Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008647.1 Hibiscus syriacus cultivar Beakdansim tig00111634_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: 1422586
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:483892 original size:12 final size:12
Alignment explanation
Indices: 483875--483926 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
483865 AAGCGAAGAG
483875 AACAAAGAAAAA
1 AACAAAGAAAAA
*
483887 AACAAAGAGAAGA
1 AACAAAGA-AAAA
* *
483900 AGCAAAGAAAAG
1 AACAAAGAAAAA
*
483912 AGCAAAGAACAAA
1 AACAAAGAA-AAA
483925 AA
1 AA
483927 GATAACAAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
12 19 0.59
13 13 0.41
ACGTcount: A:0.73, C:0.10, G:0.17, T:0.00
Consensus pattern (12 bp):
AACAAAGAAAAA
Found at i:483907 original size:13 final size:12
Alignment explanation
Indices: 483877--483920 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
483867 GCGAAGAGAA
* *
483877 CAAAGAAAAAAA
1 CAAAGAAAAGAG
*
483889 CAAAGAGAAGAAG
1 CAAAGAAAAG-AG
483902 CAAAGAAAAGAG
1 CAAAGAAAAGAG
483914 CAAAGAA
1 CAAAGAA
483921 CAAAAAGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.70, C:0.09, G:0.20, T:0.00
Consensus pattern (12 bp):
CAAAGAAAAGAG
Found at i:483917 original size:25 final size:26
Alignment explanation
Indices: 483863--483919 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
483853 AAGATCATAT
*
483863 CAAAGCGAAGAGAACAAAGAAAAAAA
1 CAAAGAGAAGAGAACAAAGAAAAAAA
* * *
483889 CAAAGAGAAGA-AGCAAAGAAAAGAG
1 CAAAGAGAAGAGAACAAAGAAAAAAA
483914 CAAAGA
1 CAAAGA
483920 ACAAAAAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 17 0.63
26 10 0.37
ACGTcount: A:0.67, C:0.11, G:0.23, T:0.00
Consensus pattern (26 bp):
CAAAGAGAAGAGAACAAAGAAAAAAA
Found at i:484996 original size:33 final size:32
Alignment explanation
Indices: 484936--484998 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
484926 AAGAAATATT
* *
484936 GAATGTTGGGGCATCTTTGGAGATTCAACATC
1 GAATATTGGGGCATATTTGGAGATTCAACATC
484968 GAATATTGGAGGCATATCTTGGAG-TTCAACA
1 GAATATTGG-GGCATAT-TTGGAGATTCAACA
484999 AATATCTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 8 0.30
33 13 0.48
34 6 0.22
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (32 bp):
GAATATTGGGGCATATTTGGAGATTCAACATC
Found at i:485791 original size:107 final size:105
Alignment explanation
Indices: 485603--485848 Score: 290
Period size: 107 Copynumber: 2.3 Consensus size: 105
485593 GTCTAGGACA
* * * *
485603 ATTTCTCTT-AAAACAAACTTCGTCTTGCTTGAGACATTCTTTCCTTTGATATACAAATTTTGAA
1 ATTTCT-TTCAAAACAAATTTCGTCTCGCTTGAGACATTCTTTCCTTTGAAATACAAATTTCGAA
*
485667 TTTGATTCACTTGAAACAAAAATTAATCTCACTTGAGATTGTT
65 TTTGATTCACTTGAAAC-AAAATTAATCTCACTTGAGATCG-T
*
485710 ATTTCTTTCAAAACAAATTTCGTCTCGTTTGAGACATT-TTTCCTTTGAGAATACAAATTTCGAA
1 ATTTCTTTCAAAACAAATTTCGTCTCGCTTGAGACATTCTTTCCTTTGA-AATACAAATTTCGAA
* * * *
485774 TTTGTTTCACATT-AAACAAAGTTGATCTCCCTTGAGATCGT
65 TTTGATTCAC-TTGAAACAAAATTAATCTCACTTGAGATCGT
485815 -TTTC--TCAAAAACAAACTTT-GTCTCGCTTGAGACA
1 ATTTCTTTC-AAAACAAA-TTTCGTCTCGCTTGAGACA
485849 ATTTCTCTAA
Statistics
Matches: 123, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
102 2 0.02
103 22 0.18
104 7 0.06
105 1 0.01
106 31 0.25
107 58 0.47
108 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.39
Consensus pattern (105 bp):
ATTTCTTTCAAAACAAATTTCGTCTCGCTTGAGACATTCTTTCCTTTGAAATACAAATTTCGAAT
TTGATTCACTTGAAACAAAATTAATCTCACTTGAGATCGT
Found at i:485871 original size:36 final size:36
Alignment explanation
Indices: 485815--485924 Score: 132
Period size: 36 Copynumber: 3.1 Consensus size: 36
485805 TTGAGATCGT
*
485815 TTTCTC-AAAAACAAACTTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
* * * *
485850 TTTCTCTAAAGACAATTTTTGTCTTGTTTGAGACAA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
* * * *
485886 TTTCTTTAAAAACAAATGTTGTCTCACTTGAGATAA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
485922 TTT
1 TTT
485925 TCCAAATTAT
Statistics
Matches: 61, Mismatches: 13, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
35 6 0.10
36 55 0.90
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (36 bp):
TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
Found at i:485998 original size:30 final size:31
Alignment explanation
Indices: 485962--486020 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
485952 AACAAACATC
**
485962 ATCTTTGAGT-TGTTTCTTTTGAAACAAAGG
1 ATCTTTGAGTCTGTTTCACTTGAAACAAAGG
*
485992 ATCTTTGAGTCTTTTTCACTTGAAACAAA
1 ATCTTTGAGTCTGTTTCACTTGAAACAAA
486021 ATAAAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (31 bp):
ATCTTTGAGTCTGTTTCACTTGAAACAAAGG
Found at i:486320 original size:28 final size:28
Alignment explanation
Indices: 486289--486370 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
486279 AAAACACATC
*
486289 ATCTTTGAGTTTATTT-TTCTTGAAACAA
1 ATCTTTGAGTATATTTCTT-TTGAAACAA
* **
486317 ATCTTTGAGTATGTTTCTTTTGAAACTT
1 ATCTTTGAGTATATTTCTTTTGAAACAA
486345 ATCTTTGAGTCA-ATTTCTTTTGAAAC
1 ATCTTTGAGT-ATATTTCTTTTGAAAC
486371 CAATATCCCT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
28 44 0.94
29 3 0.06
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.50
Consensus pattern (28 bp):
ATCTTTGAGTATATTTCTTTTGAAACAA
Found at i:486619 original size:134 final size:134
Alignment explanation
Indices: 486379--486869 Score: 668
Period size: 134 Copynumber: 3.7 Consensus size: 134
486369 ACCAATATCC
* ** * *
486379 CTAAAGATGGCCAGAACTCTTCATCATATATGAGTCGTGTCATCCCCCGACCAGATCTCCTCATC
1 CTAAAAATGGCCAGAACTCTTCATCACGTATGAGTCGTGCCATTCCCCGACCAGATCTCCTCATC
* * *
486444 GCGTAGGAGTCATGTCACCCTTAGATAACCAACCGTCCTCATCACGTAGGAACCGAGTTATCATC
66 ACGTAGGAGCCGTGTCACCCTTAGATAACCAACCGTCCTCATCACGTAGGAACCGAGTTATCATC
486509 CTTT
131 CTTT
* *
486513 CTAAAAATGGACATAACTCTTCATCACGTATGAGTCGTGCCATTCCCCGACCAGATCTCCTCATC
1 CTAAAAATGGCCAGAACTCTTCATCACGTATGAGTCGTGCCATTCCCCGACCAGATCTCCTCATC
* *
486578 GCGTAGGAGCCGTGTCACCCTTAGATAACCAACCGTCCTCATCACGTCGGAACCGAGTTATCATC
66 ACGTAGGAGCCGTGTCACCCTTAGATAACCAACCGTCCTCATCACGTAGGAACCGAGTTATCATC
486643 CTTT
131 CTTT
* * * *
486647 CTAAAAATGGCCAGAACTCTTTATCACGTATGAGCCGTACCATTCCCCGACCAGACCTCCTCATC
1 CTAAAAATGGCCAGAACTCTTCATCACGTATGAGTCGTGCCATTCCCCGACCAGATCTCCTCATC
* * * * * *
486712 ACGTAGGAGCCGTATCACCCATAGATAACCAGCAGTCCTCATCGCGTAGGAACTGAGTTATCA-C
66 ACGTAGGAGCCGTGTCACCCTTAGATAACCAACCGTCCTCATCACGTAGGAACCGAGTTATCATC
486776 CTTT
131 CTTT
* * *
486780 CCTAAAGATGGCCAAGAACTCTTCATCACGTATGAG-CAGTGTCA-TCCCCTGACTAGA--TCCT
1 -CTAAAAATGGCC-AGAACTCTTCATCACGTATGAGTC-GTGCCATTCCCC-GACCAGATCTCCT
**
486841 CATCACGTAGGAGTTGTGTCACCCTTAGA
62 CATCACGTAGGAGCCGTGTCACCCTTAGA
486870 CGACTCGAAC
Statistics
Matches: 320, Mismatches: 33, Indels: 9
0.88 0.09 0.02
Matches are distributed among these distances:
133 34 0.11
134 255 0.80
135 31 0.10
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (134 bp):
CTAAAAATGGCCAGAACTCTTCATCACGTATGAGTCGTGCCATTCCCCGACCAGATCTCCTCATC
ACGTAGGAGCCGTGTCACCCTTAGATAACCAACCGTCCTCATCACGTAGGAACCGAGTTATCATC
CTTT
Found at i:487467 original size:35 final size:35
Alignment explanation
Indices: 487421--487493 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
487411 CAAGAGATGG
487421 CAGCATGAGTATAGGGATATCATTCCCTACAAACT
1 CAGCATGAGTATAGGGATATCATTCCCTACAAACT
487456 CAGCATGAGTATAGGGATATCATTCCCTACAAACT
1 CAGCATGAGTATAGGGATATCATTCCCTACAAACT
487491 CAG
1 CAG
487494 TCATCCATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (35 bp):
CAGCATGAGTATAGGGATATCATTCCCTACAAACT
Found at i:488824 original size:2 final size:2
Alignment explanation
Indices: 488782--488806 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
488772 TATGTACATT
488782 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
488807 TTATTTGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:490830 original size:3 final size:3
Alignment explanation
Indices: 490824--490906 Score: 166
Period size: 3 Copynumber: 27.7 Consensus size: 3
490814 GTCGTAGTAG
490824 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
490872 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
490907 TATATATTAT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:490917 original size:3 final size:3
Alignment explanation
Indices: 490911--491026 Score: 223
Period size: 3 Copynumber: 38.7 Consensus size: 3
490901 ATAATATATA
490911 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
490959 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
491007 TAT TAT TAT TAT TAC TAT TA
1 TAT TAT TAT TAT TAT TAT TA
491027 CTGTGGTCCT
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 111 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:494595 original size:2 final size:2
Alignment explanation
Indices: 494588--494640 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
494578 AATGTTACAT
494588 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
494630 TA TA TA TA TA T
1 TA TA TA TA TA T
494641 GGGTTAGATC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:503553 original size:120 final size:120
Alignment explanation
Indices: 503324--503553 Score: 286
Period size: 120 Copynumber: 1.9 Consensus size: 120
503314 ATTAAATCTT
* * ** * *
503324 TCTACAACGTCATCATTTATAGGTAGATTATCACGTCGACACGGTAAATCATTATGTCAACACTG
1 TCTACAACATCATCATTTATAGGTAGATTATCACGTCAACACAATAAACCATTATGTCAACACTA
* * *
503389 TTAATTTTTATGTCACCATCATCACGATCAATGTCGATCGAATGACAAAAGTCTC
66 TTAATTTTTATGTCAACATCATCACGATCAATGTCAATCAAATGACAAAAGTCTC
* * * *
503444 TCTACAATATCATCATTTATAGGTAGTTTATTACGTTAACACAATAAACCATTATGTCAGA-ACT
1 TCTACAACATCATCATTTATAGGTAGATTATCACGTCAACACAATAAACCATTATGTCA-ACACT
*
503508 ATTAATTTTTATGTCAATATCA-CAACGATC-ATCGTCAATCAAATGA
65 ATTAATTTTTATGTCAACATCATC-ACGATCAAT-GTCAATCAAATGA
503554 TATAATTGAT
Statistics
Matches: 93, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
119 3 0.03
120 89 0.96
121 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (120 bp):
TCTACAACATCATCATTTATAGGTAGATTATCACGTCAACACAATAAACCATTATGTCAACACTA
TTAATTTTTATGTCAACATCATCACGATCAATGTCAATCAAATGACAAAAGTCTC
Found at i:504688 original size:14 final size:15
