Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 185 of 208
Found at i:57979148 original size:37 final size:37
Alignment explanation
Indices: 57979107--57979192 Score: 154
Period size: 37 Copynumber: 2.3 Consensus size: 37
57979097 TAATGCTTTC
**
57979107 TGCTATAATGTTGTCCTCCGCAAGTTTTATTTCAATT
1 TGCTATAATGTTGTCCTCCGCAAGTTTTATTGAAATT
57979144 TGCTATAATGTTGTCCTCCGCAAGTTTTATTGAAATT
1 TGCTATAATGTTGTCCTCCGCAAGTTTTATTGAAATT
57979181 TGCTATAATGTT
1 TGCTATAATGTT
57979193 TTATCTCACA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.45
Consensus pattern (37 bp):
TGCTATAATGTTGTCCTCCGCAAGTTTTATTGAAATT
Found at i:57981317 original size:33 final size:33
Alignment explanation
Indices: 57981252--57981317 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
57981242 GGTCCAACTC
*
57981252 AAATTTAATTTAAATAATAAAAAATTATTTTTA
1 AAATTTAATTTAAATAATAAAAAATTACTTTTA
*
57981285 AAATTTAAATTT-AATTAT-AAAAATATACTTTTA
1 AAATTT-AATTTAAATAATAAAAAAT-TACTTTTA
57981318 TTTTTTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 6 0.21
33 18 0.62
34 5 0.17
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (33 bp):
AAATTTAATTTAAATAATAAAAAATTACTTTTA
Found at i:57985476 original size:16 final size:16
Alignment explanation
Indices: 57985455--57985486 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
57985445 AATTTCACAC
57985455 CCTAATACAACTCATT
1 CCTAATACAACTCATT
57985471 CCTAATACAACTCATT
1 CCTAATACAACTCATT
57985487 GACTTGTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (16 bp):
CCTAATACAACTCATT
Found at i:57991714 original size:23 final size:23
Alignment explanation
Indices: 57991688--57991742 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
57991678 AATTAAAAAG
57991688 ATGAAAGCAT-TATAACTATCATT
1 ATGAAAGCATAT-TAACTATCATT
**
57991711 ATGAAAGCATATTAGTTATCATT
1 ATGAAAGCATATTAACTATCATT
57991734 ATGAAAGCA
1 ATGAAAGCA
57991743 AAAGATGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.33
Consensus pattern (23 bp):
ATGAAAGCATATTAACTATCATT
Found at i:57991775 original size:23 final size:23
Alignment explanation
Indices: 57991747--57991798 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
57991737 AAAGCAAAAG
57991747 ATGAAAGCAT-TATAGCTATCATT
1 ATGAAAGCATAT-TAGCTATCATT
*
57991770 ATGAAAGCATATTAGCTATTATT
1 ATGAAAGCATATTAGCTATCATT
57991793 ATGAAA
1 ATGAAA
57991799 CCAAGTTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (23 bp):
ATGAAAGCATATTAGCTATCATT
Found at i:57991775 original size:59 final size:59
Alignment explanation
Indices: 57991683--57991798 Score: 205
Period size: 59 Copynumber: 2.0 Consensus size: 59
57991673 TTAATAATTA
*
57991683 AAAAGATGAAAGCATTATAACTATCATTATGAAAGCATATTAGTTATCATTATGAAAGC
1 AAAAGATGAAAGCATTATAACTATCATTATGAAAGCATATTAGCTATCATTATGAAAGC
* *
57991742 AAAAGATGAAAGCATTATAGCTATCATTATGAAAGCATATTAGCTATTATTATGAAA
1 AAAAGATGAAAGCATTATAACTATCATTATGAAAGCATATTAGCTATCATTATGAAA
57991799 CCAAGTTACA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.31
Consensus pattern (59 bp):
AAAAGATGAAAGCATTATAACTATCATTATGAAAGCATATTAGCTATCATTATGAAAGC
Found at i:57991861 original size:9 final size:9
Alignment explanation
Indices: 57991849--57991880 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
57991839 ACAAATATTA
57991849 AAAATAAAC
1 AAAATAAAC
57991858 AAAATAAAC
1 AAAATAAAC
57991867 AAAATAAAC
1 AAAATAAAC
57991876 AAAAT
1 AAAAT
57991881 GCACCAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAATAAAC
Found at i:57996205 original size:36 final size:36
Alignment explanation
Indices: 57996158--57996230 Score: 121
Period size: 36 Copynumber: 2.0 Consensus size: 36
57996148 TTAATAATTA
*
57996158 AAAAGATGAAAGCA-TATTAGTTATCATTATGAAAGC
1 AAAAGATGAAAGCATTA-TAGCTATCATTATGAAAGC
57996194 AAAAGATGAAAGCATTATAGCTATCATTATGAAAGC
1 AAAAGATGAAAGCATTATAGCTATCATTATGAAAGC
57996230 A
1 A
57996231 TATTAGCTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 33 0.94
37 2 0.06
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (36 bp):
AAAAGATGAAAGCATTATAGCTATCATTATGAAAGC
Found at i:57996227 original size:23 final size:23
Alignment explanation
Indices: 57996199--57996250 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
57996189 AAAGCAAAAG
57996199 ATGAAAGCAT-TATAGCTATCATT
1 ATGAAAGCATAT-TAGCTATCATT
*
57996222 ATGAAAGCATATTAGCTATTATT
1 ATGAAAGCATATTAGCTATCATT
57996245 ATGAAA
1 ATGAAA
57996251 CCAAGTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (23 bp):
ATGAAAGCATATTAGCTATCATT
Found at i:57997897 original size:12 final size:12
Alignment explanation
Indices: 57997880--57997904 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57997870 TAGTCAATTA
57997880 AATTTTATTATT
1 AATTTTATTATT
57997892 AATTTTATTATT
1 AATTTTATTATT
57997904 A
1 A
57997905 CGTTGTGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
AATTTTATTATT
Found at i:58004715 original size:28 final size:29
Alignment explanation
Indices: 58004665--58004748 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 29
58004655 TAAATTGTTC
* * *
58004665 AGGGTTGTAGATTTTGGGGATTTTGGGTA
1 AGGGTTTTTGATTTTGGAGATTTTGGGTA
* * * * *
58004694 AGTG-TTTTGATTTTGGAAATTTTTGTTT
1 AGGGTTTTTGATTTTGGAGATTTTGGGTA
*
58004722 AGGGTTTTTAATTTTGGAGATTTTGGG
1 AGGGTTTTTGATTTTGGAGATTTTGGG
58004749 GATTTCTCAC
Statistics
Matches: 41, Mismatches: 13, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
28 20 0.49
29 21 0.51
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (29 bp):
AGGGTTTTTGATTTTGGAGATTTTGGGTA
Found at i:58006748 original size:33 final size:33
Alignment explanation
Indices: 58006711--58006776 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
58006701 AGTCCAACTC
58006711 AAATTT-AATTTAAATAATAAAA-AATTATTTTTA
1 AAATTTAAATTT-AATAATAAAATAA-TATTTTTA
*
58006744 AAATTTAAATTTAATTATAAAATAATATTTTTA
1 AAATTTAAATTTAATAATAAAATAATATTTTTA
58006777 TTTTTTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 23 0.77
34 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (33 bp):
AAATTTAAATTTAATAATAAAATAATATTTTTA
Found at i:58008899 original size:18 final size:18
Alignment explanation
Indices: 58008862--58008901 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
58008852 AGGATTTATT
* * *
58008862 TCTGTGTTTGTATTTGCA
1 TCTGTATTTGTATCTACA
58008880 TCTGTATTTGTATCTACA
1 TCTGTATTTGTATCTACA
58008898 TCTG
1 TCTG
58008902 ATTCTGCATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.17, T:0.53
Consensus pattern (18 bp):
TCTGTATTTGTATCTACA
Found at i:58009054 original size:53 final size:53
Alignment explanation
Indices: 58008974--58009076 Score: 206
Period size: 53 Copynumber: 1.9 Consensus size: 53
58008964 CTATTTCTGG
58008974 AATTGTTACTGTATTTGAGTCTATTCTGCCTGTTTGGGTTGAGTTACACATGT
1 AATTGTTACTGTATTTGAGTCTATTCTGCCTGTTTGGGTTGAGTTACACATGT
58009027 AATTGTTACTGTATTTGAGTCTATTCTGCCTGTTTGGGTTGAGTTACACA
1 AATTGTTACTGTATTTGAGTCTATTCTGCCTGTTTGGGTTGAGTTACACA
58009077 CTAAGCCTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.19, C:0.14, G:0.22, T:0.45
Consensus pattern (53 bp):
AATTGTTACTGTATTTGAGTCTATTCTGCCTGTTTGGGTTGAGTTACACATGT
Found at i:58014463 original size:3 final size:3
Alignment explanation
Indices: 58014455--58014481 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
58014445 ATTAAACCTA
58014455 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
58014482 TAATGCCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:58021963 original size:17 final size:18
Alignment explanation
Indices: 58021941--58021986 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
58021931 TATAAAATCA
*
58021941 TTTAAAAAAATCAAAAT-
1 TTTAAAAAAATAAAAATG
*
58021958 TTTAAAAATATAAAAATG
1 TTTAAAAAAATAAAAATG
*
58021976 TTTATAAAAAT
1 TTTAAAAAAAT
58021987 TATAGAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (18 bp):
TTTAAAAAAATAAAAATG
Found at i:58022006 original size:16 final size:17
Alignment explanation
Indices: 58021979--58022013 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
58021969 AAAAATGTTT
58021979 ATAAAAATTATAGAAAA
1 ATAAAAATTATAGAAAA
*
58021996 ATAAAAA-TATAGAGAA
1 ATAAAAATTATAGAAAA
58022012 AT
1 AT
58022014 TTTGTAGGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23
Consensus pattern (17 bp):
ATAAAAATTATAGAAAA
