Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 88 of 310
Found at i:28285457 original size:41 final size:40
Alignment explanation
Indices: 28285351--28285524 Score: 267
Period size: 41 Copynumber: 4.3 Consensus size: 40
28285341 GCAGTGTTTT
*
28285351 TAGCGGCGTTTTATCCAAAAACGCCGCTAAAAATAGAGCAA
1 TAGCGGCGTTTTA-CCAAAAACGCCGCTAAAAACAGAGCAA
* * *
28285392 TAGCGGCGTTTTAGCAAACACGCCGCTAAAAATAGAGCAA
1 TAGCGGCGTTTTACCAAAAACGCCGCTAAAAACAGAGCAA
28285432 TAGCGGCGTTTTTACCAAAAACGCCGCTAAAAACAGAGCAA
1 TAGCGGCG-TTTTACCAAAAACGCCGCTAAAAACAGAGCAA
*
28285473 TAGCAGCGTTTTACCAAAAACGCCGCTAAAAACCAGAGCAA
1 TAGCGGCGTTTTACCAAAAACGCCGCTAAAAA-CAGAGCAA
*
28285514 TAGCAGCGTTT
1 TAGCGGCGTTT
28285525 ATGGTCAAAA
Statistics
Matches: 125, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
40 57 0.46
41 68 0.54
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (40 bp):
TAGCGGCGTTTTACCAAAAACGCCGCTAAAAACAGAGCAA
Found at i:28285496 original size:81 final size:83
Alignment explanation
Indices: 28285351--28285545 Score: 274
Period size: 81 Copynumber: 2.4 Consensus size: 83
28285341 GCAGTGTTTT
* * * *
28285351 TAGCGGCG-TTTTATCCAAAAACGCCGCTAAAAATAGAGCAATAGCGGCGTTTTAGCAAACACGC
1 TAGCGGCGTTTTTATCCAAAAACGCCGCTAAAAACAGAGCAATAGCAGCGTTTTACCAAAAACGC
*
28285415 CGCTAAAAA-TAGAGCAA
66 CGCTAAAAACCAGAGCAA
28285432 TAGCGGCGTTTTTA-CCAAAAACGCCGCTAAAAACAGAGCAATAGCAGCGTTTTACCAAAAACGC
1 TAGCGGCGTTTTTATCCAAAAACGCCGCTAAAAACAGAGCAATAGCAGCGTTTTACCAAAAACGC
28285496 CGCTAAAAACCAGAGCAA
66 CGCTAAAAACCAGAGCAA
* **
28285514 TAGCAGCGTTTATGGT-C-AAAACGCCGCTAAAA
1 TAGCGGCGTTT-TTATCCAAAAACGCCGCTAAAA
28285546 GTCATATAAC
Statistics
Matches: 102, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
81 63 0.62
82 37 0.36
83 2 0.02
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (83 bp):
TAGCGGCGTTTTTATCCAAAAACGCCGCTAAAAACAGAGCAATAGCAGCGTTTTACCAAAAACGC
CGCTAAAAACCAGAGCAA
Found at i:28285625 original size:37 final size:39
Alignment explanation
Indices: 28285564--28285654 Score: 141
Period size: 37 Copynumber: 2.4 Consensus size: 39
28285554 ACCCCTAAAA
* *
28285564 CCCTAAACCCTTAAAAAATCATAAACACTAATCTATAAC
1 CCCTAAACCCTTAAAAAACCATAAACACTAAACTATAAC
28285603 CCCTAAACCC-T-AAAAACCATAAACACTAAACTATAAC
1 CCCTAAACCCTTAAAAAACCATAAACACTAAACTATAAC
*
28285640 CCCTAAAACCTTAAA
1 CCCTAAACCCTTAAA
28285655 CCCCAAAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
37 33 0.70
38 2 0.04
39 12 0.26
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (39 bp):
CCCTAAACCCTTAAAAAACCATAAACACTAAACTATAAC
Found at i:28285814 original size:15 final size:15
Alignment explanation
Indices: 28285785--28285828 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
28285775 GGGTTTAATA
*
28285785 TTTAAGG-TCTATGG
1 TTTAAGGTTTTATGG
*
28285799 TTTAGGGTTTTATGG
1 TTTAAGGTTTTATGG
*
28285814 TTTAAGGTTTAATGG
1 TTTAAGGTTTTATGG
28285829 CCATGGGTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.20, C:0.02, G:0.30, T:0.48
Consensus pattern (15 bp):
TTTAAGGTTTTATGG
Found at i:28286827 original size:3 final size:3
Alignment explanation
Indices: 28286819--28286874 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
28286809 TTTAGTAAAA
28286819 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28286867 AAT AAT AA
1 AAT AAT AA
28286875 AAGAGAAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:28288890 original size:3 final size:3
Alignment explanation
Indices: 28288884--28288945 Score: 51
Period size: 3 Copynumber: 21.0 Consensus size: 3
28288874 CATCATCATA
*
28288884 ATT ATT ATT GA-T ATT ATT ATT ATT ATT ATT GTT ACTT -TT -TT CATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT -ATT
*
28288929 ATT A-T ATT ATT ACT ATT
1 ATT ATT ATT ATT ATT ATT
28288946 GGTATTATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
2 7 0.14
3 37 0.76
4 5 0.10
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:28296779 original size:68 final size:68
Alignment explanation
Indices: 28296666--28297467 Score: 1185
Period size: 68 Copynumber: 11.8 Consensus size: 68
28296656 TCCCCTCTCT
*
28296666 CTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGAGGATCTCTTT
1 CTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGGATCTCTTT
28296731 CCC
66 CCC
* *
28296734 CTGAAATGGCGTTGGAGCGGCTAAAAACCACAGCAGATCTACTTGAAGTTTCAGTGGATCTCTTT
1 CTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGGATCTCTTT
28296799 CCC
66 CCC
* * *
28296802 CTAAAATGGCGTTGGAGTGGCTAAAAGCCACAGCAGATCTTCTTGAAGTTTCAGTGGATCTCTTT
1 CTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGGATCTCTTT
*
28296867 TCC
66 CCC
* * * * *
28296870 CTGAAATGGCATTGGAGTGGCTAAAAGCCACAGCAGATCTTCTTGAAGTTTCAGAGGATCTCTCT
1 CTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGGATCTCTTT
28296935 CCC
66 CCC
*
28296938 CTGAAATGGAGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGGATCTCTTT
1 CTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGGATCTCTTT
*
28297003 TCC
66 CCC
* * * *
28297006 CTGAAATGGCGTTGAAGTGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGAGGATCTCTCT
1 CTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGGATCTCTTT
28297071 CCC
66 CCC
*
28297074 CTGAAATGGAGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGGATCTCTTT
1 CTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGGATCTCTTT
*
28297139 TCC
66 CCC
* * * *
28297142 CTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGTAGATCTCCTTGAGGTTTTAGCGGATCTCTTT
1 CTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGGATCTCTTT
*
28297207 TCC
66 CCC
* * *
28297210 CTGAAATGACATTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGCGGATCTCTTT
1 CTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGGATCTCTTT
*
28297275 TCC
66 CCC
* * *
28297278 CTGAAATAGCGTTGGAGCGGCTAAAAGTCACAACAGATCTCCTTGAAGTTTCAGTGGATCTC-TT
1 CTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGGATCTCTTT
*
28297342 CTTC
66 C-CC
* *
28297346 CTGAAATGGCGTTGGAGCGGCTAAAAGCCATAGTAGATCTCCTTGAAGTTTCAGTGGATCTC-TT
1 CTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGGATCTCTTT
28297410 CTCC
66 C-CC
*** ** * * *
28297414 CTGAAATGATATTGGAGCGGCTCGAAGCCATAGTAGATCTCCTTGAACTTTCAG
1 CTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAG
28297468 CGGAGTAGAT
Statistics
Matches: 671, Mismatches: 62, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
67 2 0.00
68 669 1.00
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (68 bp):
CTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGGATCTCTTT
CCC
Found at i:28297782 original size:94 final size:94
Alignment explanation
Indices: 28297489--28297793 Score: 351
Period size: 94 Copynumber: 3.3 Consensus size: 94
28297479 GAAGTCAAAA
* *
28297489 ATCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTA
1 ATCTTATCTCCCTGAAGTTGCAGCAGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTG
* * *
28297554 CACTGGAACGGATTAAAGCTAAATTACAG
66 CAGTGGAACAGATTGAAGCTAAATTACAG
** * * * * *
28297583 ATCTTATCTCTTTGAAGTTGCAGTAGAGCAGA-TCAA-A-A-TAAATCTTATCTCTCTGAAGTTG
1 ATCTTATCTCCCTGAAGTTGCAGCAGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTG
* * * *
28297644 CAGTAGAGCAGGTCGAAG----A-TACA-
66 CAGTGGAACAGATTGAAGCTAAATTACAG
** *
28297667 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTAAAGTT
1 A-TCTTATCTCCCTGAAGTTGCAGCAGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTT
28297732 GCAGTGGAACAGATTGAAGCTAAATTACAG
65 GCAGTGGAACAGATTGAAGCTAAATTACAG
*
28297762 ATCTTATCTCTCTGAAGTTGCAGCAGAGCAGA
1 ATCTTATCTCCCTGAAGTTGCAGCAGAGCAGA
28297794 TCAACACAAG
Statistics
Matches: 169, Mismatches: 31, Indels: 22
0.76 0.14 0.10
Matches are distributed among these distances:
84 1 0.01
85 32 0.19
86 4 0.02
87 1 0.01
88 1 0.01
89 33 0.20
90 30 0.18
91 1 0.01
92 1 0.01
93 4 0.02
94 60 0.36
95 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (94 bp):
ATCTTATCTCCCTGAAGTTGCAGCAGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTG
CAGTGGAACAGATTGAAGCTAAATTACAG
Found at i:28297792 original size:179 final size:179
Alignment explanation
Indices: 28297490--28297833 Score: 553
Period size: 179 Copynumber: 1.9 Consensus size: 179
28297480 AAGTCAAAAA
*
28297490 TCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTAC
1 TCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTAAAGTTAC
* * *
28297555 ACTGGAACGGATTAAAGCTAAATTACAGATCTTATCTCTTTGAAGTTGCAGTAGAGCAGATCAAA
66 ACTGGAACAGATTAAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGCAGAGCAGATCAAA
* * *
28297620 ATAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAAGATACAAG
131 ACAAATCTCATCTCCCTGAAGTTGCAGTAGAGCAGGTCGAAGATACAAG
* *
28297669 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTAAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTAAAGTTAC
* * *
28297734 AGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGCAGAGCAGATCAAC
66 ACTGGAACAGATTAAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGCAGAGCAGATCAAA
* * *
28297799 ACAAGTCTCATCTCCCTGGAGTTGCAGTGGAGCAG
131 ACAAATCTCATCTCCCTGAAGTTGCAGTAGAGCAG
28297834 ACTAAAGATA
Statistics
Matches: 150, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
179 150 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (179 bp):
TCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTAAAGTTAC
ACTGGAACAGATTAAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGCAGAGCAGATCAAA
ACAAATCTCATCTCCCTGAAGTTGCAGTAGAGCAGGTCGAAGATACAAG
Found at i:28297830 original size:135 final size:135
Alignment explanation
Indices: 28297624--28297967 Score: 537
Period size: 135 Copynumber: 2.5 Consensus size: 135
28297614 ATCAAAATAA
*
28297624 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAAGATACAAGTCTTATCTCCCTGAAGTTGC
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATC-AA-A-ACAAGTCTTATCTCCCTGAAGTTGC
* * * * *
28297689 AGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTAAAGTTGCAGTGGAACAGATTGAAGCTA
63 AGTGGAGCAGACTAAAGATAGCAAATCTTATTTACCTAAAATTGCAGTGAAACAGATTAAAGCTA
28297754 AATTACAG
128 AATTACAG
* * * *
28297762 ATCTTATCTCTCTGAAGTTGCAGCAGAGCAGATCAACACAAGTCTCATCTCCCTGGAGTTGCAGT
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAACAAGTCTTATCTCCCTGAAGTTGCAGT
*
28297827 GGAGCAGACTAAAGATAGCAAATCTTATTTACCTAAAATTGCAGTGAAACAGTTTAAAGCTAAAT
66 GGAGCAGACTAAAGATAGCAAATCTTATTTACCTAAAATTGCAGTGAAACAGATTAAAGCTAAAT
28297892 TACAG
131 TACAG
* *
28297897 ATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCAAAACAA-CCTTATCTCCCTGAAGTTGCAGT
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAACAAGTCTTATCTCCCTGAAGTTGCAGT
28297961 GGAGCAG
66 GGAGCAG
28297968 GTTGAAATTA
Statistics
Matches: 189, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
134 27 0.14
135 128 0.68
137 2 0.01
138 32 0.17
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (135 bp):
ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAACAAGTCTTATCTCCCTGAAGTTGCAGT
GGAGCAGACTAAAGATAGCAAATCTTATTTACCTAAAATTGCAGTGAAACAGATTAAAGCTAAAT
TACAG
Found at i:28297996 original size:84 final size:85
Alignment explanation
Indices: 28297888--28298152 Score: 277
Period size: 89 Copynumber: 3.0 Consensus size: 85
28297878 GTTTAAAGCT
*
28297888 AAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCAAAAC-AACCTTATCTCCCTGA
1 AAATTACAGATCTTATCTCTCTGAAGTTGCAGTGGAGTAGATCAAAACAAACCTTATCTCCCTGA
*
28297952 AGTTGCAGTGGAGCAGGTTG
66 AGTTGCAGTGGAGCAGATTG
* * * *
28297972 AAATTAC-GAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTC
1 AAATTACAGA-TCTTATCTCTCTGAAGTTGCAGTGGAGTAGA-TCAA-A-A-CAAACCTTATCTC
* * **
28298036 CCTAAAGTTACAGTGGAATAGATTGAAG
61 CCTGAAGTTGCAGTGGAGCAGATT---G
* * *
28298064 TTAAATCACAGATCTTATCTCTC-GAAGTTACAGTGGAGTAGATCAAAACAAACCTTACCTCCCT