Alignment explanation
Indices: 504669--504706 Score: 69
Period size: 14 Copynumber: 2.6 Consensus size: 15
504659 TTTATAAAAT
504669 TTGAGTCGAGAC-AG
1 TTGAGTCGAGACGAG
504683 TTGAGTCGAGACGAG
1 TTGAGTCGAGACGAG
504698 TTGAGTCGA
1 TTGAGTCGA
504707 ATTTTTGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.26, C:0.13, G:0.37, T:0.24
Consensus pattern (15 bp):
TTGAGTCGAGACGAG
Found at i:505190 original size:21 final size:21
Alignment explanation
Indices: 505138--505191 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
505128 CAGTTTCCAG
505138 ATTCGCAATGCGATTCTGACT
1 ATTCGCAATGCGATTCTGACT
* **
505159 A-TCGCATTGCGATT-TTCCT
1 ATTCGCAATGCGATTCTGACT
505178 AATTCGCAATGCGA
1 -ATTCGCAATGCGA
505192 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 3 0.11
20 13 0.48
21 11 0.41
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (21 bp):
ATTCGCAATGCGATTCTGACT
Found at i:505204 original size:41 final size:41
Alignment explanation
Indices: 505181--505308 Score: 213
Period size: 41 Copynumber: 3.1 Consensus size: 41
505171 TTTTCCTAAT
*
505181 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGATTACGTAAATCGCAACGCGAATTTGGAAAA
505222 TCGCAATGCGATTACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGATTACGTAAATCGCAACGCGAATTTGGAAAA
* * *
505263 TCGCAATGCGATTACGTAAATCGCAATGCGAATCT-GTAAA
1 TCGCAATGCGATTACGTAAATCGCAACGCGAATTTGGAAAA
505303 TCGCAA
1 TCGCAA
505309 CGAGATTCTG
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
40 10 0.12
41 73 0.88
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (41 bp):
TCGCAATGCGATTACGTAAATCGCAACGCGAATTTGGAAAA
Found at i:505206 original size:20 final size:20
Alignment explanation
Indices: 505181--505308 Score: 132
Period size: 20 Copynumber: 6.3 Consensus size: 20
505171 TTTTCCTAAT
505181 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
505201 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
505222 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
505242 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
505263 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
505283 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
505303 TCGCAA
1 TCGCAA
505309 CGAGATTCTG
Statistics
Matches: 85, Mismatches: 20, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
19 1 0.01
20 54 0.64
21 30 0.35
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:505246 original size:61 final size:61
Alignment explanation
Indices: 505181--505310 Score: 147
Period size: 61 Copynumber: 2.1 Consensus size: 61
505171 TTTTCCTAAT
* * ** *
505181 TCGCAATGCGAA-TACGTAAATCGCAACGCGAATTTGGAAAATCGCAATGCGATTAC-GTAAA
1 TCGCAACGCGAATTACGAAAATCGCAACGCG-ATTACGAAAATCGCAATGCGAAT-CTGTAAA
** * *
505242 TCGCAACGCGAATTTGGAAAATCGCAATGCGATTACGTAAATCGCAATGCGAATCTGTAAA
1 TCGCAACGCGAATTACGAAAATCGCAACGCGATTACGAAAATCGCAATGCGAATCTGTAAA
505303 TCGCAACG
1 TCGCAACG
505311 AGATTCTGAC
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
60 1 0.02
61 43 0.74
62 14 0.24
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.22
Consensus pattern (61 bp):
TCGCAACGCGAATTACGAAAATCGCAACGCGATTACGAAAATCGCAATGCGAATCTGTAAA
Found at i:506189 original size:24 final size:24
Alignment explanation
Indices: 506131--506177 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
506121 AGTCAGTATT
*
506131 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
506155 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
506178 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:508628 original size:20 final size:20
Alignment explanation
Indices: 508603--508695 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
508593 GACATTCATT
**
508603 TGACTATCGCAATGC-GAATA
1 TGACTATCGCAACACGGAA-A
508623 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACACGGAAA
* *
508643 TGACTATCGCAACGCGGAAT
1 TGACTATCGCAACACGGAAA
* *
508663 TGACTATCGCAATACAGAAA
1 TGACTATCGCAACACGGAAA
508683 TGACTATCGCAAC
1 TGACTATCGCAAC
508696 GAGAGAATCG
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 60 0.95
21 3 0.05
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
TGACTATCGCAACACGGAAA
Found at i:508667 original size:40 final size:40
Alignment explanation
Indices: 508603--508696 Score: 145
Period size: 40 Copynumber: 2.4 Consensus size: 40
508593 GACATTCATT
* *
508603 TGACTATCGCAATGCGAATATGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGAATATGACTATCGCAACACAGAAA
*
508643 TGACTATCGCAACGCGGAAT-TGACTATCGCAATACAGAAA
1 TGACTATCGCAACGC-GAATATGACTATCGCAACACAGAAA
508683 TGACTATCGCAACG
1 TGACTATCGCAACG
508697 AGAGAATCGC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
40 46 0.92
41 4 0.08
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (40 bp):
TGACTATCGCAACGCGAATATGACTATCGCAACACAGAAA
Found at i:508784 original size:33 final size:33
Alignment explanation
Indices: 508728--508821 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 33
508718 TAATTTCGCA
508728 TTGCGATTTTCATTTTCGCATTGCGATTCA-CTCG
1 TTGCGATTTTCA-TTTCGCATTGCGATT-ATCTCG
*
508762 TTGCGATTTTCATTTCGTATTGCGATTATCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCG
** *
508795 TTGCGATAGTCATTTCCGCGTTGCGAT
1 TTGCGATTTTCATTT-CGCATTGCGAT
508822 AGTCTGTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
32 1 0.02
33 31 0.58
34 21 0.40
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTATCTCG
Found at i:508942 original size:14 final size:14
Alignment explanation
Indices: 508923--508959 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
508913 CATCAATTAA
508923 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
508937 ACAAATCATCTTTT
1 ACAAATCAACATTT
508951 ACAAATCAA
1 ACAAATCAA
508960 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:510413 original size:42 final size:42
Alignment explanation
Indices: 510334--510425 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
510324 CCTCTTCAAC
* * *
510334 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
510376 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
510418 GATGACAG
1 GATGACAG
510426 ATGAGTCGGG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
42 38 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:510949 original size:34 final size:34
Alignment explanation
Indices: 510906--511015 Score: 141
Period size: 34 Copynumber: 3.3 Consensus size: 34
510896 TGAAACTTAA
*
510906 AATCGCAATGCGAAAATGACTATCGCAATGAGAG
1 AATCGCAATGCGAAAATGACTATCGCAACGAGAG
** * * *
510940 AATCGCAATGCG-AAATGAAAATCGCAACAACAA
1 AATCGCAATGCGAAAATGACTATCGCAACGAGAG
* *
510973 AATCGCAACGCAAAAATGACTATCGCAACGAGAG
1 AATCGCAATGCGAAAATGACTATCGCAACGAGAG
511007 AATCGCAAT
1 AATCGCAAT
511016 ACGATTTTCA
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
33 25 0.41
34 36 0.59
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.15
Consensus pattern (34 bp):
AATCGCAATGCGAAAATGACTATCGCAACGAGAG
Found at i:511070 original size:20 final size:20
Alignment explanation
Indices: 511045--511170 Score: 156
Period size: 20 Copynumber: 6.6 Consensus size: 20
511035 GCGATTCTTT
**
511045 CATTGCGATAGTCAAATTCG
1 CATTGCGATAGTCATTTTCG
*
511065 CATTGCGATAGTCATTTTTG
1 CATTGCGATAGTCATTTTCG
511085 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
511105 CATTGCGAT--TC--TCTCG
1 CATTGCGATAGTCATTTTCG
511121 --TTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
511139 CGTTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
511159 CATTTCGATAGT
1 CATTGCGATAGT
511171 AAACTATTCT
Statistics
Matches: 92, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.08
16 6 0.07
18 6 0.07
20 73 0.79
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.40
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTCG
Found at i:511070 original size:34 final size:34
Alignment explanation
Indices: 511026--511147 Score: 145
Period size: 34 Copynumber: 3.4 Consensus size: 34
511016 ACGATTTTCA
*
511026 TTTCGCATTGCGATTCTTTCATTGCGATAGTCAA
1 TTTCGCATTGCGATTCTTTCATTGCGATAGTCAT
*
511060 ATTCGCATTGCGATAGTCATTTTTGCATTGCGATAGTCAT
1 TTTCGCATTGCGAT--TC---TTT-CATTGCGATAGTCAT
* *
511100 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAT
1 TTTCGCATTGCGATTCTTTCATTGCGATAGTCAT
*
511134 TTTCGCGTTGCGAT
1 TTTCGCATTGCGAT
511148 AGTCATTTTC
Statistics
Matches: 76, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
34 40 0.53
35 2 0.03
36 2 0.03
38 2 0.03
39 3 0.04
40 27 0.36
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.41
Consensus pattern (34 bp):
TTTCGCATTGCGATTCTTTCATTGCGATAGTCAT
Found at i:511147 original size:74 final size:74
Alignment explanation
Indices: 511026--511170 Score: 227
Period size: 74 Copynumber: 2.0 Consensus size: 74
511016 ACGATTTTCA
* *
511026 TTTCGCATTGCGATTCTTTCATTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTTGCATTGC
1 TTTCGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGC
511091 GATAGTCAT
66 GATAGTCAT
* ** * *
511100 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCATTTC
1 TTTCGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGC
511165 GATAGT
66 GATAGT
511171 AAACTATTCT
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 64 1.00
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (74 bp):
TTTCGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGC
GATAGTCAT
Found at i:513462 original size:22 final size:22
Alignment explanation
Indices: 513432--513489 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 22
513422 TGACCGTGAA
513432 TGATTTCGTCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGAGAC
* *
513454 TGATATCGTC---G-TGGGGAC
1 TGATTTCGTCGGAGATGGAGAC
513472 TGATTTCGTCGGAGATGG
1 TGATTTCGTCGGAGATGG
513490 GGACGGATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
18 15 0.52
19 1 0.03
21 1 0.03
22 12 0.41
ACGTcount: A:0.19, C:0.14, G:0.38, T:0.29
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGAGAC
Found at i:513493 original size:22 final size:22
Alignment explanation
Indices: 513432--513493 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
513422 TGACCGTGAA
*
