Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_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: 12876159
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 54
Found at i:3805578 original size:54 final size:54
Alignment explanation
Indices: 3805512--3805811 Score: 388
Period size: 54 Copynumber: 5.6 Consensus size: 54
3805502 TACTATAGGA
* *
3805512 ACTAAGTGTGCAACCCATAGAATTCATAATAAGTTTATGAACGACCATATCGGT
1 ACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCATATCGGC
** ** * *
3805566 TTTAAGTGTGCAACCCATGGAATTCATAAAAAGTTTATGAACGACCGTATCGGC
1 ACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCATATCGGC
* **
3805620 ACTAAGTTTGCAACCCACAGAATTCATAATAAGTTTATGAACGACTGTATCGGC
1 ACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCATATCGGC
*
3805674 ACTAAGTGTGCAACCCAC-GAAATTCATAATAAGTTTATGAACGACCATATCAGC
1 ACTAAGTGTGCAACCCACAG-AATTCATAATAAGTTTATGAACGACCATATCGGC
* * ** *
3805728 ACTAAGTGTGTAACCCACAAAATTCATAATAAGTTTATGAACGACTGTATCAGC
1 ACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCATATCGGC
* * *
3805782 ACTACGTGTGCACCCCAAAGAACTT-ATAAT
1 ACTAAGTGTGCAACCCACAGAA-TTCATAAT
3805812 GATTTGAAAA
Statistics
Matches: 217, Mismatches: 26, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
53 1 0.00
54 214 0.99
55 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (54 bp):
ACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCATATCGGC
Found at i:3816835 original size:21 final size:21
Alignment explanation
Indices: 3816809--3816853 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
3816799 GTTCTACGCT
* *
3816809 GTCCTTTGGGACATATATTTG
1 GTCCTTTGGAACATATATGTG
3816830 GTCCTTTGGAACATATATGTG
1 GTCCTTTGGAACATATATGTG
3816851 GTC
1 GTC
3816854 ATACGGGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (21 bp):
GTCCTTTGGAACATATATGTG
Found at i:3818698 original size:24 final size:24
Alignment explanation
Indices: 3818671--3818720 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
3818661 AGAGTATTGA
3818671 ATCATGAAGGAAAAGATATAACCT
1 ATCATGAAGGAAAAGATATAACCT
3818695 ATCATGAAGGAAAAGATATAACCT
1 ATCATGAAGGAAAAGATATAACCT
3818719 AT
1 AT
3818721 GTTACAAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.12, G:0.16, T:0.22
Consensus pattern (24 bp):
ATCATGAAGGAAAAGATATAACCT
Found at i:3820818 original size:21 final size:21
Alignment explanation
Indices: 3820792--3820931 Score: 73
Period size: 21 Copynumber: 6.4 Consensus size: 21
3820782 GTTCTACGCA
*
3820792 GTCCTTCGGGACATATATTTG
1 GTCCTTCGGGACATATATGTG
* *
3820813 GTCCTTTGGAACATATATGTG
1 GTCCTTCGGGACATATATGTG
* * * *
3820834 GTCCTACGGGAAAATTCTACGTG
1 GTCCTTCGGG-ACA-TATATGTG
* * * * *
3820857 GTCTTTTGGGATATTTCTATGCG
1 GTCCTTCGGGACA--TATATGTG
* *
3820880 GTCCTTTGGGACATATATATG
1 GTCCTTCGGGACATATATGTG
* * *
3820901 TTCCTTTGGGACATTTTATGTG
1 GTCCTTCGGGACA-TATATGTG
*
3820923 GTACTTCGG
1 GTCCTTCGG
3820932 TGCATTTCTA
Statistics
Matches: 89, Mismatches: 26, Indels: 7
0.73 0.21 0.06
Matches are distributed among these distances:
21 42 0.47
22 16 0.18
23 31 0.35
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.39
Consensus pattern (21 bp):
GTCCTTCGGGACATATATGTG
Found at i:3820867 original size:23 final size:23
Alignment explanation
Indices: 3820841--3820890 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
3820831 GTGGTCCTAC
* *
3820841 GGGAAAATTCTACGTGGTCTTTT
1 GGGAAAATTCTACGCGGTCCTTT
* * *
3820864 GGGATATTTCTATGCGGTCCTTT
1 GGGAAAATTCTACGCGGTCCTTT
3820887 GGGA
1 GGGA
3820891 CATATATATG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.30, T:0.38
Consensus pattern (23 bp):
GGGAAAATTCTACGCGGTCCTTT
Found at i:3823071 original size:15 final size:15
Alignment explanation
Indices: 3823051--3823080 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3823041 TTTCTATTTT
3823051 CCTTGACAATGTTTA
1 CCTTGACAATGTTTA
3823066 CCTTGACAATGTTTA
1 CCTTGACAATGTTTA
3823081 TTTGTTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (15 bp):
CCTTGACAATGTTTA
Found at i:3827327 original size:21 final size:21
Alignment explanation
Indices: 3827301--3827342 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3827291 CAATTAAGAA
*
3827301 TCAAGGAGCTTTACTTCAAAG
1 TCAAGGAGCCTTACTTCAAAG
*
3827322 TCAAGGTGCCTTACTTCAAAG
1 TCAAGGAGCCTTACTTCAAAG
3827343 CCATAGCTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (21 bp):
TCAAGGAGCCTTACTTCAAAG
Found at i:3840980 original size:46 final size:46
Alignment explanation
Indices: 3840927--3841364 Score: 642
Period size: 46 Copynumber: 9.5 Consensus size: 46
3840917 ATTTTGATGG
* * * *
3840927 CAATTATGCATCTTTATTCATTTTCATTTATGGGATCCTTTCATGC
1 CAATTATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGC
* *
3840973 CAATTATGCACCGTTATTCATTTTCATTTATGGAATCCTTTCATGC
1 CAATTATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGC
** *
3841019 CAATTATGCACCGTTATGCATTTTCATTTATTTCATCATTTCATGC
1 CAATTATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGC
* *** *
3841065 CAATTATGTACAAATATACATTTTCATTTATGGCATCCTTTCATGC
1 CAATTATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGC
* * * *
3841111 CAATTATGTATCGTTGTGCATTTTCATTTATGGCATACTTTCATGC
1 CAATTATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGC
* *
3841157 CAATTATGCATCGTTATGCATTTTCATTTATGACATCCTTTCATGC
1 CAATTATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGC
* *
3841203 CAATTATGCATCGTTATGAATTTTCATTTATGGCATCCTTTCATGC
1 CAATTATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGC
* *
3841249 CAATTATGCACCGTTATGTATTTTCATTTATGGCATCCATTCATGC
1 CAATTATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGC
*
3841295 CAATTATGCACCGTTATGTATTTTTCATTTATGGCATCCTTTCATGC
1 CAATTATGCACCGTTATGCA-TTTTCATTTATGGCATCCTTTCATGC
3841342 CAATTATGCACCGTTATGCATTT
1 CAATTATGCACCGTTATGCATTT
3841365 AATATTTTAC
Statistics
Matches: 357, Mismatches: 34, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
46 313 0.88
47 44 0.12
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.44
Consensus pattern (46 bp):
CAATTATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGC
Found at i:3840992 original size:23 final size:23
Alignment explanation
Indices: 3840966--3841035 Score: 56
Period size: 23 Copynumber: 3.0 Consensus size: 23
3840956 ATGGGATCCT
3840966 TTCATGCCAATTATGCACCGTTA
1 TTCATGCCAATTATGCACCGTTA
** * *
3840989 TTCATTTTCATTTATGGAATCC--T-
1 TTCA-TGCCAATTAT-GCA-CCGTTA
3841012 TTCATGCCAATTATGCACCGTTA
1 TTCATGCCAATTATGCACCGTTA
3841035 T
1 T
3841036 GCATTTTCAT
Statistics
Matches: 33, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
20 2 0.06
21 2 0.06
22 8 0.24
23 9 0.27
24 8 0.24
25 2 0.06
26 2 0.06
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.41
Consensus pattern (23 bp):
TTCATGCCAATTATGCACCGTTA
Found at i:3841482 original size:81 final size:81
Alignment explanation
Indices: 3841347--3841535 Score: 306
Period size: 81 Copynumber: 2.3 Consensus size: 81
3841337 CATGCCAATT
* * * * *
3841347 ATGCACCGTTATGCATTTAATATTTTACTCAAAGGCATTTAACCTTTCATCTAACTTGCATGATT
1 ATGCACAGTTAGGCATTTAATCTTTTACTCAAAGGCATTTAACATTTCATCTAACTTGCATAATT
3841412 GACACATTTCTGCCAA
66 GACACATTTCTGCCAA
3841428 ATGCACAGTTAGGCATTTAATCTTTTACTCAAAGGCATTTAACATTTCATCTAACTTGCATAATT
1 ATGCACAGTTAGGCATTTAATCTTTTACTCAAAGGCATTTAACATTTCATCTAACTTGCATAATT
* *
3841493 GGCACATTTCTTCCAA
66 GACACATTTCTGCCAA
*
3841509 ATGCACAATTAGGCATTTAATCTTTTA
1 ATGCACAGTTAGGCATTTAATCTTTTA
3841536 TTTTAAAATT
Statistics
Matches: 100, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 100 1.00
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.38
Consensus pattern (81 bp):
ATGCACAGTTAGGCATTTAATCTTTTACTCAAAGGCATTTAACATTTCATCTAACTTGCATAATT
GACACATTTCTGCCAA
Found at i:3846378 original size:55 final size:55
Alignment explanation
Indices: 3846315--3846518 Score: 261
Period size: 55 Copynumber: 3.7 Consensus size: 55
3846305 TATGTGTGAA
* **
3846315 AAAC-TAAGAAATTCATACTAAGTGTATGGATTTTTGTATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTATGTGT
*
3846369 AAACTTAAGAAATTCATACTAAGTGTATGAATTTCCATATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTATGTGT
* * * * *
3846424 AAGCTTAAGAAATTCAAACTAACTGTATGAATTTCCGTATGGGCACTTTGTGTGCA
1 AAACTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTATGTG-T
* * *
3846480 AAACTGT--GAAATTCATAATAAGTTTATGAATTTTCGTAT
1 AAACT-TAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
3846519 TAGTAGTGGG
Statistics
Matches: 131, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
54 4 0.03
55 122 0.93
56 4 0.03
57 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Consensus pattern (55 bp):
AAACTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTATGTGT
Found at i:3846874 original size:23 final size:25
Alignment explanation
Indices: 3846813--3846882 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 25
3846803 CATAAAAGGT
3846813 ATGAAAGGATGCCATAAATGAAATAC
1 ATGAAAGGATGCCATAAA-GAAATAC
* *
3846839 AT-AATGG-TG-CATAAA-AAA-GC
1 ATGAAAGGATGCCATAAAGAAATAC
3846859 ATGAAAGGATGCCATAAATGAAAT
1 ATGAAAGGATGCCATAAA-GAAAT
3846883 TAATGAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
20 3 0.09
21 7 0.20
22 2 0.06
23 12 0.34
24 2 0.06
25 7 0.20
26 2 0.06
ACGTcount: A:0.50, C:0.10, G:0.20, T:0.20
Consensus pattern (25 bp):
ATGAAAGGATGCCATAAAGAAATAC
Found at i:3851932 original size:55 final size:55
Alignment explanation
Indices: 3851863--3852127 Score: 363
Period size: 55 Copynumber: 4.8 Consensus size: 55
3851853 GGGCATTATG
**
3851863 TGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTTGTATGGGCACTTTA
1 TGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTA
* * **
3851918 TGTG-TAAACTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATGGAAACTTTA
1 TGTGCAAAAC-TAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTA
* *
3851973 TGTG-TAAACTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTG
1 TGTGCAAAAC-TAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTA
* * *
3852028 TGTGCAAAACTAAGAAATTCATATTAAGTGTATGAATTTCTGTATGGGCACTTTG
1 TGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTA
* * * *
3852083 TGTGCAAAACTATGAAATTCATAATAAATTTATGAATTTCCGTAT
1 TGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
3852128 TGGTAGTGGG
Statistics
Matches: 192, Mismatches: 16, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
54 4 0.02
55 184 0.96
56 4 0.02
