Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_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: 8285662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 35
Found at i:3596349 original size:165 final size:164
Alignment explanation
Indices: 3596052--3596363 Score: 466
Period size: 165 Copynumber: 1.9 Consensus size: 164
3596042 CTTTTGAGGC
* * *
3596052 ACATCATTTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAGTAAACCTTCGATTTCGATT
1 ACATCATTTTACAACATAACTCAAGGCGAGAAGGGCTATCTGTCAGTAAACCTTCGAGTTCGATT
* * *
3596117 ACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCGTCAA
66 ACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCGAGAAGGGATATCTATCATCAA
*
3596182 AGACCTTTGAGTTCGATACACTCAGCTCAAAGGT
131 AGACCTTTAAGTTCGATACACTCAGCTCAAAGGT
* * * *
3596216 ACATCA-TTTGCAACATAACTCAAGGCGAGAAGGGTTATTTGTC-GTCAAAGACCTTTGAGTTCG
1 ACATCATTTTACAACATAACTCAAGGCGAGAAGGGCTATCTGTCAGT--AA-ACCTTCGAGTTCG
* *
3596279 ATTACACTCAGCTCAAAGGCACATCATTTGCAGCGTAACTCAAGGCGAGAAGGGATATTTATCAT
63 ATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCGAGAAGGGATATCTATCAT
3596344 CAAAGACCTTTAAGTTCGAT
128 CAAAGACCTTTAAGTTCGAT
3596364 TGTATTCAAC
Statistics
Matches: 132, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
162 2 0.02
163 32 0.24
164 8 0.06
165 90 0.68
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (164 bp):
ACATCATTTTACAACATAACTCAAGGCGAGAAGGGCTATCTGTCAGTAAACCTTCGAGTTCGATT
ACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCGAGAAGGGATATCTATCATCAA
AGACCTTTAAGTTCGATACACTCAGCTCAAAGGT
Found at i:3598277 original size:15 final size:16
Alignment explanation
Indices: 3598252--3598283 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3598242 AAGTTTTTCG
3598252 TCTTAAAAATAATTTT
1 TCTTAAAAATAATTTT
3598268 TCTT-AAAATAATTTT
1 TCTTAAAAATAATTTT
3598283 T
1 T
3598284 GAAAGACGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (16 bp):
TCTTAAAAATAATTTT
Found at i:3598395 original size:16 final size:16
Alignment explanation
Indices: 3598374--3598406 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3598364 AAAATCACCG
3598374 AATTTTTCAAATTAAA
1 AATTTTTCAAATTAAA
3598390 AATTTTTCAAATTAAA
1 AATTTTTCAAATTAAA
3598406 A
1 A
3598407 GTTGTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTTTTCAAATTAAA
Found at i:3601579 original size:9 final size:10
Alignment explanation
Indices: 3601567--3601605 Score: 57
Period size: 9 Copynumber: 4.2 Consensus size: 10
3601557 TTTTTTCATT
3601567 TTATTTA-TA
1 TTATTTATTA
3601576 TTATTTATTA
1 TTATTTATTA
3601586 TTA-TTATTA
1 TTATTTATTA
3601595 TTA-TTATTA
1 TTATTTATTA
3601604 TT
1 TT
3601606 TTGAATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
9 24 0.83
10 5 0.17
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTATTTATTA
Found at i:3601580 original size:3 final size:3
Alignment explanation
Indices: 3601574--3601605 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
3601564 ATTTTATTTA
3601574 TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT T
3601606 TTGAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:3602178 original size:17 final size:18
Alignment explanation
Indices: 3602148--3602192 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
3602138 AAAACCGAAC
*
3602148 AAAAAAACACAACAAAGA
1 AAAAAAAGACAACAAAGA
*
3602166 AAAAAAAGA-AACAAGGA
1 AAAAAAAGACAACAAAGA
3602183 AAAACAAAGA
1 AAAA-AAAGA
3602193 GAAAGTAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.78, C:0.11, G:0.11, T:0.00
Consensus pattern (18 bp):
AAAAAAAGACAACAAAGA
Found at i:3610274 original size:16 final size:16
Alignment explanation
Indices: 3610239--3610279 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3610229 GTTTATTTCA
*
3610239 GAATGATT-AAGTGCT
1 GAATGATTCAAATGCT
*
3610254 GAATGATTCAAATGTT
1 GAATGATTCAAATGCT
3610270 GAATGATTCA
1 GAATGATTCA
3610280 GAAGCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (16 bp):
GAATGATTCAAATGCT
Found at i:3618078 original size:64 final size:64
Alignment explanation
Indices: 3618010--3618129 Score: 161
Period size: 64 Copynumber: 1.9 Consensus size: 64
3618000 TATAAATCCT
* * *
3618010 ATTCAATGTTTGCA-TTTAAGGGGGGTGCATCGATGCACTACTTGTGAATCGATACATTCATGGC
1 ATTCAATGTTTGCATTTTAA-AGGAGTGCATCGATGCACTACATGTGAATCGATACATTCATGGC
** * *
3618074 ATTCAATGTTTTTATTTTAAAGGAGTGCATCGATGCACTTCATGTGCATCGATACA
1 ATTCAATGTTTGCATTTTAAAGGAGTGCATCGATGCACTACATGTGAATCGATACA
3618130 CCTTGAACAA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
64 43 0.90
65 5 0.10
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (64 bp):
ATTCAATGTTTGCATTTTAAAGGAGTGCATCGATGCACTACATGTGAATCGATACATTCATGGC
Found at i:3618184 original size:21 final size:21
Alignment explanation
Indices: 3618160--3618208 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
3618150 TTATCCTTGA
3618160 TGCATCGGTACACATTGAATG
1 TGCATCGGTACACATTGAATG
**
3618181 TGCATCGGTATGCATTGAATG
1 TGCATCGGTACACATTGAATG
3618202 TGCATCG
1 TGCATCG
3618209 ATGCACATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (21 bp):
TGCATCGGTACACATTGAATG
Found at i:3621629 original size:20 final size:21
Alignment explanation
Indices: 3621590--3621630 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3621580 TGAATATGAA
*
3621590 CATGTAATATATCCATTCAAT
1 CATGTAATATATCAATTCAAT
*
3621611 CATGTCATATA-CAATTCAAT
1 CATGTAATATATCAATTCAAT
3621631 GTAAACAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.37
Consensus pattern (21 bp):
CATGTAATATATCAATTCAAT
Found at i:3622592 original size:19 final size:19
Alignment explanation
Indices: 3622544--3622592 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
3622534 AAGGGGGTGC
3622544 ATCGATGCACTACTTGTAA
1 ATCGATGCACTACTTGTAA
* *
3622563 ATCAATGCACTACTTGTGA
1 ATCGATGCACTACTTGTAA
*
3622582 ATCGATACACT
1 ATCGATGCACT
3622593 GATGGCATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (19 bp):
ATCGATGCACTACTTGTAA
Found at i:3631636 original size:6 final size:6
Alignment explanation
Indices: 3631625--3632625 Score: 1746
Period size: 6 Copynumber: 168.5 Consensus size: 6
3631615 ATGTCTAGAT
3631625 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
3631673 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
3631721 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
*
3631769 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATGC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
* * * * * * *
3631817 ATATAC ATATGC ATATGC ATATGC ATATGC ATATGC ATATGC ATATGC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
* *
3631865 ATATGC ATATCC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
3631913 --ATAC ATATAC ATATAC ATATAC ATATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC --ATATAC ATATAC ATATAC ATATAC
3631961 --ATAC ATATAC ATATAC ATATAC --ATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
3632005 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
3632053 ATATAC ATATAC --ATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
3632099 ATATAC ATATAC ATATAC ATATAC --ATAC ATATAC ATATAC --ATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
3632143 ATATAC ATATAC ATATAC --ATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
3632189 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
3632237 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
3632285 ATATAC ATATAC ATATAC ATATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC --ATATAC ATATAC ATATAC ATATAC ATATAC
3632335 ATATAC ATATAC ATATAC ATATAC ATATAC ATATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC --ATATAC ATATAC ATATAC
3632385 ATATAC --ATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
3632431 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
3632479 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
3632527 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
3632575 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
3632623 ATA
1 ATA
3632626 GTTACCTTTC
Statistics
Matches: 968, Mismatches: 5, Indels: 44
0.95 0.00 0.04
Matches are distributed among these distances:
4 32 0.03
6 918 0.95
8 18 0.02
ACGTcount: A:0.49, C:0.17, G:0.01, T:0.33
Consensus pattern (6 bp):
ATATAC
Found at i:3640583 original size:19 final size:20
Alignment explanation
Indices: 3640559--3640616 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 20
3640549 GCAACTGGAA
3640559 AACCGGTTTGACCGGTTC-G
1 AACCGGTTTGACCGGTTCTG
* *
3640578 AACCGGTCTGACCAG-TCTG
1 AACCGGTTTGACCGGTTCTG
*
3640597 AACCAGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTCTG
3640616 A
1 A
3640617 CCCGACCCGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
18 2 0.06
19 31 0.94
ACGTcount: A:0.21, C:0.28, G:0.28, T:0.24
Consensus pattern (20 bp):
AACCGGTTTGACCGGTTCTG
Found at i:3642470 original size:24 final size:24
Alignment explanation
Indices: 3642443--3642497 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
3642433 CTAGATTTAC
*
3642443 AGATCCGATTGATGAGATACGGGT
1 AGATCCCATTGATGAGATACGGGT
3642467 AGATCCCATTGATGAGATACGGGT
1 AGATCCCATTGATGAGATACGGGT
3642491 AGATCCC
1 AGATCCC
3642498 CTACCTCCGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (24 bp):
AGATCCCATTGATGAGATACGGGT
Found at i:3647898 original size:10 final size:11
Alignment explanation
Indices: 3647868--3647908 Score: 52
Period size: 10 Copynumber: 4.0 Consensus size: 11
3647858 GGAAAACTGG
3647868 TTCG-ACCGGT