Found at i:58022011 original size:18 final size:17
Alignment explanation
Indices: 58021979--58022012 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
58021969 AAAAATGTTT
*
58021979 ATAAAAATTATAGAAAA
1 ATAAAAATTAGAGAAAA
58021996 ATAAAAATATAGAGAAA
1 ATAAAAAT-TAGAGAAA
58022013 TTTTGTAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (17 bp):
ATAAAAATTAGAGAAAA
Found at i:58027216 original size:15 final size:15
Alignment explanation
Indices: 58027191--58027233 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
58027181 AGAATTTGCA
58027191 AAACTGAAGCAAGAAG
1 AAAC-GAAGCAAGAAG
*
58027207 AATCGAAGCAAAGAAG
1 AAACGAAGC-AAGAAG
58027223 AAAC-AAGCAAG
1 AAACGAAGCAAG
58027234 CAAAGCAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 3 0.12
15 9 0.38
16 12 0.50
ACGTcount: A:0.58, C:0.14, G:0.23, T:0.05
Consensus pattern (15 bp):
AAACGAAGCAAGAAG
Found at i:58029971 original size:28 final size:28
Alignment explanation
Indices: 58029931--58029986 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
58029921 CTTCAAGAAG
58029931 TAGACCCAGCACAACCTAGTTAAATCAT
1 TAGACCCAGCACAACCTAGTTAAATCAT
58029959 TAGACCCAGCACAACCTAGTTAAATCAT
1 TAGACCCAGCACAACCTAGTTAAATCAT
58029987 CTATGAACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.29, G:0.11, T:0.21
Consensus pattern (28 bp):
TAGACCCAGCACAACCTAGTTAAATCAT
Found at i:58031803 original size:15 final size:15
Alignment explanation
Indices: 58031783--58031820 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
58031773 TTGCAAAATT
*
58031783 GAAGCAAGAAGAATC
1 GAAGCAAGAAGAAAC
58031798 GAAGCAAAGAAGAAAC
1 GAAGC-AAGAAGAAAC
58031814 -AAGCAAG
1 GAAGCAAG
58031821 CAAAGCAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 3 0.14
15 9 0.43
16 9 0.43
ACGTcount: A:0.58, C:0.13, G:0.26, T:0.03
Consensus pattern (15 bp):
GAAGCAAGAAGAAAC
Found at i:58032293 original size:19 final size:19
Alignment explanation
Indices: 58032269--58032306 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
58032259 AAATCCGGCC
58032269 TATGAGATAAACCATTCAG
1 TATGAGATAAACCATTCAG
58032288 TATGAGATAAACCATTCAG
1 TATGAGATAAACCATTCAG
58032307 ATTGAACTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (19 bp):
TATGAGATAAACCATTCAG
Found at i:58042110 original size:26 final size:28
Alignment explanation
Indices: 58042075--58042127 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 28
58042065 GGTAATTTTC
58042075 TTTCATTTGCTTCATTCATGAC-ATGCT
1 TTTCATTTGCTTCATTCATGACTATGCT
58042102 TTTC-TTTGCTTCATTCATGACTATGC
1 TTTCATTTGCTTCATTCATGACTATGC
58042128 AATGATTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.17, C:0.23, G:0.11, T:0.49
Consensus pattern (28 bp):
TTTCATTTGCTTCATTCATGACTATGCT
Found at i:58043996 original size:45 final size:45
Alignment explanation
Indices: 58043932--58044020 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
58043922 AAAATGTCTT
58043932 GAGTGAAAGAGTAAAAATGCATGATGCAGAGAGAGACATGGCATC
1 GAGTGAAAGAGTAAAAATGCATGATGCAGAGAGAGACATGGCATC
* *
58043977 GAGTGAAAGAGTTAAAATGCATGATGCAGTGAGAGACATGGCAT
1 GAGTGAAAGAGTAAAAATGCATGATGCAGAGAGAGACATGGCAT
58044021 TGTCGATCAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.40, C:0.10, G:0.31, T:0.18
Consensus pattern (45 bp):
GAGTGAAAGAGTAAAAATGCATGATGCAGAGAGAGACATGGCATC
Found at i:58047346 original size:30 final size:30
Alignment explanation
Indices: 58047312--58047405 Score: 170
Period size: 30 Copynumber: 3.1 Consensus size: 30
58047302 TCCATATTTA
58047312 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
58047342 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
58047372 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
58047403 TGG
1 TGG
58047406 CATTATAAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
30 54 0.87
31 8 0.13
ACGTcount: A:0.40, C:0.06, G:0.27, T:0.27
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:58047352 original size:15 final size:16
Alignment explanation
Indices: 58047310--58047390 Score: 80
Period size: 15 Copynumber: 5.3 Consensus size: 16
58047300 TATCCATATT
58047310 TATGGAAAGTCAAAGA
1 TATGGAAAGTCAAAGA
** *
58047326 TATGGGTA-TCAAATA
1 TATGGAAAGTCAAAGA
58047341 T-TGGAAAGTCAAAGA
1 TATGGAAAGTCAAAGA
** *
58047356 TATGGGTA-TCAAATA
1 TATGGAAAGTCAAAGA
58047371 T-TGGAAAGTCAAAGA
1 TATGGAAAGTCAAAGA
58047386 TATGG
1 TATGG
58047391 GTATCGAGAT
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
14 8 0.16
15 28 0.57
16 13 0.27
ACGTcount: A:0.43, C:0.06, G:0.25, T:0.26
Consensus pattern (16 bp):
TATGGAAAGTCAAAGA
Found at i:58052006 original size:30 final size:31
Alignment explanation
Indices: 58051972--58052035 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
58051962 TCCATATTTA
58051972 TGGAAAGTCAAAGATATGGGTATC-AAATAT
1 TGGAAAGTCAAAGATATGGGTATCGAAATAT
*
58052002 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATCGAAATAT
58052033 TGG
1 TGG
58052036 CATTATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 24 0.75
31 8 0.25
ACGTcount: A:0.39, C:0.06, G:0.28, T:0.27
Consensus pattern (31 bp):
TGGAAAGTCAAAGATATGGGTATCGAAATAT
Found at i:58052012 original size:15 final size:16
Alignment explanation
Indices: 58051970--58052020 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 16
58051960 TATCCATATT
58051970 TATGGAAAGTCAAAGA
1 TATGGAAAGTCAAAGA
** *
58051986 TATGGGTA-TCAAATA
1 TATGGAAAGTCAAAGA
58052001 T-TGGAAAGTCAAAGA
1 TATGGAAAGTCAAAGA
58052016 TATGG
1 TATGG
58052021 GTATCGAGAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 4 0.15
15 14 0.52
16 9 0.33
ACGTcount: A:0.43, C:0.06, G:0.25, T:0.25
Consensus pattern (16 bp):
TATGGAAAGTCAAAGA
Found at i:58059559 original size:40 final size:40
Alignment explanation
Indices: 58059464--58059547 Score: 123
Period size: 40 Copynumber: 2.0 Consensus size: 40
58059454 ATTATTAACT
* * *
58059464 ATGATCAATATATTTTAAGTCATGGTAACTTTATAAATAC
1 ATGATCAATATATTTTAAGTCATGGTAACTTAATAAAAAA
58059504 ATGATCAATATATTTTAAGTCATGGTAACTTAAATAATAAAA
1 ATGATCAATATATTTTAAGTCATGGTAACTT-AATAA-AAAA
58059546 AT
1 AT
58059548 ATTTTATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
40 31 0.79
41 4 0.10
42 4 0.10
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (40 bp):
ATGATCAATATATTTTAAGTCATGGTAACTTAATAAAAAA
Found at i:58062572 original size:14 final size:15
Alignment explanation
Indices: 58062550--58062626 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
58062540 CAATCAAACA
58062550 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
58062564 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
58062579 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
58062599 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
58062613 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
58062627 ACTGCCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:58062591 original size:20 final size:20
Alignment explanation
Indices: 58062566--58062605 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
58062556 AATATTTTCC
*
58062566 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
58062586 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
58062606 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:58062611 original size:34 final size:35
Alignment explanation
Indices: 58062554--58062620 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
58062544 CAAACACCAG
*
58062554 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
58062589 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
58062621 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:58062627 original size:14 final size:14
Alignment explanation
Indices: 58062589--58062628 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
58062579 ACAGAAAAGT
*
58062589 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
58062603 AAATCATTTTACGG
1 AAAACATTTTACAG
58062617 AAAACATTTTAC
1 AAAACATTTTAC
58062629 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:58063793 original size:17 final size:17
Alignment explanation
Indices: 58063752--58063794 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
58063742 AATTCAAAAT
* * *
58063752 AATTTTTAAATTTTTAA
1 AATTTATAAAATTTCAA
58063769 ATATTTATAAAATTTCAA
1 A-ATTTATAAAATTTCAA