1 --AAATTACAGATCTTATCTCTCTGAAGTTGCAGTGGAGTAGATCAAAACAAACCTTATCTCCCT
*
28298128 GAAGTTGTAGTAGG-GCAGATTG
64 GAAGTTGCAGT-GGAGCAGATTG
28298150 AAA
1 AAA
28298153 CAATAAATTC
Statistics
Matches: 146, Mismatches: 22, Indels: 26
0.75 0.11 0.13
Matches are distributed among these distances:
83 2 0.01
84 39 0.27
85 3 0.02
86 2 0.01
87 1 0.01
88 1 0.01
89 54 0.37
90 3 0.02
91 1 0.01
92 4 0.03
93 17 0.12
94 17 0.12
95 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (85 bp):
AAATTACAGATCTTATCTCTCTGAAGTTGCAGTGGAGTAGATCAAAACAAACCTTATCTCCCTGA
AGTTGCAGTGGAGCAGATTG
Found at i:28298022 original size:178 final size:178
Alignment explanation
Indices: 28297802--28298152 Score: 508
Period size: 178 Copynumber: 2.0 Consensus size: 178
28297792 GATCAACACA
*
28297802 AGTCTCATCTCCCTGGAGTTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATTTACCTAAAATT
1 AGTCTCATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATTTACCTAAAATT
* * * *
28297867 GCAGTGAAACAGTTTAAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCA
66 ACAGTGAAACAGATTAAAGCTAAATCACAGATCTTATCTCTC-GAAGTTACAGTAGAGTAGATCA
* *
28297932 AAAC-AACCTTATCTCCCTGAAGTTGCAGT-GGAGCAGGTTGAAATTACG
130 AAACAAACCTTACCTCCCTGAAGTTGCAGTAGG-GCAGATTGAAATTACG
* * * * *
28297980 AGTCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTAAAGTT
1 AGTCTCATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATTTACCTAAAATT
* * * * *
28298045 ACAGTGGAATAGATTGAAGTTAAATCACAGATCTTATCTCTCGAAGTTACAGTGGAGTAGATCAA
66 ACAGTGAAACAGATTAAAGCTAAATCACAGATCTTATCTCTCGAAGTTACAGTAGAGTAGATCAA
*
28298110 AACAAACCTTACCTCCCTGAAGTTGTAGTAGGGCAGATTGAAA
131 AACAAACCTTACCTCCCTGAAGTTGCAGTAGGGCAGATTGAAA
28298153 CAATAAATTC
Statistics
Matches: 153, Mismatches: 18, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
177 24 0.16
178 127 0.83
179 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (178 bp):
AGTCTCATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATTTACCTAAAATT
ACAGTGAAACAGATTAAAGCTAAATCACAGATCTTATCTCTCGAAGTTACAGTAGAGTAGATCAA
AACAAACCTTACCTCCCTGAAGTTGCAGTAGGGCAGATTGAAATTACG
Found at i:28298063 original size:313 final size:313
Alignment explanation
Indices: 28297494--28298134 Score: 953
Period size: 313 Copynumber: 2.0 Consensus size: 313
28297484 CAAAAATCTT
* * * *
28297494 ATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTACACTG
1 ATCTCCCTGAAGTTGCAGCGGAGCAGACTAAAGATAGCAAATCTTATTTACCTAAAATTACACTG
* * *
28297559 GAACGGATTAAAGCTAAATTACAGATCTTATCTCTTTGAAGTTGCAGTAGAGCAGATCAAAATAA
66 AAACAGATTAAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAATAA
* *
28297624 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAAGATACAAGTCTTATCTCCCTGAAGTTGC
131 ACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTCGAAGATACAAGTCTTATCTCCCTGAAGTTGC
*
28297689 AGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTAAAGTTGCAGTGGAACAGATTGAAGCTA
196 AGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTAAAGTTACAGTGGAACAGATTGAAGCTA
*
28297754 AATTACAGATCTTATCTCTCTGAAGTTGCAGCAGAGCAGATCAACACAAGTCTC
261 AATCACAGATCTTATCTCTC-GAAGTTGCAGCAGAGCAGATCAACACAAGTCTC
* * * *
28297808 ATCTCCCTGGAGTTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATTTACCTAAAATTGCAGTG
1 ATCTCCCTGAAGTTGCAGCGGAGCAGACTAAAGATAGCAAATCTTATTTACCTAAAATTACACTG
* * *
28297873 AAACAGTTTAAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCAAAA-CA
66 AAACAGATTAAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAATAA
* * * *
28297937 ACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAA-ATTACGAGTCTTATCTCTCTGAAGTTG
131 ACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTCGAAGA-TACAAGTCTTATCTCCCTGAAGTTG
* *
28298001 CAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTAAAGTTACAGTGGAATAGATTGAAGTT
195 CAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTAAAGTTACAGTGGAACAGATTGAAGCT
* ** * * ** *
28298066 AAATCACAGATCTTATCTCTCGAAGTTACAGTGGAGTAGATCAAAACAAACCTT
260 AAATCACAGATCTTATCTCTCGAAGTTGCAGCAGAGCAGATCAACACAAGTCTC
*
28298120 ACCTCCCTGAAGTTG
1 ATCTCCCTGAAGTTG
28298135 TAGTAGGGCA
Statistics
Matches: 292, Mismatches: 34, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
312 39 0.13
313 139 0.48
314 114 0.39
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (313 bp):
ATCTCCCTGAAGTTGCAGCGGAGCAGACTAAAGATAGCAAATCTTATTTACCTAAAATTACACTG
AAACAGATTAAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAATAA
ACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTCGAAGATACAAGTCTTATCTCCCTGAAGTTGC
AGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTAAAGTTACAGTGGAACAGATTGAAGCTA
AATCACAGATCTTATCTCTCGAAGTTGCAGCAGAGCAGATCAACACAAGTCTC
Found at i:28299817 original size:3 final size:3
Alignment explanation
Indices: 28299811--28299875 Score: 55
Period size: 3 Copynumber: 22.0 Consensus size: 3
28299801 TATCATCATC
* * *
28299811 ATT ATT ATT GA-T ATT ATT ATT ATT ATT ATT ATT GTT ACTT -TT GTC
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
*
28299856 ATT ATT A-T ATT ATT ACT ATT
1 ATT ATT ATT ATT ATT ATT ATT
28299876 GGTATTATAT
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
2 5 0.10
3 42 0.84
4 3 0.06
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:28301553 original size:171 final size:170
Alignment explanation
Indices: 28301269--28301608 Score: 662
Period size: 171 Copynumber: 2.0 Consensus size: 170
28301259 CGTTTTAATT
28301269 TATTCAATCATTTTTTTAAAATTAGCATTAATACAAAGAGGGATCGTATTTTAAATTCTATTAAG
1 TATTCAATCATTTTTTTAAAATTAGCATTAATACAAAGAGGGATCGTATTTTAAATTCTATTAAG
28301334 TTTTCAAATTTTCGACACTAAGACACTAATTAATCAACTAGGTACCAATTTTGAGCGTATCGAGG
66 TTTTCAAATTTTCGACACTAAGACACTAATTAATCAACTAGGTACCAATTTTGAGCGTATCGAGG
28301399 GTGCTAACCCTTCCTCATGCGTAACCGACTCCCGAACTCG
131 GTGCTAACCCTTCCTCATGCGTAACCGACTCCCGAACTCG
28301439 TATTCAATCATTTTTTTTAAAATTAGCATTAATACAAAGAGGGATCGTATTTTAAATTCTATTAA
1 TATTCAATCA-TTTTTTTAAAATTAGCATTAATACAAAGAGGGATCGTATTTTAAATTCTATTAA
28301504 GTTTTCAAATTTTCGACACTAAGACACTAATTAATCAACTAGGTACCAATTTTGAGCGTATCGAG
65 GTTTTCAAATTTTCGACACTAAGACACTAATTAATCAACTAGGTACCAATTTTGAGCGTATCGAG
*
28301569 GGTGCTAACCCTTCCTCATGCGTAACCGACTGCCGAACTC
130 GGTGCTAACCCTTCCTCATGCGTAACCGACTCCCGAACTC
28301609 ATTTTTTGAT
Statistics
Matches: 168, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
170 10 0.06
171 158 0.94
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (170 bp):
TATTCAATCATTTTTTTAAAATTAGCATTAATACAAAGAGGGATCGTATTTTAAATTCTATTAAG
TTTTCAAATTTTCGACACTAAGACACTAATTAATCAACTAGGTACCAATTTTGAGCGTATCGAGG
GTGCTAACCCTTCCTCATGCGTAACCGACTCCCGAACTCG
Found at i:28317757 original size:19 final size:19
Alignment explanation
Indices: 28317734--28317780 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
28317724 ATTTAATCTA
*
28317734 ATTTTTATTATTTA-TTTT
1 ATTTTTATTATATATTTTT
* *
28317752 AGTTTTGATTCTATATTTTT
1 A-TTTTTATTATATATTTTT
28317772 ATTTTTATT
1 ATTTTTATT
28317781 TTAATTTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 1 0.04
19 17 0.74
20 5 0.22
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.72
Consensus pattern (19 bp):
ATTTTTATTATATATTTTT
Found at i:28318006 original size:52 final size:53
Alignment explanation
Indices: 28317926--28318030 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 53
28317916 TTTCATGACC
* *
28317926 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGG-CATGGCCTTTAGCGGCG
1 TTTAGCGGCGTTTGTGGGAAAAGAGCCGCTAAAGGCCATGACCTTTAGCGGCG
28317978 TTTAGCGGCGTTTGTGGGAAAAGAGCCGCTAAAGGCCATGACCTTTAGCGGCG
1 TTTAGCGGCGTTTGTGGGAAAAGAGCCGCTAAAGGCCATGACCTTTAGCGGCG
28318031 CTTCTAAAGG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 34 0.68
53 16 0.32
ACGTcount: A:0.21, C:0.21, G:0.35, T:0.23
Consensus pattern (53 bp):
TTTAGCGGCGTTTGTGGGAAAAGAGCCGCTAAAGGCCATGACCTTTAGCGGCG
Found at i:28318755 original size:22 final size:22
Alignment explanation
Indices: 28318702--28318757 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
28318692 TGACTTAGGT
*
28318702 GATATCGCAATACCCTGAAGAG
1 GATATCGCGATACCCTGAAGAG
*
28318724 GATATTGCGATA-CCTAGAAGAG
1 GATATCGCGATACCCT-GAAGAG
28318746 GATATCGCGATA
1 GATATCGCGATA
28318758 TCTCGGACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 3 0.10
22 27 0.90
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (22 bp):
GATATCGCGATACCCTGAAGAG
Found at i:28320120 original size:36 final size:34
Alignment explanation
Indices: 28320079--28320147 Score: 93
Period size: 36 Copynumber: 2.0 Consensus size: 34
28320069 ATCCGACAAA
* * *
28320079 GCCCGATAAGTGATAATTCTTGAAATAAATGATAAT
1 GCCCGATAAATGATAATGCTCG--ATAAATGATAAT
28320115 GCCCGATAAATGATAATGCTCGATAAATGATAA
1 GCCCGATAAATGATAATGCTCGATAAATGATAA
28320148 ATGATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 11 0.37
36 19 0.63
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (34 bp):
GCCCGATAAATGATAATGCTCGATAAATGATAAT
Found at i:28320125 original size:17 final size:17
Alignment explanation
Indices: 28320103--28320147 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
28320093 AATTCTTGAA
28320103 ATAAATGATAATGCCCG
1 ATAAATGATAATGCCCG
*
28320120 ATAAATGATAATGCTCG
1 ATAAATGATAATGCCCG
28320137 ATAAATGATAA
1 ATAAATGATAA
28320148 ATGATAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.27
Consensus pattern (17 bp):
ATAAATGATAATGCCCG
Found at i:28321979 original size:55 final size:54
Alignment explanation
Indices: 28321890--28322007 Score: 157
Period size: 55 Copynumber: 2.2 Consensus size: 54
28321880 TATTTTCGTT
28321890 CACATGGGCAGAGACACTGGCATGTGTCTCAGCCATGTGTGACACACAGCCTAG
1 CACATGGGCAGAGACACTGGCATGTGTCTCAGCCATGTGTGACACACAGCCTAG
* * * * *
28321944 CACATGGGCATGGGAC-CTGGTCGTGTGTCTTAGCCATGTGTGACACACGGCCTTG
1 CACATGGGCA-GAGACACTGG-CATGTGTCTCAGCCATGTGTGACACACAGCCTAG
*
28321999 CTCATGGGC
1 CACATGGGC
28322008 GTGTGACTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
54 14 0.25
55 42 0.75
ACGTcount: A:0.20, C:0.27, G:0.31, T:0.22
Consensus pattern (54 bp):
CACATGGGCAGAGACACTGGCATGTGTCTCAGCCATGTGTGACACACAGCCTAG
Found at i:28322024 original size:55 final size:55
Alignment explanation
Indices: 28321912--28322027 Score: 151
Period size: 55 Copynumber: 2.1 Consensus size: 55
28321902 GACACTGGCA
* *
28321912 TGTGTCTCAGCCATGTGTGACACACAGCCTAGCACATGGGCATGGGACCTGGTCG
1 TGTGTCTCAGCCATGTGTGACACACAGCCTAGCACATGGGCATGGGACCTAGCCG
* * * * * * *
28321967 TGTGTCTTAGCCATGTGTGACACACGGCCTTGCTCATGGGCGTGTGACTTAGCCG
1 TGTGTCTCAGCCATGTGTGACACACAGCCTAGCACATGGGCATGGGACCTAGCCG
28322022 TGTGTC
1 TGTGTC
28322028 ATCTACATCT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.16, C:0.26, G:0.31, T:0.27
Consensus pattern (55 bp):
TGTGTCTCAGCCATGTGTGACACACAGCCTAGCACATGGGCATGGGACCTAGCCG
Found at i:28328885 original size:38 final size:38
Alignment explanation
Indices: 28328832--28328962 Score: 118
Period size: 38 Copynumber: 3.2 Consensus size: 38
28328822 TTTCAAATTA
28328832 ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
* * * *
28328870 ACATGTTTAATCGTGGTATATCTACTTAGCACCACGTTAAT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACG-T--T
* * *
28328911 GAATCAATATATGTAACCGTGGCATATCCACTTAGCATCATGTT
1 --A-C-ATGTA--TAACCGTGGCATATCCACTTAGCACCACGTT
28328955 ACATGTAT
1 ACATGTAT
28328963 CAATATGTAT
Statistics
Matches: 72, Mismatches: 12, Indels: 18
0.71 0.12 0.18
Matches are distributed among these distances:
38 33 0.46
39 1 0.01
40 4 0.06
41 2 0.03
42 1 0.01
43 1 0.01
44 2 0.03
45 3 0.04
46 1 0.01
47 24 0.33
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (38 bp):
ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
Found at i:28331036 original size:10 final size:10
Alignment explanation
Indices: 28331008--28331037 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
28330998 AGTGCGGAGA
