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 64 of 310
Found at i:20415831 original size:37 final size:37
Alignment explanation
Indices: 20415742--20415858 Score: 164
Period size: 37 Copynumber: 3.1 Consensus size: 37
20415732 GTATCGTGAT
* *
20415742 ATATACTTGAATGTTAAGTGATTATATGAGTATTGTG
1 ATATGCTTGAATGTTATGTGATTATATGAGTATTGTG
*
20415779 ATATATGCTTGAATGTTATGTGATTGTATGAGTATTGTG
1 --ATATGCTTGAATGTTATGTGATTATATGAGTATTGTG
*
20415818 ATATGCTTGAATGTTATGTGATTATAT-ATGTAATGTG
1 ATATGCTTGAATGTTATGTGATTATATGA-GTATTGTG
20415855 ATAT
1 ATAT
20415859 ATGCTTAAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
36 1 0.01
37 37 0.51
39 34 0.47
ACGTcount: A:0.30, C:0.03, G:0.22, T:0.45
Consensus pattern (37 bp):
ATATGCTTGAATGTTATGTGATTATATGAGTATTGTG
Found at i:20419679 original size:50 final size:51
Alignment explanation
Indices: 20419616--20419749 Score: 158
Period size: 50 Copynumber: 2.8 Consensus size: 51
20419606 GAGGCCGACA
* * *
20419616 CCATGTCCTAGACATGGTCTTACACTAGCTCTCACATATCCGT-GCCGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCACACATATCCATAGCCGATG
* *
20419666 CCATGTCCCAGACATGGTCTT--A-TA-CTGACACATCT-CATAGCCGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCACACATATCCATAGCCGATG
*
20419712 -CATGTCCCAGACAT-GTCTTACACTAGCACACACATATC
1 CCATGTCCCAGACATGGTCTTACACTAGCTCACACATATC
20419750 GCCCAAATGT
Statistics
Matches: 70, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
44 5 0.07
45 16 0.23
46 16 0.23
47 4 0.06
48 9 0.13
50 20 0.29
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (51 bp):
CCATGTCCCAGACATGGTCTTACACTAGCTCACACATATCCATAGCCGATG
Found at i:20429255 original size:40 final size:40
Alignment explanation
Indices: 20429204--20429560 Score: 597
Period size: 40 Copynumber: 8.9 Consensus size: 40
20429194 ATAACCGCAA
* * * *
20429204 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
20429244 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
20429284 GCATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
20429324 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
20429364 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
20429404 GCACAAATGCCTTCGGGTCTTAGCCCGGATTTATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
20429444 GCACAAATGCCTTCGGGTCTTAGCCCGGATTTATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
20429484 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
20429524 GCATAATTGCCTTCGGGTCTTAGCCCGGATATATCAA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAA
20429561 ATGCTCATGC
Statistics
Matches: 300, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 300 1.00
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.27
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:20430058 original size:180 final size:180
Alignment explanation
Indices: 20429754--20430113 Score: 702
Period size: 180 Copynumber: 2.0 Consensus size: 180
20429744 TGACTAATCA
20429754 GTTCAATATAATTCAAGTAGGGTCATTACTCGAAGACTTAACTCGGATACTTTGAATAGTTGTGG
1 GTTCAATATAATTCAAGTAGGGTCATTACTCGAAGACTTAACTCGGATACTTTGAATAGTTGTGG
*
20429819 ATAGACTACTCGATCACTTTTTCCTTTCCTTTATCAGATTTTGACCCTCTTGTCTCTTGAGCTTG
