Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 163 of 193
Found at i:50599192 original size:160 final size:160
Alignment explanation
Indices: 50598928--50599250 Score: 565
Period size: 160 Copynumber: 2.0 Consensus size: 160
50598918 ACTACATCTG
* *
50598928 CACAACCTTTACCCTGCAGATACAGATAAAATAAATAAACATACATGCATGCGCGCGCGCACACA
1 CACAACCTTTACCCTGCAGATACAGATAAAATAAATAAACATACATGCATGCACGCGCACACACA
* * *
50598993 CACACACTCTAAATAGCGGTTATGGGAGAAAGAAGATGATCATCATTATGCAGAAAGAGAGGACC
66 CACACACTCTAAATAACAGTTATAGGAGAAAGAAGATGATCATCATTATGCAGAAAGAGAGGACC
50599058 GCAATAAAGTTACAACAACCTCATCATTAT
131 GCAATAAAGTTACAACAACCTCATCATTAT
50599088 CACAACCTTTACCCTGCAGATACAGATAAAATAAATAAACATACATGCATGCACGCGCACACACA
1 CACAACCTTTACCCTGCAGATACAGATAAAATAAATAAACATACATGCATGCACGCGCACACACA
* * *
50599153 CAGACTCTCTAAATAACAGTTATAGGAGAAAGAAGATGATCATCATTATGCAGAAAGAGAGGACT
66 CACACACTCTAAATAACAGTTATAGGAGAAAGAAGATGATCATCATTATGCAGAAAGAGAGGACC
*
50599218 GCAATAAAGTTACAACCACCTCATCATTAT
131 GCAATAAAGTTACAACAACCTCATCATTAT
50599248 CAC
1 CAC
50599251 CCGTGTAGGT
Statistics
Matches: 154, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
160 154 1.00
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.20
Consensus pattern (160 bp):
CACAACCTTTACCCTGCAGATACAGATAAAATAAATAAACATACATGCATGCACGCGCACACACA
CACACACTCTAAATAACAGTTATAGGAGAAAGAAGATGATCATCATTATGCAGAAAGAGAGGACC
GCAATAAAGTTACAACAACCTCATCATTAT
Found at i:50605008 original size:196 final size:195
Alignment explanation
Indices: 50604647--50605185 Score: 854
Period size: 196 Copynumber: 2.8 Consensus size: 195
50604637 CTTATTCAAT
* *
50604647 TGAGGCTATGGGATTTGCTTGATGAGATGAAAAAGCAATGGCATTGAGCCAAGGAATGTGCCTTC
1 TGAGGCTATGGGATTTGCTTGATGAGATGAAAAAGCAATGGTATTGAGCCAAGGGATGTGCCTTC
* * *
50604712 TTCAG-A---A-GGAATTGTCTTGGCTAATGGGTTGTATCACTGATCGGACATGAATTGTTCGAA
66 TTCAGAAGCCATGGAACTGTTTTGGCTAATGGGTTGTATCACTGATCGCACATGAATTGTTCGAA
* * * *
50604772 GAAATGACAAGGAGAGATCGTTCTTCTTCCGTTGTTTACATATTCATCCCTTTGTACAGATATAA
131 GAAATGACAA-GAGAGATTGTTCTTCTTCCGTTATTTACATATTCATCCCTTTATACAAATATAA
50604837 A
195 A
50604838 TGAGGCTATGGGATTTGCTTGATGAGATGAAAAAGCAATGGTATTGAGCCAAGGGATGTGCCTTC
1 TGAGGCTATGGGATTTGCTTGATGAGATGAAAAAGCAATGGTATTGAGCCAAGGGATGTGCCTTC
* *
50604903 TTCAGAAGCCATGGAACTGTTTTGGCTAATGGGTTGTATCACTGATCGCACACGAGTTGTTCGAA
66 TTCAGAAGCCATGGAACTGTTTTGGCTAATGGGTTGTATCACTGATCGCACATGAATTGTTCGAA
50604968 GAAATGACAACGAGAGATTGTTCTTCTTCCGTTATTTACATATTCATCCCTTTATACAAATATAA
131 GAAATGACAA-GAGAGATTGTTCTTCTTCCGTTATTTACATATTCATCCCTTTATACAAATATAA
50605033 A
195 A
* * * *
50605034 TGAGGCTATGGGATTTGCTTGATGTGATGCAAAATCAATGGTATTGAGCCAATGGATGTGCCTTC
1 TGAGGCTATGGGATTTGCTTGATGAGATGAAAAAGCAATGGTATTGAGCCAAGGGATGTGCCTTC
*
50605099 TTCAGAAGCCATGGAACTGTTTTGACTAATGGGTTGTATCACTGATCGCACATGAATTGTTCGAA
66 TTCAGAAGCCATGGAACTGTTTTGGCTAATGGGTTGTATCACTGATCGCACATGAATTGTTCGAA
* *
50605164 GAAACGACGAAAAGAGATTGTT
131 GAAATGAC-AAGAGAGATTGTT
50605186 ACATTTTCAT
Statistics
Matches: 321, Mismatches: 21, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
191 68 0.21
192 1 0.00
195 1 0.00
196 249 0.78
197 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.31
Consensus pattern (195 bp):
TGAGGCTATGGGATTTGCTTGATGAGATGAAAAAGCAATGGTATTGAGCCAAGGGATGTGCCTTC
TTCAGAAGCCATGGAACTGTTTTGGCTAATGGGTTGTATCACTGATCGCACATGAATTGTTCGAA
GAAATGACAAGAGAGATTGTTCTTCTTCCGTTATTTACATATTCATCCCTTTATACAAATATAAA
Found at i:50608679 original size:79 final size:79
Alignment explanation
Indices: 50608493--50608703 Score: 237
Period size: 79 Copynumber: 2.7 Consensus size: 79
50608483 ACTGACTAAT
* * * * *
50608493 GCTGGGCACACAATTGCGGTTTAACCGCTAGGCACTGGGTGCCAGAATTTGACGGACATTGTTGA
1 GCTGGGCTCACATTTGCGGTTTAACCGCTAAGCACTGGGTGCCAGAACTTGACAGACATTGTTGA
*
50608558 TTAATTCAACTAGA
66 TTAATCCAACTAGA
* * * * * *
50608572 GCTGGGCTCACATTTGCAGTCTAACCGCTAAGCATTGGGTGTCAGGACTTGACAGACATTGTTGG
1 GCTGGGCTCACATTTGCGGTTTAACCGCTAAGCACTGGGTGCCAGAACTTGACAGACATTGTTGA
*
50608637 TTAATCCAACTATA
66 TTAATCCAACTAGA
* * * *
50608651 GCTGGGCTCAC-TTTCGCGGTTTATCCGCTAGGCACCGGGCGCCATGAA-TTGAC
1 GCTGGGCTCACATTT-GCGGTTTAACCGCTAAGCACTGGGTGCCA-GAACTTGAC
50608704 GGAGATTATA
Statistics
Matches: 108, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
78 3 0.03
79 103 0.95
80 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (79 bp):
GCTGGGCTCACATTTGCGGTTTAACCGCTAAGCACTGGGTGCCAGAACTTGACAGACATTGTTGA
TTAATCCAACTAGA
Found at i:50618578 original size:15 final size:15
Alignment explanation
Indices: 50618560--50618600 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
50618550 TGATGAAGTT
50618560 GAAAGAGATGAGGTG
1 GAAAGAGATGAGGTG
* *
50618575 GAAAGAGATGATGTT
1 GAAAGAGATGAGGTG
50618590 GAAAGAGATGA
1 GAAAGAGATGA
50618601 AGACTCTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.39, T:0.17
Consensus pattern (15 bp):
GAAAGAGATGAGGTG
Found at i:50624818 original size:24 final size:22
Alignment explanation
Indices: 50624786--50624838 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
50624776 TTTAGTTTAC
*
50624786 AATAAAATTTAATCTTAGTAAAA
1 AATATAATTTAATCTTA-TAAAA
* *
50624809 TAATATAATTTATTTTTATAAAA
1 -AATATAATTTAATCTTATAAAA
50624832 AATATAA
1 AATATAA
50624839 ATGGTAGTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 7 0.27
23 5 0.19
24 14 0.54
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
AATATAATTTAATCTTATAAAA
Found at i:50624910 original size:9 final size:9
Alignment explanation
Indices: 50624898--50624932 Score: 56
Period size: 8 Copynumber: 4.1 Consensus size: 9
50624888 TATTTAGATC
50624898 TTTTAAAAT
1 TTTTAAAAT
50624907 TTTT-AAAT
1 TTTTAAAAT
50624915 TTTTAAAA-
1 TTTTAAAAT
50624923 TTTTAAAAT
1 TTTTAAAAT
50624932 T
1 T
50624933 AAAATTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:50624918 original size:17 final size:17
Alignment explanation
Indices: 50624898--50624932 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
50624888 TATTTAGATC
*
50624898 TTTTAAAATTTTTAAAT
1 TTTTAAAATTTTAAAAT
50624915 TTTTAAAATTTTAAAAT
1 TTTTAAAATTTTAAAAT
50624932 T
1 T
50624933 AAAATTATAT
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTAAAATTTTAAAAT
Found at i:50624975 original size:29 final size:27
Alignment explanation
Indices: 50624923--50624986 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 27
50624913 ATTTTTAAAA
*
50624923 TTTTAAAATTAAAATTATATTTTAACC
1 TTTTAAAATTAAAATTATAATTTAACC
* **
50624950 TTTTAAAATGATAAAATTTTAATTTAATT
1 TTTTAAAAT--TAAAATTATAATTTAACC
50624979 TTTTAAAA
1 TTTTAAAA
50624987 ATTTTAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 9 0.29
29 22 0.71
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (27 bp):
TTTTAAAATTAAAATTATAATTTAACC
Found at i:50627003 original size:164 final size:164
Alignment explanation
Indices: 50626718--50627025 Score: 501
Period size: 164 Copynumber: 1.9 Consensus size: 164
50626708 CGAGGTAACT
* * *
50626718 AAACAATTACTTGTTGAAGAAGCTTTATGAGTGTTTAGATTTTGATGGGGATGCAATGGTTTAGT
1 AAACAAATACTTGTTGAAGAAGCTTTATGAGTGTTTAGATTTTGATGAGGAGGCAATGGTTTAGT
* * * *
50626783 TTGTATCAAGATAATAAAGGATAAACACCATGATTGTTGAAAGAGATAATCTCGAACCTTGAGCA
66 TTGTATCAAGATAATAAACGAAAAACACCATGATTGTTGAAAGAGATAACCTCGAACCTTGAACA
*
50626848 TTAACTGCAAAACGTGCATGGTCCCGATGTAAAA
131 TGAACTGCAAAACGTGCATGGTCCCGATGTAAAA
*
50626882 AAACAAATACTTGTTGAAGAAGCTTTATGGGTGTTTAGATTTTGATGAGGAGGCAATGGTTTAGT
1 AAACAAATACTTGTTGAAGAAGCTTTATGAGTGTTTAGATTTTGATGAGGAGGCAATGGTTTAGT
*
50626947 TTGTATCAAGATAATAAACGAAAAACACCATGATTGTTGAGAA-CGATAACCTCGAACCTTGAAC
66 TTGTATCAAGATAATAAACGAAAAACACCATGATTGTTGA-AAGAGATAACCTCGAACCTTGAAC
*
50627011 ATGAACTGTAAAACG
130 ATGAACTGCAAAACG
50627026 AATATGGACT
Statistics
Matches: 132, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
164 130 0.98
165 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (164 bp):
AAACAAATACTTGTTGAAGAAGCTTTATGAGTGTTTAGATTTTGATGAGGAGGCAATGGTTTAGT
TTGTATCAAGATAATAAACGAAAAACACCATGATTGTTGAAAGAGATAACCTCGAACCTTGAACA
TGAACTGCAAAACGTGCATGGTCCCGATGTAAAA
Found at i:50636857 original size:10 final size:9
Alignment explanation
Indices: 50636840--50636864 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
50636830 CTCAACTATA
50636840 TATTTTTTT
1 TATTTTTTT
50636849 TATTTTTTT
1 TATTTTTTT
50636858 TATTTTT
1 TATTTTT
50636865 ACATTTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TATTTTTTT
Found at i:50637003 original size:13 final size:13
Alignment explanation
Indices: 50636985--50637010 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50636975 CACAACAAAC
50636985 CTATTTTATTTCT
1 CTATTTTATTTCT
50636998 CTATTTTATTTCT
1 CTATTTTATTTCT
50637011 TTAACAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (13 bp):
CTATTTTATTTCT
Found at i:50647986 original size:30 final size:31
Alignment explanation
Indices: 50647923--50647991 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
50647913 AAAAAAATAT
*
50647923 AAATTTAACTCTTTTTAAAAGATTCATGGTC
1 AAATTTAACTCTTTTTAAAAGATTCAAGGTC
* * *
50647954 AAATTTGAGTCTTTTTAAAAGGTT-AAGGTC
1 AAATTTAACTCTTTTTAAAAGATTCAAGGTC
50647984 AAATTTAA
1 AAATTTAA
50647992 TTCAAAAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 12 0.36
31 21 0.64
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.41
Consensus pattern (31 bp):
AAATTTAACTCTTTTTAAAAGATTCAAGGTC
Found at i:50662636 original size:155 final size:157
Alignment explanation
Indices: 50662264--50662656 Score: 673
Period size: 155 Copynumber: 2.5 Consensus size: 157
50662254 TAAAAACGTC
50662264 TGGTCCCGTAGCTCAGTTGGTTAGAGCGTTGGTCTTATGAGCCGAAGGTCGCGGGTTCGAGCCCC
1 TGGTCCCGTAGCTCAGTTGGTTAGAGCGTTGGTCTTATGAGCCGAAGGTCGCGGGTTCGAGCCCC
* * *
50662329 GCTGGGACCAATTTATACTCCTCTCCATAATTTTAACTATGAATTTTATTCGTTAATAAGCGATA
66 GCCGGGACCAATTTATACTCCGCTCCATAATTTTAAC-AT-AATTTTATTCGTTAATAAGCCATA
50662394 AATAAAATTAAAAAAAATGGTTATTTCAT
129 AATAAAATTAAAAAAAATGGTTATTTCAT
50662423 TGGTCCCGTAGCTCAGTTGGTTAGAGCGTTGGTCTTATGAGCCGAAGGTCGCGGGTTCGAGCCCC
1 TGGTCCCGTAGCTCAGTTGGTTAGAGCGTTGGTCTTATGAGCCGAAGGTCGCGGGTTCGAGCCCC
* *
50662488 GCCGGGACCAATTTATACTCCGCTTCATAATTTTAAC-T-ATTTTATTCGTTCATAAGCCATAAA
66 GCCGGGACCAATTTATACTCCGCTCCATAATTTTAACATAATTTTATTCGTTAATAAGCCATAAA
* *
50662551 TAAAATTAAAATATATGGTTATTTCAT
131 TAAAATTAAAAAAAATGGTTATTTCAT
*