58063787 AATTTATA
1 AATTTATA
58063795 TTTTAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTTATAAAATTTCAA
Found at i:58063813 original size:25 final size:24
Alignment explanation
Indices: 58063772--58063820 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
58063762 TTTTTAAATA
* * *
58063772 TTTATAAAATTTCAAAATTTATAT
1 TTTAAAAAATTTAAAAATATATAT
58063796 TTTAAAAAATTCTAAAAATATATAT
1 TTTAAAAAATT-TAAAAATATATAT
58063821 AAATAAAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTAAAAAATTTAAAAATATATAT
Found at i:58077044 original size:26 final size:27
Alignment explanation
Indices: 58077015--58077068 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
58077005 TATCTACTTT
58077015 CTTTAATTTGCTTCATTCATGAC-ATG
1 CTTTAATTTGCTTCATTCATGACTATG
**
58077041 CTTTTCTTTGCTTCATTCATGACTATG
1 CTTTAATTTGCTTCATTCATGACTATG
58077068 C
1 C
58077069 AATGATTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.48
Consensus pattern (27 bp):
CTTTAATTTGCTTCATTCATGACTATG
Found at i:58089956 original size:14 final size:14
Alignment explanation
Indices: 58089937--58089965 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
58089927 TCATGCATAA
58089937 ATGAAAATGTTCCG
1 ATGAAAATGTTCCG
58089951 ATGAAAATGTTCCG
1 ATGAAAATGTTCCG
58089965 A
1 A
58089966 CATGGTCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (14 bp):
ATGAAAATGTTCCG
Found at i:58092054 original size:44 final size:44
Alignment explanation
Indices: 58091963--58092056 Score: 111
Period size: 45 Copynumber: 2.1 Consensus size: 44
58091953 AAACTAATAG
* * * *
58091963 AAAAGAAAAAAAAACCCAGAAATTTATAAACATGAGATAAAATGA
1 AAAACAAAAAAAAACCCAGAAA-TTAAAAACATAAGATAAAAAGA
58092008 AAAACAAAAAAAAACCCAGAAA-TAAAAACATAAGA-AATGAAAGA
1 AAAACAAAAAAAAACCCAGAAATTAAAAACATAAGATAA--AAAGA
58092052 AAAAC
1 AAAAC
58092057 TAGATGATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
42 2 0.05
43 11 0.26
44 9 0.21
45 21 0.49
ACGTcount: A:0.69, C:0.11, G:0.10, T:0.11
Consensus pattern (44 bp):
AAAACAAAAAAAAACCCAGAAATTAAAAACATAAGATAAAAAGA
Found at i:58092578 original size:21 final size:23
Alignment explanation
Indices: 58092546--58092588 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
58092536 TATTTATTTC
58092546 TTTTAAATATTAA-A-AAAATTA
1 TTTTAAATATTAATATAAAATTA
58092567 TTTT-AATAATTAATATAAAATT
1 TTTTAAAT-ATTAATATAAAATT
58092589 TTGACATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 3 0.16
21 9 0.47
22 1 0.05
23 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTTAAATATTAATATAAAATTA
Found at i:58094809 original size:31 final size:30
Alignment explanation
Indices: 58094768--58094826 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
58094758 TACAAAACGA
*
58094768 TTACTAAACTATTCGAAAGTTTTCATTTAAG
1 TTACTAAACTATTCGAAAATTTT-ATTTAAG
* *
58094799 TTACTTAACTATTTGAAAATTTTATTTA
1 TTACTAAACTATTCGAAAATTTTATTTA
58094827 GGCCATTAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (30 bp):
TTACTAAACTATTCGAAAATTTTATTTAAG
Found at i:58096632 original size:60 final size:60
Alignment explanation
Indices: 58096506--58096624 Score: 148
Period size: 60 Copynumber: 2.0 Consensus size: 60
58096496 TATATTTTTT
* ** * * * * *
58096506 AATTTTTAGAGTTAGGACTAAATTAATAGATTTTGTAAATATTGAGGGTTAAATTTATTA
1 AATTTTTAGAATTAAAACTAAAATAATAAATTTTGTAAACATTGAGAGATAAATTTATTA
* *
58096566 AATTTTTAGAATTAAAACTAAAATGATAAATTTTGTAAACATTTAGAGATAAATTTATT
1 AATTTTTAGAATTAAAACTAAAATAATAAATTTTGTAAACATTGAGAGATAAATTTATT
58096625 GATTTTTTTA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.43, C:0.03, G:0.13, T:0.42
Consensus pattern (60 bp):
AATTTTTAGAATTAAAACTAAAATAATAAATTTTGTAAACATTGAGAGATAAATTTATTA
Found at i:58099883 original size:26 final size:26
Alignment explanation
Indices: 58099852--58099954 Score: 102
Period size: 26 Copynumber: 4.0 Consensus size: 26
58099842 TTTTATCATC
*
58099852 ATTTATTTTAAGTTTTTATATATATT
1 ATTTATTTTAAATTTTTATATATATT
* * *
58099878 ATTTATTTTAAGCTATTT-TACATATT
1 ATTTATTTTAA-ATTTTTATATATATT
* *
58099904 ATTTA-TTTAAATTTCTTTTATGTATT
1 ATTTATTTTAAATTT-TTATATATATT
* *
58099930 ATTTATTTTAAACTATTATATATAT
1 ATTTATTTTAAATTTTTATATATAT
58099955 CTTTCAAATT
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
24 2 0.03
25 7 0.11
26 42 0.68
27 11 0.18
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (26 bp):
ATTTATTTTAAATTTTTATATATATT
Found at i:58099969 original size:21 final size:24
Alignment explanation
Indices: 58099945--58099995 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 24
58099935 TTTTAAACTA
*
58099945 TTATATATA-TCTTTCAAA-T-TT
1 TTATATATATTCTTTAAAACTGTT
*
58099966 TTATATTTATTCTTTAAAACTGTT
1 TTATATATATTCTTTAAAACTGTT
58099990 TTATAT
1 TTATAT
58099996 GTTATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.32
22 8 0.32
23 1 0.04
24 8 0.32
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.59
Consensus pattern (24 bp):
TTATATATATTCTTTAAAACTGTT
Found at i:58100013 original size:37 final size:38
Alignment explanation
Indices: 58099963--58100039 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
58099953 ATCTTTCAAA
*
58099963 TTTTTATATTTA-TTCTTTAAAACTGTTTTATATGTTAT
1 TTTTTATATTTATTTATTTAAAACTGTTTTAT-TGTTAT
* *
58100001 TTTTTATA-TTATTTATTTTAAATTGTTTTATTGTTAT
1 TTTTTATATTTATTTATTTAAAACTGTTTTATTGTTAT
58100038 TT
1 TT
58100040 ATTTTTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
37 11 0.31
38 24 0.69
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.68
Consensus pattern (38 bp):
TTTTTATATTTATTTATTTAAAACTGTTTTATTGTTAT
Found at i:58100062 original size:25 final size:24
Alignment explanation
Indices: 58099999--58100067 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 24
58099989 TTTATATGTT
58099999 ATTTTTTATA-TTATTTATTTTAA
1 ATTTTTTATATTTATTTATTTTAA
**
58100022 ATTGTTTTAT-TGTTATTTATTTTTC
1 ATT-TTTTATAT-TTATTTATTTTAA
*
58100047 ATTTTTTATATTT-TATATTTT
1 ATTTTTTATATTTATTTATTTT
58100068 GTTTATTTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 10 0.26
24 14 0.36
25 15 0.38
ACGTcount: A:0.23, C:0.01, G:0.03, T:0.72
Consensus pattern (24 bp):
ATTTTTTATATTTATTTATTTTAA
Found at i:58100067 original size:14 final size:14
Alignment explanation
Indices: 58099988--58100067 Score: 51
Period size: 14 Copynumber: 5.8 Consensus size: 14
58099978 TTTAAAACTG
* *
58099988 TTTTATATGTTATT
1 TTTTATATTTTATA
58100002 TTTTATATTATT-TA
1 TTTTATATT-TTATA
* *
58100016 TTTTAAATTGTTTTA
1 TTTTATATT-TTATA
*
58100031 TTGT-TA-TTTAT-
1 TTTTATATTTTATA
*
58100042 TTTTCATTTTTTATA
1 TTTT-ATATTTTATA
58100057 TTTTATATTTT
1 TTTTATATTTT
58100068 GTTTATTTGA
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
11 3 0.06
12 3 0.06
13 2 0.04
14 31 0.62
15 11 0.22
ACGTcount: A:0.23, C:0.01, G:0.04, T:0.72
Consensus pattern (14 bp):
TTTTATATTTTATA
Found at i:58100686 original size:30 final size:30
Alignment explanation
Indices: 58100650--58100710 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
58100640 AAAAAGATCA
58100650 TATTTTAAAATCTTTTTCAAAATTTCAACT
1 TATTTTAAAATCTTTTTCAAAATTTCAACT
58100680 TATTTTAAAATCTTTTTCAAAATTTCAACT
1 TATTTTAAAATCTTTTTCAAAATTTCAACT
58100710 T
1 T
58100711 TCGGCATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (30 bp):
TATTTTAAAATCTTTTTCAAAATTTCAACT
Found at i:58104055 original size:32 final size:33
Alignment explanation
Indices: 58103973--58104056 Score: 107
Period size: 38 Copynumber: 2.4 Consensus size: 33
58103963 AGAATAGCAT
58103973 ATGTTGGAATCCCTATAATTAAAGATAGAAATC
1 ATGTTGGAATCCCTATAATTAAAGATAGAAATC
*
58104006 TGATGGTATTGGAATCCCTATAATTAAGGATAGAAATC
1 --AT-G--TTGGAATCCCTATAATTAAAGATAGAAATC
58104044 -TGTTGGAATCCCT
1 ATGTTGGAATCCCT
58104057 TGTAAATAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
32 11 0.24
34 1 0.02
35 3 0.07
36 1 0.02
38 29 0.64
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (33 bp):
ATGTTGGAATCCCTATAATTAAAGATAGAAATC
Found at i:58107897 original size:32 final size:33
Alignment explanation
Indices: 58107816--58107898 Score: 114
Period size: 38 Copynumber: 2.4 Consensus size: 33
58107806 TGAGGGGGAG
58107816 TGTTGGAATCCCTATAATTAAGGATAGAAATCTGA
1 TGTTGGAATCCCTATAATTAAGGATAGAAATC--A
58107851 TGGTATTGGAATCCCTATAATTAAGGATAGAAATC-
1 T-G--TTGGAATCCCTATAATTAAGGATAGAAATCA
58107886 TGTTGGAATCCCT