66 ATAGACTACTCGATCACTTTTTCCTTTCCTTTATCAGATTTTGACCCTCTTGGCTCTTGAGCTTG
20429884 ATTCAACAAGTAGATTTTATTAAATAACTTATCAATTTAGCGATTCGATT
131 ATTCAACAAGTAGATTTTATTAAATAACTTATCAATTTAGCGATTCGATT
*
20429934 GTTCAATATAATTCAAGTAGGGTCATTACTCGAAGACTTACCTCGGATACTTTGAATAGTTGTGG
1 GTTCAATATAATTCAAGTAGGGTCATTACTCGAAGACTTAACTCGGATACTTTGAATAGTTGTGG
20429999 ATAGACTACTCGATCACTTTTTCCTTTCCTTTATCAGATTTTGACCCTCTTGGCTCTTGAGCTTG
66 ATAGACTACTCGATCACTTTTTCCTTTCCTTTATCAGATTTTGACCCTCTTGGCTCTTGAGCTTG
20430064 ATTCAACAAGTAGATTTTATTAAATAACTTATCAATTTAGCGATTCGATT
131 ATTCAACAAGTAGATTTTATTAAATAACTTATCAATTTAGCGATTCGATT
20430114 TAATACATGT
Statistics
Matches: 178, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
180 178 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (180 bp):
GTTCAATATAATTCAAGTAGGGTCATTACTCGAAGACTTAACTCGGATACTTTGAATAGTTGTGG
ATAGACTACTCGATCACTTTTTCCTTTCCTTTATCAGATTTTGACCCTCTTGGCTCTTGAGCTTG
ATTCAACAAGTAGATTTTATTAAATAACTTATCAATTTAGCGATTCGATT
Found at i:20437328 original size:40 final size:40
Alignment explanation
Indices: 20437277--20437473 Score: 340
Period size: 40 Copynumber: 4.9 Consensus size: 40
20437267 ATAACCGCAA
* * * *
20437277 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
20437317 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
20437357 GCACAAATGCCTTCGGGTTTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
20437397 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
20437437 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAA
20437474 ATGCTCATGC
Statistics
Matches: 149, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 149 1.00
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:20450343 original size:20 final size:20
Alignment explanation
Indices: 20450306--20450344 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20450296 TTCTCATATT
* *
20450306 AATCTCGTTGAATTTCTCAG
1 AATCTCGATGAATATCTCAG
*
20450326 AATCTCGATGGATATCTCA
1 AATCTCGATGAATATCTCA
20450345 TTCACCGTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (20 bp):
AATCTCGATGAATATCTCAG
Found at i:20456959 original size:48 final size:48
Alignment explanation
Indices: 20456887--20457032 Score: 247
Period size: 48 Copynumber: 3.0 Consensus size: 48
20456877 CAAGATAAAT
20456887 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
20456935 ATATGTTTATGTGGTAAAGTCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* * *
20456983 ATATGTATATGTGGTAAAGCCGAAGGGCTAGTGTGAAATATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
20457031 AT
1 AT
20457033 GTGTGTATAT
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 91 1.00
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:20457223 original size:37 final size:37
Alignment explanation
Indices: 20457173--20457244 Score: 119
Period size: 37 Copynumber: 1.9 Consensus size: 37
20457163 GGAAATATAT
20457173 TCCGGGTAAGACCCGA-AGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATA-ACTACGTGTGGAGATTTTG
*
20457210 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATAACTACGTGTGGAGATTT
20457245 CATCTGAGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
37 32 0.97
38 1 0.03
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATAACTACGTGTGGAGATTTTG
Found at i:20458393 original size:18 final size:17
Alignment explanation
Indices: 20458374--20458481 Score: 63
Period size: 18 Copynumber: 5.9 Consensus size: 17
20458364 CATCAATAAT
*
20458374 AATCAGTTTTTCAGTAAT
1 AATCA-TTTTTCAGTAAC
*
20458392 AATCATCTATTCAGTAAC
1 AATCAT-TTTTCAGTAAC
*
20458410 AGTCATTTATTCAGTAAC
1 AATCATTT-TTCAGTAAC
* *
20458428 GATCAGTTTTTTTTAGTAAC
1 AATCA---TTTTTCAGTAAC
* *
20458448 AATAAATTATTCAGTAAC
1 AAT-CATTTTTCAGTAAC
* *
20458466 AGTCAGTTATTCAGTA
1 AATCA-TTTTTCAGTA
20458482 CCTTTTTTAC
Statistics
Matches: 70, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
17 3 0.04
18 53 0.76
20 10 0.14
21 4 0.06
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (17 bp):
AATCATTTTTCAGTAAC
Found at i:20458603 original size:6 final size:6
Alignment explanation
Indices: 20458592--20458632 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
20458582 TACACCATAT
*
20458592 CAGTAA CAGTAA TAGTAGA -AGTAA CAGTAA CAGTAA CAGTA
1 CAGTAA CAGTAA CAGTA-A CAGTAA CAGTAA CAGTAA CAGTA
20458633 GCGGTACACA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 1 0.03
6 30 0.94
7 1 0.03
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.20
Consensus pattern (6 bp):
CAGTAA
Found at i:20458722 original size:51 final size:53
Alignment explanation
Indices: 20458614--20458732 Score: 161
Period size: 51 Copynumber: 2.3 Consensus size: 53
20458604 TAGTAGAAGT
*
20458614 AACAGTAACAGTAACAGTAGCGGTACACAGAGTACCTCATCGAAACAAATCTAG
1 AACAGTAACAGTAACAGTAGAGGTA-ACAGAGTACCTCATCGAAACAAATCTAG
* * * * *
20458668 AACAGTAACAGTAACAGTA-AGGT-ACGGAGTACCTCTTCGGAACGAATCTGG
1 AACAGTAACAGTAACAGTAGAGGTAACAGAGTACCTCATCGAAACAAATCTAG
20458719 AACAGTAACAGTAA
1 AACAGTAACAGTAA
20458733 GGCAACACTT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
51 37 0.63
53 3 0.05
54 19 0.32
ACGTcount: A:0.41, C:0.20, G:0.21, T:0.18
Consensus pattern (53 bp):
AACAGTAACAGTAACAGTAGAGGTAACAGAGTACCTCATCGAAACAAATCTAG
Found at i:20459928 original size:5 final size:5
Alignment explanation
Indices: 20459918--20459950 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
20459908 ATGTTTTAAT
20459918 TATAA TATAA TATAA TATAA TATAA TATAA TAT
1 TATAA TATAA TATAA TATAA TATAA TATAA TAT
20459951 TATTCTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:20460056 original size:9 final size:9
Alignment explanation
Indices: 20460042--20460078 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
20460032 TACACTTGTC
20460042 TTTATTTAA
1 TTTATTTAA
20460051 TTTATTTAA
1 TTTATTTAA
*
20460060 -TTATTTAC
1 TTTATTTAA
20460068 TTTATTTAA
1 TTTATTTAA
20460077 TT
1 TT
20460079 AATATAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTATTTAA
Found at i:20460065 original size:17 final size:17
Alignment explanation
Indices: 20460043--20460079 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
20460033 ACACTTGTCT
20460043 TTATTTAATTTATTTAA
1 TTATTTAATTTATTTAA
*
20460060 TTATTTACTTTATTTAA
1 TTATTTAATTTATTTAA
20460077 TTA
1 TTA
20460080 ATATAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTAATTTATTTAA
Found at i:20460162 original size:20 final size:20
Alignment explanation