1 TTCGAACCGGT
*
3647878 TTTGAACCGGT
1 TTCGAACCGGT
3647889 TTCG-ACCGG-
1 TTCGAACCGGT
3647898 TTCGAACCGGT
1 TTCGAACCGGT
3647909 CTGACTGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 4 0.15
10 13 0.50
11 9 0.35
ACGTcount: A:0.15, C:0.27, G:0.29, T:0.29
Consensus pattern (11 bp):
TTCGAACCGGT
Found at i:3647904 original size:20 final size:21
Alignment explanation
Indices: 3647868--3647908 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
3647858 GGAAAACTGG
*
3647868 TTCGACCGGTTTTGAACCGGT
1 TTCGACCGGTTTCGAACCGGT
3647889 TTCGACCGG-TTCGAACCGGT
1 TTCGACCGGTTTCGAACCGGT
3647909 CTGACTGATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.15, C:0.27, G:0.29, T:0.29
Consensus pattern (21 bp):
TTCGACCGGTTTCGAACCGGT
Found at i:3647929 original size:19 final size:20
Alignment explanation
Indices: 3647901--3647952 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
3647891 CGACCGGTTC
3647901 GAACCGGTCTGACT-GATCT
1 GAACCGGTCTGACTCGATCT
* *
3647920 GAATCGGTCTGACTCGGTCT
1 GAACCGGTCTGACTCGATCT
*
3647940 GAACCGGTTTGAC
1 GAACCGGTCTGAC
3647953 CGGTCTGACC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.19, C:0.25, G:0.29, T:0.27
Consensus pattern (20 bp):
GAACCGGTCTGACTCGATCT
Found at i:3647936 original size:10 final size:10
Alignment explanation
Indices: 3647905--3647961 Score: 57
Period size: 10 Copynumber: 5.9 Consensus size: 10
3647895 CGGTTCGAAC
3647905 CGGTCTGACT
1 CGGTCTGACT
* *
3647915 -GATCTGAAT
1 CGGTCTGACT
3647924 CGGTCTGACT
1 CGGTCTGACT
3647934 CGGTCTGAAC-
1 CGGTCTG-ACT
*
3647944 CGGTTTGAC-
1 CGGTCTGACT
3647953 CGGTCTGAC
1 CGGTCTGAC
3647962 CCGACCCGAC
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
9 17 0.44
10 20 0.51
11 2 0.05
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (10 bp):
CGGTCTGACT
Found at i:3647956 original size:9 final size:9
Alignment explanation
Indices: 3647903--3647962 Score: 57
Period size: 9 Copynumber: 6.3 Consensus size: 9
3647893 ACCGGTTCGA
3647903 ACCGGTCTG
1 ACCGGTCTG
* *
3647912 ACTGATCTG
1 ACCGGTCTG
*
3647921 AATCGGTCTG
1 -ACCGGTCTG
3647931 ACTCGGTCTG
1 AC-CGGTCTG
*
3647941 AACCGGTTTG
1 -ACCGGTCTG
3647951 ACCGGTCTG
1 ACCGGTCTG
3647960 ACC
1 ACC
3647963 CGACCCGACC
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
9 19 0.47
10 19 0.47
11 2 0.05
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.27
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:3652467 original size:2 final size:2
Alignment explanation
Indices: 3652460--3652498 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
3652450 ATCGAACTTC
* *
3652460 AT AT AT AT AT GT GT 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 AT A
3652499 CTGCAGATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3655212 original size:57 final size:57
Alignment explanation
Indices: 3655149--3655267 Score: 204
Period size: 57 Copynumber: 2.1 Consensus size: 57
3655139 GCAACTACCT
* *
3655149 GTCCCAAGAAGTATTTAAGACAACCA-AAGTCCTTAGTCTCAAATTTAGTTTCTAACA
1 GTCCCAAGAAGTATCTAAGACAA-CAGAAGTCCTTAGTCTCAAATTTAGTTGCTAACA
3655206 GTCCCAAGAAGTATCTAAGACAACAGAAGTCCTTAGTCTCAAATTTAGTTGCTAACA
1 GTCCCAAGAAGTATCTAAGACAACAGAAGTCCTTAGTCTCAAATTTAGTTGCTAACA
3655263 GTCCC
1 GTCCC
3655268 TTTAATATGC
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
56 2 0.03
57 57 0.97
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (57 bp):
GTCCCAAGAAGTATCTAAGACAACAGAAGTCCTTAGTCTCAAATTTAGTTGCTAACA
Found at i:3659876 original size:20 final size:21
Alignment explanation
Indices: 3659851--3659902 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3659841 TTTTACCAAT
*
3659851 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
3659871 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
3659892 TCGCAATGCGA
1 TCGCAATGCGA
3659903 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:3659916 original size:20 final size:20
Alignment explanation
Indices: 3659891--3659984 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
3659881 AATTGGGAAA
3659891 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
3659911 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
3659931 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
3659952 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
3659972 TTCGCAACGCGAT
1 ATCGCAATGCGAT
3659985 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:3660550 original size:19 final size:19
Alignment explanation
Indices: 3660500--3660571 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
3660490 ATAGTTTCGA
*
3660500 GAATGAAAATCGCAACGCG
1 GAATAAAAATCGCAACGCG
**
3660519 GAAATAACTATCGCAACGCG
1 G-AATAAAAATCGCAACGCG
3660539 GAATAAAAATCGCAACGCG
1 GAATAAAAATCGCAACGCG
* **
3660558 AAACCAAAATCGCA
1 GAATAAAAATCGCA
3660572 TTGCGATTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 28 0.64
20 16 0.36
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
GAATAAAAATCGCAACGCG
Found at i:3660589 original size:19 final size:19
Alignment explanation
Indices: 3660567--3660636 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
3660557 GAAACCAAAA
3660567 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
3660586 TCGCGTTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
3660605 TCG-AGTTGCGATTTTCATT
1 TCGCA-TTGCGATTTTCATT
*
3660624 TCGCGTTGCGATT
1 TCGCATTGCGATT
3660637 CTCTCGTTGC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:3660656 original size:33 final size:34
Alignment explanation
Indices: 3660609--3660672 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
3660599 TTTATTTCGA
**
3660609 GTTGCGATTTTCATTT-CGCGTTGCGATTCTCTC
1 GTTGCGATAGTCATTTCCGCGTTGCGATTCTCTC
3660642 GTTGCGATAGTCATTTCCGCGTTGCGATTCT
1 GTTGCGATAGTCATTTCCGCGTTGCGATTCT
3660673 TATTATCTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 14 0.50
34 14 0.50
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.42
Consensus pattern (34 bp):
GTTGCGATAGTCATTTCCGCGTTGCGATTCTCTC
Found at i:3662867 original size:42 final size:42
Alignment explanation
Indices: 3662791--3662879 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
3662781 GACTCGCCTG
* * *
3662791 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCACTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
* * * *
3662833 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
3662875 TCATC
1 TCATC
3662880 GTTGAAGAGG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
Found at i:3664288 original size:14 final size:14
Alignment explanation
Indices: 3664269--3664304 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3664259 ATTGTTTAAT
3664269 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
3664283 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
3664297 TGATTTGT
1 TGATTTGT
3664305 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:3664456 original size:33 final size:33
Alignment explanation
Indices: 3664411--3664500 Score: 126
Period size: 33 Copynumber: 2.7 Consensus size: 33
3664401 AAAAAGTACT
* *
3664411 ATCGCAATGCGAAATGAAAATCGTAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
3664444 ATCGCAACGCGAAATGAAAATGGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* * *
3664477 ATCACAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
3664501 GTTGCGATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:3664542 original size:33 final size:33
Alignment explanation
Indices: 3664500--3664626 Score: 177
Period size: 33 Copynumber: 3.8 Consensus size: 33
3664490 ATTAAATTCG
*
3664500 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
*
3664533 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AGT
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCACT
*
3664567 -GTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
* *
3664599 CGTTGCGATTTTTATTTCGCATTACGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
3664627 AGTAATTTTC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
32 1 0.01
33 76 0.90
34 1 0.01
35 3 0.04
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:3664559 original size:19 final size:19
Alignment explanation
Indices: 3664496--3664626 Score: 76
Period size: 19 Copynumber: 7.7 Consensus size: 19
3664486 CGAAATTAAA
*
3664496 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
3664515 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
3664531 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
**
3664548 TTCGCATTGCGAAATT-A-
1 TTCGCATTGCGATTTTCAT
*
3664565 GT-G--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
3664581 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
* *
3664597 CTCG--TTGCGATTTTTAT
1 TTCGCATTGCGATTTTCAT
*
3664614 TTCGCATTACGAT
1 TTCGCATTGCGAT
3664627 AGTAATTTTC
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 20 0.24
15 1 0.01
16 14 0.17
17 15 0.18
18 1 0.01
19 31 0.38
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:3666935 original size:12 final size:12
Alignment explanation
Indices: 3666918--3666942 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3666908 TCTTCGGGGA
3666918 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3666930 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3666942 C
1 C
3666943 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3667151 original size:24 final size:24
Alignment explanation
Indices: 3667117--3667170 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
3667107 CTGAAACATC
* *