50662578 TGGTCCCGTAGCTCAGTTGGTTAGAGCGTTGGTCTTATGAGTCGAAGGTCGCGGGTTCGAGCCCC
1 TGGTCCCGTAGCTCAGTTGGTTAGAGCGTTGGTCTTATGAGCCGAAGGTCGCGGGTTCGAGCCCC
*
50662643 GCCAGGACCAATTT
66 GCCGGGACCAATTT
50662657 TAATTAAATT
Statistics
Matches: 225, Mismatches: 9, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
155 125 0.56
157 1 0.00
159 99 0.44
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (157 bp):
TGGTCCCGTAGCTCAGTTGGTTAGAGCGTTGGTCTTATGAGCCGAAGGTCGCGGGTTCGAGCCCC
GCCGGGACCAATTTATACTCCGCTCCATAATTTTAACATAATTTTATTCGTTAATAAGCCATAAA
TAAAATTAAAAAAAATGGTTATTTCAT
Found at i:50673071 original size:21 final size:21
Alignment explanation
Indices: 50673047--50673113 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
50673037 TTTTTTATTC
* * *
50673047 TAAATTTTAAATTTCGAATTT
1 TAAATCTTAAACTTTGAATTT
50673068 TAAATCTTAAACTTTGAATTT
1 TAAATCTTAAACTTTGAATTT
* * *
50673089 AAAAATC-GAAAC-TTAAATTT
1 -TAAATCTTAAACTTTGAATTT
50673109 TAAAT
1 TAAAT
50673114 TCGAATCCTA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 4 0.11
20 7 0.18
21 22 0.58
22 5 0.13
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (21 bp):
TAAATCTTAAACTTTGAATTT
Found at i:50675905 original size:55 final size:54
Alignment explanation
Indices: 50675821--50675930 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 54
50675811 CTAAACTTAG
50675821 AATAACCATAATCTAAAATAACTCGACCCCAAAACTCAATCGAAAAAAAACATAA
1 AATAACCATAATCTAAAATAACTCGACCCCAAAACTCAATC-AAAAAAAACATAA
*
50675876 AATAACCATAATCTAAAATAACTCGACCCCAAAACTCAATCAAAAAAAACCTAA
1 AATAACCATAATCTAAAATAACTCGACCCCAAAACTCAATCAAAAAAAACATAA
50675930 A
1 A
50675931 TTATTTGAAG
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
54 13 0.24
55 41 0.76
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.16
Consensus pattern (54 bp):
AATAACCATAATCTAAAATAACTCGACCCCAAAACTCAATCAAAAAAAACATAA
Found at i:50675952 original size:16 final size:17
Alignment explanation
Indices: 50675928--50675971 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
50675918 AAAAAAACCT
* *
50675928 AAATTATTTGAAGTC-A
1 AAATGATTTGAAATCGA
50675944 AAATGATTT-AAATCGA
1 AAATGATTTGAAATCGA
50675960 AAATGATTTGAA
1 AAATGATTTGAA
50675972 CCCAAAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.17
16 18 0.75
17 2 0.08
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.34
Consensus pattern (17 bp):
AAATGATTTGAAATCGA
Found at i:50676297 original size:17 final size:17
Alignment explanation
Indices: 50676252--50676298 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
50676242 TAAATCGTAG
*
50676252 AATAATTTTTAAATCAT
1 AATAATTTTTAAAACAT
* *
50676269 AATAA-ATTTAAAACTT
1 AATAATTTTTAAAACAT
*
50676285 TATAATTTTTAAAA
1 AATAATTTTTAAAA
50676299 AGATTAAATC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (17 bp):
AATAATTTTTAAAACAT
Found at i:50677089 original size:24 final size:24
Alignment explanation
Indices: 50677046--50677093 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
50677036 AGAAATAACC
** *
50677046 TTTCAATTAAATTCTGTTTATTTG
1 TTTCAATTAAACCCTATTTATTTG
50677070 TTTCAATTAAACCCTATTTATTTG
1 TTTCAATTAAACCCTATTTATTTG
50677094 AGTCAAACTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.54
Consensus pattern (24 bp):
TTTCAATTAAACCCTATTTATTTG
Found at i:50677099 original size:24 final size:24
Alignment explanation
Indices: 50677048--50677099 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
50677038 AAATAACCTT
** * **
50677048 TCAATTAAATTCTGTTTATTTGTT
1 TCAATTAAACCCTATTTATTTGAG
50677072 TCAATTAAACCCTATTTATTTGAG
1 TCAATTAAACCCTATTTATTTGAG
50677096 TCAA
1 TCAA
50677100 ACTCTTATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.48
Consensus pattern (24 bp):
TCAATTAAACCCTATTTATTTGAG
Found at i:50679007 original size:24 final size:24
Alignment explanation
Indices: 50678980--50679042 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
50678970 AGAAATAATC
*
50678980 TTTCAGTTAAACTTTGTTTAATTG
1 TTTCAGTTAAACTCTGTTTAATTG
* * *
50679004 TTTCAATTAAACCCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTAATTG
* *
50679028 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
50679043 TCTTAATCTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTAATTG
Found at i:50680892 original size:16 final size:15
Alignment explanation
Indices: 50680867--50680914 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
50680857 GGGATCAAGA
*
50680867 TAAAAGAAAATTAAAT
1 TAAAATAAAA-TAAAT
*
50680883 TAAATTAAAA-AAAT
1 TAAAATAAAATAAAT
50680897 TAAAAATAAAATAAAT
1 T-AAAATAAAATAAAT
50680913 TA
1 TA
50680915 TTTTTTAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 5 0.19
15 9 0.33
16 13 0.48
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (15 bp):
TAAAATAAAATAAAT
Found at i:50682840 original size:19 final size:21
Alignment explanation
Indices: 50682796--50682840 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
50682786 ACATCAGTAA
50682796 TTTCATCTTGAATTTCAATAT
1 TTTCATCTTGAATTTCAATAT
* *
50682817 TTTCAT-TTGGATTT-AATTT
1 TTTCATCTTGAATTTCAATAT
50682836 TTTCA
1 TTTCA
50682841 GAATAAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 9 0.41
20 7 0.32
21 6 0.27
ACGTcount: A:0.24, C:0.11, G:0.07, T:0.58
Consensus pattern (21 bp):
TTTCATCTTGAATTTCAATAT
Found at i:50683272 original size:23 final size:25
Alignment explanation
Indices: 50683223--50683272 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
50683213 TTTTAGAGCT
50683223 AATATAGACAAAAATTACAAAAATC
1 AATATAGACAAAAATTACAAAAATC
* *
50683248 AATAT-GA-AAAAATTACCAAATTC
1 AATATAGACAAAAATTACAAAAATC
50683271 AA
1 AA
50683273 AGATTAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 2 0.09
25 5 0.22
ACGTcount: A:0.62, C:0.12, G:0.04, T:0.22
Consensus pattern (25 bp):
AATATAGACAAAAATTACAAAAATC
Found at i:50686336 original size:20 final size:20
Alignment explanation
Indices: 50686311--50686349 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
50686301 AAATTATTTA
50686311 ATTT-AAGAAAAATGAAAAAC
1 ATTTAAAGAAAAA-GAAAAAC
50686331 ATTTAAAAGAAAAAGAAAA
1 ATTT-AAAGAAAAAGAAAA
50686350 CTCACCTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 5 0.29
22 8 0.47
ACGTcount: A:0.69, C:0.03, G:0.10, T:0.18
Consensus pattern (20 bp):
ATTTAAAGAAAAAGAAAAAC
Found at i:50686848 original size:3 final size:3
Alignment explanation
Indices: 50686840--50686865 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
50686830 AGAAGCTATA
50686840 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
50686866 TGAGATTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:50687226 original size:23 final size:23
Alignment explanation
Indices: 50687171--50687227 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
50687161 ATAATAAAAA
*
50687171 TATAATTAAATTATTTTAATAATTT
1 TATAATT--ATTAATTTAATAATTT
*
50687196 TATTATTATTAATTTAA-AATTT
1 TATAATTATTAATTTAATAATTT
50687218 TATAAATTAT
1 TAT-AATTAT
50687228 AAAGAGTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 8 0.29
23 14 0.50
25 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATAATTATTAATTTAATAATTT
Found at i:50688523 original size:29 final size:29
Alignment explanation
Indices: 50688490--50688562 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
50688480 CAATTAGACC
*
50688490 TAAATTTTTAAATTTAAAAA-ATAATAAAT
1 TAAATTTCTAAATTTAAAAATATAA-AAAT
* **
50688519 TAAATTCCTAAAAATAAAAATATAAAAAT
1 TAAATTTCTAAATTTAAAAATATAAAAAT
50688548 TAAA-TTCTAAATTTA
1 TAAATTTCTAAATTTA
50688563 TGAATAATAC
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 8 0.22
29 24 0.67
30 4 0.11
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (29 bp):
TAAATTTCTAAATTTAAAAATATAAAAAT
Found at i:50688558 original size:14 final size:14
Alignment explanation
Indices: 50688515--50688558 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
50688505 AAAAAATAAT
50688515 AAATTAAATTCCTAA
1 AAATTAAATT-CTAA
* * *
50688530 AAATAAAAATATAA
1 AAATTAAATTCTAA
50688544 AAATTAAATTCTAA
1 AAATTAAATTCTAA
50688558 A
1 A
50688559 TTTATGAATA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATTAAATTCTAA
Found at i:50688568 original size:28 final size:30
Alignment explanation
Indices: 50688504--50688558 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
50688494 TTTTTAAATT
50688504 TAAAAA-ATAATAAATTAAATTCCTAAAAA
1 TAAAAATATAATAAATTAAATTCCTAAAAA
50688533 TAAAAATATAA-AAATTAAATT-CTAAA
1 TAAAAATATAATAAATTAAATTCCTAAA
50688559 TTTATGAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
28 5 0.20
29 16 0.64
30 4 0.16
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.29
Consensus pattern (30 bp):
TAAAAATATAATAAATTAAATTCCTAAAAA
Found at i:50691718 original size:21 final size:21
Alignment explanation
Indices: 50691692--50691731 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
50691682 TTTTTCATTT
50691692 TGAAGAAGGGAGGAAAATAAA
1 TGAAGAAGGGAGGAAAATAAA
*
50691713 TGAAGAATGGAGGAAAATA
1 TGAAGAAGGGAGGAAAATA
50691732 GAGGGAGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.33, T:0.12
Consensus pattern (21 bp):
TGAAGAAGGGAGGAAAATAAA
Found at i:50693032 original size:30 final size:29
Alignment explanation
Indices: 50692998--50693061 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
50692988 AATTTACAAG
*
50692998 AATTGAATC-AAATCAAAATTTTATGTATAC
1 AATTGAA-CAAAATC-AAAGTTTATGTATAC
*
50693028 AATTGCACAAAATCAAAGTTTATGTATAC
1 AATTGAACAAAATCAAAGTTTATGTATAC
50693057 AATTG
1 AATTG
50693062 CACATTAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.34
Consensus pattern (29 bp):
AATTGAACAAAATCAAAGTTTATGTATAC
Found at i:50693050 original size:29 final size:30
Alignment explanation
Indices: 50693007--50693065 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
50692997 GAATTGAATC
*
50693007 AAATCAAAATTTTATGTATACAATTGCACA
1 AAATCAAAAGTTTATGTATACAATTGCACA
50693037 AAATC-AAAGTTTATGTATACAATTGCACA
1 AAATCAAAAGTTTATGTATACAATTGCACA
50693066 TTAAACCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (30 bp):
AAATCAAAAGTTTATGTATACAATTGCACA
Found at i:50697215 original size:28 final size:28
Alignment explanation
Indices: 50697141--50697230 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
50697131 CCGCTCATAT
* *
50697141 TATTTTTTATTTTTTTTAAAATATTTATATTA
1 TATTTTTTA-TTTATTTAATA-ATTT-TA-TA