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (55 bp):
TGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTA
Found at i:3852531 original size:46 final size:45
Alignment explanation
Indices: 3852415--3852537 Score: 142
Period size: 44 Copynumber: 2.7 Consensus size: 45
3852405 TCTATTTGAC
*
3852415 ATAAAAGGTATGAAAGGATGCCATAAATGAAATGAATAACGGTAT
1 ATAAAAGGCATGAAAGGATGCCATAAATGAAATGAATAACGGTAT
* * * * * *
3852460 ATTAAA-GCATGAAAGAATTCCATAAATTAAATGCATAATGGTGCAT
1 ATAAAAGGCATGAAAGGATGCCATAAATGAAATGAATAACGGT--AT
*
3852506 A-AAAAGGCATGAAAGGATGCTATAAATGAAAT
1 ATAAAAGGCATGAAAGGATGCCATAAATGAAAT
3852538 TAATGAATAA
Statistics
Matches: 63, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
44 30 0.48
45 8 0.13
46 25 0.40
ACGTcount: A:0.49, C:0.08, G:0.20, T:0.24
Consensus pattern (45 bp):
ATAAAAGGCATGAAAGGATGCCATAAATGAAATGAATAACGGTAT
Found at i:3853957 original size:36 final size:36
Alignment explanation
Indices: 3853863--3853974 Score: 143
Period size: 36 Copynumber: 3.1 Consensus size: 36
3853853 GAAAAAATAT
* * *
3853863 AAATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAAC
1 AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
*
3853899 TAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
1 -AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
* * * *
3853936 AAATTTCGTCTCTCTTAAGACAGTTTCCCTTAAAAC
1 AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
3853972 AAA
1 AAA
3853975 ATCTTTGAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
36 34 0.52
37 32 0.48
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (36 bp):
AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
Found at i:3854066 original size:67 final size:67
Alignment explanation
Indices: 3853923--3854105 Score: 219
Period size: 65 Copynumber: 2.7 Consensus size: 67
3853913 CTTGAGACAG
* * * * * * **
3853923 TTTCTCTTGAAACAAATTTCGTCTCTCTTAAGACAGTTTCCCTT-AAA-ACAAAATCTTTGAATT
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
3853986 TA
66 TA
*
3853988 TTTCTCC-TAAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAAAATCTTCAAAT
1 TTTC-CCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAAT
3854052 TTA
65 TTA
* * *
3854055 TTTCCCTTAAAACAAAATTTTGTTTCCCTTGAGACAGTTTTTCATGAAACA
1 TTTCCCTTAAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
3854106 ATATATATCT
Statistics
Matches: 100, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
65 35 0.35
66 6 0.06
67 26 0.26
68 33 0.33
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.39
Consensus pattern (67 bp):
TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
TA
Found at i:3854714 original size:32 final size:32
Alignment explanation
Indices: 3854673--3854750 Score: 122
Period size: 32 Copynumber: 2.4 Consensus size: 32
3854663 AAGTAAAGGC
3854673 TCAACTTCACGACGAATG-GGCCATCCGCGATT
1 TCAACTTCACGACGAA-GAGGCCATCCGCGATT
*
3854705 TCAACTTCACAACGAAGAGGCCATCCGCGATT
1 TCAACTTCACGACGAAGAGGCCATCCGCGATT
*
3854737 TCAACTCCACGACG
1 TCAACTTCACGACG
3854751 GAGGATATCA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
31 1 0.02
32 41 0.98
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.19
Consensus pattern (32 bp):
TCAACTTCACGACGAAGAGGCCATCCGCGATT
Found at i:3855062 original size:110 final size:110
Alignment explanation
Indices: 3854854--3855062 Score: 285
Period size: 110 Copynumber: 1.9 Consensus size: 110
3854844 GTTTCAAAGC
* * * * * *
3854854 CAATTTTAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAAATTCATAATGAAG
1 CAATTTCAAATTCACAGCGAAGAATATTGAACTCAAGACAACACAAGCTCAAATTCACAATGAAG
* * *
3854919 GGGCGACTGATTGTCAACAAATAAGTTTTCAGTTTCATTCAGAGT
66 GGGCGACTGACTGTCAACAAACAAGTTTCCAGTTTCATTCAGAGT
* *
3854964 CAATTTCAAATTCACAGCGAAGAATATTGAACTCGAGACAACACAAGCTCAACTTCACAATGAAG
1 CAATTTCAAATTCACAGCGAAGAATATTGAACTCAAGACAACACAAGCTCAAATTCACAATGAAG
* *
3855029 GGGCGGCTGGCTGTCAACAAACAA-TTTCCCAGTT
66 GGGCGACTGACTGTCAACAAACAAGTTT-CCAGTT
3855063 CCAGAACCAA
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
109 3 0.04
110 82 0.96
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (110 bp):
CAATTTCAAATTCACAGCGAAGAATATTGAACTCAAGACAACACAAGCTCAAATTCACAATGAAG
GGGCGACTGACTGTCAACAAACAAGTTTCCAGTTTCATTCAGAGT
Found at i:3856507 original size:2 final size:2
Alignment explanation
Indices: 3856500--3856550 Score: 70
Period size: 2 Copynumber: 26.0 Consensus size: 2
3856490 TTATTTTTAT
*
3856500 TA TA TA TA TC T- TA TA TCA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
3856541 TA TA TA TA TA
1 TA TA TA TA TA
3856551 GATGTATTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
1 2 0.04
2 41 0.91
3 2 0.04
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3856513 original size:14 final size:15
Alignment explanation
Indices: 3856483--3856549 Score: 64
Period size: 16 Copynumber: 4.2 Consensus size: 15
3856473 CTTTTTTTTG
* *
3856483 TATTATAT-TATTTT
1 TATTATATATATATA
3856497 TATTATATATATCTTATA
1 TATTATATATA---TATA
3856515 TCATTATATATATATA
1 T-ATTATATATATATA
3856531 TATATATATATATATA
1 TAT-TATATATATATA
3856547 TAT
1 TAT
3856550 AGATGTATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
14 8 0.18
15 4 0.09
16 20 0.44
18 3 0.07
19 10 0.22
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTATATATATATA
Found at i:3856513 original size:25 final size:27
Alignment explanation
Indices: 3856500--3856550 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
3856490 TTATTTTTAT
3856500 TATATATATCTTATATCATTATATATA
1 TATATATATCTTATATCATTATATATA
*
3856527 TATATATAT-ATATAT-A-TATATATA
1 TATATATATCTTATATCATTATATATA
3856551 GATGTATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 8 0.35
25 1 0.04
26 5 0.22
27 9 0.39
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (27 bp):
TATATATATCTTATATCATTATATATA
Found at i:3869249 original size:2 final size:2
Alignment explanation
Indices: 3869242--3869289 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
3869232 ATTAAAAATA
3869242 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
3869284 AT AT AT
1 AT AT AT
3869290 GAAACTTGGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3871215 original size:15 final size:15
Alignment explanation
Indices: 3871195--3871224 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3871185 CAAGTTCCTC
3871195 TGCTTTGTGAACATG
1 TGCTTTGTGAACATG
3871210 TGCTTTGTGAACATG
1 TGCTTTGTGAACATG
3871225 GTAAGTCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (15 bp):
TGCTTTGTGAACATG
Found at i:3881614 original size:13 final size:13
Alignment explanation
Indices: 3881596--3881623 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3881586 ATATTGCGCA
3881596 CACTCATCTAACT
1 CACTCATCTAACT
3881609 CACTCATCTAACT
1 CACTCATCTAACT
3881622 CA
1 CA
3881624 TGTACCATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.39, G:0.00, T:0.29
Consensus pattern (13 bp):
CACTCATCTAACT
Found at i:3884360 original size:41 final size:41
Alignment explanation
Indices: 3884278--3884634 Score: 258
Period size: 41 Copynumber: 8.6 Consensus size: 41
3884268 TAGCGGCATT
* *
3884278 TTTAGCGGCGTTTTTAGAACAAACGCCGCTAAAGACT-GTAC
1 TTTAGTGGCGTTTTTA-TACAAACGCCGCTAAAGACTCGTAC
* * * * *
3884319 TTTAGTGGCATTTTTATACAAATGTCGCTATAGATTCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * * *
3884360 TTTAGTGGCGTTTTTAGAACAAACACCGCTACAGACTCATAC
1 TTTAGTGGCGTTTTTA-TACAAACGCCGCTAAAGACTCGTAC
** * * *
3884402 TTTAGTGATGTTTTTATACAAACGCCGCTAAATTA-T-ATCC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAA-GACTCGTAC
* * * * * *
3884442 TTTAGTGGCCTTCTTAAACAAATC-TCGTTAAAGACTAGTAC
1 TTTAGTGGCGTTTTTATACAAA-CGCCGCTAAAGACTCGTAC
* * * * ** *
3884483 TATAGCGACGTTTGTT-TAAAAAACGCCGCTATTGATTCGTAC
1 TTTAGTGGCGTTT-TTAT-ACAAACGCCGCTAAAGACTCGTAC
* * * * *
3884525 TTTAGTGGCG-TTTTAGAACAAGCGACGCTACAGACTAGTAC
1 TTTAGTGGCGTTTTTA-TACAAACGCCGCTAAAGACTCGTAC
*
3884566 TTTAGTGGCGTTTTTATACAAATGCCGCTAAAGACTCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* *
3884607 TTTAGTGGCATTTGTGTTTACAAACGCC
1 TTTAGTGGCGTTT-T-TATACAAACGCC
3884635 TTAATTTTAC
Statistics
Matches: 237, Mismatches: 65, Indels: 26
0.72 0.20 0.08
Matches are distributed among these distances:
39 1 0.00
40 44 0.19
41 119 0.50
42 63 0.27
43 10 0.04
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
Found at i:3884396 original size:82 final size:83
Alignment explanation
Indices: 3884278--3884615 Score: 336
Period size: 82 Copynumber: 4.1 Consensus size: 83
3884268 TAGCGGCATT
* * * * *
3884278 TTTAGCGGCGTTTTTAGAACAAACGCCGCTAAAGACT-GTACTTTAGTGGCATTTTTATACAAAT
1 TTTAGTGGCGTTTTTAGAACAAACACCGCTAAAGACTAGTACTTTAGTGACGTTTTTATACAAAC
*
3884342 GTCGCTATAGATTCGTAC
66 GCCGCTATAGATTCGTAC
* *
3884360 TTTAGTGGCGTTTTTAGAACAAACACCGCTACAGACTCA-TACTTTAGTGATGTTTTTATACAAA
1 TTTAGTGGCGTTTTTAGAACAAACACCGCTAAAGACT-AGTACTTTAGTGACGTTTTTATACAAA
*
3884424 CGCCGCTA-A-ATT-ATATCC
65 CGCCGCTATAGATTCGTA--C
* * * * * * *
3884442 TTTAGTGGCCTTCTTA-AACAAATC-TCGTTAAAGACTAGTACTATAGCGACGTTTGTT-TAAAA
1 TTTAGTGGCGTTTTTAGAACAAA-CACCGCTAAAGACTAGTACTTTAGTGACGTTT-TTAT-ACA
*
3884504 AACGCCGCTATTGATTCGTAC
63 AACGCCGCTATAGATTCGTAC
* * *
3884525 TTTAGTGGCG-TTTTAGAACAAGCGA-CGCTACAGACTAGTACTTTAGTGGCGTTTTTATACAAA
1 TTTAGTGGCGTTTTTAGAACAAAC-ACCGCTAAAGACTAGTACTTTAGTGACGTTTTTATACAAA
* * *
3884588 TGCCGCTAAAGACTCGTAC
65 CGCCGCTATAGATTCGTAC
3884607 TTTAGTGGC
1 TTTAGTGGC
3884616 ATTTGTGTTT
Statistics
Matches: 208, Mismatches: 33, Indels: 30
0.77 0.12 0.11
Matches are distributed among these distances:
80 3 0.01
81 32 0.15
82 100 0.48
83 68 0.33
84 3 0.01
85 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (83 bp):
TTTAGTGGCGTTTTTAGAACAAACACCGCTAAAGACTAGTACTTTAGTGACGTTTTTATACAAAC
GCCGCTATAGATTCGTAC
Found at i:3887706 original size:42 final size:42
Alignment explanation
Indices: 3887646--3887863 Score: 217
Period size: 42 Copynumber: 5.1 Consensus size: 42
3887636 GCGTTAAATA
* * * *
3887646 GCGGCGTTTGTTCCAAAAATGCCGCTATATATCCTACCTTTT
1 GCGGCGTTTGTTCAAAAAACGCCGCTATAGATCCGACCTTTT
* * *
3887688 GCGGCGTTT-TCTAAAAAAACACCGCTATAGATCTCGACCTATT
1 GCGGCGTTTGT-TCAAAAAACGCCGCTATAGATC-CGACCTTTT
* * *
3887731 ACGGCGTTTGTTCCAAAAACGCC-ATCATAGATCCGACCTTTT
1 GCGGCGTTTGTTCAAAAAACGCCGCT-ATAGATCCGACCTTTT
* * *
3887773 GCTGCGTTTGTTCCAAAAACGCCGCTATATAGT-CGACCTTTT
1 GCGGCGTTTGTTCAAAAAACGCCGCTATAGA-TCCGACCTTTT