3667117 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
3667141 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
3667165 ATCAAA
1 ATCAAA
3667171 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:3668251 original size:20 final size:20
Alignment explanation
Indices: 3668226--3668283 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
3668216 ATTCATTTGA
3668226 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
3668246 CTATCGCAATGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
3668266 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
3668284 CGCAATGCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:3668343 original size:19 final size:19
Alignment explanation
Indices: 3668302--3668388 Score: 139
Period size: 19 Copynumber: 4.8 Consensus size: 19
3668292 GAAATGAAAA
3668302 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
3668318 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3668335 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3668354 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3668373 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
3668389 TCGTTGCGAT
Statistics
Matches: 66, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.17
16 3 0.05
17 3 0.05
19 49 0.74
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:3668372 original size:38 final size:33
Alignment explanation
Indices: 3668302--3668417 Score: 151
Period size: 33 Copynumber: 3.4 Consensus size: 33
3668292 GAAATGAAAA
3668302 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
3668335 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTC---TCG--TTGCGATTTTCATT
***
3668373 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
*
3668406 TCGCGTTGCGAT
1 TCGCATTGCGAT
3668418 AGTCTGTTTT
Statistics
Matches: 74, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
33 38 0.51
35 3 0.04
36 3 0.04
38 30 0.41
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
Found at i:3668522 original size:14 final size:14
Alignment explanation
Indices: 3668503--3668539 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3668493 CATCAATTAA
3668503 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3668517 ACAAATCATCTTTT
1 ACAAATCAACATTT
3668531 ACAAATCAA
1 ACAAATCAA
3668540 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3670378 original size:20 final size:20
Alignment explanation
Indices: 3670355--3670422 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
3670345 GAAACTTAAA
3670355 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
3670375 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
* **
3670395 ATCGCAATGC-AAAATGAAA
1 ATCGCAACGCGAAAATGACT
3670414 ATCGCAACG
1 ATCGCAACG
3670423 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 13 0.32
20 27 0.68
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:3670428 original size:14 final size:14
Alignment explanation
Indices: 3670411--3670468 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
3670401 ATGCAAAATG
3670411 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
3670425 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
3670441 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
3670457 AAAATCGCAACG
1 AAAATCGCAACG
3670469 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3670453 original size:32 final size:33
Alignment explanation
Indices: 3670395--3670473 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
3670385 GGAAATGGCT
* *
3670395 ATCGCAATGCAAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
3670428 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
3670460 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
3670474 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 30 0.68
33 14 0.32
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:3670502 original size:19 final size:18
Alignment explanation
Indices: 3670480--3670542 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
3670470 GAAACACAAA
3670480 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
* *
3670499 TCGCGTTGCGATTT--TG
1 TCGCATTGCGATTTCATT
3670515 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
3670531 TCGCATTGCGAT
1 TCGCATTGCGAT
3670543 AGCCATTTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 9 0.24
16 8 0.22
18 10 0.27
19 10 0.27
ACGTcount: A:0.13, C:0.21, G:0.22, T:0.44
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:3670561 original size:20 final size:19
Alignment explanation
Indices: 3670527--3670581 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
3670517 GTTGCGATTT
*
3670527 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
3670546 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
3670566 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
3670582 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:3671089 original size:18 final size:18
Alignment explanation
Indices: 3671063--3671102 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3671053 GTCGATCAGA
* *
3671063 TGATGGCTCTGGGTGAGG
1 TGATAGCTCTGGGCGAGG
3671081 TGATAGCTCTGGGCGAGG
1 TGATAGCTCTGGGCGAGG
3671099 TGAT
1 TGAT
3671103 GACTCCCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.12, G:0.45, T:0.28
Consensus pattern (18 bp):
TGATAGCTCTGGGCGAGG
Found at i:3672408 original size:20 final size:20
Alignment explanation
Indices: 3672385--3672430 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
3672375 AAATGAAAAC
3672385 CGCAACACGAAAATGACTAT
1 CGCAACACGAAAATGACTAT
* **
3672405 CGCAACGCGAATTTGACTAT
1 CGCAACACGAAAATGACTAT
3672425 CGCAAC
1 CGCAAC
3672431 GAGAGAATCA
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:0.37, C:0.28, G:0.17, T:0.17
Consensus pattern (20 bp):
CGCAACACGAAAATGACTAT
Found at i:3672721 original size:22 final size:22
Alignment explanation
Indices: 3672694--3672737 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3672684 TATGGAGATA
3672694 GACGGATTTCACCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
**
3672716 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
3672738 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCACCGGAGATGGG
Found at i:3672950 original size:20 final size:20
Alignment explanation
Indices: 3672924--3673037 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
3672914 GATTATGTAT
3672924 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
3672944 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
3672964 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
3672984 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
3673005 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
3673025 TATCGCATTGCGA
1 TATCGCGTTGCGA
3673038 TTTTCCCAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 3 0.04
20 63 0.79
21 12 0.15
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:3673041 original size:41 final size:41
Alignment explanation
Indices: 3672904--3673039 Score: 159
Period size: 41 Copynumber: 3.3 Consensus size: 41
3672894 CGCTTTGAAA
*
3672904 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * * *
3672945 ATCGCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * * * *
3672985 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
3673026 ATCGCATTGCGATT
1 ATCGCATTGCGATT
3673040 TTCCCAATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
39 3 0.04
40 31 0.40
41 42 0.54
42 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:3673057 original size:41 final size:41
Alignment explanation
Indices: 3672904--3673059 Score: 109
Period size: 41 Copynumber: 3.8 Consensus size: 41
3672894 CGCTTTGAAA
* ** * * * *
3672904 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
* *** * *
3672945 ATCGCGTTGCGAAAGT-CAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
* * ** * * *
3672985 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
3673026 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
3673060 TTACTTATTC
Statistics
Matches: 90, Mismatches: 23, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
40 32 0.36
41 56 0.62
42 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
Found at i:3673696 original size:29 final size:29
Alignment explanation
Indices: 3673654--3673711 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
3673644 AAATACTCCC
3673654 ATCCTCTGTTACTTTCATCACACCATATT
1 ATCCTCTGTTACTTTCATCACACCATATT
*
3673683 ATCCTTTGTTACTTTCATCACACCATATT
1 ATCCTCTGTTACTTTCATCACACCATATT
3673712 CTTTTGAGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.29, G:0.03, T:0.43
Consensus pattern (29 bp):
ATCCTCTGTTACTTTCATCACACCATATT
Found at i:3674323 original size:49 final size:51
Alignment explanation
Indices: 3674260--3674365 Score: 126
Period size: 51 Copynumber: 2.1 Consensus size: 51
3674250 TACCTGCACC
* *
3674260 GCGCTATATGTAATTAT-TCAGATA-AAAGGTATAGCGCTGAGCAGGGGCG
1 GCGCTAAATATAATTATGTCAGATACAAAGGTATAGCGCTGAGCAGGGGCG
* ** * * *
3674309 GCGCTAAATATAATTCTGTCAGATACCCAGGTATAGCGTTGAGTAGGGGTG
1 GCGCTAAATATAATTATGTCAGATACAAAGGTATAGCGCTGAGCAGGGGCG
3674360 GCGCTA
1 GCGCTA
3674366 TACTCCTACA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
49 14 0.30
50 7 0.15
51 26 0.55
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.25
Consensus pattern (51 bp):
GCGCTAAATATAATTATGTCAGATACAAAGGTATAGCGCTGAGCAGGGGCG
Found at i:3674481 original size:51 final size:51
Alignment explanation
Indices: 3674378--3674492 Score: 126