*
50697173 TATTATTTTA-ATATTTAATAATTTTATA
1 TATT-TTTTATTTATTTAATAATTTTATA
* **
50697201 TATTTTTTATTTATTAAATTTTTTTATA
1 TATTTTTTATTTATTTAATAATTTTATA
50697229 TA
1 TA
50697231 ATCATCTTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
27 5 0.10
28 22 0.45
29 2 0.04
30 4 0.08
31 7 0.14
32 4 0.08
33 5 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (28 bp):
TATTTTTTATTTATTTAATAATTTTATA
Found at i:50701658 original size:29 final size:30
Alignment explanation
Indices: 50701615--50701677 Score: 119
Period size: 29 Copynumber: 2.1 Consensus size: 30
50701605 ACTTGGGTTT
50701615 TTATTGTTCATTTGTTGAATAATTTCATCA
1 TTATTGTTCATTTGTTGAATAATTTCATCA
50701645 TTATTG-TCATTTGTTGAATAATTTCATCA
1 TTATTGTTCATTTGTTGAATAATTTCATCA
50701674 TTAT
1 TTAT
50701678 GCAGTAATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 27 0.82
30 6 0.18
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.54
Consensus pattern (30 bp):
TTATTGTTCATTTGTTGAATAATTTCATCA
Found at i:50709823 original size:47 final size:47
Alignment explanation
Indices: 50709749--50709909 Score: 259
Period size: 47 Copynumber: 3.4 Consensus size: 47
50709739 TTCTGTTGAT
* * *
50709749 CTCATAAAATGTTTTCAATGTTTGGTTGTAGTCCATGCTTCTAGTAC
1 CTCATATAATGTTTTCGATGTTCGGTTGTAGTCCATGCTTCTAGTAC
*
50709796 CTCATTTAATGTTTTCGATGTTCGGTTGTAGTCCATGCTTCTAGTAC
1 CTCATATAATGTTTTCGATGTTCGGTTGTAGTCCATGCTTCTAGTAC
* *
50709843 CTCATATAATGTTTTTGATGTTCGGTTGTAGTCCATGCTTCTGGTAC
1 CTCATATAATGTTTTCGATGTTCGGTTGTAGTCCATGCTTCTAGTAC
*
50709890 CTCATATAATGTTTTTGATG
1 CTCATATAATGTTTTCGATG
50709910 CTTCTGGTAT
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 107 1.00
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.45
Consensus pattern (47 bp):
CTCATATAATGTTTTCGATGTTCGGTTGTAGTCCATGCTTCTAGTAC
Found at i:50709913 original size:30 final size:30
Alignment explanation
Indices: 50709877--50709939 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
50709867 GTTGTAGTCC
*
50709877 ATGCTTCTGGTACCTCATATAATGTTTTTG
1 ATGCTTCTGGTACCTCATATAATGTTTTCG
*
50709907 ATGCTTCTGGTATCTCATATAATGTTTTCG
1 ATGCTTCTGGTACCTCATATAATGTTTTCG
50709937 ATG
1 ATG
50709940 TTCGGTTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.46
Consensus pattern (30 bp):
ATGCTTCTGGTACCTCATATAATGTTTTCG
Found at i:50712841 original size:23 final size:24
Alignment explanation
Indices: 50712810--50712858 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
50712800 TTTAATTTTA
*
50712810 TTTTGTAATT-TACTCG-AATATAT
1 TTTTATAATTGTACT-GTAATATAT
50712833 TTTTATAATTGTACTGTAATATAT
1 TTTTATAATTGTACTGTAATATAT
50712857 TT
1 TT
50712859 GTAAACCCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.55
Consensus pattern (24 bp):
TTTTATAATTGTACTGTAATATAT
Found at i:50713145 original size:22 final size:20
Alignment explanation
Indices: 50713110--50713152 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 20
50713100 TAAAGTTTTG
50713110 TTTAATTTATTTATTTATACAT
1 TTTAATTTATTTA--TATACAT
50713132 TTTAATTT-TATTATATACAT
1 TTTAATTTAT-TTATATACAT
50713152 T
1 T
50713153 CTATTACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 8 0.40
21 1 0.05
22 11 0.55
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTAATTTATTTATATACAT
Found at i:50715518 original size:26 final size:26
Alignment explanation
Indices: 50715489--50715541 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
50715479 GTGAGAAAGT
50715489 ATGAGGGACTAAATAGCAATTTAGCC
1 ATGAGGGACTAAATAGCAATTTAGCC
50715515 ATGAGGGACTAAATAGCAATTTAGCC
1 ATGAGGGACTAAATAGCAATTTAGCC
50715541 A
1 A
50715542 AAATGAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.23
Consensus pattern (26 bp):
ATGAGGGACTAAATAGCAATTTAGCC
Found at i:50717124 original size:6 final size:6
Alignment explanation
Indices: 50717113--50717147 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
50717103 TGATCAAAAT
50717113 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAA
50717148 TTGGAATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.31, T:0.17
Consensus pattern (6 bp):
TGAAAG
Found at i:50718407 original size:19 final size:19
Alignment explanation
Indices: 50718383--50718421 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
50718373 ATCACTATAT
* *
50718383 AAAATTTTTTAATAAATAA
1 AAAATTATTAAATAAATAA
*
50718402 AAAATTATTAAATAATTAA
1 AAAATTATTAAATAAATAA
50718421 A
1 A
50718422 TATTAAAATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATTATTAAATAAATAA
Found at i:50718430 original size:16 final size:15
Alignment explanation
Indices: 50718395--50718445 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
50718385 AATTTTTTAA
50718395 TAAATAA-AAAATTAT
1 TAAATAATAAAA-TAT
*
50718410 TAAATAATTAAATAT
1 TAAATAATAAAATAT
*
50718425 TAAAATCATAAAATA-
1 T-AAATAATAAAATAT
50718440 TAAATA
1 TAAATA
50718446 TTTTAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 4 0.13
15 12 0.40
16 14 0.47
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAATAATAAAATAT
Found at i:50719283 original size:2 final size:2
Alignment explanation
Indices: 50719278--50719303 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
50719268 TTTTTGTTTT
50719278 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
50719304 AAACAAAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:50724923 original size:332 final size:335
Alignment explanation
Indices: 50724379--50725575 Score: 1297
Period size: 334 Copynumber: 3.6 Consensus size: 335
50724369 CCCTTTTTGA
50724379 ACACTCACAC-CTGAATCCAAGCACCATAGCACCCAAAGCCAAAAAGCTAACACTTCCCTTGCTT
1 ACACTCACACTC-GAATCCAAGCACCATAGCACCCAAAGCCAAAAAGCTAACACTTCCCTTGCTT
* * ** * * *
50724443 TTCTTGAATTAATTGTGTCCAACACATAC-T-AATTAGACTTGTCCAAGGACCTATGTGCAAAGC
65 TTCTTGAAGTAATCGTGTCTGACACATACTTGAACTAGACTTGTCCAAGGACCCATGAGCAAAGC
* * * * *
50724506 CCCA-CTGGTATTTGGGAAGGTTTAGACAAAAATATTAGGCCCGATAATGAACTTGGCCAAAATA
130 CTCACCAGGTATTTGGGAAGGTTTAGACAAAAATATAAAGCCCGAGAATGAACTTGGCCAAAATA
* * * * *
50724570 TGAGACCTATATA-CTGTTGATGCTACATATGAGTTTGGTCCAACTCATAGATACCTTTGATCTG
195 TGAGACCTATATAGC-GTTGATGCTACACATGAGCTTGGTCCAACTCATAGATACCTCTGACCCG
* *
50724634 AACACGAGTATAGGAATAT-ATC-T-AAAAATCCTCTTAATACATAGAAAATACCC-TTTCGAAC
259 AACACGAGTATAGGAATATGATCTTCAAAAATCCTATTAATACATAGAAAATACCCTTTTTGAAC
*
50724695 ACA-TCCGTGTGC
324 ACACT-TGTGTGC
* * *
50724707 ACATTGACACTCGAATCCAAGCACCATAGCACTCAAAGCCAAAAAGCTAACACTTCCCTTTGCTT
1 ACACTCACACTCGAATCCAAGCACCATAGCACCCAAAGCCAAAAAGCTAACACTTCCC-TTGCTT
* * *
50724772 TTCTTGAAGTAATTGTGTCTGACACCTACTTGAACTAGACCTT-TCCAAGGACCCATGACCAAAG
65 TTCTTGAAGTAATCGTGTCTGACACATACTTGAACTAGA-CTTGTCCAAGGACCCATGAGCAAAG
* * * * * *** *
50724836 CCTTACCAAGTATTCGAGAAGGTTTAGACAAAAATATCAAGCCCGAGAATGAACTTGGTTGAAAC
129 CCTCACCAGGTATTTGGGAAGGTTTAGACAAAAATATAAAGCCCGAGAATGAACTTGGCCAAAAT
** *
50724901 ATGAGACCTATATAGCGTTGATGCTACACATGAGCTACGTCCAACTCATAGATACCTCTGACCCA
194 ATGAGACCTATATAGCGTTGATGCTACACATGAGCTTGGTCCAACTCATAGATACCTCTGACCCG
** * * * **
50724966 AACAAAAGTATAGGAATATGATCTTCCAAAGATCTTTTTAATACATAGAAAATACCCTTTTTGGC
259 AACACGAGTATAGGAATATGATCTT-CAAAAATCCTATTAATACATAGAAAATACCCTTTTTGAA
* *
50725031 CTCACTTGTGTAC
323 CACACTTGTGTGC
* * * * * ** * *
50725044 ACACTCACACTCGAACCCAAGAACTATATCTCCTGAAGCCAAAAAGTTAACACTTCCCCT-CTTT
1 ACACTCACACTCGAATCCAAGCACCATAGCACCCAAAGCCAAAAAGCTAACACTTCCCTTGCTTT
* * *
50725108 TCTT-CAGTAATCGTGTCTGACACATACTTGTACTAGACTTGTCCAAAGACCCATGAGCAAAG-C
66 TCTTGAAGTAATCGTGTCTGACACATACTTGAACTAGACTTGTCCAAGGACCCATGAGCAAAGCC
* * * ** *
50725171 TCCACCCGGTATTTGGGAAGGTTTAAACAAAAATATAAAGTCTAAGAATCAACTTGGCCAAAATA
131 T-CACCAGGTATTTGGGAAGGTTTAGACAAAAATATAAAGCCCGAGAATGAACTTGGCCAAAATA
* * * * * * *
50725236 TGAGACCTATGTAGTGTTGATGCTACACATGAGCCTGATCCATCTCATAGACACCTCAGACCCGA
195 TGAGACCTATATAGCGTTGATGCTACACATGAGCTTGGTCCAACTCATAGATACCTCTGACCCGA
* ** * * *
50725301 ACACGAATATAACAGTATGATCTTCCAGATATCCTATTAATACATAGAAAATACACCCTTTTTGA
260 ACACGAGTATAGGAATATGATCTT-CAAAAATCCTATTAATACATAGAAAAT--ACCCTTTTTGA
*
50725366 ACACGCTTGTGTGC
322 ACACACTTGTGTGC
* * * * * *
50725380 ACACTCACACGCAAATCCAAGTACCTTAGCACCCGAAGCCAAAAAGCTATCACTTTCCCTTGCTT
1 ACACTCACACTCGAATCCAAGCACCATAGCACCCAAAGCCAAAAAGCTAACAC-TTCCCTTGCTT
* * * * * *
50725445 TTCTTGCAGTAATCATGTCTGACACATACTTGAACTAGACCTGTCCAATGACTCATGTGCAAAGC
65 TTCTTGAAGTAATCGTGTCTGACACATACTTGAACTAGACTTGTCCAAGGACCCATGAGCAAAGC
* * ** * * * * *
50725510 CCCACCTGGTATTTGGGAAAATTTATACAAAAATGTTAGGCTCGAGAATGAACTTGGCCAAAATA
130 CTCACCAGGTATTTGGGAAGGTTTAGACAAAAATATAAAGCCCGAGAATGAACTTGGCCAAAATA
50725575 T
195 T
50725576 AGTGTTGATG
Statistics
Matches: 716, Mismatches: 132, Indels: 31
0.81 0.15 0.04
Matches are distributed among these distances:
328 53 0.07
329 32 0.04
330 1 0.00
331 27 0.04
332 123 0.17
333 9 0.01
334 194 0.27
335 8 0.01
336 90 0.13
337 65 0.09
338 9 0.01
339 104 0.15
340 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.26
Consensus pattern (335 bp):
ACACTCACACTCGAATCCAAGCACCATAGCACCCAAAGCCAAAAAGCTAACACTTCCCTTGCTTT
TCTTGAAGTAATCGTGTCTGACACATACTTGAACTAGACTTGTCCAAGGACCCATGAGCAAAGCC
TCACCAGGTATTTGGGAAGGTTTAGACAAAAATATAAAGCCCGAGAATGAACTTGGCCAAAATAT
GAGACCTATATAGCGTTGATGCTACACATGAGCTTGGTCCAACTCATAGATACCTCTGACCCGAA
CACGAGTATAGGAATATGATCTTCAAAAATCCTATTAATACATAGAAAATACCCTTTTTGAACAC
ACTTGTGTGC
Found at i:50727405 original size:18 final size:20
Alignment explanation
Indices: 50727384--50727425 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
50727374 ATATATATTT
50727384 AAAATAG-AAA-AAATTATA
1 AAAATAGTAAAGAAATTATA
*
50727402 AAAATAGTAAAGAATTTATA
1 AAAATAGTAAAGAAATTATA
50727422 AAAA
1 AAAA
50727426 AATGTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 3 0.14
20 11 0.52
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (20 bp):
AAAATAGTAAAGAAATTATA
Found at i:50727944 original size:37 final size:38
Alignment explanation
Indices: 50727903--50728003 Score: 95
Period size: 37 Copynumber: 2.7 Consensus size: 38
50727893 AGAGATATGA
** *
50727903 TAATTTTTATAAACTTTTATCCATTTTTATAT-TTTTT
1 TAATTTTTATAAACTTTTATAAAATTTTATATATTTTT
*
50727940 TAATTTTCT-TACGA-TTTTATAAAATTTTATATATTTTT
1 TAATTTT-TATA-AACTTTTATAAAATTTTATATATTTTT
* *
50727978 TAATTTTAAT-AACTTTTA-AATATTTT
1 TAATTTTTATAAACTTTTATAAAATTTT
50728004 TTATTAAATT
