAGAGAATA
1 AAT-AAAT-AAATAGAAAAAAATA-AATA
*
4172437 AA-AAATAAATA-AATAAAATAAATA
1 AATAAATAAATAGAAAAAAATAAATA
4172461 AGATAA
1 A-ATAA
4172467 GAAAAAAATA
Statistics
Matches: 85, Mismatches: 13, Indels: 25
0.69 0.11 0.20
Matches are distributed among these distances:
24 7 0.08
25 29 0.34
26 12 0.14
27 25 0.29
28 11 0.13
29 1 0.01
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.18
Consensus pattern (26 bp):
AATAAATAAATAGAAAAAAATAAATA
Found at i:4172380 original size:29 final size:28
Alignment explanation
Indices: 4172331--4172477 Score: 113
Period size: 29 Copynumber: 5.0 Consensus size: 28
4172321 GAAAAAAAGG
*
4172331 AATAAATAAATAGAAAAAAATAATAAATA
1 AATAAATAAATAGAATAAAA-AATAAATA
* **
4172360 AATAAATAAATATGAATAAATAA-AACGA
1 AATAAATAAATA-GAATAAAAAATAAATA
* *
4172388 AGATAAAGAAA-AAAATAAAAAAATAAAATAA
1 A-ATAAATAAATAGAAT-AAAAAAT-AAAT-A
*
4172419 AATAAAATAAAGAGAATAAAAAATAAATA
1 AAT-AAATAAATAGAATAAAAAATAAATA
4172448 AATAAAATAAATA-AGATAAGAAAA-AAATA
1 AAT-AAATAAATAGA-ATAA-AAAATAAATA
4172477 A
1 A
4172478 TAGTAAAGAA
Statistics
Matches: 96, Mismatches: 12, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
27 3 0.03
28 11 0.11
29 45 0.47
30 18 0.19
31 15 0.16
32 4 0.04
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.18
Consensus pattern (28 bp):
AATAAATAAATAGAATAAAAAATAAATA
Found at i:4172398 original size:74 final size:70
Alignment explanation
Indices: 4172313--4172454 Score: 178
Period size: 74 Copynumber: 2.0 Consensus size: 70
4172303 TGAAGAGAAA
* * *
4172313 AAGATAAAGAAAAAAAGGAATAAATAAATAGAAAAAAATAATAAATA-AATAAATAAATATGAAT
1 AAGATAAAGAAAAAAAGAAAAAAATAAA-AGAAAAAAA-AATAAAGAGAATAAA-AAATA--AAT
4172377 AAATAAAACG
61 AAATAAAACG
* * *
4172387 AAGATAAAGAAAAAAATAAAAAAATAAAATAAAATAAAATAAAGAGAATAAAAAATAAATAAATA
1 AAGATAAAGAAAAAAAGAAAAAAATAAAAGAAAAAAAAATAAAGAGAATAAAAAATAAATAAATA
4172452 AAA
66 AAA
4172455 TAAATAAGAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
70 11 0.18
72 12 0.20
73 13 0.21
74 25 0.41
ACGTcount: A:0.75, C:0.01, G:0.08, T:0.16
Consensus pattern (70 bp):
AAGATAAAGAAAAAAAGAAAAAAATAAAAGAAAAAAAAATAAAGAGAATAAAAAATAAATAAATA
AAACG
Found at i:4172415 original size:5 final size:5
Alignment explanation
Indices: 4172399--4172477 Score: 62
Period size: 5 Copynumber: 16.4 Consensus size: 5
4172389 GATAAAGAAA
*
4172399 AAAAT -AAA- AAAAT AAAAT AAAAT AAAAT AAAGAG AATAA- AAAAT -AAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AA-AAT AAAAT AAAAT
* *
4172447 -AAAT AAAAT -AAAT AAGAT AAGAAA AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT AA
4172478 TAGTAAAGAA
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
4 20 0.33
5 33 0.54
6 7 0.11
7 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:4172472 original size:70 final size:70
Alignment explanation
Indices: 4172313--4172454 Score: 164
Period size: 70 Copynumber: 2.0 Consensus size: 70
4172303 TGAAGAGAAA
* * * *
4172313 AAGATAAAGAAAAAAAGGAATAAATAAATAGAAAAAAATAATAAATAAATAAATAAATATGAATA
1 AAGATAAAG--AAAAA--AATAAAAAAATAGAAAAAAATAATAAATAAAGAAATAAAAATAAATA
4172378 AATAAAACG
62 AATAAAACG
4172387 AAGATAAAGAAAAAAATAAAAAAATA-AAATAAAAT-A-AAATAAAGAGAATAAAAAATAAATAA
1 AAGATAAAGAAAAAAATAAAAAAATAGAAA-AAAATAATAAATAAAGA-AAT-AAAAATAAATAA
4172449 ATAAAA
63 ATAAAA
4172455 TAAATAAGAT
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
68 8 0.13
69 7 0.11
70 32 0.52
72 5 0.08
74 9 0.15
ACGTcount: A:0.75, C:0.01, G:0.08, T:0.16
Consensus pattern (70 bp):
AAGATAAAGAAAAAAATAAAAAAATAGAAAAAAATAATAAATAAAGAAATAAAAATAAATAAATA
AAACG
Found at i:4172474 original size:20 final size:19
Alignment explanation
Indices: 4172387--4172477 Score: 52
Period size: 18 Copynumber: 4.9 Consensus size: 19
4172377 AAATAAAACG
4172387 AAGATAAAGAAAAAAATAAA
1 AAGAT-AAGAAAAAAATAAA
* *
4172407 AAAATAA-AATAAAATAAA
1 AAGATAAGAAAAAAATAAA
* *
4172425 ATA-A-AGAGAATAAAA-AAT
1 A-AGATA-AGAAAAAAATAAA
*
4172443 AA-AT-A-AATAAAATAAA
1 AAGATAAGAAAAAAATAAA
4172459 TAAGATAAGAAAAAAATAA
1 -AAGATAAGAAAAAAATAA
4172478 TAGTAAAGAA
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
15 7 0.12
16 3 0.05
17 5 0.09
18 18 0.32
19 11 0.19
20 13 0.23
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (19 bp):
AAGATAAGAAAAAAATAAA
Found at i:4172490 original size:43 final size:41
Alignment explanation
Indices: 4172331--4172490 Score: 120
Period size: 43 Copynumber: 3.9 Consensus size: 41
4172321 GAAAAAAAGG
*
4172331 AATAAATAAATAGAA-AAAAAT-AA-TAAATAAATAAATAA
1 AATAAATAAATAAAACAAAAATAAAGTAAATAAATAAATAA
* * * *
4172369 ATATGAATAAATAAAACGAAGATAAAG-AAAAAAATAAA-AA
1 A-ATAAATAAATAAAACAAAAATAAAGTAAATAAATAAATAA
*
4172409 AATAAAATAAAATAAAATAAAGAGAATAAA--AAATAAATAAATAA
1 AAT-AAAT-AAATAAAA-CAA-A-AATAAAGTAAATAAATAAATAA
*
4172453 AATAAATAAGATAAGAA-AAAAATAATAGTAAAGAAATA
1 AATAAATAA-ATAA-AACAAAAATAA-AGTAAATAAATA
4172491 TATATATATA
Statistics