Period size: 51 Copynumber: 2.3 Consensus size: 51
3674368 CTCCTACATG
* * **
3674378 GCGTATAGCACGGATCAGGGGGTGCGCTATACCCATGTGTACGACATGTCA
1 GCGTATAGCGCGGATCAGGGGGTGCGCTATACCCACGTGTACGACAAATCA
* * *
3674429 GCGTATAGCGCGG-TACAGGGGGTGTGCTATATCCCACGTG-GCGCCAAATCA
1 GCGTATAGCGCGGAT-CAGGGGGTGCGCTATA-CCCACGTGTACGACAAATCA
*
3674480 GCATATAGCGCGG
1 GCGTATAGCGCGG
3674493 GGCAAGGAGC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
50 1 0.02
51 46 0.85
52 7 0.13
ACGTcount: A:0.23, C:0.24, G:0.33, T:0.20
Consensus pattern (51 bp):
GCGTATAGCGCGGATCAGGGGGTGCGCTATACCCACGTGTACGACAAATCA
Found at i:3675954 original size:19 final size:19
Alignment explanation
Indices: 3675930--3675970 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3675920 AATATTTACA
*
3675930 ATAAAAAT-AATTTTAAAAT
1 ATAAAAATGAATTAT-AAAT
3675949 ATAAAAATGAATTATAAAT
1 ATAAAAATGAATTATAAAT
3675968 ATA
1 ATA
3675971 TTAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
ATAAAAATGAATTATAAAT
Found at i:3676068 original size:16 final size:16
Alignment explanation
Indices: 3676047--3676114 Score: 84
Period size: 16 Copynumber: 4.1 Consensus size: 16
3676037 TAAATTAAAC
3676047 TTTTATAATTTAATAT
1 TTTTATAATTTAATAT
3676063 TTTTATAATTTAATAT
1 TTTTATAATTTAATAT
*
3676079 TTTTATATTTTTAAATTAT
1 TTTTATA-ATTT-AA-TAT
3676098 ATTTTA-AATTTAATAT
1 -TTTTATAATTTAATAT
3676114 T
1 T
3676115 AAATATAAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
15 1 0.02
16 26 0.57
17 5 0.11
18 5 0.11
19 4 0.09
20 5 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTATAATTTAATAT
Found at i:3676088 original size:8 final size:8
Alignment explanation
Indices: 3676047--3676091 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
3676037 TAAATTAAAC
*
3676047 TTTTATAA
1 TTTTATAT
*
3676055 TTTAATAT
1 TTTTATAT
*
3676063 TTTTATAA
1 TTTTATAT
*
3676071 TTTAATAT
1 TTTTATAT
3676079 TTTTATAT
1 TTTTATAT
3676087 TTTTA
1 TTTTA
3676092 AATTATATTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTTATAT
Found at i:3678159 original size:22 final size:22
Alignment explanation
Indices: 3678133--3678181 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
3678123 TTAAATTAAA
*
3678133 AAAAATAAAAT-TATATATATTTT
1 AAAAATAAAATGCATA-A-ATTTT
*
3678156 AAAAAGAAAATGCATAAATTTT
1 AAAAATAAAATGCATAAATTTT
3678178 AAAA
1 AAAA
3678182 TAACCTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 9 0.39
23 11 0.48
24 3 0.13
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (22 bp):
AAAAATAAAATGCATAAATTTT
Found at i:3678689 original size:3 final size:3
Alignment explanation
Indices: 3678683--3678762 Score: 115
Period size: 3 Copynumber: 26.0 Consensus size: 3
3678673 TTACCCATTT
* *
3678683 TTA TTA TTA TAA TTA TAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
3678731 TTA TTA TTA TTA TTAA TTA TTTA TTA ATA TTA
1 TTA TTA TTA TTA TT-A TTA -TTA TTA TTA TTA
3678763 CAAAGCCCAA
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
3 63 0.91
4 6 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3680081 original size:13 final size:13
Alignment explanation
Indices: 3680042--3680082 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
3680032 AATAATAATT
3680042 TATTT-TTTTCAA
1 TATTTATTTTCAA
*
3680054 TAAATTATTTT-AA
1 T-ATTTATTTTCAA
3680067 TATTTATTTTCAA
1 TATTTATTTTCAA
3680080 TAT
1 TAT
3680083 CGAAGAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
12 9 0.38
13 11 0.46
14 4 0.17
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTTATTTTCAA
Found at i:3691275 original size:5 final size:5
Alignment explanation
Indices: 3691265--3691334 Score: 72
Period size: 5 Copynumber: 13.8 Consensus size: 5
3691255 CTTAAAGAGA
* *
3691265 AAAAG AAAAG -AAAG AAAAAA AAAAG AAAAAG AAAAG AAAAG AAAAA AAAAG
1 AAAAG AAAAG AAAAG -AAAAG AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG
*
3691316 AAAA- AAAGAA AAAAG AAAA
1 AAAAG AAA-AG AAAAG AAAA
3691335 AAGGGGGTCA
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
4 7 0.13
5 37 0.67
6 11 0.20
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:3691283 original size:1 final size:1
Alignment explanation
Indices: 3691264--3691336 Score: 56
Period size: 1 Copynumber: 73.0 Consensus size: 1
3691254 GCTTAAAGAG
* * * * * * * * *
3691264 AAAAAGAAAAGAAAGAAAAAAAAAAGAAAAAGAAAAGAAAAGAAAAAAAAAGAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
3691329 AGAAAAAA
1 AAAAAAAA
3691337 GGGGGTCAAG
Statistics
Matches: 52, Mismatches: 20, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (1 bp):
A
Found at i:3691297 original size:26 final size:26
Alignment explanation
Indices: 3691262--3691336 Score: 109
Period size: 26 Copynumber: 2.9 Consensus size: 26
3691252 ATGCTTAAAG
3691262 AGAAAAAGAAAAGAAAGAAAAAAAAA
1 AGAAAAAGAAAAGAAAGAAAAAAAAA
3691288 AGAAAAAGAAAAGAAA-AGAAAAAAAA
1 AGAAAAAGAAAAGAAAGA-AAAAAAAA
*
3691314 AGAAAAA-AAGAAAAAAGAAAAAA
1 AGAAAAAGAA-AAGAAAGAAAAAA
3691337 GGGGGTCAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
25 3 0.07
26 41 0.91
27 1 0.02
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (26 bp):
AGAAAAAGAAAAGAAAGAAAAAAAAA
Found at i:3691336 original size:15 final size:16
Alignment explanation
Indices: 3691258--3691334 Score: 108
Period size: 15 Copynumber: 4.9 Consensus size: 16
3691248 TATTATGCTT
3691258 AAAGAGAAAAAGAAAAG
1 AAAGA-AAAAAGAAAAG
3691275 AAAGAAAAAA-AAAAG
1 AAAGAAAAAAGAAAAG
3691290 AAA-AAGAAAAGAAAAG
1 AAAGAA-AAAAGAAAAG
3691306 AAA-AAAAAAGAAAA-
1 AAAGAAAAAAGAAAAG
3691320 AAAGAAAAAAGAAAA
1 AAAGAAAAAAGAAAA
3691335 AAGGGGGTCA
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.09
15 32 0.56
16 15 0.26
17 5 0.09
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAGAAAAG
Found at i:3692873 original size:83 final size:84
Alignment explanation
Indices: 3692728--3693000 Score: 350
Period size: 83 Copynumber: 3.1 Consensus size: 84
3692718 GAACCAATCA
*
3692728 TTGGAATAAAACCAATCATTGAATTTGAAAGATGAATGTGCTCAAAGCATCTTCTGGAAGTGTTC
1 TTGG-ATAAAACCAATCATTGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTC
* *
3692793 TTTGAGTTATTTGATCTGGT
65 TTTGAGTTATCTGATTTGGT
* *
3692813 TTGG-TAAAACCAATCATTGATTTTGAAAGATGAATGTGCTCATAGCATCTTCTAGAAGTGTTCT
1 TTGGATAAAACCAATCATTGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCT
3692877 TTGAGTTATCTGATTTGGT
66 TTGAGTTATCTGATTTGGT
* * * * *
3692896 TTGGTATGAACCACAGAACCAGTTATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGA
1 TTGG-AT-----A-A-AACCAATCATTGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTGGA
3692961 AGTGTTCTTTGAGTTATCTGATTTGGT
58 AGTGTTCTTTGAGTTATCTGATTTGGT
*
3692988 TTGATATAAAACC
1 TTG-GATAAAACC
3693001 CAGAACCAAT
Statistics
Matches: 165, Mismatches: 13, Indels: 20
0.83 0.07 0.10
Matches are distributed among these distances:
83 78 0.47
85 9 0.05
86 1 0.01
87 1 0.01
90 1 0.01
91 1 0.01
92 74 0.45
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (84 bp):
TTGGATAAAACCAATCATTGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCT
TTGAGTTATCTGATTTGGT
Found at i:3692977 original size:92 final size:91
Alignment explanation
Indices: 3692737--3693020 Score: 363
Period size: 92 Copynumber: 3.2 Consensus size: 91
3692727 ATTGGAATAA
3692737 AACCAATCATTGAATTTGAAAGATGAATGTGCTCAA-AGCATCTTCTGGAAGTGTTCTTTGAGTT
1 AACCAATCATTGAATTTGAAAGATGAATGTGCT-AATAGCATCTTCTGGAAGTGTTCTTTGAGTT
* *
3692801 ATTTGATCTGGTTTGG--T----A-A-
65 ATCTGATTTGGTTTGGTATAACCACAG
* * *
3692820 AACCAATCATTGATTTTGAAAGATGAATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTA
1 AACCAATCATTGAATTTGAAAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
3692885 TCTGATTTGGTTTGGTATGAACCACAG
66 TCTGATTTGGTTTGGTAT-AACCACAG
* * * *
3692912 AACCAGTTATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
1 AACCAATCATTGAATTTGAAAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
*
3692977 TCTGATTTGGTTTGATATAAAACC-CAG
66 TCTGATTTGGTTTGGTAT--AACCACAG
3693004 AACCAATCATTGGAATT
1 AACCAATCATT-GAATT
3693021 AAAAGGTGAA
Statistics
Matches: 173, Mismatches: 16, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
82 1 0.01
83 73 0.42
85 1 0.01
90 1 0.01
91 1 0.01
92 87 0.50
93 9 0.05
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (91 bp):
AACCAATCATTGAATTTGAAAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
TCTGATTTGGTTTGGTATAACCACAG
Found at i:3693907 original size:113 final size:113
Alignment explanation
Indices: 3693710--3695583 Score: 3311
Period size: 113 Copynumber: 16.6 Consensus size: 113
3693700 GCAAAGATTT
* * * *
3693710 AAATCCATCA-TTCAATGGATCAGCTTTT-CAATTCAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTT-GATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAA
* *
3693773 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTTCTC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
3693822 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCTTAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
* *
3693887 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTACTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
3693935 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
* *
3694000 AAGGAAGAAGAAGTTAATAATGAGAAGAATTTGTTTAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
3694048 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
3694113 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
3694161 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAA
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
* *
3694226 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACATTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
3694274 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
3694339 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
3694387 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
3694452 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
3694500 AAATCCATCACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
3694565 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
3694613 AAATCCATCACTTGATGGATCAGCTTTTCTAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
*
3694678 AAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
3694726 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAAATCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
3694791 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
3694839 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
3694904 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
3694952 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCAAGTTCATAATAAGAAGAACTCATCTGAAA
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
*
3695017 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
3695065 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
*
3695130 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACATTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
3695178 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
* *
3695243 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACATTTTTCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
3695291 AAATCCATCACTTGATGGATCAGCTTTTCCAATTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
3695356 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
3695404 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
* * * *
3695469 AAGGAAGAAGAAGTTCGTAATGAGAAGAACTTGTTTAACCTTTTGTTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * * * **** *
3695517 AAATTCATCACTTAATGGATCAACCTTTACGGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
3695582 AA
66 AA
3695584 TAATAAGTTC
Statistics
Matches: 1706, Mismatches: 54, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
112 24 0.01
113 1682 0.99
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (113 bp):
AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:3695861 original size:3 final size:3
Alignment explanation
Indices: 3695853--3695949 Score: 131
Period size: 3 Copynumber: 31.7 Consensus size: 3
3695843 ATGTTATTTA
*
3695853 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
3695901 AAT TAT AAT TAT TAT TAT TAT TAT TAA TAT ATAT TATT TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA-T TAT TAT TAT
3695948 TA
1 TA
3695950 CAAAACCCAA
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
3 76 0.93
4 6 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:3701818 original size:15 final size:16
Alignment explanation
Indices: 3701798--3701837 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
3701788 TTTACTTCAT
*
3701798 AATGATT-AAGCGCTG
1 AATGATTCAAACGCTG
*
3701813 AATGATTCAAATGCTG
1 AATGATTCAAACGCTG
3701829 AATGATTCA
1 AATGATTCA
3701838 GAGACTCTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (16 bp):
AATGATTCAAACGCTG
Found at i:3702078 original size:6 final size:6
Alignment explanation
Indices: 3702067--3702097 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3702057 TATAATCAAC
3702067 ATACAA ATACAA ATACAA ATACAA ATACAA A
1 ATACAA ATACAA ATACAA ATACAA ATACAA A
3702098 ACCAATTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (6 bp):
ATACAA
Found at i:3710880 original size:59 final size:60
Alignment explanation
Indices: 3710777--3710905 Score: 161
Period size: 59 Copynumber: 2.1 Consensus size: 60
3710767 CGAACTCGAA
* * *
3710777 AAAACTCAAACTGAAAAATAAATTCAAAAGATCAACTAAAACTCGAATTTCAAGCTCAATT
1 AAAACTC-AACTCAAAAATAAATTCAAAAGATCAACTAAAACTCGAAATTCAAACTCAATT
* * * * *
3710838 AAAACTCAACTCAAAAA-AATTTCAAGAGCTCGATTAAAACTCGAAATTCAAACTCAATT
1 AAAACTCAACTCAAAAATAAATTCAAAAGATCAACTAAAACTCGAAATTCAAACTCAATT
*
3710897 CAAACTCAA
1 AAAACTCAA
3710906 TTGAAGCTCA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
59 43 0.73
60 9 0.15
61 7 0.12
ACGTcount: A:0.51, C:0.20, G:0.06, T:0.22
Consensus pattern (60 bp):
AAAACTCAACTCAAAAATAAATTCAAAAGATCAACTAAAACTCGAAATTCAAACTCAATT
Found at i:3710896 original size:11 final size:11
Alignment explanation
Indices: 3710882--3710929 Score: 69
Period size: 11 Copynumber: 4.4 Consensus size: 11
3710872 TAAAACTCGA
3710882 AATTCAAACTC
1 AATTCAAACTC
3710893 AATTCAAACTC
1 AATTCAAACTC
* *
3710904 AATTGAAGCTC
1 AATTCAAACTC
*
3710915 AATTCAAACTT
1 AATTCAAACTC
3710926 AATT
1 AATT
3710930 GAAGCTCGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.31
Consensus pattern (11 bp):
AATTCAAACTC
Found at i:3710915 original size:22 final size:22
Alignment explanation
Indices: 3710890--3710936 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3710880 GAAATTCAAA
3710890 CTCAATTCAAACTCAATTGAAG
1 CTCAATTCAAACTCAATTGAAG
*
3710912 CTCAATTCAAACTTAATTGAAG
1 CTCAATTCAAACTCAATTGAAG
3710934 CTC
1 CTC
3710937 GAGAATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.30
Consensus pattern (22 bp):
CTCAATTCAAACTCAATTGAAG
Found at i:3712300 original size:2 final size:2
Alignment explanation
Indices: 3712293--3712325 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3712283 ATCAATTTTA
3712293 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3712326 CTTATACTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3712650 original size:21 final size:21
Alignment explanation
Indices: 3712621--3712673 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3712611 TATAATCGGA
* * * *
3712621 TTTAGGGTTTATGGTTTATAT
1 TTTAAGGTTTATGATTTAGAG
*
3712642 TTTAAGGTTTATGATTTAGGG
1 TTTAAGGTTTATGATTTAGAG
3712663 TTTAAGGTTTA
1 TTTAAGGTTTA
3712674 GATATTAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.53
Consensus pattern (21 bp):
TTTAAGGTTTATGATTTAGAG
Found at i:3712743 original size:7 final size:7
Alignment explanation
Indices: 3712719--3712809 Score: 155
Period size: 7 Copynumber: 13.0 Consensus size: 7
3712709 GTAAGTATGA
3712719 TTTAGGG
1 TTTAGGG
* *
3712726 TTTATGA
1 TTTAGGG
*
3712733 TTTAGAG
1 TTTAGGG
3712740 TTTAGGG
1 TTTAGGG
3712747 TTTAGGG
1 TTTAGGG
3712754 TTTAGGG
1 TTTAGGG
3712761 TTTAGGG
1 TTTAGGG
3712768 TTTAGGG
1 TTTAGGG
3712775 TTTAGGG
1 TTTAGGG
3712782 TTTAGGG
1 TTTAGGG
3712789 TTTAGGG
1 TTTAGGG
3712796 TTTAGGG
1 TTTAGGG
3712803 TTTAGGG
1 TTTAGGG
3712810 CTCATTGCAA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 78 1.00
ACGTcount: A:0.16, C:0.00, G:0.40, T:0.44
Consensus pattern (7 bp):
TTTAGGG
Found at i:3741537 original size:31 final size:31
Alignment explanation
Indices: 3741480--3741539 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
3741470 AGTTTCTACC
* * *
3741480 TATTTTTTATTATTGATAATATTATTTTACT
1 TATTTTTTAATATTAATAATAATATTTTACT
3741511 TATTTTTTAATATTAAATAA-AATATTTTA
1 TATTTTTTAATATT-AATAATAATATTTTA
3741540 AAAAAACTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (31 bp):
TATTTTTTAATATTAATAATAATATTTTACT
Found at i:3742041 original size:4 final size:4
Alignment explanation
Indices: 3742032--3742071 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
3742022 CGATAATTTG
* * *
3742032 TATA TATA TATA TATA TATA TATT TATT TATA TTTA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
3742072 AAAGAAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (4 bp):
TATA
Found at i:3742043 original size:6 final size:6
Alignment explanation
Indices: 3742032--3742071 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
3742022 CGATAATTTG
* * *
3742032 TATATA TATATA TATATA TATATT TATTTA TATTTA TATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATA
3742072 AAAGAAAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (6 bp):
TATATA
Found at i:3742047 original size:10 final size:10
Alignment explanation
Indices: 3742032--3742071 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
3742022 CGATAATTTG
3742032 TATATATATA
1 TATATATATA
3742042 TATATATATA
1 TATATATATA
* *
3742052 TATTTATTTA
1 TATATATATA
*
3742062 TATTTATATA
1 TATATATATA
3742072 AAAGAAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TATATATATA
Found at i:3752204 original size:197 final size:199
Alignment explanation
Indices: 3751871--3752266 Score: 737
Period size: 197 Copynumber: 2.0 Consensus size: 199
3751861 TTTCCAACAA
3751871 TCTGATTCTTTTCCAATAGCCAATATTGAATAAACCATAGTTTTGTAGAAGTAAATGAGCCACAA
1 TCTGATTCTTTTCCAATAGCCAATATTGAATAAACCATAGTTTTGTAGAAGTAAATGAGCCACAA
3751936 AATCATCTCTGGGAACTTTAGAGGCAGGCAAGGATTATGCCCAGATATTTTCAGAAACAAGGCCA
66 AATCATCTCTGGGAACTTTAGAGGCAGGCAAGGATTATGCCCAGATATTTTCAGAAACAAGGCCA
3752001 GTAATT-AAAAGAAAGTCAAGTTTAGGAAAAGGACGGAGCA-CTTGA-T-TTGGACTGTAGTGAT
131 GTAATTAAAAAGAAAGTCAAGTTTAGGAAAAGGACGGAGCAGCTTGATTCTTGGACTGTAGTGAT
3752062 CAAT
196 CAAT
3752066 TCTGATTCTTTTCCAATAGCCAATATTGAAATAAACCATAGTTTTGTAGAAGTAAATGAGCCACA
1 TCTGATTCTTTTCCAATAGCCAATATTG-AATAAACCATAGTTTTGTAGAAGTAAATGAGCCACA
3752131 AAATTCATCTCTGGGAACTTTAGAGGCAGGCAAGGATTATGCCCAGATATTTTCAGAAACAAGGC
65 AAA-TCATCTCTGGGAACTTTAGAGGCAGGCAAGGATTATGCCCAGATATTTTCAGAAACAAGGC
3752196 CAGTAATTAAAAAGAAAGTCAAGTTTAGGAAAAGGACGGAGCAGCTTGATTCCTTGGACTGTAGT
