Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 102 of 235
Found at i:35219898 original size:41 final size:41
Alignment explanation
Indices: 35219853--35219933 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
35219843 AAACATTCTT
35219853 GTAAATTTTGTTTTTTGTTTGACTTATAAAGCAAATAGGAA
1 GTAAATTTTGTTTTTTGTTTGACTTATAAAGCAAATAGGAA
35219894 GTAAATTTTGTTTTTTGTTTGACTTATAAAGCAAATAGGA
1 GTAAATTTTGTTTTTTGTTTGACTTATAAAGCAAATAGGA
35219934 CTATTTGAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.44
Consensus pattern (41 bp):
GTAAATTTTGTTTTTTGTTTGACTTATAAAGCAAATAGGAA
Found at i:35237196 original size:26 final size:26
Alignment explanation
Indices: 35237164--35237215 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
35237154 TTTTAATCCT
35237164 TTAAATTCATGTTTTAATGCTTAATA
1 TTAAATTCATGTTTTAATGCTTAATA
35237190 TTAAATTCATGTTTTAATGCTTAATA
1 TTAAATTCATGTTTTAATGCTTAATA
35237216 GAGCACTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.50
Consensus pattern (26 bp):
TTAAATTCATGTTTTAATGCTTAATA
Found at i:35238019 original size:60 final size:59
Alignment explanation
Indices: 35237939--35238070 Score: 185
Period size: 60 Copynumber: 2.2 Consensus size: 59
35237929 TTAATAGGGG
* * **
35237939 AATCCATAGCATGAGTTAATGTGATAATAG-GAGTTTTATTTAGTGATAAATTTCAAATGA
1 AATCCATAGCATGAGTTAATGTGACAATAGTG-GTTTTAATTAGAAATAAATTTCAAAT-A
*
35237999 AATCCATAGCATTAGTTAATGTGACAATAGTGGTTTTAATTAGAAATAAATTTCAAATA
1 AATCCATAGCATGAGTTAATGTGACAATAGTGGTTTTAATTAGAAATAAATTTCAAATA
*
35238058 AATCTATAGCATG
1 AATCCATAGCATG
35238071 CAATCCACAG
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
59 12 0.19
60 51 0.80
61 1 0.02
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (59 bp):
AATCCATAGCATGAGTTAATGTGACAATAGTGGTTTTAATTAGAAATAAATTTCAAATA
Found at i:35254076 original size:14 final size:14
Alignment explanation
Indices: 35254057--35254084 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35254047 TTAATGCGAC
35254057 AATAGGGGTTTTAA
1 AATAGGGGTTTTAA
35254071 AATAGGGGTTTTAA
1 AATAGGGGTTTTAA
35254085 TTAGAAAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.29, T:0.36
Consensus pattern (14 bp):
AATAGGGGTTTTAA
Found at i:35255821 original size:18 final size:18
Alignment explanation
Indices: 35255798--35255832 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35255788 AGAAATAGTT
*
35255798 GCAAAATAATACATAAAA
1 GCAAAACAATACATAAAA
35255816 GCAAAACAATACATAAA
1 GCAAAACAATACATAAA
35255833 TGCTCAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.14, G:0.06, T:0.14
Consensus pattern (18 bp):
GCAAAACAATACATAAAA
Found at i:35256778 original size:36 final size:36
Alignment explanation
Indices: 35256704--35256811 Score: 110
Period size: 36 Copynumber: 3.0 Consensus size: 36
35256694 CAATCAGTAA
* * * * * *
35256704 TATTCATTAATAATCAGTCAATCAG-AACAATTATT
1 TATTCAATAACAATCAGTTATTCAGTAACAATCAAT
* * *
35256739 TATTCAGTAACAGTCAGTTATTCGGTAACAATCAAT
1 TATTCAATAACAATCAGTTATTCAGTAACAATCAAT
* *
35256775 TATTCAATAATAATCAGTTATTCAGTATCAATCAAT
1 TATTCAATAACAATCAGTTATTCAGTAACAATCAAT
35256811 T
1 T
35256812 GATCGGTTAT
Statistics
Matches: 59, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
35 19 0.32
36 40 0.68
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (36 bp):
TATTCAATAACAATCAGTTATTCAGTAACAATCAAT
Found at i:35256883 original size:19 final size:19
Alignment explanation
Indices: 35256738--35256885 Score: 81
Period size: 18 Copynumber: 7.7 Consensus size: 19
35256728 GAACAATTAT
* *
35256738 TTATTCAGTAACAGTC-AG
1 TTATTCAGTAACAATCAAA
*
35256756 TTATTCGGTAACAATC-AA
1 TTATTCAGTAACAATCAAA
* * *
35256774 TTATTCAATAATAATC-AG
1 TTATTCAGTAACAATCAAA
*
35256792 TTATTCAGTATCAATCAATTGA
1 TTATTCAGTAACAATCAA---A
* *
35256814 TCGGTTATCCAGTAACAGTC-AA
1 ----TTATTCAGTAACAATCAAA
* *
35256836 TTATTCAGTAAAAATCAGA
1 TTATTCAGTAACAATCAAA
* *
35256855 -TATACAGTAACAATTAAA
1 TTATTCAGTAACAATCAAA
35256873 TTATTCAGTAACA
1 TTATTCAGTAACA
35256886 GTCGATCTTT
Statistics
Matches: 97, Mismatches: 23, Indels: 19
0.70 0.17 0.14
Matches are distributed among these distances:
18 69 0.71
19 13 0.13
22 1 0.01
25 1 0.01
26 13 0.13
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.34
Consensus pattern (19 bp):
TTATTCAGTAACAATCAAA
Found at i:35257130 original size:12 final size:12
Alignment explanation
Indices: 35257113--35257137 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35257103 AGTGCCGAAT
35257113 CGGTAACAGTAA
1 CGGTAACAGTAA
35257125 CGGTAACAGTAA
1 CGGTAACAGTAA
35257137 C
1 C
35257138 AGTAGTCGGC
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:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:35257310 original size:19 final size:20
Alignment explanation
Indices: 35257263--35257310 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
35257253 CACTTTCCAG
*
35257263 TTTTCAATTAATTCATATTT
1 TTTTCAATTAACTCATATTT
*
35257283 TAATT-AATTAACT-ATATTT
1 T-TTTCAATTAACTCATATTT
35257302 TTTTCAATT
1 TTTTCAATT
35257311 CAATATAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
18 2 0.09
19 11 0.48
20 8 0.35
21 2 0.09
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTCAATTAACTCATATTT
Found at i:35257353 original size:20 final size:20
Alignment explanation
Indices: 35257323--35257360 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35257313 ATATAATTCC
35257323 ATTCAATTTTCACTAATAAAT
1 ATTCAATTTTCAC-AATAAAT
35257344 ATTCAA-TTTCACAATAA
1 ATTCAATTTTCACAATAA
35257361 TCACAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTCAATTTTCACAATAAAT
Found at i:35258958 original size:19 final size:19
Alignment explanation
Indices: 35258893--35258965 Score: 78
Period size: 18 Copynumber: 3.9 Consensus size: 19
35258883 AATTGATCGG
* *
35258893 TTATCCAGTAACAGTC-AA
1 TTATTCAGTAACAATCAAA
*
35258911 TTATTCAGTAAAAATCAAA
1 TTATTCAGTAACAATCAAA
* *
35258930 -TATACAGTAACAATTAAA
1 TTATTCAGTAACAATCAAA
*
35258948 TTATTCAGTAACAGTCAA
1 TTATTCAGTAACAATCAA
35258966 TATTTCCAGT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
18 28 0.64
19 16 0.36
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (19 bp):
TTATTCAGTAACAATCAAA
Found at i:35258975 original size:19 final size:18
Alignment explanation
Indices: 35258896--35258975 Score: 54
Period size: 18 Copynumber: 4.3 Consensus size: 18
35258886 TGATCGGTTA
*
35258896 TCCAGTAACAGTC-AATT
1 TCCAGTAACAATCAAATT
* * *
35258913 ATTCAGTAAAAATCAAATA
1 -TCCAGTAACAATCAAATT
* *
35258932 TACAGTAACAATTAAATT
1 TCCAGTAACAATCAAATT
* *
35258950 ATTCAGTAACAGTCAATATT
1 -TCCAGTAACAATCAA-ATT
35258970 TCCAGT
1 TCCAGT
35258976 TCCTTTATTT
Statistics
Matches: 47, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
18 24 0.51
19 20 0.43
20 3 0.06
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (18 bp):
TCCAGTAACAATCAAATT
Found at i:35259205 original size:12 final size:12
Alignment explanation
Indices: 35259188--35259212 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35259178 AGTGCCGAAT
35259188 CGGTAACAGTAA
1 CGGTAACAGTAA
35259200 CGGTAACAGTAA
1 CGGTAACAGTAA
35259212 C
1 C
35259213 AGTAGTCGGC
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:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:35259386 original size:20 final size:21
Alignment explanation
Indices: 35259338--35259386 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
35259328 CACTTTCCAG
*
35259338 TTTTCAATTAATTCATATTTT
1 TTTTCAATTAACTCATATTTT
**
35259359 AATT-AATTAACT-ATATTTT
1 TTTTCAATTAACTCATATTTT
35259378 TTTTCAATT
1 TTTTCAATT
35259387 CAATATAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
19 9 0.41
20 11 0.50
21 2 0.09
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTCAATTAACTCATATTTT
Found at i:35263550 original size:26 final size:26
Alignment explanation
Indices: 35263513--35263568 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
35263503 TAAAAAGTAT
*
35263513 AAAATATTAAAAAT-ATAAAATTCAGA
1 AAAATATAAAAAATAATAAAATT-AGA
*
35263539 AAAATATAAAAATTAATAAAATTAGA
1 AAAATATAAAAAATAATAAAATTAGA
35263565 AAAA
1 AAAA
35263569 ACAATTAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 19 0.70
27 8 0.30
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.25
Consensus pattern (26 bp):
AAAATATAAAAAATAATAAAATTAGA
Found at i:35263559 original size:17 final size:16
Alignment explanation
Indices: 35263502--35263560 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
35263492 AACAAATAAT
*
35263502 TTAAAAAGTATAAAATA
1 TTAAAAAATATAAAA-A
35263519 TT-AAAAATAT-AAAA
1 TTAAAAAATATAAAAA
35263533 TTCAGAAAAATATAAAAA
1 TT-A-AAAAATATAAAAA
35263551 TTAATAAAAT
1 TTAA-AAAAT
35263561 TAGAAAAAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 3 0.08
15 3 0.08
16 8 0.22
17 16 0.44
18 6 0.17
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (16 bp):
TTAAAAAATATAAAAA
Found at i:35264043 original size:3 final size:3
Alignment explanation
Indices: 35264035--35264083 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
35264025 GAACTCTTCT
* *
35264035 ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA AAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
35264083 A
1 A
35264084 CGTGCAGTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:35266857 original size:24 final size:24
Alignment explanation
Indices: 35266791--35266858 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 24
35266781 TGGAGGATCA
35266791 ATAATACTTCCATTGAAAATATCC
1 ATAATACTTCCATTGAAAATATCC
*
35266815 ---ATA-TT--ATTGAGAAA-CTCC
1 ATAATACTTCCATTGA-AAATATCC
35266833 ATAATACTTCCATTGAAAATATCC
1 ATAATACTTCCATTGAAAATATCC
35266857 AT
1 AT
35266859 GTTATTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 16
0.65 0.04 0.31
Matches are distributed among these distances:
18 8 0.24
19 3 0.09
20 2 0.06
21 6 0.18
22 2 0.06
23 3 0.09
24 10 0.29
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.34
Consensus pattern (24 bp):
ATAATACTTCCATTGAAAATATCC
Found at i:35272873 original size:21 final size:21
Alignment explanation
Indices: 35272847--35272887 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
35272837 ATCTGCTCAA
* *
35272847 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
35272868 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
35272888 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:35277131 original size:18 final size:19
Alignment explanation
Indices: 35277100--35277135 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
35277090 ATATTTATTT
*
35277100 TAAACATAATATTAAATAA
1 TAAAAATAATATTAAATAA
35277119 TAAAAATAA-ATTAAATA
1 TAAAAATAATATTAAATA
35277136 GTATTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAAATAATATTAAATAA
Found at i:35297610 original size:16 final size:16
Alignment explanation
Indices: 35297589--35297636 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
35297579 TTCATTTCGG
35297589 GAAGAAAAAAGGAGAA
1 GAAGAAAAAAGGAGAA
35297605 GAAGAAAAGAA-GAGAA
1 GAAGAAAA-AAGGAGAA
*
35297621 GAAG-AATAAGGAGAA
1 GAAGAAAAAAGGAGAA
35297636 G
1 G
35297637 GAGGCAGCAC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 2 0.07
15 8 0.28
16 17 0.59
17 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (16 bp):
GAAGAAAAAAGGAGAA
Found at i:35298167 original size:16 final size:16
Alignment explanation
Indices: 35298146--35298201 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
35298136 AAAAATAGCA
35298146 TAAAAAAATAAAATAC
1 TAAAAAAATAAAATAC
*** *
35298162 TAAAAAAATATCTTAA
1 TAAAAAAATAAAATAC
*
35298178 TGAAAAAATAAAATAC
1 TAAAAAAATAAAATAC
*
35298194 GAAAAAAA
1 TAAAAAAA
35298202 ATAATTTTTT
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.71, C:0.05, G:0.04, T:0.20
Consensus pattern (16 bp):
TAAAAAAATAAAATAC
Found at i:35298481 original size:151 final size:150
Alignment explanation
Indices: 35298239--35298922 Score: 1054
Period size: 151 Copynumber: 4.6 Consensus size: 150
35298229 GCGGGTTTTT
35298239 TACTAAAATAATAT-AAAAATAAAATACGAAAATAGTATATTTTTAAAAAATAAAAT-------T