1 TGTTGGAATCCCT
58107899 TGTAAATAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
32 11 0.24
34 1 0.02
35 2 0.04
36 1 0.02
38 30 0.67
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (33 bp):
TGTTGGAATCCCTATAATTAAGGATAGAAATCA
Found at i:58110536 original size:13 final size:13
Alignment explanation
Indices: 58110518--58110543 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58110508 CTTTTGTAAC
58110518 TTAGTGAAGATGG
1 TTAGTGAAGATGG
58110531 TTAGTGAAGATGG
1 TTAGTGAAGATGG
58110544 CCTCCGGTTA
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:0.31, C:0.00, G:0.38, T:0.31
Consensus pattern (13 bp):
TTAGTGAAGATGG
Found at i:58112026 original size:16 final size:16
Alignment explanation
Indices: 58111994--58112027 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
58111984 CAAGAGCGTT
**
58111994 TGCAAAGAAGATTACA
1 TGCAAAGAAGAAGACA
58112010 TGCAAAGAAGAAGACA
1 TGCAAAGAAGAAGACA
58112026 TG
1 TG
58112028 TTTCAATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.24, T:0.15
Consensus pattern (16 bp):
TGCAAAGAAGAAGACA
Found at i:58113591 original size:16 final size:17
Alignment explanation
Indices: 58113570--58113602 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
58113560 TTCAATGGTA
58113570 ATTTTGAATTT-ATTTG
1 ATTTTGAATTTAATTTG
*
58113586 ATTTTGTATTTAATTTG
1 ATTTTGAATTTAATTTG
58113603 TCAAATACGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (17 bp):
ATTTTGAATTTAATTTG
Found at i:58118196 original size:20 final size:21
Alignment explanation
Indices: 58118171--58118215 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
58118161 AAATATAAAA
* *
58118171 TTTGAAATTTTTATAAA-TAT
1 TTTGAAATTTTAAAAAATTAT
58118191 TTTG-AATTTTAAAAAATTAT
1 TTTGAAATTTTAAAAAATTAT
58118211 TTTGA
1 TTTGA
58118216 TTTTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (21 bp):
TTTGAAATTTTAAAAAATTAT
Found at i:58118198 original size:19 final size:20
Alignment explanation
Indices: 58118171--58118220 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
58118161 AAATATAAAA
*
58118171 TTTGAAATTTTTATAAA-TAT
1 TTTG-AATTTTTAAAAATTAT
*
58118191 TTTGAATTTTAAAAAATTAT
1 TTTGAATTTTTAAAAATTAT
58118211 TTTG-ATTTTT
1 TTTGAATTTTT
58118221 TTTTATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (20 bp):
TTTGAATTTTTAAAAATTAT
Found at i:58120346 original size:20 final size:20
Alignment explanation
Indices: 58120321--58120370 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
58120311 TGATGAAATT
*
58120321 ACTTCATTGTGCTTAGTGGC
1 ACTTCATTGTGCTTAGTGAC
*
58120341 ACTTCATTATGCTTAGTGAC
1 ACTTCATTGTGCTTAGTGAC
*
58120361 ACTTCCTTGT
1 ACTTCATTGT
58120371 TCTTCTGCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (20 bp):
ACTTCATTGTGCTTAGTGAC
Found at i:58121930 original size:17 final size:17
Alignment explanation
Indices: 58121900--58121934 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
58121890 AATCAAGCAC
*
58121900 CCTTAATGCTAGAATGG
1 CCTTAATGCAAGAATGG
*
58121917 CCTTAGTGCAAGAATGG
1 CCTTAATGCAAGAATGG
58121934 C
1 C
58121935 ATCCTGGTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (17 bp):
CCTTAATGCAAGAATGG
Found at i:58126313 original size:18 final size:18
Alignment explanation
Indices: 58126287--58126322 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
58126277 TTTTATATAT
* *
58126287 TTTTTAAAACATTATAAA
1 TTTTAAAAAAATTATAAA
58126305 TTTTAAAAAAATTATAAA
1 TTTTAAAAAAATTATAAA
58126323 GAATATATAA
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:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTTAAAAAAATTATAAA
Found at i:58129548 original size:16 final size:16
Alignment explanation
Indices: 58129527--58129559 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
58129517 CATTTGACCG
58129527 ATTAATACATAAATAT
1 ATTAATACATAAATAT
58129543 ATTAATACATAAATAT
1 ATTAATACATAAATAT
58129559 A
1 A
58129560 AATTTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTAATACATAAATAT
Found at i:58129618 original size:42 final size:38
Alignment explanation
Indices: 58129535--58129619 Score: 91
Period size: 38 Copynumber: 2.1 Consensus size: 38
58129525 CGATTAATAC
* * *
58129535 ATAAATATATTAATACATAAATATAAATTTTTTATGTT
1 ATAAATATATTAATACATAAAAATAAATTTTATATATT
58129573 ATAAAT-TATATAATACATAAAAATAACATAATTTAATATATT
1 ATAAATATAT-TAATACATAAAAATAA-AT--TTT-ATATATT
58129615 ATAAA
1 ATAAA
58129620 ATTAAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
37 3 0.08
38 21 0.54
39 2 0.05
41 3 0.08
42 10 0.26
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (38 bp):
ATAAATATATTAATACATAAAAATAAATTTTATATATT
Found at i:58135795 original size:18 final size:18
Alignment explanation
Indices: 58135772--58135828 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
58135762 CCCAACTACT
*
58135772 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
58135790 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
58135808 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
58135826 GTA
1 GTA
58135829 AACGGTCGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:58146705 original size:18 final size:18
Alignment explanation
Indices: 58146663--58146697 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
58146653 AAGAATCTGT
58146663 GATAGATGAGGAATTTCA
1 GATAGATGAGGAATTTCA
58146681 GATAGATGAGGAATTTC
1 GATAGATGAGGAATTTC
58146698 CGGTAGATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.06, G:0.29, T:0.29
Consensus pattern (18 bp):
GATAGATGAGGAATTTCA
Found at i:58146975 original size:64 final size:64
Alignment explanation
Indices: 58146874--58146997 Score: 239
Period size: 64 Copynumber: 1.9 Consensus size: 64
58146864 ATATATGTCC
58146874 AATATGAATAAATTTGAAGAGTACATCTCCTTATCCATGTTTAAATATATATCCAACATGTTTA
1 AATATGAATAAATTTGAAGAGTACATCTCCTTATCCATGTTTAAATATATATCCAACATGTTTA
*
58146938 AATATGAATAAATTTGAAGAGTACATCTCCTTATCCATGTTTAAATATGTATCCAACATG
1 AATATGAATAAATTTGAAGAGTACATCTCCTTATCCATGTTTAAATATATATCCAACATG
58146998 GATACAAAGA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (64 bp):
AATATGAATAAATTTGAAGAGTACATCTCCTTATCCATGTTTAAATATATATCCAACATGTTTA
Found at i:58161538 original size:18 final size:18
Alignment explanation
Indices: 58161510--58161545 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
58161500 AAATTTATAT
*
58161510 TTTTTAAAAAATTATAAA
1 TTTTAAAAAAATTATAAA
*
58161528 TTTTAAAAAAATTCTAAA
1 TTTTAAAAAAATTATAAA
58161546 GAATATATAA
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:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTTAAAAAAATTATAAA
Found at i:58175309 original size:26 final size:27
Alignment explanation
Indices: 58175263--58175319 Score: 66
Period size: 26 Copynumber: 2.1 Consensus size: 27
58175253 GAATGAAAAG
58175263 AAATTTTATAATTAATATA-TTAATTA
1 AAATTTTATAATTAATATATTTAATTA
*
58175289 AAATTTTAT-A-TAATGAGTATTTAATTG
1 AAATTTTATAATTAAT-A-TATTTAATTA
58175316 AAAT
1 AAAT
58175320 CATAAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 4 0.15
25 2 0.07
26 11 0.41
27 10 0.37
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (27 bp):
AAATTTTATAATTAATATATTTAATTA
Found at i:58175590 original size:52 final size:52
Alignment explanation
Indices: 58175528--58175632 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
58175518 CAGCTGCTGG
* * *
58175528 ACCTGCCAGGAAAAGTCTTTTGTTTGGACCCAAAATCTGGAAAAATATGTGT
1 ACCTGCCAGGAAAAGTCTTTGGTTTGGACCCAAAAACAGGAAAAATATGTGT
58175580 ACCTGCCAGGAAAAGTCTTTGGTTTGGACCCAAAAACAGGAAAAATATGTGT
1 ACCTGCCAGGAAAAGTCTTTGGTTTGGACCCAAAAACAGGAAAAATATGTGT
58175632 A
1 A
58175633 TCTCCAATGA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (52 bp):
ACCTGCCAGGAAAAGTCTTTGGTTTGGACCCAAAAACAGGAAAAATATGTGT
Found at i:58179435 original size:111 final size:111
Alignment explanation
Indices: 58179100--58179435 Score: 484
Period size: 111 Copynumber: 3.0 Consensus size: 111
58179090 AAAAAAAATT
* *
58179100 ATTTATTTTTATTTTTTTCGTATTTTTTTATCTGATTCTGACACGAAAAAAAAATAATTTTTTTT
1 ATTTTTTTTTA-TTTTTTCGTA-TTTTTTATCTGATTCTGACACG-AAAAAAAATAAATTTTTTT
*
58179165 CTTTCTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCC-AAA
63 CTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAA
58179213 ATTTTTTTATT-TTTTTTCGTATTTTTTATCTGATTCTGACAC--AAAAAAATAAATTTTTTTTT