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
36 8 0.15
37 29 0.56
38 15 0.29
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (38 bp):
TAATTTTTATAAACTTTTATAAAATTTTATATATTTTT
Found at i:50727977 original size:10 final size:10
Alignment explanation
Indices: 50727954--50728036 Score: 50
Period size: 9 Copynumber: 8.6 Consensus size: 10
50727944 TTTCTTACGA
* *
50727954 TTTTATAAAA
1 TTTTATATAT
50727964 TTTTATATAT
1 TTTTATATAT
50727974 TTTT-TA-AT
1 TTTTATATAT
* *
50727982 TTTAATA-AC
1 TTTTATATAT
*
50727991 TTTTAAATATT
1 TTTTATATA-T
*
50728002 TTTTATTAAAT
1 TTTTA-TATAT
*
50728013 TTTAAT-TAT
1 TTTTATATAT
50728022 TTTTATAT-T
1 TTTTATATAT
50728031 TTTTAT
1 TTTTAT
50728037 TTTTATCATT
Statistics
Matches: 56, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
8 5 0.09
9 24 0.43
10 15 0.27
11 10 0.18
12 2 0.04
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTATATAT
Found at i:50727983 original size:27 final size:27
Alignment explanation
Indices: 50727953--50728006 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
50727943 TTTTCTTACG
*
50727953 ATTTT-ATAAAATTTTATATATTTTTTA
1 ATTTTAAT-AAATTTTAAATATTTTTTA
*
50727980 ATTTTAATAACTTTTAAATATTTTTTA
1 ATTTTAATAAATTTTAAATATTTTTTA
50728007 TTAAATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 22 0.92
28 2 0.08
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (27 bp):
ATTTTAATAAATTTTAAATATTTTTTA
Found at i:50728006 original size:21 final size:21
Alignment explanation
Indices: 50727981--50728025 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
50727971 TATTTTTTAA
*
50727981 TTTTAATAACTTTTAAATATT
1 TTTTAATAAATTTTAAATATT
* *
50728002 TTTTATTAAATTTTAATTATT
1 TTTTAATAAATTTTAAATATT
50728023 TTT
1 TTT
50728026 ATATTTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTAATAAATTTTAAATATT
Found at i:50728017 original size:31 final size:29
Alignment explanation
Indices: 50727953--50728037 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 29
50727943 TTTTCTTACG
* *
50727953 ATTTTATAAAATTTT-ATATATTTT-TT-A
1 ATTTTA-ATAATTTTAATATTTTTTATTAA
50727980 ATTTTAATAACTTTTAAATATTTTTTATTAA
1 ATTTTAATAA-TTTT-AATATTTTTTATTAA
* *
50728011 ATTTTAATTATTTTTATATTTTTTATT
1 ATTTTAATAATTTTAATATTTTTTATT
50728038 TTTATCATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
26 3 0.06
27 10 0.20
29 20 0.41
30 6 0.12
31 10 0.20
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (29 bp):
ATTTTAATAATTTTAATATTTTTTATTAA
Found at i:50728030 original size:29 final size:29
Alignment explanation
Indices: 50727964--50728037 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
50727954 TTTTATAAAA
*
50727964 TTTTATATATTTT-TTAATTTTAATAACT
1 TTTTATATTTTTTATTAATTTTAATAACT
* *
50727992 TTTAAATATTTTTTATTAAATTTTAATTA-T
1 TTT-TATATTTTTTATT-AATTTTAATAACT
50728022 TTTTATATTTTTTATT
1 TTTTATATTTTTTATT
50728038 TTTATCATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
28 3 0.08
29 20 0.51
30 6 0.15
31 10 0.26
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (29 bp):
TTTTATATTTTTTATTAATTTTAATAACT
Found at i:50728038 original size:15 final size:16
Alignment explanation
Indices: 50728018--50728050 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
50728008 TAAATTTTAA
50728018 TTATTTTTAT-ATTTT
1 TTATTTTTATCATTTT
50728033 TTATTTTTATCATTTT
1 TTATTTTTATCATTTT
50728049 TT
1 TT
50728051 GCCACATGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (16 bp):
TTATTTTTATCATTTT
Found at i:50729954 original size:8 final size:8
Alignment explanation
Indices: 50729941--50729967 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
50729931 TTCAAATAAA
50729941 TTCAAATT
1 TTCAAATT
50729949 TTCAAATT
1 TTCAAATT
50729957 TTCAAATT
1 TTCAAATT
50729965 TTC
1 TTC
50729968 TTATTTAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (8 bp):
TTCAAATT
Found at i:50730241 original size:14 final size:14
Alignment explanation
Indices: 50730198--50730245 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
50730188 AATAATTATA
50730198 ATTAATATTTGATTAT
1 ATTAATATTT-ATT-T
*
50730214 ATTTAA-ATTCATTT
1 A-TTAATATTTATTT
50730228 ATTAATATTTATTT
1 ATTAATATTTATTT
50730242 ATTA
1 ATTA
50730246 GTCATTATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 4 0.14
14 13 0.46
15 3 0.11
16 4 0.14
17 4 0.14
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (14 bp):
ATTAATATTTATTT
Found at i:50735024 original size:9 final size:8
Alignment explanation
Indices: 50735011--50735044 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
50735001 CAATTGAACC
50735011 AATTTTTA
1 AATTTTTA
50735019 ATATTTTTA
1 A-ATTTTTA
*
50735028 AATATTTA
1 AATTTTTA
50735036 AATTTTTA
1 AATTTTTA
50735044 A
1 A
50735045 TAATTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
AATTTTTA
Found at i:50735954 original size:24 final size:22
Alignment explanation
Indices: 50735911--50735954 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
50735901 ATCCCCTTTA
*
50735911 ATTATTTAAAAAATAATGTTAT
1 ATTATTTAAAAAACAATGTTAT
*
50735933 ATTATTTTTAAAAACAACTGTT
1 ATTA-TTTAAAAAACAA-TGTT
50735955 GATACAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (22 bp):
ATTATTTAAAAAACAATGTTAT
Found at i:50747433 original size:2 final size:2
Alignment explanation
Indices: 50747420--50747463 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
50747410 ATGACATTCA
* *
50747420 AT AT AT AC AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50747462 AT
1 AT
50747464 GCGTGAAGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:50753277 original size:29 final size:30
Alignment explanation
Indices: 50753236--50753296 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
50753226 AATTTTAAAA
50753236 TCTAAAAAGTAAAAAAAAAAAAACTAAATT
1 TCTAAAAAGTAAAAAAAAAAAAACTAAATT
* * *
50753266 TCTAAAAA-TAAAAATACAAAGACTAAATT
1 TCTAAAAAGTAAAAAAAAAAAAACTAAATT
50753295 TC
1 TC
50753297 AAATTTACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.64, C:0.10, G:0.03, T:0.23
Consensus pattern (30 bp):
TCTAAAAAGTAAAAAAAAAAAAACTAAATT
Found at i:50753341 original size:39 final size:40
Alignment explanation
Indices: 50753295--50753386 Score: 111
Period size: 38 Copynumber: 2.4 Consensus size: 40
50753285 AGACTAAATT
*
50753295 TCAAATTTACAAAAAAATAC-AGAAATTTATGGCATAAAGA
1 TCAAATTTACAAAAAAATACAAG-AACTTATGGCATAAAGA
** *
50753335 -CAAATTTAC-AAAAGGTACAAGGACTTATGGCATAAAGA
1 TCAAATTTACAAAAAAATACAAGAACTTATGGCATAAAGA
50753373 TC-AATTTACAAAAA
1 TCAAATTTACAAAAA
50753387 GGCACAGGGA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
38 29 0.64
39 16 0.36
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (40 bp):
TCAAATTTACAAAAAAATACAAGAACTTATGGCATAAAGA
Found at i:50753371 original size:38 final size:39
Alignment explanation
Indices: 50753321--50753406 Score: 122
Period size: 39 Copynumber: 2.2 Consensus size: 39
50753311 ATACAGAAAT
* *
50753321 TTATGGCATAAAGA-CAAATTTAC-AAAAGGTACAAGGAC
1 TTATGGCATAAAGATC-AATTTACAAAAAGGCACAAGGAA
*
50753359 TTATGGCATAAAGATCAATTTACAAAAAGGCACAGGGAA
1 TTATGGCATAAAGATCAATTTACAAAAAGGCACAAGGAA
50753398 TTATGGCAT
1 TTATGGCAT
50753407 GGCCAAAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
38 21 0.49
39 22 0.51
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.23
Consensus pattern (39 bp):
TTATGGCATAAAGATCAATTTACAAAAAGGCACAAGGAA
Found at i:50755498 original size:167 final size:169
Alignment explanation
Indices: 50755083--50755533 Score: 554
Period size: 167 Copynumber: 2.7 Consensus size: 169
50755073 ACAAGTAATG
* * * *
50755083 AAGACTAAGAGAT-GACATTCTCGACCGCCAGTGAAGCTTATTC-GGTTCTCGTAAAACCGTATC
1 AAGACTACGAGATCAACATTC-CGACCG-CAGTGAAGCTCA-TCGGGTTCTCGTAAAACCGTATT
* * * * *
50755146 GTTATAGAACTCACACAAGTAAACTAAACTACAACAGAGGGCAATTTAGCACCAAATCTCCTTAT
63 GTTATAGAACTCACACAAGTAACCTAAACTATATCATACGGCAATTTAGCACCAAATCTCCTTAT
* **
50755211 AATCACACAAATGACAAAAATGATGAAGCATGCAAGTAATGA
128 AATCACACAAATGACAAAAATAATGAAGCATGCAAGTAACAA
** ** * * * * *
50755253 AAGACTACGAGATGTAGTTTCCAACCATCATTGAAGCTCATAAGGATTCTCGTAAAACCGTATTG
1 AAGACTACGAGATCAACATTCCGACC-GCAGTGAAGCTCAT-CGGGTTCTCGTAAAACCGTATTG
* *
50755318 TTATAGAACTCACACAAGTAACCTAAA-T-TATCATACGGCAATTTAGCACCAAATCTCCTTGTG
64 TTATAGAACTCACACAAGTAACCTAAACTATATCATACGGCAATTTAGCACCAAATCTCCTTATA
*
50755381 ATTACAC-AATGACAAAAATAATGAAGCATGCAAGTAACAA
129 ATCACACAAATGACAAAAATAATGAAGCATGCAAGTAACAA
* *
50755421 AAGGCTACGAGA-CAACATTCCGACCGCAGGTGAAGCTCATCGGGGTTCTCATAAAACCGTATTG
1 AAGACTACGAGATCAACATTCCGACCGCA-GTGAAGCTCATC-GGGTTCTCGTAAAACCGTATTG
*
50755485 TTATAGAACTCACACAAGTAACCTAAATTATATCATACGGCAATTTAGC
64 TTATAGAACTCACACAAGTAACCTAAACTATATCATACGGCAATTTAGC
50755534 TCTAAACATG
Statistics
Matches: 240, Mismatches: 33, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
166 2 0.01
167 65 0.27
168 42 0.17
169 55 0.23
170 27 0.11
171 49 0.20
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (169 bp):
AAGACTACGAGATCAACATTCCGACCGCAGTGAAGCTCATCGGGTTCTCGTAAAACCGTATTGTT
ATAGAACTCACACAAGTAACCTAAACTATATCATACGGCAATTTAGCACCAAATCTCCTTATAAT
CACACAAATGACAAAAATAATGAAGCATGCAAGTAACAA
Found at i:50756803 original size:31 final size:31
Alignment explanation
Indices: 50756768--50756826 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
50756758 AACAACCAAG
*
50756768 TAACTGAAATAACAACTTTCAAATAATTCAA
1 TAACTGAAATAAAAACTTTCAAATAATTCAA
* *
50756799 TAACTTAAATAAAAACTTTCGAATAATT
1 TAACTGAAATAAAAACTTTCAAATAATT
50756827 TAATGACTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.32
Consensus pattern (31 bp):
TAACTGAAATAAAAACTTTCAAATAATTCAA
Found at i:50757039 original size:41 final size:44
Alignment explanation
Indices: 50756937--50757039 Score: 104
Period size: 46 Copynumber: 2.4 Consensus size: 44
50756927 TAGCTTCCAT
* * *
50756937 ATATTTATAATTAAATTTAAATAAAATATTTTATTAACATGTATAT
1 ATATGTATAAATAAATTTAAATAAAATATTTTATT-A-ATGTATAA
* * * *
50756983 ATATTTATAATTAAATTTAAATAAAATATTTTATT-ATTTTTAA
1 ATATGTATAAATAAATTTAAATAAAATATTTTATTAATGTATAA
50757026 ATA-GTA-AAATAAAT
1 ATATGTATAAATAAAT
50757040 CATTTGAGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
41 7 0.13
42 2 0.04
43 8 0.15
46 35 0.67
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.48
Consensus pattern (44 bp):
ATATGTATAAATAAATTTAAATAAAATATTTTATTAATGTATAA