28331008 AAAACTAAAG
1 AAAACTAAAG
28331018 AAAACCTAAAG
1 AAAA-CTAAAG
28331029 AAAACTAAA
1 AAAACTAAA
28331038 CCTAAACTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.70, C:0.13, G:0.07, T:0.10
Consensus pattern (10 bp):
AAAACTAAAG
Found at i:28333947 original size:19 final size:20
Alignment explanation
Indices: 28333918--28333957 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
28333908 AAAAACCTGT
* *
28333918 AAAACTTTTTATTTTCTCCC
1 AAAACTTTTTACTCTCTCCC
28333938 AAAA-TTTTTACTCTCTCCC
1 AAAACTTTTTACTCTCTCCC
28333957 A
1 A
28333958 CTTTCCCCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAACTTTTTACTCTCTCCC
Found at i:28335097 original size:29 final size:29
Alignment explanation
Indices: 28335065--28335131 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
28335055 CATTTATGGT
*
28335065 TGATTCTGTTTTATGAGAG-CCTTTGTAGC
1 TGATTCTGTTATATGAGAGTCC-TTGTAGC
* *
28335094 TGATTCT-ATATATGAGAGTCCTTGTGGC
1 TGATTCTGTTATATGAGAGTCCTTGTAGC
*
28335122 TGATTATGTT
1 TGATTCTGTT
28335132 CAATGCACCT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
28 21 0.68
29 10 0.32
ACGTcount: A:0.19, C:0.12, G:0.24, T:0.45
Consensus pattern (29 bp):
TGATTCTGTTATATGAGAGTCCTTGTAGC
Found at i:28337939 original size:12 final size:12
Alignment explanation
Indices: 28337924--28337953 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28337914 AATGATTAAA
28337924 TAAATTAGAAAT
1 TAAATTAGAAAT
*
28337936 TAAATTGGAAAT
1 TAAATTAGAAAT
28337948 TAAATT
1 TAAATT
28337954 CGGATTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (12 bp):
TAAATTAGAAAT
Found at i:28342896 original size:35 final size:35
Alignment explanation
Indices: 28342852--28343018 Score: 183
Period size: 35 Copynumber: 4.6 Consensus size: 35
28342842 TCCTCATTGA
** *
28342852 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* ***
28342887 AATGCCATACCTACATTTGTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
* *
28342927 AATACCATACCTATATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
28342962 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
28342997 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
28343019 CTTTGCCATG
Statistics
Matches: 114, Mismatches: 13, Indels: 10
0.83 0.09 0.07
Matches are distributed among these distances:
35 86 0.75
39 3 0.03
40 25 0.22
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:28342935 original size:75 final size:73
Alignment explanation
Indices: 28342847--28343018 Score: 208
Period size: 75 Copynumber: 2.4 Consensus size: 73
28342837 GGTTTTCCTC
** * * ***
28342847 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTGTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
28342911 TCAGTATGG
65 TCAGTATGG
* *
28342920 ATTTGATAATACCATACCTATATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
28342985 CTCAGTATGG
64 CTCAGTATGG
28342995 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
28343019 CTTTGCCATG
Statistics
Matches: 86, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
70 20 0.23
73 3 0.03
74 7 0.08
75 56 0.65
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.32
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:28350387 original size:35 final size:35
Alignment explanation
Indices: 28350343--28350509 Score: 183
Period size: 35 Copynumber: 4.6 Consensus size: 35
28350333 TCCTCATTGA
** *
28350343 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* ***
28350378 AATGCCATACCTACATTTGTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
* *
28350418 AATACCATACCTATATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
28350453 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
28350488 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
28350510 CTTTGCCATG
Statistics
Matches: 114, Mismatches: 13, Indels: 10
0.83 0.09 0.07
Matches are distributed among these distances:
35 86 0.75
39 3 0.03
40 25 0.22
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:28350426 original size:75 final size:73
Alignment explanation
Indices: 28350338--28350509 Score: 208
Period size: 75 Copynumber: 2.4 Consensus size: 73
28350328 GGTTTTCCTC
** * * ***
28350338 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTGTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
28350402 TCAGTATGG
65 TCAGTATGG
* *
28350411 ATTTGATAATACCATACCTATATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
28350476 CTCAGTATGG
64 CTCAGTATGG
28350486 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
28350510 CTTTGCCATG
Statistics
Matches: 86, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
70 20 0.23
73 3 0.03
74 7 0.08
75 56 0.65
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.32
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:28353433 original size:43 final size:43
Alignment explanation
Indices: 28353372--28353527 Score: 170
Period size: 43 Copynumber: 3.6 Consensus size: 43
28353362 CAATGTCATA
* * * * **
28353372 TCCTAGATATGGTCTTACATGTTATCACATATTTATGCCAATG
1 TCCTAGACATCGTCTTACACGTAATCACATATCAATGCCAATG
* * * * *
28353415 TCCTAGACATGGTCTTACACGAAATCATATAACGATGCCAATG
1 TCCTAGACATCGTCTTACACGTAATCACATATCAATGCCAATG
*
28353458 TCCTAGACATCGTCTTACACGTAATCACA-ATACAATGCCAATT
1 TCCTAGACATCGTCTTACACGTAATCACATAT-CAATGCCAATG
* *
28353501 TCCCAGACATCGTCTTACATGTAATCA
1 TCCTAGACATCGTCTTACACGTAATCA
28353528 TATCTCGGAA
Statistics
Matches: 96, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 1 0.01
43 95 0.99
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (43 bp):
TCCTAGACATCGTCTTACACGTAATCACATATCAATGCCAATG
Found at i:28355745 original size:17 final size:17
Alignment explanation
Indices: 28355723--28355756 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28355713 AACTTGAGCC
*
28355723 TTTATTTATGTATTCAT
1 TTTATTCATGTATTCAT
*
28355740 TTTATTCATTTATTCAT
1 TTTATTCATGTATTCAT
28355757 GTACAAGCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.09, G:0.03, T:0.65
Consensus pattern (17 bp):
TTTATTCATGTATTCAT
Found at i:28357033 original size:22 final size:22
Alignment explanation
Indices: 28357008--28357050 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
28356998 CAAATGAATT
*
28357008 CCAACCGATAGCATCA-AAATAG
1 CCAACC-ACAGCATCACAAATAG
*
28357030 CCAATCACAGCATCACAAATA
1 CCAACCACAGCATCACAAATA
28357051 TTTAGCATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.47, C:0.30, G:0.09, T:0.14
Consensus pattern (22 bp):
CCAACCACAGCATCACAAATAG
Found at i:28370787 original size:5 final size:5
Alignment explanation
Indices: 28370750--28370783 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
28370740 ATATAACTAT
* *
28370750 TATTA TATTA TATTA TATTA TATTG TATTG TATT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATT
28370784 GTATAGTAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (5 bp):
TATTA
Found at i:28370975 original size:17 final size:18
Alignment explanation
Indices: 28370953--28371013 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
28370943 TCATTGCAGC
28370953 ATATATATAAACTAT-TA
1 ATATATATAAACTATATA
*
28370970 ATATATTATATACTATATA
1 ATATA-TATAAACTATATA
*
28370989 GTATGATAT-AACATCATATA
1 ATAT-ATATAAAC-T-ATATA
28371009 ATATA
1 ATATA
28371014 GTAGGAGGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 5 0.14
18 11 0.31
19 10 0.29
20 9 0.26
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (18 bp):
ATATATATAAACTATATA
Found at i:28372640 original size:53 final size:53
Alignment explanation
Indices: 28372557--28372659 Score: 172
Period size: 53 Copynumber: 1.9 Consensus size: 53
28372547 GACACTAAAC
28372557 GACCATATCGTGTAAGACCATAACTAGTGGGTTATGACATCATATGGAAAGAA
1 GACCATATCGTGTAAGACCATAACTAGTGGGTTATGACATCATATGGAAAGAA
* *
28372610 GACCATATCGTGTAAGATCC-TAACTGGTGGGTTATGGCATCATATGGAAA
1 GACCATATCGTGTAAGA-CCATAACTAGTGGGTTATGACATCATATGGAAA
28372660 ATTTTAAGGA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
53 45 0.96
54 2 0.04
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (53 bp):
GACCATATCGTGTAAGACCATAACTAGTGGGTTATGACATCATATGGAAAGAA
Found at i:28372933 original size:57 final size:58
Alignment explanation
Indices: 28372790--28373289 Score: 525
Period size: 57 Copynumber: 8.8 Consensus size: 58
28372780 GCCTTTTCGG
* * * * * *
28372790 CAAAACTCTAGAAAGGTAAGCCTATGTGGAAAACCTATTAAAGGACAACCTTTTTTGGA
1 CAAAACTCTAGAAAGGTAAGCCTTTGTGGCAAACCTGTTAAAGGATAGCC-TTTGTGGA
* * ** * * *
28372849 -AAAACTCTGGAAATGTAAGCCTTTGTGGTGAACCTGTTAAAGGATAGTCTTTAT-CA
1 CAAAACTCTAGAAAGGTAAGCCTTTGTGGCAAACCTGTTAAAGGATAGCCTTTGTGGA
* * ** *
28372905 CAAAACTCTAGAAAGTTAAGCCTATGTGGTGAACCTATTAAAGGATAGCCTTTGTGG-
1 CAAAACTCTAGAAAGGTAAGCCTTTGTGGCAAACCTGTTAAAGGATAGCCTTTGTGGA
* * * * * * **
28372962 CAAAACACTGGAAAGGTAAGCCTTTATGGCACACCTATTAAAGGATAGACTTCATGGA
1 CAAAACTCTAGAAAGGTAAGCCTTTGTGGCAAACCTGTTAAAGGATAGCCTTTGTGGA
* * * * * *
28373020 -AAAACTCTAAAAAGGTAAGCCTATATGGCGAACTTGTTAAATGATAGCCTTTGTGGA
1 CAAAACTCTAGAAAGGTAAGCCTTTGTGGCAAACCTGTTAAAGGATAGCCTTTGTGGA
* * * * *
28373077 -AAAACTCTGGAAAGGTAAACCTTTGTGGCAAACATATTAAAGGATAGCCTTTG-GGG
1 CAAAACTCTAGAAAGGTAAGCCTTTGTGGCAAACCTGTTAAAGGATAGCCTTTGTGGA
* *
28373133 CAAAACTCTAGAAATGTAAGCCTTTGTGGCAAACCTGTTAAAGGAGAGCCTTTGTGG-
1 CAAAACTCTAGAAAGGTAAGCCTTTGTGGCAAACCTGTTAAAGGATAGCCTTTGTGGA
* * *
28373190 CAAAACTCTAGAAAGGTAAGCCTTTGTAGCGAACCTGTTAAAGGATAGCCTTTATGGA
1 CAAAACTCTAGAAAGGTAAGCCTTTGTGGCAAACCTGTTAAAGGATAGCCTTTGTGGA
*
28373248 -AAAACTCTAGAAA-GT-AGACCTTTGTGGAAAACCTGTTAAAGG
1 CAAAACTCTAGAAAGGTAAG-CCTTTGTGGCAAACCTGTTAAAGG
28373290 GCATCTTTTG
Statistics
Matches: 368, Mismatches: 66, Indels: 17
0.82 0.15 0.04
Matches are distributed among these distances:
55 2 0.01
56 26 0.07
57 298 0.81
58 42 0.11
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (58 bp):
CAAAACTCTAGAAAGGTAAGCCTTTGTGGCAAACCTGTTAAAGGATAGCCTTTGTGGA
Found at i:28373117 original size:171 final size:171
Alignment explanation
Indices: 28372779--28373289 Score: 616
Period size: 171 Copynumber: 3.0 Consensus size: 171
28372769 GGAGAAGAAA
* *
28372779 AGCCTTT-TCGGCAAAACTCTAGAAAGGTAAGCCTATGTGGAAAACCTATTAAAGGACA-ACCTT
1 AGCCTTTGT-GGCAAAACTCTAGAAAGGTAAGCCTTTGTGGCAAACCTATTAAAGGACAGA-C-T
* * * * * *
28372842 TTTTGGAAAAACTCTGGAAATGTAAGCCTTTGTGGTGAACCTGTTAAAGGATAGTCTTTAT-CAC
63 TTATGGAAAAACTCTAGAAAGGTAAGCCTTTGTGGCGAACCTGTTAAAGGATAGCCTTTATGGA-
* * * **
28372906 AAAACTCTAGAAAGTTAAGCCTATGTGGTGAACCTATTAAAGGAT
127 AAAACTCTAGAAAGGTAAACCTTTGTGGAAAACCTATTAAAGGAT
* * * * * *
28372951 AGCCTTTGTGGCAAAACACTGGAAAGGTAAGCCTTTATGGCACACCTATTAAAGGATAGACTTCA
1 AGCCTTTGTGGCAAAACTCTAGAAAGGTAAGCCTTTGTGGCAAACCTATTAAAGGACAGACTTTA
* * * * * *
28373016 TGGAAAAACTCTAAAAAGGTAAGCCTATATGGCGAACTTGTTAAATGATAGCCTTTGTGGAAAAA
66 TGGAAAAACTCTAGAAAGGTAAGCCTTTGTGGCGAACCTGTTAAAGGATAGCCTTTATGGAAAAA
* * *
28373081 CTCTGGAAAGGTAAACCTTTGTGGCAAACATATTAAAGGAT
131 CTCTAGAAAGGTAAACCTTTGTGGAAAACCTATTAAAGGAT
* * * * * *
28373122 AGCCTTTGGGGCAAAACTCTAGAAATGTAAGCCTTTGTGGCAAACCTGTTAAAGGAGAGCCTTTG
1 AGCCTTTGTGGCAAAACTCTAGAAAGGTAAGCCTTTGTGGCAAACCTATTAAAGGACAGACTTTA
* *
28373187 TGGCAAAACTCTAGAAAGGTAAGCCTTTGTAGCGAACCTGTTAAAGGATAGCCTTTATGGAAAAA
66 TGGAAAAACTCTAGAAAGGTAAGCCTTTGTGGCGAACCTGTTAAAGGATAGCCTTTATGGAAAAA
* *
28373252 CTCTAGAAA-GTAGACCTTTGTGGAAAACCTGTTAAAGG
131 CTCTAGAAAGGTAAACCTTTGTGGAAAACCTATTAAAGG
28373290 GCATCTTTTG
Statistics
Matches: 285, Mismatches: 51, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
170 25 0.09
171 207 0.73
172 51 0.18
173 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (171 bp):
AGCCTTTGTGGCAAAACTCTAGAAAGGTAAGCCTTTGTGGCAAACCTATTAAAGGACAGACTTTA
TGGAAAAACTCTAGAAAGGTAAGCCTTTGTGGCGAACCTGTTAAAGGATAGCCTTTATGGAAAAA
CTCTAGAAAGGTAAACCTTTGTGGAAAACCTATTAAAGGAT