1 ATTTTTTT-TTATTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAAATAAA--TTTTTTT
*
58179275 CTTTGTACTGTGTACTGGGTGCCGGCTATTGACAGGCCAGCACCCAAAA
63 CTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAA
* ****
58179324 ATTTTTTTTTAATTTTTTCGTATTTTTTATCTTATTCTGACACGAAAAAAAATAAAAAAATTT-T
1 ATTTTTTTTT-ATTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAAATAAATTTTTTTCT
*
58179388 TTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGAACCCAAAA
65 TTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAA
58179435 A
1 A
58179436 AATAATTTTT
Statistics
Matches: 204, Mismatches: 11, Indels: 18
0.88 0.05 0.08
Matches are distributed among these distances:
108 10 0.05
110 52 0.25
111 79 0.39
112 43 0.21
113 7 0.03
114 13 0.06
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (111 bp):
ATTTTTTTTTATTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAAATAAATTTTTTTCTT
TGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAA
Found at i:58179807 original size:11 final size:11
Alignment explanation
Indices: 58179788--58179839 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
58179778 AAAAAAAGCC
58179788 TACTATTTTCT
1 TACTATTTTCT
* **
58179799 TACTGTTTTGA
1 TACTATTTTCT
*
58179810 TACTATTTTTT
1 TACTATTTTCT
*
58179821 TATTATTTTCT
1 TACTATTTTCT
58179832 TACT-TTTT
1 TACTATTTT
58179840 TACTATCATT
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
10 4 0.12
11 28 0.88
ACGTcount: A:0.17, C:0.12, G:0.04, T:0.67
Consensus pattern (11 bp):
TACTATTTTCT
Found at i:58179857 original size:33 final size:32
Alignment explanation
Indices: 58179791--58179859 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 32
58179781 AAAAGCCTAC
*
58179791 TATTTTCTTACTGTTTTGATACTATTTTTTTAT
1 TATTTTCTTACTGTTTT-ATACTATTTTATTAT
58179824 TATTTTCTTACT-TTTT-TACTATCATTTCATTAT
1 TATTTTCTTACTGTTTTATACTAT--TTT-ATTAT
58179857 TAT
1 TAT
58179860 GTTACTACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
30 6 0.19
32 7 0.22
33 19 0.59
ACGTcount: A:0.20, C:0.12, G:0.03, T:0.65
Consensus pattern (32 bp):
TATTTTCTTACTGTTTTATACTATTTTATTAT
Found at i:58179999 original size:13 final size:13
Alignment explanation
Indices: 58179981--58180005 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58179971 TATTTAAGTA
58179981 TAAATTTATTTTT
1 TAAATTTATTTTT
58179994 TAAATTTATTTT
1 TAAATTTATTTT
58180006 CAATTTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TAAATTTATTTTT
Found at i:58186891 original size:22 final size:22
Alignment explanation
Indices: 58186850--58186891 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
58186840 AAAAAAAAAC
* *
58186850 TACTATTTTCTTGTTGTTTTGA
1 TACTATTTTCTTATTATTTTGA
58186872 TACTATTTTCTTATTATTTT
1 TACTATTTTCTTATTATTTT
58186892 CTTACTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.67
Consensus pattern (22 bp):
TACTATTTTCTTATTATTTTGA
Found at i:58186897 original size:22 final size:22
Alignment explanation
Indices: 58186850--58186902 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
58186840 AAAAAAAAAC
* * *
58186850 TACTATTTTCTTGTTGTTTTGA
1 TACTATTTTCTTATTATTTTCA
*
58186872 TACTATTTTCTTATTATTTTCT
1 TACTATTTTCTTATTATTTTCA
*
58186894 TACTTTTTT
1 TACTATTTT
58186903 ACTATCATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.15, C:0.11, G:0.06, T:0.68
Consensus pattern (22 bp):
TACTATTTTCTTATTATTTTCA
Found at i:58187061 original size:13 final size:13
Alignment explanation
Indices: 58187043--58187067 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58187033 TATTTAAGTA
58187043 TAAATTTATTTTT
1 TAAATTTATTTTT
58187056 TAAATTTATTTT
1 TAAATTTATTTT
58187068 CAATTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TAAATTTATTTTT
Found at i:58187137 original size:16 final size:17
Alignment explanation
Indices: 58187098--58187139 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
58187088 ATTTTAATGT
58187098 TTTTTTATA-TTTTAGA
1 TTTTTTATATTTTTAGA
* *
58187114 TGTATTATATTTTTA-A
1 TTTTTTATATTTTTAGA
58187130 TTTTTTATAT
1 TTTTTTATAT
58187140 ATAAAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (17 bp):
TTTTTTATATTTTTAGA
Found at i:58199119 original size:3 final size:3
Alignment explanation
Indices: 58199111--58199148 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
58199101 CTATTTTTCG
*
58199111 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
58199149 GTTCGTTAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:58205656 original size:82 final size:82
Alignment explanation
Indices: 58205519--58205682 Score: 328
Period size: 82 Copynumber: 2.0 Consensus size: 82
58205509 AAATAAACTT
58205519 AATAAAAATGAAATTTTATTGAATAAATGAAAGGAACAAAAGTAGAGCTTTTTGGGAGAGGGAGC
1 AATAAAAATGAAATTTTATTGAATAAATGAAAGGAACAAAAGTAGAGCTTTTTGGGAGAGGGAGC
58205584 TTTTACAGAAAAGATGA
66 TTTTACAGAAAAGATGA
58205601 AATAAAAATGAAATTTTATTGAATAAATGAAAGGAACAAAAGTAGAGCTTTTTGGGAGAGGGAGC
1 AATAAAAATGAAATTTTATTGAATAAATGAAAGGAACAAAAGTAGAGCTTTTTGGGAGAGGGAGC
58205666 TTTTACAGAAAAGATGA
66 TTTTACAGAAAAGATGA
58205683 GTGAAATTTG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.46, C:0.05, G:0.23, T:0.26
Consensus pattern (82 bp):
AATAAAAATGAAATTTTATTGAATAAATGAAAGGAACAAAAGTAGAGCTTTTTGGGAGAGGGAGC
TTTTACAGAAAAGATGA
Found at i:58206935 original size:22 final size:22
Alignment explanation
Indices: 58206910--58206952 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
58206900 TATCTTAATA
*
58206910 ATAACAACAAAATTGTAACAAC
1 ATAACAACAAAATAGTAACAAC
* *
58206932 ATAATAATAAAATAGTAACAA
1 ATAACAACAAAATAGTAACAA
58206953 AGTAGTGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.63, C:0.12, G:0.05, T:0.21
Consensus pattern (22 bp):
ATAACAACAAAATAGTAACAAC
Found at i:58212763 original size:72 final size:71
Alignment explanation
Indices: 58212684--58212892 Score: 222
Period size: 72 Copynumber: 2.9 Consensus size: 71
58212674 GAATTCATCA
* * *
58212684 ACTCAATTGGTTTCTTGACAAGCCTAATTGAGTGAGTTGCAATAGGTTTCCCAATGATTTTGGAA
1 ACTCAATTGG-TTCTTGACAAGCCTAAATGAGTGAGTTGCAAGAGGTTTCCCAATGATCTTGGAA
58212749 TCTGTCC
65 TCTGTCC
* * * * * **
58212756 ACTCAATTGGTTCTAATG-GAAGCTTAAATAAGTGAGTTGCAAGATGTTACCCAATGATCTTAAA
1 ACTCAATTGGTTCT--TGACAAGCCTAAATGAGTGAGTTGCAAGAGGTTTCCCAATGATCTTGGA
*
58212820 ATTTGTCC
64 ATCTGTCC
** * * * *
58212828 ACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGTTGCAAGAGATTTTCCAGTGATCTTGGAA
1 ACTCAATTGGTTC-TTGACAAGCCTAAATGAGTGAGTTGCAAGAGGTTTCCCAATGATCTTGGAA
58212893 CCGTTGTTGA
Statistics
Matches: 109, Mismatches: 24, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
71 5 0.05
72 102 0.94
73 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (71 bp):
ACTCAATTGGTTCTTGACAAGCCTAAATGAGTGAGTTGCAAGAGGTTTCCCAATGATCTTGGAAT
CTGTCC
Found at i:58215253 original size:11 final size:11
Alignment explanation
Indices: 58215216--58215305 Score: 50
Period size: 11 Copynumber: 8.5 Consensus size: 11
58215206 ATATTTTTTA
*
58215216 TTTTTAAAAAT
1 TTTTTAAAATT
*
58215227 ATTTTAAAATACT
1 TTTTTAAAAT--T
58215240 TTTTTAAAA-T
1 TTTTTAAAATT
58215250 TTTTT---A--
1 TTTTTAAAATT
*
58215256 TTTTTAAAATA
1 TTTTTAAAATT
58215267 TTTTTAAAATACT
1 TTTTTAAAAT--T
*
58215280 TTTTTAAAAAT
1 TTTTTAAAATT
*
58215291 TTTCT-AAATT
1 TTTTTAAAATT
58215301 TTTTT
1 TTTTT
58215306 GTGTTTATTT
Statistics
Matches: 62, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
6 5 0.08
7 1 0.02
9 1 0.02
10 14 0.23
11 23 0.37
13 18 0.29
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTTAAAATT
Found at i:58215261 original size:16 final size:17
Alignment explanation
Indices: 58215240--58215272 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
58215230 TTAAAATACT
58215240 TTTTTAAAAT-TTTTTA
1 TTTTTAAAATATTTTTA
58215256 TTTTTAAAATATTTTTA
1 TTTTTAAAATATTTTTA
58215273 AAATACTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTAAAATATTTTTA
Found at i:58215265 original size:39 final size:41
Alignment explanation
Indices: 58215208--58215293 Score: 149
Period size: 40 Copynumber: 2.1 Consensus size: 41
58215198 ATAAATATAT
58215208 ATTTTTTATTTTTAAAAATA-TTTTAAAATACTTTTTTAAA
1 ATTTTTTATTTTTAAAAATATTTTTAAAATACTTTTTTAAA
58215248 ATTTTTTATTTTT-AAAATATTTTTAAAATACTTTTTTAAA
1 ATTTTTTATTTTTAAAAATATTTTTAAAATACTTTTTTAAA