1 TACTAAAATAATATAAAAAATAAAATACGAAAATAGTATA-TTTTAAAAAATAAAATCCGAAAAT
* * *
35298296 TAAAAAATACAAACAAAGGGCCAAAATCAGGGTTATTTACTAAATTAATATAAAAAA-ACTTAAA
65 AAAAAAATACCAACAAAGGGCCAAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTT-AA
35298360 ATAATACATTT-AAACATTATG
129 ATAATACATTTGAAACATTATG
* *
35298381 TACTAAAATAATATAAAAAAATAAAATACGAAAATAGTAAATTTTAAAAAATAAAATCTGAAAAT
1 TACTAAAATAATAT-AAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAAT
* * * *
35298446 AAAAAAATAACCAACAAAGTGTCAAAATAAAGGTTATTTATTAAATTAATAT-AAAAACACTTAA
65 AAAAAAAT-ACCAACAAAGGGCCAAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTTAA
35298510 ATAATACATTTGAAACATTATG
129 ATAATACATTTGAAACATTATG
35298532 TACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTT--AAAATAAAATCCGAAAATA
1 TACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATA
*
35298595 AAAAAATACCAACAAAGGGCCAAAATCAGGGTTATTTATTAAATTAATATAAAAAATACTTAAAT
66 AAAAAATACCAACAAAGGGCCAAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTTAAAT
*
35298660 AATACATTTAAAACATTATG
131 AATACATTTGAAACATTATG
* *
35298680 TACTAAAATAATATAAAAAATAAAATATGAAAATAGTATATTTTAAAAAATAAAATCCAAAAATA
1 TACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAAT-
* * *
35298745 AAAAAAATACCAACAAAGGGTCAAAATTAGGGTTATTTATTAAATTAATAGAAAAAACACTTAAA
65 AAAAAAATACCAACAAAGGGCCAAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTTAAA
*
35298810 TAATACATTTGAAATATTATG
130 TAATACATTTGAAACATTATG
**
35298831 TACTAAAATAATAT-AAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATAAGAAAATA
1 TACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATA
35298895 AAAAAATACCAACAAAGGGCCAAAATCA
66 AAAAAATACCAACAAAGGGCCAAAATCA
35298923 CCGAAAAATT
Statistics
Matches: 496, Mismatches: 30, Indels: 25
0.90 0.05 0.05
Matches are distributed among these distances:
142 14 0.03
143 16 0.03
144 24 0.05
147 39 0.08
148 100 0.20
149 27 0.05
150 117 0.24
151 159 0.32
ACGTcount: A:0.58, C:0.08, G:0.07, T:0.27
Consensus pattern (150 bp):
TACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATA
AAAAAATACCAACAAAGGGCCAAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTTAAAT
AATACATTTGAAACATTATG
Found at i:35298665 original size:298 final size:296
Alignment explanation
Indices: 35298239--35298922 Score: 1103
Period size: 298 Copynumber: 2.3 Consensus size: 296
35298229 GCGGGTTTTT
* *
35298239 TACTAAAATAATATAAAAATAAAATACGAAAATAGTATATTTT-TAA-AAAAT-AAAATTTAAAA
1 TACTAAAATAATATAAAAATAAAATACGAAAATAGTATATTTTAAAATAAAATGAAAA-TAAAAA
*
35298301 AATACAAACAAAGGGCCAAAATCAGGGTTATTTACTAAATTAATATAAAAAAACTTAAAATAATA
65 AATACCAACAAAGGGCCAAAATCAGGGTTATTTACTAAATTAATATAAAAAAACTTAAAATAATA
35298366 CATTT-AAACATTATGTACTAAAATAATATAAAAAAATAAAATACGAAAATAGTAAATTTTAAAA
130 CATTTAAAACATTATGTACTAAAATAATAT-AAAAAATAAAATACGAAAATAGTAAATTTTAAAA
** *
35298430 AATAAAATCTGAAAAT-AAAAAAATAACCAACAAAGTGTCAAAATAAAGGTTATTTATTAAATTA
194 AATAAAATCCAAAAATAAAAAAAAT-ACCAACAAAGGGTCAAAATAAAGGTTATTTATTAAATTA
*
35298494 ATA-TAAAAACACTTAAATAATACATTTGAAACATTATG
258 ATAGAAAAAACACTTAAATAATACATTTGAAACATTATG
35298532 TACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAATAAAATCCGAAAATAAA
1 TACTAAAATAATAT-AAAAATAAAATACGAAAATAGTATATTTTAAAATAAAAT--GAAAATAAA
*
35298597 AAAATACCAACAAAGGGCCAAAATCAGGGTTATTTATTAAATTAATATAAAAAATACTT-AAATA
63 AAAATACCAACAAAGGGCCAAAATCAGGGTTATTTACTAAATTAATATAAAAAA-ACTTAAAATA
* *
35298661 ATACATTTAAAACATTATGTACTAAAATAATATAAAAAATAAAATATGAAAATAGTATATTTTAA
127 ATACATTTAAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTAAATTTTAA
* *
35298726 AAAATAAAATCCAAAAATAAAAAAAATACCAACAAAGGGTCAAAATTAGGGTTATTTATTAAATT
192 AAAATAAAATCCAAAAATAAAAAAAATACCAACAAAGGGTCAAAATAAAGGTTATTTATTAAATT
*
35298791 AATAGAAAAAACACTTAAATAATACATTTGAAATATTATG
257 AATAGAAAAAACACTTAAATAATACATTTGAAACATTATG
35298831 TACTAAAATAATATAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATAAGAAAATAA
1 TACTAAAATAATATAAAAATAAAATACGAAAATAGTATATTTT--AAAATAAAAT--GAAAATAA
35298896 AAAAATACCAACAAAGGGCCAAAATCA
62 AAAAATACCAACAAAGGGCCAAAATCA
35298923 CCGAAAAATT
Statistics
Matches: 364, Mismatches: 15, Indels: 17
0.92 0.04 0.04
Matches are distributed among these distances:
293 14 0.04
294 29 0.08
295 2 0.01
296 5 0.01
298 182 0.50
299 87 0.24
300 45 0.12
ACGTcount: A:0.58, C:0.08, G:0.07, T:0.27
Consensus pattern (296 bp):
TACTAAAATAATATAAAAATAAAATACGAAAATAGTATATTTTAAAATAAAATGAAAATAAAAAA
ATACCAACAAAGGGCCAAAATCAGGGTTATTTACTAAATTAATATAAAAAAACTTAAAATAATAC
ATTTAAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTAAATTTTAAAAAA
TAAAATCCAAAAATAAAAAAAATACCAACAAAGGGTCAAAATAAAGGTTATTTATTAAATTAATA
GAAAAAACACTTAAATAATACATTTGAAACATTATG
Found at i:35303381 original size:28 final size:29
Alignment explanation
Indices: 35303350--35303404 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
35303340 AAAACTAAAG
*
35303350 AAAAAAATAAAAATATT-TTAAATTTATT
1 AAAAAAATAAAAAAATTGTTAAATTTATT
* *
35303378 AAAAATATAAAAAAATTGTTAGATTTA
1 AAAAAAATAAAAAAATTGTTAAATTTA
35303405 AAGTTGTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (29 bp):
AAAAAAATAAAAAAATTGTTAAATTTATT
Found at i:35303877 original size:18 final size:19
Alignment explanation
Indices: 35303856--35303893 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
35303846 AAAAGCTAAT
35303856 AAAAGA-AGAAAAAGGCCC
1 AAAAGAGAGAAAAAGGCCC
* *
35303874 AAAAGAGAGTAAATGGCCC
1 AAAAGAGAGAAAAAGGCCC
35303893 A
1 A
35303894 CAAAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.55, C:0.16, G:0.24, T:0.05
Consensus pattern (19 bp):
AAAAGAGAGAAAAAGGCCC
Found at i:35309444 original size:49 final size:49
Alignment explanation
Indices: 35309412--35309508 Score: 144
Period size: 49 Copynumber: 2.0 Consensus size: 49
35309402 TTAAATATAG
* *
35309412 AGTGTTGAAATAAATTTATAAATAATAGTTAT-ATTAGCTCATGGAAATC
1 AGTGTTGAAATAAATTTATAAACAATAGTTATAATTA-CTCATGAAAATC
35309461 AGTGTTGAAATAAATTTATAAACAATAGTTAT-ATTAGCTCATGAAAAT
1 AGTGTTGAAATAAATTTATAAACAATAGTTATAATTA-CTCATGAAAAT
35309509 ATAATTGCAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.36
Consensus pattern (49 bp):
AGTGTTGAAATAAATTTATAAACAATAGTTATAATTACTCATGAAAATC
Found at i:35311645 original size:786 final size:786
Alignment explanation
Indices: 35310133--35311704 Score: 3045
Period size: 786 Copynumber: 2.0 Consensus size: 786
35310123 CCTAATTGAT
35310133 ATAACATAAATAGTTTGAGAATGTAATTAAAATGTTTTGAAATTTAAGAACCAATTTAAAGAATG
1 ATAACATAAATAGTTTGAGAATGTAATTAAAATGTTTTGAAATTTAAGAACCAATTTAAAGAATG
*
35310198 CTTTGGTGCAATTAGGTCTTTAAAGAAAATTGTCTGAAACCCTATATGTTAAATACTATATTTTA
66 CTTTGGTGCAATTAGGTCTTTAAAGAAAATTGTCTGAAACCCTATATGTCAAATACTATATTTTA
35310263 ACTTTCTTTTTTTGTCTGAAACCCTCCTGTATCTAGTAAATTGAATCAAGTTGAACCTTTAAACG
131 ACTTTCTTTTTTTGTCTGAAACCCTCCTGTATCTAGTAAATTGAATCAAGTTGAACCTTTAAACG
35310328 AGATAAATATTTTTTTCTACAGTCTCACACCTATCTCCCAAATACCAATCATCCATTAAATAATA
196 AGATAAATATTTTTTTCTACAGTCTCACACCTATCTCCCAAATACCAATCATCCATTAAATAATA
35310393 AATTCAATTATCAGCTCAATAGCAATTGACACTTAAAACATAGCTGTCAAATAGATTATAGGTCA
261 AATTCAATTATCAGCTCAATAGCAATTGACACTTAAAACATAGCTGTCAAATAGATTATAGGTCA
35310458 TAGCTCATAATCAGTTATATGTTGGTCATCACAGTTGTTTCAAGAAAAGAAATATCACATTGATG
326 TAGCTCATAATCAGTTATATGTTGGTCATCACAGTTGTTTCAAGAAAAGAAATATCACATTGATG
*
35310523 TATTGGACAAAGCAATTCTTGATGACTAGTGTTGCTAAGAAAAACATAAGGAATGAAGTTTGCTT
391 TATTAGACAAAGCAATTCTTGATGACTAGTGTTGCTAAGAAAAACATAAGGAATGAAGTTTGCTT
35310588 ACACTTTTGAAAAGATAGTCATAATCAATAATCCTTTCTATATCCTCGTTATTGTTTACCATAGA
456 ACACTTTTGAAAAGATAGTCATAATCAATAATCCTTTCTATATCCTCGTTATTGTTTACCATAGA
35310653 TCTTTGAGAATTTTTTCTTTAGTGTTCATCTTATGGCTTTCATCTTTTTGTGATGTGTTATTCTT
521 TCTTTGAGAATTTTTTCTTTAGTGTTCATCTTATGGCTTTCATCTTTTTGTGATGTGTTATTCTT
35310718 AATTTTTTATGAAACTATATTATTTTATCTAATTATATATTTATGGTTTTATGTCGGTTGACATT
586 AATTTTTTATGAAACTATATTATTTTATCTAATTATATATTTATGGTTTTATGTCGGTTGACATT
35310783 TAAAATCAAAATAATAATAATAGATGGTAAAGACATAAATTTGTGGAGGGAGATAGTACATTAGC
651 TAAAATCAAAATAATAATAATAGATGGTAAAGACATAAATTTGTGGAGGGAGATAGTACATTAGC
35310848 AACAAAAGCTGTTTGGGATGATGAGTTGACGTTGATATTTTGTGAACTTTGCATGAATGAAGTCA
716 AACAAAAGCTGTTTGGGATGATGAGTTGACGTTGATATTTTGTGAACTTTGCATGAATGAAGTCA
35310913 ATGCTA
781 ATGCTA
*
35310919 ATAACATAAATAGTTTGAGAATGTAATTAAAATGTTTTGAAATTTAATAACCAATTTAAAGAATG
1 ATAACATAAATAGTTTGAGAATGTAATTAAAATGTTTTGAAATTTAAGAACCAATTTAAAGAATG
35310984 CTTTGGTGCAATTAGGTCTTTAAAGAAAATTGTCTGAAACCCTATATGTCAAATACTATATTTTA
66 CTTTGGTGCAATTAGGTCTTTAAAGAAAATTGTCTGAAACCCTATATGTCAAATACTATATTTTA
* *
35311049 ACTTTCTTTTTTTGTTTGAAACCCTCTTGTATCTAGTAAATTGAATCAAGTTGAACCTTTAAACG
131 ACTTTCTTTTTTTGTCTGAAACCCTCCTGTATCTAGTAAATTGAATCAAGTTGAACCTTTAAACG
*
35311114 AGATAAATATTTTTTTCTATAGTCTCACACCTATCTCCCAAATACCAATCATCCATTAAATAATA
196 AGATAAATATTTTTTTCTACAGTCTCACACCTATCTCCCAAATACCAATCATCCATTAAATAATA
35311179 AATTCAATTATCAGCTCAATAGCAATTGACACTTAAAACATAGCTGTCAAATAGATTATAGGTCA
261 AATTCAATTATCAGCTCAATAGCAATTGACACTTAAAACATAGCTGTCAAATAGATTATAGGTCA
*
35311244 TAGCTCATAATCAGTTATCTGTTGGTCATCACAGTTGTTTCAAGAAAAGAAATATCACATTGATG
326 TAGCTCATAATCAGTTATATGTTGGTCATCACAGTTGTTTCAAGAAAAGAAATATCACATTGATG
35311309 TATTAGACAAAGCAATTCTTGATGACTAGTGTTGCTAAGAAAAACATAAGGAATGAAGTTTGCTT
391 TATTAGACAAAGCAATTCTTGATGACTAGTGTTGCTAAGAAAAACATAAGGAATGAAGTTTGCTT
* * * *
35311374 ACACTTTTGAGAAGATAGTCATAATCAATTATCCTTTCTATGTCCTTGTTATTGTTTACCATAGA
456 ACACTTTTGAAAAGATAGTCATAATCAATAATCCTTTCTATATCCTCGTTATTGTTTACCATAGA
35311439 TCTTTGAGAATTTTTTCTTTAGTGTTCATCTTATGGCTTTCATCTTTTTGTGATGTGTTATTCTT
521 TCTTTGAGAATTTTTTCTTTAGTGTTCATCTTATGGCTTTCATCTTTTTGTGATGTGTTATTCTT
35311504 AATTTTTTATGAAACTATATTATTTTATCTAATTATATATTTATGGTTTTATGTCGGTTGACATT
586 AATTTTTTATGAAACTATATTATTTTATCTAATTATATATTTATGGTTTTATGTCGGTTGACATT
35311569 TAAAATCAAAATAATAATAATAGATGGTAAAGACATAAATTTGTGGAGGGAGATAGTACATTAGC
651 TAAAATCAAAATAATAATAATAGATGGTAAAGACATAAATTTGTGGAGGGAGATAGTACATTAGC
35311634 AACAAAAGCTGTTTGGGATGATGAGTTGACGTTGATATTTTGTGAACTTTGCATGAATGAAGTCA
716 AACAAAAGCTGTTTGGGATGATGAGTTGACGTTGATATTTTGTGAACTTTGCATGAATGAAGTCA
35311699 ATGCTA
781 ATGCTA
35311705 GTAATAGACC
Statistics
Matches: 775, Mismatches: 11, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
786 775 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (786 bp):
ATAACATAAATAGTTTGAGAATGTAATTAAAATGTTTTGAAATTTAAGAACCAATTTAAAGAATG
CTTTGGTGCAATTAGGTCTTTAAAGAAAATTGTCTGAAACCCTATATGTCAAATACTATATTTTA
ACTTTCTTTTTTTGTCTGAAACCCTCCTGTATCTAGTAAATTGAATCAAGTTGAACCTTTAAACG
AGATAAATATTTTTTTCTACAGTCTCACACCTATCTCCCAAATACCAATCATCCATTAAATAATA
AATTCAATTATCAGCTCAATAGCAATTGACACTTAAAACATAGCTGTCAAATAGATTATAGGTCA
TAGCTCATAATCAGTTATATGTTGGTCATCACAGTTGTTTCAAGAAAAGAAATATCACATTGATG
TATTAGACAAAGCAATTCTTGATGACTAGTGTTGCTAAGAAAAACATAAGGAATGAAGTTTGCTT
ACACTTTTGAAAAGATAGTCATAATCAATAATCCTTTCTATATCCTCGTTATTGTTTACCATAGA
TCTTTGAGAATTTTTTCTTTAGTGTTCATCTTATGGCTTTCATCTTTTTGTGATGTGTTATTCTT
AATTTTTTATGAAACTATATTATTTTATCTAATTATATATTTATGGTTTTATGTCGGTTGACATT
TAAAATCAAAATAATAATAATAGATGGTAAAGACATAAATTTGTGGAGGGAGATAGTACATTAGC
AACAAAAGCTGTTTGGGATGATGAGTTGACGTTGATATTTTGTGAACTTTGCATGAATGAAGTCA
ATGCTA
Found at i:35312792 original size:32 final size:32
Alignment explanation
Indices: 35312756--35312819 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
35312746 TATAACTATA
35312756 CTACTTTTTTATATGTAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
35312788 CTACTTTTTTATATGTAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
35312820 ANNNNNNNNN
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:0.34, C:0.09, G:0.09, T:0.47
Consensus pattern (32 bp):
CTACTTTTTTATATGTAAAACTAATGTATGAT
Found at i:35317496 original size:32 final size:32
Alignment explanation
Indices: 35317460--35317521 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
35317450 AACTATACTA
35317460 ACTTTTTTATATGTAAAACTAATGTATGATCT
1 ACTTTTTTATATGTAAAACTAATGTATGATCT
35317492 ACTTTTTTATATGTAAAACTAATGTATGAT
1 ACTTTTTTATATGTAAAACTAATGTATGAT
35317522 ATTTTTTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (32 bp):
ACTTTTTTATATGTAAAACTAATGTATGATCT