513432 TGATTTCGTCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
513454 TGATATCGTC---G-TGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
513472 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
513494 GGATGTCGCC
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
18 15 0.45
19 1 0.03
21 1 0.03
22 16 0.48
ACGTcount: A:0.19, C:0.15, G:0.39, T:0.27
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:513713 original size:20 final size:20
Alignment explanation
Indices: 513690--513783 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
513680 CGATAGTCAG
513690 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
513710 ATTCGAATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
513730 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
513751 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
513771 ATTCGCATTGCGA
1 ATTCGCATTGCGA
513784 ATTAGGAAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 46 0.75
21 15 0.25
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:513765 original size:61 final size:60
Alignment explanation
Indices: 513670--513783 Score: 174
Period size: 61 Copynumber: 1.9 Consensus size: 60
513660 GCGCTATGTA
*
513670 AATCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGTATTCGAATTGCGATTTACGT
1 AATCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGTATTCGAATTGCGATTTACGT
** * *
513730 AATCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCATTGCGA
1 AATCGCATTGCGATAGT-CAAATTCGCATTGCGATTTACGTATTCGAATTGCGA
513784 ATTAGGAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 15 0.31
61 33 0.69
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (60 bp):
AATCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGTATTCGAATTGCGATTTACGT
Found at i:513825 original size:21 final size:21
Alignment explanation
Indices: 513773--513825 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
513763 ATTTACGTAT
*
513773 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* * * *
513794 TCGTAACGCGAATTTGGGAAA
1 TCGCAATGCGAATTAGGAAAA
513815 TCGCAATGCGA
1 TCGCAATGCGA
513826 TAGTCAGAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:515100 original size:2 final size:2
Alignment explanation
Indices: 515093--515130 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
515083 ATTCGAAGGA
515093 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
515131 TGTTAGGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:516279 original size:29 final size:28
Alignment explanation
Indices: 516242--516318 Score: 118
Period size: 29 Copynumber: 2.6 Consensus size: 28
516232 TTAAGCACAC
*
516242 AAATGGTCATCCGACTATTAAAAGTTACA
1 AAATAGTCA-CCGACTATTAAAAGTTACA
516271 AAATAGTCACCCGACTATTAAAAGTTACA
1 AAATAGTCA-CCGACTATTAAAAGTTACA
516300 AAATAGTCACCTGACTATT
1 AAATAGTCACC-GACTATT
516319 CGTTATGTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 2 0.04
29 43 0.96
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (28 bp):
AAATAGTCACCGACTATTAAAAGTTACA
Found at i:516652 original size:60 final size:59
Alignment explanation
Indices: 516525--516661 Score: 134
Period size: 60 Copynumber: 2.3 Consensus size: 59
516515 ATAGTCGAGT
* * *
516525 GACCATTTTGTAACTTTTAATAACCGATGAACTTAATAAAGTAATATTCTATAATCAGAT
1 GACCATTTTGT-ACTTTTAATAACCGAAGAACTTAATAAAGTAATATCCTATAATCAGAG
* * * * * *
516585 GATCATTTTGTATCTTTTAATAATCGAAGGACTTAATAAAGTAGTA-CCATATAGT-GGAG
1 GACCATTTTGTA-CTTTTAATAACCGAAGAACTTAATAAAGTAATATCC-TATAATCAGAG
516644 GAACCATTTCTGTACTTT
1 G-ACCATTT-TGTACTTT
516662 ACCCTAATTT
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
59 5 0.08
60 54 0.86
61 4 0.06
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (59 bp):
GACCATTTTGTACTTTTAATAACCGAAGAACTTAATAAAGTAATATCCTATAATCAGAG
Found at i:517613 original size:35 final size:35
Alignment explanation
Indices: 517533--517921 Score: 265
Period size: 35 Copynumber: 10.5 Consensus size: 35
517523 TGATTTTATT
* *
517533 TATAT-ATATATAG-TTTGCAAATATTTTTGAAATA
1 TATATAATATATAGTTTTGAAAACATTTTT-AAATA
* * *
517567 CATATGGTATATATAGTTTTGAAAACGGTTTTTAAATATATA
1 TATAT--AATATATAGTTTTGAAAAC-ATTTTT--A-A-ATA
* *
517609 TATATATATATATAATTTTTGGAAAGC-TTTTTGGAAATA
1 TATATA-ATATAT-AGTTTT-GAAAACATTTTT--AAATA
* * *
517648 TATATAATATATGATTTTTGAAAACATTTAAATATATA
1 TATATAATATAT-AGTTTTGAAAACATTT--TTAAATA
* *
517686 TATATATATAATATAGTTTTTGAAAATATTTTGAAAATA
1 TATATA-AT-ATATAG-TTTTGAAAACATTTT-TAAATA
* *
517725 TATATAATATATAGTTTTGAAATCATTTTTAAAACATT
1 TATATAATATATAGTTTTGAAAACATTTTT--AA-ATA
517763 TATATAATATATAGTTTT-AAAACATTTTTGAAA-A
1 TATATAATATATAGTTTTGAAAACATTTTT-AAATA
** *
517797 CTATATAATATATAGTTTAAAAAAATATTTTTGAAA-A
1 -TATATAATATATAGTTT-TGAAAACATTTTT-AAATA
*
517834 TTTATAATATATAGTTTT-AAAACATTTTTTAAA-A
1 TATATAATATATAGTTTTGAAAACA-TTTTTAAATA
* *
517868 CTATATAATATATAATTTTGAAAACATTTTTTTAA-A
1 -TATATAATATATAGTTTTGAAAACA-TTTTTAAATA
517904 TATATAATATATAGTTTT
1 TATATAATATATAGTTTT
517922 TTAAAATATT
Statistics
Matches: 292, Mismatches: 36, Indels: 53
0.77 0.09 0.14
Matches are distributed among these distances:
34 13 0.04
35 56 0.19
36 46 0.16
37 46 0.16
38 54 0.18
39 27 0.09
40 20 0.07
41 13 0.04
42 12 0.04
43 5 0.02
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (35 bp):
TATATAATATATAGTTTTGAAAACATTTTTAAATA
Found at i:517615 original size:37 final size:36
Alignment explanation
Indices: 517533--517942 Score: 300
Period size: 37 Copynumber: 11.0 Consensus size: 36
517523 TGATTTTATT
* * *
517533 TATATATATATAG-TTTGCAAATATTTTTGAAATACA
1 TATATATATATAGTTTTGAAAACATTTTTGAAA-ATA
* * *
517569 TATGGTATATATAGTTTTGAAAACGGTTTTTAAATATATATA
1 TAT-ATATATATAGTTTTGAAAAC-ATTTTT-GA-A-A-ATA
* * *
517611 TATATATATATAATTTTTGGAAAGC-TTTTTGGAAATA
1 TATATATATAT-AGTTTT-GAAAACATTTTTGAAAATA
* * *
517648 TATATAATATATGATTTTTGAAAACATTTAAAT-ATATATA
1 TATAT-ATATAT-AGTTTTGAAAACATTT--TTGA-AAATA
*
517688 TATATATAATATAGTTTTTGAAAATA-TTTTGAAAATA
1 TATATAT-ATATAG-TTTTGAAAACATTTTTGAAAATA
* * *
517725 TATATAATATATAGTTTTGAAATCATTTTTAAAACATT
1 TATAT-ATATATAGTTTTGAAAACATTTTTGAAA-ATA
517763 TATATAATATATAGTTTT-AAAACATTTTTGAAAACTA
1 TATAT-ATATATAGTTTTGAAAACATTTTTGAAAA-TA
** * *
517800 TATA-ATATATAGTTTAAAAAAATATTTTTGAAAATT
1 TATATATATATAGTTT-TGAAAACATTTTTGAAAATA
*
517836 TATA-ATATATAGTTTT-AAAACATTTTTTAAAACTA
1 TATATATATATAGTTTTGAAAACATTTTTGAAAA-TA
* **
517871 TATA-ATATATAATTTTGAAAACATTTTTTTAAATA
1 TATATATATATAGTTTTGAAAACATTTTTGAAAATA
* * *
517906 TATA-ATATATAGTTTTTTAAAATATTTTTTAAAATA
1 TATATATATATAG-TTTTGAAAACATTTTTGAAAATA
517942 T
1 T
517943 TTTACATATT
Statistics
Matches: 309, Mismatches: 40, Indels: 50
0.77 0.10 0.13
Matches are distributed among these distances:
34 14 0.05
35 40 0.13
36 65 0.21
37 78 0.25
38 46 0.15
39 11 0.04
40 25 0.08
41 13 0.04
42 12 0.04
43 5 0.02
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (36 bp):
TATATATATATAGTTTTGAAAACATTTTTGAAAATA
Found at i:517694 original size:77 final size:76
Alignment explanation
Indices: 517575--517814 Score: 244
Period size: 77 Copynumber: 3.1 Consensus size: 76
517565 TACATATGGT
* *
517575 ATATATAGTTTTGAAAACGGTTTTTAAATATATATATATATAT-ATATAATTTTTGGAAAGCT-T
1 ATATATAGTTTTGAAAAC---ATTTAAATATATATATATATATAATATAATTTTT-GAAA-ATAT
*
517638 TTTGGAAATATATATA
61 TTTGAAAATATATATA
* *
517654 ATATATGATTTTTGAAAACATTTAAATATATATATATATATAATATAGTTTTTGAAAATATTTTG
1 ATATAT-AGTTTTGAAAACATTTAAATATATATATATATATAATATAATTTTTGAAAATATTTTG
517719 AAAATATATATA
65 AAAATATATATA
* * * * *
517731 ATATATAGTTTTGAAATCATTTTTAA-A-ACAT-T-TATATAATATATAGTTTT-AAAACATTTT
1 ATATATAGTTTTGAAAACA-TTTAAATATATATATATATATAATATA-ATTTTTGAAAATA-TTT
*
517791 TGAAAA-CTATATA
63 TGAAAATATATATA
517804 ATATATAGTTT
1 ATATATAGTTT
517815 AAAAAAATAT
Statistics
Matches: 142, Mismatches: 13, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
73 33 0.23
74 14 0.10
75 3 0.02
76 13 0.09
77 52 0.37
78 10 0.07
79 6 0.04
80 11 0.08
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (76 bp):
ATATATAGTTTTGAAAACATTTAAATATATATATATATATAATATAATTTTTGAAAATATTTTGA
AAATATATATA
Found at i:517934 original size:35 final size:35
Alignment explanation
Indices: 517685--517967 Score: 208
Period size: 36 Copynumber: 7.9 Consensus size: 35
517675 TTAAATATAT
* *
517685 ATATATATATAATATAGTTTTTGAAAATATTTTGAAAA
1 ATATATA-AT-ATATAGTTTTTTAAAATATTTT-TAAA
*
517723 TATATATAATATATAG--TTTTGAAATCATTTTTAAAA
1 -ATATATAATATATAGTTTTTTAAAAT-ATTTTT-AAA
*
517759 CATTTATATAATATATAG--TTTTAAAACATTTTTGAAA
1 -A--TATATAATATATAGTTTTTTAAAATATTTTT-AAA
***
517796 ACTATATAATATATAGTTTAAAAAAATATTTTTGAAA
1 A-TATATAATATATAGTTTTTTAAAATATTTTT-AAA
* *
517833 ATTTATAATATATAG--TTTTAAAACATTTTTTAAA
1 ATATATAATATATAGTTTTTTAAAATA-TTTTTAAA
* * * *
517867 ACTATATAATATATA-ATTTTGAAAACATTTTTTTAA
1 A-TATATAATATATAGTTTTTTAAAATA-TTTTTAAA
517903 ATATATAATATATAGTTTTTTAAAATATTTTTTAAA
1 ATATATAATATATAGTTTTTTAAAATA-TTTTTAAA
* *
517939 ATAT-T-TTACATA-TTTTTTAAAAATATTTT
1 ATATATAATATATAGTTTTTT-AAAATATTTT
517968 ATATATTTTT
Statistics
Matches: 206, Mismatches: 26, Indels: 30
0.79 0.10 0.11
Matches are distributed among these distances:
33 10 0.05
34 21 0.10
35 52 0.25
36 62 0.30
37 31 0.15
38 23 0.11
39 7 0.03
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (35 bp):
ATATATAATATATAGTTTTTTAAAATATTTTTAAA
Found at i:517945 original size:11 final size:12
Alignment explanation
Indices: 517918--517989 Score: 73
Period size: 11 Copynumber: 6.3 Consensus size: 12
517908 TAATATATAG
517918 TTTTTTAAAATA
1 TTTTTTAAAATA
517930 TTTTTTAAAATA
1 TTTTTTAAAATA
*
517942 --TTTT-ACATA
1 TTTTTTAAAATA
517951 TTTTTTAAAA-A
1 TTTTTTAAAATA
* *
517962 TATTTT-ATATA
1 TTTTTTAAAATA
517973 TTTTTTAAAAATA
1 TTTTTT-AAAATA
517986 TTTT
1 TTTT
517990 ATATATAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
9 4 0.08
10 6 0.12
11 16 0.33
12 14 0.29
13 8 0.17
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTTTTAAAATA
Found at i:517953 original size:21 final size:22
Alignment explanation
Indices: 517927--517995 Score: 122
Period size: 22 Copynumber: 3.2 Consensus size: 22
517917 GTTTTTTAAA
*