** *
3887815 GCGGCGTTTGTTCCAAAAAATTCCGCTATAGATCTCGACCTATT
1 GCGGCGTTTGTT-CAAAAAACGCCGCTATAGATC-CGACCTTTT
3887859 GCGGC
1 GCGGC
3887864 ATTTTTTTTT
Statistics
Matches: 144, Mismatches: 23, Indels: 16
0.79 0.13 0.09
Matches are distributed among these distances:
41 1 0.01
42 81 0.56
43 48 0.33
44 14 0.10
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (42 bp):
GCGGCGTTTGTTCAAAAAACGCCGCTATAGATCCGACCTTTT
Found at i:3887791 original size:85 final size:84
Alignment explanation
Indices: 3887647--3887868 Score: 241
Period size: 85 Copynumber: 2.6 Consensus size: 84
3887637 CGTTAAATAG
* * *
3887647 CGGCGTTTGTTCCAAAAATGCCGCTATATATCCTACCTTTTGCGGCGTTTTCTAAAAAAACACCG
1 CGGCGTTTGTTCCAAAAACGCCGCTATAGATCCGACCTTTTGCGGCGTTTTCTAAAAAAACACCG
3887712 CTATAGATCTCGACCTATTA
66 CTATAGA-CTCGACCTATTA
* * ** *
3887732 CGGCGTTTGTTCCAAAAACGCC-ATCATAGATCCGACCTTTTGCTGCGTTTGT-TCCAAAAACGC
1 CGGCGTTTGTTCCAAAAACGCCGCT-ATAGATCCGACCTTTTGCGGCGTTT-TCTAAAAAAACAC
* * * *
3887795 CGCTATATAGTCGACCTTTTG
64 CGCTATAGACTCGACCTATTA
** * *
3887816 CGGCGTTTGTTCCAAAAAATTCCGCTATAGATCTCGACCTATTGCGGCATTTT
1 CGGCGTTTGTTCC-AAAAACGCCGCTATAGATC-CGACCTTTTGCGGCGTTTT
3887869 TTTTTCACAA
Statistics
Matches: 114, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
84 23 0.20
85 74 0.65
86 17 0.15
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (84 bp):
CGGCGTTTGTTCCAAAAACGCCGCTATAGATCCGACCTTTTGCGGCGTTTTCTAAAAAAACACCG
CTATAGACTCGACCTATTA
Found at i:3920568 original size:18 final size:18
Alignment explanation
Indices: 3920531--3920564 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3920521 TTTTAGGATT
*
3920531 TTATATTCGATTTTAATA
1 TTATATTCGATTTAAATA
3920549 TTATATTCGA-TTAAAT
1 TTATATTCGATTTAAAT
3920565 TATTCGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (18 bp):
TTATATTCGATTTAAATA
Found at i:3920961 original size:44 final size:44
Alignment explanation
Indices: 3920911--3921009 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 44
3920901 TACCATGTTA
** *
3920911 GGTATCGATACTACTTTACATGGTAGTATCGATACTCACTAGAC
1 GGTATCGATACTACTGCACATAGTAGTATCGATACTCACTAGAC
* * *
3920955 GGTATCGATACTACTGCATATAGTAGTATCGATACTCTCTGGAC
1 GGTATCGATACTACTGCACATAGTAGTATCGATACTCACTAGAC
*
3920999 AGTATCGATAC
1 GGTATCGATAC
3921010 CGTTGGTTTG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Consensus pattern (44 bp):
GGTATCGATACTACTGCACATAGTAGTATCGATACTCACTAGAC
Found at i:3921092 original size:22 final size:23
Alignment explanation
Indices: 3921047--3921092 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
3921037 TAATTTTATA
**
3921047 CAGGTAGTATCGATACCCCTATG
1 CAGGTAGTATCGATACCCAAATG
3921070 CAGG-AGTATCGATACCCAAATG
1 CAGGTAGTATCGATACCCAAATG
3921092 C
1 C
3921093 TCCCAGCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (23 bp):
CAGGTAGTATCGATACCCAAATG
Found at i:3932814 original size:75 final size:76
Alignment explanation
Indices: 3932654--3932822 Score: 236
Period size: 76 Copynumber: 2.2 Consensus size: 76
3932644 TGGGTTAAAC
* *
3932654 TTAA-ATTTAGGATAATATTTTAAATATTATATTTTATCTTTGTATTTTAGTTTAAATAGATTTT
1 TTAAGATTTAGGATATTATTTTAAATATTATATTTTATCTTTGTATTTTAGTTTAAATAGAGTTT
3932718 TAGTATTTTAA
66 TAGTATTTTAA
* * *
3932729 TTAAGTTTTAGGATATTATGTTTATATTTTATA-TTTATCTTTGTATTTTAGTTTAAATAG-GTT
1 TTAAGATTTAGGATATTAT-TTTAAATATTATATTTTATCTTTGTATTTTAGTTTAAATAGAGTT
*
3932792 TTATTATTTTAA
65 TTAGTATTTTAA
* *
3932804 TTAGGATTTAGAATATTAT
1 TTAAGATTTAGGATATTAT
3932823 ATTATTTTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
75 33 0.40
76 39 0.47
77 11 0.13
ACGTcount: A:0.32, C:0.01, G:0.10, T:0.57
Consensus pattern (76 bp):
TTAAGATTTAGGATATTATTTTAAATATTATATTTTATCTTTGTATTTTAGTTTAAATAGAGTTT
TAGTATTTTAA
Found at i:3932840 original size:76 final size:76
Alignment explanation
Indices: 3932680--3932833 Score: 222
Period size: 75 Copynumber: 2.0 Consensus size: 76
3932670 ATTTTAAATA
* * *
3932680 TTATATTTTATCTTTGTATTTTAGTTTAAATAGATTTTTAGTATTTTAATTAAGTTTTAGGATAT
1 TTATA-TTTATCTTTGTATTTTAGTTTAAATAGAGTTTTAGTATTTTAATTAAGATTTAGAATAT
*
3932745 TATGTTTATATT
65 TATGATTATATT
* *
3932757 TTATATTTATCTTTGTATTTTAGTTTAAATAG-GTTTTATTATTTTAATTAGGATTTAGAATATT
1 TTATATTTATCTTTGTATTTTAGTTTAAATAGAGTTTTAGTATTTTAATTAAGATTTAGAATATT
*
3932821 AT-ATTATTTT
66 ATGATTATATT
3932831 TTA
1 TTA
3932834 GGTATTTTAG
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
74 9 0.13
75 29 0.41
76 27 0.39
77 5 0.07
ACGTcount: A:0.29, C:0.01, G:0.10, T:0.60
Consensus pattern (76 bp):
TTATATTTATCTTTGTATTTTAGTTTAAATAGAGTTTTAGTATTTTAATTAAGATTTAGAATATT
ATGATTATATT
Found at i:3944997 original size:77 final size:80
Alignment explanation
Indices: 3944915--3945069 Score: 185
Period size: 83 Copynumber: 2.0 Consensus size: 80
3944905 TAAACTCAAA
*
3944915 TTTAGGATAATA-TTTTA-A-ACAT-TATAT-TTTATCTTTGGATTTTAGTTTAAATAGATTTTT
1 TTTAGGATAATATTTTTATATACATCTATATCTTTATCTTTGGATTTTAGTTTAAATAG--GTTT
3944975 TAGTATTTTAATTAAGT
64 TAGTATTTTAATTAAGT
* ** * * *
3944992 TTTAGGATATTATTTTTATATTTTATCTTTATCTTTATCTTTGTATTTTAGTTTAAATTGGTTTT
1 TTTAGGATAATATTTTTATA-TACATCTATATCTTTATCTTTGGATTTTAGTTTAAATAGGTTTT
3945057 AGTATTTTAATTA
65 AGTATTTTAATTA
3945070 GGATATAGAA
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
77 11 0.17
78 5 0.08
79 1 0.02
81 19 0.29
82 4 0.06
83 25 0.38
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (80 bp):
TTTAGGATAATATTTTTATATACATCTATATCTTTATCTTTGGATTTTAGTTTAAATAGGTTTTA
GTATTTTAATTAAGT
Found at i:3945106 original size:83 final size:81
Alignment explanation
Indices: 3944939--3945096 Score: 203
Period size: 81 Copynumber: 2.0 Consensus size: 81
3944929 TTAAACATTA
* * * *
3944939 TATTTTATCTTTGGATTTTAGTTTAAATAGATTTTTTAGTATTTTAATTAAGTTTTAGGATATTA
1 TATTTTATCTTTGGATTTTAGTTTAAATAGA-GTTTTAGTATTTTAATTAAGATATAGAATATTA
*
3945004 TTTTTATATTTTATCTT
65 TTATTATATTTTATCTT
* * *
3945021 TATCTTTATCTTTGTATTTTAGTTTAAATTG-GTTTTAGTATTTTAATTAGGATATAGAATATTA
1 TAT-TTTATCTTTGGATTTTAGTTTAAATAGAGTTTTAGTATTTTAATTAAGATATAGAATATTA
*
3945085 -TATTATTTTTTA
65 TTATTATATTTTA
3945097 GGTATTTTAT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
80 10 0.15
81 28 0.42
82 3 0.05
83 25 0.38
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (81 bp):
TATTTTATCTTTGGATTTTAGTTTAAATAGAGTTTTAGTATTTTAATTAAGATATAGAATATTAT
TATTATATTTTATCTT
Found at i:3945758 original size:21 final size:22
Alignment explanation
Indices: 3945733--3945773 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3945723 CTTTAATTTG
3945733 TTTATTTAATTATT-TTTTTCT
1 TTTATTTAATTATTATTTTTCT
*
3945754 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
3945774 TATTTTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTAATTATTATTTTTCT
Found at i:3948277 original size:22 final size:22
Alignment explanation
Indices: 3948243--3948297 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
3948233 TTGAAAGTGG
*
3948243 TTTAATTGGTTTA-AAATTATTAA
1 TTTAATT--TTTAGAAATTAATAA
*
3948266 TTTATATTTTTAGAACTTAATAA
1 TTTA-ATTTTTAGAAATTAATAA
3948289 TTTAATTTT
1 TTTAATTTT
3948298 AATAGGTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 9 0.32
23 16 0.57
24 3 0.11
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.56
Consensus pattern (22 bp):
TTTAATTTTTAGAAATTAATAA
Found at i:3950907 original size:21 final size:21
Alignment explanation
Indices: 3950875--3950953 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 21
3950865 ACTTTTCCAA
3950875 AAAATAGATTGATCCCTTTGAT
1 AAAAT-GATTGATCCCTTTGAT
* *
3950897 AAAATGATTGATTCCTTTTCA-
1 AAAATGATTGA-TCCCTTTGAT
* * *
3950918 AAAAGGATTGATCCCTTGGTT
1 AAAATGATTGATCCCTTTGAT
**
3950939 TGAATGATTGATCCC
1 AAAATGATTGATCCC
3950954 AAACTCACTA
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
20 5 0.11
21 28 0.62
22 12 0.27
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (21 bp):
AAAATGATTGATCCCTTTGAT
Found at i:3954365 original size:30 final size:30
Alignment explanation
Indices: 3954329--3954392 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
3954319 CAACCAGTAG
*
3954329 CAGGTGAAGCCACAACCTTAGTTGCAACAA
1 CAGGTGAAGCCACAACCTTAGTTACAACAA
*
3954359 CAGGTGATGCCACAACCTTAGTTACAACAA
1 CAGGTGAAGCCACAACCTTAGTTACAACAA
3954389 CAGG
1 CAGG
3954393 CCACACAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (30 bp):
CAGGTGAAGCCACAACCTTAGTTACAACAA
Found at i:3959766 original size:20 final size:18
Alignment explanation
Indices: 3959734--3959776 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
3959724 TTTTTAAGAT
3959734 CATA-TTTAAATTACTTTAG
1 CATATTTTAAATTA-TTT-G
*
3959753 CATATTTTACATTATTTG
1 CATATTTTAAATTATTTG
3959771 CATATT
1 CATATT
3959777 GGAAATGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 7 0.32
20 8 0.36
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.51
Consensus pattern (18 bp):
CATATTTTAAATTATTTG
Found at i:3965774 original size:65 final size:65
Alignment explanation
Indices: 3965668--3965793 Score: 157
Period size: 65 Copynumber: 1.9 Consensus size: 65
3965658 CGATGCACAT
* * * *
3965668 CCATGCATCGATGCACTCTGGATTTTATTGGAACGTCGAATGC-ATTTGATGCACCGATGCATAG
1 CCATGCATCGATGCACTCTGGATTGTATTGAAACATCGAATGCAATTAG-TGCACCGATGCATAG
3965732 A
65 A
* * *
3965733 CCATGCATCGATGCACTCCTGGCTTGT-TTGAAACATTGAATGTAATTAGTGCACCGATGCA
1 CCATGCATCGATGCACT-CTGGATTGTATTGAAACATCGAATGCAATTAGTGCACCGATGCA
3965794 CCCCTAGTGT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
65 41 0.79
66 11 0.21
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (65 bp):
CCATGCATCGATGCACTCTGGATTGTATTGAAACATCGAATGCAATTAGTGCACCGATGCATAGA
Found at i:3968333 original size:22 final size:22
Alignment explanation
Indices: 3968301--3968374 Score: 107
Period size: 22 Copynumber: 3.5 Consensus size: 22
3968291 ACACTAGATA
*
3968301 GTGCATTGATGCATTCTTGAAT
1 GTGCATCGATGCATTCTTGAAT
3968323 GTGCATCGATGCATTCTTGAAT
1 GTGCATCGATGCATTCTTGAAT
* *
3968345 GTGCATCGATGCACTC-TG-TT
1 GTGCATCGATGCATTCTTGAAT
3968365 GTGCATCGAT
1 GTGCATCGAT
3968375 ACACCCATCG
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
20 11 0.22
21 2 0.04
22 36 0.73
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.36
Consensus pattern (22 bp):
GTGCATCGATGCATTCTTGAAT
Found at i:3971129 original size:65 final size:64
Alignment explanation
Indices: 3970995--3971137 Score: 155
Period size: 65 Copynumber: 2.2 Consensus size: 64
3970985 AATGCATTTT
* * * * * * *