Matches: 96, Mismatches: 11, Indels: 25
0.73 0.08 0.19
Matches are distributed among these distances:
38 1 0.01
39 14 0.15
40 15 0.16
41 22 0.23
42 5 0.05
43 27 0.28
44 12 0.12
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.18
Consensus pattern (41 bp):
AATAAATAAATAAAACAAAAATAAAGTAAATAAATAAATAA
Found at i:4172493 original size:2 final size:2
Alignment explanation
Indices: 4172488--4172524 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4172478 TAGTAAAGAA
4172488 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4172525 GTCATCAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4172574 original size:11 final size:13
Alignment explanation
Indices: 4172487--4172574 Score: 67
Period size: 14 Copynumber: 6.7 Consensus size: 13
4172477 ATAGTAAAGA
4172487 AATATATATATAT
1 AATATATATATAT
4172500 ATATATATATATAT
1 A-ATATATATATAT
4172514 ATATATATATAGTCAT
1 A-ATATATATA-T-AT
*
4172530 CAAAATAT-TA-AT
1 -AATATATATATAT
* *
4172542 AA-A-ACAAATAT
1 AATATATATATAT
4172553 AATATATATATAT
1 AATATATATATAT
*
4172566 AATAAATAT
1 AATATATAT
4172575 TAAAAAACTA
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
9 1 0.02
10 2 0.03
11 6 0.10
12 3 0.05
13 15 0.25
14 23 0.38
15 3 0.05
16 7 0.11
17 1 0.02
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (13 bp):
AATATATATATAT
Found at i:4172668 original size:133 final size:135
Alignment explanation
Indices: 4172514--4172804 Score: 471
Period size: 134 Copynumber: 2.1 Consensus size: 135
4172504 ATATATATAT
* *
4172514 ATATATATATAGTCATCAAAATATTAATAAAACAAATATAATATATATATATAATAAATATTAAA
1 ATATATATATA-T-AT-AAAATATTAATAAAACAAATAGAATATATATACATAATAAATATTAAA
*
4172579 AAAC-TACCCC-TCACTTCACCGAAAGTGGGGGGACTTTGGTCAGAGACAAAACAAAAAGAGGGG
63 AAACTTACCCCATCACTTCACCGAAAGT-GGGGGACTTTGGTCAGAGACAAAACAAAAAGAGAGG
4172642 CCCCATGTA
127 CCCCATGTA
*
4172651 ATATATAT-TATATAAAATATTAATAAAACAAATAGAATATATGTACATAATAAATATTAAAAAA
1 ATATATATATATATAAAATATTAATAAAACAAATAGAATATATATACATAATAAATATTAAAAAA
*
4172715 CTTCCCCCATCACTTCACCGAAAGTGGGGGACTTTGGTCAGAGACAAAACAAAAAGAGAGGCCCC
66 CTTACCCCATCACTTCACCGAAAGTGGGGGACTTTGGTCAGAGACAAAACAAAAAGAGAGGCCCC
4172780 ATGTA
131 ATGTA
*
4172785 ATATATATATATATATAATA
1 ATATATATATATATAAAATA
4172805 CACAATAATA
Statistics
Matches: 145, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
133 49 0.34
134 59 0.41
135 27 0.19
136 2 0.01
137 8 0.06
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.26
Consensus pattern (135 bp):
ATATATATATATATAAAATATTAATAAAACAAATAGAATATATATACATAATAAATATTAAAAAA
CTTACCCCATCACTTCACCGAAAGTGGGGGACTTTGGTCAGAGACAAAACAAAAAGAGAGGCCCC
ATGTA
Found at i:4172830 original size:33 final size:32
Alignment explanation
Indices: 4172783--4172857 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 32
4172773 AGGCCCCATG
* *
4172783 TAATATATATATATATATAATACACAATAATA-A
1 TAATATA-AAATATATATAATA-ACAATAAAACA
*
4172816 TAATAATAAAATATATATGATAACAATAAAACA
1 TAAT-ATAAAATATATATAATAACAATAAAACA
4172849 TAATATAAA
1 TAATATAAA
4172858 TAAAAATAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
32 13 0.35
33 21 0.57
34 3 0.08
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.32
Consensus pattern (32 bp):
TAATATAAAATATATATAATAACAATAAAACA
Found at i:4172846 original size:134 final size:131
Alignment explanation
Indices: 4172539--4172838 Score: 397
Period size: 134 Copynumber: 2.2 Consensus size: 131
4172529 TCAAAATATT
4172539 AATAAAACAAATATA-ATATATATATATAATAAATATTAAAAAACTACCCCTCACTTCACCGAAA
1 AATAAAA-AAA-ATAGA-ATATATATATAATAAATATTAAAAAACTACCCCTCACTTCACCGAAA
*
4172603 GTGGGGGGACTTTGGTCAGAGACAAAACAAAAAGAGGGGCCCCATGTAATATATATTATATAAAA
63 GTGGGGGGACTTTGGTCAGAGACAAAACAAAAAGAGAGGCCCCATGTAATATATATTATATAAAA
**
4172668 TATT
128 TAAC
* * *
4172672 AATAAAACAAATAGAATATATGTACATAATAAATATTAAAAAACTTCCCCCATCACTTCACCGAA
1 AATAAAAAAAATAGAATATA--TATATAATAAATATTAAAAAAC-TACCCC-TCACTTCACCGAA
*
4172737 AGT-GGGGGACTTTGGTCAGAGACAAAACAAAAAGAGAGGCCCCATGTAATATATATATATATAT
62 AGTGGGGGGACTTTGGTCAGAGACAAAACAAAAAGAGAGGCCCCATGTAATATATAT-TATATAA
4172801 AATACAC
126 AATA-AC
*
4172808 AATAATAATAATAATAAAATATATATGATAA
1 AATAA-AA-AA-AATAGAATATATAT-ATAA
4172839 CAATAAAACA
Statistics
Matches: 146, Mismatches: 10, Indels: 17
0.84 0.06 0.10
Matches are distributed among these distances:
131 8 0.05
132 3 0.02
133 28 0.19
134 57 0.39
135 26 0.18
136 5 0.03
137 4 0.03
138 5 0.03
139 10 0.07
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.25
Consensus pattern (131 bp):
AATAAAAAAAATAGAATATATATATAATAAATATTAAAAAACTACCCCTCACTTCACCGAAAGTG
GGGGGACTTTGGTCAGAGACAAAACAAAAAGAGAGGCCCCATGTAATATATATTATATAAAATAA
C
Found at i:4174435 original size:46 final size:47
Alignment explanation
Indices: 4174294--4174447 Score: 238
Period size: 47 Copynumber: 3.3 Consensus size: 47
4174284 TATTTGATCT
* *
4174294 ATTTTGGGTATGAACTGCCCAATTCATTTTTATACGATATTTGAATG
1 ATTTCGGGTATGAATTGCCCAATTCATTTTTATACGATATTTGAATG