517927 ATATTTTTT-AAAATATTTTAC
1 ATATTTTTTAAAAATATTTTAT
517948 ATATTTTTTAAAAATATTTTAT
1 ATATTTTTTAAAAATATTTTAT
517970 ATATTTTTTAAAAATATTTTAT
1 ATATTTTTTAAAAATATTTTAT
517992 ATAT
1 ATAT
517996 AATATATTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
21 9 0.20
22 37 0.80
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATTTTTTAAAAATATTTTAT
Found at i:523321 original size:22 final size:22
Alignment explanation
Indices: 523295--523355 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
523285 GTAGGGCAGA
523295 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
* * * *
523317 GGGAACCGATTCCCCCCTGTAG
1 GGGAATCGATACCCCCTTGAAG
523339 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
523356 AGAGGTTCTG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.18
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:524954 original size:18 final size:18
Alignment explanation
Indices: 524933--524973 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
524923 AGAACAACAC
* *
524933 GAGGAACAAGCACGAGCA
1 GAGGAACAAGCACAACCA
524951 GAGGAACAAGCACAACCA
1 GAGGAACAAGCACAACCA
524969 GAGGA
1 GAGGA
524974 TCAAATGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.32, T:0.00
Consensus pattern (18 bp):
GAGGAACAAGCACAACCA
Found at i:526895 original size:12 final size:12
Alignment explanation
Indices: 526878--526908 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
526868 TCGACTCGAT
526878 CCGACCCGAGAC
1 CCGACCCGAGAC
526890 CCGACCCGAGAC
1 CCGACCCGAGAC
526902 CCGACCC
1 CCGACCC
526909 ACGGGTAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.23, C:0.55, G:0.23, T:0.00
Consensus pattern (12 bp):
CCGACCCGAGAC
Found at i:527143 original size:17 final size:18
Alignment explanation
Indices: 527117--527150 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
527107 TATATATATA
527117 TATTA-GTTTTTTATTTC
1 TATTATGTTTTTTATTTC
*
527134 TATTATTTTTTTTATTT
1 TATTATGTTTTTTATTT
527151 TTTACTTTTC
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:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (18 bp):
TATTATGTTTTTTATTTC
Found at i:527364 original size:3 final size:3
Alignment explanation
Indices: 527358--527416 Score: 77
Period size: 3 Copynumber: 19.7 Consensus size: 3
527348 TTTTCCTTCT
*
527358 TTA TTA TTA TTA TTA TAA TTA TTA -TA TATA TT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
527402 TTA TTA TTA TATA TT
1 TTA TTA TTA T-TA TT
527417 TTTTCTCTTA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
2 4 0.08
3 40 0.80
4 6 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:527399 original size:29 final size:29
Alignment explanation
Indices: 527361--527420 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
527351 TCCTTCTTTA
527361 TTATTATTATTATAATTATTATATATATT
1 TTATTATTATTATAATTATTATATATATT
* *
527390 TTATTATTATTATTATTATTATATATTTT
1 TTATTATTATTATAATTATTATATATATT
527419 TT
1 TT
527421 CTCTTAACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (29 bp):
TTATTATTATTATAATTATTATATATATT
Found at i:527494 original size:2 final size:2
Alignment explanation
Indices: 527489--527513 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
527479 TATCTTGCAT
527489 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
527514 TGTCATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:527569 original size:14 final size:14
Alignment explanation
Indices: 527552--527590 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
527542 TTATCTTCTA
527552 CTTTTTTTTTCTTT
1 CTTTTTTTTTCTTT
*
527566 CTTTTCTTTTCTTT
1 CTTTTTTTTTCTTT
*
527580 ATTTTATTTTT
1 CTTTT-TTTTT
527591 TTATTTCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (14 bp):
CTTTTTTTTTCTTT
Found at i:527572 original size:36 final size:35
Alignment explanation
Indices: 527519--527620 Score: 100
Period size: 36 Copynumber: 2.8 Consensus size: 35
527509 TATATTGTCA
527519 TTATTGTCTTTATTTTCTTTATC-TTATCTTCTACTTTT
1 TTATT-TCTTTATTTTCTTT-TCTTTAT-TT-TACTTTT
* *
527557 TT-TTTCTTTCTTTTCTTTTCTTTATTTTATTTTT
1 TTATTTCTTTATTTTCTTTTCTTTATTTTACTTTT
* * *
527591 TTATTTCTTTTGTTTTATTTTATTTATTTT
1 TTATTTC-TTTATTTTCTTTTCTTTATTTT
527621 TTTATTTTCC
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
34 8 0.14
35 8 0.14
36 36 0.64
37 2 0.04
38 2 0.04
ACGTcount: A:0.11, C:0.11, G:0.02, T:0.76
Consensus pattern (35 bp):
TTATTTCTTTATTTTCTTTTCTTTATTTTACTTTT
Found at i:527590 original size:31 final size:31
Alignment explanation
Indices: 527555--527627 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
527545 TCTTCTACTT
* *
527555 TTTTTTTCTTTCTTTTCTTTT-CTTTATTTTA
1 TTTTTTTATTTCTTTTCTTTTATTTTA-TTTA
*
527586 TTTTTTTATTTCTTTTGTTTTATTTTATTTA
1 TTTTTTTATTTCTTTTCTTTTATTTTATTTA
527617 TTTTTTTATTT
1 TTTTTTTATTT
527628 TCCTTATCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 34 0.89
32 4 0.11
ACGTcount: A:0.10, C:0.07, G:0.01, T:0.82
Consensus pattern (31 bp):
TTTTTTTATTTCTTTTCTTTTATTTTATTTA
Found at i:527640 original size:31 final size:32
Alignment explanation
Indices: 527527--527639 Score: 92
Period size: 31 Copynumber: 3.6 Consensus size: 32
527517 CATTATTGTC
* *
527527 TTTATTTTCTTTATCTTATCTTCTACTT-TTTT
1 TTTATTTTCCTTATCTTATCTT-TATTTATTTT
* * *
527559 TTT-CTTT-CTTTTCTTTTCTTTATTTTATTTT
1 TTTATTTTCCTTATCTTATCTTTA-TTTATTTT
* * *
527590 TTTA-TTTCTTTTGTTTTAT-TTTATTTATTTT
1 TTTATTTTC-CTTATCTTATCTTTATTTATTTT
527621 TTTATTTTCCTTATCTTAT
1 TTTATTTTCCTTATCTTAT
527640 TCATTTTCAC
Statistics
Matches: 63, Mismatches: 12, Indels: 13
0.72 0.14 0.15
Matches are distributed among these distances:
29 2 0.03
30 12 0.19
31 32 0.51
32 11 0.17
33 6 0.10
ACGTcount: A:0.12, C:0.12, G:0.01, T:0.76
Consensus pattern (32 bp):
TTTATTTTCCTTATCTTATCTTTATTTATTTT
Found at i:529609 original size:14 final size:15
Alignment explanation
Indices: 529575--529613 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
529565 CTCTGGGTTT
*
529575 GCAACGCTACATGTA
1 GCAATGCTACATGTA
529590 GC-ATGCTAC-TGTA
1 GCAATGCTACATGTA
529603 GCAATGCTACA
1 GCAATGCTACA
529614 AAAATCTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 6 0.29
14 13 0.62
15 2 0.10
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.23
Consensus pattern (15 bp):
GCAATGCTACATGTA
Found at i:529718 original size:10 final size:10
Alignment explanation
Indices: 529705--529738 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
529695 TTTTTTGTAA
529705 TTTTTCTGAT
1 TTTTTCTGAT
*
529715 TTTTTAT-AT
1 TTTTTCTGAT
529724 TTTTTCTGAT
1 TTTTTCTGAT
529734 TTTTT
1 TTTTT
529739 AAAATTTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (10 bp):
TTTTTCTGAT
Found at i:529719 original size:19 final size:19
Alignment explanation
Indices: 529695--529745 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
529685 CATACTAATT
*
529695 TTTTTTGTAATTTTTCTGA
1 TTTTTTATAATTTTTCTGA
*
529714 TTTTTTATATTTTTTCTGA
1 TTTTTTATAATTTTTCTGA
*
529733 TTTTTTAAAATTT
1 TTTTTTATAATTT
529746 ACAAAATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.71
Consensus pattern (19 bp):
TTTTTTATAATTTTTCTGA
Found at i:534678 original size:14 final size:14
Alignment explanation
Indices: 534656--534690 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
534646 GAAAAGAATA
534656 ATAAAAATATTAAT
1 ATAAAAATATTAAT
*
534670 ATAATAATATTAAT
1 ATAAAAATATTAAT
534684 A-AAAAAT
1 ATAAAAAT
534691 GAAAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAAAAATATTAAT
Found at i:534797 original size:20 final size:22
Alignment explanation
Indices: 534757--534800 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
534747 TTAAAATTAG
534757 GAGAAAATGAAAAATATATATA
1 GAGAAAATGAAAAATATATATA
534779 GAGAAAATGAAAAATATATATA
1 GAGAAAATGAAAAATATATATA
534801 AAGTAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.23
Consensus pattern (22 bp):
GAGAAAATGAAAAATATATATA
Found at i:534808 original size:22 final size:22
Alignment explanation
Indices: 534758--534808 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
534748 TAAAATTAGG
*
534758 AGAAAATGAAAAATATATATAG
1 AGAAAATGAAAAATATATATAA
534780 AGAAAATGAAAAATATATATAA
1 AGAAAATGAAAAATATATATAA
*
534802 AGTAAAT
1 AGAAAAT
534809 AAATAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (22 bp):
AGAAAATGAAAAATATATATAA
Found at i:535620 original size:13 final size:12
Alignment explanation
Indices: 535602--535644 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
535592 AAATACATGT
535602 TATATAATTATAG
1 TATATAA-TATAG
535615 TATATAATATAG
1 TATATAATATAG
* *
535627 TATGT-ATATAT
1 TATATAATATAG
535638 TATATAA
1 TATATAA
535645 CATAATACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 9 0.35
12 10 0.38
13 7 0.27
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (12 bp):
TATATAATATAG
Found at i:535635 original size:16 final size:14
Alignment explanation
Indices: 535602--535643 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
535592 AAATACATGT
535602 TATATAAT-TATAG
1 TATATAATATATAG
535615 TATATAATATAGTATG
1 TATATAATATA-TA-G
*
535631 TATATATTATATA
1 TATATAATATATA
535644 ACATAATACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 8 0.32
14 2 0.08
15 4 0.16
16 11 0.44
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
TATATAATATATAG
Found at i:536826 original size:165 final size:165
Alignment explanation
Indices: 536382--537527 Score: 1402
Period size: 165 Copynumber: 6.9 Consensus size: 165
536372 TGCACCTTGG
* * * * * *
536382 AGCTGAGCGAAATCGAACTCAAAGGTCTTTTGTGACAGATA-ACCCTTCTAGCCTTGAGTTATGC
1 AGCTGAGCGTAATCGAACTCGAAGGTC-TTTG-G-CAGATAGA-CCTTCTCGACTTAAGTTATTC
* * * * * * *
536446 TGTAAATGATGTGCCCTCGAAGCTGAGCGTAATTGAACTCAAGGGTC-TTTGG---CAGATAGCC
62 TGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACC
* * * * * * * * *
536507 CTTCTTGGCTTAAGCTATTCTGCAAATGATGTG-TCTTGG
126 CTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGA
* * * * *
536546 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATA-ACCCTTCTAGCCTTGAGTTATGC
1 AGCTGAGCGTAATCGAACTCGAAGGTCTTT-G-G-CAGATAGA-CCTTCTCGACTTAAGTTATTC
* * * * *