Indices: 20460139--20460179 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20460129 TTACAAATGT
*
20460139 ATGTATAATATTTATTACAC
1 ATGTATAATATTTATCACAC
* *
20460159 ATGTATTATTTTTATCACAC
1 ATGTATAATATTTATCACAC
20460179 A
1 A
20460180 CTTGGCATTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.46
Consensus pattern (20 bp):
ATGTATAATATTTATCACAC
Found at i:20465959 original size:16 final size:16
Alignment explanation
Indices: 20465938--20465971 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
20465928 GGAGTAGTAG
20465938 TTGTGTAAGGTGGTTC
1 TTGTGTAAGGTGGTTC
20465954 TTGTGTAAGGTGGTTC
1 TTGTGTAAGGTGGTTC
20465970 TT
1 TT
20465972 ATGATACGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.06, G:0.35, T:0.47
Consensus pattern (16 bp):
TTGTGTAAGGTGGTTC
Found at i:20467242 original size:21 final size:22
Alignment explanation
Indices: 20467218--20467266 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
20467208 ATTGTTGGAG
*
20467218 TATTGGCAACTTATC-GCAACT
1 TATTGGCAACTTATCTGCAAAT
* *
20467239 TATTGGCAGCTTGTCTGCAAAT
1 TATTGGCAACTTATCTGCAAAT
20467261 TATTGG
1 TATTGG
20467267 TAGTTCTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.37
Consensus pattern (22 bp):
TATTGGCAACTTATCTGCAAAT
Found at i:20471459 original size:20 final size:21
Alignment explanation
Indices: 20471434--20471473 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
20471424 CTCTTGAAAC
20471434 AGGGC-ACACGCCCGTGTGGA
1 AGGGCAACACGCCCGTGTGGA
*
20471454 AGGGCAACACGCTCGTGTGG
1 AGGGCAACACGCCCGTGTGG
20471474 TCATTATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.20, C:0.28, G:0.40, T:0.12
Consensus pattern (21 bp):
AGGGCAACACGCCCGTGTGGA
Found at i:20473180 original size:73 final size:71
Alignment explanation
Indices: 20473092--20473237 Score: 238
Period size: 73 Copynumber: 2.0 Consensus size: 71
20473082 TTAAAATAAG
*
20473092 CTATAATGACATTATTCACATATGTACTTATCTCGACACAAAATGATAGGAACGAGCAAAATCCT
1 CTATAATGACATTATTCACATATGTACTTACCTCGACACAAAATGATAGGAACGAGCAAAATCCT
*
20473157 TGTAAA
66 CGTAAA
* *
20473163 CTATAATGGCACATTATTCACATATGTACTTACCTCGACACAAAATGATGGGAACGAGCCAAATC
1 CTATAAT-G-ACATTATTCACATATGTACTTACCTCGACACAAAATGATAGGAACGAGCAAAATC
20473228 CTCGTAAA
64 CTCGTAAA
20473236 CT
1 CT
20473238 TTGTTCCTCC
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 7 0.10
72 1 0.01
73 61 0.88
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (71 bp):
CTATAATGACATTATTCACATATGTACTTACCTCGACACAAAATGATAGGAACGAGCAAAATCCT
CGTAAA
Found at i:20487228 original size:44 final size:43
Alignment explanation
Indices: 20487165--20487321 Score: 146
Period size: 44 Copynumber: 3.7 Consensus size: 43
20487155 CTGTTTTGCG
20487165 TGTAAGACCACGTCTGGGACGTTGGCATCGACT-TCTATTTTACA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGA-TAT-TATTTTACA
* * * * *
20487209 TGTAAGACCATGTCTGGGACATTAGCATCGTATATGATTTT--G
1 TGTAAGACCACGTCTGGGACGTTGGCATCG-ATATTATTTTACA
* *
20487251 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATGTT-TGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTAT-TTTACA
*
20487294 TGTAAGACCACGTCTAGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
20487322 TATATTTACT
Statistics