*
4174341 ATTTCGGGTATGAATTGCCCAATTCATTTTTATATGATATTTGAATG
1 ATTTCGGGTATGAATTGCCCAATTCATTTTTATACGATATTTGAATG
* * *
4174388 ATTTCGGGTATGAATTGTCCAATT-AATTTTATACGGTATTTGAATG
1 ATTTCGGGTATGAATTGCCCAATTCATTTTTATACGATATTTGAATG
*
4174434 ATTTCGAGTATGAA
1 ATTTCGGGTATGAA
4174448 CTACCCAAGG
Statistics
Matches: 99, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
46 32 0.32
47 67 0.68
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.43
Consensus pattern (47 bp):
ATTTCGGGTATGAATTGCCCAATTCATTTTTATACGATATTTGAATG
Found at i:4174446 original size:93 final size:94
Alignment explanation
Indices: 4174280--4174475 Score: 252
Period size: 93 Copynumber: 2.1 Consensus size: 94
4174270 ATTTTGCTAA
* * *
4174280 ATGATATTTGATCTATTTTGGGTATGAACTGCCCAATTCATTTTTATACGATATTTGAATGATTT
1 ATGATATTTGATCGATTTCGGGTATGAACTGCCCAATTCAATTTTATACGATATTTGAATGATTT
* * * ** *
4174345 CGGGTATGAATTGCCCAATTCATTTTTAT
66 CGAGTATGAACTACCCAAGGCATTATTAT
* * *
4174374 ATGATATTTGAAT-GATTTCGGGTATGAATTGTCCAATT-AATTTTATACGGTATTTGAATGATT
1 ATGATATTTG-ATCGATTTCGGGTATGAACTGCCCAATTCAATTTTATACGATATTTGAATGATT
4174437 TCGAGTATGAACTACCCAAGGCATTATTAT
65 TCGAGTATGAACTACCCAAGGCATTATTAT
*
4174467 ATGAGATTT
1 ATGATATTT
4174476 TGATATATTC
Statistics
Matches: 88, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
93 55 0.62
94 31 0.35
95 2 0.02
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.42
Consensus pattern (94 bp):
ATGATATTTGATCGATTTCGGGTATGAACTGCCCAATTCAATTTTATACGATATTTGAATGATTT
CGAGTATGAACTACCCAAGGCATTATTAT
Found at i:4176510 original size:44 final size:44
Alignment explanation
Indices: 4176456--4176542 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
4176446 AATAATAATA
*
4176456 TTATGTTAATAAATAATTAATATACTTAATAATAT-GTTATTTTT
1 TTATGTTAATAAATAATTAATATAATT-ATAATATAGTTATTTTT
* * *
4176500 TTATTTTAATAAATATTTAATATAATTATAATATATTTATTTT
1 TTATGTTAATAAATAATTAATATAATTATAATATAGTTATTTT
4176543 AATAAAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 7 0.18
44 31 0.82
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (44 bp):
TTATGTTAATAAATAATTAATATAATTATAATATAGTTATTTTT
Found at i:4186330 original size:20 final size:20
Alignment explanation
Indices: 4186305--4186344 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
4186295 ATATTGAGAG
4186305 GAATTTTGATAGAGGAAGTT
1 GAATTTTGATAGAGGAAGTT
4186325 GAATTTTGATAGAGGAAGTT
1 GAATTTTGATAGAGGAAGTT
4186345 TAGTGCATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.30, T:0.35
Consensus pattern (20 bp):
GAATTTTGATAGAGGAAGTT
Found at i:4187252 original size:18 final size:17
Alignment explanation
Indices: 4187238--4187272 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4187228 AAAAAATACT
* *
4187238 TTAAAAATTTTAAATTA
1 TTAAAAAATTTAAAATA
4187255 TTAAAAAATTTAAAATA
1 TTAAAAAATTTAAAATA
4187272 T
1 T
4187273 ATATTATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAAAAATTTAAAATA
Found at i:4189542 original size:20 final size:20
Alignment explanation
Indices: 4189517--4189563 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
4189507 CATGATACCT
4189517 ATACTACAAGTAGATTATCG
1 ATACTACAAGTAGATTATCG
4189537 ATACTACAAGTAGATTATCG
1 ATACTACAAGTAGATTATCG
4189557 ATACTAC
1 ATACTAC
4189564 CCACCCTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (20 bp):
ATACTACAAGTAGATTATCG
Found at i:4190534 original size:17 final size:17
Alignment explanation
Indices: 4190512--4190545 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4190502 CCCTCAGCCG
4190512 CACCATGATGCCCGCCA
1 CACCATGATGCCCGCCA
*
4190529 CACCATGATGCCTGCCA
1 CACCATGATGCCCGCCA
4190546 TAACATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.44, G:0.18, T:0.15
Consensus pattern (17 bp):
CACCATGATGCCCGCCA
Found at i:4196434 original size:32 final size:32
Alignment explanation
Indices: 4196393--4196473 Score: 144
Period size: 32 Copynumber: 2.5 Consensus size: 32
4196383 TAATCGAGTT
*
4196393 AGTATTGCATTCAGATAGTGCATAGAAACATC
1 AGTATTGCATTCAGATAGTGCATAAAAACATC
4196425 AGTATTGCATTCAGATAGTGCATAAAAACATC
1 AGTATTGCATTCAGATAGTGCATAAAAACATC
*
4196457 AGTATTGCATTTAGATA
1 AGTATTGCATTCAGATA
4196474 ATACGTAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (32 bp):
AGTATTGCATTCAGATAGTGCATAAAAACATC
Found at i:4199681 original size:25 final size:24
Alignment explanation
Indices: 4199653--4199716 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
4199643 ATTTTATTTA
*
4199653 TTTTTTATATTTTAATTTT-AACAT
1 TTTTTTATTTTTTAATTTTAAAC-T
* *
4199677 GTTTTTCATTTTATTATTTTTAAACT
1 -TTTTTTATTTT-TTAATTTTAAACT
4199703 TTTTTTATTTTTTA
1 TTTTTTATTTTTTA
4199717 TTTATTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
24 3 0.09
25 19 0.58
26 8 0.24
27 3 0.09
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTTTTATTTTTTAATTTTAAACT
Found at i:4199726 original size:37 final size:37
Alignment explanation