536610 TGTAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACC
62 TGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACC
* *
536675 CTTATAGCCTTGAGTTATACTGTAAATGATGTGCTCC-CGA
126 CTTCTAGCCTTGAGTTATGCTGTAAATGATGTGC-CCTCGA
536715 AGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAGACCTTCTCGACTTAAGTTATTCTGCA
1 AGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAGACCTTCTCGACTTAAGTTATTCTGCA
*
536780 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACATATAACCCTTCT
66 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCT
* *
536845 AGCCTTGAGTTATGTTGTAAATGATGTGCCCTCAA
131 AGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGA
* * * *
536880 AGTTGAGCGTAATCGAACTCGAGGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGTTATTCTGCA
1 AGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAGACCTTCTCGACTTAAGTTATTCTGCA
* *
536945 AATTATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCT
66 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCT
*
537010 AGCCTTGAGTTATGCTGTAAATGATGTACCCTCGA
131 AGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGA
** * * * * *
537045 AGCTGAGTATAATCAAACCCG-AGGTTTTTGGCAGATAGTCCTTCTCGACTTAAGCTATTCTGCA
1 AGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAGACCTTCTCGACTTAAGTTATTCTGCA
* * * * * * *
537109 AATGATGCGCCTTTAGAGTTGAGCTTAGTCAAACTCGAAGGTC-TTTGGTGACAGATAACCCTTC
66 AATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTC
*
537173 TAGCCTTAAGTTATGCTGTAAATGATGTGCCCTCGA
130 TAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGA
* * * *
537209 AGCTGAGCGTAATCGAGCTCGAGGGTCTTTGG-ATGATAG-CTTTTCTCGACTTAAGCTATTCTG
1 AGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCA-GATAGAC-CTTCTCGACTTAAGTTATTCTG
*
537272 CAAATGATGCGCCTTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCT
64 CAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCT
*
537337 TCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGA
128 TCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGA
* * *
537375 AGCTGAGTGTAATCAAACTC-AAGGGTCTTTAGCAGATA-ACCCTTCTCGACTTAAGTTATTCTG
1 AGCTGAGCGTAATCGAACTCGAA-GGTCTTTGGCAGATAGA-CCTTCTCGACTTAAGTTATTCTG
* * *
537438 CAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGGTCACAGATAACCATT
64 CAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTT
537503 CTAGCCTTGAGTTATGCTGTAAATG
129 CTAGCCTTGAGTTATGCTGTAAATG
537528 TTGTCTTTTA
Statistics
Matches: 872, Mismatches: 92, Indels: 35
0.87 0.09 0.04
Matches are distributed among these distances:
163 3 0.00
164 220 0.25
165 430 0.49
166 149 0.17
167 4 0.00
168 35 0.04
169 30 0.03
170 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (165 bp):
AGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAGACCTTCTCGACTTAAGTTATTCTGCA
AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCT
AGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGA
Found at i:537404 original size:495 final size:495
Alignment explanation
Indices: 536633--537527 Score: 1546
Period size: 495 Copynumber: 1.8 Consensus size: 495
536623 CCCTCGAAGC
* *
536633 TGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTATAGCCTTGAGTTATACTGT
1 TGAGCGTAGTCAAACTCGAAGGTCTTTTGGTGACAGATAACCCTTATAGCCTTAAGTTATACTGT
536698 AAATGATGTGCTCCCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAGACCTTCTCG
66 AAATGATGTGCTCCCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAGACCTTCTCG
* *
536763 ACTTAAGTTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGG
131 ACTTAAGCTATTCTGCAAATGATGCGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGG
* *
536828 TCACATATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCAAAGTTGAGCGTAAT
196 TCACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCAAAGCTGAGCGTAAT
* * * *
536893 CGAACTCGAGGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGTTATTCTGCAAATTATATGCCTT
261 CAAACTCAAGGGTCTTTAGCAGATAACCCTTCTCGACTTAAGTTATTCTGCAAATGATATGCCTT
* *
536958 GGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTAT
326 GGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGGTCACAGATAACCATTCTAGCCTTGAGTTAT
537023 GCTGTAAATGATGTACCCTCGAAGCTGAGTATAATCAAACCCGAGGTTTTTGGCAGATAGTCCTT
391 GCTGTAAATGATGTACCCTCGAAGCTGAGTATAATCAAACCCGAGGTTTTTGGCAGATAGTCCTT
537088 CTCGACTTAAGCTATTCTGCAAATGATGCGCCTTTAGAGT
456 CTCGACTTAAGCTATTCTGCAAATGATGCGCCTTTAGAGT
* * *
537128 TGAGCTTAGTCAAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGCCTTAAGTTATGCTGT
1 TGAGCGTAGTCAAACTCGAAGGTCTTTTGGTGACAGATAACCCTTATAGCCTTAAGTTATACTGT
* * *
537192 AAATGATGTGC-CCTCGAAGCTGAGCGTAATCGAGCTCGAGGGTCTTTGG-ATGATAG-CTTTTC
66 AAATGATGTGCTCC-CGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCA-GATAGAC-CTTC
537254 TCGACTTAAGCTATTCTGCAAATGATGCGCCTTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTT
128 TCGACTTAAGCTATTCTGCAAATGATGCGCC-TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTT
* *
537319 TTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTG
192 TTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCAAAGCTGAGCG
537384 TAATCAAACTCAAGGGTCTTTAGCAGATAACCCTTCTCGACTTAAGTTATTCTGCAAATGATATG
257 TAATCAAACTCAAGGGTCTTTAGCAGATAACCCTTCTCGACTTAAGTTATTCTGCAAATGATATG
537449 CCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGGTCACAGATAACCATTCTAGCCTTGAG
322 CCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGGTCACAGATAACCATTCTAGCCTTGAG
537514 TTATGCTGTAAATG
387 TTATGCTGTAAATG
537528 TTGTCTTTTA
Statistics
Matches: 376, Mismatches: 20, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
493 4 0.01
494 118 0.31
495 254 0.68
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (495 bp):
TGAGCGTAGTCAAACTCGAAGGTCTTTTGGTGACAGATAACCCTTATAGCCTTAAGTTATACTGT
AAATGATGTGCTCCCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAGACCTTCTCG
ACTTAAGCTATTCTGCAAATGATGCGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGG
TCACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCAAAGCTGAGCGTAAT
CAAACTCAAGGGTCTTTAGCAGATAACCCTTCTCGACTTAAGTTATTCTGCAAATGATATGCCTT
GGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGGTCACAGATAACCATTCTAGCCTTGAGTTAT
GCTGTAAATGATGTACCCTCGAAGCTGAGTATAATCAAACCCGAGGTTTTTGGCAGATAGTCCTT
CTCGACTTAAGCTATTCTGCAAATGATGCGCCTTTAGAGT
Found at i:542207 original size:14 final size:14
Alignment explanation
Indices: 542168--542208 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
542158 ATTGATTACA
* *
542168 TTTCTGGAAAACGT
1 TTTCCGGAAAATGT
542182 TTTCCGGAAAATGT
1 TTTCCGGAAAATGT
*
542196 TTTCCGTAAAATG
1 TTTCCGGAAAATG
542209 AATTACATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37
Consensus pattern (14 bp):
TTTCCGGAAAATGT
Found at i:542420 original size:49 final size:47
Alignment explanation
Indices: 542330--542437 Score: 112
Period size: 49 Copynumber: 2.2 Consensus size: 47
542320 ATTAAATATA
*
542330 AAAAATAATCTTATTTATCATAAAACTTAATATTATTATTTTA-AAAT
1 AAAAATAAT-TTATTTATCATAAAACTTAATATTATAATTTTATAAAT
* * * *
542377 ATTAAAATAATTTATTTATTATTAAATA-TTATTTTTATAATTTTATTAAT
1 A--AAAATAATTTATTTATCA-TAAA-ACTTAATATTATAATTTTATAAAT
542427 AAAAATAATTT
1 AAAAATAATTT
542438 TTATATTTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
47 1 0.02
48 19 0.37
49 26 0.51
50 5 0.10
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (47 bp):
AAAAATAATTTATTTATCATAAAACTTAATATTATAATTTTATAAAT
Found at i:542421 original size:27 final size:26
Alignment explanation
Indices: 542391--542462 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 26
542381 AAATAATTTA
*
542391 TTTATTATTAAATATTATTTTTATAAT
1 TTTATTAATAAATATTATTTTTAT-AT
* *
542418 TTTATTAATAAAAATAATTTTTATAT
1 TTTATTAATAAATATTATTTTTATAT
*
542444 TTTAGTGAATAAATATTAT
1 TTTA-TTAATAAATATTAT
542463 AAATTATATT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 6 0.16
27 32 0.84
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (26 bp):
TTTATTAATAAATATTATTTTTATAT
Found at i:542497 original size:83 final size:80
Alignment explanation
Indices: 542373--542530 Score: 178
Period size: 83 Copynumber: 1.9 Consensus size: 80
542363 TATTATTTTA
* * *
542373 AAATATTAAAATAATTTATTTATTATTAAATATTATTTTTATAATTTTA-TTAATAAA-AATAAT
1 AAATATTAAAATAATTTAATTATTATTAAATA-TATGTTTAT-ATTATATTTAA-AAATAATAAT
*
542436 TTTTATATTTTAGTGAAT
63 TATTATATTTTAGTGAAT
* *
542454 AAATATTATAAATTATATTAATTATTATTAAAGTA-AGTGTTTATATTATATTTAAAAATATTAA
1 AAATATTA-AAATAAT-TTAATTATTATTAAA-TATA-TGTTTATATTATATTTAAAAATAATAA
542518 TTATTATATTTTA
62 TTATTATATTTTA
542531 AATATATTTA
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
81 8 0.12
82 15 0.23
83 40 0.62
84 2 0.03
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (80 bp):
AAATATTAAAATAATTTAATTATTATTAAATATATGTTTATATTATATTTAAAAATAATAATTAT
TATATTTTAGTGAAT
Found at i:542556 original size:12 final size:12
Alignment explanation
Indices: 542522--542562 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
542512 TATTAATTAT
542522 TATA-TTTTAAA
1 TATATTTTTAAA
542533 TATATTTATTAAA
1 TATATTT-TTAAA
542546 -ATATTATTTAAA
1 TATATT-TTTAAA
542558 TATAT
1 TATAT
542563 AAATAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 4 0.15
12 12 0.46
13 10 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TATATTTTTAAA
Found at i:542561 original size:25 final size:24
Alignment explanation
Indices: 542500--542562 Score: 74
Period size: 23 Copynumber: 2.6 Consensus size: 24
542490 GTGTTTATAT
* **
542500 TATATTTAAAAATATTAATTATTA
1 TATATTTAAATATATTAATTAAAA
*
542524 TAT-TTTAAATATATTTATTAAAA
1 TATATTTAAATATATTAATTAAAA
542547 TATTATTTAAATATAT
1 TA-TATTTAAATATAT
542563 AAATAATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 18 0.55
24 4 0.12
25 11 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TATATTTAAATATATTAATTAAAA
Found at i:542602 original size:28 final size:27
Alignment explanation
Indices: 542547--542611 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
542537 TTTATTAAAA
* *
542547 TATTATTTAAATATATAAATAATATTAT
1 TATTA-TTAAATACATAAAGAATATTAT
* *
542575 TCATTATTAAATACATAAAGATTTTTAT
1 T-ATTATTAAATACATAAAGAATATTAT
542603 TATATATTA
1 TAT-TATTA
542612 TTAAAATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