Found at i:28373359 original size:113 final size:114
Alignment explanation
Indices: 28372791--28373362 Score: 331
Period size: 114 Copynumber: 5.0 Consensus size: 114
28372781 CCTTTTCGGC
* * * * * *
28372791 AAAACTCTAGAAAGGTAAGCCTATGTGGAAAACCTATTAAAGGACAACCTTTTTTGGA-AAAACT
1 AAAACTCTAGAAATGTAAGCCTTTGTGGAAAACCTGTTAAAGGAGAGCC-TTTGT-GACAAAACT
* * * * * * * * * * * *
28372855 CTGGAAATGTAAGCCTTTGTGGTGAACCTGTTAAAGGATAGTCTTTAT-CA
64 CTAGAAAGGTAAACATTTATAGCGAACCTGTCAAAGGAAAGCCTCTATGGA
* ** * * * *
28372905 CAAAACTCTAGAAA-GTTAAGCCTATGTGGTGAACCTATTAAAGGATAGCCTTTGTGGCAAAACA
1 -AAAACTCTAGAAATG-TAAGCCTTTGTGGAAAACCTGTTAAAGGAGAGCCTTTGTGACAAAACT
* * * * * * * *
28372969 CTGGAAAGGTAAGCCTTTATGGC-ACACCTATTAAAGGATAGACT-TCATGGA
64 CTAGAAAGGTAAACATTTATAGCGA-ACCTGTCAAAGGAAAGCCTCT-ATGGA
* * * * ** * * *
28373020 AAAACTCTAAAAAGGTAAGCCTATATGGCGAACTTGTTAAATGATAGCCTTTGTGGA-AAAACTC
1 AAAACTCTAGAAATGTAAGCCTTTGTGGAAAACCTGTTAAAGGAGAGCCTTTGT-GACAAAACTC
* * * * * * * * * * ** *
28373084 TGGAAAGGTAAACCTTTGTGGCAAACATATTAAAGGATAGCCTTTGGGGC
65 TAGAAAGGTAAACATTTATAGCGAACCTGTCAAAGGAAAGCCTCTATGGA
* *
28373134 AAAACTCTAGAAATGTAAGCCTTTGTGGCAAACCTGTTAAAGGAGAGCCTTTGTGGCAAAACTCT
1 AAAACTCTAGAAATGTAAGCCTTTGTGGAAAACCTGTTAAAGGAGAGCCTTTGTGACAAAACTCT
* * * * * *
28373199 AGAAAGGTAAGCCTTTGTAGCGAACCTGTTAAAGGATAGCCTTTATGGA
66 AGAAAGGTAAACATTTATAGCGAACCTGTCAAAGGAAAGCCTCTATGGA
* * *
28373248 AAAACTCTAGAAA-GT-AGACCTTTGTGGAAAACCTGTTAAAGG-GCATCTTTTGTGACAAATCT
1 AAAACTCTAGAAATGTAAG-CCTTTGTGGAAAACCTGTTAAAGGAG-AGCCTTTGTGACAAAACT
* * *
28373310 CTA-AAAGG-AAACATATTATGGC-CACCTTTGTCAAAGGAAAGTCTCTATGGA
64 CTAGAAAGGTAAACAT-TTATAGCGAACC--TGTCAAAGGAAAGCCTCTATGGA
28373361 AA
1 AA
28373363 TATCTGTAAA
Statistics
Matches: 382, Mismatches: 60, Indels: 32
0.81 0.13 0.07
Matches are distributed among these distances:
111 7 0.02
112 13 0.03
113 67 0.18
114 247 0.65
115 48 0.13
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (114 bp):
AAAACTCTAGAAATGTAAGCCTTTGTGGAAAACCTGTTAAAGGAGAGCCTTTGTGACAAAACTCT
AGAAAGGTAAACATTTATAGCGAACCTGTCAAAGGAAAGCCTCTATGGA
Found at i:28376036 original size:45 final size:45
Alignment explanation
Indices: 28375970--28376059 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
28375960 GTGAATGCTG
*
28375970 GGGAAAAATTAATAACCGAGCTTGTTATAGTTGTGGTTCAAGAAA
1 GGGAAAAATTAATAACCGAGCTTGTTACAGTTGTGGTTCAAGAAA
* *
28376015 GGGAAAGAA-TAATAACTGAGCTTGTTACAGTTGTGGTTCACGAAA
1 GGGAAA-AATTAATAACCGAGCTTGTTACAGTTGTGGTTCAAGAAA
28376060 CCATTTTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 39 0.95
46 2 0.05
ACGTcount: A:0.37, C:0.10, G:0.26, T:0.28
Consensus pattern (45 bp):
GGGAAAAATTAATAACCGAGCTTGTTACAGTTGTGGTTCAAGAAA
Found at i:28378522 original size:18 final size:18
Alignment explanation
Indices: 28378499--28378539 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
28378489 GATTTGTCAG
28378499 CAAGTTAATGCTGAACAT
1 CAAGTTAATGCTGAACAT
28378517 CAAGTTAATGCTGAACAT
1 CAAGTTAATGCTGAACAT
28378535 CAAGT
1 CAAGT
28378540 GCCATCTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (18 bp):
CAAGTTAATGCTGAACAT
Found at i:28380737 original size:46 final size:45
Alignment explanation
Indices: 28380681--28380855 Score: 210
Period size: 46 Copynumber: 3.8 Consensus size: 45
28380671 TGTTTGGGCA
*
28380681 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
28380727 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
28380774 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
28380820 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATG
28380856 AGCGGGTTAC
Statistics
Matches: 109, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 66 0.61
47 33 0.30
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (45 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:28380836 original size:93 final size:93
Alignment explanation
Indices: 28380677--28380849 Score: 319
Period size: 93 Copynumber: 1.9 Consensus size: 93
28380667 ATGATGTTTG
* *
28380677 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
28380742 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
*
28380770 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
28380835 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
28380850 CTTATGAGCG
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:28385346 original size:80 final size:80
Alignment explanation
Indices: 28385246--28385407 Score: 238
Period size: 81 Copynumber: 2.0 Consensus size: 80
28385236 AGTTTTATAT
* * * *
28385246 TTATAAGCTGAATTTTGTGTACAGATTTGACTAAAA-ATCATTAGAATAATCAAAGTTTAAGTAG
1 TTATAAGCTAAATTCTGTGTACAAATTTGACTAAAACATCAGTAGAATAATCAAAGTTTAAGTAG
28385310 -GAAAAGAAATCAGAG
66 AG-AAAGAAATCAGAG
* *
28385325 TNTATAGGCTAAATTCTGTGTACAAATTTGACTAAAACATCCGTAGAATAATCAAAGTTTAAGTA
1 T-TATAAGCTAAATTCTGTGTACAAATTTGACTAAAACATCAGTAGAATAATCAAAGTTTAAGTA
28385390 GAGAAAGAAATCAGAG
65 GAGAAAGAAATCAGAG
28385406 TT
1 TT
28385408 TAACCGGGAG
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
79 1 0.01
80 32 0.43
81 40 0.54
82 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.30
Consensus pattern (80 bp):
TTATAAGCTAAATTCTGTGTACAAATTTGACTAAAACATCAGTAGAATAATCAAAGTTTAAGTAG
AGAAAGAAATCAGAG
Found at i:28386281 original size:108 final size:108
Alignment explanation
Indices: 28386092--28386309 Score: 427
Period size: 108 Copynumber: 2.0 Consensus size: 108
28386082 ATTCTTGATT
*
28386092 ATTTCTTGAATTTTTTTGTGTTTTTGTGACTTTTACAACTAGGTCCTATTGTTGAATTCATTAGT
1 ATTTCTTGAATTTTCTTGTGTTTTTGTGACTTTTACAACTAGGTCCTATTGTTGAATTCATTAGT
28386157 TTTTTATTCTATGAAAGAAATTGAAAGTTTCTATGAATATGTG
66 TTTTTATTCTATGAAAGAAATTGAAAGTTTCTATGAATATGTG
28386200 ATTTCTTGAATTTTCTTGTGTTTTTGTGACTTTTACAACTAGGTCCTATTGTTGAATTCATTAGT
1 ATTTCTTGAATTTTCTTGTGTTTTTGTGACTTTTACAACTAGGTCCTATTGTTGAATTCATTAGT
28386265 TTTTTATTCTATGAAAGAAATTGAAAGTTTCTATGAATATGTG
66 TTTTTATTCTATGAAAGAAATTGAAAGTTTCTATGAATATGTG
28386308 AT
1 AT
28386310 GGAAGTATAT
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 109 1.00
ACGTcount: A:0.26, C:0.09, G:0.16, T:0.50
Consensus pattern (108 bp):
ATTTCTTGAATTTTCTTGTGTTTTTGTGACTTTTACAACTAGGTCCTATTGTTGAATTCATTAGT
TTTTTATTCTATGAAAGAAATTGAAAGTTTCTATGAATATGTG
Found at i:28387785 original size:39 final size:39
Alignment explanation
Indices: 28387739--28387839 Score: 148
Period size: 39 Copynumber: 2.6 Consensus size: 39
28387729 GCTCTGATGA
28387739 GCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATGT
**
28387778 GCTTCAGTTAGCCTTCGGGCTTCTGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATGT
* * **
28387817 GCTTTAGCTAGATTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
28387840 AGATCACGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.14, C:0.24, G:0.23, T:0.40
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATGT
Found at i:28389169 original size:50 final size:51
Alignment explanation
Indices: 28389092--28389220 Score: 179
Period size: 50 Copynumber: 2.5 Consensus size: 51
28389082 GACCATGGCA
* *
28389092 ACAAGTGATAAGTAATAGCTTCGGCTACACTTAACTGATCAAGGACAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTAACTGATCAAGGACAAATG
* * *
28389143 A-AAGTGATAAGTGATAACTTCGGCTACACTTATCTGATCAATGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTAACTGATCAAGGACAAATG
* * *
28389193 ACAAGTGAAAAGTGGTAGCTTCGACTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
28389221 TTGATCAGTG
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 45 0.66
51 23 0.34
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTAACTGATCAAGGACAAATG
Found at i:28389234 original size:31 final size:31
Alignment explanation
Indices: 28389196--28389313 Score: 173
Period size: 31 Copynumber: 3.8 Consensus size: 31
28389186 ACAAATGACA
* *
28389196 AGTGAAAAGTGGTAGCTTCGACTACTTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
28389227 AGTGAAAAGTGGTAGCTTCTGCTACCTGGTT
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
28389258 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
28389289 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
28389314 AAGTGACAAG
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:28389293 original size:62 final size:62
Alignment explanation
Indices: 28389196--28389313 Score: 191
Period size: 62 Copynumber: 1.9 Consensus size: 62
28389186 ACAAATGACA
* * *
28389196 AGTGAAAAGTGGTAGCTTCGACTACTTGATCAGTGAAAAGTGGTAGCTTCTGCTACCTGGTT
1 AGTGAAAAGTGGTAGCTCCGACTACCTGATCAGTGAAAAGTGGTAGCTTCGGCTACCTGGTT
* *
28389258 AGTGAAAAGTGGTAGCTCCGGCTACCTGATCAGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTCCGACTACCTGATCAGTGAAAAGTGGTAGCTTCGGCTAC
28389314 AAGTGACAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 51 1.00
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (62 bp):
AGTGAAAAGTGGTAGCTCCGACTACCTGATCAGTGAAAAGTGGTAGCTTCGGCTACCTGGTT
Found at i:28392677 original size:39 final size:39
Alignment explanation
Indices: 28392629--28392729 Score: 166
Period size: 39 Copynumber: 2.6 Consensus size: 39
28392619 GCTCTGATGA
* *
28392629 GCTTTAGTTAGCCTTCGGGCTTTCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
28392668 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
**
28392707 GCTTCAGTTAGATTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
28392730 AGATCGCGAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.13, C:0.23, G:0.24, T:0.41
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:28392711 original size:21 final size:21
Alignment explanation
Indices: 28392647--28392711 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
28392637 TAGCCTTCGG
*
28392647 GCTTTCGTTTAGCACTTATGT
1 GCTTCCGTTTAGCACTTATGT
* * *
28392668 GCTTCAG-TTAGC-CTT-CGG
1 GCTTCCGTTTAGCACTTATGT
28392686 GCTTCCGTTTAGCACTTATGT
1 GCTTCCGTTTAGCACTTATGT
28392707 GCTTC
1 GCTTC
28392712 AGTTAGATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
18 7 0.21
19 8 0.24
20 8 0.24
21 11 0.32
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.42
Consensus pattern (21 bp):
GCTTCCGTTTAGCACTTATGT
Found at i:28396427 original size:79 final size:79
Alignment explanation
Indices: 28396296--28396448 Score: 306
Period size: 79 Copynumber: 1.9 Consensus size: 79
28396286 CAATTCGGAC
28396296 TACTTCGTTATTTGCGCACCTCAAATCAATAGTCTTGCTCTTGCAATTCACAACCGCATCATGCG
1 TACTTCGTTATTTGCGCACCTCAAATCAATAGTCTTGCTCTTGCAATTCACAACCGCATCATGCG
28396361 CGGTCAACCTGGAT
66 CGGTCAACCTGGAT
28396375 TACTTCGTTATTTGCGCACCTCAAATCAATAGTCTTGCTCTTGCAATTCACAACCGCATCATGCG
1 TACTTCGTTATTTGCGCACCTCAAATCAATAGTCTTGCTCTTGCAATTCACAACCGCATCATGCG
28396440 CGGTCAACC
66 CGGTCAACC
28396449 AATCCAAACC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 74 1.00
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (79 bp):
TACTTCGTTATTTGCGCACCTCAAATCAATAGTCTTGCTCTTGCAATTCACAACCGCATCATGCG
CGGTCAACCTGGAT
Found at i:28400518 original size:27 final size:27
Alignment explanation
Indices: 28400469--28400544 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
28400459 TCCCAAAATA
**
28400469 GGTAAAATGACTGTAATACCCCCTATAG
1 GGTAAAATGACCATAATA-CCCCTATAG
* *
28400497 GGTAAAATGACCATAATACCCCTGTAT
1 GGTAAAATGACCATAATACCCCTATAG
* *
28400524 GGTAAAATGACGATTATACCC
1 GGTAAAATGACCATAATACCC
28400545 TTGTGCTCCG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 26 0.62
28 16 0.38
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (27 bp):
GGTAAAATGACCATAATACCCCTATAG
Found at i:28400698 original size:26 final size:26
Alignment explanation
Indices: 28400669--28400727 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
28400659 TTGGAGGAAG
*
28400669 TTCTGTACTAGAGGTTTTGCCACGTA
1 TTCTGTACTAGAGGTTCTGCCACGTA
* * *
28400695 TTCTGATTCTAGTGGTTCTGCCACGTT