Found at i:35319561 original size:21 final size:20
Alignment explanation
Indices: 35319514--35319566 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
35319504 CACCATTGTT
35319514 TCTAATCTCACCGCTAAGTA
1 TCTAATCTCACCGCTAAGTA
*
35319534 TCCAATCTCACCGCTACAGTAA
1 TCTAATCTCACCGCTA-AGT-A
35319556 T-TAATCTCACC
1 TCTAATCTCACC
35319567 ACCACCGCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 15 0.52
21 12 0.41
22 2 0.07
ACGTcount: A:0.30, C:0.34, G:0.08, T:0.28
Consensus pattern (20 bp):
TCTAATCTCACCGCTAAGTA
Found at i:35320191 original size:14 final size:14
Alignment explanation
Indices: 35320172--35320206 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
35320162 CTAACATAAC
35320172 ATAATTTTTTTAAA
1 ATAATTTTTTTAAA
*
35320186 ATAATTATTTTAAA
1 ATAATTTTTTTAAA
35320200 ATAATTT
1 ATAATTT
35320207 ATCTACAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATAATTTTTTTAAA
Found at i:35321644 original size:28 final size:28
Alignment explanation
Indices: 35321565--35321669 Score: 83
Period size: 28 Copynumber: 3.8 Consensus size: 28
35321555 TTACTTAGGC
*
35321565 TTTTATATTTTTA-ATATTTTTGTAAT--
1 TTTTATATTTTTATAAATTTTT-TAATAA
* * **
35321591 TTTAAAATTTTTATAGAAAAATTTTAATAA
1 TTTTATATTTTTAT--AAATTTTTTAATAA
*
35321621 TATTT-TATTTTTATATATTTTTTAATAA
1 T-TTTATATTTTTATAAATTTTTTAATAA
*
35321649 TTTTATTTTTTTATAAATTTT
1 TTTTATATTTTTATAAATTTT
35321670 ATCATTTTTA
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
26 11 0.18
27 3 0.05
28 30 0.50
29 5 0.08
30 9 0.15
31 2 0.03
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (28 bp):
TTTTATATTTTTATAAATTTTTTAATAA
Found at i:35321655 original size:16 final size:16
Alignment explanation
Indices: 35321636--35321685 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
35321626 TATTTTTATA
35321636 TATTTTTTAATAATTT
1 TATTTTTTAATAATTT
*
35321652 TATTTTTTTATAAATTT
1 TATTTTTTAAT-AATTT
*
35321669 TATCATTTTTACTAATT
1 TAT--TTTTTAATAATT
35321686 ATAATCATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 10 0.36
17 8 0.29
18 4 0.14
19 6 0.21
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (16 bp):
TATTTTTTAATAATTT
Found at i:35321658 original size:17 final size:18
Alignment explanation
Indices: 35321638--35321685 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
35321628 TTTTTATATA
35321638 TTTTTTAATAATTTTAT-
1 TTTTTTAATAATTTTATC
35321655 TTTTTT-ATAAATTTTATC
1 TTTTTTAAT-AATTTTATC
* *
35321673 ATTTTTACTAATT
1 TTTTTTAATAATT
35321686 ATAATCATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 2 0.08
17 14 0.54
18 9 0.35
19 1 0.04
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTTAATAATTTTATC
Found at i:35321670 original size:26 final size:28
Alignment explanation
Indices: 35321609--35321670 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 28
35321599 TTTTATAGAA
35321609 AAATTTTAATAATATTTTATTTTTATAT
1 AAATTTTAATAATATTTTATTTTTATAT
** *
35321637 ATTTTTTAAT-A-ATTTTATTTTTTTAT
1 AAATTTTAATAATATTTTATTTTTATAT
35321663 AAATTTTA
1 AAATTTTA
35321671 TCATTTTTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 20 0.69
27 1 0.03
28 8 0.28
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (28 bp):
AAATTTTAATAATATTTTATTTTTATAT
Found at i:35321678 original size:26 final size:26
Alignment explanation
Indices: 35321609--35321679 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
35321599 TTTTATAGAA
35321609 AAATTTTAATAATATTTTATTTTTATAT
1 AAATTTTAAT-AT-TTTTATTTTTATAT
** * *
35321637 ATTTTTTAATAATTTTATTTTTTTAT
1 AAATTTTAATATTTTTATTTTTATAT
35321663 AAATTTT-ATCATTTTTA
1 AAATTTTAAT-ATTTTTA
35321680 CTAATTATAA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
25 2 0.06
26 24 0.69
27 1 0.03
28 8 0.23
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (26 bp):
AAATTTTAATATTTTTATTTTTATAT
Found at i:35321841 original size:24 final size:24
Alignment explanation
Indices: 35321808--35321856 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
35321798 ATGAATTATC
*
35321808 TATATTTTTAATATTATAATAATT
1 TATATATTTAATATTATAATAATT
* *
35321832 TATATATTTATTATTTTAATAATT
1 TATATATTTAATATTATAATAATT
35321856 T
1 T
35321857 TTTTAAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TATATATTTAATATTATAATAATT
Found at i:35323700 original size:25 final size:25
Alignment explanation
Indices: 35323672--35323724 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
35323662 TCCAAATGAC
35323672 AAAATTAATGAGCCAAATTTTAATT
1 AAAATTAATGAGCCAAATTTTAATT
35323697 AAAATTAATGAGCCAAATTTTAATT
1 AAAATTAATGAGCCAAATTTTAATT
35323722 AAA
1 AAA
35323725 CTTTACTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.34
Consensus pattern (25 bp):
AAAATTAATGAGCCAAATTTTAATT
Found at i:35327610 original size:578 final size:579
Alignment explanation
Indices: 35326510--35327669 Score: 2214
Period size: 578 Copynumber: 2.0 Consensus size: 579
35326500 CTTACCTTTA
35326510 GGAAGTTTCACAAGATCCCATGTTTTGTTTTTGTGAAGTGATTCCATGTCCTCTTGCATAGTAAA
1 GGAAGTTTCACAAGATCCCATGTTTTGTTTTTGTGAAGTGATTCCATGTCCTCTTGCATAGTAAA
35326575 CATCCATTTTTCTGAGTCTTCATAGCTAACCGCCTCAGAATAATTAGATGGCTCTTGGTTTGCAT
66 CATCCATTTTTCTGAGTCTTCATAGCTAACCGCCTCAGAATAATTAGATGGCTCTTGGTTTGCAT
*
35326640 CTATATCTTCAGCCACATTTAAAGCATAAGCAACTAAATCAACTTCGGCATACTTCTTTGGAGGT
131 CTATATCTTCAGCCACATTTAAAGCATAAGCAACTAAATCAACCTCGGCATACTTCTTTGGAGGT
*
35326705 TTAATTTCTCTTTTAGTTCTGTTTTTGGCGATAGAGTATTGTGGTGAAGAAGCAACTCTATTCTC
196 TTAATTTCTCTTCTAGTTCTGTTTTTGGCGATAGAGTATTGTGGTGAAGAAGCAACTCTATTCTC
35326770 AATTTTTGCACTGGCTTGAGGAGTTGACTCTGTATTAATCTGATGCTCCACCTGCTTTTGATTTT
261 AATTTTTGCACTGGCTTGAGGAGTTGACTCTGTATTAATCTGATGCTCCACCTGCTTTTGATTTT
*
35326835 CTTTATTGGAAGAGTCTTTAAGAGATAAGTTAGGTAGCATAGTAGTTTCATCAAAAACAACATCT
326 CTTTATTGGAAGAGTCTTTAAGAGATAAGTTAGGTAGCATAGCAGTTTCATCAAAAACAACATCT
35326900 CTACTAATCACAACTTTTCTATTTTCAGGACACCATAACTTATACCCTTTTACACCAGCTTTATA
391 CTACTAATCACAACTTTTCTATTTTCAGGACACCATAACTTATACCCTTTTACACCAGCTTTATA
*
35326965 ACCAAGAAAAACGCATTTAATGGATCTCGGTTCCAATTTTCCATTATCAACATGAGCATACGCAG
456 ACCAAGAAAAACACATTTAATGGATCTCGGTTCCAATTTTCCATTATCAACATGAGCATACGCAG
* *
35327030 GACACCCAAAGATCTTTAAATCAGAATAATTAGCAGGATTACCAGGCCATACCTCTTGT
521 GACACCCAAAAATCTTTAAATCAGAATAATTAGCAGGATTACCAGACCATACCTCTTGT
35327089 GGAA-TTTCACAAGATCCCATGTTTTGTTTTTGTGAAGTGATTCCATGTCCTCTTGCATAGTAAA
1 GGAAGTTTCACAAGATCCCATGTTTTGTTTTTGTGAAGTGATTCCATGTCCTCTTGCATAGTAAA
35327153 CATCCATTTTTCTGAGTCTTCATAGCTAACCGCCTCAGAATAATTAGATGGCTCTTGGTTTGCAT
66 CATCCATTTTTCTGAGTCTTCATAGCTAACCGCCTCAGAATAATTAGATGGCTCTTGGTTTGCAT
* *
35327218 CTATATCTTCAGCCACATTTAAAGCATAAGCAACTAGATCAGCCTCGGCATACTTCTTTGGAGGT
131 CTATATCTTCAGCCACATTTAAAGCATAAGCAACTAAATCAACCTCGGCATACTTCTTTGGAGGT
35327283 TTAATTTCTCTTCTAGTTCTGTTTTTGGCGATAGAGTATTGTGGTGAAGAAGCAACTCTATTCTC
196 TTAATTTCTCTTCTAGTTCTGTTTTTGGCGATAGAGTATTGTGGTGAAGAAGCAACTCTATTCTC
**
35327348 AATTTTTGTTCTGGCTTGAGGAGTTGACTCTGTATTAATCTGATGCTCCACCTGCTTTTGATTTT
261 AATTTTTGCACTGGCTTGAGGAGTTGACTCTGTATTAATCTGATGCTCCACCTGCTTTTGATTTT
35327413 CTTTATTGGAAGAGTCTTTAAGAGATAAGTTAGGTAGCATAGCAGTTTCATCAAAAACAACATCT
326 CTTTATTGGAAGAGTCTTTAAGAGATAAGTTAGGTAGCATAGCAGTTTCATCAAAAACAACATCT
*
35327478 CTGCTAATCACAACTTTTCTATTTTCAGGACACCATAACTTATACCCTTTTACACCAGCTTTATA
391 CTACTAATCACAACTTTTCTATTTTCAGGACACCATAACTTATACCCTTTTACACCAGCTTTATA
35327543 ACCAAGAAAAACACATTTAATGGATCTCGGTTCCAATTTTCCATTATCAACATGAGCATACGCAG
456 ACCAAGAAAAACACATTTAATGGATCTCGGTTCCAATTTTCCATTATCAACATGAGCATACGCAG
35327608 GACACCCAAAAATCTTTAAATCAGAATAATTAGCAGGATTACCAGACCATACCTCTTGT
521 GACACCCAAAAATCTTTAAATCAGAATAATTAGCAGGATTACCAGACCATACCTCTTGT
35327667 GGA
1 GGA
35327670 GTCTTTTTCT
Statistics
Matches: 570, Mismatches: 11, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
578 566 0.99
579 4 0.01
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (579 bp):
GGAAGTTTCACAAGATCCCATGTTTTGTTTTTGTGAAGTGATTCCATGTCCTCTTGCATAGTAAA
CATCCATTTTTCTGAGTCTTCATAGCTAACCGCCTCAGAATAATTAGATGGCTCTTGGTTTGCAT
CTATATCTTCAGCCACATTTAAAGCATAAGCAACTAAATCAACCTCGGCATACTTCTTTGGAGGT
TTAATTTCTCTTCTAGTTCTGTTTTTGGCGATAGAGTATTGTGGTGAAGAAGCAACTCTATTCTC
AATTTTTGCACTGGCTTGAGGAGTTGACTCTGTATTAATCTGATGCTCCACCTGCTTTTGATTTT
CTTTATTGGAAGAGTCTTTAAGAGATAAGTTAGGTAGCATAGCAGTTTCATCAAAAACAACATCT
CTACTAATCACAACTTTTCTATTTTCAGGACACCATAACTTATACCCTTTTACACCAGCTTTATA
ACCAAGAAAAACACATTTAATGGATCTCGGTTCCAATTTTCCATTATCAACATGAGCATACGCAG
GACACCCAAAAATCTTTAAATCAGAATAATTAGCAGGATTACCAGACCATACCTCTTGT
Found at i:35329642 original size:11 final size:11
Alignment explanation
Indices: 35329623--35329651 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
35329613 CAATTTGTGA
35329623 AAAAT-AAAAT
1 AAAATAAAAAT
35329633 AAAATAAAAAT
1 AAAATAAAAAT
35329644 AAAATAAA
1 AAAATAAA
35329652 GAACACACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:35330845 original size:17 final size:17
Alignment explanation
Indices: 35330823--35330857 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
35330813 CAAATTGACA
*
35330823 TAGTTTTGTCTTTTAAC
1 TAGTTTTGACTTTTAAC
35330840 TAGTTTTGACTTTTAAC
1 TAGTTTTGACTTTTAAC
35330857 T
1 T
35330858 TTAGAAAATG
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:0.20, C:0.11, G:0.11, T:0.57
Consensus pattern (17 bp):
TAGTTTTGACTTTTAAC
Found at i:35333463 original size:16 final size:17
Alignment explanation
Indices: 35333439--35333472 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
35333429 TATTAGTTAA
*
35333439 AAATTATTTATTT-TTT
1 AAATAATTTATTTATTT
35333455 AAATAATTTATTTATTT
1 AAATAATTTATTTATTT
35333472 A
1 A
35333473 TCTTTTCTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
AAATAATTTATTTATTT
Found at i:35334675 original size:3 final size:3
Alignment explanation
Indices: 35334669--35334712 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
35334659 TTTTTTGTAA
35334669 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
35334713 ACTAATGATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:35334723 original size:11 final size:11
Alignment explanation
Indices: 35334666--35334724 Score: 50
Period size: 12 Copynumber: 5.4 Consensus size: 11
35334656 ACTTTTTTTG
*
35334666 TAAAATAATAA
1 TAAACTAATAA
35334677 T-AA-TAATAA
1 TAAACTAATAA
*
35334686 TAATAATAATAA
1 TAA-ACTAATAA
*
35334698 TAATAATAATAA
1 TAA-ACTAATAA
*
35334710 TAAACTAATGA
1 TAAACTAATAA
35334721 TAAA
1 TAAA
35334725 GTTTCTAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
9 7 0.16
10 3 0.07
11 12 0.28
12 21 0.49
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (11 bp):
TAAACTAATAA
Found at i:35335069 original size:33 final size:33
Alignment explanation
Indices: 35335027--35335089 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
35335017 ATAAAGTAAG
35335027 TTAAATCAAGTAAGATTCGTCGTTTTAATTAAA
1 TTAAATCAAGTAAGATTCGTCGTTTTAATTAAA
35335060 TTAAATCAAGTAAGATTCGTCGTTTTAATT
1 TTAAATCAAGTAAGATTCGTCGTTTTAATT
35335090 TGGTTAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.41
Consensus pattern (33 bp):
TTAAATCAAGTAAGATTCGTCGTTTTAATTAAA
Found at i:35341624 original size:11 final size:11
Alignment explanation
Indices: 35341610--35341641 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
35341600 TTGTGGTAGT
35341610 ATATTTTGATG
1 ATATTTTGATG
*
35341621 ATATTTTAATG
1 ATATTTTGATG
35341632 ATATTTTGAT
1 ATATTTTGAT
35341642 TTACTCAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (11 bp):
ATATTTTGATG
Found at i:35344092 original size:14 final size:14
Alignment explanation
Indices: 35344073--35344099 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35344063 TTATCAACTC
35344073 TTATTATTTTATTA
1 TTATTATTTTATTA
35344087 TTATTATTTTATT
1 TTATTATTTTATT
35344100 CCAAATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTATTTTATTA
Found at i:35345107 original size:24 final size:23
Alignment explanation
Indices: 35345080--35345131 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
35345070 AAAACTTAGT
* *
35345080 TTTATTTCCAGAATACTAAAGTTA
1 TTTATTTACAAAATACTAAAG-TA
*
35345104 TTTAATTTACAAAATACTCAAGTA