Indices: 4199685--4199845 Score: 106
Period size: 36 Copynumber: 4.4 Consensus size: 37
4199675 ATGTTTTTCA
*
4199685 TTTTATTATTTTTAA-ACTTTTTTTATTTT-TTATTTAT
1 TTTTATT-TTTTTAACA-TTTTTATATTTTATTATTTAT
*
4199722 TTTTATTTTTTTAACATTTTTATATTTTATTATTT-C
1 TTTTATTTTTTTAACATTTTTATATTTTATTATTTAT
*** *
4199758 TTTTA-AAATTTAAAATTTTCT-TCATTTTATTTTATTT-T
1 TTTTATTTTTTTAACATTTT-TAT-ATTTTA--TTATTTAT
* *
4199796 GTTTT-TCTCTTTTAACATTTTT-TATTTTACTATTT-T
1 -TTTTAT-TTTTTTAACATTTTTATATTTTATTATTTAT
*
4199832 TTTTATTTTCTTAA
1 TTTTATTTTTTTAA
4199846 TTTAACCTTT
Statistics
Matches: 100, Mismatches: 14, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
35 21 0.21
36 37 0.37
37 14 0.14
38 12 0.12
39 6 0.06
40 10 0.10
ACGTcount: A:0.22, C:0.06, G:0.01, T:0.71
Consensus pattern (37 bp):
TTTTATTTTTTTAACATTTTTATATTTTATTATTTAT
Found at i:4199741 original size:27 final size:28
Alignment explanation
Indices: 4199711--4199768 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
4199701 CTTTTTTTAT
* *
4199711 TTTTTAT-TTATTTTTATTT-TTTTAACA
1 TTTTTATATT-TTATTATTTCTTTTAAAA
4199738 TTTTTATATTTTATTATTTCTTTTAAAA
1 TTTTTATATTTTATTATTTCTTTTAAAA
4199766 TTT
1 TTT
4199769 AAAATTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 15 0.56
28 12 0.44
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.72
Consensus pattern (28 bp):
TTTTTATATTTTATTATTTCTTTTAAAA
Found at i:4199742 original size:34 final size:36
Alignment explanation
Indices: 4199685--4199756 Score: 96
Period size: 34 Copynumber: 2.1 Consensus size: 36
4199675 ATGTTTTTCA
* *
4199685 TTTTATTATTTTTAAACTTTTTTTATTTTTTATTTAT
1 TTTTATTATTTTTAAACTATTTTTATATTTTA-TTAT
4199722 TTTTATT-TTTTT-AAC-ATTTTTATATTTTATTAT
1 TTTTATTATTTTTAAACTATTTTTATATTTTATTAT
4199755 TT
1 TT
4199757 CTTTTAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 6 0.18
34 12 0.36
35 3 0.09
36 5 0.15
37 7 0.21
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (36 bp):
TTTTATTATTTTTAAACTATTTTTATATTTTATTAT
Found at i:4211816 original size:37 final size:37
Alignment explanation
Indices: 4211771--4211905 Score: 143
Period size: 37 Copynumber: 3.7 Consensus size: 37
4211761 TAATATAATG
* *
4211771 TAGTTTTTAAAAATATTTTTTGAAAACAAATAATATA
1 TAGTTTTTAAAAATAGTTTTTGAAAACATATAATATA
* *
4211808 TAGTTTTTATAAAA-GGTTTTTGAAAGCATATAATATA
1 TAGTTTTTA-AAAATAGTTTTTGAAAACATATAATATA
* *
4211845 TAGCTTTTAAAAATTAGTTTTTGAAAATATAT-A-ATA
1 TAGTTTTTAAAAA-TAGTTTTTGAAAACATATAATATA
* *
4211881 T-GGTTTTGAAAATACGTTTTTGAAA
1 TAGTTTTTAAAAATA-GTTTTTGAAA
4211906 TATATATTAT
Statistics
Matches: 84, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
34 2 0.02
35 19 0.23
36 8 0.10
37 37 0.44
38 18 0.21
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (37 bp):
TAGTTTTTAAAAATAGTTTTTGAAAACATATAATATA
Found at i:4212001 original size:24 final size:24
Alignment explanation
Indices: 4211957--4212026 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 24
4211947 TTTATTTTTT
* *
4211957 TTTTGAAAATGTA-TATAATATAG
1 TTTTGAAAATATATTATTATATAG
*
4211980 TTTTGAAAACATATTATTATATAG
1 TTTTGAAAATATATTATTATATAG
* **
4212004 TTTTTATTATATATTATTATATA
1 TTTTGAAAATATATTATTATATA
4212027 TTTATATTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 11 0.28
24 28 0.72
ACGTcount: A:0.40, C:0.01, G:0.07, T:0.51
Consensus pattern (24 bp):
TTTTGAAAATATATTATTATATAG
Found at i:4212004 original size:59 final size:59
Alignment explanation
Indices: 4211897--4212011 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 59
4211887 TGAAAATACG
* * *
4211897 TTTTTGAAATATATATTATATTCTTTTAAAAACGTATAATATACATAGTTTTTATTTTT
1 TTTTTGAAATATATATAATATACTTTTAAAAACATATAATATACATAGTTTTTATTTTT
* * * * *
4211956 TTTTTGAAAATGTATATAATATAGTTTTGAAAACATATTAT-TATATAGTTTTTATT
1 TTTTTG-AAATATATATAATATACTTTTAAAAACATATAATATACATAGTTTTTATT
4212012 ATATATTATT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 20 0.43
60 27 0.57
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (59 bp):
TTTTTGAAATATATATAATATACTTTTAAAAACATATAATATACATAGTTTTTATTTTT
Found at i:4212022 original size:10 final size:10
Alignment explanation
Indices: 4212007--4212064 Score: 54
Period size: 10 Copynumber: 6.2 Consensus size: 10
4211997 TATATAGTTT
4212007 TTATTATATA
1 TTATTATATA
4212017 TTATTATATA
1 TTATTATATA
4212027 -T-TTATATTA
1 TTATTATA-TA
* *
4212036 ATATTATTTA
1 TTATTATATA
4212046 TT-TT-TAT-
1 TTATTATATA
4212053 TTATTATATA
1 TTATTATATA
4212063 TT
1 TT
4212065 TATATTATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
7 2 0.05
8 9 0.23
9 8 0.21
10 16 0.41
11 4 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTATTATATA
Found at i:4213311 original size:20 final size:20
Alignment explanation
Indices: 4213270--4213313 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
4213260 AAATTGATCC
*
4213270 TTTAAATTTTTATTTATTTT
1 TTTAAATTTTTATTTATATT
* *
4213290 TTTATATTTTTATTT-TAAT