Found at i:50780143 original size:5 final size:5
Alignment explanation
Indices: 50780135--50780175 Score: 64
Period size: 5 Copynumber: 8.0 Consensus size: 5
50780125 ATTTGAAAAT
*
50780135 TTTAA TTTAA TTTAG TTTAA TTTAA TTTAA TTTTAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA -TTTAA TTTAA
50780176 AAGTGCTGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 28 0.85
6 5 0.15
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (5 bp):
TTTAA
Found at i:50781323 original size:31 final size:31
Alignment explanation
Indices: 50781231--50781323 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
50781221 TTAACCCAAT
* *
50781231 ATGAGAATAATTGTCAAATTTAAGGACTAAC
1 ATGAAAATAATTATCAAATTTAAGGACTAAC
* * * * *
50781262 ATGATAAT-TTTATCACATTTTAGGCTCTAAC
1 ATGAAAATAATTATCAAATTTAAGG-ACTAAC
*
50781293 ATGAAAATAATTATCAAATTTAAAGACTAAC
1 ATGAAAATAATTATCAAATTTAAGGACTAAC
50781324 TTAAATAGAA
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
30 12 0.25
31 24 0.50
32 12 0.25
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (31 bp):
ATGAAAATAATTATCAAATTTAAGGACTAAC
Found at i:50782507 original size:17 final size:19
Alignment explanation
Indices: 50782473--50782518 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
50782463 AATATTAAAA
*
50782473 AATATATTATATATATTA-T
1 AATATTTTA-ATATATTATT
50782492 AATATTTTAATA-ATTATT
1 AATATTTTAATATATTATT
50782510 AAT-TTTTAA
1 AATATTTTAA
50782519 AAATAGCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 10 0.40
18 7 0.28
19 8 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATTTTAATATATTATT
Found at i:50787427 original size:23 final size:22
Alignment explanation
Indices: 50787388--50787436 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
50787378 ATGATTTGAC
**
50787388 AAAAAAAAAAAGTTTAA-GAGCT
1 AAAAAAAAAAAAATTAATG-GCT
50787410 AAAAAAAGAAAAAATTAATGGCT
1 AAAAAAA-AAAAAATTAATGGCT
50787433 AAAA
1 AAAA
50787437 TGATTTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 7 0.30
23 15 0.65
24 1 0.04
ACGTcount: A:0.67, C:0.04, G:0.12, T:0.16
Consensus pattern (22 bp):
AAAAAAAAAAAAATTAATGGCT
Found at i:50787980 original size:16 final size:18
Alignment explanation
Indices: 50787949--50787981 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
50787939 TTGATAGTTC
50787949 TAAATATTGTATAAAAAA
1 TAAATATTGTATAAAAAA
50787967 TAAATA-TG-ATAAAAA
1 TAAATATTGTATAAAAA
50787982 CTTATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (18 bp):
TAAATATTGTATAAAAAA
Found at i:50788918 original size:18 final size:18
Alignment explanation
Indices: 50788895--50788942 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
50788885 CAGGTATATC
50788895 TTCTTTGCATCCGTCTAT
1 TTCTTTGCATCCGTCTAT
50788913 TTCTTTGCATCCGTCTAT
1 TTCTTTGCATCCGTCTAT
*
50788931 CTCTTTGCATCC
1 TTCTTTGCATCC
50788943 TAATCATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.10, C:0.31, G:0.10, T:0.48
Consensus pattern (18 bp):
TTCTTTGCATCCGTCTAT
Found at i:50800645 original size:117 final size:117
Alignment explanation
Indices: 50800307--50800941 Score: 603
Period size: 117 Copynumber: 5.3 Consensus size: 117
50800297 CAGTTCCCGA
** * * * *
50800307 CAATCACATAAAAACCAACTGCAAAAAACTCACTCGTAAACCGAGCTCACCGAC-TGTTCAAAAG
1 CAATCACATACCAACCAACTGC-AATAATTCACTCGAAAACCGAACTCACCGACGT-TTC--AAG
* ** * * * *
50800371 ACTAAAATCTTCACTCCCATACATAAATCTCAAATACCATAAACTCGGTTTTCTAG
62 ACTAAAATCTTCACTCCTATATGTATATCTCAAACACCCTAAACTCGGTTTTCCAG
* * * * * *
50800427 CAATCACATACCAACCAACTGCAAAAAACTCACTCGTAAACCAAACTCGCCGACGTTTCAAGACC
1 CAATCACATACCAACCAACTGC-AATAATTCACTCGAAAACCGAACTCACCGACGTTTCAAGACT
* * * *
50800492 AAAATCTTCACTCCTATACGT-TAATCTCAAACGCCCTAACCTCAGTTTTCCAG
65 AAAATCTTCACTCCTATATGTAT-ATCTCAAACACCCTAAACTCGGTTTTCCAG
* * * * **
50800545 CAATCACGTACCAACCAACTGCAATAATTCACTCGAAAACTGAACTCACTGATGTTTTGAGACTA
1 CAATCACATACCAACCAACTGCAATAATTCACTCGAAAACCGAACTCACCGACGTTTCAAGACTA
* ** *
50800610 AAATCCTCACTCCTATATGTATATCTCAAATGCCCTAAACTCAGTTTTCCAG
66 AAATCTTCACTCCTATATGTATATCTCAAACACCCTAAACTCGGTTTTCCAG
* * ** * * *
50800662 CAACCACATACCAACCAAATGCAATAAACCACTTGTAAACCGAACTCACCAACAG-TTCAAGACT
1 CAATCACATACCAACCAACTGCAATAATTCACTCGAAAACCGAACTCACCGAC-GTTTCAAGACT
* * *
50800726 AAAATCTTCACTCCTATATGTATATTTCAAACACCATAAACTCGGTTTTCCGG
65 AAAATCTTCACTCCTATATGTATATCTCAAACACCCTAAACTCGGTTTTCCAG
** *
50800779 CAATCACATACCAAGTTACCAACCAAATGCAATAATTCACTCGAAAATTGAACTCACAGACGTTT
1 CAATCACATACC-A---ACCAA-C---TGCAATAATTCACTCGAAAACCGAACTCACCGACGTTT
* * * * **
50800844 CTAGACAAAAATCCTCACTCCTATACT-TAAATCTCAAACACCCTAAACTCGGTTTTCTGG
58 CAAGACTAAAATCTTCACTCCTATA-TGTATATCTCAAACACCCTAAACTCGGTTTTCCAG
* * *
50800904 CAATCACAAACCAATCAACTGCAATAATTCACTTGAAA
1 CAATCACATACCAACCAACTGCAATAATTCACTCGAAA
50800942 CATCGAATCA
Statistics
Matches: 430, Mismatches: 71, Indels: 31
0.81 0.13 0.06
Matches are distributed among these distances:
117 202 0.47
118 72 0.17
120 53 0.12
121 10 0.02
124 2 0.00
125 90 0.21
126 1 0.00
ACGTcount: A:0.38, C:0.29, G:0.09, T:0.24
Consensus pattern (117 bp):
CAATCACATACCAACCAACTGCAATAATTCACTCGAAAACCGAACTCACCGACGTTTCAAGACTA
AAATCTTCACTCCTATATGTATATCTCAAACACCCTAAACTCGGTTTTCCAG
Found at i:50800859 original size:242 final size:234
Alignment explanation
Indices: 50800369--50800930 Score: 682
Period size: 242 Copynumber: 2.4 Consensus size: 234
50800359 ACTGTTCAAA
* * * *
50800369 AGACTAAAATCTTCACTCCCATACATAAATCTCAAATACCATAAACTCGGTTTTCTAGCAATCAC
1 AGACTAAAATCCTCACTCCTATA-TTAAATCTCAAATACCCTAAACTCGGTTTTCTAGCAATCAC
* * *
50800434 ATACCAACCAACTGCAAAAAACTCACTCGTAAACCAAACTCGCCGACGTTTCAAGACCAAAATCT
65 ATACCAACCAACTGCAATAAACTCACTCGTAAACCAAACTCACCAACGTTTCAAGACCAAAATCT
* * * *
50800499 TCACTCCTATACGTTAATCTCAAACGCCCTAACCTCAGTTTTCCAGCAATCACGTACCAACCAAC
130 TCACTCCTATACGTTAATCTCAAACACCATAAACTCAGTTTTCCAGCAATCACGTACCAACCAAA
* *
50800564 TGCAATAATTCACTCGAAAACTGAACTCACTGATGTTTTG
195 TGCAATAATTCACTCGAAAACTGAACTCACAGACGTTTTG
* * * * *
50800604 AGACTAAAATCCTCACTCCTATATGTATATCTCAAATGCCCTAAACTCAGTTTTCCAGCAACCAC
1 AGACTAAAATCCTCACTCCTATAT-TAAATCTCAAATACCCTAAACTCGGTTTTCTAGCAATCAC
* * * *
50800669 ATACCAACCAAATGCAATAAAC-CACTTGTAAACCGAACTCACCAACAG-TTCAAGACTAAAATC
65 ATACCAACCAACTGCAATAAACTCACTCGTAAACCAAACTCACCAAC-GTTTCAAGACCAAAATC
* * * *
50800732 TTCACTCCTATATG-TATATTTCAAACACCATAAACTCGGTTTTCCGGCAATCACATACCAAGTT
129 TTCACTCCTATACGTTA-ATCTCAAACACCATAAACTCAGTTTTCCAGCAAT--C--A-C--G-T
*
50800796 ACCAACCAAATGCAATAATTCACTCGAAAATTGAACTCACAGACGTTTCT-
185 ACCAACCAAATGCAATAATTCACTCGAAAACTGAACTCACAGACGTTT-TG
* * *
50800846 AGACAAAAATCCTCACTCCTATACTTAAATCTCAAACACCCTAAACTCGGTTTTCTGGCAATCAC
1 AGACTAAAATCCTCACTCCTATA-TTAAATCTCAAATACCCTAAACTCGGTTTTCTAGCAATCAC
* *
50800911 AAACCAATCAACTGCAATAA
65 ATACCAACCAACTGCAATAA
50800931 TTCACTTGAA
Statistics
Matches: 276, Mismatches: 38, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
233 2 0.01
234 75 0.27
235 76 0.28
236 1 0.00
238 1 0.00
239 1 0.00
241 1 0.00
242 117 0.42
243 2 0.01
ACGTcount: A:0.37, C:0.29, G:0.09, T:0.25
Consensus pattern (234 bp):
AGACTAAAATCCTCACTCCTATATTAAATCTCAAATACCCTAAACTCGGTTTTCTAGCAATCACA
TACCAACCAACTGCAATAAACTCACTCGTAAACCAAACTCACCAACGTTTCAAGACCAAAATCTT
CACTCCTATACGTTAATCTCAAACACCATAAACTCAGTTTTCCAGCAATCACGTACCAACCAAAT
GCAATAATTCACTCGAAAACTGAACTCACAGACGTTTTG
Found at i:50801373 original size:16 final size:17
Alignment explanation
Indices: 50801352--50801387 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
50801342 ACCAAAAGCC
50801352 AAAATTAAAACTA-AGA
1 AAAATTAAAACTATAGA
*
50801368 AAAATTGAAACTATAGA
1 AAAATTAAAACTATAGA
50801385 AAA
1 AAA
50801388 TGAATGATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.19
Consensus pattern (17 bp):
AAAATTAAAACTATAGA
Found at i:50803400 original size:32 final size:32
Alignment explanation
Indices: 50803355--50803425 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 32
50803345 GAATAAATTT
* *
50803355 TCAAATTTTAAAAAGTAAAGGGACTA-AATTTGA
1 TCAAA-TTCAAAAAATAAAGGGACTAGAA-TTGA
* *
50803388 T-AAATTCAAAAAATACATGGACTAGAATTGA
1 TCAAATTCAAAAAATAAAGGGACTAGAATTGA
50803419 TCAAATT
1 TCAAATT
50803426 AAACTATAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
31 21 0.66
32 10 0.31
33 1 0.03
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (32 bp):
TCAAATTCAAAAAATAAAGGGACTAGAATTGA
Found at i:50805752 original size:15 final size:15
Alignment explanation
Indices: 50805712--50805754 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
50805702 TACATTCGAA
*
50805712 ATCAAAAATCAATAG
1 ATCAAAAATCAATAC
*
50805727 A-CGAAAA-CAATAC
1 ATCAAAAATCAATAC
50805740 ATCAAAAATCAATAC
1 ATCAAAAATCAATAC
50805755 GAGCAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 6 0.26
14 10 0.43
15 7 0.30
ACGTcount: A:0.60, C:0.19, G:0.05, T:0.16
Consensus pattern (15 bp):
ATCAAAAATCAATAC
Found at i:50805762 original size:15 final size:15
Alignment explanation
Indices: 50805714--50805763 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 15
50805704 CATTCGAAAT
50805714 CAAAAATCAATA-GA
1 CAAAAATCAATACGA
*
50805728 CGAAAA-CAATAC-A
1 CAAAAATCAATACGA
50805741 TCAAAAATCAATACGA
1 -CAAAAATCAATACGA
50805757 GCAAAAA
1 -CAAAAA
50805764 ACGAAGCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 6 0.21
14 10 0.34
15 6 0.21
16 7 0.24
ACGTcount: A:0.62, C:0.18, G:0.08, T:0.12
Consensus pattern (15 bp):
CAAAAATCAATACGA
Found at i:50806958 original size:60 final size:60
Alignment explanation
Indices: 50806894--50807069 Score: 205
Period size: 60 Copynumber: 3.0 Consensus size: 60
50806884 TTGACCTTCG
* * *
50806894 AACTTCTCCAAAATCATATTTTAACCCCTAAACTTCTCCAAAATTTTATTTTGATCCCAA
1 AACTTCTCCAAAATCATATTTTAACCCCTAAACTTCTCCAAAATTATATTTTAACCCCAA
* * * *
50806954 AACTTCTCCAAAATCATGTTTTGACCCCTAAACTT-TCCAAAATTACATTTTAACCCCTA
1 AACTTCTCCAAAATCATATTTTAACCCCTAAACTTCTCCAAAATTATATTTTAACCCCAA
* * * * *
50807013 AACTTTTCTAAAATTACATTTTAA-CCCTCAAACTTC-CCTAAAATTATATTTTTACCC
1 AACTTCTCCAAAATCATATTTTAACCCCT-AAACTTCTCC-AAAATTATATTTTAACCC
50807070 TCGAACTTTT
Statistics
Matches: 98, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
58 4 0.04
59 45 0.46
60 49 0.50
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.37
Consensus pattern (60 bp):
AACTTCTCCAAAATCATATTTTAACCCCTAAACTTCTCCAAAATTATATTTTAACCCCAA