1 TTT-ATTTACAAAATACTAAAGTA
35345128 TTTA
1 TTTA
35345132 GAAGATTGCG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
23 1 0.04
24 8 0.33
25 15 0.62
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (23 bp):
TTTATTTACAAAATACTAAAGTA
Found at i:35349546 original size:31 final size:31
Alignment explanation
Indices: 35349510--35349569 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
35349500 TTTAGAGAGT
35349510 CACACGCCCGTGTGGGTAAGCCGTGTGGCCA
1 CACACGCCCGTGTGGGTAAGCCGTGTGGCCA
** *
35349541 CACACGCCCGTGTGTTTAGGCCGTGTGGC
1 CACACGCCCGTGTGGGTAAGCCGTGTGGC
35349570 GAATTAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.13, C:0.32, G:0.35, T:0.20
Consensus pattern (31 bp):
CACACGCCCGTGTGGGTAAGCCGTGTGGCCA
Found at i:35355116 original size:3 final size:3
Alignment explanation
Indices: 35355110--35355143 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
35355100 TTTGAATCAC
35355110 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
35355144 TTTTATTACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:35356345 original size:12 final size:12
Alignment explanation
Indices: 35356328--35356352 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35356318 TCACTCAAAA
35356328 ACCTAAGCTCTT
1 ACCTAAGCTCTT
35356340 ACCTAAGCTCTT
1 ACCTAAGCTCTT
35356352 A
1 A
35356353 ATTAGTTTAA
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:0.28, C:0.32, G:0.08, T:0.32
Consensus pattern (12 bp):
ACCTAAGCTCTT
Found at i:35359827 original size:14 final size:14
Alignment explanation
Indices: 35359810--35359848 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
35359800 ATCATTATAG
35359810 TTTAGGGTTTATGA
1 TTTAGGGTTTATGA
* *
35359824 TTTAGGGTATATGG
1 TTTAGGGTTTATGA
*
35359838 TTCAGGGTTTA
1 TTTAGGGTTTA
35359849 AAGTGTAGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.21, C:0.03, G:0.31, T:0.46
Consensus pattern (14 bp):
TTTAGGGTTTATGA
Found at i:35362826 original size:8 final size:8
Alignment explanation
Indices: 35362812--35362867 Score: 67
Period size: 8 Copynumber: 7.0 Consensus size: 8
35362802 GTGATTATGA
35362812 TAATAGTG
1 TAATAGTG
*
35362820 GAATAGTG
1 TAATAGTG
*
35362828 GAATAGTG
1 TAATAGTG
* *
35362836 TAATTGCG
1 TAATAGTG
35362844 TAATAGTG
1 TAATAGTG
*
35362852 TAATAGAG
1 TAATAGTG
35362860 TAATAGTG
1 TAATAGTG
35362868 GAATTTTTTG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
8 40 1.00
ACGTcount: A:0.38, C:0.02, G:0.29, T:0.32
Consensus pattern (8 bp):
TAATAGTG
Found at i:35362848 original size:32 final size:32
Alignment explanation
Indices: 35362812--35362872 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
35362802 GTGATTATGA
* *
35362812 TAATAGTGGAATAGTGGAATAGTGTAATTGCG
1 TAATAGTGGAATAGAGGAATAGTGGAATTGCG
* *
35362844 TAATAGTGTAATAGAGTAATAGTGGAATT
1 TAATAGTGGAATAGAGGAATAGTGGAATT
35362873 TTTTGATTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.38, C:0.02, G:0.28, T:0.33
Consensus pattern (32 bp):
TAATAGTGGAATAGAGGAATAGTGGAATTGCG
Found at i:35363719 original size:48 final size:48
Alignment explanation
Indices: 35363667--35363815 Score: 148
Period size: 48 Copynumber: 3.2 Consensus size: 48
35363657 TTTTGTCTAC
*
35363667 TTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTATTTAAAG
1 TTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTATTTATAG
** * * ** * * *
35363715 TTTTATTTTA-TTTTATTTTA-ATCACGAAA--AAACTT-T-TGTCTAC
1 TTTTATTTTATTTTTAAATTACCTAATTAAATTAAA-TTGTATTTATAG
*
35363758 TTTTATTTTATTTATAAATTACCTAATTAAATTAAATTGTATTTATAG
1 TTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTATTTATAG
35363806 TTTTATTTTA
1 TTTTATTTTA
35363816 AGTATTTTAT
Statistics
Matches: 74, Mismatches: 20, Indels: 14
0.69 0.19 0.13
Matches are distributed among these distances:
43 13 0.18
44 11 0.15
45 7 0.09
46 7 0.09
47 12 0.16
48 24 0.32
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (48 bp):
TTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTATTTATAG
Found at i:35364108 original size:10 final size:9
Alignment explanation
Indices: 35364092--35364198 Score: 76
Period size: 9 Copynumber: 11.7 Consensus size: 9
35364082 AAATATATAT
*
35364092 CATATTTTA
1 CATAATTTA
35364101 CATAATTTA
1 CATAATTTA
*
35364110 CATAACTTA
1 CATAATTTA
*
35364119 TATAA--TA
1 CATAATTTA
35364126 CATAAATATATA
1 CAT-AAT-T-TA
35364138 TCAT-ATCTTA
1 -CATAAT-TTA
35364148 CATAATTTA
1 CATAATTTA
**
35364157 CATAATTCG
1 CATAATTTA
* *
35364166 GATAACTTA
1 CATAATTTA
35364175 CATAATTTA
1 CATAATTTA
*
35364184 CATAACTTA
1 CATAATTTA
35364193 CATAAT
1 CATAAT
35364199 ACATAAATAT
Statistics
Matches: 76, Mismatches: 15, Indels: 14
0.72 0.14 0.13
Matches are distributed among these distances:
7 4 0.05
8 2 0.03
9 58 0.76
10 4 0.05
11 3 0.04
12 2 0.03
13 3 0.04
ACGTcount: A:0.44, C:0.14, G:0.02, T:0.40
Consensus pattern (9 bp):
CATAATTTA
Found at i:35364123 original size:18 final size:18
Alignment explanation
Indices: 35364098--35364198 Score: 89
Period size: 18 Copynumber: 5.5 Consensus size: 18
35364088 ATATCATATT
35364098 TTACATAATTTACATAAC
1 TTACATAATTTACATAAC
* *
35364116 TTATATAA--TACATAAA
1 TTACATAATTTACATAAC
* *
35364132 TATATATCATATCTTACATAAT
1 T-TACAT-A-AT-TTACATAAC
***
35364154 TTACATAATTCGGATAAC
1 TTACATAATTTACATAAC
35364172 TTACATAATTTACATAAC
1 TTACATAATTTACATAAC
35364190 TTACATAAT
1 TTACATAAT
35364199 ACATAAATAT
Statistics
Matches: 66, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
16 8 0.12
17 5 0.08
18 37 0.56
19 3 0.05
20 1 0.02
21 4 0.06
22 8 0.12
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.40
Consensus pattern (18 bp):
TTACATAATTTACATAAC
Found at i:35369284 original size:13 final size:14
Alignment explanation
Indices: 35369268--35369296 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
35369258 TTATAAATAT
35369268 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
35369281 TTATAATGGTTTAA
1 TTATAATGGTTTAA
35369295 TT
1 TT
35369297 CGTCGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:35370061 original size:31 final size:31
Alignment explanation
Indices: 35370014--35370079 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
35370004 GTATTTTTTT
*
35370014 ATGCTACATTTGCTGTTTTTGGTTGGATTTC
1 ATGCTACATTTGCTGTTTTTGGTTGGATTTA
* *
35370045 ATGCTATATTTTCTGTTTTTGGTTGGATTTA
1 ATGCTACATTTGCTGTTTTTGGTTGGATTTA
35370076 ATGC
1 ATGC
35370080 AGGAAGGTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.15, C:0.11, G:0.21, T:0.53
Consensus pattern (31 bp):
ATGCTACATTTGCTGTTTTTGGTTGGATTTA
Found at i:35370175 original size:43 final size:43
Alignment explanation
Indices: 35370153--35370245 Score: 116
Period size: 43 Copynumber: 2.2 Consensus size: 43
35370143 AAAAAAGCGT
*
35370153 CGCTAAAAACAATGATTTTTAGCGGCGCTTTTACAAGAAACGC
1 CGCTAAAAACAATGACTTTTAGCGGCGCTTTTACAAGAAACGC
* * * * *
35370196 CGCTAAAAGCCATGACTTTTAGCGGCACTTTT-CTGACAAACGC
1 CGCTAAAAACAATGACTTTTAGCGGCGCTTTTAC-AAGAAACGC
35370239 CGCTAAA
1 CGCTAAA
35370246 TTTTGTAGCG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 1 0.02
43 42 0.98
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (43 bp):
CGCTAAAAACAATGACTTTTAGCGGCGCTTTTACAAGAAACGC
Found at i:35372067 original size:14 final size:14
Alignment explanation
Indices: 35372050--35372078 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
35372040 AATTTTTATT
35372050 AATGAATTATTAAA
1 AATGAATTATTAAA
35372064 AATGAATTATTAAA
1 AATGAATTATTAAA
35372078 A
1 A
35372079 TATAACATTT
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:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (14 bp):
AATGAATTATTAAA
Found at i:35376956 original size:29 final size:30
Alignment explanation
Indices: 35376900--35376970 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
35376890 ACAAAAATAA
* *
35376900 AAAATTATATTTTGGCCCCTAAACTTTT-T
1 AAAAGTATATTTTGACCCCTAAACTTTTCT
* * *
35376929 GAAAGTATATTTTGACCCCTAGATTTTTCT
1 AAAAGTATATTTTGACCCCTAAACTTTTCT
*
35376959 AAAATTATATTT
1 AAAAGTATATTT
35376971 AAACCTCTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 23 0.68
30 11 0.32
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.45
Consensus pattern (30 bp):
AAAAGTATATTTTGACCCCTAAACTTTTCT
Found at i:35376970 original size:30 final size:29
Alignment explanation
Indices: 35376900--35377066 Score: 88
Period size: 30 Copynumber: 5.7 Consensus size: 29
35376890 ACAAAAATAA
*
35376900 AAAATTATATTTTGGCCCCTAAACTTTTT
1 AAAATTATATTTTGACCCCTAAACTTTTT
* * * *
35376929 GAAAGTATATTTTGACCCCTAGATTTTTCT
1 AAAATTATATTTTGACCCCTAAACTTTT-T
** * *
35376959 AAAATTATATTTAAACCTCTAAAATATTTTT
1 AAAATTATATTTTGACCCCT-AAA-CTTTTT
* * **
35376990 AAAA-TAGATTTTAACCTATAAA-TGTTTT
1 AAAATTATATTTTGACCCCTAAACT-TTTT
* * * *
35377018 GAAATTACATTATGACCCCT-AAGTTTTCT
1 AAAATTATATTTTGACCCCTAAACTTTT-T
* *
35377047 CAAAATTATGTTTTGGCCCC
1 -AAAATTATATTTTGACCCC
35377067 AGAGGTTTTG
Statistics
Matches: 104, Mismatches: 26, Indels: 15
0.72 0.18 0.10
Matches are distributed among these distances:
27 1 0.01
28 12 0.12
29 38 0.37
30 42 0.40
31 7 0.07
32 4 0.04
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (29 bp):
AAAATTATATTTTGACCCCTAAACTTTTT
Found at i:35377326 original size:14 final size:16
Alignment explanation
Indices: 35377285--35377328 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
35377275 AGAAAATAGG
35377285 AGAGAAAAGAGAAAGA
1 AGAGAAAAGAGAAAGA
*
35377301 AGAGGAAGAA-AGGAAGA
1 AGA-GAA-AAGAGAAAGA
35377318 AGAGAAAAGAG
1 AGAGAAAAGAG
35377329 GGGAAGGCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
15 2 0.08
16 8 0.33
17 12 0.50
18 2 0.08
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (16 bp):
AGAGAAAAGAGAAAGA
Found at i:35377676 original size:28 final size:26
Alignment explanation
Indices: 35377637--35377736 Score: 83
Period size: 22 Copynumber: 4.0 Consensus size: 26
35377627 CCCAGCAGAA
35377637 AAAAAAAG-AGAAAATGAAGAAAAAAGG
1 AAAAAAAGAAGAAAA-GAAGAAAAAA-G
*
35377664 AAAAAAAGAAGAAAA-AAG--AGAAG
1 AAAAAAAGAAGAAAAGAAGAAAAAAG
*
35377687 -AAAATAGAAGAAAA-AAG-AAAAAG
1 AAAAAAAGAAGAAAAGAAGAAAAAAG
35377710 AGAAAAAAG-AGAAAAAGAA-AAAAAAG
1 A-AAAAAAGAAG-AAAAGAAGAAAAAAG
35377736 A
1 A
35377737 GGTTCAATTC
Statistics
Matches: 62, Mismatches: 4, Indels: 15
0.77 0.05 0.19
Matches are distributed among these distances:
22 16 0.26
23 5 0.08
24 5 0.08
25 10 0.16
26 12 0.19
27 8 0.13
28 6 0.10
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (26 bp):
AAAAAAAGAAGAAAAGAAGAAAAAAG
Found at i:35377689 original size:40 final size:38
Alignment explanation
Indices: 35377633--35377722 Score: 118
Period size: 37 Copynumber: 2.4 Consensus size: 38
35377623 GCAGCCCAGC
35377633 AGAA-AAAAAA-AG-AGAAAAT-GAAGAAAAAAGGAAAAAA
1 AGAAGAAAAAAGAGAAGAAAATAGAAGAAAAAA-G--AAAA
35377670 AGAAGAAAAAAGAGAAGAAAATAGAAGAAAAAAGAAAA
1 AGAAGAAAAAAGAGAAGAAAATAGAAGAAAAAAGAAAA
35377708 AG-AGAAAAAAGAGAA
1 AGAAGAAAAAAGAGAA
35377723 AAAGAAAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
37 17 0.35
38 12 0.24
39 2 0.04
40 8 0.16
41 10 0.20
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (38 bp):
AGAAGAAAAAAGAGAAGAAAATAGAAGAAAAAAGAAAA
Found at i:35377728 original size:40 final size:41
Alignment explanation
Indices: 35377633--35377730 Score: 123
Period size: 40 Copynumber: 2.5 Consensus size: 41
35377623 GCAGCCCAGC
*
35377633 AGAAAAAA-AAAGAGAAAATGAAGAAAAAAGGAAAAAAAGA
1 AGAAAAAAGAAAAAGAAAATGAAGAAAAAAGGAAAAAAAGA
* *
35377673 AGAAAAAAG-AGAAGAAAATAGAAGAAAAAA-GAAAAAGAGA
1 AGAAAAAAGAAAAAGAAAAT-GAAGAAAAAAGGAAAAAAAGA
*
35377713 A-AAAAGAGAAAAAGAAAA
1 AGAAAAAAGAAAAAGAAAA
35377731 AAAAGAGGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
39 6 0.12
40 34 0.68
41 10 0.20
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (41 bp):
AGAAAAAAGAAAAAGAAAATGAAGAAAAAAGGAAAAAAAGA
Found at i:35377736 original size:9 final size:9
Alignment explanation
Indices: 35377636--35377734 Score: 69
Period size: 9 Copynumber: 10.6 Consensus size: 9
35377626 GCCCAGCAGA
35377636 AAAAAAAAG
1 AAAAAAAAG