3970995 ATGCACCGATGCACAGCCATGCATCGATGCACTCTGGATTTTATTGGAACATCGAATTCATTTG
1 ATGCACTGATGCACAGCCATGCATCGATGCACTCTGGATTGTATTGAAACAACCAATTAATTAG
* *
3971059 ATGCACTGATGCACAGACCATGTATCGATGCACTCCTGGCTTGT-TTGAAACAACCAATGTAATT
1 ATGCACTGATGCACAG-CCATGCATCGATGCACT-CTGGATTGTATTGAAACAACCAAT-TAATT
3971123 AG
63 AG
*
3971125 -TGCACTCATGCAC
1 ATGCACTGATGCAC
3971138 CCCTAGTGTA
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
64 15 0.23
65 39 0.59
66 12 0.18
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (64 bp):
ATGCACTGATGCACAGCCATGCATCGATGCACTCTGGATTGTATTGAAACAACCAATTAATTAG
Found at i:3985112 original size:2 final size:2
Alignment explanation
Indices: 3985107--3985171 Score: 114
Period size: 2 Copynumber: 33.0 Consensus size: 2
3985097 TACACACGTG
*
3985107 TA TA TA TA TA TA TA TA TA GA 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
3985149 TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
3985172 AAAGACAAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3985489 original size:13 final size:13
Alignment explanation
Indices: 3985471--3985496 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3985461 TGTATAGCCC
3985471 ATCTATTATTTCT
1 ATCTATTATTTCT
3985484 ATCTATTATTTCT
1 ATCTATTATTTCT
3985497 TGATATCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (13 bp):
ATCTATTATTTCT
Found at i:3986809 original size:129 final size:131
Alignment explanation
Indices: 3986569--3986820 Score: 490
Period size: 129 Copynumber: 1.9 Consensus size: 131
3986559 TGGTTTTATT
3986569 TTGAGGTAATATGGGATCCTTAATTGAGCTTTAAGTTAATGTGTTCTTGTTACTATTACTAGTGC
1 TTGAGGTAATATGGGATCCTTAATTGAGCTTTAAGTTAATGTGTTCTTGTTACTATTACTAGTGC
3986634 ATAAGTGACCTATAATGACCTATGTTGTACTTTGATTCTTGATTAAGTAGTGAAATGATTGTTTT
66 ATAAGTGACCTATAATGACCTATGTTGTACTTTGATTCTTGATTAAGTAGTGAAATGATTGTTTT
3986699 A
131 A
3986700 TTGAGGT-A-ATGGGATCCTTAATTGAGCTTTAAGTTAATGTGTTCTTGTTACTATTACTAGTGC
1 TTGAGGTAATATGGGATCCTTAATTGAGCTTTAAGTTAATGTGTTCTTGTTACTATTACTAGTGC
3986763 ATAAGTGACCTATAATGACCTATGTTGTACTTTGATTCTTGATTAAGTAGTGAAATGA
66 ATAAGTGACCTATAATGACCTATGTTGTACTTTGATTCTTGATTAAGTAGTGAAATGA
3986821 CTATTATTGA
Statistics
Matches: 121, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
129 113 0.93
130 1 0.01
131 7 0.06
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (131 bp):
TTGAGGTAATATGGGATCCTTAATTGAGCTTTAAGTTAATGTGTTCTTGTTACTATTACTAGTGC
ATAAGTGACCTATAATGACCTATGTTGTACTTTGATTCTTGATTAAGTAGTGAAATGATTGTTTT
A
Found at i:3988868 original size:15 final size:14
Alignment explanation
Indices: 3988831--3988871 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3988821 ATTTAGGAAC
*
3988831 TTGCATATATAATG
1 TTGCATATTTAATG
*
3988845 TTGCATATTTAATT
1 TTGCATATTTAATG
3988859 TTGTCATATTTAA
1 TTG-CATATTTAA
3988872 GGAATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 15 0.62
15 9 0.38
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (14 bp):
TTGCATATTTAATG
Found at i:3990662 original size:22 final size:22
Alignment explanation
Indices: 3990634--3990680 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
3990624 CCTTCACATA
3990634 TTGAATTTATTACTTTGCTATC
1 TTGAATTTATTACTTTGCTATC
* *
3990656 TTGAATTTATTAGTTTGTTATC
1 TTGAATTTATTACTTTGCTATC
3990678 TTG
1 TTG
3990681 TTTTTGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.21, C:0.09, G:0.13, T:0.57
Consensus pattern (22 bp):
TTGAATTTATTACTTTGCTATC
Found at i:3992830 original size:74 final size:72
Alignment explanation
Indices: 3992706--3992841 Score: 209
Period size: 74 Copynumber: 1.9 Consensus size: 72
3992696 TTTTATCTTT
* * *
3992706 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTATATTTTATC
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAATATTATATTAT-TTTTATC
3992771 TTGTTTAG
65 TTGTTTAG
* *
3992779 GTATTTTAGTTTAAATAGGTTTTTCGTATTTTAATTAGGATTTAGAATATTATATTATTTTTA
1 GTATTTTAGTTTAAATAGG-TTTTAGTATTTTAATTAAGATTTAGAATATTATATTATTTTTA
3992842 GGTATTTTAG
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
73 24 0.42
74 33 0.58
ACGTcount: A:0.29, C:0.01, G:0.13, T:0.57
Consensus pattern (72 bp):
GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAATATTATATTATTTTTATCT
TGTTTAG
Found at i:3993474 original size:23 final size:22
Alignment explanation
Indices: 3993448--3993501 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
3993438 TCTCAATCTC
*
3993448 TTTAATTTGTTTATTTAATTATT
1 TTTAATTTATTTATTT-ATTATT
* *
3993471 TTTATTTTATTTATTTCTTATT
1 TTTAATTTATTTATTTATTATT
*
3993493 TTTATTTTA
1 TTTAATTTA
3993502 AAAACAACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTAATTTATTTATTTATTATT
Found at i:3999117 original size:30 final size:30
Alignment explanation
Indices: 3999083--3999140 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
3999073 CTAAATTAAA
* * *
3999083 AAAAACAGACATTTAAAAGACTAAAATAGC
1 AAAAACAGAAAGTTAAAAGACCAAAATAGC
* *
3999113 AAAAATAGAAAGTTAAAGGACCAAAATA
1 AAAAACAGAAAGTTAAAAGACCAAAATA
3999141 AATTACATAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.62, C:0.10, G:0.12, T:0.16
Consensus pattern (30 bp):
AAAAACAGAAAGTTAAAAGACCAAAATAGC
Found at i:4000235 original size:31 final size:32
Alignment explanation
Indices: 4000176--4000235 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
4000166 TAAAAAAAAC
*
4000176 ATTAGTAAATAATATAATAATATGATATATGT
1 ATTAGTAAATAATATAATAATATCATATATGT
*
4000208 ATTA-TAAATAATATAGT-ATACTCATATA
1 ATTAGTAAATAATATAATAATA-TCATATA
4000236 AATTTGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 3 0.12
31 18 0.72
32 4 0.16
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (32 bp):
ATTAGTAAATAATATAATAATATCATATATGT
Found at i:4000440 original size:41 final size:41
Alignment explanation
Indices: 4000395--4000490 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
4000385 GTTGGTTGTG
* * * * *
4000395 GAGTGCCCTTTTCCACCCCTGGTGTACCCATCGAAGCCCCT
1 GAGTGCCCTCTGCCACCCATGGTGTACCCACCAAAGCCCCT
4000436 GAGTGCCCTCTGCCACCCATGGTGTACCCACCAAAGCCCCT
1 GAGTGCCCTCTGCCACCCATGGTGTACCCACCAAAGCCCCT
4000477 GAGTGCCCTCTGCC
1 GAGTGCCCTCTGCC
4000491 GCCCCTACGA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.16, C:0.43, G:0.21, T:0.21
Consensus pattern (41 bp):
GAGTGCCCTCTGCCACCCATGGTGTACCCACCAAAGCCCCT
Found at i:4001125 original size:15 final size:15
Alignment explanation
Indices: 4001105--4001143 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
4001095 ATATGTGCTT
4001105 TGGAATATTTGTTCA
1 TGGAATATTTGTTCA
4001120 TGGAATATTTGTTCA
1 TGGAATATTTGTTCA
*
4001135 TGAAATATT
1 TGGAATATT
4001144 GTTAATAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.31, C:0.05, G:0.18, T:0.46
Consensus pattern (15 bp):
TGGAATATTTGTTCA
Found at i:4005819 original size:18 final size:18
Alignment explanation
Indices: 4005796--4005840 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
4005786 TAGTTTGATT
4005796 AATGAACTAAAATTATTC
1 AATGAACTAAAATTATTC
**
4005814 AATGAACTAACTTTATTC
1 AATGAACTAAAATTATTC
*
4005832 AATGCACTA
1 AATGAACTA
4005841 GATTCATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (18 bp):
AATGAACTAAAATTATTC
Found at i:4008360 original size:221 final size:222
Alignment explanation
Indices: 4007977--4008415 Score: 871
Period size: 221 Copynumber: 2.0 Consensus size: 222
4007967 TTCTAGAACC
4007977 TTCCATCTTATTTTCCACACCATTTATCTTCTTCTTCCTCTCGATTCATTCATCTCTTTTCTTTT
1 TTCCATCTTATTTTCCACACCATTTATCTTCTTCTTCCTCTCGATTCATTCATCTCTTTTCTTTT
4008042 GTGAGTATCAAATGTGGGAACTTGGTTGTCCAACAAGGCTAGTCTAAGTTTATAAAGATAAGAAC
66 GTGAGTATCAAATGTGGGAACTTGGTTGTCCAACAAGGCTAGTCTAAGTTTATAAAGATAAGAAC
4008107 ATTAATCTCCTCTCTTAGAGTTTCATTTCTAGCCCAACATCTCATGGTTTTGTTATG-TGCACAA
131 ATTAATCTCCTCTCTTAGAGTTTCATTTCTAGCCCAACATCTCATGGTTTTGTTATGTTGCACAA
4008171 GGTAGGGGTTTTAGAGAGGTTTTAACT
196 GGTAGGGGTTTTAGAGAGGTTTTAACT
4008198 TTCCATCTTATTTTCCACACCATTTATCTTCTTCTTCCTCTCGATTCATTCATCTCTTTTCTTTT
1 TTCCATCTTATTTTCCACACCATTTATCTTCTTCTTCCTCTCGATTCATTCATCTCTTTTCTTTT
4008263 GTGAGTATCAAATGTGGGAACTTGGTTGTCCAACAAGGCTAGTCTAAGTTTATAAAGATAAGAAC
66 GTGAGTATCAAATGTGGGAACTTGGTTGTCCAACAAGGCTAGTCTAAGTTTATAAAGATAAGAAC
4008328 ATTAATCTCCTCTCTTAGAGTTTCATTTCTAGCCCAACATCTCATGGTTTTGTTATGTTGCACAA
131 ATTAATCTCCTCTCTTAGAGTTTCATTTCTAGCCCAACATCTCATGGTTTTGTTATGTTGCACAA
4008393 GGTAGGGGTTTTAGAGAGGTTTT
196 GGTAGGGGTTTTAGAGAGGTTTT
4008416 GAGTTTTAAG
Statistics
Matches: 217, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
221 187 0.86
222 30 0.14
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.41
Consensus pattern (222 bp):
TTCCATCTTATTTTCCACACCATTTATCTTCTTCTTCCTCTCGATTCATTCATCTCTTTTCTTTT
GTGAGTATCAAATGTGGGAACTTGGTTGTCCAACAAGGCTAGTCTAAGTTTATAAAGATAAGAAC
ATTAATCTCCTCTCTTAGAGTTTCATTTCTAGCCCAACATCTCATGGTTTTGTTATGTTGCACAA
GGTAGGGGTTTTAGAGAGGTTTTAACT
Found at i:4013507 original size:21 final size:21
Alignment explanation
Indices: 4013483--4013524 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4013473 ATTAAAAGCC
4013483 AAGGCAACAC-TATTACAAAGT
1 AAGGCAAC-CTTATTACAAAGT
*
4013504 AAGGCAACCTTATTGCAAAGT
1 AAGGCAACCTTATTACAAAGT
4013525 CATAGCTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (21 bp):
AAGGCAACCTTATTACAAAGT
Found at i:4022886 original size:16 final size:16
Alignment explanation
Indices: 4022849--4022891 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
4022839 TGGCTTAAAA
*
4022849 ATGAATATTATTAGGT
1 ATGAATATTATTAGGC
4022865 AT-AATATTAGTTA-GC
1 ATGAATATTA-TTAGGC
4022880 ATGAATATTATT
1 ATGAATATTATT
4022892 TTACTGGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.44
Consensus pattern (16 bp):
ATGAATATTATTAGGC
Found at i:4026445 original size:16 final size:16
Alignment explanation
Indices: 4026424--4026457 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
4026414 AAGGGAGTGT
4026424 CTTAGGGCCTAAGAGC
1 CTTAGGGCCTAAGAGC
4026440 CTTAGGGCCTAAGAGC
1 CTTAGGGCCTAAGAGC
4026456 CT
1 CT
4026458 ACCCAAGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.26, G:0.29, T:0.21
Consensus pattern (16 bp):
CTTAGGGCCTAAGAGC
Found at i:4030465 original size:77 final size:79
Alignment explanation
Indices: 4030325--4030479 Score: 206
Period size: 77 Copynumber: 2.0 Consensus size: 79
4030315 ATATAGTAAG
*
4030325 TAAACATTAAAAGAATGTAATTCTGATTACAACTCTTTTAAAGGATATTTAATTCAAAATAATTA
1 TAAACATTAAAAGAATGTAATTCGGATTACAACTCTTTTAAAGGATATTTAATTCAAAATAATTA
*
4030390 AATAAGAGTTTAAA
66 AATAAAAGTTTAAA