Found at i:50807034 original size:89 final size:90
Alignment explanation
Indices: 50806864--50807099 Score: 257
Period size: 89 Copynumber: 2.6 Consensus size: 90
50806854 TAGGTCCCTG
* * *
50806864 AACTT-TCCAAAAATCATATTTTGACCTTCGAACTTCTCCAAAATCATATTTTAACCCCTAAACT
1 AACTTCTCCAAAAATCATATTTTGACCCTCGAACTT-TCCAAAATTACATTTTAACCCCTAAACT
** *
50806928 TCTCCAAAATTTTATTTTGATCCC-AA
65 TCTCCAAAATTACATTTT-AACCCTAA
* *
50806954 AACTTCTCC-AAAATCATGTTTTGACCC-CTAAACTTTCCAAAATTACATTTTAACCCCTAAACT
1 AACTTCTCCAAAAATCATATTTTGACCCTC-GAACTTTCCAAAATTACATTTTAACCCCTAAACT
* * *
50807017 TTTCTAAAATTACATTTTAACCCTCA
65 TCTCCAAAATTACATTTTAACCCTAA
* * * * *
50807043 AACTTC-CCTAAAATTATATTTTTACCCTCGAACTTTTCTAAAATTACATTTTGACCC
1 AACTTCTCCAAAAATCATATTTTGACCCTCGAAC-TTTCCAAAATTACATTTTAACCC
50807100 AGTATTCTCT
Statistics
Matches: 123, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
88 6 0.05
89 66 0.54
90 48 0.39
91 3 0.02
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (90 bp):
AACTTCTCCAAAAATCATATTTTGACCCTCGAACTTTCCAAAATTACATTTTAACCCCTAAACTT
CTCCAAAATTACATTTTAACCCTAA
Found at i:50807070 original size:30 final size:28
Alignment explanation
Indices: 50806868--50807099 Score: 149
Period size: 30 Copynumber: 7.8 Consensus size: 28
50806858 TCCCTGAACT
* * * *
50806868 TTCCAAAAATCATATTTTGACCTTCGAAC
1 TTCCCAAAATTATATTTTGACC-CCAAAC
* *
50806897 TTCTCCAAAATCATATTTTAACCCCTAAAC
1 TTC-CCAAAATTATATTTTGACCCC-AAAC
* *
50806927 TTCTCCAAAATTTTATTTTGATCCCAAAAC
1 TTC-CCAAAATTATATTTTGA-CCCCAAAC
* *
50806957 TTCTCCAAAATCATGTTTTGACCCCTAAAC
1 TTC-CCAAAATTATATTTTGACCCC-AAAC
* * *
50806987 TTTCCAAAATTACATTTTAACCCCTAAAC
1 TTCCCAAAATTATATTTTGACCCC-AAAC
* * * *
50807016 TTTTCTAAAATTACATTTTAACCCTCAAAC
1 -TTCCCAAAATTATATTTTGACCC-CAAAC
* *
50807046 TTCCCTAAAATTATATTTTTACCCTCGAAC
1 TTCCC-AAAATTATATTTTGACCC-CAAAC
* * *
50807076 TTTTCTAAAATTACATTTTGACCC
1 -TTCCCAAAATTATATTTTGACCC
50807100 AGTATTCTCT
Statistics
Matches: 168, Mismatches: 27, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
29 32 0.19
30 129 0.77
31 7 0.04
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.38
Consensus pattern (28 bp):
TTCCCAAAATTATATTTTGACCCCAAAC
Found at i:50807077 original size:60 final size:58
Alignment explanation
Indices: 50806859--50807099 Score: 196
Period size: 60 Copynumber: 4.0 Consensus size: 58
50806849 CCCAGTAGGT
* * * * * *
50806859 CCCTGAACTTTCCAAAAATCATATTTTGACCTTCGAACTTCTCCAAAATCATATTTTAAC
1 CCCTAAAC-TTCCCAAAATTATATTTTGACC-CCAAACTTCTCCAAAATCACATTTTAAC
* * ** *
50806919 CCCTAAACTTCTCCAAAATTTTATTTTGATCCCAAAACTTCTCCAAAATCATGTTTTGAC
1 CCCTAAACTTC-CCAAAATTATATTTTGA-CCCCAAACTTCTCCAAAATCACATTTTAAC
* * * * * *
50806979 CCCTAAACTTTCCAAAATTACATTTTAACCCCTAAACTTTTCTAAAATTACATTTTAA-
1 CCCTAAACTTCCCAAAATTATATTTTGACCCC-AAACTTCTCCAAAATCACATTTTAAC
* * * * * *
50807037 CCCTCAAACTTCCCTAAAATTATATTTTTACCCTCGAACTTTTCTAAAATTACATTTTGAC
1 CCCT-AAACTTCCC-AAAATTATATTTTGACCC-CAAACTTCTCCAAAATCACATTTTAAC
50807098 CC
1 CC
50807100 AGTATTCTCT
Statistics
Matches: 149, Mismatches: 25, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
58 7 0.05
59 44 0.30
60 93 0.62
61 5 0.03
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.37
Consensus pattern (58 bp):
CCCTAAACTTCCCAAAATTATATTTTGACCCCAAACTTCTCCAAAATCACATTTTAAC
Found at i:50807974 original size:315 final size:316
Alignment explanation
Indices: 50807387--50807978 Score: 882
Period size: 315 Copynumber: 1.9 Consensus size: 316
50807377 AAATAATTTT
* ** *
50807387 AAAACCGAGGAAAATATCATTTCGTGTGAAATTTCGAAAAATTATGCCCTAACGTGTTGGGTGTG
1 AAAACCGAGGAAAATATCATTTCGTGTGAAACTTCGAAAAACCATGCCCTAACGTGCTGGGTGTG
* *
50807452 ATTTTTCGTATAATTCGCGCGATCGAATATCCTCTTTAAAACTTTTCAAAATGTCATTCAATTTC
66 ATTTTTCGTATAATTCGCGCGATCGAATATCCTCTTTAAAACCTTACAAAATGTCATTCAATTTC
* * * *
50807517 GAAATTCCAAGAACATCGTGCCCTAACGTGTTGGACACGACTTCAATTCTCTGAGAAATTCGAAA
131 GAAATCCCAAGAACATCGTGCCCTAACATGTTAGACACGACTTCAATTCTCCGAGAAATTCGAAA
* *** *
50807582 CACACGGGCATTTTTCTTCAAATCTAATTTTTAAAAATCACGCGAAATAAGTTATGTGTCCGAGG
196 CACACAGGCATTTTTCTTCAAATCTAATTTTTAAAAATCACGCGAAATAAGTTATGTGTAAAAAG
*
50807647 ATCGCATTTTAAACTTCATTCGAAATTTCAAGTTCTAAAAAAATAATTTTAAACAA
261 ATCACATTTTAAACTTCATTCGAAATTTCAAGTTCTAAAAAAATAATTTTAAACAA
* *
50807703 AAAACCGAGG-CAATATCATTTCGTGTGAAAACTTCGAAAAACCATGCCCTAATGTGCTGGGTGT
1 AAAACCGAGGAAAATATCATTTCGTGTG-AAACTTCGAAAAACCATGCCCTAACGTGCTGGGTGT
* *
50807767 GA-TTTTCGTATAATTCGCGCGATCGAATATCCTTTTTAAAACCTTACAAAATGTCCTTCAATTT
65 GATTTTTCGTATAATTCGCGCGATCGAATATCCTCTTTAAAACCTTACAAAATGTCATTCAATTT
* ** *
50807831 CGAAATCCCGAGAATGTCGTGCCCTAACATGTTAGACACGACTTCAATTCTCCGAGAAATTTGAA
130 CGAAATCCCAAGAACATCGTGCCCTAACATGTTAGACACGACTTCAATTCTCCGAGAAATTCGAA
* * * * *
50807896 ACACACAGGCATTTTTCTTCAAATTTGATTTTTGAAAATCATGCGAAATGAGTTATGTGTAAAAA
195 ACACACAGGCATTTTTCTTCAAATCTAATTTTTAAAAATCACGCGAAATAAGTTATGTGTAAAAA
**
50807961 GATCATTTTTTAAACTTC
260 GATCACATTTTAAACTTC
50807979 GCTCAATATT
Statistics
Matches: 244, Mismatches: 31, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
315 201 0.82
316 43 0.18
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (316 bp):
AAAACCGAGGAAAATATCATTTCGTGTGAAACTTCGAAAAACCATGCCCTAACGTGCTGGGTGTG
ATTTTTCGTATAATTCGCGCGATCGAATATCCTCTTTAAAACCTTACAAAATGTCATTCAATTTC
GAAATCCCAAGAACATCGTGCCCTAACATGTTAGACACGACTTCAATTCTCCGAGAAATTCGAAA
CACACAGGCATTTTTCTTCAAATCTAATTTTTAAAAATCACGCGAAATAAGTTATGTGTAAAAAG
ATCACATTTTAAACTTCATTCGAAATTTCAAGTTCTAAAAAAATAATTTTAAACAA
Found at i:50811430 original size:9 final size:9
Alignment explanation
Indices: 50811378--50811435 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
50811368 TAATTTAACA
50811378 TTTGATCATT
1 TTTGAT-ATT
* *
50811388 ATTGATATC
1 TTTGATATT
50811397 TTT-ATTATGT
1 TTTGA-TAT-T
50811407 TTT-ATATT
1 TTTGATATT
50811415 TTT-ATATT
1 TTTGATATT
50811423 TTTGATATT
1 TTTGATATT
50811432 TTTG
1 TTTG
50811436 GTGGACATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
8 13 0.32
9 19 0.46
10 9 0.22
ACGTcount: A:0.22, C:0.03, G:0.09, T:0.66
Consensus pattern (9 bp):
TTTGATATT
Found at i:50811432 original size:17 final size:19
Alignment explanation
Indices: 50811389--50811434 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 19
50811379 TTGATCATTA
*
50811389 TTGATATCTTTATTATGTT
1 TTGATATTTTTATTATGTT
50811408 TT-ATATTTTTA-TAT-TT
1 TTGATATTTTTATTATGTT
50811424 TTGATATTTTT
1 TTGATATTTTT
50811435 GGTGGACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 4 0.16
17 11 0.44
18 8 0.32
19 2 0.08
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.70
Consensus pattern (19 bp):
TTGATATTTTTATTATGTT
Found at i:50820027 original size:24 final size:24
Alignment explanation
Indices: 50820000--50820046 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
50819990 AAGAGGGCAT
50820000 AGATAAAATTT-TAAAAATTTTAAA
1 AGAT-AAATTTCTAAAAATTTTAAA
* *
50820024 AGATTAATTTCTTAAAATTTTAA
1 AGATAAATTTCTAAAAATTTTAA
50820047 GCGTCCTCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (24 bp):
AGATAAATTTCTAAAAATTTTAAA
Found at i:50826058 original size:18 final size:17
Alignment explanation
Indices: 50826032--50826079 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
50826022 ATTACTTCTC
*
50826032 AAAAA-ATTTTTGAGAT
1 AAAAATATTTTTAAGAT
50826048 AAAAAATATTTTTAAGAT
1 -AAAAATATTTTTAAGAT
*
50826066 AAAAATATTATTAA
1 AAAAATATTTTTAA
50826080 ACAAAATGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 18 0.64
18 10 0.36
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
AAAAATATTTTTAAGAT
Found at i:50828346 original size:29 final size:31
Alignment explanation
Indices: 50828287--50828348 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 31
50828277 TAAATTCGGC
**
50828287 ATAAATTTTTTTAAGAGATCAAAATTGAATT
1 ATAAATTTTTTTAAGAGATCAAAATAAAATT
* *
50828318 ATAAA-TTTTTTAGGAG-TTAAAATAAAATT
1 ATAAATTTTTTTAAGAGATCAAAATAAAATT
50828347 AT
1 AT
50828349 GCTGTCCCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 12 0.44
30 10 0.37
31 5 0.19
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.42
Consensus pattern (31 bp):
ATAAATTTTTTTAAGAGATCAAAATAAAATT
Found at i:50840139 original size:29 final size:30
Alignment explanation
Indices: 50840101--50840177 Score: 88
Period size: 28 Copynumber: 2.6 Consensus size: 30
50840091 ATTTTTTTTT
* *
50840101 AATTTTAAAATTCA-AAAAATTATTTTTAAA
1 AATTATAAAATTCATAAAAACTA-TTTTAAA
*
50840131 AATTA-AAAA-TCATTAAAACTATTTTAAA
1 AATTATAAAATTCATAAAAACTATTTTAAA
*
50840159 AATTATAAAATTTATAAAA
1 AATTATAAAATTCATAAAA
50840178 GTACTTTTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
28 15 0.38
29 14 0.36
30 10 0.26
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (30 bp):
AATTATAAAATTCATAAAAACTATTTTAAA
Found at i:50843844 original size:23 final size:23
Alignment explanation
Indices: 50843818--50843861 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
50843808 GATCTAAATT
50843818 TTAAAATT-TGAAAAGTAAAAGAA
1 TTAAAATTCTGAAAA-TAAAAGAA
*
50843841 TTAAATTTCTGAAAATAAAAG
1 TTAAAATTCTGAAAATAAAAG
50843862 TACAGTGACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.57, C:0.02, G:0.11, T:0.30
Consensus pattern (23 bp):
TTAAAATTCTGAAAATAAAAGAA
Found at i:50846244 original size:18 final size:18
Alignment explanation
Indices: 50846223--50846261 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
50846213 TTTATTAACC
*
50846223 CAAAGTTATACATAACTT
1 CAAAGTTATACACAACTT
50846241 CAAAGTTATACACAACTT
1 CAAAGTTATACACAACTT
50846259 CAA
1 CAA
50846262 CCATGGATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.46, C:0.21, G:0.05, T:0.28
Consensus pattern (18 bp):
CAAAGTTATACACAACTT
Found at i:50848898 original size:29 final size:30
Alignment explanation
Indices: 50848860--50848916 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
50848850 AATTTGAATC
*
50848860 AAATCAAAAATTTATATATAAAATTACACA
1 AAATCAAAAATTCATATATAAAATTACACA
*
50848890 AAATC-AAAATTCATGTATAAAATTACA
1 AAATCAAAAATTCATATATAAAATTACA
50848917 TATTAAACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.30
Consensus pattern (30 bp):
AAATCAAAAATTCATATATAAAATTACACA
Found at i:50850586 original size:12 final size:13
Alignment explanation
Indices: 50850562--50850594 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