129 CAGTAATTAAAAAGAAAGTCAAGTTTAGGAAAAGGACGGAGCAGCTTGATT-CTTGGACTGTAGT
3752261 GATCAA
193 GATCAA
3752267 AGTCAAATTG
Statistics
Matches: 194, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
195 28 0.14
196 39 0.20
197 69 0.36
198 34 0.18
199 5 0.03
200 1 0.01
202 18 0.09
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (199 bp):
TCTGATTCTTTTCCAATAGCCAATATTGAATAAACCATAGTTTTGTAGAAGTAAATGAGCCACAA
AATCATCTCTGGGAACTTTAGAGGCAGGCAAGGATTATGCCCAGATATTTTCAGAAACAAGGCCA
GTAATTAAAAAGAAAGTCAAGTTTAGGAAAAGGACGGAGCAGCTTGATTCTTGGACTGTAGTGAT
CAAT
Found at i:3758529 original size:19 final size:19
Alignment explanation
Indices: 3758505--3758543 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3758495 AATTCACATT
*
3758505 AAATTTGAATTTAACATAA
1 AAATTTGAAATTAACATAA
* *
3758524 AAATTTTAAATTAAGATAA
1 AAATTTGAAATTAACATAA
3758543 A
1 A
3758544 TTTTAATTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (19 bp):
AAATTTGAAATTAACATAA
Found at i:3758600 original size:88 final size:88
Alignment explanation
Indices: 3758502--3758679 Score: 356
Period size: 88 Copynumber: 2.0 Consensus size: 88
3758492 GTAAATTCAC
3758502 ATTAAATTTGAATTTAACATAAAAATTTTAAATTAAGATAAATTTTAATTATTATTGATGAAGAC
1 ATTAAATTTGAATTTAACATAAAAATTTTAAATTAAGATAAATTTTAATTATTATTGATGAAGAC
3758567 TTTGCCAAAATTAAAATATTAAT
66 TTTGCCAAAATTAAAATATTAAT
3758590 ATTAAATTTGAATTTAACATAAAAATTTTAAATTAAGATAAATTTTAATTATTATTGATGAAGAC
1 ATTAAATTTGAATTTAACATAAAAATTTTAAATTAAGATAAATTTTAATTATTATTGATGAAGAC
3758655 TTTGCCAAAATTAAAATATTAAT
66 TTTGCCAAAATTAAAATATTAAT
3758678 AT
1 AT
3758680 ACTTAAATCA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 90 1.00
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (88 bp):
ATTAAATTTGAATTTAACATAAAAATTTTAAATTAAGATAAATTTTAATTATTATTGATGAAGAC
TTTGCCAAAATTAAAATATTAAT
Found at i:3758615 original size:19 final size:19
Alignment explanation
Indices: 3758593--3758631 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3758583 TATTAATATT
*
3758593 AAATTTGAATTTAACATAA
1 AAATTTGAAATTAACATAA
* *
3758612 AAATTTTAAATTAAGATAA
1 AAATTTGAAATTAACATAA
3758631 A
1 A
3758632 TTTTAATTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (19 bp):
AAATTTGAAATTAACATAA
Found at i:3768451 original size:23 final size:23
Alignment explanation
Indices: 3768407--3768451 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3768397 ATTATTATAT
*
3768407 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
3768430 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
3768452 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:3769957 original size:19 final size:20
Alignment explanation
Indices: 3769933--3769973 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
3769923 CTAGCTCAGT
3769933 ACCAAC-AAAAGGGGAAGAG
1 ACCAACAAAAAGGGGAAGAG
3769952 ACCAACAAAAAGGGGAAGAG
1 ACCAACAAAAAGGGGAAGAG
3769972 AC
1 AC
3769974 TCGGGATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.54, C:0.17, G:0.29, T:0.00
Consensus pattern (20 bp):
ACCAACAAAAAGGGGAAGAG
Found at i:3790671 original size:51 final size:51
Alignment explanation
Indices: 3790595--3790697 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
3790585 TTAATGGAGT
3790595 TAAATTTAAATAAATTTAATTTATGTATATTTATAGATTAAACTATTCAAA
1 TAAATTTAAATAAATTTAATTTATGTATATTTATAGATTAAACTATTCAAA
3790646 TAAATTTAAATAAATTTAATTTATGTATATTTATAGATTAAACTATTCAAA
1 TAAATTTAAATAAATTTAATTTATGTATATTTATAGATTAAACTATTCAAA
3790697 T
1 T
3790698 TCGAATTATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (51 bp):
TAAATTTAAATAAATTTAATTTATGTATATTTATAGATTAAACTATTCAAA
Found at i:3799735 original size:19 final size:19
Alignment explanation
Indices: 3799711--3799752 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
3799701 TCTTTTTAAT
3799711 ATTACAATT-TCATCTCAAA
1 ATTACAATTCTCAT-TCAAA
*
3799730 ATTACAATTCTCATTCTAA
1 ATTACAATTCTCATTCAAA
3799749 ATTA
1 ATTA
3799753 TCATAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTACAATTCTCATTCAAA
Found at i:3804628 original size:27 final size:27
Alignment explanation
Indices: 3804597--3804650 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
3804587 TAGTAAATTT
3804597 GTCACTTTCCACATCACTATAAATAAC
1 GTCACTTTCCACATCACTATAAATAAC
3804624 GTCACTTTCCACATCACTATAAATAAC
1 GTCACTTTCCACATCACTATAAATAAC
3804651 ATCTAATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.30, G:0.04, T:0.30
Consensus pattern (27 bp):
GTCACTTTCCACATCACTATAAATAAC
Found at i:3819156 original size:202 final size:201
Alignment explanation
Indices: 3818799--3819219 Score: 520
Period size: 202 Copynumber: 2.1 Consensus size: 201
3818789 ATGAGATACC
* * * * ** *
3818799 GCAACTTGTCTTTAATTTGAGCCTAATATCACCACATTTGAGACATTCTAAGTTGGATAAAAATC
1 GCAACTTATCTTTAAGTTGAGCATAATATCACCACATTCGAGACATTCTAAGCGGGATAAAAAAC
* * * * **
3818864 ATCCTGAAAATGGATCGAAAGCATGATTTTGATCATCAAGTGTAAGGCAAAATGGTTTCATAGGC
66 ACCCTGAAAATGGATAGAAAGAATGATTTTGATCATAAAGTGTAAGGCAAAATGACTTCATAGGC
* *
3818929 ATGTTCGATTATTATTTCCGGGTTGTAAATAGCAGATTTTTCGTAATTTATAAGCATAAAGACCT
131 ATGTTCGAGTATTATTTCCGGGTTGTAAATAACAGATTTTTCGTAATTTATAAGCATAAAGACCT
3818994 AGTATT
196 AGTATT
* ** *
3819000 GTAACTTATCTTTAAGTTGAGCATAATATTGCCACATTCGAGACATTCTAAGCGGGGTAAAAAAC
1 GCAACTTATCTTTAAGTTGAGCATAATATCACCACATTCGAGACATTCTAAGCGGGATAAAAAAC
* * * * * *
3819065 ACCCTGGAAATGGTTAGGAAGAATGCTTTTCG-TCATAAAGTTTTAAGGCAACATGACTTCATAG
66 ACCCTGAAAATGGATAGAAAGAATGATTTT-GATCATAAAG-TGTAAGGCAAAATGACTTCATAG
* * * * * * *
3819129 GCGTGTTCGAGTATTATTTTCGGGTTGTAAATAACATATTTTTCGTAATTTGTAAGCTTAGAGGC
129 GCATGTTCGAGTATTATTTCCGGGTTGTAAATAACAGATTTTTCGTAATTTATAAGCATAAAGAC
3819194 CTAGTATT
194 CTAGTATT
*
3819202 GCAACTTTTCTTTAAGTT
1 GCAACTTATCTTTAAGTT
3819220 TAGCCAAATA
Statistics
Matches: 184, Mismatches: 34, Indels: 3
0.83 0.15 0.01
Matches are distributed among these distances:
201 84 0.46
202 100 0.54
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (201 bp):
GCAACTTATCTTTAAGTTGAGCATAATATCACCACATTCGAGACATTCTAAGCGGGATAAAAAAC
ACCCTGAAAATGGATAGAAAGAATGATTTTGATCATAAAGTGTAAGGCAAAATGACTTCATAGGC
ATGTTCGAGTATTATTTCCGGGTTGTAAATAACAGATTTTTCGTAATTTATAAGCATAAAGACCT
AGTATT
Found at i:3819295 original size:202 final size:201
Alignment explanation
Indices: 3818799--3819301 Score: 465
Period size: 202 Copynumber: 2.5 Consensus size: 201
3818789 ATGAGATACC
* * * ** * * *** * *
3818799 GCAACTTGTCTTTAATTTGAGCCTAATATCACCACATTTGAGACATTCTAAGTTGGATAAAAATC
1 GCAACTTATCTTTAAGTTGAGCATAATATGGCCACATTCGAGACATTCAAAACAGGGTAAAAAAC
* * * * * * * * **
3818864 ATC-CTGAAAATGGATCGAAAGCATGATTTTGATCATCAAG-TGTAAGGCAAAATGGTTTCATAG
66 A-CACTGGAAATGGTTAGGAAGAATGCTTTTG-TCATAAAGTTTTAAGGCAAAATGACTTCATAG
* *
3818927 GCATGTTCGATTATTATTTCCGGGTTGTAAATAGCAGATTTTTCGTAATTTATAAGCATAAAGAC
129 GCATGTTCGAGTATTATTTCCGGGTTGTAAATAACAGATTTTTCGTAATTTATAAGCATAAAGAC
3818992 CTAGTATT
194 CTAGTATT
* * * * *
3819000 GTAACTTATCTTTAAGTTGAGCATAATATTGCCACATTCGAGACATTCTAAGCGGGGTAAAAAAC
1 GCAACTTATCTTTAAGTTGAGCATAATATGGCCACATTCGAGACATTCAAAACAGGGTAAAAAAC
* *
3819065 ACCCTGGAAATGGTTAGGAAGAATGCTTTTCGTCATAAAGTTTTAAGGCAACATGACTTCATAGG
66 ACACTGGAAATGGTTAGGAAGAATGCTTTT-GTCATAAAGTTTTAAGGCAAAATGACTTCATAGG
* * * * * * *
3819130 CGTGTTCGAGTATTATTTTCGGGTTGTAAATAACATATTTTTCGTAATTTGTAAGCTTAGAGGCC
130 CATGTTCGAGTATTATTTCCGGGTTGTAAATAACAGATTTTTCGTAATTTATAAGCATAAAGACC
3819195 TAGTATT
195 TAGTATT
* * ** * * * * **
3819202 GCAACTTTTCTTTAAGTTTAGCCA-AATATGGTTATATTCGAGATATTCAAAACATGTTAAAAGT
1 GCAACTTATCTTTAAGTTGAG-CATAATATGGCCACATTCGAGACATTCAAAACAGGGTAAAAAA
* * * *
3819266 CA-AGTTGAAATTGGTTCGGAAGCATGCTTTTGTCAT
65 CACACTGGAAA-TGGTTAGGAAGAATGCTTTTGTCAT
3819302 CAATTACAAT
Statistics
Matches: 246, Mismatches: 51, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
200 1 0.00
201 93 0.38
202 150 0.61
203 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (201 bp):
GCAACTTATCTTTAAGTTGAGCATAATATGGCCACATTCGAGACATTCAAAACAGGGTAAAAAAC
ACACTGGAAATGGTTAGGAAGAATGCTTTTGTCATAAAGTTTTAAGGCAAAATGACTTCATAGGC
ATGTTCGAGTATTATTTCCGGGTTGTAAATAACAGATTTTTCGTAATTTATAAGCATAAAGACCT
AGTATT
Found at i:3820487 original size:23 final size:23
Alignment explanation
Indices: 3820461--3820528 Score: 109
Period size: 23 Copynumber: 3.0 Consensus size: 23
3820451 CACCACAACT
*
3820461 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
3820484 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
3820507 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
3820529 ATATAATAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.24, C:0.26, G:0.29, T:0.21
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:3820716 original size:103 final size:103
Alignment explanation
Indices: 3820545--3820757 Score: 390
Period size: 103 Copynumber: 2.1 Consensus size: 103
3820535 TAATGTCCAT
* *
3820545 AAGGACCACATATCATTCCTTAAGAATCATATATATATACTAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
3820610 GACTTCACACATGTTCCAAATAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
3820648 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
3820713 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
3820751 AAGGACC
1 AAGGACC
3820758 GCGTAGACCC
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:3821597 original size:20 final size:20
Alignment explanation
Indices: 3821574--3821619 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
3821564 CTTTTTATAA
3821574 ACATCTATTTCTATTTCCCT
1 ACATCTATTTCTATTTCCCT
3821594 ACATCTATTTCTATTTCCCT
1 ACATCTATTTCTATTTCCCT