* *
35377645 -AGAAAATG
1 AAAAAAAAG
35377653 AAGAAAAAAG
1 AA-AAAAAAG
*
35377663 GAAAAAAAG
1 AAAAAAAAG
35377672 AAGAAAAAAG
1 AA-AAAAAAG
35377682 AGAAGAAAATAG
1 A-AA-AAAA-AG
35377694 AAGAAAAAAG
1 AA-AAAAAAG
*
35377704 -AAAAAGAG
1 AAAAAAAAG
*
35377712 AAAAAAGAG
1 AAAAAAAAG
35377721 AAAAAGAAA-
1 AAAAA-AAAG
35377730 AAAAA
1 AAAAA
35377735 GAGGTTCAAT
Statistics
Matches: 73, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
8 12 0.16
9 28 0.38
10 19 0.26
11 10 0.14
12 4 0.05
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:35378080 original size:18 final size:18
Alignment explanation
Indices: 35378059--35378559 Score: 192
Period size: 17 Copynumber: 28.1 Consensus size: 18
35378049 ATTGTAAATA
35378059 TTCAAAAAATTTCGTGTT
1 TTCAAAAAATTTCGTGTT
*
35378077 TTCACAAAAAATTTCCT-TGT
1 TT--CAAAAAATTTCGTGT-T
* * **
35378097 TTC-GAAATTTTCGTGGC
1 TTCAAAAAATTTCGTGTT
35378114 TTCAAAATAATTTTTC-TCGTGT
1 TTCAAAA-AA--TTTCGT-GT-T
35378136 TTC-AAAAATATTCGTGTT
1 TTCAAAAAAT-TTCGTGTT
* * *
35378154 TTCAAAAGATTCCAT-TT
1 TTCAAAAAATTTCGTGTT
*
35378171 TTC-AAAATTTTCCGTGTT
1 TTCAAAAAATTT-CGTGTT
* *
35378189 TTCTAAAAATTTCCATG-T
1 TTCAAAAAATTT-CGTGTT
*
35378207 TTC-TAAAATTT-GTG-T
1 TTCAAAAAATTTCGTGTT
* *
35378222 TTCAAAAATTTTCGTGTA
1 TTCAAAAAATTTCGTGTT
**
35378240 TTC-AAAAATTTTTTGTAT
1 TTCAAAAAATTTCGTGT-T
** *
35378258 TTTGAACAATTCTCGTG-T
1 TTCAAAAAATT-TCGTGTT
* *
35378276 TTCACAAATTTTCGTGTT
1 TTCAAAAAATTTCGTGTT
**** **
35378294 TT-AATTTTTTTTATGTT
1 TTCAAAAAATTTCGTGTT
*
35378311 TTAAAAAAAATTATCGTG-T
1 TT-CAAAAAATT-TCGTGTT
*
35378330 TTCAAAAAATTGTCGTCTT
1 TTCAAAAAATT-TCGTGTT
* *
35378349 TT-AAAAATTTTTGTG-T
1 TTCAAAAAATTTCGTGTT
* * *
35378365 TTCTAAAATTTTCGT-AT
1 TTCAAAAAATTTCGTGTT
*
35378382 TTCAAAAATTTTCGTGTT
1 TTCAAAAAATTTCGTGTT
*
35378400 TTC-AAAAATTCCG-GTGT
1 TTCAAAAAATTTCGTGT-T
*
35378417 TTCAAAAAATTCCCGTGTT
1 TTCAAAAAATT-TCGTGTT
35378436 TT--AAAAATTTCCGTGTT
1 TTCAAAAAATTT-CGTGTT
*
35378453 TTC-AAAAATTTCGTGGT
1 TTCAAAAAATTTCGTGTT
**
35378470 TTC--AAAATTTTTTGTAT
1 TTCAAAAAATTTCGTGT-T
* *
35378487 TTC-AAAAATCCTCATGTT
1 TTCAAAAAAT-TTCGTGTT
*
35378505 TTC-AAAAATTTCAGTGTG
1 TTCAAAAAATTTC-GTGTT
* *
35378523 TT-GAAAATTTTCGTGTT
1 TTCAAAAAATTTCGTGTT
*
35378540 TTCAAAAAAATCTCGTGTT
1 TTC-AAAAAATTTCGTGTT
35378559 T
1 T
35378560 CATAAATTTT
Statistics
Matches: 363, Mismatches: 77, Indels: 85
0.69 0.15 0.16
Matches are distributed among these distances:
15 6 0.02
16 25 0.07
17 129 0.36
18 103 0.28
19 62 0.17
20 27 0.07
21 8 0.02
22 3 0.01
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.47
Consensus pattern (18 bp):
TTCAAAAAATTTCGTGTT
Found at i:35378152 original size:17 final size:17
Alignment explanation
Indices: 35378130--35378570 Score: 250
Period size: 17 Copynumber: 25.1 Consensus size: 17
35378120 ATAATTTTTC
*
35378130 TCGTGTTTCAAAAATAT
1 TCGTGTTTCAAAAATTT
35378147 TCGTGTTTTCAAAAGA-TT
1 TCGTG-TTTCAAAA-ATTT
* * *
35378165 CCATTTTTC-AAAATTT
1 TCGTGTTTCAAAAATTT
35378181 TCCGTGTTTTCTAAAAATTT
1 T-CGTG-TTTC-AAAAATTT
* * *
35378201 CCATGTTTCTAAAA-TT
1 TCGTGTTTCAAAAATTT
35378217 T-GTGTTTCAAAAATTT
1 TCGTGTTTCAAAAATTT
35378233 TCGTGTATTCAAAAATTTT
1 TCGTGT-TTCAAAAA-TTT
* * * * *
35378252 TTGTATTTTGAACAATTC
1 TCGT-GTTTCAAAAATTT
*
35378270 TCGTGTTTCACAAATTT
1 TCGTGTTTCAAAAATTT
* ***
35378287 TCGTGTTTTAATTTTTT
1 TCGTGTTTCAAAAATTT
** * *
35378304 TTATGTTTTAAAAAAAATTA
1 TCGTG-TTT--CAAAAATTT
*
35378324 TCGTGTTTCAAAAAATTG
1 TCGTGTTTC-AAAAATTT
* *
35378342 TCGTCTTTTAAAAATTT
1 TCGTGTTTCAAAAATTT
* *
35378359 TTGTGTTTCTAAAATTT
1 TCGTGTTTCAAAAATTT
*
35378376 TCGTATTTCAAAAATTT
1 TCGTGTTTCAAAAATTT
35378393 TCGTGTTTTCAAAAA-TT
1 TCGTG-TTTCAAAAATTT
* *
35378410 CCGGTGTTTCAAAAAATTC
1 TC-GTGTTTC-AAAAATTT
* *
35378429 CCGTGTTTTAAAAATTT
1 TCGTGTTTCAAAAATTT
*
35378446 CCGTGTTTTCAAAAA-TT
1 TCGTG-TTTCAAAAATTT
*
35378463 TCGTGGTTTCAAAATTTT
1 TCGT-GTTTCAAAAATTT
* * **
35378481 TTGTATTTCAAAAATCC
1 TCGTGTTTCAAAAATTT
*
35378498 TCATGTTTTCAAAAA-TT
1 TCGTG-TTTCAAAAATTT
*
35378515 TCAGTGTGTT-GAAAATTT
1 TC-GTGT-TTCAAAAATTT
* *
35378533 TCGTGTTTTCAAAAAAATC
1 TCGTG-TTTC-AAAAATTT
*
35378552 TCGTGTTTCATAAATTT
1 TCGTGTTTCAAAAATTT
35378569 TC
1 TC
35378571 ATTTTTTTAA
Statistics
Matches: 318, Mismatches: 76, Indels: 60
0.70 0.17 0.13
Matches are distributed among these distances:
15 11 0.03
16 10 0.03
17 142 0.45
18 108 0.34
19 32 0.10
20 15 0.05
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (17 bp):
TCGTGTTTCAAAAATTT
Found at i:35378224 original size:15 final size:15
Alignment explanation
Indices: 35378204--35378250 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
35378194 AAAATTTCCA
*
35378204 TGTTTCTAAAATTTG
1 TGTTTCAAAAATTTG
35378219 TGTTTCAAAAATTTTCG
1 TGTTTCAAAAA-TTT-G
35378236 TGTATTCAAAAATTT
1 TGT-TTCAAAAATTT
35378251 TTTGTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 10 0.36
16 3 0.11
17 7 0.25
18 8 0.29
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.49
Consensus pattern (15 bp):
TGTTTCAAAAATTTG
Found at i:35378285 original size:54 final size:51
Alignment explanation
Indices: 35378170--35378616 Score: 199
Period size: 52 Copynumber: 8.5 Consensus size: 51
35378160 AGATTCCATT
** *
35378170 TTTC-AAAATTTTCCGTGTTTTCTAAAAATTTCCATGTTTCTAAAATT-T-GTG
1 TTTCAAAAATTTT-CGTG-TTTC-AAAAATTTTTATGTTTTTAAAATTATCGTG
*
35378221 TTTCAAAAATTTTCGTGTATTCAAAAATTTTT-TGTATTTTGAACAATTCTCGTG
1 TTTCAAAAATTTTCGTGT-TTCAAAAATTTTTATGT-TTTT-AA-AATTATCGTG
* * *** *
35378275 TTTCACAAATTTTCGTGTTTTAATTTTTTTTATGTTTTAAAAAAAATTATCGTG
1 TTTCAAAAATTTTCGTGTTTCAAAAATTTTTATGTTTT---TAAAATTATCGTG
* * * * * * *
35378329 TTTCAAAAAATTGTCGTCTTTTAAAAATTTTTGTGTTTCTAAAATTTTCGTA
1 TTTC-AAAAATTTTCGTGTTTCAAAAATTTTTATGTTTTTAAAATTATCGTG
**** ** **
35378381 TTTCAAAAATTTTCGTGTTTTCAAAAATTCCGGTGTTTCAAAAAATTCCCGTG
1 TTTCAAAAATTTTCGTG-TTTCAAAAATTTTTATGTTT-TTAAAATTATCGTG
* * ** * * * * *
35378434 TTTTAAAAATTTCCGTGTTTTCAAAAA-TTTCGTGGTTTCAAAATTTTTTGTA
1 TTTCAAAAATTTTCGTG-TTTCAAAAATTTTTATGTTTTTAAAA-TTATCGTG
** * * * * *
35378486 TTTCAAAAATCCTCATGTTTTCAAAAA-TTTCAGTGTGTTGAAAATTTTCGTG
1 TTTCAAAAATTTTCGTG-TTTCAAAAATTTTTA-TGTTTTTAAAATTATCGTG
* * * * * * *
35378538 TTTTCAAAAAAATCTCGTGTTTCATAAATTTTCATTTTTTTAAAAAATAAT--TA
1 -TTTC-AAAAATTTTCGTGTTTCAAAAATTTTTATGTTTTT--AAAATTATCGTG
* *
35378591 TTTCAAAAATCTTCGTGTTTTAAAAA
1 TTTCAAAAATTTTCGTGTTTCAAAAA
35378617 AAATTCGTTT
Statistics
Matches: 305, Mismatches: 70, Indels: 42
0.73 0.17 0.10
Matches are distributed among these distances:
49 3 0.01
50 12 0.04
51 45 0.15
52 88 0.29
53 72 0.24
54 51 0.17
55 34 0.11
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.47
Consensus pattern (51 bp):
TTTCAAAAATTTTCGTGTTTCAAAAATTTTTATGTTTTTAAAATTATCGTG
Found at i:35378420 original size:35 final size:34
Alignment explanation
Indices: 35378059--35378617 Score: 240
Period size: 35 Copynumber: 15.8 Consensus size: 34
35378049 ATTGTAAATA
* *
35378059 TTCAAAAAATTTCGTGTTTTCACAAAAAATTTCCTTGT
1 TTCAAAAATTTTCGTGTTTT--C-AAAAA-TTCCGTGT
* **
35378097 TTC-GAAATTTTCGTGGCTTCAAAATAATTTTTCTCGTGT
1 TTCAAAAATTTTCGTGTTTTC-AAA-AA---TTC-CGTGT
* * *
35378136 TTCAAAAATATTCGTGTTTTCAAAAGATTCCATTT
1 TTCAAAAATTTTCGTGTTTTCAAAA-ATTCCGTGT
*
35378171 TTC-AAAATTTTCCGTGTTTTCTAAAAATTTCCATGT
1 TTCAAAAATTTT-CGTGTTTTC-AAAAA-TTCCGTGT
* *
35378207 TTCTAAAA-TTT-GTG-TTTCAAAAATTTTCGTGT
1 TTCAAAAATTTTCGTGTTTTCAAAAA-TTCCGTGT
* * * *
35378239 ATTCAAAAATTTTTTGTATTTTGAACAATTCTCGTGT
1 -TTCAAAAA-TTTTCGTGTTTTCAAAAATTC-CGTGT
* *** ***
35378276 TTCACAAATTTTCGTGTTTT-AATTTTTTTTATGTT
1 TTCAAAAATTTTCGTGTTTTCAA-AAATTCCGTG-T
* * * *
35378311 TTAAAAAAAATTATCGTG-TTTCAAAAAATTGTCGTCT
1 TT--CAAAAATTTTCGTGTTTTC-AAAAATT-CCGTGT
* * * * *
35378348 TTTAAAAATTTTTGTG-TTTCTAAAATTTTCGTAT
1 TTCAAAAATTTTCGTGTTTTC-AAAAATTCCGTGT
35378382 TTCAAAAATTTTCGTGTTTTCAAAAATTCCGGTGT
1 TTCAAAAATTTTCGTGTTTTCAAAAATTCC-GTGT
**
35378417 TTCAAAAAATTCCCGTGTTTT-AAAAATTTCCGTGTT
1 TTC-AAAAATTTTCGTGTTTTCAAAAA-TTCCGTG-T
* * ** *
35378453 TTCAAAAA-TTTCGTGGTTTCAAAATTTTTTGTAT
1 TTCAAAAATTTTCGTGTTTTCAAAA-ATTCCGTGT
** * *
35378487 TTCAAAAATCCTCATGTTTTCAAAAATTTCAGTGT
1 TTCAAAAATTTTCGTGTTTTCAAAAA-TTCCGTGT
* *
35378522 GTT-GAAAATTTTCGTGTTTTCAAAAAAATCTCGTGT
1 -TTCAAAAATTTTCGTGTTTTC-AAAAATTC-CGTGT
* * * * * *** *
35378558 TTCATAAATTTTCATTTTTTTAAAAAATAATTAT
1 TTCAAAAATTTTCGTGTTTTCAAAAATTCCGTGT
* *
35378592 TTCAAAAATCTTCGTGTTTTAAAAAA
1 TTCAAAAATTTTCGTGTTTTCAAAAA
35378618 AATTCGTTTT
Statistics
Matches: 399, Mismatches: 86, Indels: 76
0.71 0.15 0.14
Matches are distributed among these distances:
32 12 0.03
33 11 0.03
34 80 0.20
35 133 0.33
36 83 0.21
37 44 0.11
38 12 0.03
39 11 0.03
40 13 0.03
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.46
Consensus pattern (34 bp):
TTCAAAAATTTTCGTGTTTTCAAAAATTCCGTGT
Found at i:35378505 original size:87 final size:87
Alignment explanation
Indices: 35378153--35378570 Score: 246
Period size: 87 Copynumber: 4.8 Consensus size: 87
35378143 ATATTCGTGT
* * * * *
35378153 TTTCAAAAGATT-CCAT-TTTTCAAAATTTTCCGTGTTTTCTAAAAATTTCCATGTTTCTAAAA-
1 TTTCAAAAAATTCCCGTGTTTTAAAAATTTT-CGTGTTTTCAAAAAATTT-CGTGTTTC-AAAAT
** *
35378215 TTT-GTG-TTTCAAAAATTTTCGTG
63 TTTCGTGTTTTCAAAAATTCCCATG
* *** * * * * * * **
35378238 TATTCAAAAATTTTTTGTATTTTGAACAATTCTCGTG-TTTCACAAATTTTCGTGTTTTAATTTT
1 T-TTCAAAAAATTCCCGTGTTTT-AAAAATTTTCGTGTTTTCAAAAAATTTCGTGTTTCAA-AAT
** * ** *
35378302 TTTTATGTTTTAAAAAAAATTATCGTG
63 TTTCGTGTTTT--CAAAAATTCCCATG
** * * * * *
35378329 TTTCAAAAAATTGTCGTCTTTTAAAAATTTTTGTG-TTTCTAAAATTTTCGTATTTCAAAAATTT
1 TTTCAAAAAATTCCCGTGTTTTAAAAATTTTCGTGTTTTCAAAAAATTTCGTGTTTC-AAAATTT
**
35378393 TCGTGTTTTCAAAAATTCCGGTG
65 TCGTGTTTTCAAAAATTCCCATG
*
35378416 TTTCAAAAAATTCCCGTGTTTTAAAAATTTCCGTGTTTTC-AAAAATTTCGTGGTTTCAAAATTT
1 TTTCAAAAAATTCCCGTGTTTTAAAAATTTTCGTGTTTTCAAAAAATTTCGT-GTTTCAAAATTT
*
35378480 T-TTGTATTTCAAAAA-TCCTCATG
65 TCGTGT-TTTCAAAAATTCC-CATG
* * * * *
35378503 TTTTC-AAAAATTTCAGTGTGTTGAAAATTTTCGTGTTTTCAAAAAAATCTCGTGTTTCATAAAT
1 -TTTCAAAAAATTCCCGTGTTTTAAAAATTTTCGTGTTTTC-AAAAAATTTCGTGTTTCA-AAAT
35378567 TTTC
63 TTTC
35378571 ATTTTTTTAA
Statistics
Matches: 260, Mismatches: 53, Indels: 35
0.75 0.15 0.10
Matches are distributed among these distances:
85 3 0.01
86 21 0.08
87 113 0.43
88 28 0.11
89 63 0.24
90 19 0.07
91 13 0.05
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (87 bp):
TTTCAAAAAATTCCCGTGTTTTAAAAATTTTCGTGTTTTCAAAAAATTTCGTGTTTCAAAATTTT
CGTGTTTTCAAAAATTCCCATG
Found at i:35389521 original size:29 final size:28
Alignment explanation
Indices: 35389485--35389562 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
35389475 TCATGAGATT
35389485 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
35389515 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
35389542 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
35389563 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:35389780 original size:174 final size:174
Alignment explanation
Indices: 35389515--35389842 Score: 602
Period size: 174 Copynumber: 1.9 Consensus size: 174
35389505 AAATTGTACA
*
35389515 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* * *
35389580 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTATCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
35389645 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
*
35389689 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
*
35389754 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
35389819 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
35389843 ACCTTGAGTT
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
174 148 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:35394343 original size:30 final size:31
Alignment explanation
Indices: 35394309--35394414 Score: 139
Period size: 30 Copynumber: 3.5 Consensus size: 31
35394299 AAGATAACAG
* *
35394309 TATAATAAAATTGCTCACACAAGCTT-TCAT
1 TATAATAGATTTGCTCACACAAGCTTGTCAT
*
35394339 TATAATAGATTTGCTCACACAAG-TTGTCCT
1 TATAATAGATTTGCTCACACAAGCTTGTCAT