50850552 AATAGTATTT
*
50850562 TAATAAAAATAAA
1 TAATAATAATAAA
50850575 TAA-AATAATAAA
1 TAATAATAATAAA
50850587 TAATAATA
1 TAATAATA
50850595 TTTTAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
TAATAATAATAAA
Found at i:50851194 original size:16 final size:16
Alignment explanation
Indices: 50851156--50851194 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
50851146 GTCATTATTC
50851156 TAAATATTCAAAAATT
1 TAAATATTCAAAAATT
50851172 TATAATATT-AAAAATAT
1 TA-AATATTCAAAAAT-T
50851189 TAAATA
1 TAAATA
50851195 AAAAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATATTCAAAAATT
Found at i:50851454 original size:17 final size:18
Alignment explanation
Indices: 50851432--50851465 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
50851422 TTTATTAACT
50851432 AAAATAAAAT-TATAAAA
1 AAAATAAAATATATAAAA
*
50851449 AAAATATAATATATAAA
1 AAAATAAAATATATAAA
50851466 TATATATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATAAAATATATAAAA
Found at i:50854188 original size:31 final size:31
Alignment explanation
Indices: 50854150--50854210 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
50854140 TTACAAGATG
*
50854150 GTCATTGAATTATTC-AAATGTTTTTATTTAT
1 GTCATTGAACTATTCGAAA-GTTTTTATTTAT
50854181 GTCATTGAACTATTCGAAAGTTTTTATTTA
1 GTCATTGAACTATTCGAAAGTTTTTATTTA
50854211 AGACATTGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 25 0.89
32 3 0.11
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.51
Consensus pattern (31 bp):
GTCATTGAACTATTCGAAAGTTTTTATTTAT
Found at i:50854218 original size:31 final size:31
Alignment explanation
Indices: 50854152--50854218 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
50854142 ACAAGATGGT
* * *
50854152 CATTGAATTATTCAAATGTTTTTATTTATGT
1 CATTGAACTATTCAAATGTTTTTATTTAAGA
50854183 CATTGAACTATTCGAAA-GTTTTTATTTAAGA
1 CATTGAACTATTC-AAATGTTTTTATTTAAGA
50854214 CATTG
1 CATTG
50854219 GGTTGTTAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 29 0.91
32 3 0.09
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (31 bp):
CATTGAACTATTCAAATGTTTTTATTTAAGA
Found at i:50858566 original size:104 final size:104
Alignment explanation
Indices: 50858378--50858567 Score: 299
Period size: 104 Copynumber: 1.8 Consensus size: 104
50858368 TGTGCACGCG
50858378 TGTTTGTTTATATATATGATGAGTGTAAATGGGATTGCTTTAACTGTTATTGTGGAAAAATTCTC
1 TGTTTGTTTATATATATGATGAGTGTAAATGGGATTGCTTTAACTGTTATTGTGGAAAAATTCTC
* * * * *
50858443 ATATATGTGTGTGTGTGTGTGAGAGAGAGAGCATGTACC
66 ATATATATATATATATGTGTGAGAGAGAGAGCATGTACC
* ** *
50858482 TGTTTGTTTATATATATGATGAGTGTAAATGGGATTGCTTTAACTGTTATTGTGGGAATTTTTTC
1 TGTTTGTTTATATATATGATGAGTGTAAATGGGATTGCTTTAACTGTTATTGTGGAAAAATTCTC
50858547 ATATATATATATATATGTGTG
66 ATATATATATATATATGTGTG
50858568 TGTGTGTGTG
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
104 77 1.00
ACGTcount: A:0.27, C:0.05, G:0.24, T:0.44
Consensus pattern (104 bp):
TGTTTGTTTATATATATGATGAGTGTAAATGGGATTGCTTTAACTGTTATTGTGGAAAAATTCTC
ATATATATATATATATGTGTGAGAGAGAGAGCATGTACC
Found at i:50871805 original size:268 final size:268
Alignment explanation
Indices: 50871109--50871906 Score: 1123
Period size: 261 Copynumber: 3.0 Consensus size: 268
50871099 AGGGCATAAC
* ** * *
50871109 TCCTACAAACAAGAAAATCAATGAAACCTCCATATAAATAAAGATTCAACTAACCAAGCTAATTC
1 TCCTACAAACAAGAAAATCAAAGAAATTTTCATAAAAATAAAGATTCAACTAACCAAGCTAATTC
50871174 AAATCTTAAAA-AGGATAAAAAAAAAATCCTT-CAAATATAGTTTCAATTTAAAATACTTTTCTA
66 AAATCTTAAAATA-G---AAAAAAAAA-CCTTCCAAATATAGTTTCAATTTAAAATACTTTTCTA
* *
50871237 ACACTCCAGTTCAAGTTAAATCCTAAAATTCTAAATCCAATTTAATTTCAATTTTAAAA-TTTAA
126 GCACTCCAGTTCAAGTTAAACCCTAAAATTCTAAATCCAATTTAATTTC-A-TTTAAAATTTTAA
* *
50871301 TCCTTCAAAACTAAAAAGCTTGGATCTGAGTCTAACACTTAGAAAAAACTAATATACGTGTGAAG
189 TCCTTCAAAACTAAAAAGCTTGGATCTGAGTCTAACTCTTAGAAAAAACTAATATACATGTGAAG
50871366 GAAATTAAATTCAAA
254 GAAATTAAATTCAAA
* *
50871381 TCCTACAGACAAGAAAATCAAAGAATTTTTCATAAAAATAAAGATTCAACTAACCAAGCTAATTC
1 TCCTACAAACAAGAAAATCAAAGAAATTTTCATAAAAATAAAGATTCAACTAACCAAGCTAATTC
* * *
50871446 AAATCTT----T--TAAAAAAATCC-TCCAAATATAGTTTCAATTTAAAATACTTTCCTAGCACT
66 AAATCTTAAAATAGAAAAAAAAACCTTCCAAATATAGTTTCAATTTAAAATACTTTTCTAGCACT
*
50871504 CCAGTTCAAGTTAAACCCTAAAAGTCTAAATCCAATTTAATTTCATTTAAAATTTTAATCCTTCA
131 CCAGTTCAAGTTAAACCCTAAAATTCTAAATCCAATTTAATTTCATTTAAAATTTTAATCCTTCA
*
50871569 AAACTAAAAAGCTTGGATCTGAGTCTAACTCTTAGAAAAAACTAATATATATGTGAAGGAAATTA
196 AAACTAAAAAGCTTGGATCTGAGTCTAACTCTTAGAAAAAACTAATATACATGTGAAGGAAATTA
50871634 AATTCAAA
261 AATTCAAA
*
50871642 TCCTACAAACAAGAAAATCAAAGAAATTTTCATAAAAATAAAGATTCAACTAACCAAGCTAATCC
1 TCCTACAAACAAGAAAATCAAAGAAATTTTCATAAAAATAAAGATTCAACTAACCAAGCTAATTC
* *
50871707 AAATCTTAAAATAGAAAAAAAAACCTTCCAAATGTAGTTTCGATTTAAAATACTTTTCTAGCACT
66 AAATCTTAAAATAGAAAAAAAAACCTTCCAAATATAGTTTCAATTTAAAATACTTTTCTAGCACT
50871772 CCAGTTCAAGTTAAACCCTAAAATTCTAAATCC------A----ATTTAAAATTTTAATCCTTCA
131 CCAGTTCAAGTTAAACCCTAAAATTCTAAATCCAATTTAATTTCATTTAAAATTTTAATCCTTCA
** * * *
50871827 AAACTAAAAAAATTTGGATCTGAGTCTAACTCTTAGGAAAAAATTAAAAATTTTACATATGAAGG
196 AAACT-AAAAAGCTTGGATCTGAGTCTAACTCTTA-GAAAAAACT---AA-TATACATGTGAAGG
50871892 AAATTAAATTCAAA
255 AAATTAAATTCAAA
50871906 T
1 T
50871907 GCGAGGTGAA
Statistics
Matches: 479, Mismatches: 31, Indels: 40
0.87 0.06 0.07
Matches are distributed among these distances:
258 26 0.05
259 27 0.06
260 15 0.03
261 153 0.32
262 80 0.17
263 9 0.02
264 26 0.05
265 1 0.00
267 9 0.02
268 68 0.14
272 65 0.14
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (268 bp):
TCCTACAAACAAGAAAATCAAAGAAATTTTCATAAAAATAAAGATTCAACTAACCAAGCTAATTC
AAATCTTAAAATAGAAAAAAAAACCTTCCAAATATAGTTTCAATTTAAAATACTTTTCTAGCACT
CCAGTTCAAGTTAAACCCTAAAATTCTAAATCCAATTTAATTTCATTTAAAATTTTAATCCTTCA
AAACTAAAAAGCTTGGATCTGAGTCTAACTCTTAGAAAAAACTAATATACATGTGAAGGAAATTA
AATTCAAA
Found at i:50876105 original size:22 final size:22
Alignment explanation
Indices: 50876080--50876130 Score: 52
Period size: 21 Copynumber: 2.3 Consensus size: 22
50876070 AGGGGATATT
*
50876080 GGGGTAGGGTTT-GGGGTTTAAA
1 GGGGTAGGGTTTAAGGG-TTAAA
*
50876102 GGGG-AAGGTTTAAGGGTTAAA
1 GGGGTAGGGTTTAAGGGTTAAA
50876123 GAGGGTAG
1 G-GGGTAG
50876131 AGAGTAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
21 12 0.52
22 10 0.43
23 1 0.04
ACGTcount: A:0.25, C:0.00, G:0.49, T:0.25
Consensus pattern (22 bp):
GGGGTAGGGTTTAAGGGTTAAA
Found at i:50880451 original size:29 final size:30
Alignment explanation
Indices: 50880389--50880453 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
50880379 AATGAAAACA
50880389 AAAATAAATTCAAATATTAATATCTAAAATT
1 AAAA-AAATTCAAATATTAATATCTAAAATT
*
50880420 AAAAAAATTTAAA-ATTAAGTGATC-AAAA-T
1 AAAAAAATTCAAATATTAA-T-ATCTAAAATT
50880449 AAAAA
1 AAAAA
50880454 CATGAATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
29 11 0.35
30 13 0.42
31 7 0.23
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (30 bp):
AAAAAAATTCAAATATTAATATCTAAAATT
Found at i:50884627 original size:130 final size:129
Alignment explanation
Indices: 50884235--50884710 Score: 618
Period size: 130 Copynumber: 3.6 Consensus size: 129
50884225 TTTTGAATTG
* *
50884235 ATTTGAATTTTTATTGATTCAGTGTTGCTGGTTT-AGTTTAGATTTAG-TTTTTGAGATGAACAA
1 ATTTGAATTTTTATTGATTCAGTGTTGCTGGTTTAAGTTTAGATTTAGTTTTTTTAGTTGAACAA
* * * * * *
50884298 TGTGATTTTTGAGCTGATTGTTTTTTTTTGGTAGTTTTTGCTAGTATTGAGTCTGTGATTTCTAT
66 TGTGATTTTTGAGC------CTTTTTTTT-GTCGTTTTTGCTAGCATTGACTTTGAGATTTCTAT
50884363 GTACTA
124 GTACTA
* *
50884369 TTTTTGAATTTTTATTGATTCAGTGTTGCTGGTTTAAGTTTAGATTTACTTTTTTTTTGTAGTTG
1 -ATTTGAATTTTTATTGATTCAGTGTTGCTGGTTTAAGTTTAGATTTA---GTTTTTT-TAGTTG
* *
50884434 AACAATGTGAGTTTTT-AGCCTTTTTTTTGTCCTTTTTGTTAGCATTGACTTTGAGATTTCTATG
61 AACAATGTGA-TTTTTGAGCCTTTTTTTTGTCGTTTTTGCTAGCATTGACTTTGAGATTTCTATG
50884498 TACTA
125 TACTA
*
50884503 ATTTGAATTTTTATTGATTCTGTGTTGCTGGTTTAAGTTTAGATTTAGTTTTTTTTAGTTGAACA
1 ATTTGAATTTTTATTGATTCAGTGTTGCTGGTTTAAGTTTAGATTTAG-TTTTTTTAGTTGAACA
* * *
50884568 ACGTGATTTTTGAGCCCTTTTTTTGTCGTTTTTGGTAGCATTGACTTTGAGATTTCTATGTACTA
65 ATGTGATTTTTGAGCCTTTTTTTTGTCGTTTTTGCTAGCATTGACTTTGAGATTTCTATGTACTA
* * * *
50884633 AATTGAATTTTTATTGATTCAGTGTTGCTGG-TTAAGTTTAGATTTAGGTTTTTCAGTTGAGCAA
1 ATTTGAATTTTTATTGATTCAGTGTTGCTGGTTTAAGTTTAGATTTAGTTTTTTTAGTTGAACAA
50884697 TGTGATTTTTGAGC
66 TGTGATTTTTGAGC
50884711 TTTCTTTCTT
Statistics
Matches: 307, Mismatches: 25, Indels: 25
0.86 0.07 0.07
Matches are distributed among these distances:
128 27 0.09
129 21 0.07
130 94 0.31
131 6 0.02
133 45 0.15
134 34 0.11
135 41 0.13
136 12 0.04
140 5 0.02
141 17 0.06
142 5 0.02
ACGTcount: A:0.20, C:0.08, G:0.20, T:0.52
Consensus pattern (129 bp):
ATTTGAATTTTTATTGATTCAGTGTTGCTGGTTTAAGTTTAGATTTAGTTTTTTTAGTTGAACAA
TGTGATTTTTGAGCCTTTTTTTTGTCGTTTTTGCTAGCATTGACTTTGAGATTTCTATGTACTA
Found at i:50892577 original size:23 final size:21
Alignment explanation
Indices: 50892529--50892586 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 21
50892519 AAATAACATT
*
50892529 AAAAACAACAAAAACAATAAC
1 AAAAACAACAAAAACAACAAC
50892550 AAAAACAACACGAAAACAACAAC
1 AAAAACAACA--AAAACAACAAC
* *
50892573 CAAAACAATAAAAA
1 AAAAACAACAAAAA
50892587 AAAGAACCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 14 0.44
23 18 0.56
ACGTcount: A:0.74, C:0.21, G:0.02, T:0.03
Consensus pattern (21 bp):
AAAAACAACAAAAACAACAAC
Found at i:50892588 original size:23 final size:23
Alignment explanation
Indices: 50892538--50892609 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
50892528 TAAAAACAAC
* * * *
50892538 AAAAACAATAACAAAAACAACAC
1 AAAAACAACAACCAAAACAATAA
*
50892561 GAAAACAACAACCAAAACAAT-A
1 AAAAACAACAACCAAAACAATAA
* * *
50892583 AAAAA-AAGAACCAAAATAGTAA
1 AAAAACAACAACCAAAACAATAA
50892605 AAAAA
1 AAAAA
50892610 AATCGCACAA
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
21 12 0.31
22 10 0.26
23 17 0.44
ACGTcount: A:0.74, C:0.17, G:0.04, T:0.06
Consensus pattern (23 bp):
AAAAACAACAACCAAAACAATAA
Found at i:50892589 original size:12 final size:12
Alignment explanation
Indices: 50892535--50892588 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 12
50892525 CATTAAAAAC
50892535 AACAAAAACAAT
1 AACAAAAACAAT
50892547 AACAAAAACAA-
1 AACAAAAACAAT
* * *
50892558 CACGAAAACAAC
1 AACAAAAACAAT
*