3821614 ACATCT
1 ACATCT
3821620 CTCGACTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.22, C:0.30, G:0.00, T:0.48
Consensus pattern (20 bp):
ACATCTATTTCTATTTCCCT
Found at i:3822196 original size:20 final size:22
Alignment explanation
Indices: 3822132--3822211 Score: 128
Period size: 23 Copynumber: 3.7 Consensus size: 22
3822122 TCGTTTGAGG
*
3822132 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCCATTGAAT
3822154 GGGTACCGATTCCCCCATTGAAT
1 GGGTACCGATT-CCCCATTGAAT
3822177 GGGTACCGATT-CCC-TTGAAT
1 GGGTACCGATTCCCCATTGAAT
3822197 GGGTACCGATTCCCC
1 GGGTACCGATTCCCC
3822212 TTGCCCATAA
Statistics
Matches: 55, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
20 17 0.31
21 6 0.11
22 10 0.18
23 22 0.40
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.28
Consensus pattern (22 bp):
GGGTACCGATTCCCCATTGAAT
Found at i:3822950 original size:43 final size:43
Alignment explanation
Indices: 3822879--3823157 Score: 330
Period size: 43 Copynumber: 6.5 Consensus size: 43
3822869 GCTAAAGTTC
* * *** *
3822879 GCGGCGTTTAGTAACAAAAAACGCCGCAATAGGTAACGATATATA
1 GCGGCGTTT-GT-CCAACAAACGCCGCAATAGGTGTTGATATTTA
*
3822924 GCGGCGTTTGTCCAACAAACGCCGCAATAGGTGTTGATATTTG
1 GCGGCGTTTGTCCAACAAACGCCGCAATAGGTGTTGATATTTA
* * *
3822967 GTGGC-TTTTTCCAACAAACGCCGCAATAGGTGTTGAGATTTA
1 GCGGCGTTTGTCCAACAAACGCCGCAATAGGTGTTGATATTTA
* * *
3823009 GCGGCGTTTTTCCAACAAACGCCGCAATATGTGTTGAGATTTA
1 GCGGCGTTTGTCCAACAAACGCCGCAATAGGTGTTGATATTTA
**
3823052 GCGGCGTTT-TTTACACAAACGCCGCAATAGGTGTTGATATTTA
1 GCGGCGTTTGTCCA-ACAAACGCCGCAATAGGTGTTGATATTTA
* *
3823095 GCGGCGTTTTGTCC-ACAAAAGCCGCAATAGGTCTTGATATTTA
1 GCGGCG-TTTGTCCAACAAACGCCGCAATAGGTGTTGATATTTA
* *
3823138 GCGGCGTTTTTCCCACAAAC
1 GCGGCGTTTGTCCAACAAAC
3823158 ACCGGAAAAG
Statistics
Matches: 206, Mismatches: 23, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
42 46 0.22
43 145 0.70
44 5 0.02
45 10 0.05
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (43 bp):
GCGGCGTTTGTCCAACAAACGCCGCAATAGGTGTTGATATTTA
Found at i:3823199 original size:86 final size:85
Alignment explanation
Indices: 3822897--3823205 Score: 288
Period size: 86 Copynumber: 3.6 Consensus size: 85
3822887 TAGTAACAAA
*** * * *
3822897 AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTGTCCA-ACAAACGCCGCAATAGGTGTTGA
1 AAACGCCGCAATAGGTGTTGGTATTTAGCGGCGTTT-T-GATACAAACGCCGCAATAGGTGTTGA
* * *
3822961 TATTTGGTGGC-TTTTTCCAAC
64 TATTTAGCGGCGTTTTTCCCAC
* *
3822982 AAACGCCGCAATAGGTGTTGAG-ATTTAGCGGCGTTTTTCCA-ACAAACGCCGCAATATGTGTTG
1 AAACGCCGCAATAGGTGTTG-GTATTTAGCGGCG-TTTT-GATACAAACGCCGCAATAGGTGTTG
* **
3823045 AGATTTAGCGGCGTTTTTTACAC
63 ATATTTAGCGGCGTTTTTCCCAC
* * *
3823068 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTG-TCCACAAAAGCCGCAATAGGTCTTGA
1 AAACGCCGCAATAGGTGTTGGTATTTAGCGGCGTTTTGAT--ACAAACGCCGCAATAGGTGTTGA
3823132 TATTTAGCGGCGTTTTTCCCAC
64 TATTTAGCGGCGTTTTTCCCAC
* * * * * *
3823154 AAACACCGGAAAAGAT-CTGGTATATAGCGGCGTTTTAAGATACAAACGCCGC
1 AAACGCCGCAATAGGTGTTGGTATTTAGCGGCGTTTT--GATACAAACGCCGC
3823206 TAATTACCTC
Statistics
Matches: 186, Mismatches: 28, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
85 82 0.44
86 102 0.55
87 1 0.01
88 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (85 bp):
AAACGCCGCAATAGGTGTTGGTATTTAGCGGCGTTTTGATACAAACGCCGCAATAGGTGTTGATA
TTTAGCGGCGTTTTTCCCAC
Found at i:3823199 original size:129 final size:128
Alignment explanation
Indices: 3822919--3823205 Score: 341
Period size: 129 Copynumber: 2.2 Consensus size: 128
3822909 AGGTAACGAT
** * *
3822919 ATATAGCGGCGTTTGTCCA-ACAAACGCCGCAATAGGTGTTGATATTTGGTGGCTTTTTCCAACA
1 ATATAGCGGCGTTT-TAGACACAAACGCCGCAATAGGTGTTGATATTTAGCGGCTTTTTCCAACA
* * * * *
3822983 AACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAACAAACGCCGCAATATGTGTTGAG
65 AAAGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCAACAAACACCGCAATAAGTGCTGAG
* **
3823047 ATTTAGCGGCGTTTTTTACACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTGTCC-AC
1 ATATAGCGGCGTTTTAGACACAAACGCCGCAATAGGTGTTGATATTTAGCGGC-TTTT-TCCAAC
* * *
3823111 AAAAGCCGCAATAGGTCTTGATATTTAGCGGCGTTTTTCCCACAAACACCGGAA-AAGAT-CTG-
64 AAAAGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCAACAAACACCGCAATAAG-TGCTGA
3823173 G
128 G
*
3823174 TATATAGCGGCGTTTTAAGATACAAACGCCGC
1 -ATATAGCGGCGTTTT-AGACACAAACGCCGC
3823206 TAATTACCTC
Statistics
Matches: 136, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
127 3 0.02
128 63 0.46
129 67 0.49
130 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.29
Consensus pattern (128 bp):
ATATAGCGGCGTTTTAGACACAAACGCCGCAATAGGTGTTGATATTTAGCGGCTTTTTCCAACAA
AAGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCAACAAACACCGCAATAAGTGCTGAG
Found at i:3823343 original size:21 final size:21
Alignment explanation
Indices: 3823330--3823375 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
3823320 CTTGACATCG
3823330 ATAACAACAAACTTAAAATCC
1 ATAACAACAAACTTAAAATCC
* ** *
3823351 ATAACAAGAAAAATGAAATCC
1 ATAACAACAAACTTAAAATCC
3823372 ATAA
1 ATAA
3823376 TAATAAATCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.61, C:0.17, G:0.04, T:0.17
Consensus pattern (21 bp):
ATAACAACAAACTTAAAATCC
Found at i:3828241 original size:83 final size:83
Alignment explanation
Indices: 3828130--3828523 Score: 481
Period size: 83 Copynumber: 4.8 Consensus size: 83
3828120 TATGATAATT
* *
3828130 GCGGCATTTGGTATTAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTTATTAAAACGCC
1 GCGGCGTTT-GTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTTATTAAAACGCC
3828195 ACAAAAGTACGTGTCTATA
65 ACAAAAGTACGTGTCTATA
* * * *
3828214 GCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAATCTATTGCGGCGTTTGATATTAAAACGCCA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTTATTAAAACGCCA
3828279 CAAAAGTACGTGTCTATA
66 CAAAAGTACGTGTCTATA
* * * ** *
3828297 GCGGCGTTTGTGTAAAAATGCCACTAAAGTATGAGTCTATAGCATCGTTTGGTATTAAAACGCCA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTTATTAAAACGCCA
3828362 CAAAAGTACGTGTCTATA
66 CAAAAGTACGTGTCTATA
* * * * * *
3828380 GCAGCGTTTGTATAAAAACGCCACTAAAATACTAGTTTATAGCGGCATTTG-TATAAAAACGCCA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTTATTAAAACGCCA
* * * *
3828444 CTACATTACGAT-TCTTTA
66 CAAAAGTACG-TGTCTATA
* * * * * * *
3828462 GCGGCGTTTTTATACAAACGCCACTAAAGTA-TAGTATTTTGCGGCGTTTGTTA-AAAAACGCC
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTTATTAAAACGCC
3828524 GCTATATGTA
Statistics
Matches: 272, Mismatches: 36, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
81 24 0.09
82 53 0.19
83 187 0.69
84 8 0.03
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (83 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTTATTAAAACGCCA
CAAAAGTACGTGTCTATA
Found at i:3828244 original size:41 final size:41
Alignment explanation
Indices: 3828130--3828492 Score: 406
Period size: 41 Copynumber: 8.8 Consensus size: 41
3828120 TATGATAATT
* * *
3828130 GCGGCATTTGGTATTAAAACGCCACTAAAGTACGAGTCTATA
1 GCGGCGTTT-GTATAAAAACGCCACTAAAGTACGTGTCTATA
* *
3828172 GCGGCGTTTGTTATTAAAACGCCACAAAAGTACGTGTCTATA
1 GCGGCGTTTG-TATAAAAACGCCACTAAAGTACGTGTCTATA
* ** *
3828214 GCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAATCTATT
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGTGTCTATA
* *
3828255 GCGGCGTTTGATATTAAAACGCCACAAAAGTACGTGTCTATA
1 GCGGCGTTTG-TATAAAAACGCCACTAAAGTACGTGTCTATA
* * * *
3828297 GCGGCGTTTGTGTAAAAATGCCACTAAAGTATGAGTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGTGTCTATA
** * *
3828338 GCATCGTTTGGTATTAAAACGCCACAAAAGTACGTGTCTATA
1 GCGGCGTTT-GTATAAAAACGCCACTAAAGTACGTGTCTATA
* * *
3828380 GCAGCGTTTGTATAAAAACGCCACTAAAATAC-TAGTTTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGT-GTCTATA
* * * *
3828421 GCGGCATTTGTATAAAAACGCCACTACATTACGAT-TCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACG-TGTCTATA
* *
3828462 GCGGCGTTTTTATACAAACGCCACTAAAGTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTA
3828493 TAGTATTTTG
Statistics
Matches: 270, Mismatches: 45, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
40 1 0.00
41 152 0.56
42 116 0.43
43 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACGTGTCTATA
Found at i:3830918 original size:15 final size:14
Alignment explanation
Indices: 3830899--3830940 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
3830889 ACCACTACAT
3830899 CCCGAAGGACTACG
1 CCCGAAGGACTACG
*
3830913 TTCCGAAGGACTACG
1 -CCCGAAGGACTACG
3830928 CCCTGAAGGACTA
1 CCC-GAAGGACTA
3830941 TTATACCCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 2 0.08
15 22 0.92
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (14 bp):
CCCGAAGGACTACG
Found at i:3831079 original size:29 final size:29
Alignment explanation
Indices: 3831027--3831099 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 29
3831017 TCATATGTTT
* * *
3831027 ATGTA-CTCATGTTATTTCTCTTGTGATC
1 ATGTAGCTCATGTCATATCTATTGTGATC
3831055 ATGTAGCTCATGTCATATCTATTGTGATC
1 ATGTAGCTCATGTCATATCTATTGTGATC
3831084 ATGTAGCTCATGTCAT
1 ATGTAGCTCATGTCAT
3831100 GTTCTCATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.44
Consensus pattern (29 bp):
ATGTAGCTCATGTCATATCTATTGTGATC
Found at i:3831548 original size:64 final size:63
Alignment explanation
Indices: 3831479--3831635 Score: 169
Period size: 64 Copynumber: 2.5 Consensus size: 63
3831469 TAATGAAGGT
* *
3831479 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAAT-GCATTCGAT-GTTTTATTATTAATG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT--AATCGCATTCGATCGTTTTATT-TTAA-A