* *
35394369 TATAATAGATTTGCTCACACAAGC-TGACAG
1 TATAATAGATTTGCTCACACAAGCTTGTCAT
35394399 TATAATAGATTT-CTCA
1 TATAATAGATTTGCTCA
35394415 TCCGGGCTAA
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
29 6 0.09
30 62 0.91
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (31 bp):
TATAATAGATTTGCTCACACAAGCTTGTCAT
Found at i:35405130 original size:14 final size:12
Alignment explanation
Indices: 35405092--35405148 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 12
35405082 GTACATGTTC
35405092 ATAAAATAAATAT
1 ATAAAAT-AATAT
35405105 ATAAAATAATAT
1 ATAAAATAATAT
*
35405117 ATAACACATGATAT
1 ATAA-A-ATAATAT
**
35405131 ATGCAATATATAT
1 ATAAAATA-ATAT
35405144 ATAAA
1 ATAAA
35405149 TGAAATGACT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
12 11 0.31
13 16 0.46
14 8 0.23
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.32
Consensus pattern (12 bp):
ATAAAATAATAT
Found at i:35405692 original size:14 final size:13
Alignment explanation
Indices: 35405673--35405709 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
35405663 AGTAAGATAT
35405673 AATAATAATATAAA
1 AATAATAATAT-AA
*
35405687 AATAATAATGTAA
1 AATAATAATATAA
35405700 AATAATAATA
1 AATAATAATA
35405710 ATTTGTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (13 bp):
AATAATAATATAA
Found at i:35407850 original size:205 final size:205
Alignment explanation
Indices: 35407403--35407984 Score: 850
Period size: 206 Copynumber: 2.8 Consensus size: 205
35407393 CTGCTTCTTG
* * * *
35407403 GATTTGTTCTCTGACAATACAGAGACGCCAAATCATCTTAGATTTGC-TCCAGCGTAAGCACGCG
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCC-TCGTAAACACGTG
* * *
35407467 AAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGAATGCCAAATCATCTTGGA
65 AAAGCCAAATCAGCTATGTCTTTGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGA
* ** *
35407532 TCTTGCTTCAGTGA-GATTATCTGAAGATG--ATATCTGCTATGTATCTGCTCCCCGTTGAAGTG
130 TC-TGCTTCAGT-ATAAACATCTGAA-A-GCCAGATCTGCTATGTATCTGCTCCCCGTTGAAGTG
* *
35407594 GAGATGCCAGACTTT
191 GAGATGCCAAACTTC
*
35407609 GATTTGTTCTCTGAAAATACAGAGATGCCAAATCATCTTAGATTTGCTTCCTCGTAAACACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCCTCGTAAACACGTGA
* *
35407674 AAGCCAAATCAGCTACGTCTTTGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTTGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGAT
35407739 CTGCTTCAGTATAAACATCTGAAAGCCAGATCTGCTATGTATCTGCTCCCCGTTGAAGTGGAGAT
131 CTGCTTCAGTATAAACATCTGAAAGCCAGATCTGCTATGTATCTGCTCCCCGTTGAAGTGGAGAT
35407804 GCCAAACTTC
196 GCCAAACTTC
* * * *
35407814 GATTTGCTCTCTGACAATACAGAGATGACC-AATCATCTTAGATTTGCTTCATTGTAAACACATG
1 GATTTGTTCTCTGACAATACAGAGATG-CCAAATCATCTTAGATTTGCTTCCTCGTAAACACGTG
* * *
35407878 AAAGTCAAATCAGCTATGTCTTTGATTTGTTCCTTGTAAGCACAAGGATGCCCAAATCATTTTGG
65 AAAGCCAAATCAGCTATGTCTTTGATTTGCTCCTTGTAAGCACAAGGATG-CCAAATCATCTTGG
*
35407943 ATCTGCTTCAGTATAAACATCTGAATGCCAGATCTGCTATGT
129 ATCTGCTTCAGTATAAACATCTGAAAGCCAGATCTGCTATGT
35407985 TGTGGCTTGT
Statistics
Matches: 343, Mismatches: 27, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
203 1 0.00
204 2 0.01
205 165 0.48
206 172 0.50
207 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (205 bp):
GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCCTCGTAAACACGTGA
AAGCCAAATCAGCTATGTCTTTGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGAT
CTGCTTCAGTATAAACATCTGAAAGCCAGATCTGCTATGTATCTGCTCCCCGTTGAAGTGGAGAT
GCCAAACTTC
Found at i:35411554 original size:133 final size:133
Alignment explanation
Indices: 35411316--35411583 Score: 536
Period size: 133 Copynumber: 2.0 Consensus size: 133
35411306 TCGACTTCAA
35411316 TTTCTTTTTTACTGACTACGAAGCCTAATAACTTTCCTGATCTGGCTCCAAAAGTACACTTTGCT
1 TTTCTTTTTTACTGACTACGAAGCCTAATAACTTTCCTGATCTGGCTCCAAAAGTACACTTTGCT
35411381 GGATTGAGCTTCAGTTGAAATTTTCTCAACCTCAAGAACAATCTTCTCAAGACCTCAATGTGCTC
66 GGATTGAGCTTCAGTTGAAATTTTCTCAACCTCAAGAACAATCTTCTCAAGACCTCAATGTGCTC
35411446 TTT
131 TTT
35411449 TTTCTTTTTTACTGACTACGAAGCCTAATAACTTTCCTGATCTGGCTCCAAAAGTACACTTTGCT
1 TTTCTTTTTTACTGACTACGAAGCCTAATAACTTTCCTGATCTGGCTCCAAAAGTACACTTTGCT
35411514 GGATTGAGCTTCAGTTGAAATTTTCTCAACCTCAAGAACAATCTTCTCAAGACCTCAATGTGCTC
66 GGATTGAGCTTCAGTTGAAATTTTCTCAACCTCAAGAACAATCTTCTCAAGACCTCAATGTGCTC
35411579 TTT
131 TTT
35411582 TT
1 TT
35411584 CTGTGCGCGA
Statistics
Matches: 135, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
133 135 1.00
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (133 bp):
TTTCTTTTTTACTGACTACGAAGCCTAATAACTTTCCTGATCTGGCTCCAAAAGTACACTTTGCT
GGATTGAGCTTCAGTTGAAATTTTCTCAACCTCAAGAACAATCTTCTCAAGACCTCAATGTGCTC
TTT
Found at i:35417780 original size:15 final size:15
Alignment explanation
Indices: 35417738--35417787 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
35417728 ATAACTTTGA
*
35417738 ATGCAAATG-ATGTG
1 ATGCAAATGCATGAG
35417752 ATG-AAATGCTATGAG
1 ATGCAAATGC-ATGAG
35417767 ATGCAAATGCATGA-
1 ATGCAAATGCATGAG
35417781 ATGCAAA
1 ATGCAAA
35417788 AAGGATATCG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.31
15 11 0.34
16 6 0.19
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.24
Consensus pattern (15 bp):
ATGCAAATGCATGAG
Found at i:35423865 original size:12 final size:13
Alignment explanation
Indices: 35423840--35423868 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
35423830 GTACATGTTC
35423840 ATAAAATAAATAT
1 ATAAAATAAATAT
35423853 ATAAAAT-AATAT
1 ATAAAATAAATAT
35423865 ATAA
1 ATAA
35423869 CACATGATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAAAATAAATAT
Found at i:35424445 original size:12 final size:13
Alignment explanation
Indices: 35424420--35424448 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
35424410 GTACATGTTC
35424420 ATAAAATAAATAT
1 ATAAAATAAATAT
35424433 ATAAAAT-AATAT
1 ATAAAATAAATAT
35424445 ATAA
1 ATAA
35424449 CACATGATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAAAATAAATAT
Found at i:35424633 original size:580 final size:580
Alignment explanation
Indices: 35423533--35424695 Score: 2326
Period size: 580 Copynumber: 2.0 Consensus size: 580
35423523 CCTTATTTTT
35423533 AAAAAAACATGATGCATGGGGAATTATATTGTATTATAAATCATACATAGTAACATATTATTGTA
1 AAAAAAACATGATGCATGGGGAATTATATTGTATTATAAATCATACATAGTAACATATTATTGTA
35423598 GTAGGTAAATAATACATGCATTTAAACAAAATGATGGCAATAATATAAAGATCGCGCATTAGATA
66 GTAGGTAAATAATACATGCATTTAAACAAAATGATGGCAATAATATAAAGATCGCGCATTAGATA
35423663 CATACATATAAAAATAATATATACATAGCAAATATTAACCATATGCATACAAGGATATATATATA
131 CATACATATAAAAATAATATATACATAGCAAATATTAACCATATGCATACAAGGATATATATATA
35423728 TAGCATGTATTGAGAAATGAATAAACAACACGTACAAACATACAAAGTAATAATTAAATAATGCA
196 TAGCATGTATTGAGAAATGAATAAACAACACGTACAAACATACAAAGTAATAATTAAATAATGCA
35423793 TGATATACACAAAAAAAAATACAATATCAATATCAATGTACATGTTCATAAAATAAATATATAAA
261 TGATATACACAAAAAAAAATACAATATCAATATCAATGTACATGTTCATAAAATAAATATATAAA
35423858 ATAATATATAACACATGATATATGCAATATATATATATATAAAATGAAATGAGTTATTATTAACA
326 ATAATATATAACACATGATATATGCAATATATATATATATAAAATGAAATGAGTTATTATTAACA
35423923 AAATATACGTATAATATAAATAAAAACATAATATTTAATAATAATCTTAAAATAGTGTTTGCTAT
391 AAATATACGTATAATATAAATAAAAACATAATATTTAATAATAATCTTAAAATAGTGTTTGCTAT
35423988 ACAATATATAAAACATAATAACAAAATATTTATAAAAGAATAATAATTATATATAAAATATACTG
456 ACAATATATAAAACATAATAACAAAATATTTATAAAAGAATAATAATTATATATAAAATATACTG
35424053 GGTTTAAAAAACATAAAATAAAAGTATGTAAAAGAATTTATAAAATAACGCATAACATAA
521 GGTTTAAAAAACATAAAATAAAAGTATGTAAAAGAATTTATAAAATAACGCATAACATAA
35424113 AAAAAAACATGATGCATGGGGAATTATATTGTATTATAAATCATACATAGTAACATATTATTGTA
1 AAAAAAACATGATGCATGGGGAATTATATTGTATTATAAATCATACATAGTAACATATTATTGTA
35424178 GTAGGTAAATAATACATGCATTTAAACAAAATGATGGCAATAATATAAAGATCGCGCATTAGATA
66 GTAGGTAAATAATACATGCATTTAAACAAAATGATGGCAATAATATAAAGATCGCGCATTAGATA
35424243 CATACATATAAAAATAATATATACATAGCAAATATTAACCATATGCATACAAGGATATATATATA
131 CATACATATAAAAATAATATATACATAGCAAATATTAACCATATGCATACAAGGATATATATATA
35424308 TAGCATGTATTGAGAAATGAATAAACAACACGTACAAACATACAAAGTAATAATTAAATAATGCA
196 TAGCATGTATTGAGAAATGAATAAACAACACGTACAAACATACAAAGTAATAATTAAATAATGCA
35424373 TGATATACACAAAAAAAAATACAATATCAATATCAATGTACATGTTCATAAAATAAATATATAAA
261 TGATATACACAAAAAAAAATACAATATCAATATCAATGTACATGTTCATAAAATAAATATATAAA
35424438 ATAATATATAACACATGATATATGCAATATATATATATATAAAATGAAATGAGTTATTATTAACA
326 ATAATATATAACACATGATATATGCAATATATATATATATAAAATGAAATGAGTTATTATTAACA
35424503 AAATATACGTATAATATAAATAAAAACATAATATTTAATAATAATCTTAAAATAGTGTTTGCTAT
391 AAATATACGTATAATATAAATAAAAACATAATATTTAATAATAATCTTAAAATAGTGTTTGCTAT
35424568 ACAATATATAAAACATAATAACAAAATATTTATAAAAGAATAATAATTATATATAAAATATACTG
456 ACAATATATAAAACATAATAACAAAATATTTATAAAAGAATAATAATTATATATAAAATATACTG
35424633 GGTTTAAAAAACATAAAATAAAAGTATGTAAAAGAATTTATAAAATAACGCATAACATAA
521 GGTTTAAAAAACATAAAATAAAAGTATGTAAAAGAATTTATAAAATAACGCATAACATAA
35424693 AAA
1 AAA
35424696 TATCATTTTA
Statistics
Matches: 583, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
580 583 1.00
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.30
Consensus pattern (580 bp):
AAAAAAACATGATGCATGGGGAATTATATTGTATTATAAATCATACATAGTAACATATTATTGTA
GTAGGTAAATAATACATGCATTTAAACAAAATGATGGCAATAATATAAAGATCGCGCATTAGATA
CATACATATAAAAATAATATATACATAGCAAATATTAACCATATGCATACAAGGATATATATATA
TAGCATGTATTGAGAAATGAATAAACAACACGTACAAACATACAAAGTAATAATTAAATAATGCA
TGATATACACAAAAAAAAATACAATATCAATATCAATGTACATGTTCATAAAATAAATATATAAA
ATAATATATAACACATGATATATGCAATATATATATATATAAAATGAAATGAGTTATTATTAACA
AAATATACGTATAATATAAATAAAAACATAATATTTAATAATAATCTTAAAATAGTGTTTGCTAT
ACAATATATAAAACATAATAACAAAATATTTATAAAAGAATAATAATTATATATAAAATATACTG
GGTTTAAAAAACATAAAATAAAAGTATGTAAAAGAATTTATAAAATAACGCATAACATAA
Found at i:35425030 original size:16 final size:16
Alignment explanation
Indices: 35424970--35425051 Score: 55
Period size: 16 Copynumber: 5.1 Consensus size: 16
35424960 TAAGAACAAT
35424970 ATATATAAATAATTAATAA
1 ATATA-AAATAA-TAAT-A
* *
35424989 ATATATAATACA-AGTA
1 ATATAAAATA-ATAATA
* *
35425005 AGATATAATAATAATA
1 ATATAAAATAATAATA
35425021 ATAT--AA-AATAATA
1 ATATAAAATAATAATA
*
35425034 ATGTAAAATAATAATA
1 ATATAAAATAATAATA
35425050 AT
1 AT
35425052 TTGTGAAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
13 10 0.19
14 2 0.04
15 3 0.06
16 25 0.48
17 2 0.04
18 4 0.08
19 6 0.12
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (16 bp):
ATATAAAATAATAATA
Found at i:35425032 original size:13 final size:13
Alignment explanation
Indices: 35425007--35425049 Score: 68
Period size: 13 Copynumber: 3.2 Consensus size: 13
35424997 TACAAGTAAG
35425007 ATATAATAATAATA
1 ATATAA-AATAATA
35425021 ATATAAAATAATA
1 ATATAAAATAATA
*
35425034 ATGTAAAATAATA
1 ATATAAAATAATA
35425047 ATA
1 ATA
35425050 ATTTGTGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 21 0.78
14 6 0.22
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (13 bp):
ATATAAAATAATA
Found at i:35425079 original size:32 final size:30
Alignment explanation
Indices: 35425003--35425094 Score: 91
Period size: 29 Copynumber: 3.0 Consensus size: 30
35424993 ATAATACAAG
35425003 TAAGATATAATAATAATAA-TATAAAATAA
1 TAAGATATAATAATAATAATTATAAAATAA
* *
35425032 TAATG-TAAAATAATAATAATTTGTGAAAA-AA
1 TAA-GATATAATAATAATAA-TTAT-AAAATAA
*
35425063 TAAGATATAATAAATAATAATATATATAATAA
1 TAAGATATAAT-AATAATAAT-TATAAAATAA
35425095 AATAATCTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
29 16 0.32
30 2 0.04
31 16 0.32
32 16 0.32
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (30 bp):
TAAGATATAATAATAATAATTATAAAATAA
Found at i:35431092 original size:21 final size:20
Alignment explanation
Indices: 35431056--35431102 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
35431046 CACACGATCG
*
35431056 TGTGGCTTCACACATGGCCA
1 TGTGGCTTCACACATGCCCA
* *
35431076 TGTGGCTTCCCCACATGCCCG
1 TGTGGCTT-CACACATGCCCA
35431097 TGTGGC
1 TGTGGC
35431103 CAGACTATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.13, C:0.34, G:0.28, T:0.26
Consensus pattern (20 bp):
TGTGGCTTCACACATGCCCA
Found at i:35443316 original size:44 final size:44
Alignment explanation