1 TTCTG-TACTAGAGGTTCTGCCACGTA
28400722 TTCTGT
1 TTCTGT
28400728 TATTAGCAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 6 0.21
27 22 0.79
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.44
Consensus pattern (26 bp):
TTCTGTACTAGAGGTTCTGCCACGTA
Found at i:28406413 original size:14 final size:14
Alignment explanation
Indices: 28406394--28406428 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
28406384 CTGATTAGGT
*
28406394 AAATTTCGAGGCTG
1 AAATTTCGAGGCTA
28406408 AAATTTCGAGGCTA
1 AAATTTCGAGGCTA
28406422 AAATTTC
1 AAATTTC
28406429 TTTAAGGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.31
Consensus pattern (14 bp):
AAATTTCGAGGCTA
Found at i:28408457 original size:28 final size:27
Alignment explanation
Indices: 28408421--28408486 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 27
28408411 CCCCAAAATA
*
28408421 GGTAAAATGACTGTAATACCTCCTATAG
1 GGTAAAATGACCGTAATACC-CCTATAG
* *
28408449 GGTAAAATGACCGTAATACCCCTGTAT
1 GGTAAAATGACCGTAATACCCCTATAG
28408476 GGTAAAATGAC
1 GGTAAAATGAC
28408487 AATTATGCCC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
27 16 0.46
28 19 0.54
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (27 bp):
GGTAAAATGACCGTAATACCCCTATAG
Found at i:28417175 original size:40 final size:40
Alignment explanation
Indices: 28417084--28417346 Score: 343
Period size: 40 Copynumber: 6.6 Consensus size: 40
28417074 TCCTCGTTCA
* * * * *
28417084 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
28417123 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
28417163 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
28417203 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
28417243 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
28417283 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
28417323 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
28417347 CAGCATTCAA
Statistics
Matches: 202, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 37 0.18
40 157 0.78
41 8 0.04
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:28421680 original size:42 final size:42
Alignment explanation
Indices: 28421621--28421704 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
28421611 ATACGGAGCT
*
28421621 ATCGAAATCGGCGTAGTCCCAGGTACAAGCTCAATCCCAAAC
1 ATCGAAATCGGCGTAGTCCCAGGTACAAGCTCAATACCAAAC
28421663 ATCGAAATCGGCGTAGTCCCAGGTACAAGCTCAATACCAAAC
1 ATCGAAATCGGCGTAGTCCCAGGTACAAGCTCAATACCAAAC
28421705 TCTACCTCCC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.35, C:0.30, G:0.19, T:0.17
Consensus pattern (42 bp):
ATCGAAATCGGCGTAGTCCCAGGTACAAGCTCAATACCAAAC
Found at i:28441009 original size:43 final size:42
Alignment explanation
Indices: 28440836--28440998 Score: 154
Period size: 43 Copynumber: 3.9 Consensus size: 42
28440826 ATAATCACAT
** * * *
28440836 ATATCG-TGCCAACGTCCCAGATGTGGTTTTACATGCTATCAC
1 ATATCGATGCCAACGTCCCAGACATGGTCTTACATG-AATCAA
* * *
28440878 ATATCGATGCC-ACTATCCCAGACAGGGTCTTACACGAATCAA
1 ATATCGATGCCAAC-GTCCCAGACATGGTCTTACATGAATCAA
* * * *
28440920 ATA-CAATGCCGATGTCCTAGACATGGTCTTACGCAT-AATCAA
1 ATATCGATGCCAACGTCCCAGACATGGTCTTA--CATGAATCAA
28440962 ATATCGATGCCAACGTCCCAGACATGGTCTTACATGA
1 ATATCGATGCCAACGTCCCAGACATGGTCTTACATGA
28440999 GAACACATAT
Statistics
Matches: 96, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
41 24 0.25
42 26 0.27
43 46 0.48
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (42 bp):
ATATCGATGCCAACGTCCCAGACATGGTCTTACATGAATCAA
Found at i:28442551 original size:33 final size:34
Alignment explanation
Indices: 28442514--28442590 Score: 88
Period size: 33 Copynumber: 2.3 Consensus size: 34
28442504 ATGGTAACCA
*
28442514 TTTATCATATTC-A-TCATTCAACTTAATTCA-CAT
1 TTTATCATATTCAATTCA-TCAAC-CAATTCATCAT
*
28442547 TTTATCATTTTCAATTCATCAACCAATTCATCAT
1 TTTATCATATTCAATTCATCAACCAATTCATCAT
*
28442581 TTCATCATAT
1 TTTATCATAT
28442591 AACATAACAC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
33 17 0.46
34 17 0.46
35 3 0.08
ACGTcount: A:0.32, C:0.22, G:0.00, T:0.45
Consensus pattern (34 bp):
TTTATCATATTCAATTCATCAACCAATTCATCAT
Found at i:28443750 original size:3 final size:3
Alignment explanation
Indices: 28443744--28443773 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
28443734 ACATTATCAT
*
28443744 CAC CAC CAC CAC CAC TAC CAC CAC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
28443774 TATTATTACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.63, G:0.00, T:0.03
Consensus pattern (3 bp):
CAC
Found at i:28443765 original size:15 final size:15
Alignment explanation
Indices: 28443745--28443775 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28443735 CATTATCATC
28443745 ACCACCACCACCACT
1 ACCACCACCACCACT
28443760 ACCACCACCACCACT
1 ACCACCACCACCACT
28443775 A
1 A
28443776 TTATTACCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.58, G:0.00, T:0.06
Consensus pattern (15 bp):
ACCACCACCACCACT
Found at i:28447969 original size:13 final size:13
Alignment explanation
Indices: 28447951--28447975 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28447941 TAATTTATAT
28447951 GTGTGAAAATTTC
1 GTGTGAAAATTTC
28447964 GTGTGAAAATTT
1 GTGTGAAAATTT
28447976 TATCATTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:28448354 original size:17 final size:18
Alignment explanation
Indices: 28448325--28448359 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28448315 GTTTTGCTCG
*
28448325 ATTTTTGATGATTTTTAC
1 ATTTTTGATGATTGTTAC
28448343 ATTTTTGA-GATTGTTAC
1 ATTTTTGATGATTGTTAC
28448360 TTTGAATACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.23, C:0.06, G:0.14, T:0.57
Consensus pattern (18 bp):
ATTTTTGATGATTGTTAC
Found at i:28449246 original size:43 final size:44
Alignment explanation
Indices: 28449089--28449247 Score: 121
Period size: 43 Copynumber: 3.7 Consensus size: 44
28449079 ATGTGTTTTT
* * *
28449089 CATGTAAGACCATGTCTAGGATGTTGGCATCGATTTGTGATTTA
1 CATGTAAGACCACGTCTAGGATGTTGGCATCGATATGTGAGTTA
* * * * ** ** * *
28449133 CGTGTAAGACCATGTTTGGGACATCAGAATCG-TATATGAGTT-
1 CATGTAAGACCACGTCTAGGATGTTGGCATCGATATGTGAGTTA
* *
28449175 CGTGTAAGACC-CTGTCTAGGACAG-TGGCATCGATATGTGA-TTA
1 CATGTAAGACCAC-GTCTAGGA-TGTTGGCATCGATATGTGAGTTA
*
28449218 CATGTAAGACCACGTCTGGGATGTTGGCAT
1 CATGTAAGACCACGTCTAGGATGTTGGCAT
28449248 TGTACGAGCT
Statistics
Matches: 86, Mismatches: 23, Indels: 13
0.70 0.19 0.11
Matches are distributed among these distances:
42 25 0.29
43 36 0.42
44 25 0.29
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (44 bp):
CATGTAAGACCACGTCTAGGATGTTGGCATCGATATGTGAGTTA
Found at i:28451198 original size:15 final size:16
Alignment explanation
Indices: 28451180--28451210 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28451170 GCAGTTATCA
28451180 ATTTTA-TTTTATTTT
1 ATTTTATTTTTATTTT
28451195 ATTTTATTTTTATTTT
1 ATTTTATTTTTATTTT
28451211 CTGTCTCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (16 bp):
ATTTTATTTTTATTTT
Found at i:28451207 original size:6 final size:5
Alignment explanation
Indices: 28451180--28451210 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
28451170 GCAGTTATCA
28451180 ATTTT ATTTT ATTTT ATTTT ATTTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT A-TTTT ATTTT
28451211 CTGTCTCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
ATTTT
Found at i:28451767 original size:12 final size:12
Alignment explanation
Indices: 28451750--28451777 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28451740 CACTGGCGTA
28451750 TGGTCACCCATG
1 TGGTCACCCATG
28451762 TGGTCACCCATG
1 TGGTCACCCATG
28451774 TGGT
1 TGGT
28451778 AGGCTCATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (12 bp):
TGGTCACCCATG
Found at i:28470220 original size:29 final size:29
Alignment explanation
Indices: 28470150--28470249 Score: 107
Period size: 29 Copynumber: 3.5 Consensus size: 29
28470140 ACCCCTACAT
* *
28470150 ACATGCATATGGCCTA-CTAGACCCAA-TC
1 ACATTCATATGGCCCATC-AGACCCAATTC
* * *
28470178 TCATTTATATGGCCCATCCGACCCAATTC
1 ACATTCATATGGCCCATCAGACCCAATTC
* *
28470207 ACGTTCATATGGCCCATCAGGCCCAATTC
1 ACATTCATATGGCCCATCAGACCCAATTC
28470236 ACATTC-TATGGCCC
1 ACATTCATATGGCCC
28470250 TTTAGGATCA
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
28 27 0.46
29 32 0.54
ACGTcount: A:0.26, C:0.34, G:0.14, T:0.26
Consensus pattern (29 bp):
ACATTCATATGGCCCATCAGACCCAATTC
Found at i:28470261 original size:28 final size:29
Alignment explanation
Indices: 28470179--28470300 Score: 85
Period size: 28 Copynumber: 4.3 Consensus size: 29
28470169 GACCCAATCT
* *
28470179 CATTTATATGGCCCATC-CGACCCAATTCA
1 CATTCATATGGCCCATCAGGA-CCAATTCA
* *
28470208 CGTTCATATGGCCCATCAGGCCCAATTCA
1 CATTCATATGGCCCATCAGGACCAATTCA
* * *
28470237 CATTC-TATGGCCCTTTAGGATCAATAT-A
1 CATTCATATGGCCCATCAGGACCAAT-TCA
* * *
28470265 -ATTTATATGGCCCATTC-GGCCCAAATCA
1 CATTCATATGGCCCA-TCAGGACCAATTCA
28470293 CATT-ATAT
1 CATTCATAT
28470301 TCATGTTCAC
Statistics
Matches: 72, Mismatches: 15, Indels: 13
0.72 0.15 0.13
Matches are distributed among these distances:
27 4 0.06
28 35 0.49
29 32 0.44
30 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.30
Consensus pattern (29 bp):
CATTCATATGGCCCATCAGGACCAATTCA
Found at i:28472300 original size:19 final size:18
Alignment explanation
Indices: 28472276--28472315 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28472266 TGATCACATG
28472276 TTCATTAAACGGTTTTAAT
1 TTCATT-AACGGTTTTAAT
* *
28472295 TTCATTTACGGTTTTTAT
1 TTCATTAACGGTTTTAAT
28472313 TTC
1 TTC
28472316 CTATTCTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.23, C:0.12, G:0.10, T:0.55
Consensus pattern (18 bp):
TTCATTAACGGTTTTAAT
Found at i:28487636 original size:40 final size:39
Alignment explanation
Indices: 28487592--28487696 Score: 122
Period size: 39 Copynumber: 2.6 Consensus size: 39
28487582 AGTGACCATA
*
28487592 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGACTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
* *
28487632 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGACTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
28487670 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGACTAAG-CCCGAAGGCATTTG
28487697 AACGAGTAGC
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
38 2 0.03
39 32 0.55
40 24 0.41
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGACTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:28487653 original size:39 final size:40
Alignment explanation
Indices: 28487552--28487715 Score: 169
Period size: 40 Copynumber: 4.1 Consensus size: 40
28487542 TTGAATGATG
* *
28487552 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATA
*
28487592 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-A
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTATA
*
28487631 TTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATA
* * **
28487671 ACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATA-CTATA
28487711 TCCGG
1 TCCGG
28487716 TTAAATTCCG
Statistics
Matches: 106, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
39 36 0.34
40 59 0.56
41 10 0.09
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATA
Found at i:28487715 original size:79 final size:80
Alignment explanation
Indices: 28487552--28487702 Score: 191
Period size: 79 Copynumber: 1.9 Consensus size: 80
28487542 TTGAATGATG
*
28487552 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
**
28487617 GTGCGAGATACTAAT
66 GAACGAGATACTAAT
* * * * *
28487632 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCAT
28487694 TTGAACGAG
64 TTGAACGAG
28487703 TAGCTATATC
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
78 1 0.02
79 42 0.69
80 18 0.30