1 TTTAAATTTTTATTTATATT
4213309 TTTAA
1 TTTAA
4213314 CATGTTCTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTAAATTTTTATTTATATT
Found at i:4230318 original size:26 final size:26
Alignment explanation
Indices: 4230289--4230338 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
4230279 AGAGCTATTA
* *
4230289 AATCTCTTTTAATTAAAGAGATAATG
1 AATCTCTTTTAATAAAAGAAATAATG
4230315 AATCTCTTTTAATAAAAGAAATAA
1 AATCTCTTTTAATAAAAGAAATAA
4230339 ATATCTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (26 bp):
AATCTCTTTTAATAAAAGAAATAATG
Found at i:4231070 original size:47 final size:46
Alignment explanation
Indices: 4231019--4231132 Score: 165
Period size: 47 Copynumber: 2.4 Consensus size: 46
4231009 ACTAGAGTTA
*
4231019 GTTTCAGACACCTCTAGCATTTCTTGAATATGTAACAACAAGAGTCG
1 GTTTCAG-CACCTCTAGCAATTCTTGAATATGTAACAACAAGAGTCG
* * *
4231066 GTTTCGGGCACCTCTAGCAATTCTTGACTATGTAACAACTAGAGTCG
1 GTTTC-AGCACCTCTAGCAATTCTTGAATATGTAACAACAAGAGTCG
4231113 GTTTCATGCACCTCTAGCAA
1 GTTTCA-GCACCTCTAGCAA
4231133 GAGTTTTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
47 59 0.98
48 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (46 bp):
GTTTCAGCACCTCTAGCAATTCTTGAATATGTAACAACAAGAGTCG
Found at i:4239308 original size:49 final size:48
Alignment explanation
Indices: 4239233--4239331 Score: 155
Period size: 49 Copynumber: 2.0 Consensus size: 48
4239223 CTTTCTATTC
4239233 AAACCATTAAAAATCCTATAATTTATAAG-TTTAATTTCATTTAATTTA
1 AAACCATTAAAAATCCTATAATTTATAAGCTTT-ATTTCATTTAATTTA
* *
4239281 AAACCATTAAAAATTCCTATAATTTATAAGCTTTATTTGATTTGATTTA
1 AAACCATTAAAAA-TCCTATAATTTATAAGCTTTATTTCATTTAATTTA
4239330 AA
1 AA
4239332 TTTATTTTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
48 13 0.28
49 31 0.66
50 3 0.06
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.43
Consensus pattern (48 bp):
AAACCATTAAAAATCCTATAATTTATAAGCTTTATTTCATTTAATTTA
Found at i:4241080 original size:13 final size:13
Alignment explanation
Indices: 4241062--4241110 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
4241052 ATGAAATTAC
4241062 TTTTCTTTTTAAT
1 TTTTCTTTTTAAT
*
4241075 TTTTCTTTTCTTTAT
1 TTTTC-TTT-TTAAT
* *
4241090 TTTTCTTTTCAAG
1 TTTTCTTTTTAAT
4241103 TTTTCTTT
1 TTTTCTTT
4241111 ACTTTTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 15 0.50
14 6 0.20
15 9 0.30
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTTCTTTTTAAT
Found at i:4241094 original size:28 final size:28
Alignment explanation
Indices: 4241062--4241115 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
4241052 ATGAAATTAC
* * *
4241062 TTTTCTTTTTAATTTTTCTTTTCTTTAT
1 TTTTCTTTTCAAGTTTTCTTTACTTTAT
4241090 TTTTCTTTTCAAGTTTTCTTTACTTT
1 TTTTCTTTTCAAGTTTTCTTTACTTT
4241116 TAAAATGCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.11, C:0.13, G:0.02, T:0.74
Consensus pattern (28 bp):
TTTTCTTTTCAAGTTTTCTTTACTTTAT
Found at i:4248108 original size:21 final size:21
Alignment explanation
Indices: 4248034--4248110 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
4248024 CGAAATTTCC
* *
4248034 CAGGTATCGATACCCTCCATA
1 CAGGTATCGATACTCTTCATA
* *
4248055 TAGGTATCGATATCTTTTTCATA
1 CAGGTATCGATA-C-TCTTCATA
* * *
4248078 -TGGTACCGATACTGTTCATA
1 CAGGTATCGATACTCTTCATA
4248098 CAGGTATCGATAC
1 CAGGTATCGATAC
4248111 CCCATGAGTT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
20 7 0.16
21 22 0.50
22 10 0.23
23 5 0.11
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (21 bp):
CAGGTATCGATACTCTTCATA
Found at i:4257273 original size:36 final size:36
Alignment explanation
Indices: 4257226--4257299 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
4257216 TATAACAAAA
4257226 TCGTTATCACCAGACCTCTTGAAATAAGCACAAGGG
1 TCGTTATCACCAGACCTCTTGAAATAAGCACAAGGG
4257262 TCGTTATCACCAGACCTCTTGAAATAAGCACAAGGG
1 TCGTTATCACCAGACCTCTTGAAATAAGCACAAGGG
4257298 TC
1 TC
4257300 TGCATTAAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (36 bp):
TCGTTATCACCAGACCTCTTGAAATAAGCACAAGGG
Found at i:4261544 original size:51 final size:51
Alignment explanation
Indices: 4261448--4261544 Score: 140
Period size: 51 Copynumber: 1.9 Consensus size: 51
4261438 CTATGCACCG
* * *
4261448 CGCCTTGCATAATTGTCTCAGAGTTAAAGAAAATGAGCGGTCCCTGAATCA
1 CGCCTTGCATAATTGTCTCAGAATTAAAGAAAAGGAGCGGCCCCTGAATCA
* * *
4261499 CGCCTTGCATAATTGTGTCAGAATTAAAGTAAAGGTGCGGCCCCTG
1 CGCCTTGCATAATTGTCTCAGAATTAAAGAAAAGGAGCGGCCCCTG
4261545 CACCGCGCTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.26
Consensus pattern (51 bp):
CGCCTTGCATAATTGTCTCAGAATTAAAGAAAAGGAGCGGCCCCTGAATCA
Found at i:4266856 original size:22 final size:22
Alignment explanation
Indices: 4266828--4266882 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
4266818 TTCAGTATTT
*
4266828 GTCCCGAATGACCACTAGATAC
1 GTCCCGAAGGACCACTAGATAC
*
4266850 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTAGATAC
*
4266872 GTTCCGAAGGA