Matches: 91, Mismatches: 13, Indels: 19
0.74 0.11 0.15
Matches are distributed among these distances:
40 1 0.01
41 5 0.05
42 26 0.29
43 23 0.25
44 34 0.37
45 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATTATTTTACA
Found at i:20494822 original size:44 final size:43
Alignment explanation
Indices: 20494758--20494931 Score: 176
Period size: 44 Copynumber: 4.0 Consensus size: 43
20494748 CATAGGATTT
**
20494758 TCGATATATGTTTTGTGTGTAAGACCACGTCTGGGACATTGGCA
1 TCGATATATG-TTTACGTGTAAGACCACGTCTGGGACATTGGCA
* *
20494802 TCGACT-TCTGTTTTACGTGTAAGACCATGTCTGGGACATTGGCA
1 TCGA-TATATG-TTTACGTGTAAGACCACGTCTGGGACATTGGCA
*
20494846 TCG-TATATGATTT-CGTGTAAGACC-CTGTCTGGGACAGTGGCA
1 TCGATATATG-TTTACGTGTAAGACCAC-GTCTGGGACATTGGCA
* * * * * *
20494888 TCGATGTTTGATTACATGTAAGACCACGTCTAGGACGTTGGCA
1 TCGATATATGTTTACGTGTAAGACCACGTCTGGGACATTGGCA
20494931 T
1 T
20494932 TGTATTTACT
Statistics
Matches: 109, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
42 32 0.29
43 34 0.31
44 42 0.39
45 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (43 bp):
TCGATATATGTTTACGTGTAAGACCACGTCTGGGACATTGGCA
Found at i:20494876 original size:42 final size:42
Alignment explanation
Indices: 20494774--20494936 Score: 168
Period size: 43 Copynumber: 3.8 Consensus size: 42
20494764 TATGTTTTGT
* *
20494774 GTGTAAGACCACGTCTGGGACATTGGCATCG-ACTTCTGTTTTAC
1 GTGTAAGACCACGTCTGGGACATTGGCATCGTA--TATGATTT-C
*
20494818 GTGTAAGACCATGTCTGGGACATTGGCATCGTATATGATTTC
1 GTGTAAGACCACGTCTGGGACATTGGCATCGTATATGATTTC
* * * *
20494860 GTGTAAGACC-CTGTCTGGGACAGTGGCATCGATGTTTGATTAC
1 GTGTAAGACCAC-GTCTGGGACATTGGCATCG-TATATGATTTC
* * * *
20494903 ATGTAAGACCACGTCTAGGACGTTGGCATTGTAT
1 GTGTAAGACCACGTCTGGGACATTGGCATCGTAT
20494937 TTACTTTTCA
Statistics
Matches: 101, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
42 31 0.31
43 38 0.38
44 31 0.31
45 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (42 bp):
GTGTAAGACCACGTCTGGGACATTGGCATCGTATATGATTTC
Found at i:20494877 original size:86 final size:85
Alignment explanation
Indices: 20494774--20494936 Score: 213
Period size: 85 Copynumber: 1.9 Consensus size: 85
20494764 TATGTTTTGT
* * * * *
20494774 GTGTAAGACCACGTCTGGGACATTGGCATCGACT-TCTGTTTTACGTGTAAGACCATGTCTGGGA
1 GTGTAAGACCACGTCTGGGACAGTGGCATCGA-TGTCTG-ATTACATGTAAGACCACGTCTAGGA
20494838 CATTGGCATCGTATATGATTTC
64 CATTGGCATCGTATATGATTTC
*
20494860 GTGTAAGACC-CTGTCTGGGACAGTGGCATCGATGTTTGATTACATGTAAGACCACGTCTAGGAC
1 GTGTAAGACCAC-GTCTGGGACAGTGGCATCGATGTCTGATTACATGTAAGACCACGTCTAGGAC
* *
20494924 GTTGGCATTGTAT
65 ATTGGCATCGTAT
20494937 TTACTTTTCA
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
85 35 0.52
86 32 0.48
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (85 bp):
GTGTAAGACCACGTCTGGGACAGTGGCATCGATGTCTGATTACATGTAAGACCACGTCTAGGACA
TTGGCATCGTATATGATTTC
Found at i:20495932 original size:37 final size:37
Alignment explanation
Indices: 20495872--20495943 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 37
20495862 AGCTCAGATG
20495872 AAATCTCCACACGAAGTTATCGGGACTTACCCGGACA
1 AAATCTCCACACGAAGTTATCGGGACTTACCCGGACA
* *
20495909 AAATCTCCACACGTAGTCT-TCGGGTCTTACCCGGA
1 AAATCTCCACACGAAGT-TATCGGGACTTACCCGGA