27 2 0.06
28 25 0.81
29 4 0.13
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (27 bp):
TATTATTAAATACATAAAGAATATTAT
Found at i:542652 original size:23 final size:23
Alignment explanation
Indices: 542622--542695 Score: 71
Period size: 23 Copynumber: 3.1 Consensus size: 23
542612 TTAAAATAAA
*
542622 AATATAATATCTTATATTATTAT
1 AATATAATATATTATATTATTAT
*
542645 AATATAAT-TGATTATTTTA-TAT
1 AATATAATAT-ATTATATTATTAT
542667 AATATTAAAAATATATTATATTATTAT
1 AATA-T---AATATATTATATTATTAT
542694 AA
1 AA
542696 ATATTAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
22 8 0.20
23 16 0.39
26 11 0.27
27 6 0.15
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (23 bp):
AATATAATATATTATATTATTAT
Found at i:542718 original size:27 final size:29
Alignment explanation
Indices: 542661--542718 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 29
542651 ATTGATTATT
* *
542661 TTATATAATATTAAAAATATATTATATTA
1 TTATATAATATTAAAAATATATAATAGTA
542690 TTATA-AATATT-AAAATA-ATAAATAGTA
1 TTATATAATATTAAAAATATAT-AATAGTA
542717 TT
1 TT
542719 TTGATGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 2 0.08
27 13 0.50
28 6 0.23
29 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (29 bp):
TTATATAATATTAAAAATATATAATAGTA
Found at i:542950 original size:42 final size:42
Alignment explanation
Indices: 542892--543007 Score: 160
Period size: 42 Copynumber: 2.8 Consensus size: 42
542882 ATGAATTACA
* *
542892 TTCCGGAAAATCAATTACATGAAACAAACACGGGAAAACATT
1 TTCCGGAAAATAAATTACGTGAAACAAACACGGGAAAACATT
* * *
542934 TTCCGGAAAATGAATTACGTGAAACAAATACGGGAAAATATT
1 TTCCGGAAAATAAATTACGTGAAACAAACACGGGAAAACATT
* * *
542976 TTCCGAAAAACAAATTACGTGAAATAAACACG
1 TTCCGGAAAATAAATTACGTGAAACAAACACG
543008 AGAATTCAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (42 bp):
TTCCGGAAAATAAATTACGTGAAACAAACACGGGAAAACATT
Found at i:544448 original size:20 final size:19
Alignment explanation
Indices: 544423--544481 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 19
544413 AATTTACAAC
*
544423 ACGAATATGTAAATCGCAA
1 ACGAATCTGTAAATCGCAA
*
544442 TACGAATCTGTAAATCGTAA
1 -ACGAATCTGTAAATCGCAA
*
544462 ATCGAATCTGTAATTCGCAA
1 A-CGAATCTGTAAATCGCAA
544482 CACATAAGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.03
20 33 0.97
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (19 bp):
ACGAATCTGTAAATCGCAA
Found at i:544498 original size:20 final size:20
Alignment explanation
Indices: 544473--544563 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
544463 TCGAATCTGT
*
544473 AATTCGCAACACATAAGTCA
1 AATTCGCAACACAGAAGTCA
544493 AATTCGCAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
**
544513 AATTCGCAA-AGC-GATTTCCA
1 AATTCGCAACA-CAGAAGT-CA
* *
544533 AATTCGCAACACTGAATTTCA
1 AATTCGCAACACAGAA-GTCA
544554 AATTCGCAAC
1 AATTCGCAAC
544564 TCGATTTCTG
Statistics
Matches: 62, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
19 4 0.06
20 41 0.66
21 15 0.24
22 2 0.03
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.22
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:544569 original size:41 final size:40
Alignment explanation
Indices: 544491--544644 Score: 166
Period size: 41 Copynumber: 3.8 Consensus size: 40
544481 ACACATAAGT
* **
544491 CAAATTCGCAACACAGAA-GTCAAATTCGCAAAGCGATTTC
1 CAAATTCGCAACAC-GAATTTCAAATTCGCAACTCGATTTC
544531 CAAATTCGCAACACTGAATTTCAAATTCGCAACTCGATTTC
1 CAAATTCGCAACAC-GAATTTCAAATTCGCAACTCGATTTC
** * * * *
544572 TGAATTCGCAACGCGAATTTGGAAAATCGCAACTCGATTTT
1 CAAATTCGCAACACGAATTT-CAAATTCGCAACTCGATTTC
* * *
544613 CGAATTCGCAACACGAATTTTAATTTCGCAAC
1 CAAATTCGCAACACGAATTTCAAATTCGCAAC
544645 ACAAATGTTT
Statistics
Matches: 97, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
40 32 0.33
41 65 0.67
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (40 bp):
CAAATTCGCAACACGAATTTCAAATTCGCAACTCGATTTC
Found at i:544579 original size:20 final size:20
Alignment explanation
Indices: 544513--544624 Score: 77
Period size: 20 Copynumber: 5.5 Consensus size: 20
544503 ACAGAAGTCA
* **
544513 AATTCGCAAAGCGATTTCCA
1 AATTCGCAACGCGATTTCTG
* *
544533 AATTCGCAACACTGAATTTC-A
1 AATTCGCAACGC-G-ATTTCTG
*
544554 AATTCGCAACTCGATTTCTG
1 AATTCGCAACGCGATTTCTG
*
544574 AATTCGCAACGCGAATTT-GG
1 AATTCGCAACGCG-ATTTCTG
* *
544594 AAAATCGCAACTCGATTT-TCG
1 -AATTCGCAACGCGATTTCT-G
544615 AATTCGCAAC
1 AATTCGCAAC
544625 ACGAATTTTA
Statistics
Matches: 76, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
19 5 0.07
20 37 0.49
21 29 0.38
22 5 0.07
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (20 bp):
AATTCGCAACGCGATTTCTG
Found at i:544640 original size:20 final size:19
Alignment explanation
Indices: 544533--544646 Score: 79
Period size: 20 Copynumber: 5.6 Consensus size: 19
544523 GCGATTTCCA
*
544533 AATTCGCAACACTGAATTTCA
1 AATTCGCAACAC-GAATTT-T
*
544554 AATTCGCAACTCG-ATTTCT
1 AATTCGCAACACGAATTT-T
* *
544573 GAATTCGCAACGCGAATTTGGA
1 -AATTCGCAACACGAATTT--T
* *
544595 AAATCGCAACTCG-ATTTT
1 AATTCGCAACACGAATTTT
544613 CGAATTCGCAACACGAATTTT
1 --AATTCGCAACACGAATTTT
544634 AATTTCGCAACAC
1 AA-TTCGCAACAC
544647 AAATGTTTTG
Statistics
Matches: 76, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
19 7 0.09
20 38 0.50
21 31 0.41
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (19 bp):
AATTCGCAACACGAATTTT
Found at i:544801 original size:14 final size:15
Alignment explanation
Indices: 544782--544820 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
544772 TTCCCATCTC
544782 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
544796 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
544812 TAATTTTTT
1 TAATTTTTT
544821 AATGATTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 7 0.32
15 5 0.23
16 10 0.45
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:545610 original size:24 final size:24
Alignment explanation
Indices: 545559--545612 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
545549 GTATTCAAAA
*
545559 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
545583 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
545607 TTTGAT
1 TTTGAT
545613 GATGTTTTAG
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:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:546161 original size:9 final size:9
Alignment explanation
Indices: 546133--546274 Score: 57
Period size: 9 Copynumber: 15.3 Consensus size: 9
546123 AATAATAATT
546133 AAATAAATGA
1 AAATAAAT-A
**
546143 AAGGAAATA
1 AAATAAATA
546152 AAATAAATA
1 AAATAAATA
546161 ATAAT-AATA
1 A-AATAAATA
*
546170 ATAAT-ATTA
1 A-AATAAATA
546179 AAAT-AATA
1 AAATAAATA
546187 AAATAAA-A
1 AAATAAATA
546195 AATATTAAAT-
1 AA-A-TAAATA
546205 AAATCAAA-A
1 AAAT-AAATA
* *
546214 GGGAAAGAAAAA
1 ---AAATAAATA
546226 ACAAT-AATA
1 A-AATAAATA
*
546235 AAATAAAACA
1 AAAT-AAATA
546245 AAAGT-AATA
1 AAA-TAAATA
*
546254 AAATAAATG
1 AAATAAATA
546263 AAATAAATA
1 AAATAAATA
546272 AAA
1 AAA
546275 AACTATAATA
Statistics
Matches: 103, Mismatches: 13, Indels: 33
0.69 0.09 0.22
Matches are distributed among these distances:
8 18 0.17
9 54 0.52
10 23 0.22
11 4 0.04
12 4 0.04
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.20
Consensus pattern (9 bp):
AAATAAATA
Found at i:546165 original size:3 final size:3
Alignment explanation
Indices: 546148--546192 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
546138 AATGAAAGGA
*
546148 AAT AA- AAT AAAT AAT AAT AAT AAT AAT ATT AA- AAT AAT AA- AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
546191 AA
1 AA
546193 AAAATATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
2 6 0.17
3 27 0.75
4 3 0.08
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:546182 original size:23 final size:23
Alignment explanation
Indices: 546150--546203 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 23
546140 TGAAAGGAAA
546150 TAAAATAAATAATAATAATAATAATAT
1 TAAAAT-AATAA-AATAA-AA-AATAT
546177 TAAAATAATAAAATAAAAAATAT
1 TAAAATAATAAAATAAAAAATAT
546200 TAAA
1 TAAA
546204 TAAATCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 9 0.33
24 2 0.07
25 5 0.19
26 5 0.19
27 6 0.22
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (23 bp):
TAAAATAATAAAATAAAAAATAT
Found at i:546198 original size:7 final size:8
Alignment explanation
Indices: 546148--546203 Score: 60
Period size: 9 Copynumber: 6.8 Consensus size: 8
546138 AATGAAAGGA
546148 AATAAAAT
1 AATAAAAT
546156 AAATAATAAT
1 -AATAA-AAT
546166 AATAATAAT
1 AATAA-AAT
*
546175 ATTAAAAT
1 AATAAAAT
546183 AATAAAAT
1 AATAAAAT
546191 AA-AAAAT
1 AATAAAAT
*
546198 ATTAAA
1 AATAAA
546204 TAAATCAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
7 6 0.14
8 15 0.36
9 18 0.43
10 3 0.07
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
AATAAAAT
Found at i:547826 original size:12 final size:12
Alignment explanation
Indices: 547809--547858 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
547799 GTGGGGTAAA
547809 AAAAATATTAAT
1 AAAAATATTAAT
547821 AAAAATATTAAT
1 AAAAATATTAAT
*
547833 -AAAATAATAAT
1 AAAAATATTAAT
*
547844 AATAAT-TTACAT
1 AAAAATATTA-AT
547856 AAA
1 AAA
547859 TGTATATTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 12 0.38
12 20 0.62
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAAATATTAAT
Found at i:547843 original size:23 final size:23
Alignment explanation
Indices: 547810--547858 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
547800 TGGGGTAAAA
*
547810 AAAATATTAATAAAAATATTA-AT
1 AAAATAATAATAAAAAT-TTACAT
*
547833 AAAATAATAATAATAATTTACAT
1 AAAATAATAATAAAAATTTACAT
547856 AAA
1 AAA
547859 TGTATATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAATAATAATAAAAATTTACAT
Found at i:549100 original size:100 final size:102
Alignment explanation
Indices: 548919--549225 Score: 404
Period size: 100 Copynumber: 3.0 Consensus size: 102
548909 TGAAATTGAA
* * *
548919 AGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTATGAAGTTGAGCTTGTGTTGTCTCGAGTCTAA
1 AGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCTAA
* *
548984 TATCCTTCGTTATGAAGTTGAAATTGACTCTGAAA-T