1 GTCCCGAAGGA
4266883 TTAATATACC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.16
Consensus pattern (22 bp):
GTCCCGAAGGACCACTAGATAC
Found at i:4271597 original size:18 final size:18
Alignment explanation
Indices: 4271571--4271605 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4271561 GTTCAGTATT
* *
4271571 TGTCTCGAAGGACCACTA
1 TGTCCCGAAGAACCACTA
4271589 TGTCCCGAAGAACCACT
1 TGTCCCGAAGAACCACT
4271606 GGATACATCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGAACCACTA
Found at i:4278810 original size:17 final size:18
Alignment explanation
Indices: 4278788--4278821 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4278778 TCAGCCGGTC
4278788 CGGTTC-GAACGGTTCAA
1 CGGTTCTGAACGGTTCAA
*
4278805 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
4278822 CTAGTAGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAA
Found at i:4285549 original size:2 final size:2
Alignment explanation
Indices: 4285537--4285600 Score: 112
Period size: 2 Copynumber: 32.0 Consensus size: 2
4285527 CTGTGTTCTG
4285537 TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4285580 TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
4285601 AGCTCAAGAA
Statistics
Matches: 60, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 57 0.95
3 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4288718 original size:25 final size:24
Alignment explanation
Indices: 4288690--4288762 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
4288680 GTTTAGGGTC
4288690 TTTGAAAAGATAGA-ATAGGATTTTA
1 TTTGAAAA-AT-GATATAGGATTTTA
* *
4288715 TTTGGAAAATGATTTAGGATTTTA
1 TTTGAAAAATGATATAGGATTTTA
* * *
4288739 TTTGGAAAATGATTTAGGGTTTTA
1 TTTGAAAAATGATATAGGATTTTA
4288763 AATATTAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
23 2 0.05
24 35 0.80
25 7 0.16
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (24 bp):
TTTGAAAAATGATATAGGATTTTA
Found at i:4288733 original size:24 final size:24
Alignment explanation
Indices: 4288705--4288762 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
4288695 AAAGATAGAA
4288705 TAGGATTTTATTTGGAAAATGATT
1 TAGGATTTTATTTGGAAAATGATT
4288729 TAGGATTTTATTTGGAAAATGATT
1 TAGGATTTTATTTGGAAAATGATT
*
4288753 TAGGGTTTTA
1 TAGGATTTTA
4288763 AATATTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (24 bp):
TAGGATTTTATTTGGAAAATGATT
Found at i:4296913 original size:45 final size:45
Alignment explanation
Indices: 4296846--4296931 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 45
4296836 TAAAAAACTT
* * *
4296846 ACCTGATGGGAATGTGGTTTTGGAGCAGGCCAAGTGAGAGAACAA
1 ACCTGATGGGAACGTGGATTTGGAGCAGGCCAAGGGAGAGAACAA
* * *
4296891 ACCTGATGGGGACGTGGATTTGGAGCGGGTCAAGGGAGAGA
1 ACCTGATGGGAACGTGGATTTGGAGCAGGCCAAGGGAGAGA
4296932 CCCAAGTAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.28, C:0.13, G:0.41, T:0.19
Consensus pattern (45 bp):
ACCTGATGGGAACGTGGATTTGGAGCAGGCCAAGGGAGAGAACAA
Found at i:4315385 original size:2 final size:2
Alignment explanation
Indices: 4315378--4315407 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4315368 TTTAATATTC
4315378 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
4315408 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4316557 original size:20 final size:20
Alignment explanation
Indices: 4316532--4316582 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
4316522 TTAACCCATG
4316532 GTATTGATACCATGCCCTTA
1 GTATTGATACCATGCCCTTA
4316552 GTATTGATACCATGCCCTTA
1 GTATTGATACCATGCCCTTA
4316572 GTATTGATACC
1 GTATTGATACC
4316583 TGATGAATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (20 bp):
GTATTGATACCATGCCCTTA
Found at i:4322198 original size:33 final size:33
Alignment explanation
Indices: 4322130--4322203 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
4322120 ACCCCCTACA
* *
4322130 TCCGAATCTGACCTCTATTTTGTTGGAACATGC
1 TCCGAATCTGACCTCTATTTTGTTAGAACAAGC
*
4322163 TCCGAATCTGACCTCTATTTTGTTAGTACAAGC
1 TCCGAATCTGACCTCTATTTTGTTAGAACAAGC
*
4322196 TCCAAATC
1 TCCGAATC
4322204 CAATCAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (33 bp):
TCCGAATCTGACCTCTATTTTGTTAGAACAAGC
Found at i:4324165 original size:2 final size:2
Alignment explanation
Indices: 4324154--4324274 Score: 125
Period size: 2 Copynumber: 64.5 Consensus size: 2
4324144 TATGCATAAC
* * *
4324154 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA -A TT TT TCA -A GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
* *
4324194 -A T- TA TA TA T- TT TA TA -A TA CA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4324232 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4324272 TA T
1 TA T
4324275 GTGTGTGTTT
Statistics
Matches: 104, Mismatches: 5, Indels: 20
0.81 0.04 0.16
Matches are distributed among these distances:
1 9 0.09
2 95 0.91
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4325224 original size:74 final size:73