** * * * * * *
4030404 TAAACATT-AAAGTGTGTAATTCGGATTATAAGTC-TTTAATGTATATTTAATTTAAATTAATTA
1 TAAACATTAAAAGAATGTAATTCGGATTACAACTCTTTTAAAGGATATTTAATTCAAAATAATTA
4030467 AATAAAAGTTTAA
66 AATAAAAGTTTAA
4030480 TTAATTCGAA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
77 37 0.56
78 21 0.32
79 8 0.12
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.39
Consensus pattern (79 bp):
TAAACATTAAAAGAATGTAATTCGGATTACAACTCTTTTAAAGGATATTTAATTCAAAATAATTA
AATAAAAGTTTAAA
Found at i:4030964 original size:14 final size:14
Alignment explanation
Indices: 4030954--4030984 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
4030944 ATTTTATTTC
4030954 TTACTTTTTATCAT
1 TTACTTTTTATCAT
4030968 TTACTTTTTATCAT
1 TTACTTTTTATCAT
4030982 TTA
1 TTA
4030985 AAGGTCAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.65
Consensus pattern (14 bp):
TTACTTTTTATCAT
Found at i:4032555 original size:6 final size:7
Alignment explanation
Indices: 4032528--4032576 Score: 59
Period size: 7 Copynumber: 7.3 Consensus size: 7
4032518 TTTTTAGCAA
4032528 TTTA-AT
1 TTTATAT
*
4032534 TTTAAAT
1 TTTATAT
4032541 TTTAATAT
1 TTT-ATAT
4032549 TTT-TAT
1 TTTATAT
4032555 TTT-TAT
1 TTTATAT
4032561 TTTATAT
1 TTTATAT
4032568 TTTATAT
1 TTTATAT
4032575 TT
1 TT
4032577 AAAATATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
6 16 0.41
7 17 0.44
8 6 0.15
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTATAT
Found at i:4032562 original size:20 final size:20
Alignment explanation
Indices: 4032539--4032576 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4032529 TTAATTTTAA
4032539 ATTTTAATATTTT-TATTTTT
1 ATTTT-ATATTTTATATTTTT
4032559 ATTTTATATTTTATATTT
1 ATTTTATATTTTATATTT
4032577 AAAATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
ATTTTATATTTTATATTTTT
Found at i:4032585 original size:35 final size:34
Alignment explanation
Indices: 4032528--4032595 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
4032518 TTTTTAGCAA
*
4032528 TTTAATTTTAAATTTTAATATTTTTA-TTTTTAT
1 TTTAATTTTAAATTTAAATATTTTTAGTTTTTAT
*
4032561 TTTATATTTTATATTTAAAATATTTTTAGTTTTTA
1 TTTA-ATTTTAAATTT-AAATATTTTTAGTTTTTA
4032596 AAAAAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 4 0.13
34 10 0.33
35 10 0.33
36 6 0.20
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (34 bp):
TTTAATTTTAAATTTAAATATTTTTAGTTTTTAT
Found at i:4032595 original size:18 final size:17
Alignment explanation
Indices: 4032544--4032598 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
4032534 TTTAAATTTT
*
4032544 AATATTTTTATTTTTAT
1 AATATTTTTATTTTTAA
** *
4032561 TTTATATTTTATATTTAA
1 AATAT-TTTTATTTTTAA
4032579 AATATTTTTAGTTTTTAA
1 AATATTTTTA-TTTTTAA
4032597 AA
1 AA
4032599 AAATTAAATA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
17 8 0.28
18 21 0.72
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
AATATTTTTATTTTTAA
Found at i:4033120 original size:20 final size:21
Alignment explanation
Indices: 4033091--4033138 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
4033081 AAAGTTTAGA
*
4033091 TAAA-TAAAAT-ATATATTTT
1 TAAATTAAAATAAAATATTTT
4033110 TAAATTAAAATAAAATATTTT
1 TAAATTAAAATAAAATATTTT
*
4033131 AAAATTAA
1 TAAATTAA
4033139 GTTAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 4 0.16
20 6 0.24
21 15 0.60
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATTAAAATAAAATATTTT
Found at i:4033146 original size:49 final size:50
Alignment explanation
Indices: 4033061--4033158 Score: 121
Period size: 49 Copynumber: 2.0 Consensus size: 50
4033051 TTAATTTTAA
* *
4033061 TAAATTAAAATAAAATTGTAAAAGTTTAGATAAATAA-AATATATATTTT
1 TAAATTAAAATAAAATTGTAAAAGTTAAGATAAATAATAAAATATATTTT
* *
4033110 TAAATTAAAATAAAATATTTTAAAA-TTAAG-TTAATAATAAAATATATTT
1 TAAATTAAAAT-AAA-ATTGTAAAAGTTAAGATAAATAATAAAATATATTT
4033159 AATAAGTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
49 17 0.40
50 17 0.40
51 8 0.19
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (50 bp):
TAAATTAAAATAAAATTGTAAAAGTTAAGATAAATAATAAAATATATTTT
Found at i:4033152 original size:27 final size:27
Alignment explanation
Indices: 4033109--4033160 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
4033099 ATATATATTT
4033109 TTAAATTAAAATAAAATAT-TTTAAAA
1 TTAAATTAAAATAAAATATATTTAAAA
*
4033135 TTAAGTTAATAATAAAATATATTTAA
1 TTAAATTAA-AATAAAATATATTTAA
4033161 TAAGTTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 8 0.35
27 10 0.43
28 5 0.22
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (27 bp):
TTAAATTAAAATAAAATATATTTAAAA
Found at i:4033170 original size:25 final size:25
Alignment explanation
Indices: 4033093--4033170 Score: 79
Period size: 25 Copynumber: 3.0 Consensus size: 25
4033083 AGTTTAGATA
** *
4033093 AATAAAATATATATTTTTAAATTAA-
1 AATAAAATATAT-TTAATAAGTTAAT
4033118 AATAAAATAT-TTTAAAATTAAGTTAAT
1 AATAAAATATATTT--AA-TAAGTTAAT
4033145 AATAAAATATATTTAATAAGTTAAT
1 AATAAAATATATTTAATAAGTTAAT
4033170 A
1 A
4033171 TAATTTTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
23 2 0.04
24 1 0.02
25 20 0.44
26 9 0.20
27 10 0.22
28 3 0.07
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (25 bp):
AATAAAATATATTTAATAAGTTAAT
Found at i:4034102 original size:17 final size:17
Alignment explanation
Indices: 4034063--4034103 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
4034053 CTCAAATCCT
*
4034063 CTCAAACCCTCTTAAAG
1 CTCAAACCCTCTTAAAA
*
4034080 CCCAAACCCTCTTAAAA
1 CTCAAACCCTCTTAAAA
*
4034097 TTCAAAC
1 CTCAAAC
4034104 TCGGTCAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.39, C:0.37, G:0.02, T:0.22
Consensus pattern (17 bp):
CTCAAACCCTCTTAAAA
Found at i:4036064 original size:3 final size:3
Alignment explanation
Indices: 4036056--4036096 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
4036046 TATCTGCTCC
* * *
4036056 TGA TGA TGA TGG TGA TGA AGG TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
4036097 GGAGAAAGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.29, C:0.00, G:0.39, T:0.32
Consensus pattern (3 bp):
TGA
Found at i:4041795 original size:30 final size:30
Alignment explanation
Indices: 4041761--4041826 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
4041751 GGGTAGTCGA
* *
4041761 TGCTTTGGAATTTATCCCCGGTACTAAGGT
1 TGCTTAGGAATTTATCCCCGGTACTAAGGG
4041791 TGCTTAGGAATTTATCCCCGGTACTAAGGG
1 TGCTTAGGAATTTATCCCCGGTACTAAGGG
4041821 TGCTTA
1 TGCTTA
4041827 TCGAGCAAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (30 bp):
TGCTTAGGAATTTATCCCCGGTACTAAGGG
Found at i:4042899 original size:4 final size:4
Alignment explanation
Indices: 4042892--4042936 Score: 54
Period size: 4 Copynumber: 11.0 Consensus size: 4
4042882 GCATACAGGC
* * *
4042892 ATGT ATGT ATGT ATGT ACGT ATGT ACGT ACGT ATGT ATGGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT-GT ATGT
4042937 GTGCATACCG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
4 32 0.89
5 4 0.11
ACGTcount: A:0.24, C:0.07, G:0.27, T:0.42
Consensus pattern (4 bp):
ATGT
Found at i:4042907 original size:12 final size:12
Alignment explanation
Indices: 4042892--4042930 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
4042882 GCATACAGGC
*
4042892 ATGTATGTATGT
1 ATGTACGTATGT
4042904 ATGTACGTATGT
1 ATGTACGTATGT
*
4042916 ACGTACGTATGT
1 ATGTACGTATGT
4042928 ATG
1 ATG
4042931 GTATGTGTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (12 bp):
ATGTACGTATGT
Found at i:4043439 original size:39 final size:40
Alignment explanation
Indices: 4043371--4043459 Score: 108
Period size: 39 Copynumber: 2.2 Consensus size: 40
4043361 TATAAACAAC
* * * * *
4043371 ACAAACGTAAATGAGCACCATCAAATAC-AACTAACATAA
1 ACAAACGTAAACGAACACAACCAAATACAAACGAACATAA
*
4043410 ACAAACGTAAACGAACACAACCAATTACAAACGAACATAA
1 ACAAACGTAAACGAACACAACCAAATACAAACGAACATAA
*
4043450 ACAAAAGTAA
1 ACAAACGTAA
4043460 GTGTATAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 23 0.55
40 19 0.45
ACGTcount: A:0.57, C:0.22, G:0.08, T:0.12
Consensus pattern (40 bp):
ACAAACGTAAACGAACACAACCAAATACAAACGAACATAA
Found at i:4044694 original size:21 final size:22
Alignment explanation
Indices: 4044662--4044702 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4044652 GTCCCTGGCA
4044662 CGGGGACGGTA-CGGGGACGGC
1 CGGGGACGGTACCGGGGACGGC
4044683 CGGGGTAC-GTACCGGGGACG
1 CGGGG-ACGGTACCGGGGACG
4044703 TGCCACGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.15, C:0.24, G:0.54, T:0.07
Consensus pattern (22 bp):
CGGGGACGGTACCGGGGACGGC
Found at i:4045543 original size:4 final size:4
Alignment explanation
Indices: 4045514--4045556 Score: 50
Period size: 4 Copynumber: 10.2 Consensus size: 4
4045504 ATTTGTATAT
* *
4045514 ATAA CTAA ATATA ATCA ATAAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATA-A ATAA AT-AA ATAA ATAA ATAA ATAA ATAA A
4045557 ATATTTCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 27 0.82
5 6 0.18
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:4046423 original size:13 final size:13
Alignment explanation
Indices: 4046405--4046430 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4046395 AAATATAAAC
4046405 CCATCTCAAAGAA
1 CCATCTCAAAGAA
4046418 CCATCTCAAAGAA
1 CCATCTCAAAGAA
4046431 TTGTCTGCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.31, G:0.08, T:0.15
Consensus pattern (13 bp):
CCATCTCAAAGAA
Found at i:4050338 original size:16 final size:17
Alignment explanation
Indices: 4050312--4050344 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
4050302 TTTATATTTA
4050312 ATGATTTTAGTAATGAT
1 ATGATTTTAGTAATGAT
4050329 ATGA-TTTAGTAATGAT
1 ATGATTTTAGTAATGAT
4050345 TACTAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (17 bp):
ATGATTTTAGTAATGAT
Found at i:4050426 original size:14 final size:14
Alignment explanation
Indices: 4050394--4050465 Score: 50
Period size: 14 Copynumber: 5.5 Consensus size: 14
4050384 ATTAGTGATT
4050394 TAATAATG-ATTAG
1 TAATAATGAATTAG
4050407 TAATAATGACATTA-
1 TAATAATGA-ATTAG
*
4050421 TAATAATG-ATTTG
1 TAATAATGAATTAG
*
4050434 ATACTAATG-ATT--
1 -TAATAATGAATTAG
*
4050446 TAATAATG-ATTAC
1 TAATAATGAATTAG
4050459 TAATAAT
1 TAATAAT
4050466 TATTTAATAA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
11 10 0.20
12 3 0.06
13 15 0.30
14 18 0.36
15 4 0.08
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (14 bp):
TAATAATGAATTAG
Found at i:4050595 original size:17 final size:15
Alignment explanation