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
GAACGAGATACTAAT
Found at i:28494986 original size:79 final size:81
Alignment explanation
Indices: 28494851--28495034 Score: 225
Period size: 79 Copynumber: 2.3 Consensus size: 81
28494841 TGAATGATGT
*
28494851 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
*
28494915 GTGCGAGATACTA-ATT
66 GTGCGAGATACTATA-A
* * * * **
28494931 TCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCATT
*
28494993 TGTGCGAGTTACTATAA
65 TGTGCGAGATACTATAA
*
28495010 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
28495035 AACGAGTAGC
Statistics
Matches: 89, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.64
80 31 0.35
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTATAA
Found at i:28495041 original size:40 final size:40
Alignment explanation
Indices: 28494850--28495034 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
28494840 TTGAATGATG
* * * *
28494850 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
28494890 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28494930 TTCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28494969 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
28495010 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28495035 AACGAGTAGC
Statistics
Matches: 125, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
39 34 0.27
40 81 0.65
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28495056 original size:79 final size:79
Alignment explanation
Indices: 28494903--28495067 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
28494893 GGACTAAGAT
** **
28494903 CCGAAGGCATTTGTGCGAGATACTAATTTCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
28494968 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
28494982 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
28495045 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
28495061 CCGAAGG
1 CCGAAGG
28495068 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:28497953 original size:16 final size:15
Alignment explanation
Indices: 28497925--28497958 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
28497915 GTTTTATGGA
28497925 AAAAGAAAAAAAAAG
1 AAAAGAAAAAAAAAG
*
28497940 AAAATAAAATAAAAAG
1 AAAAGAAAA-AAAAAG
28497956 AAA
1 AAA
28497959 TTATATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (15 bp):
AAAAGAAAAAAAAAG
Found at i:28507602 original size:39 final size:39
Alignment explanation
Indices: 28507548--28507765 Score: 321
Period size: 39 Copynumber: 5.5 Consensus size: 39
28507538 TAATGGAGAA
28507548 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
28507587 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
28507626 TTATATTCGAGCTAAG-CCCTGAAGGCATTTGTGCTGGTG
1 TTATATCCGGGCTAAGTCCC-GAAGGCATTCGTGCTGGTG
*
28507665 TTATATCCGGGCTAAGCCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * * *
28507704 TTATATCCAGGCTAAGCCCCAAAGGCATTCGTGCTGGTA
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
28507743 TTATATTCGGGCTTAAAGTCCCG
1 TTATATCCGGGC-T-AAGTCCCG
28507766 CATGCTTTGT
Statistics
Matches: 162, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
38 3 0.02
39 149 0.92
40 4 0.02
41 6 0.04
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.29
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:28519794 original size:29 final size:29
Alignment explanation
Indices: 28519752--28519810 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
28519742 CTTGATTAAA
28519752 TCTTATTTGAAATCGTGCATTAGAACTCC
1 TCTTATTTGAAATCGTGCATTAGAACTCC
28519781 TCTTATTTGAAATCGTGCATTAGAACTCC
1 TCTTATTTGAAATCGTGCATTAGAACTCC
28519810 T
1 T
28519811 TGGTTTTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (29 bp):
TCTTATTTGAAATCGTGCATTAGAACTCC
Found at i:28520381 original size:35 final size:35
Alignment explanation
Indices: 28520333--28520405 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
28520323 TATTTGAACC
28520333 CTTGCAAAATTAGCCATCACTTCTCTCTTAACTAT
1 CTTGCAAAATTAGCCATCACTTCTCTCTTAACTAT
*
28520368 CTTGCAAATTTAGCCATCACTTCTCTCTTAACTAT
1 CTTGCAAAATTAGCCATCACTTCTCTCTTAACTAT
28520403 CTT
1 CTT
28520406 AAAATTGTCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.26, C:0.29, G:0.05, T:0.40
Consensus pattern (35 bp):
CTTGCAAAATTAGCCATCACTTCTCTCTTAACTAT
Found at i:28522100 original size:23 final size:23
Alignment explanation
Indices: 28522070--28522115 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
28522060 GTCGGCTAAG
28522070 AGTGCTCGGAGCGTGGATTAACT
1 AGTGCTCGGAGCGTGGATTAACT
28522093 AGTGCTCGGAGCGTGGATTAACT
1 AGTGCTCGGAGCGTGGATTAACT
28522116 CCAGTCTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.35, T:0.26
Consensus pattern (23 bp):
AGTGCTCGGAGCGTGGATTAACT
Found at i:28522591 original size:108 final size:108
Alignment explanation
Indices: 28522445--28523303 Score: 1149
Period size: 108 Copynumber: 8.0 Consensus size: 108
28522435 GTACTCCCGA
* * * * * *
28522445 TTTATAGAATTACTGTTTTACCCTCGATTTGTAAAATTACCGTTTTACCCTCAGTTTACAGAATT
1 TTTACAGAATTACTATTTTACCCTCGATTTATAGAATTACTGTTTTACCCTCAGTTTACAAAATT
* * *
28522510 ACCGTTTTACCCTCGATTTACAGAATTACCATTTTACCATCAC
66 ACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCAT
**
28522553 TTTACAGAATTACTATTTTACCCTCGATTTATAGAATTACTGTTTTACCCTC-GATTTGTAAAAT
1 TTTACAGAATTACTATTTTACCCTCGATTTATAGAATTACTGTTTTACCCTCAG-TTTACAAAAT
* * *
28522617 TACTGTTTTACCCTCGATTTATAGAATTACCGTTTTACCCTCAA
65 TACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCAT
**
28522661 TTTACAGAATTACTATTTTACCCTCGATTTATAGAATTACTGTTTTACCCTC-GATTTGTAAAAT
1 TTTACAGAATTACTATTTTACCCTCGATTTATAGAATTACTGTTTTACCCTCAG-TTTACAAAAT
* * *
28522725 TACTGTTTTACCCTCGATTTATAGAATTACCGTTTTACCCTCAA
65 TACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCAT
* * * *
28522769 TTTACAGAATTACTATTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCATTTTACAGAATT
1 TTTACAGAATTACTATTTTACCCTCGATTTATAGAATTACTGTTTTACCCTCAGTTTACAAAATT
* * * *
28522834 ATCGTTTTACCCTCGATTTACATAATTACTGTTTTACCCTCAG
66 ACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCAT
* * *
28522877 TTTACAGAATTACTATTTTACCCTCGATTTATAGAATTACCGTTTTACCCTCAGTTTATAGAATT
1 TTTACAGAATTACTATTTTACCCTCGATTTATAGAATTACTGTTTTACCCTCAGTTTACAAAATT
* *
28522942 ACTGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTTGAT
66 ACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCC-TCAT
* * * *
28522986 TTGTA-A-AATTACTACTTTACCCTTGATTTATAGAATTACTGGTTTACCCTTAGTTTACAAAAT
1 TT-TACAGAATTACTATTTTACCCTCGATTTATAGAATTACTGTTTTACCCTCAGTTTACAAAAT
* *
28523049 TATCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTTGAT
65 TACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCC-TCAT
* * * *
28523094 TTGTA-A-AATTACTACTTTACCCTTGATTTATAGAATTACTGGTTTACCCTTAGTTTACAAAAT
1 TT-TACAGAATTACTATTTTACCCTCGATTTATAGAATTACTGTTTTACCCTCAGTTTACAAAAT
* *
28523157 TATCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTTGAT
65 TACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCC-TCAT
* * * *
28523202 TTGTA-A-AATTACTACTTTACCCTTGATTTATAGAATTACTGGTTTACCCTTAGTTTACAAAAT
1 TT-TACAGAATTACTATTTTACCCTCGATTTATAGAATTACTGTTTTACCCTCAGTTTACAAAAT
*
28523265 TATCGTTTTACCCTCGATTTACAGAATTACCGTTTTACC
65 TACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACC
28523304 ATTGATTGTG
Statistics
Matches: 704, Mismatches: 43, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
107 1 0.00
108 696 0.99
109 5 0.01
110 2 0.00
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.42
Consensus pattern (108 bp):
TTTACAGAATTACTATTTTACCCTCGATTTATAGAATTACTGTTTTACCCTCAGTTTACAAAATT
ACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCAT
Found at i:28523310 original size:27 final size:27
Alignment explanation
Indices: 28522442--28523303 Score: 911
Period size: 27 Copynumber: 31.9 Consensus size: 27
28522432 AAAGTACTCC
*
28522442 CGATTTATAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
** * *
28522469 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
*
28522496 C-AGTTTACAGAATTACCGTTTTACCCT
1 CGA-TTTACAGAATTACTGTTTTACCCT
** *
28522523 CGATTTACAGAATTACCATTTTACCAT
1 CGATTTACAGAATTACTGTTTTACCCT
*
28522550 C-ACTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACTGTTTTACCCT
*
28522577 CGATTTATAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
** *
28522604 CGATTTGTAAAATTACTGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
* *
28522631 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
* *
28522658 CAATTTACAGAATTACTATTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
*
28522685 CGATTTATAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
** *
28522712 CGATTTGTAAAATTACTGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
* *
28522739 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
* *
28522766 CAATTTACAGAATTACTATTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
*
28522793 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
28522820 C-ATTTTACAGAATTA-TCGTTTTACCCT
1 CGA-TTTACAGAATTACT-GTTTTACCCT
*
28522847 CGATTTACATAATTACTGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
*
28522874 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACTGTTTTACCCT
* *
28522901 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
*
28522928 C-AGTTTATAGAATTACTGTTTTACCCT
1 CGA-TTTACAGAATTACTGTTTTACCCT
*
28522955 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
* ** * **
28522982 TGATTTGTAAAATTACTACTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
* * *
28523009 TGATTTATAGAATTACTGGTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
* *
28523036 -TAGTTTACAAAATTA-TCGTTTTACCCT
1 CGA-TTTACAGAATTACT-GTTTTACCCT
*
28523063 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
* ** * **
28523090 TGATTTGTAAAATTACTACTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
* * *
28523117 TGATTTATAGAATTACTGGTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
* *
28523144 -TAGTTTACAAAATTA-TCGTTTTACCCT
1 CGA-TTTACAGAATTACT-GTTTTACCCT
*
28523171 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
* ** * **
28523198 TGATTTGTAAAATTACTACTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
* * *
28523225 TGATTTATAGAATTACTGGTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
* *
28523252 -TAGTTTACAAAATTA-TCGTTTTACCCT
1 CGA-TTTACAGAATTACT-GTTTTACCCT
*
28523279 CGATTTACAGAATTACCGTTTTACC
1 CGATTTACAGAATTACTGTTTTACC
28523304 ATTGATTGTG
Statistics
Matches: 711, Mismatches: 100, Indels: 48
0.83 0.12 0.06
Matches are distributed among these distances:
26 11 0.02
27 691 0.97
28 9 0.01
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.42
Consensus pattern (27 bp):
CGATTTACAGAATTACTGTTTTACCCT
Found at i:28523353 original size:27 final size:27
Alignment explanation
Indices: 28523315--28523511 Score: 241
Period size: 27 Copynumber: 7.3 Consensus size: 27
28523305 TTGATTGTGA
* *
28523315 AATTACCGAAATACCCCTATAGGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
* *
28523342 AATTTCCAAAATACCCCTATAGGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
* * *
28523369 AATTACTAAAATACCCTTGTAGGATAG
1 AATTACCAAAATACCCCTGTAGGGTAG
28523396 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
* * *
28523423 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
*
28523450 AAATACCAAAATACCCCTGTAGGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAG
* * * * * *
28523477 AATTACCGAGATACCCTTATGGGGTAA
1 AATTACCAAAATACCCCTGTAGGGTAG
28523504 AATTACCA
1 AATTACCA
28523512 TTTTGCCCTT
Statistics
Matches: 145, Mismatches: 25, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 145 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.25
Consensus pattern (27 bp):