Alignment explanation
Indices: 4325146--4325331 Score: 232
Period size: 74 Copynumber: 2.5 Consensus size: 73
4325136 TAAGCCAATA
* * *
4325146 TTGATTCTTTAGATGACTCCCCTTTGAGGGTCTAAGTCAAGTGAGACCTCTCCCATTCACGGTTT
1 TTGATTCTTTGGATGACTCCCCTTCGAGGGTCTAAGTCAAGTGAGACCACTCCC-TTCACGGTTT
*
4325211 AAGCTGGTC
65 AAGCTAGTC
* * ** * * *
4325220 TTGATTATTTGGATGACTCCCATTCGCTGGTCTAAGTCAAGTGAGACGACTCTCTTCGCGGTTTA
1 TTGATTCTTTGGATGACTCCCCTTCGAGGGTCTAAGTCAAGTGAGACCACTCCCTTCACGGTTTA
4325285 AGCTAGTC
66 AGCTAGTC
*
4325293 TTGATTCTTTGGATAACTCCCCTTC-ATGGGTCT-AGTCAA
1 TTGATTCTTTGGATGACTCCCCTTCGA-GGGTCTAAGTCAA
4325332 ATTAAATGAC
Statistics
Matches: 95, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
72 6 0.06
73 44 0.46
74 45 0.47
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (73 bp):
TTGATTCTTTGGATGACTCCCCTTCGAGGGTCTAAGTCAAGTGAGACCACTCCCTTCACGGTTTA
AGCTAGTC
Found at i:4325312 original size:73 final size:74
Alignment explanation
Indices: 4325146--4325359 Score: 227
Period size: 73 Copynumber: 2.9 Consensus size: 74
4325136 TAAGCCAATA
* * * *
4325146 TTGATTCTTTAGATGACTCCCCTTTGAGGGTCTAAGTCAAGTGAGACCTCTCCCATTCACGGTTT
1 TTGATTCTTTGGATGACTCCCATTCGAGGGTCTAAGTCAAGTGAGACCACTCCCATTCACGGTTT
*
4325211 AAGCTGGTC
66 AAGCTAGTC
* ** * * *
4325220 TTGATTATTTGGATGACTCCCATTCGCTGGTCTAAGTCAAGTGAGACGACTCTC-TTCGCGGTTT
1 TTGATTCTTTGGATGACTCCCATTCGAGGGTCTAAGTCAAGTGAGACCACTCCCATTCACGGTTT
4325284 AAGCTAGTC
66 AAGCTAGTC
* * * * * ** *
4325293 TTGATTCTTTGGATAACTCCCCTTC-ATGGGTCT-AGTCAAATTAAATGACTCCCATTCATGGTT
1 TTGATTCTTTGGATGACTCCCATTCGA-GGGTCTAAGTCAAGTGAGACCACTCCCATTCACGGTT
4325356 TAAG
65 TAAG
4325360 ACAATCTTAA
Statistics
Matches: 115, Mismatches: 23, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
72 15 0.13
73 55 0.48
74 45 0.39
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (74 bp):
TTGATTCTTTGGATGACTCCCATTCGAGGGTCTAAGTCAAGTGAGACCACTCCCATTCACGGTTT
AAGCTAGTC
Found at i:4336386 original size:6 final size:6
Alignment explanation
Indices: 4335182--4336379 Score: 1944
Period size: 6 Copynumber: 205.3 Consensus size: 6
4335172 CTCAAAATCA
4335182 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
* *
4335230 ATATG- -TATGT ATATG- -TATGT ATATGT AGAGGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
4335274 ATATGT ATATGT ATATGT ATATGT ATATGT A-ATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
4335321 ATATGT A-ATGT ATATGT ATATGT ATATGT ATA--T ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
4335366 ATATGT AT-TGT AGATATGT ATATGT ATATGT ATATGT ATATGT AT-TGT
1 ATATGT ATATGT --ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
4335414 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATG- --ATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
4335459 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
4335507 ATATGT ATATGT ATATGT ATATGT ATATGT ATA-GT ATATG- -TATG-
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
4335551 ATATGT ATATG- -TATGT ATATGT ATGTATGT ATATG- ATATGT ATAT-T
1 ATATGT ATATGT ATATGT ATATGT A--TATGT ATATGT ATATGT ATATGT
4335597 ATATGT ATATGT ATATGT ATATGT ATATGT ATATG- -TATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
*
4335643 AT-TGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGGT ATATAT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATAT-GT ATATGT
* *
4335691 GTATGT ATATGT A-ATGT ATATGT ATATGT ATATGT CTATGT ATATG-
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
4335737 -TATGT ATATGT ATATGT ATATGT A-ATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
4335783 ATATGT ATATGT ATATGTAT ATATGT ATATGT ATATGT ATATGT ATATGTAT
1 ATATGT ATATGT ATATG--T ATATGT ATATGT ATATGT ATATGT ATATG--T
4335835 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATG- -TATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
4335881 ATATGT ATATGT A-ATGT ATATGT ATATGT ATATG- -TATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
*
4335926 ATATG- -TATGT ATATGT ATATGT ATATGT ATATGGT GTATGT ATATG-
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATAT-GT ATATGT ATATGT
4335972 -TATGT ATATGT ATATGT ATATGT ATATGT ATATGT -TATG- -TATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
4336016 ATATGT ATATGT ATATGT ATATGT -TATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
4336063 ATATGT ATATGT ATATG- ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
4336110 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
4336158 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
4336206 ATATG- -TATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
4336252 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
4336300 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
4336348 ATATGT ATATGT ATATGT ATATGT ATATGT AT
1 ATATGT ATATGT ATATGT ATATGT ATATGT AT
4336380 GAATATGTCA
Statistics
Matches: 1128, Mismatches: 12, Indels: 104