66 TATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACT
* * * *
549020 -TTTTTTTGTTGACAGTCAGTCGCCCCTTCGCTGTAAAGTTGAGCTTGTGTTGTCTTGAGTCAAA
1 AGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCTAA
* *
549084 TATCATTCGGTGTGAAGTTGAAATTGACTCTGAATGAAACT
66 TATCCTTCGCTGTGAAGTTGAAATTGACTC----TGAAACT
*
549125 GAAAAGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGCCTCT-AG
1 ----AGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCT-TGAG
549189 TCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG
61 TCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG
549226 GATGAAACTA
Statistics
Matches: 179, Mismatches: 16, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
100 85 0.47
104 5 0.03
105 1 0.01
106 2 0.01
110 85 0.47
111 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (102 bp):
AGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCTAA
TATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACT
Found at i:549157 original size:110 final size:110
Alignment explanation
Indices: 549024--549249 Score: 355
Period size: 110 Copynumber: 2.1 Consensus size: 110
549014 TGAAATTTTT
*
549024 TTTGTTGACAGTCAGTCGCCCCTTCGCTGTAAAGTTGAGCTTGTGTTGTCT-TGAGTCAAATATC
1 TTTGTTGACAGTCAGTCGCCCCTTCGCTGTAAAGTTGAGCTTGTGTTGCCTCT-AGTCAAATATC
* *
549088 ATTCGGTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTA
65 ATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTAAAAAGTTA
* * *
549134 TTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGCCTCTAGTCTAATATCC
1 TTTGTTGACAGTCAGTCGCCCCTTCGCTGTAAAGTTGAGCTTGTGTTGCCTCTAGTCAAATATCA
* * *
549199 TTCGCTGTGAAGTTGAAATTGACTCTGGATGAAACTAAAAATTTG
66 TTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTAAAAAGTTA
549244 TTTGTT
1 TTTGTT
549250 TCGCCCCTTC
Statistics
Matches: 106, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
110 105 0.99
111 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (110 bp):
TTTGTTGACAGTCAGTCGCCCCTTCGCTGTAAAGTTGAGCTTGTGTTGCCTCTAGTCAAATATCA
TTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTAAAAAGTTA
Found at i:553008 original size:3 final size:3
Alignment explanation
Indices: 553000--553028 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
552990 AAATAAAAGA
553000 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
553029 GAAAGAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:553078 original size:35 final size:35
Alignment explanation
Indices: 553039--553106 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
553029 GAAAGAAAAT
* *
553039 AAAGAAAATAAAAAAT-ATTAAATAAATCAAAAGGG
1 AAAGAAAA-AAAAAATAATAAAATAAAACAAAAGGG
*
553074 AAAGAAAAAAATAATAATAAAATAAAACAAAAG
1 AAAGAAAAAAAAAATAATAAAATAAAACAAAAG
553107 TAATAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 6 0.21
35 23 0.79
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.15
Consensus pattern (35 bp):
AAAGAAAAAAAAAATAATAAAATAAAACAAAAGGG
Found at i:553125 original size:14 final size:14
Alignment explanation
Indices: 552976--553132 Score: 61
Period size: 14 Copynumber: 10.6 Consensus size: 14
552966 AATAATAATT
* **
552976 AAATAAATGAAAGG
1 AAATAAAAGAAATA
552990 AAATAAAAGAAATA
1 AAATAAAAGAAATA
*
553004 ATAATAATAA-TAATA
1 A-AATAA-AAGAAATA
*
553019 ATAATAATAAGAAAGA
1 A-AATAA-AAGAAATA
553035 AAAT-AAAGAAAATAAA
1 AAATAAAAG-AAAT--A
*
553051 AAATATTAAATAAATCA
1 AAATA--AAAGAAAT-A
**
553068 AAAGGGAAAGAAA-A
1 AAA-TAAAAGAAATA
*
553082 AAATAATAATAAAATA
1 AAATAA-AA-GAAATA
* *
553098 AAACAAAAGTAATA
1 AAATAAAAGAAATA
*
553112 AAATAAATGAAAT-
1 AAATAAAAGAAATA
553125 AAATAAAA
1 AAATAAAA
553133 AAACCATAAT
Statistics
Matches: 108, Mismatches: 22, Indels: 27
0.69 0.14 0.17
Matches are distributed among these distances:
13 11 0.10
14 36 0.33
15 27 0.25
16 23 0.21
17 4 0.04
18 4 0.04
19 3 0.03
ACGTcount: A:0.72, C:0.01, G:0.08, T:0.18
Consensus pattern (14 bp):
AAATAAAAGAAATA
Found at i:556776 original size:18 final size:18
Alignment explanation
Indices: 556743--556778 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
556733 AAGCAAAAGG
**
556743 AAATCAAAATTGCAATCA
1 AAATCAAAATCCCAATCA
556761 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
556779 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:557092 original size:49 final size:49
Alignment explanation
Indices: 557020--557117 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 49
557010 ACGATTTTTT
*
557020 GTTGCGATTGTTGCAAAAGTCAAATTCGCAACGCAAAAGTAAAATTCGC
1 GTTGCGATTGTTGCAAAAGTCAAATTCGAAACGCAAAAGTAAAATTCGC
*
557069 GTTGCGATTGTTGCGAAAA-TCAAATTCGAAACGCGAAAGTAAAATTCGC
1 GTTGCGATTGTTGC-AAAAGTCAAATTCGAAACGCAAAAGTAAAATTCGC
557118 AACGCGCATT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
49 42 0.91
50 4 0.09
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.24
Consensus pattern (49 bp):
GTTGCGATTGTTGCAAAAGTCAAATTCGAAACGCAAAAGTAAAATTCGC
Found at i:557106 original size:20 final size:20
Alignment explanation
Indices: 557081--557123 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
557071 TGCGATTGTT
*
557081 GCGAAAATCAAATTCGAAAC
1 GCGAAAATAAAATTCGAAAC
* *
557101 GCGAAAGTAAAATTCGCAAC
1 GCGAAAATAAAATTCGAAAC
557121 GCG
1 GCG
557124 CATTTGACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.14
Consensus pattern (20 bp):
GCGAAAATAAAATTCGAAAC
Found at i:558676 original size:21 final size:21
Alignment explanation
Indices: 558650--558743 Score: 109
Period size: 21 Copynumber: 4.5 Consensus size: 21
558640 TGTGAATCGG
* *
558650 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGGTGAGAGGGGC
* * *
558671 CTCTTGAACGATGACAGGGGT
1 CTCTTGAACGGTGAGAGGGGC
*
558692 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGGTGAGAGGGGC
*
558713 CTCTTGAA-GGATGATAGGGGC
1 CTCTTGAACGG-TGAGAGGGGC
558734 CTCTTGAACG
1 CTCTTGAACG
558744 ATAGGAGATG
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 2 0.03
21 57 0.95
22 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.38, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGGTGAGAGGGGC
Found at i:558709 original size:42 final size:41
Alignment explanation
Indices: 558650--558772 Score: 165
Period size: 42 Copynumber: 2.9 Consensus size: 41
558640 TGTGAATCGG
*
558650 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGT
1 CTCTTGAACGGTGGGAGGG-CCTCTTGAACGATGACAGGGGC
* *
558692 CTCTTGAACGGTGGGAGGGGCCTCTTGAAGGATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGCCTCTTGAACGATGACAGGGGC
* * *
558734 CTCTTGAACGATAGGAGATGCCTCTTGAACGATGACAGG
1 CTCTTGAACGGTGGGAG-GGCCTCTTGAACGATGACAGG
558773 TGAATCGGGC
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
41 1 0.01
42 67 0.94
43 3 0.04
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGCCTCTTGAACGATGACAGGGGC
Found at i:560943 original size:19 final size:20
Alignment explanation
Indices: 560904--560989 Score: 131
Period size: 20 Copynumber: 4.4 Consensus size: 20
560894 TCTGAAACTT
560904 AAAATCGCAACGCGAAAATG
1 AAAATCGCAACGCGAAAATG
560924 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
*
560943 AAAATCGCAATGCGAAAATG
1 AAAATCGCAACGCGAAAATG
* *
560963 AAAATCGTAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
560982 AAAATCGC
1 AAAATCGC
560990 GTTGCGATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
19 25 0.42
20 35 0.58
ACGTcount: A:0.49, C:0.20, G:0.19, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:560996 original size:39 final size:39
Alignment explanation
Indices: 560897--560989 Score: 143
Period size: 39 Copynumber: 2.4 Consensus size: 39
560887 AATAGTTTCT
*
560897 GAAACTTAAAATCGCAACGCGAAAATGAAAATCGCAACGC
1 GAAAC-TAAAATCGCAATGCGAAAATGAAAATCGCAACGC
*
560937 GAAA-TGAAAATCGCAATGCGAAAATGAAAATCGTAACGC
1 GAAACT-AAAATCGCAATGCGAAAATGAAAATCGCAACGC
560976 GAAACTAAAATCGC
1 GAAACTAAAATCGC
560990 GTTGCGATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
38 1 0.02
39 43 0.88
40 5 0.10
ACGTcount: A:0.48, C:0.19, G:0.18, T:0.14
Consensus pattern (39 bp):
GAAACTAAAATCGCAATGCGAAAATGAAAATCGCAACGC
Found at i:561338 original size:22 final size:22
Alignment explanation
Indices: 561307--561364 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
561297 GATGGAAATA
*
561307 GACGGCTTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
* *
561329 GACGGATTTCGTTGGATATGGG
1 GACGGATTTCGTCGGAGATGGG
*
561351 GACGGATGTCGTCG
1 GACGGATTTCGTCG
561365 TAGAGAGTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.16, C:0.16, G:0.43, T:0.26
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:561490 original size:19 final size:20
Alignment explanation
Indices: 561468--561505 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
561458 AATATTGTGT
561468 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
*
561487 TTCGCATTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
561506 CGCGCTTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:561537 original size:20 final size:20
Alignment explanation
Indices: 561512--561560 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
561502 TAAACGCGCT
*
561512 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTA
*
561532 TTGCGAATTTGACTTTTGTA
1 TTGCGAATTTGACTTCTGTA
*
561552 TAGCGAATT
1 TTGCGAATT
561561 ACAGATTCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.12, G:0.22, T:0.45
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTA
Found at i:561575 original size:40 final size:38
Alignment explanation
Indices: 561531--561622 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 38
561521 TGACTTCTGT
*
561531 GTTGCGAATTTGACTTT-TGTATAGCGAATTACAGATTCGC
1 GTTGCGAATTTGA-TTTGCGT-T-GCGAATTACAGATTCGC
* *
561571 GTTGCGAATTATAGATTTGCGTTGCGATTTACATATTCGC
1 GTTGCGAATT-T-GATTTGCGTTGCGAATTACAGATTCGC
561611 GTTGCGAATTTG
1 GTTGCGAATTTG
561623 GAAACTGAGT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
38 1 0.02
39 1 0.02
40 35 0.76
41 5 0.11
42 4 0.09
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.39
Consensus pattern (38 bp):
GTTGCGAATTTGATTTGCGTTGCGAATTACAGATTCGC
Found at i:561577 original size:20 final size:20
Alignment explanation