AATTACCAAAATACCCCTGTAGGGTAG
Found at i:28523520 original size:27 final size:28
Alignment explanation
Indices: 28523490--28523553 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 28
28523480 TACCGAGATA
*
28523490 CCCTTATGGG-GTAAAATTACCATTTTG
1 CCCTTATGGGTGTAAAATGACCATTTTG
* **
28523517 CCCTTA-GGGTGTTAAATGACTGTTTTG
1 CCCTTATGGGTGTAAAATGACCATTTTG
*
28523544 CCCTTGTGGG
1 CCCTTATGGG
28523554 CAAGTGACTG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
26 3 0.10
27 24 0.80
28 3 0.10
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (28 bp):
CCCTTATGGGTGTAAAATGACCATTTTG
Found at i:28523748 original size:27 final size:26
Alignment explanation
Indices: 28523710--28523792 Score: 85
Period size: 27 Copynumber: 3.1 Consensus size: 26
28523700 CGGAGGAAGC
*
28523710 GTTCTGGTGGCTATTCCACAAATATCT
1 GTTCTGGTGGCTATGCCAC-AATATCT
*
28523737 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTATGCCACAATATCT
* * * **
28523763 GTATTTGGTGACTCTATCACAATATCT
1 GT-TCTGGTGGCTATGCCACAATATCT
28523790 GTT
1 GTT
28523793 GACCGATCGA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
26 10 0.20
27 39 0.80
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (26 bp):
GTTCTGGTGGCTATGCCACAATATCT
Found at i:28523912 original size:22 final size:22
Alignment explanation
Indices: 28523880--28523938 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
28523870 CCCGTTATTA
*
28523880 ATGGCTCTGTGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
* * * *
28523902 ATGGCTTTGTGCCATCTTGACT
1 ATGGCTTTGTGCCAACCTAAAT
*
28523924 ATGGCTTCGTGCCAA
1 ATGGCTTTGTGCCAA
28523939 ACGTATTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Found at i:28524149 original size:27 final size:26
Alignment explanation
Indices: 28524118--28524176 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 26
28524108 TATTATTTGA
*
28524118 TTCTGGTGGCTCTGCCACAATATCTG
1 TTCTGGTGACTCTGCCACAATATCTG
* *
28524144 TATCTGGTGACTCTGTCACGATATCTG
1 T-TCTGGTGACTCTGCCACAATATCTG
28524171 TTCTGG
1 TTCTGG
28524177 CAGCCATGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 6 0.21
27 23 0.79
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (26 bp):
TTCTGGTGACTCTGCCACAATATCTG
Found at i:28524322 original size:6 final size:6
Alignment explanation
Indices: 28524313--28524463 Score: 132
Period size: 6 Copynumber: 24.8 Consensus size: 6
28524303 CTGTCACGTA
* * *
28524313 ATTCTG ATTCTG ATTCTG ATTCTG -TCACGTA ATTCTG ATTCTG ATTTTG
1 ATTCTG ATTCTG ATTCTG ATTCTG AT-TC-TG ATTCTG ATTCTG ATTCTG
* *
28524362 ATTCTG -TTACTA ATACTG ATTCTG ATTCTG ATTCTG -TTACTG ATTCTG
1 ATTCTG ATT-CTG ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG
* * *
28524410 ATTCTG -TCACCTA ATTCTG ATTCTG ATTCTG -TTATTG ATTCTG ATTCTG
1 ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG
28524459 ATTCT
1 ATTCT
28524464 CATTTTGGTT
Statistics
Matches: 117, Mismatches: 16, Indels: 24
0.75 0.10 0.15
Matches are distributed among these distances:
5 8 0.07
6 98 0.84
7 9 0.08
8 2 0.02
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:28524329 original size:31 final size:30
Alignment explanation
Indices: 28524294--28524415 Score: 181
Period size: 31 Copynumber: 4.0 Consensus size: 30
28524284 TTGCATTCAC
28524294 ATTCTGATTCTGTCACGTAATTCTGATTCTG
1 ATTCTGATTCTGTCAC-TAATTCTGATTCTG
28524325 ATTCTGATTCTGTCACGTAATTCTGATTCTG
1 ATTCTGATTCTGTCAC-TAATTCTGATTCTG
* * *
28524356 ATTTTGATTCTGTTACTAATACTGATTCTG
1 ATTCTGATTCTGTCACTAATTCTGATTCTG
* *
28524386 ATTCTGATTCTGTTACTGATTCTGATTCTG
1 ATTCTGATTCTGTCACTAATTCTGATTCTG
28524416 TCACCTAATT
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
30 40 0.47
31 45 0.53
ACGTcount: A:0.20, C:0.17, G:0.16, T:0.48
Consensus pattern (30 bp):
ATTCTGATTCTGTCACTAATTCTGATTCTG
Found at i:28524437 original size:73 final size:74
Alignment explanation
Indices: 28524313--28524463 Score: 198
Period size: 79 Copynumber: 2.0 Consensus size: 74
28524303 CTGTCACGTA
*
28524313 ATTCTGATTCTGATTCTGATTCTGTCACGTAATTCTGATTCTGATTTTGATTCTGTTACTAATAC
1 ATTCTGATTCTGATTCTGATTCTGTCACCTAATTCTGATTC-----TTGATTCTGTTACTAATAC
28524378 TGATTCTGATTCTG
61 TGATTCTGATTCTG
* * *
28524392 ATTCTG-TTACTGATTCTGATTCTGTCACCTAATTCTGATTC-TGATTCTGTTATTGATTCTGAT
1 ATTCTGATT-CTGATTCTGATTCTGTCACCTAATTCTGATTCTTGATTCTGTTACTAATACTGAT
28524455 TCTGATTCT
65 TCTGATTCT
28524464 CATTTTGGTT
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
73 28 0.42
78 2 0.03
79 37 0.55
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (74 bp):
ATTCTGATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTTGATTCTGTTACTAATACTGATT
CTGATTCTG
Found at i:28529795 original size:26 final size:26
Alignment explanation
Indices: 28529765--28529816 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
28529755 CATAGGTATG
28529765 GATGTATCCCGAAAATGATCCACTAT
1 GATGTATCCCGAAAATGATCCACTAT
*
28529791 GATGTATCCCGAAAGTGATCCACTAT
1 GATGTATCCCGAAAATGATCCACTAT
28529817 CCTGCACGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (26 bp):
GATGTATCCCGAAAATGATCCACTAT
Found at i:28533590 original size:83 final size:83
Alignment explanation
Indices: 28533367--28533802 Score: 658
Period size: 83 Copynumber: 5.2 Consensus size: 83
28533357 TTCGATTTGT
* * * * * *
28533367 AAGGATGTCAAATCATTTTGAGTCTGCTTGAGAACATTTGAGAATCATATCTGCAAGGTCCTCGA
1 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
*
28533432 CTTGTTCCTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
* *
28533450 AAGGATGCCTAAACCATCTTAAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATATCCTCG
1 AAGGATGCC-AAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCG
*
28533515 ATTTGTTCTTTGTAAGCAC
65 ATTTGTTCCTTGTAAGCAC
* *
28533534 AAGGATGCCAAACCGTCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATTTCCTCGA
1 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
28533599 TTTGTTCCTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
*
28533617 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGAAATGTCCTCGA
1 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
*
28533682 TTTGTTCTTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
* *
28533700 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATCTGAGAGTC-TAATCTGCTATGTCCTCG
1 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCAT-ATCTGCAATGTCCTCG
* *
28533764 GTTTGTTCCTTGTAAACAC
65 ATTTGTTCCTTGTAAGCAC
* * *
28533783 AAGAATACCAAATCATCTTG
1 AAGGATGCCAAACCATCTTG
28533803 GATCTATTTC
Statistics
Matches: 324, Mismatches: 27, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
82 1 0.00
83 249 0.77
84 74 0.23
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (83 bp):
AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
TTTGTTCCTTGTAAGCAC
Found at i:28534196 original size:119 final size:119
Alignment explanation
Indices: 28533726--28534177 Score: 735
Period size: 119 Copynumber: 3.8 Consensus size: 119
28533716 CTTGAGTCTG
* * *
28533726 TTTGAGAACATCTGAGAGTCTAATCTGCTATGTCCTCGGTTTGTTCCTTGTAAACACAAGAATAC
1 TTTGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
** *
28533791 CAAATCATCTTGGATCTATTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
66 CAAATCATCTTGGATCTGCTTCAGCATAAACATCTGAAGGTTAGATCTGCTATA
*
28533845 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
1 TTTGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
* * *
28533910 CAAATCATCTTGGATTTCCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
66 CAAATCATCTTGGATCTGCTTCAGCATAAACATCTGAAGGTTAGATCTGCTATA
28533964 TTTGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
1 TTTGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
** *
28534029 CAAATCATCTTGGATCTGCTTCAGCATAAATGTCTGAA-GTCTAGATCTGTTATA
66 CAAATCATCTTGGATCTGCTTCAGCATAAACATCTGAAGGT-TAGATCTGCTATA
* *
28534083 TTTGAGAACGTCTAAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
1 TTTGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
* *
28534148 CAAATTATCTTGGATCTGCTTTAGCATAAA
66 CAAATCATCTTGGATCTGCTTCAGCATAAA
28534178 TGTTTGAAGT
Statistics
Matches: 314, Mismatches: 18, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
118 2 0.01
119 312 0.99
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Consensus pattern (119 bp):
TTTGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
CAAATCATCTTGGATCTGCTTCAGCATAAACATCTGAAGGTTAGATCTGCTATA
Found at i:28539022 original size:28 final size:28
Alignment explanation
Indices: 28538959--28539081 Score: 158
Period size: 28 Copynumber: 4.4 Consensus size: 28
28538949 ATATTAAGTC
* *
28538959 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATACAATCAAACT
*
28538986 TGCACACTTAGTGCTATACAATCAAACT
1 CGCACACTTAGTGCTATACAATCAAACT
* *
28539014 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATACAATCAAACT
* * *
28539042 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATACAA-TCAAACT
28539071 CGCACACTTAG
1 CGCACACTTAG
28539082 CGCCAATCTC
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
27 20 0.24
28 47 0.57
29 16 0.19
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATACAATCAAACT
Found at i:28545475 original size:14 final size:15
Alignment explanation
Indices: 28545456--28545485 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
28545446 TTCAATCTCG
28545456 TTTAGAAAAA-AATA
1 TTTAGAAAAAGAATA
28545470 TTTAGAAAAAGAATA
1 TTTAGAAAAAGAATA
28545485 T
1 T
28545486 CTTTACATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (15 bp):
TTTAGAAAAAGAATA
Found at i:28552019 original size:34 final size:33
Alignment explanation
Indices: 28551976--28552040 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 33
28551966 AAGACGTCGA
28551976 AGACTCGATCACACTATCAATTGAATATTTGNAG
1 AGACTCGATCACACTATCAATTGAATATTTG-AG
28552010 AGACTCGATCACACTATCAATTGAATATTTG
1 AGACTCGATCACACTATCAATTGAATATTTG
28552041 GGTATAGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.31
Consensus pattern (33 bp):
AGACTCGATCACACTATCAATTGAATATTTGAG
Found at i:28553954 original size:79 final size:82
Alignment explanation
Indices: 28553843--28554027 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
28553833 GCTACTCGTT
* *
28553843 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
28553906 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
28553923 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
28553986 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
28554003 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28554028 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:28554027 original size:40 final size:40
Alignment explanation
Indices: 28553824--28554027 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
28553814 CGGAATTTAA
** *
28553824 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
28553864 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
28553904 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
28553943 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
28553983 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
28554023 CCGGA
1 CCGGA
28554028 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:28564481 original size:34 final size:34
Alignment explanation
Indices: 28564443--28564581 Score: 129
Period size: 34 Copynumber: 4.1 Consensus size: 34
28564433 TTGATTTATC
* * *
28564443 ATAAGCACATTATTTGTTACCGTATCAATCTGCT
1 ATAAGCATATTAATTGTTACCGTATCAATCTGTT
* ** *
28564477 ATAAGCATATTAAGTGTTA-C-TATTGATCTATT
1 ATAAGCATATTAATTGTTACCGTATCAATCTGTT
* * **
28564509 TTAAGTATATTAATTACTACCGTATCAATCTGTT
1 ATAAGCATATTAATTGTTACCGTATCAATCTGTT
* ** *
28564543 ATAAGCATATTAATTGTTATCGTATTGATCTATT
1 ATAAGCATATTAATTGTTACCGTATCAATCTGTT
28564577 ATAAG
1 ATAAG
28564582 TATGTCATAT
Statistics