0.91 0.01 0.08
Matches are distributed among these distances:
3 3 0.00
4 52 0.05
5 71 0.06
6 968 0.86
7 13 0.01
8 21 0.02
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (6 bp):
ATATGT
Found at i:4343531 original size:32 final size:36
Alignment explanation
Indices: 4343468--4343544 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 36
4343458 TTGGGCCGGG
4343468 TATATATATTTAAATTAAATATATAAATATT-AT-T
1 TATATATATTTAAATTAAATATATAAATATTAATAT
* *
4343502 TATATAT-TTTAATTTAAAT-TA-AATTTATTAATAT
1 TATATATATTTAAATTAAATATATAA-ATATTAATAT
4343536 TATATATAT
1 TATATATAT
4343545 ATAATAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
31 2 0.05
32 6 0.16
33 13 0.35
34 15 0.41
35 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (36 bp):
TATATATATTTAAATTAAATATATAAATATTAATAT
Found at i:4343553 original size:38 final size:37
Alignment explanation
Indices: 4343468--4343553 Score: 111
Period size: 38 Copynumber: 2.3 Consensus size: 37
4343458 TTGGGCCGGG
*
4343468 TATATAT-ATTTAAATTAAATATATAAATATTATTTA
1 TATATATAATTTAAATTAAATATATAAATATTATATA
* * *
4343504 TATATTTTAATTTAAATTAAATTTATTAATATTATATA
1 TATA-TATAATTTAAATTAAATATATAAATATTATATA
4343542 TATATAATAATT
1 TATAT-ATAATT
4343554 ATTTTTAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
36 4 0.10
37 3 0.07
38 35 0.83
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (37 bp):
TATATATAATTTAAATTAAATATATAAATATTATATA
Found at i:4351137 original size:2 final size:2
Alignment explanation
Indices: 4351068--4351118 Score: 86
Period size: 2 Copynumber: 25.5 Consensus size: 2
4351058 TAAATAAAAA
4351068 AT AT AT ACT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4351110 AT AT AT AT A
1 AT AT AT AT A
4351119 GTTTTTCAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 44 0.94
3 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4351143 original size:17 final size:17
Alignment explanation
Indices: 4351123--4351161 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
4351113 TATATAGTTT
4351123 TTCAAGAACTATATATA
1 TTCAAGAACTATATATA
* *
4351140 TTCAAGAACTATTTATT
1 TTCAAGAACTATATATA
4351157 TTCAA
1 TTCAA
4351162 ATATATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.41
Consensus pattern (17 bp):
TTCAAGAACTATATATA
Found at i:4353752 original size:110 final size:110
Alignment explanation
Indices: 4353608--4353843 Score: 454
Period size: 110 Copynumber: 2.1 Consensus size: 110
4353598 CATCAGAAAC
* *
4353608 AAAACTTAAAATGTGAAAATTGTATTGAATCAGAAGATTAAATACTGAAAAACAGCTTACCATAT
1 AAAACCTAAAATATGAAAATTGTATTGAATCAGAAGATTAAATACTGAAAAACAGCTTACCATAT
4353673 TTGCATTTGGTGAAATAAACCCTAATAATGAACTCAAGACGTCAA
66 TTGCATTTGGTGAAATAAACCCTAATAATGAACTCAAGACGTCAA
4353718 AAAACCTAAAATATGAAAATTGTATTGAATCAGAAGATTAAATACTGAAAAACAGCTTACCATAT
1 AAAACCTAAAATATGAAAATTGTATTGAATCAGAAGATTAAATACTGAAAAACAGCTTACCATAT
4353783 TTGCATTTGGTGAAATAAACCCTAATAATGAACTCAAGACGTCAA
66 TTGCATTTGGTGAAATAAACCCTAATAATGAACTCAAGACGTCAA
4353828 AAAACCTAAAATATGA
1 AAAACCTAAAATATGA
4353844 CTTTTCGAGA
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 124 1.00
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.26
Consensus pattern (110 bp):
AAAACCTAAAATATGAAAATTGTATTGAATCAGAAGATTAAATACTGAAAAACAGCTTACCATAT
TTGCATTTGGTGAAATAAACCCTAATAATGAACTCAAGACGTCAA
Found at i:4370676 original size:187 final size:190
Alignment explanation
Indices: 4370314--4370692 Score: 689
Period size: 187 Copynumber: 2.0 Consensus size: 190
4370304 CTAAAATGAA
4370314 ACAAAAACTAAACGTTATGTATGATTTTGAAAAAAAAATGAAAATTTAAGTATTAAAATGAACCA
1 ACAAAAACTAAACGTTATGTATGATTTTGAAAAAAAAATGAAAATTTAAGTATTAAAATGAACCA
4370379 AACTGATAGTTTAGGTACTAAACGCGGTAATTTATTCCTAAAGTTTATGCATGATTAAGCATAGT
66 AACTGATAGTTTAGGTACTAAACGCGGTAATTTATTCCTAAAGTTTATGCATGATTAAGCATAGT
4370444 TATCGATTCATTAAAAAAACTCTAAATGTAAATTATTATTTTTAGTTTATA-TTTTTTAC
131 TATCGATTCATTAAAAAAACTCTAAATGTAAATTATTATTTTTAGTTTATATTTTTTTAC
4370503 ACAAAAACTAAACGTTATGTATGATTTTG-AAAAAAAATG-AAATTTAAGTATTAAAATGAACCA
1 ACAAAAACTAAACGTTATGTATGATTTTGAAAAAAAAATGAAAATTTAAGTATTAAAATGAACCA
4370566 AACTGATAGTTTAGGTACTAAACGC-GTAATTTATTCCTAAAGTTTATGCATGATT-AGCATAGT
66 AACTGATAGTTTAGGTACTAAACGCGGTAATTTATTCCTAAAGTTTATGCATGATTAAGCATAGT
4370629 TATCGATTCATTAAAAAAACTCTAAATGT-AATATATTATTATTTTAGTTTATATTTTTTTAC
131 TATCGATTCATTAAAAAAACTCTAAATGTAAAT-TATTA-T-TTTTAGTTTATATTTTTTTAC
4370691 AC
1 AC
4370693 GAAAGTTTAG
Statistics
Matches: 186, Mismatches: 0, Indels: 9
0.95 0.00 0.05
Matches are distributed among these distances:
184 3 0.02
185 42 0.23
186 31 0.17
187 61 0.33
188 20 0.11
189 29 0.16
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.37
Consensus pattern (190 bp):
ACAAAAACTAAACGTTATGTATGATTTTGAAAAAAAAATGAAAATTTAAGTATTAAAATGAACCA
AACTGATAGTTTAGGTACTAAACGCGGTAATTTATTCCTAAAGTTTATGCATGATTAAGCATAGT
TATCGATTCATTAAAAAAACTCTAAATGTAAATTATTATTTTTAGTTTATATTTTTTTAC
Done.