Indices: 4050561--4050600 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
4050551 AGACACATGC
4050561 ATATTTAATATTATA
1 ATATTTAATATTATA
*
4050576 ATATTTAAGTTTTAATA
1 ATATTTAA-TATT-ATA
4050593 ATATTTAA
1 ATATTTAA
4050601 CATTTGCAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 3 0.14
17 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATATTTAATATTATA
Found at i:4053385 original size:11 final size:12
Alignment explanation
Indices: 4053363--4053442 Score: 76
Period size: 11 Copynumber: 6.9 Consensus size: 12
4053353 GCTCGGTTAC
*
4053363 CTTTCTTTCTTT
1 CTTTCTTCCTTT
4053375 C-TTCTTCCTTT
1 CTTTCTTCCTTT
*
4053386 CTTTTTTCCTTT
1 CTTTCTTCCTTT
* *
4053398 CCTTC-ACCTTT
1 CTTTCTTCCTTT
*
4053409 CTTTTTTCCTTT
1 CTTTCTTCCTTT
* *
4053421 CCTTC-ACCTTT
1 CTTTCTTCCTTT
4053432 CTTTCTTCCTT
1 CTTTCTTCCTT
4053443 CTTACAACCG
Statistics
Matches: 52, Mismatches: 13, Indels: 6
0.73 0.18 0.08
Matches are distributed among these distances:
11 27 0.52
12 25 0.48
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.64
Consensus pattern (12 bp):
CTTTCTTCCTTT
Found at i:4053396 original size:12 final size:12
Alignment explanation
Indices: 4053379--4053421 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
4053369 TTCTTTCTTC
4053379 TTCCTTTCTTTT
1 TTCCTTTCTTTT
*
4053391 TTCCTTTC-CTT
1 TTCCTTTCTTTT
**
4053402 CACCTTTCTTTT
1 TTCCTTTCTTTT
4053414 TTCCTTTC
1 TTCCTTTC
4053422 CTTCACCTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (12 bp):
TTCCTTTCTTTT
Found at i:4053397 original size:23 final size:23
Alignment explanation
Indices: 4053381--4053442 Score: 115
Period size: 23 Copynumber: 2.7 Consensus size: 23
4053371 CTTTCTTCTT
4053381 CCTTTCTTTTTTCCTTTCCTTCA
1 CCTTTCTTTTTTCCTTTCCTTCA
4053404 CCTTTCTTTTTTCCTTTCCTTCA
1 CCTTTCTTTTTTCCTTTCCTTCA
*
4053427 CCTTTCTTTCTTCCTT
1 CCTTTCTTTTTTCCTT
4053443 CTTACAACCG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.03, C:0.35, G:0.00, T:0.61
Consensus pattern (23 bp):
CCTTTCTTTTTTCCTTTCCTTCA
Found at i:4053830 original size:29 final size:29
Alignment explanation
Indices: 4053749--4053834 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 29
4053739 CTCCAATTAG
* *
4053749 TTGGTCGTCGGGACTGCATGGCAACATGC
1 TTGGTCGTCGGGACTGCATGGCGACCTGC
*
4053778 TTGGGCGCTCGGG-CGTGCATGGCGACCTGC
1 TTGGTCG-TCGGGAC-TGCATGGCGACCTGC
4053808 TTGGTCG-CGGGACTTGCATGGCGACCT
1 TTGGTCGTCGGGAC-TGCATGGCGACCT
4053835 AGAGGTTGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
28 4 0.08
29 21 0.43
30 24 0.49
ACGTcount: A:0.12, C:0.27, G:0.38, T:0.23
Consensus pattern (29 bp):
TTGGTCGTCGGGACTGCATGGCGACCTGC
Found at i:4055786 original size:37 final size:36
Alignment explanation
Indices: 4055685--4055797 Score: 115
Period size: 37 Copynumber: 3.2 Consensus size: 36
4055675 TTAAAATATG
* *
4055685 AATATATTA-TTACGAATTTATATTCAATTGAATT-
1 AATATATTATTTATGAATTTATATTCAATTAAATTA
** * **
4055719 AGGA-ATTATTTATAAATTTATATTTGATTAAATGTA
1 AATATATTATTTATGAATTTATATTCAATTAAAT-TA
*
4055755 AATATATTATTTATGAATTTATATTCAATTAAAATA
1 AATATATTATTTATGAATTTATATTCAATTAAATTA
*
4055791 AAAATAT
1 AATATAT
4055798 ATCATTTCAA
Statistics
Matches: 61, Mismatches: 14, Indels: 6
0.75 0.17 0.07
Matches are distributed among these distances:
33 4 0.07
34 21 0.34
35 1 0.02
36 10 0.16
37 25 0.41
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (36 bp):
AATATATTATTTATGAATTTATATTCAATTAAATTA
Found at i:4061859 original size:14 final size:14
Alignment explanation
Indices: 4061840--4061866 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4061830 ATTTAATTAA
4061840 AATATGAATTTATT
1 AATATGAATTTATT
4061854 AATATGAATTTAT
1 AATATGAATTTAT
4061867 GTTCGATTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
AATATGAATTTATT
Found at i:4061865 original size:37 final size:38
Alignment explanation
Indices: 4061812--4061982 Score: 152
Period size: 37 Copynumber: 4.6 Consensus size: 38
4061802 CATAATGGTT
* * * *
4061812 TATTATTTAAGGATTTATATTTAATTAAAATATGAATT
1 TATTATTTATGAATTTATATTCAATTAAAATATGAATA
* * * * * *
4061850 TATTA-ATATGAATTTATGTTCGATTGAAACATGGATA
1 TATTATTTATGAATTTATATTCAATTAAAATATGAATA
* ** ***
4061887 TATTATTTATAAATTTATATTTGATT-AAATGCAAATA
1 TATTATTTATGAATTTATATTCAATTAAAATATGAATA
4061924 TATTATTTATGAATTTATATTCAATTAAAATATGAATA
1 TATTATTTATGAATTTATATTCAATTAAAATATGAATA
*
4061962 TATTGTTTCA--AATTTATATTC
1 TATTATTT-ATGAATTTATATTC
4061983 GTTTAGAATA
Statistics
Matches: 104, Mismatches: 26, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
37 67 0.64
38 36 0.35
39 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (38 bp):
TATTATTTATGAATTTATATTCAATTAAAATATGAATA
Found at i:4061944 original size:17 final size:17
Alignment explanation
Indices: 4061885--4061944 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
4061875 GAAACATGGA
*
4061885 TATATTATTTATAAATT
1 TATATTATTTATGAATT
* *
4061902 TATATTTGATTAAATGCAA-A
1 TATA-TT-ATT-TATG-AATT
4061922 TATATTATTTATGAATT
1 TATATTATTTATGAATT
4061939 TATATT
1 TATATT
4061945 CAATTAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
16 2 0.06
17 13 0.39
18 5 0.15
19 5 0.15
20 6 0.18
21 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (17 bp):
TATATTATTTATGAATT
Found at i:4070187 original size:108 final size:108
Alignment explanation
Indices: 4069985--4070222 Score: 267
Period size: 106 Copynumber: 2.2 Consensus size: 108
4069975 TGATTGGATC
* * *
4069985 TTTTCAGTGATATATCACTTCATTTCAAAAAAACATTCTTTTTCTCATAGACCATTTAATGCACA
1 TTTTCAGTGATATATCACTTCATTTCAAAAAAACATACTTTTTCTCATACACCATTTAATACACA
*
4070050 ATGAAATAAACTTTTCAATTCCCAATTACTTTATTTTAGAAAT
66 ATGAAATAAACTTTTCAATTCACAATTACTTTATTTTAGAAAT
* * * *
4070093 TTTTCAGTGATATATCACTTTATTT-AGAAAAACGTAC-TTTTGTCATACACCATTTAATACACA
1 TTTTCAGTGATATATCACTTCATTTCAAAAAAACATACTTTTTCTCATACACCATTTAATACACA
* * * *
4070156 ATGATAA-AAACATTTT-AGTT---AATTACTTTACTTCATAAACT
66 ATGA-AATAAAC-TTTTCAATTCACAATTACTTTATTTTAGAAA-T
* *
4070197 TTTT-AGTAATATATAACTTCATTTCA
1 TTTTCAGTGATATATCACTTCATTTCA
4070223 GAAACTTTAC
Statistics
Matches: 112, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
103 33 0.29
104 6 0.05
106 34 0.30
107 15 0.13
108 24 0.21
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.42
Consensus pattern (108 bp):
TTTTCAGTGATATATCACTTCATTTCAAAAAAACATACTTTTTCTCATACACCATTTAATACACA
ATGAAATAAACTTTTCAATTCACAATTACTTTATTTTAGAAAT
Found at i:4072461 original size:20 final size:21
Alignment explanation
Indices: 4072396--4072453 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
4072386 AAATGAATTG
*
4072396 AAAG-GTTAAGATCATTTAAC
1 AAAGAGTTAAGATCATTTGAC
4072416 AAAGAGTTAAGATCATTTGAC
1 AAAGAGTTAAGATCATTTGAC
4072437 AAAGAGTTAAGATCATT
1 AAAGAGTTAAGATCATT
4072454 GATGAAGAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 4 0.11
21 32 0.89
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.29
Consensus pattern (21 bp):
AAAGAGTTAAGATCATTTGAC
Found at i:4073961 original size:26 final size:26
Alignment explanation
Indices: 4073923--4074009 Score: 94
Period size: 26 Copynumber: 3.5 Consensus size: 26
4073913 GAATTCTCTA
4073923 AGAAA-AAATTTTTATAGATAGGGATT
1 AGAAACAAA-TTTTATAGATAGGGATT
*
4073949 AGAAACAAA-TTT-TAG-T-GGAATT
1 AGAAACAAATTTTATAGATAGGGATT
* **
4073971 AGAAACAAATTTTACAGATAAAGATT
1 AGAAACAAATTTTATAGATAGGGATT
4073997 AGAAACAAATTTT
1 AGAAACAAATTTT
4074010 CTAAGAAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
22 14 0.27
23 4 0.08
24 5 0.10
25 4 0.08
26 21 0.41
27 3 0.06
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.31
Consensus pattern (26 bp):
AGAAACAAATTTTATAGATAGGGATT
Found at i:4074665 original size:2 final size:2
Alignment explanation
Indices: 4074648--4074704 Score: 87
Period size: 2 Copynumber: 28.0 Consensus size: 2
4074638 TCATGACATC
* *
4074648 AT AT AC AT AC 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
4074690 AT AT AT AT AT CAT AT
1 AT AT AT AT AT -AT AT
4074705 TATGAACATG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 48 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4075499 original size:22 final size:23
Alignment explanation
Indices: 4075440--4075501 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
4075430 AATTTAATAA
*
4075440 CTTATTATAAAAAATTACTAAAT
1 CTTATTATAAAATATTACTAAAT
* * *
4075463 ATCTAATAT-AAATATTA-TTAAT
1 CT-TATTATAAAATATTACTAAAT
4075485 CTTATTATAAAATATTA
1 CTTATTATAAAATATTA
4075502 ACTATATTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
21 5 0.16
22 13 0.42
23 8 0.26
24 5 0.16
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (23 bp):
CTTATTATAAAATATTACTAAAT
Found at i:4076858 original size:3 final size:3
Alignment explanation
Indices: 4076852--4076970 Score: 65
Period size: 3 Copynumber: 38.7 Consensus size: 3
4076842 TAATATTATT
*
4076852 TAA TAA TAA TAA TAA TAT TAA T-A TAA T-A TATA TAA -AA TAA CGTATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA --TA-A
*
4076898 TAA TAA -AA -ACA TATA TAA TTAA TAG T-A TATA TAA TTAA TAA T-A
1 TAA TAA TAA TA-A TA-A TAA -TAA TAA TAA TA-A TAA -TAA TAA TAA
4076941 TAA TTAA TAA TAA T-A TATA TAA TAA TAA TA
1 TAA -TAA TAA TAA TAA TA-A TAA TAA TAA TA
4076971 TAAACGAACA
Statistics
Matches: 94, Mismatches: 5, Indels: 34
0.71 0.04 0.26
Matches are distributed among these distances:
2 14 0.15
3 53 0.56
4 24 0.26
5 2 0.02
6 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:4086051 original size:3 final size:3
Alignment explanation
Indices: 4086004--4086101 Score: 53
Period size: 3 Copynumber: 31.7 Consensus size: 3
4085994 GGGTCATATG
* * * *
4086004 TAA TAT TAA TTAA TAA TAT TAA TAT TAT TAA T-A TAA T-A TATA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
4086049 TAA TAA CGTATA TAA TAA -AA -AA TATA TAA TTAA TAA T-A TATA TAA
1 TAA TAA --TA-A TAA TAA TAA TAA TA-A TAA -TAA TAA TAA TA-A TAA
4086094 TAA TAA TA
1 TAA TAA TA
4086102 TAAACGGACA
Statistics
Matches: 77, Mismatches: 6, Indels: 24
0.72 0.06 0.22
Matches are distributed among these distances:
2 10 0.13
3 47 0.61
4 17 0.22
5 2 0.03
6 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:4086053 original size:12 final size:13
Alignment explanation
Indices: 4086004--4086104 Score: 79
Period size: 12 Copynumber: 7.8 Consensus size: 13
4085994 GGGTCATATG
4086004 TAATAT-TAATTAA
1 TAATATATAA-TAA
*
4086017 TAATAT-TAATAT
1 TAATATATAATAA
*
4086029 TATTA-AT-ATAA