*
58215288 AATTTT
1 ATTTTT
58215294 CTAAATTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
39 6 0.14
40 38 0.86
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.59
Consensus pattern (41 bp):
ATTTTTTATTTTTAAAAATATTTTTAAAATACTTTTTTAAA
Found at i:58215305 original size:23 final size:24
Alignment explanation
Indices: 58215228--58215305 Score: 70
Period size: 23 Copynumber: 3.1 Consensus size: 24
58215218 TTTAAAAATA
58215228 TTTTAAAATACTTTTTTAAAATTTTTTAT
1 TTTTAAAATA--TTTTTAAAA--TTTT-T
**
58215257 TTTTAAAATATTTTTAAAATACTT
1 TTTTAAAATATTTTTAAAATTTTT
58215281 TTTTAAAA-ATTTTCT-AAATTTTT
1 TTTTAAAATATTTT-TAAAATTTTT
58215304 TT
1 TT
58215306 GTGTTTATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
23 13 0.30
24 10 0.23
25 2 0.05
27 9 0.20
29 10 0.23
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTAAAATATTTTTAAAATTTTT
Found at i:58221786 original size:31 final size:29
Alignment explanation
Indices: 58221716--58221789 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
58221706 GGTTCAAGTT
* *
58221716 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* *
58221745 ACGTTTTAGTCACTTATGTTATCATGATGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
58221776 ACATTTTAGTCACT
1 ACATTTTAGTCACT
58221790 GAGCCGTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 19 0.50
30 2 0.05
31 17 0.45
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:58223068 original size:20 final size:19
Alignment explanation
Indices: 58223043--58223090 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
58223033 TATAATTTAT
58223043 AATTTTTTT-ATATTTTGAAG
1 AATTTTTTTGA-ATTTT-AAG
58223063 AATTTTTCTTGAATTTTAAG
1 AATTTTT-TTGAATTTTAAG
58223083 -ATTTTTTT
1 AATTTTTTT
58223091 TTTTAATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.08
19 6 0.23
20 10 0.38
21 7 0.27
22 1 0.04
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.62
Consensus pattern (19 bp):
AATTTTTTTGAATTTTAAG
Found at i:58223642 original size:17 final size:17
Alignment explanation
Indices: 58223612--58223658 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
58223602 GCACTGAAAA
58223612 TAAAAAAAATAAAATCC
1 TAAAAAAAATAAAATCC
58223629 TAAAATAAAA-AAAAT-C
1 TAAAA-AAAATAAAATCC
* *
58223645 TACAAAATATAAAA
1 TAAAAAAAATAAAA
58223659 ACAGAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 3 0.12
16 9 0.35
17 10 0.38
18 4 0.15
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.19
Consensus pattern (17 bp):
TAAAAAAAATAAAATCC
Found at i:58231619 original size:47 final size:47
Alignment explanation
Indices: 58231526--58231623 Score: 126
Period size: 47 Copynumber: 2.1 Consensus size: 47
58231516 TTATATGAAA
* * *
58231526 TATTTTTAAAAATTTTATCAAATAATAAAAAATATTTTACATATATT
1 TATTTTTAAAAATATTATCAAACAATAAAAAATATTTTACACATATT
* **
58231573 TATTTTTAGGAAATATT-TCAAACAATAAAAAATATTTTAGGCATATT
1 TATTTTTA-AAAATATTATCAAACAATAAAAAATATTTTACACATATT
58231620 TATT
1 TATT
58231624 CAAACACAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
47 38 0.86
48 6 0.14
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (47 bp):
TATTTTTAAAAATATTATCAAACAATAAAAAATATTTTACACATATT
Found at i:58232794 original size:63 final size:63
Alignment explanation
Indices: 58232695--58232820 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
58232685 TATAGTACTG
58232695 TGATTGACTGTCTTTGTAAGAATGGGTTGGTAAAGGAGGCTCTCGATCTCTCTCGGAAATGAA
1 TGATTGACTGTCTTTGTAAGAATGGGTTGGTAAAGGAGGCTCTCGATCTCTCTCGGAAATGAA
*
58232758 TGATTGACTGTCTTTGTAAGAATGGGTTGGTAAAGGAGGCTCTTGATCTCTCTCGGAAATGAA
1 TGATTGACTGTCTTTGTAAGAATGGGTTGGTAAAGGAGGCTCTCGATCTCTCTCGGAAATGAA
58232821 GGATAAAGGC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.33
Consensus pattern (63 bp):
TGATTGACTGTCTTTGTAAGAATGGGTTGGTAAAGGAGGCTCTCGATCTCTCTCGGAAATGAA
Found at i:58235832 original size:2 final size:2
Alignment explanation
Indices: 58235789--58235813 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
58235779 ATTTTCTAGT
58235789 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
58235814 TAAAAGATTT
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:58237143 original size:16 final size:16
Alignment explanation
Indices: 58237122--58237173 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
58237112 TTTGGTTCGC
58237122 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
58237138 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
58237154 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
58237170 TGTA
1 TGTA
58237174 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:58237220 original size:45 final size:44
Alignment explanation
Indices: 58237154--58237244 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
58237144 GGATTAGAGG
*
58237154 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
58237199 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
58237243 TG
1 TG
58237245 GAATAGAGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 18 0.44
45 23 0.56
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:58237582 original size:16 final size:16
Alignment explanation
Indices: 58237545--58237586 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
58237535 TTAATCATAT
*
58237545 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
58237561 TT-AAATATATTATAA
1 TTAAAATATATTATAA
58237576 TTAAAATATAT
1 TTAAAATATAT
58237587 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:58237593 original size:14 final size:15
Alignment explanation
Indices: 58237554--58237595 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
58237544 TTTAAACATA
*
58237554 ATTATTATTAAATAT
1 ATTATAATTAAATAT
58237569 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
58237583 A-TATAATTTAATA
1 ATTATAATTAAATA
58237596 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:58237645 original size:61 final size:61
Alignment explanation
Indices: 58237580--58237767 Score: 183
Period size: 61 Copynumber: 3.1 Consensus size: 61
58237570 TTATAATTAA
58237580 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * *
58237641 AATATATGATACT-GTAAAA-T-AT-A-AATTAACATAATTATTAT-TAAATATA-TTATAATTA
1 AATATATAAT-TTAATAAAATTCTTAATAATT-A-AT-ATTCTTATATGAATTTACTCA-AATCA
*
58237699 A
61 T
*
58237700 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTCATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
58237761 AATATAT
1 AATATAT
58237768 GATACTATAA
Statistics
Matches: 94, Mismatches: 21, Indels: 24
0.68 0.15 0.17
Matches are distributed among these distances:
57 4 0.04
58 5 0.05
59 27 0.29
60 15 0.16
61 34 0.36
62 5 0.05
63 4 0.04
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
Found at i:58237673 original size:120 final size:121
Alignment explanation
Indices: 58237543--58237840 Score: 503
Period size: 120 Copynumber: 2.5 Consensus size: 121
58237533 ATTTAATCAT
*
58237543 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* * *
58237608 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAA
66 ATTAATATTCTCATATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AA
58237665 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
58237728 ATTAATATTCTCATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
66 ATTAATATTCTCATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
* * *
58237784 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
58237841 TAAAATAATT
Statistics
Matches: 168, Mismatches: 6, Indels: 6
0.93 0.03 0.03
Matches are distributed among these distances:
119 3 0.02
120 160 0.95
121 4 0.02
122 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTCATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
Found at i:58237713 original size:14 final size:15
Alignment explanation
Indices: 58237664--58237715 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
58237654 GTAAAATATA
58237664 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
58237679 TATTAAATATATTAT
1 AATTAAATATATTAT
58237694 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
58237707 AATTTAATA
1 AATTAAATA
58237716 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:58237950 original size:101 final size:93
Alignment explanation
Indices: 58237783--58238063 Score: 277