Matches: 80, Mismatches: 23, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
32 22 0.28
33 2 0.03
34 56 0.70
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (34 bp):
ATAAGCATATTAATTGTTACCGTATCAATCTGTT
Found at i:28572449 original size:43 final size:43
Alignment explanation
Indices: 28572401--28572487 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
28572391 CATTAGAAGG
28572401 GTTTACCAGCTAAATAATTCAACCTTAGAAGATAAAGTTGATA
1 GTTTACCAGCTAAATAATTCAACCTTAGAAGATAAAGTTGATA
*
28572444 GTTTACCAGCTAAGTAATTCAACCTTAGAAGATAAAGTTGATA
1 GTTTACCAGCTAAATAATTCAACCTTAGAAGATAAAGTTGATA
28572487 G
1 G
28572488 ACTTACTAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (43 bp):
GTTTACCAGCTAAATAATTCAACCTTAGAAGATAAAGTTGATA
Found at i:28576487 original size:7 final size:7
Alignment explanation
Indices: 28576470--28576550 Score: 53
Period size: 7 Copynumber: 11.3 Consensus size: 7
28576460 GGCAACCCAA
28576470 TTTTTAT
1 TTTTTAT
28576477 TTTTT-T
1 TTTTTAT
*
28576483 CTTTTTCT
1 -TTTTTAT
28576491 TTTATTAT
1 TTT-TTAT
28576499 TTTTTAT
1 TTTTTAT
28576506 TTTATT-T
1 TTT-TTAT
28576513 TATTTTAT
1 T-TTTTAT
*
28576521 TATTTAT
1 TTTTTAT
*
28576528 TACTTTA-
1 T-TTTTAT
28576535 -TTTTAT
1 TTTTTAT
28576541 TTTATTAT
1 TTT-TTAT
28576549 TT
1 TT
28576551 ATTACTTTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
5 4 0.07
6 1 0.02
7 32 0.53
8 23 0.38
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTAT
Found at i:28576501 original size:20 final size:19
Alignment explanation
Indices: 28576471--28576566 Score: 72
Period size: 20 Copynumber: 4.9 Consensus size: 19
28576461 GCAACCCAAT
*
28576471 TTTTATTTT-TTTCTTTTTC
1 TTTTATTTTATTT-TTTTTA
28576490 TTTTATTATT-TTTTATTTTA
1 TTTTATT-TTATTTT-TTTTA
*
28576510 TTTTATTTTATTATTTATTA
1 TTTTATTTTATT-TTTTTTA
*
28576530 CTTTATTTTATTTTATTATT-
1 TTTTATTTTATTTT-TT-TTA
* *
28576550 TATTACTTTATTTTTTT
1 TTTTATTTTATTTTTTT
28576567 GGATATTAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
18 1 0.02
19 14 0.22
20 45 0.70
21 4 0.06
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTATTTTATTTTTTTTA
Found at i:28576508 original size:5 final size:5
Alignment explanation
Indices: 28576471--28576546 Score: 70
Period size: 5 Copynumber: 15.4 Consensus size: 5
28576461 GCAACCCAAT
*
28576471 TTTTA TTTT- TTTCT- TTTTC TTTTA TTATT- TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTT-TA TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA
* *
28576520 TTATT- TATTA CTTTA TTTTA TTTTA TT
1 TT-TTA TTTTA TTTTA TTTTA TTTTA TT
28576547 ATTTATTACT
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
4 8 0.13
5 48 0.80
6 4 0.07
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:28576519 original size:25 final size:25
Alignment explanation
Indices: 28576485--28576563 Score: 131
Period size: 25 Copynumber: 3.2 Consensus size: 25
28576475 ATTTTTTTCT
* * *
28576485 TTTTCTTTTATTATTTTTTATTTTA
1 TTTTATTTTATTATTTATTACTTTA
28576510 TTTTATTTTATTATTTATTACTTTA
1 TTTTATTTTATTATTTATTACTTTA
28576535 TTTTATTTTATTATTTATTACTTTA
1 TTTTATTTTATTATTTATTACTTTA
28576560 TTTT
1 TTTT
28576564 TTTGGATATT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (25 bp):
TTTTATTTTATTATTTATTACTTTA
Found at i:28576537 original size:30 final size:33
Alignment explanation
Indices: 28576501--28576561 Score: 101
Period size: 30 Copynumber: 1.9 Consensus size: 33
28576491 TTTATTATTT
28576501 TTTATTTTATTTTA-T-TTTATTA-TTTATTAC
1 TTTATTTTATTTTATTATTTATTACTTTATTAC
28576531 TTTATTTTATTTTATTATTTATTACTTTATT
1 TTTATTTTATTTTATTATTTATTACTTTATT
28576562 TTTTTGGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 14 0.50
31 1 0.04
32 7 0.25
33 6 0.21
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (33 bp):
TTTATTTTATTTTATTATTTATTACTTTATTAC
Found at i:28576559 original size:8 final size:7
Alignment explanation
Indices: 28576491--28576561 Score: 52
Period size: 7 Copynumber: 8.9 Consensus size: 7
28576481 TTCTTTTTCT
28576491 TTTATTA
1 TTTATTA
*
28576498 TTTTTTA
1 TTTATTA
28576505 TTTTATTTTA
1 -TTTA--TTA
28576515 TTTTATTA
1 -TTTATTA
28576523 TTTATTA
1 TTTATTA
28576530 CTTTATTTTA
1 -TTTA--TTA
28576540 TTTTATTA
1 -TTTATTA
28576548 TTTATTA
1 TTTATTA
28576555 CTTTATT
1 -TTTATT
28576562 TTTTTGGATA
Statistics
Matches: 54, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
7 20 0.37
8 19 0.35
10 15 0.28
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTATTA
Found at i:28576561 original size:15 final size:15
Alignment explanation
Indices: 28576516--28576561 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
28576506 TTTATTTTAT
28576516 TTTATTATTTATTAC
1 TTTATTATTTATTAC
28576531 TTTA-T-TTTA-T--
1 TTTATTATTTATTAC
28576541 TTTATTATTTATTAC
1 TTTATTATTTATTAC
28576556 TTTATT
1 TTTATT
28576562 TTTTTGGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
10 4 0.15
11 1 0.04
12 5 0.19
13 5 0.19
14 1 0.04
15 10 0.38
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATTATTTATTAC
Found at i:28577915 original size:17 final size:17
Alignment explanation
Indices: 28577893--28577925 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
28577883 TATTCTTAAG
28577893 CAAAAAAAAGGAAAAAA
1 CAAAAAAAAGGAAAAAA
28577910 CAAAAAAAAGGAAAAA
1 CAAAAAAAAGGAAAAA
28577926 GAAAGAAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (17 bp):
CAAAAAAAAGGAAAAAA
Found at i:28580481 original size:57 final size:58
Alignment explanation
Indices: 28580391--28580530 Score: 203
Period size: 57 Copynumber: 2.4 Consensus size: 58
28580381 TAACATATAA
** *
28580391 CAGGATTACCAGTCCAGGCTAAATCCTTTTTGTAACATATGCTC-AGAAGAGCTCA-AT
1 CAGGATTACCAGTCCAGGCTAAATCCTAATTGTAACATATGCTCGAGAA-AGATCATAT
* *
28580448 TAGGATTACCAGTCCAGGCTAAATCCTAATTGTAACATATGCTCGAGAAAGATTATAT
1 CAGGATTACCAGTCCAGGCTAAATCCTAATTGTAACATATGCTCGAGAAAGATCATAT
*
28580506 CAGGATTACCAGTCCATGCTAAATC
1 CAGGATTACCAGTCCAGGCTAAATC
28580531 ATGTTAGCAA
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
57 45 0.61
58 29 0.39
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (58 bp):
CAGGATTACCAGTCCAGGCTAAATCCTAATTGTAACATATGCTCGAGAAAGATCATAT
Found at i:28582803 original size:23 final size:22
Alignment explanation
Indices: 28582773--28582816 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
28582763 TATCCAATGT
*
28582773 GTGGTGATAGAGTCCACTTATAG
1 GTGGTGATAAAGTCC-CTTATAG
28582796 GTGGTGATAAAGTCCCTTATA
1 GTGGTGATAAAGTCCCTTATA
28582817 TGTTTCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (22 bp):
GTGGTGATAAAGTCCCTTATAG
Found at i:28582900 original size:17 final size:17
Alignment explanation
Indices: 28582880--28582928 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
28582870 CGATGTGGTA
*
28582880 TGAATGAATTATTATAT
1 TGAATGAACTATTATAT
28582897 TGAATGAACTATTATAT
1 TGAATGAACTATTATAT
*
28582914 TGCATGAACTATTAT
1 TGAATGAACTATTAT
28582929 TTCATCTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (17 bp):
TGAATGAACTATTATAT
Found at i:28582938 original size:17 final size:16
Alignment explanation
Indices: 28582883--28582947 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 16
28582873 TGTGGTATGA
* *
28582883 ATGAATTATTATATTGA
1 ATGAACTATTAT-TTGC
28582900 ATGAACTATTATATTGC
1 ATGAACTATTAT-TTGC
28582917 ATGAACTATTATTT-C
1 ATGAACTATTATTTGC
28582932 ATCTGAACTATTATTT
1 A--TGAACTATTATTT
28582948 TATGCGAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.05
16 2 0.05
17 40 0.91
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.46
Consensus pattern (16 bp):
ATGAACTATTATTTGC
Found at i:28587634 original size:30 final size:31
Alignment explanation
Indices: 28587566--28587637 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
28587556 AGGGTTAATT
*
28587566 TTAATTTTTTAATATTATTTAATATTTTTAC
1 TTAATTTTTTAATATTAATTAATATTTTTAC
* * *
28587597 TTCATTTTTTAA-GTTAATTAATATTTTT-T
1 TTAATTTTTTAATATTAATTAATATTTTTAC
28587626 TATAATTTTTTA
1 T-TAATTTTTTA
28587638 TAACAGTCAG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 1 0.03
30 23 0.66
31 11 0.31
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (31 bp):
TTAATTTTTTAATATTAATTAATATTTTTAC
Found at i:28589464 original size:33 final size:33
Alignment explanation
Indices: 28589414--28589600 Score: 137
Period size: 33 Copynumber: 5.6 Consensus size: 33
28589404 AAGACAAATT
* *
28589414 GCATTCT-TATGTAAGACCATAGTTGGGTTATG
1 GCATTCTGGATGTAAGACCATAGCTGGGTTATG
*
28589446 GCATTCT-GATGATAAGACCATAACTGGGTTATG
1 GCATTCTGGATG-TAAGACCATAGCTGGGTTATG
* * * * * * ***
28589479 ACACTATGGACGTAAGACCATGGTTGGACCATG
1 GCATTCTGGATGTAAGACCATAGCTGGGTTATG
* ** * *
28589512 GCAGTGTTTATATGTAAAACCATAGCTGGGCTATG
1 GCA-T-TCTGGATGTAAGACCATAGCTGGGTTATG
*
28589547 GCATTCT-GATGATAAGACCATAACTGGGTTATG
1 GCATTCTGGATG-TAAGACCATAGCTGGGTTATG
* *
28589580 GCATTATGGACGTAAGACCAT
1 GCATTCTGGATGTAAGACCAT
28589601 GGTTGGACCA
Statistics
Matches: 118, Mismatches: 31, Indels: 11
0.74 0.19 0.07
Matches are distributed among these distances:
32 13 0.11
33 75 0.64
34 7 0.06
35 23 0.19
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (33 bp):
GCATTCTGGATGTAAGACCATAGCTGGGTTATG
Found at i:28589596 original size:101 final size:101
Alignment explanation
Indices: 28589421--28589650 Score: 379
Period size: 101 Copynumber: 2.3 Consensus size: 101
28589411 ATTGCATTCT
* *
28589421 TATGTAAGACCATAGTTGGGTTATGGCATTCTGATGATAAGACCATAACTGGGTTATGACACTAT
1 TATGTAAAACCATAGTTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGACACTAT
* *
28589486 GGACGTAAGACCATGGTTGGACCATGGCAGTGTTTA
66 GGACGTAAGACCATGGTTGGACCATGACAATGTTTA
* * *
28589522 TATGTAAAACCATAGCTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCATTAT
1 TATGTAAAACCATAGTTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGACACTAT
28589587 GGACGTAAGACCATGGTTGGACCATGACAATGTTTA
66 GGACGTAAGACCATGGTTGGACCATGACAATGTTTA
* *
28589623 TATGTAAAGCCATAGTTGGACTATGGCA
1 TATGTAAAACCATAGTTGGGCTATGGCA
28589651 CAAAAGAAAC
Statistics
Matches: 119, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
101 119 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (101 bp):
TATGTAAAACCATAGTTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGACACTAT
GGACGTAAGACCATGGTTGGACCATGACAATGTTTA
Found at i:28592639 original size:59 final size:59
Alignment explanation
Indices: 28592547--28592728 Score: 233
Period size: 59 Copynumber: 3.1 Consensus size: 59
28592537 ATGCATTGAT
* * *
28592547 TTTTTAATATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTG
1 TTTTAAATATATTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTA
* * *
28592606 TTTTAAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGACGTTC
1 TTTTAAATATATTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTA
* *** * *
28592665 TTTTGAATA-AGACAGTACAAATTATTTTT-TATTGTTTCATTTAATAAATTAGGAGTTA
1 TTTTAAATATA-TTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTA
28592723 TTTTAA
1 TTTTAA
28592729 TTTGGACATG
Statistics
Matches: 107, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
58 30 0.28
59 77 0.72
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (59 bp):
TTTTAAATATATTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTA
Found at i:28594834 original size:46 final size:46
Alignment explanation
Indices: 28594767--28594858 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
28594757 GATAGATCAA
* * *
28594767 CATTATGCATATAGGCTGGAGGCGAGTACGCCGTGAATCGTGAATT
1 CATTATGCATATAAGCTGGAGGCGAGTACACCATGAATCGTGAATT
28594813 CATTATGCATATAAGCTGGAGGCGAGTACACCATGAATCGTGAATT
1 CATTATGCATATAAGCTGGAGGCGAGTACACCATGAATCGTGAATT
28594859 TTCTTCTTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.26
Consensus pattern (46 bp):
CATTATGCATATAAGCTGGAGGCGAGTACACCATGAATCGTGAATT
Done.