1 TAATATATAATAA
4086040 T-ATATATAATAA
1 TAATATATAATAA
4086052 TAACGTATATAATAAA
1 TAA--TATATAAT-AA
*
4086068 AAATATATAATTAA
1 TAATATATAA-TAA
4086082 TAATATAT-ATAA
1 TAATATATAATAA
4086094 TAATAATATAA
1 TAAT-ATATAA
4086105 ACGGACAAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 19
0.74 0.06 0.20
Matches are distributed among these distances:
10 2 0.03
11 6 0.08
12 19 0.26
13 15 0.21
14 17 0.24
15 9 0.12
16 4 0.06
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (13 bp):
TAATATATAATAA
Found at i:4086054 original size:15 final size:15
Alignment explanation
Indices: 4085999--4086103 Score: 103
Period size: 15 Copynumber: 7.2 Consensus size: 15
4085989 CCTCCGGGTC
* *
4085999 ATATGTAATATTAAT
1 ATATATAATAATAAT
*
4086014 -TA-ATAATATTAAT
1 ATATATAATAATAAT
4086027 AT-TATTAAT-ATAAT
1 ATATA-TAATAATAAT
*
4086041 ATATATAATAATAAC
1 ATATATAATAATAAT
* *
4086056 GTATATAATAA-AAA
1 ATATATAATAATAAT
4086070 ATATATAATTAATAAT
1 ATATATAA-TAATAAT
4086086 ATATATAATAATAAT
1 ATATATAATAATAAT
4086101 ATA
1 ATA
4086104 AACGGACAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 14
0.78 0.07 0.14
Matches are distributed among these distances:
13 10 0.13
14 23 0.30
15 33 0.43
16 10 0.13
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (15 bp):
ATATATAATAATAAT
Found at i:4088947 original size:73 final size:73
Alignment explanation
Indices: 4088856--4088995 Score: 253
Period size: 73 Copynumber: 1.9 Consensus size: 73
4088846 TTAAATATTA
4088856 TATTTTATCTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATT
1 TATTTTATCTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATT
4088921 TAGGGTAT
66 TAGGGTAT
* * *
4088929 TATTTTATCTTATTTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAATTATTTTAATTATGATT
1 TATTTTATCTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATT
4088994 TA
66 TA
4088996 TTTTCTTTAT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 64 1.00
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.59
Consensus pattern (73 bp):
TATTTTATCTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATT
TAGGGTAT
Found at i:4107978 original size:73 final size:73
Alignment explanation
Indices: 4107829--4107967 Score: 253
Period size: 72 Copynumber: 1.9 Consensus size: 73
4107819 TTAAATATTA
4107829 TATTTTATCTTATCTTTGTTTTCAGTATTATAGTTTAAATAGTTTTAAGTATTTTAATTAGGATT
1 TATTTTATCTTATCTTTGTTTTCAGTATTATAGTTTAAATAGTTTTAAGTATTTTAATTAGGATT
4107894 TAGGATAT
66 TAGGATAT
* *
4107902 TATTTTATCTTATCTTTGTTTT-GGTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATT
1 TATTTTATCTTATCTTTGTTTTCAGTATTATAGTTTAAATAGTTTTAAGTATTTTAATTAGGATT
4107966 TA
66 TA
4107968 TTTTCTTTAT
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
72 42 0.66
73 22 0.34
ACGTcount: A:0.27, C:0.04, G:0.12, T:0.57
Consensus pattern (73 bp):
TATTTTATCTTATCTTTGTTTTCAGTATTATAGTTTAAATAGTTTTAAGTATTTTAATTAGGATT
TAGGATAT
Found at i:4108003 original size:72 final size:72
Alignment explanation
Indices: 4107853--4108005 Score: 175
Period size: 72 Copynumber: 2.1 Consensus size: 72
4107843 TTTGTTTTCA
* * **
4107853 GTATTATAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTAGGATATTATTTTATCTTATCTT
1 GTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTAGGATATTATTATAGATTATCTT
***
4107918 TGTTTTG
66 TACCTTG
*** *
4107925 GTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTATTTTCTTTATTATAGGATTATC
1 GTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTAGGAT-ATTATTATA-GATTATC
4107990 TTTACCTT-
64 TTTACCTTG
4107998 G-ATTTTAG
1 GTATTTTAG
4108006 GATTTTGAAG
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
72 50 0.74
73 8 0.12
74 10 0.15
ACGTcount: A:0.27, C:0.04, G:0.13, T:0.56
Consensus pattern (72 bp):
GTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTAGGATATTATTATAGATTATCTT
TACCTTG
Found at i:4108737 original size:4 final size:4
Alignment explanation
Indices: 4108724--4108758 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
4108714 CTTTATCTCA
*
4108724 ATTT ATTTT ATTT ATTT ATTT ATTT ATTT GTTT AT
1 ATTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT AT
4108759 CTAATTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:4119416 original size:5 final size:5
Alignment explanation
Indices: 4119406--4119460 Score: 58
Period size: 5 Copynumber: 10.6 Consensus size: 5
4119396 ATAATTTTAA
* *
4119406 AAAAT AAAAT AACAAT AATAG AAAAT AAAA- AAAAT AAAAAAT AAAAT
1 AAAAT AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT --AAAAT AAAAT
4119453 AAAAT AAA
1 AAAAT AAA
4119461 CACTAGTACA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
4 4 0.10
5 28 0.67
6 5 0.12
7 5 0.12
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:4119432 original size:21 final size:18
Alignment explanation
Indices: 4119404--4119460 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 18
4119394 ACATAATTTT
4119404 AAAAAATAAAATAACAATA
1 AAAAAATAAAATAA-AATA
4119423 ATAGAAAATAAAA-AAAAT-
1 A-A-AAAATAAAATAAAATA
4119441 AAAAAATAAAATAAAATA
1 AAAAAATAAAATAAAATA
4119459 AA
1 AA
4119461 CACTAGTACA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
16 9 0.26
17 6 0.18
18 3 0.09
19 4 0.12
20 3 0.09
21 9 0.26
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.16
Consensus pattern (18 bp):
AAAAAATAAAATAAAATA
Found at i:4121596 original size:64 final size:63
Alignment explanation
Indices: 4121391--4121598 Score: 224
Period size: 65 Copynumber: 3.2 Consensus size: 63
4121381 TTTCAAAGTG
*
4121391 ATGCATCGATGCACCAATCCATGCATCGATGCAC-CATGGAATATTTTG-AACATCGAATGCATT
1 ATGCATCGATGCACCAA-CCATGCATCGATGCACTC-TGG--TATTTTGAAACATCGAATGAATT
4121454 TC
62 TC
* * * * * *
4121456 ATGCATCGATGCA-CATACTATGCCTCGATGCACTCAGAGTTTTATTAAAACATCGAATGTATTT
1 ATGCATCGATGCACCA-ACCATGCATCGATGCACTCTG-GTATT-TTGAAACATCGAATGAATTT
*
4121520 G
63 C
* * *
4121521 ATACATCGATGCACCAGCCATGCATCGATACACTCTGGCTATTTTGAAACATCGAATGAATTTC
1 ATGCATCGATGCACCAACCATGCATCGATGCACTCTGG-TATTTTGAAACATCGAATGAATTTC
4121585 ATGCATCGATGCAC
1 ATGCATCGATGCAC
4121599 TAAGGGTCCA
Statistics
Matches: 118, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
63 3 0.03
64 51 0.43
65 62 0.53
66 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (63 bp):
ATGCATCGATGCACCAACCATGCATCGATGCACTCTGGTATTTTGAAACATCGAATGAATTTC
Found at i:4129436 original size:29 final size:28
Alignment explanation
Indices: 4129404--4129462 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
4129394 GGATGTTTAA
4129404 ATTTGATGGTTCT-TGGATGTTTTGAACTT
1 ATTTG-TGGTTCTATGGAT-TTTTGAACTT
* *
4129433 ATTTGTTGTTTTATGGATTTTTGAACTT
1 ATTTGTGGTTCTATGGATTTTTGAACTT
4129461 AT
1 AT
4129463 ATTTATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 17 0.63
29 10 0.37
ACGTcount: A:0.19, C:0.05, G:0.20, T:0.56
Consensus pattern (28 bp):
ATTTGTGGTTCTATGGATTTTTGAACTT
Found at i:4130317 original size:64 final size:63
Alignment explanation
Indices: 4130111--4130318 Score: 235
Period size: 65 Copynumber: 3.2 Consensus size: 63
4130101 TTTCAAAGTG
* * *
4130111 ATGCACCGATGCACCAATCCATGCATCGGTGCAC-CATGGAATATTTTG-AACATCGAATGCATT
1 ATGCATCGATGCACC-ATACATGCATCGATGCACTC-TGG--TATTTTGAAACATCGAATGCATT
4130174 TC
62 TC
* *
4130176 ATGCATCGATGC-CTATACTATGCATCGATGCACTCAGAGT-TTTATGAAAACATCGAATGCATT
1 ATGCATCGATGCACCATAC-ATGCATCGATGCACTCTG-GTATTT-TG-AAACATCGAATGCATT
4130239 TC
62 TC
* **
4130241 ATGCATCAATGCACCAGGCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCATTTC
1 ATGCATCGATGCACCATACATGCATCGATGCACTCTGG-TATTTTGAAACATCGAATGCATTTC
4130305 ATGCATCGATGCAC
1 ATGCATCGATGCAC
4130319 TCTTAGTGCA
Statistics
Matches: 123, Mismatches: 11, Indels: 19
0.80 0.07 0.12
Matches are distributed among these distances:
62 3 0.02
63 6 0.05
64 47 0.38
65 61 0.50
66 6 0.05
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (63 bp):
ATGCATCGATGCACCATACATGCATCGATGCACTCTGGTATTTTGAAACATCGAATGCATTTC
Found at i:4130334 original size:64 final size:64
Alignment explanation
Indices: 4130152--4130338 Score: 210
Period size: 65 Copynumber: 2.9 Consensus size: 64
4130142 CACCATGGAA
*
4130152 TATTTTG-AACATCGAATGCATTTCATGCATCGATGC-CTATACTA-TGCATCGATGCACTCAGA
1 TATTTTGAAACATCGAATGCATTTCATGCATCGATGCACTCT--TAGTGCATCGATGCACTCAGA
4130214 G
64 G
*
4130215 T-TTTATGAAAACATCGAATGCATTTCATGCATCAATGCAC-C--AGGCATGCATCGATGCACTC
1 TATTT-TG-AAACATCGAATGCATTTCATGCATCGATGCACTCTTA-G--TGCATCGATGCACTC
*
4130276 TG-G
61 AGAG
*
4130279 CTATTTTGAAACATCGAATGCATTTCATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 -TATTTTGAAACATCGAATGCATTTCATGCATCGATGCACTCTTAGTGCATCGATGCACT
4130339 AAGGGTTCAA
Statistics
Matches: 106, Mismatches: 5, Indels: 25
0.78 0.04 0.18
Matches are distributed among these distances:
61 1 0.01
62 3 0.03
63 3 0.03
64 45 0.42
65 48 0.45
66 5 0.05
67 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (64 bp):
TATTTTGAAACATCGAATGCATTTCATGCATCGATGCACTCTTAGTGCATCGATGCACTCAGAG
Found at i:4146225 original size:18 final size:17
Alignment explanation
Indices: 4146185--4146272 Score: 81
Period size: 18 Copynumber: 5.1 Consensus size: 17
4146175 TAAATTATAA
*
4146185 ATATTTACAGTTATCGG
1 ATATTTACAGTTATCAG
* *
4146202 ACATTTCACTGTTATCAG
1 ATATTT-ACAGTTATCAG
*
4146220 ATATTTACAATTATC-G
1 ATATTTACAGTTATCAG
4146236 -TATGATTACAGTTATCAG
1 ATAT--TTACAGTTATCAG
*
4146254 ATGTTTTACAGTTATCAG
1 AT-ATTTACAGTTATCAG
4146272 A
1 A
4146273 CGTAGATTAA
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
15 3 0.05
16 1 0.02
17 22 0.39
18 29 0.51
19 1 0.02
20 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (17 bp):
ATATTTACAGTTATCAG
Found at i:4148039 original size:20 final size:21
Alignment explanation
Indices: 4148016--4148057 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
4148006 CAATTTCACC
*
4148016 TTCTAATATCAAATT-CAACA
1 TTCTAACATCAAATTCCAACA
*
4148036 TTCTAACATTAAATTCCAACA
1 TTCTAACATCAAATTCCAACA
4148057 T
1 T
4148058 AGTACATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (21 bp):
TTCTAACATCAAATTCCAACA
Found at i:4151468 original size:46 final size:46
Alignment explanation
Indices: 4151349--4151659 Score: 480
Period size: 46 Copynumber: 6.7 Consensus size: 46
4151339 TAATATGCAA
* ** * *
4151349 TTATGTATTTTCATTGGTGGCATCCTTTCATGCCAATTATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACCG
* *
4151395 TTTAAGCATTTTCATTTATGGCATCCTTTCATTCCTATAATGCACCG