Indices: 35443076--35443301 Score: 328
Period size: 44 Copynumber: 5.1 Consensus size: 44
35443066 TCACCGATAG
*
35443076 CAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
*
35443120 CAGATTTGGCGTCTCTGTATTGACAGACAGCAGATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* * *
35443164 TAGATTTGGCGTCTCTGTATTGATAGAGAGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* * * *
35443208 CATATTTGGCTTCTCTGTATTGACAGAAAGCAAATCGAAGAT-A
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* * *
35443251 GCAGATTTGGCGTCTCTGTATTGACAGAGGGCAGGTCCAAGATGA
1 -CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
35443296 CAGATT
1 CAGATT
35443302 CGGTTTCTCC
Statistics
Matches: 161, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
43 1 0.01
44 159 0.99
45 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.27
Consensus pattern (44 bp):
CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
Found at i:35444897 original size:12 final size:11
Alignment explanation
Indices: 35444864--35444910 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 11
35444854 ATAAATTGTA
35444864 TATATATTATTTT
1 TATATATTA--TT
35444877 TATATATTATT
1 TATATATTATT
35444888 TATCATATTATT
1 TAT-ATATTATT
35444900 TATATTATTAT
1 TATA-TATTAT
35444911 ACATTTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.19
12 17 0.53
13 9 0.28
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATATTATT
Found at i:35444905 original size:21 final size:21
Alignment explanation
Indices: 35444879--35444924 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
35444869 ATTATTTTTA
35444879 TATATTATT-TATCATATTATT
1 TATATTATTATA-CATATTATT
*
35444900 TATATTATTATACATTTTATT
1 TATATTATTATACATATTATT
35444921 TATA
1 TATA
35444925 AATTTTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (21 bp):
TATATTATTATACATATTATT
Found at i:35453362 original size:61 final size:61
Alignment explanation
Indices: 35453292--35453425 Score: 178
Period size: 61 Copynumber: 2.2 Consensus size: 61
35453282 TCAATTTGAC
* ** * *
35453292 CTAAATCTAAAAAAATTAATAAATTTAGCCCTCAATGTTTATAAAAGTTGTCATTTTAGTT
1 CTAATTCTAAAAAAATTAATAAATTTAGCCCTCAACATTTACAAAAGTTGTCAATTTAGTT
* * * * *
35453353 TTAGTTCTAAAAAATTTAATAAATTTAGCCCTCAACATTTACAAAATTTTTCAATTTAGTT
1 CTAATTCTAAAAAAATTAATAAATTTAGCCCTCAACATTTACAAAAGTTGTCAATTTAGTT
35453414 CTAATTCTAAAA
1 CTAATTCTAAAA
35453426 GTTAAAAATA
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.40
Consensus pattern (61 bp):
CTAATTCTAAAAAAATTAATAAATTTAGCCCTCAACATTTACAAAAGTTGTCAATTTAGTT
Found at i:35456639 original size:14 final size:15
Alignment explanation
Indices: 35456615--35456651 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
35456605 ATATTAATGA
35456615 AAATA-TTTAAT-AT
1 AAATATTTTAATAAT
*
35456628 TAATATTTTAATAAT
1 AAATATTTTAATAAT
35456643 AAATATTTT
1 AAATATTTT
35456652 TTACAATTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 4 0.20
14 6 0.30
15 10 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AAATATTTTAATAAT
Found at i:35457646 original size:16 final size:16
Alignment explanation
Indices: 35457625--35457673 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
35457615 TTTTTTATAT
35457625 AATTATAAAATTAAAA
1 AATTATAAAATTAAAA
*
35457641 AATTATAAAAAATT-GAA
1 AATTAT--AAAATTAAAA
*
35457658 AATTATAAAAATAAAA
1 AATTATAAAATTAAAA
35457674 CTCATTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
15 5 0.19
16 8 0.30
17 8 0.30
18 6 0.22
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (16 bp):
AATTATAAAATTAAAA
Found at i:35463990 original size:44 final size:43
Alignment explanation
Indices: 35463902--35464025 Score: 108
Period size: 44 Copynumber: 2.9 Consensus size: 43
35463892 GACAGGATTC
* *
35463902 CGATATGTGATTTCGTGTAAGACCACGTCTGGGACGTTGACAT
1 CGATATGTGATTTCGTGTAAAACCACGTCTGGGACGTAGACAT
* *
35463945 CGATTTGTGATTTGTGTGTAAAACC-CTGTCTGGGACAGTAG-CAT
1 CGATATGTGATTT-CGTGTAAAACCAC-GTCTGGGAC-GTAGACAT
* * * * * * *
35463989 CGTTATGTAATTACATGTAAGACCATGTCTAGGACGT
1 CGATATGTGATTTCGTGTAAAACCACGTCTGGGACGT
35464026 TGATGTTGTA
Statistics
Matches: 64, Mismatches: 13, Indels: 9
0.74 0.15 0.10
Matches are distributed among these distances:
42 2 0.03
43 29 0.45
44 30 0.47
45 3 0.05
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (43 bp):
CGATATGTGATTTCGTGTAAAACCACGTCTGGGACGTAGACAT
Found at i:35480966 original size:40 final size:40
Alignment explanation
Indices: 35480922--35481145 Score: 308
Period size: 40 Copynumber: 5.6 Consensus size: 40
35480912 AAGTGAATAT
* * * * **
35480922 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAA
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTGTTAA
35480962 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
35481002 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
35481042 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
* * **
35481082 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
* * *
35481121 AACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATT
35481146 TGAACGAGGA
Statistics
Matches: 171, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.20
40 136 0.80
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
Found at i:35481020 original size:80 final size:80
Alignment explanation
Indices: 35480883--35481145 Score: 318
Period size: 80 Copynumber: 3.3 Consensus size: 80
35480873 TTGAATGCTG
* * * * *
35480883 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAG-TGAATATATCCGGATTAAGAT-CCGAAGGCC
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTTG-TTAAATCCGGGTTAAG-TCCCGAAGGCC
*
35480945 TTTGTGCGAGATACTAAA
63 TTTGTGCGAGTTACTAAA
* * *
35480963 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCCTTT
**
35481028 GTGCGAGTTGTTAAA
66 GTGCGAGTTACTAAA
* * *
35481043 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGG-CATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCCTTT
*
35481107 GTGTGAGTTACTAAA
66 GTGCGAGTTACTAAA
* *
35481122 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
35481146 TGAACGAGGA
Statistics
Matches: 159, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
79 35 0.22
80 116 0.73
81 8 0.05
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCCTTT
GTGCGAGTTACTAAA
Found at i:35481097 original size:120 final size:120
Alignment explanation
Indices: 35480883--35481145 Score: 318
Period size: 120 Copynumber: 2.2 Consensus size: 120
35480873 TTGAATGCTG
* * *
35480883 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGATTAAGATCCGAAGGCCTT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
* **
35480947 TGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
66 CGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* * * *
35481003 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTG-TTAAATCCGGGTTAAG-TCCCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAG-TGAATAAATCCGGATTAAGAT-CCGAAGGCA
* ** * *
35481065 TTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
64 TTCGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
35481122 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
35481146 TGAACGAGGA
Statistics
Matches: 122, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
119 34 0.28
120 80 0.66
121 8 0.07
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
CGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:35491117 original size:45 final size:45
Alignment explanation
Indices: 35490953--35491191 Score: 212
Period size: 45 Copynumber: 5.3 Consensus size: 45
35490943 ATATTTGACA
* *
35490953 TGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTATCAG
1 TGATGCCATAGTATCTTTCAACTATGGTCTTACTCA-TTTCAATC-G
* * * * ***
35491000 -GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAAAA
1 TGATGCCATAGTATCTTTCAACTATGGTCTTACTCATTTCA-ATCG
* * * * *
35491045 TGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTGAATCG
1 TGATGCCATAGTATCTTTCAACTATGGTCTTACTCATTTCAATCG
* * * * *
35491090 CGATGCCATAGCATCTTTCAGCTATGGTCTTACTCATCTGAATCG
1 TGATGCCATAGTATCTTTCAACTATGGTCTTACTCATTTCAATCG
** * * *
35491135 TGATGCCATAGCGTCTTTCAGCTATGGTCTTACTCATTTCTAGT-A
1 TGATGCCATAGTATCTTTCAACTATGGTCTTACTCATTTC-AATCG
35491180 TGATGCCATAGT
1 TGATGCCATAGT
35491192 CCAACTATGG
Statistics
Matches: 161, Mismatches: 28, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
45 89 0.55
46 72 0.45
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (45 bp):
TGATGCCATAGTATCTTTCAACTATGGTCTTACTCATTTCAATCG
Found at i:35491319 original size:33 final size:33
Alignment explanation
Indices: 35491183--35491338 Score: 81
Period size: 33 Copynumber: 4.7 Consensus size: 33
35491173 TCTAGTATGA
* * *
35491183 TGCCATAGTCC-AACTATGGTCTTACACGTGTAT
1 TGCCATAG-CCTAGCTATGGTCTTACACATATAT
** * * * **
35491216 TATCATGGCCTAGCCATGGTCTTACAC-TCGTGG
1 TGCCATAGCCTAGCTATGGTCTTACACAT-ATAT
* * *
35491249 TGCCATATCCCT-GATATGGTCTTATCATCA-AGA-
1 TGCCATA-GCCTAGCTATGGTCTTA-CA-CATATAT
35491282 TGCCATAGCCTAGCTATGGTCTTACACATATAT
1 TGCCATAGCCTAGCTATGGTCTTACACATATAT
* *
35491315 TGCCAT-GACCCAGCCATGGTCTTA
1 TGCCATAG-CCTAGCTATGGTCTTA
35491339 TCCATCAGTT
Statistics
Matches: 92, Mismatches: 21, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
31 2 0.02
32 11 0.12
33 73 0.79
34 5 0.05
35 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (33 bp):
TGCCATAGCCTAGCTATGGTCTTACACATATAT
Found at i:35506174 original size:26 final size:26
Alignment explanation
Indices: 35506145--35506245 Score: 132
Period size: 26 Copynumber: 3.9 Consensus size: 26
35506135 CCCATCGTGG
35506145 AACATTTACCTAAACCATTATCATGA
1 AACATTTACCTAAACCATTATCATGA
*
35506171 AACATTTACCT-AACGCATTATCATGT
1 AACATTTACCTAAAC-CATTATCATGA
* * * *
35506197 TATATTTACCTAATCCATTATCATGG
1 AACATTTACCTAAACCATTATCATGA
*
35506223 AACATTTACCTAACCCATTATCA
1 AACATTTACCTAAACCATTATCA
35506246 ATTTGTATCA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
25 3 0.05
26 60 0.92
27 2 0.03
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
AACATTTACCTAAACCATTATCATGA
Found at i:35512285 original size:26 final size:26
Alignment explanation
Indices: 35512254--35512361 Score: 182
Period size: 26 Copynumber: 4.2 Consensus size: 26
35512244 TGAAATGCCC
35512254 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
35512280 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
*
35512306 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
35512332 ATCATGGAACATTTACCT-AACCTATT
1 ATCATGGAACATTTACCTAAACC-ATT
35512358 ATCA
1 ATCA
35512362 ATTTGTATCA
Statistics
Matches: 79, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
25 3 0.04
26 76 0.96
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:35519395 original size:26 final size:26
Alignment explanation
Indices: 35519357--35519414 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
35519347 CATGAAATTC
35519357 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
35519383 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
35519409 TTATCA
1 TTATCA
35519415 ATTTGTATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.36
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:35521553 original size:43 final size:43
Alignment explanation
Indices: 35521488--35521580 Score: 116
Period size: 43 Copynumber: 2.2 Consensus size: 43
35521478 CGCTACAAAA
* * *
35521488 TTTAGCGGCGTTTGTCAGAAAAGTGCCGCTAAAAGTCATGGCT
1 TTTAGCGGCGTTTCTCAGAAAAGCGCCGCTAAAAATCATGGCT
* * *
35521531 TTTAGCGGCGTTTCT-TGTAAAAGCGCCGCTAAAAATCATTGTT
1 TTTAGCGGCGTTTCTCAG-AAAAGCGCCGCTAAAAATCATGGCT
35521574 TTTAGCG
1 TTTAGCG
35521581 ACGCTTTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 1 0.02
43 42 0.98
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (43 bp):
TTTAGCGGCGTTTCTCAGAAAAGCGCCGCTAAAAATCATGGCT
Found at i:35521694 original size:31 final size:31
Alignment explanation
Indices: 35521654--35521719 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
35521644 TAACCTTCCT
*
35521654 GCATTAAATCCAACCAAAAACAGAAAATATA
1 GCATGAAATCCAACCAAAAACAGAAAATATA
* *