Period size: 91 Copynumber: 3.0 Consensus size: 93
58237773 TATAAAAGAA
* * * *
58237783 AATTTGAAATAATTAATATTAAATATATTTTAATTAA-AATATATGATTTAATAAAATT-TAAAA
1 AATTTAAAATAATTAATATTAAATATAATTTAA-TAATAATATATAATTTCATAAAATTCT----
* * * *
58237846 TAATTATAACTAATAAATTATATTTTATGAATTTGTAT
61 T-A--ATAA-T-ATAAATTTTATTATATGAATTTATAC
* *
58237884 AATTTAAAATAA-TAATTATTACATATAATTTAATAATAATATATAATTTCATAAAATTCTTGAT
1 AATTTAAAATAATTAA-TATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAAT
*
58237948 -A-ATAAATTTTCTTATATGAATTTATAC
65 AATATAAATTTTATTATATGAATTTATAC
* *
58237975 AATTTAAAATAATTAATATTAAATATAATTTAATAGTGATATATAATTTCATAAAATTCTTAATA
1 AATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAATA
* * *
58238040 ATA-AGATGTTCTTATATGAATTTA
66 ATATAAATTTTATTATATGAATTTA
58238064 CTAAAATCAA
Statistics
Matches: 157, Mismatches: 17, Indels: 21
0.81 0.09 0.11
Matches are distributed among these distances:
91 77 0.49
92 23 0.15
93 1 0.01
94 1 0.01
95 2 0.01
98 1 0.01
100 6 0.04
101 45 0.29
102 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (93 bp):
AATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAATA
ATATAAATTTTATTATATGAATTTATAC
Found at i:58237951 original size:91 final size:91
Alignment explanation
Indices: 58237856--58238063 Score: 285
Period size: 91 Copynumber: 2.3 Consensus size: 91
58237846 TAATTATAAC
* * * *
58237856 TAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATTTAATAA
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAATAA
*
58237920 TAATATATAATTTCATAAAATTCTTGA
65 TAATATATAATTTCATAAAATTCTTAA
* * *
58237947 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGT
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
58238012 GATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
*
58238038 TAATAAGATGT-TCTTATATGAATTTA
1 TAATAA-AT-TATATTATATGAATTTA
58238064 CTAAAATCAA
Statistics
Matches: 105, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
91 84 0.80
92 20 0.19
93 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATATAATTTCATAAAATTCTTAA
Found at i:58238535 original size:18 final size:18
Alignment explanation
Indices: 58238514--58238567 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
58238504 GAAGAATACA
58238514 CATTAAATGCGGACGAGC
1 CATTAAATGCGGACGAGC
* *
58238532 CATT-ACTGC-AAC-A--
1 CATTAAATGCGGACGAGC
58238545 CATTAAATGCGGACGAGC
1 CATTAAATGCGGACGAGC
58238563 CATTA
1 CATTA
58238568 CTGCAACACA
Statistics
Matches: 27, Mismatches: 4, Indels: 10
0.66 0.10 0.24
Matches are distributed among these distances:
13 4 0.15
14 4 0.15
15 3 0.11
16 3 0.11
17 4 0.15
18 9 0.33
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (18 bp):
CATTAAATGCGGACGAGC
Found at i:58238549 original size:31 final size:31
Alignment explanation
Indices: 58238511--58238582 Score: 144
Period size: 31 Copynumber: 2.3 Consensus size: 31
58238501 AATGAAGAAT
58238511 ACACATTAAATGCGGACGAGCCATTACTGCA
1 ACACATTAAATGCGGACGAGCCATTACTGCA
58238542 ACACATTAAATGCGGACGAGCCATTACTGCA
1 ACACATTAAATGCGGACGAGCCATTACTGCA
58238573 ACACATTAAA
1 ACACATTAAA
58238583 ATTAGAACAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (31 bp):
ACACATTAAATGCGGACGAGCCATTACTGCA
Found at i:58238802 original size:15 final size:15
Alignment explanation
Indices: 58238782--58238817 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
58238772 GGTATATGTA
58238782 TAATTGACCTAAAAT
1 TAATTGACCTAAAAT
58238797 TAATTGACCTAAAAT
1 TAATTGACCTAAAAT
58238812 TAATTG
1 TAATTG
58238818 TTGGTATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36
Consensus pattern (15 bp):
TAATTGACCTAAAAT
Found at i:58239041 original size:6 final size:6
Alignment explanation
Indices: 58239030--58239054 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
58239020 GTTTGAACAT
58239030 TTTAAA TTTAAA TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA T
58239055 ATAATTTCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:58243540 original size:9 final size:9
Alignment explanation
Indices: 58243526--58243557 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
58243516 TATTCATGTA
58243526 TTATGTAAG
1 TTATGTAAG
*
58243535 TTATGTGAG
1 TTATGTAAG
58243544 TTATGTAAG
1 TTATGTAAG
58243553 TTATG
1 TTATG
58243558 ATATTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:58245428 original size:20 final size:21
Alignment explanation
Indices: 58245403--58245444 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
58245393 AAAGTGTTCT
*
58245403 TTGTATAT-ATAATAAATAAA
1 TTGTATATAAAAATAAATAAA
*
58245423 TTGTATTTAAAAATAAATAAA
1 TTGTATATAAAAATAAATAAA
58245444 T
1 T
58245445 AAATAAAGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
TTGTATATAAAAATAAATAAA
Found at i:58245721 original size:28 final size:26
Alignment explanation
Indices: 58245631--58245724 Score: 75
Period size: 28 Copynumber: 3.5 Consensus size: 26
58245621 TAGCATTTAA
* *
58245631 TTAATTTTTTAAAATTTTAAAAAAAATT
1 TTAATTTTTT--AATTTTTAAAATAATT
* * *
58245659 ATAATTTTAT-ATTTTT-TAATAATT
1 TTAATTTTTTAATTTTTAAAATAATT
58245683 TTAATGATTTTTAATTTTTAAAAGTAATTT
1 TTAAT--TTTTTAATTTTTAAAA-TAA-TT
58245713 TTAATTTTTTAA
1 TTAATTTTTTAA
58245725 AATTAAAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
24 10 0.19
25 5 0.10
26 4 0.08
27 6 0.12
28 17 0.33
29 3 0.06
30 7 0.13
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
TTAATTTTTTAATTTTTAAAATAATT
Found at i:58247935 original size:15 final size:14
Alignment explanation
Indices: 58247906--58247943 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
58247896 TCAGAAAAGT
58247906 AATTATTTTTTAAA
1 AATTATTTTTTAAA
*
58247920 AATTATTTTTTGAA
1 AATTATTTTTTAAA
*
58247934 AACTATTTTT
1 AATTATTTTT
58247944 AGATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (14 bp):
AATTATTTTTTAAA
Found at i:58248443 original size:43 final size:43
Alignment explanation
Indices: 58248391--58248528 Score: 161
Period size: 43 Copynumber: 3.2 Consensus size: 43
58248381 ACGGCACTAT
* * * * *
58248391 AGAATATGACCTTTAGCGGTGCTTTTCTCACAATCACTGCTAA
1 AGAACATGACATTTAGCGGTGCTTTTATCACAATCGCCGCTAA
58248434 AGAACATGACATTTAGCGGCT-CTTTTATCACAATCGCCGCTAA
1 AGAACATGACATTTAGCGG-TGCTTTTATCACAATCGCCGCTAA
* * * * *
58248477 AAAACATGACATTTAGCAGCGTTTTTATCACAAACGCCGCTAA
1 AGAACATGACATTTAGCGGTGCTTTTATCACAATCGCCGCTAA
*
58248520 AGAATATGA
1 AGAACATGA
58248529 TCTTTAGTGA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
43 80 0.99
44 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.28
Consensus pattern (43 bp):
AGAACATGACATTTAGCGGTGCTTTTATCACAATCGCCGCTAA
Found at i:58248535 original size:43 final size:43
Alignment explanation
Indices: 58248358--58248528 Score: 148
Period size: 43 Copynumber: 4.0 Consensus size: 43
58248348 GTCGCTAAAT
* * * * * *
58248358 TTTA-CAGCGTTTTTTTCACATAAACGGCACTATAGAATATGACC
1 TTTAGCAGCGTTTTTATCAC--AAACGCCGCTAAAGAACATGACA
* * * * * * *
58248402 TTTAGCGGTGCTTTTCTCACAATCACTGCTAAAGAACATGACA
1 TTTAGCAGCGTTTTTATCACAAACGCCGCTAAAGAACATGACA
* * *
58248445 TTTAGCGGC-TCTTTTATCACAATCGCCGCTAAAAAACATGACA
1 TTTAGCAGCGT-TTTTATCACAAACGCCGCTAAAGAACATGACA
*
58248488 TTTAGCAGCGTTTTTATCACAAACGCCGCTAAAGAATATGA
1 TTTAGCAGCGTTTTTATCACAAACGCCGCTAAAGAACATGA
58248529 TCTTTAGTGA
Statistics
Matches: 102, Mismatches: 22, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
43 86 0.84
44 5 0.05
45 11 0.11
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.30
Consensus pattern (43 bp):
TTTAGCAGCGTTTTTATCACAAACGCCGCTAAAGAACATGACA
Found at i:58251033 original size:9 final size:9
Alignment explanation
Indices: 58251019--58251057 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
58251009 TTTATGTATC
58251019 ATGTAAGTT
1 ATGTAAGTT
58251028 ATGTAAGTT
1 ATGTAAGTT
* *
58251037 ACGTGAGTT
1 ATGTAAGTT
58251046 ATGTAAGTT
1 ATGTAAGTT
58251055 ATG
1 ATG
58251058 ATATGATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.31, C:0.03, G:0.26, T:0.41
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:58253256 original size:17 final size:19
Alignment explanation
Indices: 58253234--58253271 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
58253224 TTAAAAGATT
58253234 ATAATTTT-AT-ATTTTTA
1 ATAATTTTAATGATTTTTA
58253251 ATAATTTTAATGATTTTTA
1 ATAATTTTAATGATTTTTA
58253270 AT