50892570 AACCAAAACAAT
1 AACAAAAACAAT
50892582 AA-AAAAA
1 AACAAAAA
50892589 AGAACCAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
11 13 0.37
12 22 0.63
ACGTcount: A:0.74, C:0.20, G:0.02, T:0.04
Consensus pattern (12 bp):
AACAAAAACAAT
Found at i:50892594 original size:21 final size:21
Alignment explanation
Indices: 50892570--50892610 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
50892560 CGAAAACAAC
50892570 AACCAAAACAATAAAAAAAAG
1 AACCAAAACAATAAAAAAAAG
* *
50892591 AACCAAAATAGTAAAAAAAA
1 AACCAAAACAATAAAAAAAA
50892611 ATCGCACAAA
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:0.76, C:0.12, G:0.05, T:0.07
Consensus pattern (21 bp):
AACCAAAACAATAAAAAAAAG
Found at i:50899342 original size:31 final size:31
Alignment explanation
Indices: 50899307--50899373 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
50899297 TAACAGCACG
*
50899307 GTGACTTAAATAAAAACTTTCGGATAGTTCA
1 GTGACTTAAATAAAAACTTTCGAATAGTTCA
* *
50899338 GTGACTTAAATGAAAACTTTCGAATAGTTTA
1 GTGACTTAAATAAAAACTTTCGAATAGTTCA
50899369 GTGAC
1 GTGAC
50899374 CATTTTGTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (31 bp):
GTGACTTAAATAAAAACTTTCGAATAGTTCA
Found at i:50904549 original size:18 final size:19
Alignment explanation
Indices: 50904511--50904550 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
50904501 AACTAAAAAA
* *
50904511 AATATTTTTTTGTAATTTT
1 AATAATTTTTTGTAATATT
50904530 AATAATTTTTTG-AATATT
1 AATAATTTTTTGTAATATT
50904548 AAT
1 AAT
50904551 TTTAATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (19 bp):
AATAATTTTTTGTAATATT
Found at i:50906259 original size:5 final size:5
Alignment explanation
Indices: 50906242--50906281 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
50906232 ATCATAAATT
*
50906242 ATATA ATAT- ATATA ATATA ATATA ATATA ATATA TTATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
50906282 ACAAAGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:50907023 original size:29 final size:30
Alignment explanation
Indices: 50906983--50907039 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
50906973 TGGCGATCAA
* *
50906983 TTAGGGATTTAATTAAAATTTTTAAAAAAT
1 TTAGGGATTTAATGAAAATTTTCAAAAAAT
*
50907013 TTAGGG-TTTAATGAGAATTTTCAAAAA
1 TTAGGGATTTAATGAAAATTTTCAAAAA
50907040 GATTAAGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.44, C:0.02, G:0.14, T:0.40
Consensus pattern (30 bp):
TTAGGGATTTAATGAAAATTTTCAAAAAAT
Found at i:50921699 original size:25 final size:24
Alignment explanation
Indices: 50921653--50921699 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
50921643 TAAGCACGGG
*
50921653 AAAATTATAAAAATATTTTTATTT
1 AAAATTATAAAAATATTATTATTT
*
50921677 AAAATTATAATTAATATTATTAT
1 AAAATTATAA-AAATATTATTAT
50921700 AATGATGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AAAATTATAAAAATATTATTATTT
Found at i:50933674 original size:22 final size:22
Alignment explanation
Indices: 50933646--50933689 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
50933636 ACACAATGGA
50933646 AAGAAGAAAGAATGAGAATATT
1 AAGAAGAAAGAATGAGAATATT
50933668 AAGAAGAAAGAATGAGAATATT
1 AAGAAGAAAGAATGAGAATATT
50933690 TTCTTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.23, T:0.18
Consensus pattern (22 bp):
AAGAAGAAAGAATGAGAATATT
Found at i:50935912 original size:30 final size:31
Alignment explanation
Indices: 50935878--50935942 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
50935868 ATCACAGAAT
50935878 TATTCAAAAGTTTTCATTTAAGTCATGAA-C
1 TATTCAAAAGTTTTCATTTAAGTCATGAAGC
* *
50935908 TATTCAAAAGTTTTTATTTAAGTCATTAAGC
1 TATTCAAAAGTTTTCATTTAAGTCATGAAGC
50935939 TATT
1 TATT
50935943 AAGTTTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 27 0.84
31 5 0.16
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45
Consensus pattern (31 bp):
TATTCAAAAGTTTTCATTTAAGTCATGAAGC
Found at i:50935957 original size:29 final size:28
Alignment explanation
Indices: 50935884--50935957 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 28
50935874 GAATTATTCA
*
50935884 AAAGTTTTCATTTAAGTCATGAACTATT
1 AAAGTTTTTATTTAAGTCATGAACTATT
*
50935912 CAAAAGTTTTTATTTAAGTCATTAAGCTATT
1 --AAAGTTTTTATTTAAGTCATGAA-CTATT
50935943 -AAGTTTTTTATTTAA
1 AAAG-TTTTTATTTAA
50935958 ATATTGACTA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
28 3 0.08
29 11 0.28
30 21 0.52
31 5 0.12
ACGTcount: A:0.35, C:0.08, G:0.09, T:0.47
Consensus pattern (28 bp):
AAAGTTTTTATTTAAGTCATGAACTATT
Found at i:50937900 original size:54 final size:54
Alignment explanation
Indices: 50937832--50937945 Score: 210
Period size: 54 Copynumber: 2.1 Consensus size: 54
50937822 TTAAATAAAA
*
50937832 AATATGGGAGAGCGCTACTTGGTGCAAATATAACCTATATACCTTAATATATAT
1 AATATGGGACAGCGCTACTTGGTGCAAATATAACCTATATACCTTAATATATAT
50937886 AATATGGGACAGCGCTACTTGGTGCAAATATAACCTATATACCTTAATATATAT
1 AATATGGGACAGCGCTACTTGGTGCAAATATAACCTATATACCTTAATATATAT
50937940 ATATAT
1 A-ATAT
50937946 ATATATATAT
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
54 54 0.93
55 4 0.07
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (54 bp):
AATATGGGACAGCGCTACTTGGTGCAAATATAACCTATATACCTTAATATATAT
Found at i:50937990 original size:2 final size:2
Alignment explanation
Indices: 50937932--50937975 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
50937922 ATATACCTTA
50937932 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50937974 AT
1 AT
50937976 GTGTGAGATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50938203 original size:7 final size:7
Alignment explanation
Indices: 50938193--50938231 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
50938183 CCAAATCCAG
50938193 AGTTTAA
1 AGTTTAA
50938200 AGTTTAA
1 AGTTTAA
*
50938207 AGTTTAG
1 AGTTTAA
*
50938214 AGTCTAA
1 AGTTTAA
*
50938221 GGTTTAA
1 AGTTTAA
50938228 AGTT
1 AGTT
50938232 CATCATGTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.36, C:0.03, G:0.21, T:0.41
Consensus pattern (7 bp):
AGTTTAA
Found at i:50938216 original size:21 final size:21
Alignment explanation
Indices: 50938191--50938231 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
50938181 GTCCAAATCC
*
50938191 AGAGTTTAAAGTTTAAAGTTT
1 AGAGTCTAAAGTTTAAAGTTT
*
50938212 AGAGTCTAAGGTTTAAAGTT
1 AGAGTCTAAAGTTTAAAGTT
50938232 CATCATGTAT
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:0.37, C:0.02, G:0.22, T:0.39
Consensus pattern (21 bp):
AGAGTCTAAAGTTTAAAGTTT
Found at i:50950448 original size:2 final size:2
Alignment explanation
Indices: 50950443--50950469 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
50950433 ATGTCTTTTT
50950443 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
50950470 TATTTCACCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50951376 original size:17 final size:17
Alignment explanation
Indices: 50951302--50951385 Score: 78
Period size: 17 Copynumber: 4.8 Consensus size: 17
50951292 TTAGATTCTT
*
50951302 AATTCATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
50951319 AATTTGTTATAAATTTAA
1 AATTTATTTTAAATTT-A
* * ** *
50951337 AACTTGTTTGGAGTTTA
1 AATTTATTTTAAATTTA
50951354 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
50951371 AATTTATTTTGAAAT
1 AATTTATTTT-AAAT
50951386 GAAAATTTAA
Statistics
Matches: 52, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
17 36 0.69
18 16 0.31
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:50951391 original size:18 final size:17
Alignment explanation
Indices: 50951353--50951394 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
50951343 TTTGGAGTTT
**
50951353 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATGA
50951370 AAATTTATTTTGAAATGA
1 AAATTTATTTT-AAATGA
50951388 AAATTTA
1 AAATTTA
50951395 AAATTTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (17 bp):
AAATTTATTTTAAATGA
Found at i:50953311 original size:29 final size:28
Alignment explanation
Indices: 50953282--50953563 Score: 148
Period size: 29 Copynumber: 9.6 Consensus size: 28
50953272 ACCTCGAAAC
50953282 TTCCAAAACTAACCATTTTACCCCCGAACT
1 TTCCAAAA-T-ACCATTTTACCCCCGAACT
* * *
50953312 TTCCAAGATTCCATTTTTAACCCCG-A-T
1 TTCCAAAATACCA-TTTTACCCCCGAACT
*
50953339 TTCACAAAAAATGACCATTTTACCCTCGAACT
1 TTC-C--AAAAT-ACCATTTTACCCCCGAACT
* * *
50953371 TTCCAAAGTTCCATTTTTAACCCCG-A-T
1 TTCCAAAATACCA-TTTTACCCCCGAACT
50953398 TTCACCAAAATTACCATTTTACCCCCGAACT
1 TT--CCAAAA-TACCATTTTACCCCCGAACT
* *
50953429 TTCCAAAATTCCATTTTTAACCCCG-A-T
1 TTCCAAAATACCA-TTTTACCCCCGAACT
* ** *
50953456 TTCACCAAAAATTACCATTTAATGCCCAAACT
1 TT--CC-AAAA-TACCATTTTACCCCCGAACT
* * * *
50953488 TTCTAAAATTCCATTTTTAACCCC--AGT
1 TTCCAAAATACCA-TTTTACCCCCGAACT
*
50953515 TTCACCAAAAATTACCATTATACCCCCGAACT
1 TT--CC-AAAA-TACCATTTTACCCCCGAACT
*
50953547 TTCCAAAATTCCATTTT
1 TTCCAAAATACCATTTT
50953564 TAAACCTCGA
Statistics
Matches: 191, Mismatches: 34, Indels: 56
0.68 0.12 0.20
Matches are distributed among these distances:
27 14 0.07
28 25 0.13
29 73 0.38
30 51 0.27
31 17 0.09
32 11 0.06
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (28 bp):
TTCCAAAATACCATTTTACCCCCGAACT
Found at i:50953435 original size:58 final size:58
Alignment explanation
Indices: 50953284--50953601 Score: 458
Period size: 59 Copynumber: 5.4 Consensus size: 58
50953274 CTCGAAACTT
* *
50953284 CCAAAACTAACCATTTTACCCCCGAACTTTCCAAGATTCCATTTTTAACCCCGATTTCA
1 CCAAAA-TTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
50953343 CAAAAAATGACCATTTTACCCTCGAACTTTCCAAAGTTCCATTTTTAACCCCGATTTCA
1 C-CAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
50953402 CCAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* ** * *
50953460 CCAAAAATTACCATTTAATGCCCAAACTTTCTAAAATTCCATTTTTAACCCC-AGTTTCA
1 CC-AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGA-TTTCA
* *
50953519 CCAAAAATTACCATTATACCCCCGAACTTTCCAAAATTCCATTTTTAAACCTCGATTTCA
1 CC-AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTT-AACCCCGATTTCA
50953579 CCAAAATTACCATTTTACCCCCG
1 CCAAAATTACCATTTTACCCCCG
50953602 GGTATCCAAA
Statistics
Matches: 232, Mismatches: 22, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
58 56 0.24
59 159 0.69
60 16 0.07
61 1 0.00
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (58 bp):
CCAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Done.