35521685 GCATGAAATCCAACCAAAAACAGCAAATGTA
1 GCATGAAATCCAACCAAAAACAGAAAATATA
35521716 GCAT
1 GCAT
35521720 AAAAAAATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.53, C:0.21, G:0.11, T:0.15
Consensus pattern (31 bp):
GCATGAAATCCAACCAAAAACAGAAAATATA
Found at i:35529937 original size:29 final size:28
Alignment explanation
Indices: 35529901--35529978 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
35529891 TCATGAGATT
35529901 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
35529931 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
35529958 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
35529979 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:35530196 original size:174 final size:174
Alignment explanation
Indices: 35529931--35530258 Score: 620
Period size: 174 Copynumber: 1.9 Consensus size: 174
35529921 AAATTGTACA
*
35529931 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
*
35529996 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
35530061 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* *
35530105 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
35530170 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
35530235 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
35530259 ACCTTGAGTT
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 150 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:35534427 original size:38 final size:38
Alignment explanation
Indices: 35534385--35534461 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
35534375 ATAGAACAAA
35534385 TCAACACTAGCAGTAAACATGCTTAACATGTATTCAAT
1 TCAACACTAGCAGTAAACATGCTTAACATGTATTCAAT
* *
35534423 TCAACACTGGTAGTAAACATGCTTAACATGTATTCAAT
1 TCAACACTAGCAGTAAACATGCTTAACATGTATTCAAT
35534461 T
1 T
35534462 GGGTGGTAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (38 bp):
TCAACACTAGCAGTAAACATGCTTAACATGTATTCAAT
Found at i:35535318 original size:22 final size:20
Alignment explanation
Indices: 35535289--35535348 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 20
35535279 AATAATTGAC
35535289 AACAAAAAGATGAAAAATAT
1 AACAAAAAGATGAAAAATAT
*
35535309 AATGCAAAAAAGA-GAAAAAAAT
1 AA--C-AAAAAGATGAAAAATAT
35535331 AA-AAAAAGATGACAAAAT
1 AACAAAAAGATGA-AAAAT
35535349 TCTAATAGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
18 7 0.21
19 2 0.06
20 6 0.18
22 11 0.33
23 7 0.21
ACGTcount: A:0.72, C:0.05, G:0.12, T:0.12
Consensus pattern (20 bp):
AACAAAAAGATGAAAAATAT
Found at i:35537410 original size:13 final size:13
Alignment explanation
Indices: 35537392--35537416 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35537382 GTCATGTGAC
35537392 AAAAATAAAATAA
1 AAAAATAAAATAA
35537405 AAAAATAAAATA
1 AAAAATAAAATA
35537417 TACTATAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAATAAAATAA
Found at i:35540326 original size:14 final size:14
Alignment explanation
Indices: 35540307--35540340 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
35540297 TTGCTTTACT
35540307 GAAAATGACTTCCG
1 GAAAATGACTTCCG
* *
35540321 GAAAATGATTTCTG
1 GAAAATGACTTCCG
35540335 GAAAAT
1 GAAAAT
35540341 AATTTACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (14 bp):
GAAAATGACTTCCG
Found at i:35542475 original size:19 final size:19
Alignment explanation
Indices: 35542451--35542519 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
35542441 TAATAATAAT
35542451 ATAAAATAATAGTATGTAC
1 ATAAAATAATAGTATGTAC
* *
35542470 ATAAAAATATATA-TATATGC
1 AT-AAAATA-ATAGTATGTAC
* *
35542490 ATATAATAAAAGTATGTA-
1 ATAAAATAATAGTATGTAC
35542508 ATAATAATAATA
1 ATAA-AATAATA
35542520 TCTACAATAA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
18 5 0.13
19 17 0.45
20 13 0.34
21 3 0.08
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (19 bp):
ATAAAATAATAGTATGTAC
Found at i:35543722 original size:17 final size:17
Alignment explanation
Indices: 35543700--35543733 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
35543690 TCTACAACTT
35543700 CAATCTACTCTTCTATC
1 CAATCTACTCTTCTATC
35543717 CAATCTACTCTTCTATC
1 CAATCTACTCTTCTATC
35543734 GCTTCAGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.35, G:0.00, T:0.41
Consensus pattern (17 bp):
CAATCTACTCTTCTATC
Found at i:35544043 original size:88 final size:85
Alignment explanation
Indices: 35543935--35544360 Score: 284
Period size: 88 Copynumber: 5.0 Consensus size: 85
35543925 AAAAACAGAC
* * *
35543935 ATTAAAAATAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
1 ATTAAAAACAGATATTGAAAATACCTC-GCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
35544000 GAGTTGATTTTTTGAAACTTA
65 GAGTTGATTTTTTGAAACTTA
* * * * * *
35544021 ACTTGAAAAGCAGATTTTGAAAATACCTCGATATGTGA-CTGAAGGTTCAACTCACCTCTCGCAA
1 A-TT-AAAAACAGATATTGAAAATACCTCG-CACGTGAGC-CAAGGCTCAACTCACCTCTCGCAA
* *
35544085 TATGAGTTGA-TTTTTGAAAAATAGAA
62 TATGAGTTGATTTTTTG-AAACT--TA
** * * * ** *** *
35544111 ATTAAAAGACTCA-ACT-CAACT--CTCGCA-GAAATTAAAAAGCTCAACTCACCTCTCGCAATA
1 ATTAAAA-ACAGATATTGAAAATACCTCGCACGTGA-GCCAAGGCTCAACTCACCTCTCGCAATA
35544171 TGAGTTGAATTTTTTTGAAA---A
64 TGAGTTG-A-TTTTTTGAAACTTA
* * * * * *
35544192 A--AAAAACAGAAATTGAAAATAGCTTAGCACGTAAGCCAAGGCTCAACTCACTTCTTGCAATAT
1 ATTAAAAACAGATATTGAAAATA-CCTCGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
*
35544255 GAGTTGA-TTTTTGAAAACATA
65 GAGTTGATTTTTTG-AAACTTA
* * * * *
35544276 ATCTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGGCTCAACTCACATCTCGCAAT
1 AT-T-AAAAACAGATATTGAAAATACCTCG-CACGTGAGCCAAGGCTCAACTCACCTCTCGCAAT
*
35544341 GTGAGTTGATTTTTTTGAAA
63 ATGAGTTGA-TTTTTTGAAA
35544361 AATATAAATT
Statistics
Matches: 260, Mismatches: 50, Indels: 57
0.71 0.14 0.16
Matches are distributed among these distances:
78 3 0.01
79 6 0.02
80 9 0.03
81 5 0.02
82 1 0.00
83 35 0.13
84 36 0.14
85 5 0.02
86 4 0.02
87 22 0.08
88 119 0.46
89 7 0.03
90 8 0.03
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (85 bp):
ATTAAAAACAGATATTGAAAATACCTCGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTTTTGAAACTTA
Found at i:35544143 original size:30 final size:30
Alignment explanation
Indices: 35544107--35544167 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
35544097 TTTGAAAAAT
35544107 AGAAATT-AAAAGACTCAACTCAACTCTCGC
1 AGAAATTAAAAAG-CTCAACTCAACTCTCGC
*
35544137 AGAAATTAAAAAGCTCAACTCACCTCTCGC
1 AGAAATTAAAAAGCTCAACTCAACTCTCGC
35544167 A
1 A
35544168 ATATGAGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.20
Consensus pattern (30 bp):
AGAAATTAAAAAGCTCAACTCAACTCTCGC
Found at i:35544486 original size:77 final size:78
Alignment explanation
Indices: 35544318--35544856 Score: 381
Period size: 77 Copynumber: 6.9 Consensus size: 78
35544308 ATGTGACCCG
* * * * *
35544318 AGGCTCAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTG--AAAATACCT
* * * *
35544383 CAGTGTGTGATCTGA
64 CAGCGCGTGAGCTCA
*
35544398 A-GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATAGCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
35544462 GCGCGTGAGC-CA
66 GCGCGTGAGCTCA
*
35544474 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAGGCAGAAATTGGAAAACGGAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAAGACAGAAATT-G---A---AA
** ** * *
35544539 ATTGAAAATACCTCGGCGTGTGAC-CTG
58 A-T--ACCT-CAGC-GCGTGAG-CTC-A
* ** * * *
35544566 AGGCTCAACTCGCCTCTTACAATACGAGTTGATTTTTTTGACA-ACAGAAATTGAAATTACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
** *
35544630 --GCGTGTCCT-G
66 GCGCGTGAGCTCA
* * *
35544640 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTGAAAAATAGAAATTGAAAATACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
* * **
35544705 --GCATG-TCTTG
66 GCGCGTGAGCTCA
** * * *
35544715 AGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTTTTTGAAAAACAGAAATTAAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTGAAAGACAGAAATTGAAAATACCT
* * *
35544780 CA--GCATG-TCTTA
64 CAGCGCGTGAGCTCA
* ** * *
35544792 AGGCTCAACTAATTTCTCGCAATATGAGTTGA--ATTTTGAAA-ACAGAAATTGAAATTACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
35544854 GCG
66 GCG
35544857 TGTCTTGAGG
Statistics
Matches: 386, Mismatches: 50, Indels: 52
0.79 0.10 0.11
Matches are distributed among these distances:
72 19 0.05
73 8 0.02
74 41 0.11
75 53 0.14
76 8 0.02
77 117 0.30
78 20 0.05
79 49 0.13
80 3 0.01
82 2 0.01
83 2 0.01
85 3 0.01
86 2 0.01
88 2 0.01
89 3 0.01
90 14 0.04
91 12 0.03
92 28 0.07
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (78 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCA
GCGCGTGAGCTCA
Found at i:35544576 original size:169 final size:165
Alignment explanation
Indices: 35544374--35544828 Score: 467
Period size: 152 Copynumber: 2.8 Consensus size: 165
35544364 ATAAATTGAA
* * * *
35544374 AAAATACCTCAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
1 AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCTCTCACAATACGAGTTGATTTTTTTGAA
*
35544439 AGACAGAAATTGAAAATAGCTCAGCGCGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGAGT
66 A-ACAGAAATTGAAAATACCTCA--GCGTG-GCCTAAGGCTCAACTCACCTCTCGCAATATGAGT
35544503 TGATTTTTTTTGAAAGGCAGAAATTGGAAAACGGAAATTG
127 TGA-TTTTTTTGAAAGGCAGAAATTGGAAAACGGAAATTG
* * * * *
35544543 AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTTACAATACGAGTTGATTTTTTTGAC
1 AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCTCTCACAATACGAGTTGATTTTTTTGAA
* * * *
35544608 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGTAATATGAGTTGAT
66 AACAGAAATTGAAAATACCTCAGCGTGGCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
35544673 TTTTTTG--A---A-AAA-T-----A--GAAATTG
131 TTTTTTGAAAGGCAGAAATTGGAAAACGGAAATTG
* * * ** *
35544694 AAAATACCTCAGCATGT--CTTGAGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTTTTTG
1 AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCTCTCACAATACGAGTTGA--TTTTTTTG
* * * * * **
35544757 AAAAACAGAAATTAAAAATACCTCAGCATGTCTTAAGGCTCAACTAATTTCTCGCAATATGAGTT
64 -AAAACAGAAATTGAAAATACCTCAGCGTGGCCTAAGGCTCAACTCACCTCTCGCAATATGAGTT
*
35544822 GAATTTT
128 GATTTTT
35544829 GAAAACAGAA
Statistics
Matches: 249, Mismatches: 33, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
149 30 0.12
151 30 0.12
152 60 0.24
153 1 0.00
158 1 0.00
159 3 0.01
160 1 0.00
163 1 0.00
165 10 0.04
166 36 0.14
168 19 0.08
169 57 0.23
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (165 bp):
AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCTCTCACAATACGAGTTGATTTTTTTGAA
AACAGAAATTGAAAATACCTCAGCGTGGCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTTTGAAAGGCAGAAATTGGAAAACGGAAATTG
Found at i:35544721 original size:75 final size:74
Alignment explanation
Indices: 35544529--35544875 Score: 410
Period size: 77 Copynumber: 4.6 Consensus size: 74
35544519 GCAGAAATTG
* * * * * *
35544529 GAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTTACAATACGAG
1 GAAAACAGAAATTGAAAATACCTCAGCGTGT--CTTGAGGCTCAACTCACCTCTCACAATATGAG
35544594 TTGATTTTTTT
64 TTGATTTTTTT
* * * **
35544605 GACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGTAATATGAGTT
1 GAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCACAATATGAGTT
35544670 GATTTTTTT
66 GATTTTTTT
* * **
35544679 GAAAAATAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGAGT
1 G-AAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCACAATATGAGT
35544744 TGATTTTTTTTT
65 TGA--TTTTTTT
* * * * ** *
35544756 GAAAAACAGAAATTAAAAATACCTCAGCATGTCTTAAGGCTCAACTAATTTCTCGCAATATGAGT
1 G-AAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCACAATATGAGT
*
35544821 TGA--ATTTT
65 TGATTTTTTT
*
35544829 GAAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCA
1 GAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCA
35544876 TTTTGAACAG
Statistics
Matches: 239, Mismatches: 29, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
72 41 0.17
73 5 0.02
74 39 0.16
75 57 0.24
76 27 0.11
77 70 0.29
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (74 bp):
GAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCACAATATGAGTT
GATTTTTTT
Done.