*
3831541 GG
62 AG
* * *
3831543 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATCGCATTCGATCTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAATCGCATTCGATCGTTTTATTTTAAAAG
*
3831606 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTGTGCATCGAT
3831636 ACACCTTCAA
Statistics
Matches: 78, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
63 6 0.08
64 63 0.81
65 9 0.12
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAATCGCATTCGATCGTTTTATTTTAAAAG
Found at i:3834039 original size:22 final size:22
Alignment explanation
Indices: 3834022--3834088 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
3834012 CTCGTATAAA
3834022 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
3834044 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
3834066 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
3834088 T
1 T
3834089 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:3835122 original size:18 final size:18
Alignment explanation
Indices: 3835099--3835133 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3835089 TTCCCTCTAG
3835099 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
3835117 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
3835134 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:3835744 original size:21 final size:21
Alignment explanation
Indices: 3835718--3835763 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
3835708 TTCATATTCG
* *
3835718 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
3835739 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
3835760 CTTG
1 CTTG
3835764 CCCAGAAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:3838878 original size:22 final size:22
Alignment explanation
Indices: 3838861--3838927 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
3838851 CTCGTATAAA
3838861 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
3838883 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
3838905 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
3838927 T
1 T
3838928 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:3839963 original size:18 final size:18
Alignment explanation
Indices: 3839942--3839976 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3839932 TCCCCTCTAG
3839942 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
3839960 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
3839977 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:3840607 original size:22 final size:21
Alignment explanation
Indices: 3840561--3840603 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3840551 TTCATATTCG
* *
3840561 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
3840582 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
3840603 C
1 C
3840604 CTTGCCCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:3844256 original size:6 final size:6
Alignment explanation
Indices: 3844245--3844302 Score: 116
Period size: 6 Copynumber: 9.7 Consensus size: 6
3844235 TTTCCCTTCT
3844245 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC
3844293 CTCTCC CTCT
1 CTCTCC CTCT
3844303 TTGAATGATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
CTCTCC
Found at i:3882260 original size:21 final size:22
Alignment explanation
Indices: 3882192--3882273 Score: 94
Period size: 22 Copynumber: 3.7 Consensus size: 22
3882182 GGGGGCAAAT
* *
3882192 GGAATCGATACCCCCTTGAAGG
1 GGAACCGATTCCCCCTTGAAGG
3882214 GGAACCGATTCCCCCTTTGAAGG
1 GGAACCGATTCCCCC-TTGAAGG
* *
3882237 GGAACCGATT-CCTCTTGTAGG
1 GGAACCGATTCCCCCTTGAAGG
* *
3882258 GGAATCGATACCCCCT
1 GGAACCGATTCCCCCT
3882274 GGGGTTCTGT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
21 14 0.27
22 20 0.39
23 17 0.33
ACGTcount: A:0.23, C:0.29, G:0.26, T:0.22
Consensus pattern (22 bp):
GGAACCGATTCCCCCTTGAAGG
Found at i:3885528 original size:29 final size:29
Alignment explanation
Indices: 3885486--3885542 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
3885476 AGTGTTGGCC
3885486 GTAGGTCGCCATGCACTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
3885515 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
3885543 ACCCTTGCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.14, C:0.35, G:0.32, T:0.19
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:3885646 original size:29 final size:29
Alignment explanation
Indices: 3885613--3885697 Score: 143
Period size: 29 Copynumber: 2.9 Consensus size: 29
3885603 TCCCAACACA
* *
3885613 TAGGTCGCCATGCCCTCCGGGTGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
3885642 TAGGTCGCCATGCACTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
*
3885671 TAGGTCGCCATGCACTCTGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
3885698 ACCCTCGCTC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.13, C:0.34, G:0.31, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:3885742 original size:33 final size:33
Alignment explanation
Indices: 3885701--3885785 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
3885691 GCGACCTACC
*
3885701 CTCGCTCGGCTT-CCCTCGGATTCCCTCGCATAG
1 CTCGCTCGG-TTGCCCTCGGATGCCCTCGCATAG
3885734 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
* * *
3885767 CTCGTTCGGATGGCCTCGG
1 CTCGCTCGGTTGCCCTCGG
3885786 TCGGATGGCC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
32 2 0.04
33 45 0.96
ACGTcount: A:0.08, C:0.39, G:0.27, T:0.26
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
Found at i:3885789 original size:14 final size:14
Alignment explanation
Indices: 3885767--3885799 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3885757 CCTCGCATAG
*
3885767 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
3885781 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
3885795 CTCGG
1 CTCGG
3885800 ATGCCCAGCG
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:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:3895233 original size:2 final size:2
Alignment explanation
Indices: 3895187--3895215 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3895177 ATCTAGACTT
3895187 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 T
3895216 GCAATTCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3896221 original size:27 final size:27
Alignment explanation
Indices: 3896191--3896246 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
3896181 CTAGGCAAAG
* *
3896191 AACAAGAAGTCAATTCAGTTACCATTA
1 AACAACAAGTCAATTCAGCTACCATTA
* *
3896218 AACAACCATTCAATTCAGCTACCATTA
1 AACAACAAGTCAATTCAGCTACCATTA
3896245 AA
1 AA
3896247 AAACCATTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.45, C:0.23, G:0.07, T:0.25
Consensus pattern (27 bp):
AACAACAAGTCAATTCAGCTACCATTA
Found at i:3896251 original size:27 final size:27
Alignment explanation
Indices: 3896200--3896257 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
3896190 GAACAAGAAG
* *
3896200 TCAATTCAGTTACCATTAAACAACCAT
1 TCAATTCAGCTACCATTAAAAAACCAT
3896227 TCAATTCAGCTACCATTAAAAAACCAT
1 TCAATTCAGCTACCATTAAAAAACCAT
3896254 TCAA
1 TCAA
3896258 GTGCAGGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.43, C:0.26, G:0.03, T:0.28
Consensus pattern (27 bp):
TCAATTCAGCTACCATTAAAAAACCAT
Found at i:3898042 original size:50 final size:50
Alignment explanation
Indices: 3897975--3898083 Score: 175
Period size: 49 Copynumber: 2.2 Consensus size: 50
3897965 TATAATTAAA
*
3897975 AATATTTTTTGCATTATTTTGGATTACAATTAAAAATATTATAAAAAATAT
1 AATATTTTTTGCATTA-TTTCGATTACAATTAAAAATATTATAAAAAATAT
* *
3898026 ATTATTTTTT-TATTATTTCGATTACAATTAAAAATATTATAAAAAATAT
1 AATATTTTTTGCATTATTTCGATTACAATTAAAAATATTATAAAAAATAT
3898075 AATATTTTT
1 AATATTTTT
3898084 ATTGTAATTG
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
49 41 0.76
50 4 0.07
51 9 0.17
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (50 bp):
AATATTTTTTGCATTATTTCGATTACAATTAAAAATATTATAAAAAATAT
Found at i:3898297 original size:39 final size:38
Alignment explanation
Indices: 3898235--3898338 Score: 102
Period size: 39 Copynumber: 2.6 Consensus size: 38
3898225 TTATATTTTT
*
3898235 ATATTATTAAAATATGTTCTTTAA-TAATTTAAAATATAAAAA
1 ATATTA-TAAAATAT-TT-TTTAACT-ATTTAAAAAAT-AAAA
*
3898277 ATATTATAAAATATTTTTTAACTATTTAAAAAATAATA
1 ATATTATAAAATATTTTTTAACTATTTAAAAAATAAAA
*
3898315 ATGCTTATAAATATATTATTTTAA
1 AT-ATTATAAA-ATATT-TTTTAA
3898339 AAAATATATT
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
38 5 0.09
39 22 0.40
40 8 0.15
41 14 0.25
42 6 0.11
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (38 bp):
ATATTATAAAATATTTTTTAACTATTTAAAAAATAAAA
Found at i:3898345 original size:17 final size:17
Alignment explanation
Indices: 3898323--3898355 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3898313 TAATGCTTAT
3898323 AAATATATTATTTTAAA
1 AAATATATTATTTTAAA
3898340 AAATATATTATTTTAA
1 AAATATATTATTTTAA
3898356 TTATTTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AAATATATTATTTTAAA
Found at i:3898380 original size:26 final size:26
Alignment explanation
Indices: 3898329--3898380 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
3898319 TTATAAATAT
*
3898329 ATTATTTTAAAAAATATATTATTTTA
1 ATTATTTTAAAAAATATAATATTTTA
* *
3898355 ATTATTTTGAAATAT-TAATATATTTA
1 ATTATTTTAAAAAATATAATAT-TTTA
3898381 CATCATGTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
ATTATTTTAAAAAATATAATATTTTA
Done.