1 AT
58253272 TTTTAAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 2 0.11
19 9 0.47
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
ATAATTTTAATGATTTTTA
Found at i:58255123 original size:8 final size:7
Alignment explanation
Indices: 58255086--58255256 Score: 94
Period size: 7 Copynumber: 24.4 Consensus size: 7
58255076 TTAAAATCAG
58255086 ACCCTAA
1 ACCCTAA
*
58255093 ACACTAA
1 ACCCTAA
*
58255100 ACCATAA
1 ACCCTAA
58255107 ACCCTAA
1 ACCCTAA
58255114 ACCTCTAA
1 ACC-CTAA
*
58255122 ACCATAA
1 ACCCTAA
**
58255129 ACTTTAA
1 ACCCTAA
*
58255136 ACTCTAA
1 ACCCTAA
* *
58255143 ATCTTAA
1 ACCCTAA
*
58255150 GCCCCTAA
1 -ACCCTAA
*
58255158 ACCATAA
1 ACCCTAA
*
58255165 ACACTAA
1 ACCCTAA
*
58255172 ACCATAA
1 ACCCTAA
*
58255179 ACACTAA
1 ACCCTAA
*
58255186 ACCAT-A
1 ACCCTAA
* *
58255192 AGCCTAC
1 ACCCTAA
58255199 ACCCTAA
1 ACCCTAA
*
58255206 ACCGTAA
1 ACCCTAA
*
58255213 ACACTAA
1 ACCCTAA
* *
58255220 ACTCT-T
1 ACCCTAA
*
58255226 ACACTAA
1 ACCCTAA
* *
58255233 ATCATAA
1 ACCCTAA
58255240 ACCCTAA
1 ACCCTAA
*
58255247 ACCTTAA
1 ACCCTAA
58255254 ACC
1 ACC
58255257 TCAAATAAAC
Statistics
Matches: 118, Mismatches: 42, Indels: 8
0.70 0.25 0.05
Matches are distributed among these distances:
6 8 0.07
7 99 0.84
8 11 0.09
ACGTcount: A:0.46, C:0.32, G:0.02, T:0.20
Consensus pattern (7 bp):
ACCCTAA
Found at i:58255137 original size:36 final size:36
Alignment explanation
Indices: 58255090--58255188 Score: 119
Period size: 36 Copynumber: 2.8 Consensus size: 36
58255080 AATCAGACCC
*
58255090 TAAACACTAAACCATAAACCCTAAACCTCTAAACCA
1 TAAACACTAAACCATAAACCCTAAACCCCTAAACCA
** * * *
58255126 TAAACTTTAAACTC-TAAATCTTAAGCCCCTAAACCA
1 TAAACACTAAAC-CATAAACCCTAAACCCCTAAACCA
*
58255162 TAAACACTAAACCATAAACACTAAACC
1 TAAACACTAAACCATAAACCCTAAACC
58255189 ATAAGCCTAC
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
35 1 0.02
36 47 0.96
37 1 0.02
ACGTcount: A:0.48, C:0.30, G:0.01, T:0.20
Consensus pattern (36 bp):
TAAACACTAAACCATAAACCCTAAACCCCTAAACCA
Found at i:58255214 original size:27 final size:28
Alignment explanation
Indices: 58255090--58255255 Score: 95
Period size: 29 Copynumber: 5.7 Consensus size: 28
58255080 AATCAGACCC
* *
58255090 TAAACACTAAACCATAAACCCTAAACCTC
1 TAAACACTAAACCATAAACACTAAACC-A
** * * *
58255119 TAAAC-CATAAACTTTAAACTCTAAATCT
1 TAAACAC-TAAACCATAAACACTAAACCA
* *
58255147 TAAGCCCCTAAACCATAAACACTAAACCA
1 TAA-ACACTAAACCATAAACACTAAACCA
*
58255176 TAAACACTAAACCATAAGCCTACACCCTAAACCG
1 TAAACACTAAACCATAA----ACA--CTAAACCA
* *
58255210 TAAACACTAAACTC-T-TACACTAAATCA
1 TAAACACTAAAC-CATAAACACTAAACCA
* *
58255237 TAAACCCTAAACCTTAAAC
1 TAAACACTAAACCATAAAC
58255256 CTCAAATAAA
Statistics
Matches: 106, Mismatches: 19, Indels: 25
0.71 0.13 0.17
Matches are distributed among these distances:
26 1 0.01
27 18 0.17
28 18 0.17
29 44 0.42
30 1 0.01
32 3 0.03
34 20 0.19
35 1 0.01
ACGTcount: A:0.47, C:0.31, G:0.02, T:0.20
Consensus pattern (28 bp):
TAAACACTAAACCATAAACACTAAACCA
Found at i:58255907 original size:115 final size:114
Alignment explanation
Indices: 58255607--58255976 Score: 392
Period size: 116 Copynumber: 3.2 Consensus size: 114
58255597 TTTTTGCGAT
* * *
58255607 GTTTTTATAAAAAACGCCACTATTGCCACTAAAGCTCAACAACAAACGACGTCGTTTT-CTCAAC
1 GTTTTT-TAAAAAGCGCCACTAATGCCACTAAAGCTCAACAACAAACGATGTCGTTTTGCTCAAC
* * ** * *
58255671 TTTTTTTGCAGTGTTTTGTGAAAAGCGCTGCTAATTCTCGATCTATTGCGGC
65 -TTTTTTGGA-CGTTTTCCGAAAAGCGCAGCTAATGCTCGATCTATTGCGGC
*
58255723 ATTATTTTATAAAA-CGCCACTAATGCCACTAAAGCTCAACAACAAACG-TCGTCGTTTTGCTCA
1 GTT-TTTTA-AAAAGCGCCACTAATGCCACTAAAGCTCAACAACAAACGAT-GTCGTTTTGCTCA
* *
58255786 ACTTTTTTGTGACGTTTTCCAAAAAGCGCAGCTAATGCTCGATCTATTGTGGC
63 ACTTTTTTG-GACGTTTTCCGAAAAGCGCAGCTAATGCTCGATCTATTGCGGC
* * *
58255839 GTTTTTTAAAAAGCGCCGCTAATGCCACTAAAGCTCAAAAACAAACGATGT-GTTTTGCTTAACT
1 GTTTTTTAAAAAGCGCCACTAATGCCACTAAAGCTCAACAACAAACGATGTCGTTTTGCTCAACT
* * * * * *
58255903 TTTTTGAGGCATTTTTCGCAAAGTGCTA-CTAATGCTCGATCTATAGCGGC
66 TTTTTG-GACGTTTTCCGAAAAGCGC-AGCTAATGCTCGATCTATTGCGGC
** * *
58255953 -TTTTTCGAGAAGCGCCGCTAATGC
1 GTTTTTTAAAAAGCGCCACTAATGC
58255977 TCAACCTATA
Statistics
Matches: 219, Mismatches: 27, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
113 21 0.10
114 55 0.25
115 40 0.18
116 89 0.41
117 14 0.06
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.32
Consensus pattern (114 bp):
GTTTTTTAAAAAGCGCCACTAATGCCACTAAAGCTCAACAACAAACGATGTCGTTTTGCTCAACT
TTTTTGGACGTTTTCCGAAAAGCGCAGCTAATGCTCGATCTATTGCGGC
Found at i:58261856 original size:24 final size:23
Alignment explanation
Indices: 58261804--58261856 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
58261794 TATAAAGATC
*
58261804 ATGCATACCAACATAACCATATA
1 ATGCATACCAACACAACCATATA
*
58261827 AT-CATACCATCACAGACACATAT-
1 ATGCATACCAACACA-AC-CATATA
58261850 ATGCATA
1 ATGCATA
58261857 ACTAGATTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 10 0.40
23 6 0.24
24 9 0.36
ACGTcount: A:0.45, C:0.26, G:0.06, T:0.23
Consensus pattern (23 bp):
ATGCATACCAACACAACCATATA
Found at i:58263223 original size:3 final size:3
Alignment explanation
Indices: 58263215--58263246 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
58263205 GTCAGTCTGC
58263215 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
58263247 AACAGGTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:58264418 original size:17 final size:17
Alignment explanation
Indices: 58264396--58264430 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
58264386 ATAATCCAAA
*
58264396 AGAGTGAATTTAGGTTC
1 AGAGTGAACTTAGGTTC
58264413 AGAGTGAACTTAGGTTC
1 AGAGTGAACTTAGGTTC
58264430 A
1 A
58264431 AGCAGTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.09, G:0.29, T:0.31
Consensus pattern (17 bp):
AGAGTGAACTTAGGTTC
Found at i:58268805 original size:3 final size:3
Alignment explanation
Indices: 58268797--58268854 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
58268787 TTAGTTTCTT
58268797 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
58268845 TTA TTA TTA T
1 TTA TTA TTA T
58268855 CTTTTAAATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:58272797 original size:25 final size:24
Alignment explanation
Indices: 58272753--58272809 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
58272743 GGAACTTTGA
58272753 ATTTGTTTGAAATTCTTATGTT-G
1 ATTTGTTTGAAATTCTTATGTTCG
* *
58272776 ATATTGTTGTGGAATTGTTATGTTCG
1 AT-TTGTT-TGAAATTCTTATGTTCG
58272802 ATTTGTTT
1 ATTTGTTT
58272810 AGATGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 2 0.07
24 6 0.21
25 18 0.62
26 3 0.10
ACGTcount: A:0.19, C:0.04, G:0.21, T:0.56
Consensus pattern (24 bp):
ATTTGTTTGAAATTCTTATGTTCG
Found at i:58282188 original size:15 final size:15
Alignment explanation
Indices: 58282156--58282202 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
58282146 CTAATGTGTG
*
58282156 TATGGCTCCTCC-CTC
1 TATGGCTCCACCAC-C
58282171 TATGGCTCCACCACC
1 TATGGCTCCACCACC
* *
58282186 TATGGTTCCATCACC
1 TATGGCTCCACCACC
58282201 TA
1 TA
58282203 CTTGGACATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 27 0.96
16 1 0.04
ACGTcount: A:0.17, C:0.40, G:0.13, T:0.30
Consensus pattern (15 bp):
TATGGCTCCACCACC
Found at i:58288674 original size:13 final size:12
Alignment explanation
Indices: 58288636--58288685 Score: 59
Period size: 13 Copynumber: 4.2 Consensus size: 12
58288626 ATATTTTTGT
58288636 AATTAATTT-TA
1 AATTAATTTATA
*
58288647 AA-TAATATATCA
1 AATTAATTTAT-A
58288659 AATTAATTTAATA
1 AATTAATTT-ATA
58288672 AATTAATTTATA
1 AATTAATTTATA
58288684 AA
1 AA
58288686 AAAATAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
10 5 0.15
11 3 0.09
12 8 0.24
13 15 0.45
14 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (12 bp):
AATTAATTTATA
Found at i:58291294 original size:32 final size:32
Alignment explanation
Indices: 58291253--58291316 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
58291243 TCTATGACTT
58291253 TCCCTTTTATCTTCTTATGTTTGTCATATATA
1 TCCCTTTTATCTTCTTATGTTTGTCATATATA
58291285 TCCCTTTTATCTTCTTATGTTTGTCATATATA
1 TCCCTTTTATCTTCTTATGTTTGTCATATATA
58291317 CGTCTTAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56
Consensus pattern (32 bp):
TCCCTTTTATCTTCTTATGTTTGTCATATATA
Done.