Indices: 561554--561620 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
561544 CTTTTGTATA
561554 GCGAATTACAGATTCGCGTT
1 GCGAATTACAGATTCGCGTT
* *
561574 GCGAATTATAGATTTGCGTT
1 GCGAATTACAGATTCGCGTT
* *
561594 GCGATTTACATATTCGCGTT
1 GCGAATTACAGATTCGCGTT
561614 GCGAATT
1 GCGAATT
561621 TGGAAACTGA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (20 bp):
GCGAATTACAGATTCGCGTT
Found at i:561635 original size:40 final size:40
Alignment explanation
Indices: 561554--561660 Score: 101
Period size: 40 Copynumber: 2.7 Consensus size: 40
561544 CTTTTGTATA
** *
561554 GCGAATTACAGATTCGCGTTGCGAATTATAGATTTGCGTT
1 GCGAATTACAGATTCGCGTTGCGAATTATAGAACTGAGTT
* * *
561594 GCGATTTACATATTCGCGTTGCGAATT-TGGAAACTGAGTT
1 GCGAATTACAGATTCGCGTTGCGAATTATAG-AACTGAGTT
** *
561634 GCGAAATTGGAG-TTCGCGTTGTGAATT
1 GCG-AATTACAGATTCGCGTTGCGAATT
561661 TGTTGATCAT
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
39 2 0.04
40 48 0.89
41 4 0.07
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (40 bp):
GCGAATTACAGATTCGCGTTGCGAATTATAGAACTGAGTT
Found at i:563856 original size:32 final size:32
Alignment explanation
Indices: 563820--563905 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 32
563810 GGTTCTGATC
*
563820 AATATTGAATCGGTTGATTTTTAGGTCGGGTT
1 AATATTGAATCGGTTGATTTTTAGGTCAGGTT
* ** * *
563852 AATATCGGGTTGGTTGATTTTTGGGTCAGGTT
1 AATATTGAATCGGTTGATTTTTAGGTCAGGTT
*
563884 AATACTGAATCGGTTGGATTTT
1 AATATTGAATCGGTT-GATTTT
563906 GGGTCGTGTC
Statistics
Matches: 42, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
32 36 0.86
33 6 0.14
ACGTcount: A:0.21, C:0.07, G:0.29, T:0.43
Consensus pattern (32 bp):
AATATTGAATCGGTTGATTTTTAGGTCAGGTT
Found at i:564660 original size:16 final size:16
Alignment explanation
Indices: 564641--564685 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
564631 TTAAATTCGG
564641 TTTGGGTTGCTTTTGA
1 TTTGGGTTGCTTTTGA
* **
564657 TTTGGATTAATTTTGA
1 TTTGGGTTGCTTTTGA
564673 TTTGGGTTGCTTT
1 TTTGGGTTGCTTT
564686 CGGTTTATGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.11, C:0.04, G:0.27, T:0.58
Consensus pattern (16 bp):
TTTGGGTTGCTTTTGA
Found at i:564699 original size:16 final size:16
Alignment explanation
Indices: 564678--564735 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
564668 TTTGATTTGG
564678 GTTGCTTTCGGTTTAT
1 GTTGCTTTCGGTTTAT
*
564694 GTTGCTTTCGGTTCT-G
1 GTTGCTTTCGGTT-TAT
** *
564710 GTTAATTTCGGTTCAT
1 GTTGCTTTCGGTTTAT
564726 GTTGCTTTCG
1 GTTGCTTTCG
564736 ATTCGAGTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
16 32 0.97
17 1 0.03
ACGTcount: A:0.07, C:0.16, G:0.26, T:0.52
Consensus pattern (16 bp):
GTTGCTTTCGGTTTAT
Found at i:569813 original size:11 final size:11
Alignment explanation
Indices: 569797--569829 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
569787 TTGTAAAGGG
569797 TTTTCCATTTT
1 TTTTCCATTTT
569808 TTTTCCA--TT
1 TTTTCCATTTT
569817 TTTTCCATTTT
1 TTTTCCATTTT
569828 TT
1 TT
569830 GGTGGGAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.45
11 11 0.55
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTCCATTTT
Found at i:572852 original size:121 final size:119
Alignment explanation
Indices: 572512--572928 Score: 401
Period size: 121 Copynumber: 3.4 Consensus size: 119
572502 AAATGTTTTG
*
572512 GTGATATATCACTTCAATTCAGTGATATATTAAACCATTGAATGATGTTTTTGACATATTCTTTA
1 GTGATATATCACTTCAATTCAGTGATATATCAAA-CATTGAATGATG-TTTTGACATATTCTTTA
* * * * * * *
572577 ATAAAAACATCTTTTTTTTTTCAGAGACCATTTAATGCACAATGACATAAACTTTTTA
64 ATGAAAA-AT-GTCTTTTTTTCAAAGACTATTTAATGCACAATGAAATAAACTTTTCA
* * * *
572635 GTGATATATAATTTCAATTCAGTGATATATCACACAATTGAATGATGTCTTTAACATATTCTTTA
1 GTGATATATCACTTCAATTCAGTGATATATCAAAC-ATTGAATGATGT-TTTGACATATTCTTTA
* * * *
572700 ATGAAAAACGTCATTTCTTT-AAGAGATTATTTAATGCACAAGGAAATAAACTTTTCA
64 ATGAAAAATGTC-TTTTTTTCAA-AGACTATTTAATGCACAATGAAATAAACTTTTCA
* * * * * * *
572757 GTGATATATCACAT-AATTCAATGATGTACCAGAACATTGAATGATATTGTTGACAAATGCTTTA
1 GTGATATATCACTTCAATTCAGTGATATATCA-AACATTGAATGATGTT-TTGACATATTCTTTA
* *
572821 ATGAAAAATGTCTTTTTTCTCAAACACTATTTAATACACAATGATAA-AAACTTTTCA
64 ATGAAAAATGTCTTTTTT-TCAAAGACTATTTAATGCACAATGA-AATAAACTTTTCA
* * * * * *
572878 ATGCTCA-ATCACTTCATTTCAGTGATATATCATACAATTGAGTGATATTTT
1 GTGAT-ATATCACTTCAATTCAGTGATATATCAAAC-ATTGAATGATGTTTT
572929 TAACCATATT
Statistics
Matches: 240, Mismatches: 42, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
120 6 0.03
121 91 0.38
122 81 0.34
123 62 0.26
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.39
Consensus pattern (119 bp):
GTGATATATCACTTCAATTCAGTGATATATCAAACATTGAATGATGTTTTGACATATTCTTTAAT
GAAAAATGTCTTTTTTTCAAAGACTATTTAATGCACAATGAAATAAACTTTTCA
Found at i:573074 original size:25 final size:25
Alignment explanation
Indices: 573040--573103 Score: 119
Period size: 25 Copynumber: 2.6 Consensus size: 25
573030 GAGTTATTGT
573040 TTCTAATGTAATGTACGATTTAATG
1 TTCTAATGTAATGTACGATTTAATG
*
573065 TTCTAATGTAATGTAGGATTTAATG
1 TTCTAATGTAATGTACGATTTAATG
573090 TTCTAATGTAATGT
1 TTCTAATGTAATGT
573104 TTGTATTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.45
Consensus pattern (25 bp):
TTCTAATGTAATGTACGATTTAATG
Found at i:573583 original size:30 final size:30
Alignment explanation
Indices: 573512--573570 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
573502 AAAAAATCAC
*
573512 AAATCGATCATTAACGTTATCATTTGTTACA
1 AAAT-GATCACTAACGTTATCATTTGTTACA
*
573543 AAATGGTCACTAACGTTATCATTTGTTA
1 AAATGATCACTAACGTTATCATTTGTTA
573571 TATATTGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (30 bp):
AAATGATCACTAACGTTATCATTTGTTACA
Found at i:574509 original size:44 final size:44
Alignment explanation
Indices: 574455--574541 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
574445 AGTCAAACGA
* * * *
574455 TTAGTTAAATATGTTGAGTTAATTGGTTTAACGTGTCACGTCAG
1 TTAGTCAAATATGTTGAGTTAATTGATTTAACGAGTCAAGTCAG
*
574499 TTAGTCAAATATGTTGGGTTAATTGATTTAACGAGTCAAGTCA
1 TTAGTCAAATATGTTGAGTTAATTGATTTAACGAGTCAAGTCA
574542 ATATTTCGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (44 bp):
TTAGTCAAATATGTTGAGTTAATTGATTTAACGAGTCAAGTCAG
Found at i:578155 original size:26 final size:28
Alignment explanation
Indices: 578126--578180 Score: 101
Period size: 29 Copynumber: 1.9 Consensus size: 28
578116 GTCGACAACT
578126 ACCATTAAAGTTGATGTTGTCGTCGAACC
1 ACCATTAAAGTTGATGTTGTCGTCGAA-C
578155 ACCATTAAAGTTGATGTTGTCGTCGA
1 ACCATTAAAGTTGATGTTGTCGTCGA
578181 TCAACAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (28 bp):
ACCATTAAAGTTGATGTTGTCGTCGAAC
Found at i:578582 original size:3 final size:3
Alignment explanation
Indices: 578574--578602 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
578564 AGAGATATTC
578574 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
578603 ATGTACGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:579991 original size:31 final size:31
Alignment explanation
Indices: 579953--580046 Score: 163
Period size: 31 Copynumber: 3.0 Consensus size: 31
579943 AGGGTCGAGG
579953 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
579984 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
580015 GTTTACCTAGGTTCTTCGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
580046 G
1 G
580047 GTCCTTCGGG
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 60 0.98
32 1 0.02
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:580955 original size:18 final size:18
Alignment explanation
Indices: 580912--580955 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
580902 ACTTCCGTTG
*
580912 TTAAAGGAAATGTTGTTT
1 TTAAAGGTAATGTTGTTT
580930 TTAAAGGTAATGTTGTTT
1 TTAAAGGTAATGTTGTTT
580948 TTAAAGGT
1 TTAAAGGT
580956 TATGGATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (18 bp):
TTAAAGGTAATGTTGTTT
Found at i:581005 original size:26 final size:28
Alignment explanation
Indices: 580976--581035 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
580966 AGTATCACTG
* *
580976 ACCAAA-AA-AATGATTGAGCGTTTATT
1 ACCAAATAACAATGATGGAACGTTTATT
*
581002 ACCAAATAATCTATGATGGAACGTTTATT
1 ACCAAATAA-CAATGATGGAACGTTTATT
581031 ACCAA
1 ACCAA
581036 TAGTTGAGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 6 0.21
27 2 0.07
29 20 0.71
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (28 bp):
ACCAAATAACAATGATGGAACGTTTATT
Found at i:583262 original size:230 final size:229
Alignment explanation
Indices: 582859--583343 Score: 871
Period size: 230 Copynumber: 2.1 Consensus size: 229
582849 GTAAAGTATC
* *
582859 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTGGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTGGT
*
582924 TAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAATAATCAAATAATTTTG
66 TAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTG
* * *
582989 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACATTATTAAAAAAAATT
131 TGTGTAAATAAAATTATTAAATTAATATTGTAGGTGAAAAACATGAAACACTATTAAAAAAAATT
583054 GAAACATAAATTACATAACTTTAAAAAAAATATA
196 GAAACATAAATTACATAACTTTAAAAAAAATATA
*
583088 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATTATATTTTG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGT-GAAAACATATTTATTATTATATTTGG
*
583153 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATATTTTT
65 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTT
*
583218 TTGTGTAAATAAAATTATTAAATTAATATTGTAGGTGAAAAACATGAAACACTATTAAAAAAAAT
130 GTGTGTAAATAAAATTATTAAATTAATATTGTAGGTGAAAAACATGAAACACTATTAAAAAAAAT
*
583283 TGAAACATAAATTACATAACTTTAAAAAAAGTATA
195 TGAAACATAAATTACATAACTTTAAAAAAAATATA
583318 TATCATTTTTATAAAAGTGTCCATAC
1 TATCATTTTTATAAAAGTGTCCATAC
583344 GTATAAAAGT
Statistics
Matches: 245, Mismatches: 10, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
229 38 0.16
230 207 0.84
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (229 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTGGT
TAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTG
TGTGTAAATAAAATTATTAAATTAATATTGTAGGTGAAAAACATGAAACACTATTAAAAAAAATT
GAAACATAAATTACATAACTTTAAAAAAAATATA
Done.