1 -TTATGCATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACCG
* * *
4151442 TTATTCA-TTTCAATTTATGGAATCCTTTCATGCTTATAATGCACCG
1 TTATGCATTTTC-ATTTATGGCATCCTTTCATGCCTATAATGCACCG
4151488 TTATGCATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACCG
*
4151534 TTCTGCATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACCG
4151580 TTATGCATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACCG
* *
4151626 TTACGTATTTTCATTTATGGCATCCTTTCATGCC
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCC
4151660 GTCATTTATG
Statistics
Matches: 243, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
45 4 0.02
46 196 0.81
47 43 0.18
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (46 bp):
TTATGCATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACCG
Found at i:4151670 original size:25 final size:25
Alignment explanation
Indices: 4151636--4151685 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
4151626 TTACGTATTT
4151636 TCATTTATGGCATCCTTTCATGCCG
1 TCATTTATGGCATCCTTTCATGCCG
4151661 TCATTTATGGCATCCTTTCATGCCG
1 TCATTTATGGCATCCTTTCATGCCG
4151686 ATAATGCACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.16, C:0.28, G:0.16, T:0.40
Consensus pattern (25 bp):
TCATTTATGGCATCCTTTCATGCCG
Found at i:4151679 original size:71 final size:71
Alignment explanation
Indices: 4151590--4151728 Score: 251
Period size: 71 Copynumber: 2.0 Consensus size: 71
4151580 TTATGCATTT
* *
4151590 TCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTACGTATTTTCATTTATGGCATCCTTTC
1 TCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTACGCATTTTCATTTATGGCATCCTTTC
4151655 ATGCCG
66 ATGCCG
*
4151661 TCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTC
1 TCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTACGCATTTTCATTTATGGCATCCTTTC
4151726 ATG
66 ATG
4151729 TCGATAATAC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.41
Consensus pattern (71 bp):
TCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTACGCATTTTCATTTATGGCATCCTTTC
ATGCCG
Found at i:4151690 original size:117 final size:117
Alignment explanation
Indices: 4151544--4151776 Score: 394
Period size: 117 Copynumber: 2.0 Consensus size: 117
4151534 TTCTGCATTT
*
4151544 TCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTC
1 TCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTC
* * *
4151609 ATGCCTATAATGCACCGTTACGTATTTTCATTTATGGCATCCTTTCATGCCG
66 ATGCCGATAATACACCGTTACGCATTTTCATTTATGGCATCCTTTCATGCCG
4151661 TCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTC
1 TCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTC
* ** *
4151726 ATGTCGATAATACATTGTTATGCATTTTCATTTATGGCATCCTTTCATGCC
66 ATGCCGATAATACACCGTTACGCATTTTCATTTATGGCATCCTTTCATGCC
4151777 AAAAGGCATT
Statistics
Matches: 108, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 108 1.00
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.42
Consensus pattern (117 bp):
TCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTC
ATGCCGATAATACACCGTTACGCATTTTCATTTATGGCATCCTTTCATGCCG
Found at i:4151713 original size:46 final size:46
Alignment explanation
Indices: 4151661--4151776 Score: 196
Period size: 46 Copynumber: 2.5 Consensus size: 46
4151651 TTTCATGCCG
*
4151661 TCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTT
1 TCATTTATGGCATCCTTTCATGCCGATAATACACCGTTATGCATTT
* **
4151707 TCATTTATGGCATCCTTTCATGTCGATAATACATTGTTATGCATTT
1 TCATTTATGGCATCCTTTCATGCCGATAATACACCGTTATGCATTT
4151753 TCATTTATGGCATCCTTTCATGCC
1 TCATTTATGGCATCCTTTCATGCC
4151777 AAAAGGCATT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 65 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (46 bp):
TCATTTATGGCATCCTTTCATGCCGATAATACACCGTTATGCATTT
Found at i:4151923 original size:81 final size:81
Alignment explanation
Indices: 4151778--4152178 Score: 511
Period size: 81 Copynumber: 5.0 Consensus size: 81
4151768 TTTCATGCCA
* * * * * * * *
4151778 AAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATCCACAGTTAGGC
1 AAAGGTATTTAACATTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATACACAGCTAGGC
4151843 AATTACTCTTTTACTC
66 AATTACTCTTTTACTC
* * * ** **
4151859 AAAGGTATTTAACATTTCAACTAATTGGCATGATTGATACCTTTCTGTTGAATGTACAGCTAGGC
1 AAAGGTATTTAACATTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATACACAGCTAGGC
*
4151924 AATTAGTCTTTTACTC
66 AATTACTCTTTTACTC
* * *
4151940 AAAGGTATTTAAC-CTTCATGTAACTGGCATAATTGACACCTTTCTGTCAAATACACAGCTAGGC
1 AAAGGTATTTAACATTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATACACAGCTAGGC
4152004 AATTAGC-CTTTTACTC
66 AATTA-CTCTTTTACTC
* * *
4152020 AAAGTTATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTGTCAAATACACAGCTAGGC
1 AAAGGTATTTAACATTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATACACAGCTAGGC
*
4152085 AATTAGTCTTTTACTC
66 AATTACTCTTTTACTC
* * * *
4152101 AAAAGTATTTAACATTTCATCTAGA-TGGCATGATTGACACCTTTCTATCAAATGCACAACTAGG
1 AAAGGTATTTAACATTTCATCTA-ACTGGCATGATTGACACCTTTCTGTCAAATACACAGCTAGG
*
4152165 CAATTAATCTTTTA
65 CAATTACTCTTTTA
4152179 TTTAAAAACA
Statistics
Matches: 276, Mismatches: 40, Indels: 8
0.85 0.12 0.02
Matches are distributed among these distances:
80 67 0.24
81 208 0.75
82 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (81 bp):
AAAGGTATTTAACATTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATACACAGCTAGGC
AATTACTCTTTTACTC
Found at i:4152081 original size:161 final size:161
Alignment explanation
Indices: 4151778--4152178 Score: 527
Period size: 161 Copynumber: 2.5 Consensus size: 161
4151768 TTTCATGCCA
* * * * * * *
4151778 AAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATCCACAGTTAGGC
1 AAAGGTATTTAACC-TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATACACAGCTAGGC
* * * *
4151843 AATTACTCTTTTACTCAAAGGTATTTAACATTTCAACTAATTGGCATGATTGATACCTTTCTGTT
65 AATTACTCTTTTACTCAAAGGTATTTAACATTTCAACTAACTAGCATGATTGACACCTTTCTGTC
* **
4151908 GAATGTACAGCTAGGCAATTAGTCTTTTACTC
130 AAATACACAGCTAGGCAATTAGTCTTTTACTC
*
4151940 AAAGGTATTTAACCTTCATGTAACTGGCATAATTGACACCTTTCTGTCAAATACACAGCTAGGCA
1 AAAGGTATTTAACCTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATACACAGCTAGGCA
* * *
4152005 ATTAGC-CTTTTACTCAAAGTTATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTGTC
66 ATTA-CTCTTTTACTCAAAGGTATTTAACATTTCAACTAACTAGCATGATTGACACCTTTCTGTC
4152069 AAATACACAGCTAGGCAATTAGTCTTTTACTC
130 AAATACACAGCTAGGCAATTAGTCTTTTACTC
* * * * * *
4152101 AAAAGTATTTAACATTTCATCTAGA-TGGCATGATTGACACCTTTCTATCAAATGCACAACTAGG
1 AAAGGTATTTAAC-CTTCATCTA-ACTGGCATAATTGACACCTTTCTGTCAAATACACAGCTAGG
*
4152165 CAATTAATCTTTTA
64 CAATTACTCTTTTA
4152179 TTTAAAAACA
Statistics
Matches: 209, Mismatches: 26, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
161 140 0.67
162 68 0.33
163 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (161 bp):
AAAGGTATTTAACCTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATACACAGCTAGGCA
ATTACTCTTTTACTCAAAGGTATTTAACATTTCAACTAACTAGCATGATTGACACCTTTCTGTCA
AATACACAGCTAGGCAATTAGTCTTTTACTC
Found at i:4152736 original size:21 final size:21
Alignment explanation
Indices: 4152710--4152761 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
4152700 TACCCACATT
4152710 AGTATCGATACTCATTGCATC
1 AGTATCGATACTCATTGCATC
4152731 AGTATCGATACTCATTGCATC
1 AGTATCGATACTCATTGCATC
4152752 AGTATCGATA
1 AGTATCGATA
4152762 TTATTCATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (21 bp):
AGTATCGATACTCATTGCATC
Found at i:4157419 original size:46 final size:46
Alignment explanation
Indices: 4157126--4157420 Score: 412
Period size: 46 Copynumber: 6.4 Consensus size: 46
4157116 TTTGTATTGG
* * * * **
4157126 TGGCATCTTTTCATGCAAATTATGTACCGTTAAACATTTTCATTTA
1 TGGCATCCTTTCATGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
4157172 TGGCATCCTTTCAAGCCTATAATGCACTGTTATGCATTTTCATTTA
1 TGGCATCCTTTCATGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
4157218 TGGCATCCTTTAATG-CATATAATGCATCGTTATACATTTTCATTTA
1 TGGCATCCTTTCATGCCA-ATAATGCACCGTTATGCATTTTCATTTA
* **
4157264 TGGCATCCTTTCATGCCTATAATGCATTGTTATGCATTTTCATTTA
1 TGGCATCCTTTCATGCCAATAATGCACCGTTATGCATTTTCATTTA
*
4157310 TGGCATCCTTTCATGCCTATAATGCACCGTTATGCATTTTCATTTA
1 TGGCATCCTTTCATGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
4157356 TGGCATCCTTTCATGCCAATAATGCACCATTATGCATTTTTATTTA
1 TGGCATCCTTTCATGCCAATAATGCACCGTTATGCATTTTCATTTA
4157402 TGGCATCCTTTCATGCCAA
1 TGGCATCCTTTCATGCCAA
4157421 AGGCATTTAA
Statistics
Matches: 223, Mismatches: 24, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
45 1 0.00
46 221 0.99
47 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (46 bp):
TGGCATCCTTTCATGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:4157514 original size:81 final size:81
Alignment explanation
Indices: 4157418--4157831 Score: 483
Period size: 81 Copynumber: 5.0 Consensus size: 81
4157408 CCTTTCATGC
* * * * * *
4157418 CAAAGGCATTTAACCTTTCATTTAACTTGCATTATTGGCACCTTTCAGCCAAATGCACAGTTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTTGCATGATTGACACCTTTCAGTCAAATGCACAGCTAGG
* * *
4157483 CAGTTAATGTTTTACT
66 CAATTAGTCTTTTACT
* *
4157499 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCACCTTTCTATCATAT
1 CAAAGGTATTTAACCTTTCATCTAACTTGCATGATTGACACC--T-T-TCA---GTC-A--A-AT
4157564 GCACAGCTAGGCAATTAGTCTTTTACT
55 GCACAGCTAGGCAATTAGTCTTTTACT
* * * *
4157591 CAAAGGTATTTAACCTTTCATTTAACTTGCATGATTGACACCTTTCTGTCAAATACATAGCTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTTGCATGATTGACACCTTTCAGTCAAATGCACAGCTAGG
*
4157656 CAATTAGTCTTTTAGT
66 CAATTAGTCTTTTACT
* * *
4157672 TAAAGGTATTTAACCTTTTATCTAACTAGCATGATTGACACCTTTCTA-TCAAATGCACAGCTAG
1 CAAAGGTATTTAACCTTTCATCTAACTTGCATGATTGACACCTTTC-AGTCAAATGCACAGCTAG
4157736 GCAATTAGTCTTTTACT
65 GCAATTAGTCTTTTACT
* *
4157753 CAAAAGTATTTAACCTTTCATCTAAC-TGTCATGATTGACACCTTT-ATGTCAAATGCACAACTA
1 CAAAGGTATTTAACCTTTCATCTAACTTG-CATGATTGACACCTTTCA-GTCAAATGCACAGCTA
*
4157816 GGCAATTAATCTTTTA
64 GGCAATTAGTCTTTTA
4157832 TTTTAAAGCA
Statistics
Matches: 286, Mismatches: 32, Indels: 30
0.82 0.09 0.09
Matches are distributed among these distances:
79 1 0.00
80 1 0.00
81 203 0.71
82 1 0.00
83 1 0.00
84 2 0.01
85 5 0.02
88 3 0.01
89 2 0.01
90 1 0.00
91 1 0.00
92 65 0.23
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.37
Consensus pattern (81 bp):
CAAAGGTATTTAACCTTTCATCTAACTTGCATGATTGACACCTTTCAGTCAAATGCACAGCTAGG
CAATTAGTCTTTTACT
Done.