20495944 ATATATTTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 31 0.97
38 1 0.03
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (37 bp):
AAATCTCCACACGAAGTTATCGGGACTTACCCGGACA
Found at i:20496142 original size:48 final size:48
Alignment explanation
Indices: 20496084--20496181 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
20496074 ATATACACAC
* *
20496084 ATCTCCTACATATTTCACACTAGCCCTTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
20496132 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
20496180 AT
1 AT
20496182 ATTTATCTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.35
Consensus pattern (48 bp):
ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:20506965 original size:12 final size:11
Alignment explanation
Indices: 20506943--20506970 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
20506933 TAAGTTAGAA
20506943 TTTTCTTTTTT
1 TTTTCTTTTTT
20506954 TTTTCTTTTTT
1 TTTTCTTTTTT
20506965 TTTTCT
1 TTTTCT
20506971 CATTCTCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:20508184 original size:18 final size:19
Alignment explanation
Indices: 20508144--20508185 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
20508134 TTTCTAAAGA
* *
20508144 AATTTTATATCATTTTGAG
1 AATTTTAAATCATTTTAAG
20508163 -ATTTTAAATC-TTTTAAG
1 AATTTTAAATCATTTTAAG
20508180 AATTTT
1 AATTTT
20508186 TCATATAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (19 bp):
AATTTTAAATCATTTTAAG
Found at i:20508273 original size:18 final size:18
Alignment explanation
Indices: 20508250--20508284 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20508240 TATTTCGTTT
*
20508250 TAAATCATTTTGGAATTA
1 TAAATCATTTAGGAATTA
*
20508268 TAAATCCTTTAGGAATT
1 TAAATCATTTAGGAATT
20508285 TTTGTAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (18 bp):
TAAATCATTTAGGAATTA
Found at i:20509534 original size:13 final size:13
Alignment explanation
Indices: 20509515--20509549 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
20509505 GAATTTAGAT
20509515 AAAAATAAATAACG
1 AAAAATAAATAA-G
20509529 -AAAATAAATAAG
1 AAAAATAAATAAG
20509541 AAAAATAAA
1 AAAAATAAA
20509550 CAAATGATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 1 0.05
13 19 0.95
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (13 bp):
AAAAATAAATAAG
Found at i:20517110 original size:27 final size:27
Alignment explanation
Indices: 20517076--20517133 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
20517066 AAGCATTACT
20517076 AATGCTTAGTAAGTTCATAAGTATATA
1 AATGCTTAGTAAGTTCATAAGTATATA
20517103 AATGCTTAGTAAGTTCATAAGTATATA
1 AATGCTTAGTAAGTTCATAAGTATATA
20517130 AATG
1 AATG
20517134 TGTATAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (27 bp):
AATGCTTAGTAAGTTCATAAGTATATA
Found at i:20518074 original size:236 final size:236
Alignment explanation
Indices: 20517477--20518098 Score: 632
Period size: 237 Copynumber: 2.6 Consensus size: 236
20517467 CTTGTCCAGA
* * ** * * *
20517477 CTAAACCTTTTATCAACACATCAAATAGCTTGGATAAAGCTGTAAATATACATGTCAAGTTACCT
1 CTAAACCTTTTATCTACACATCAAATAGTTTGGCCAAAGCTATAAATACACATGTCAAGTTACCC
* * * * *
20517542 GTCTAGGCTAAACCTTTAAAACC-ACATCAGGTTACTCGTTCGAGCAAAACCTGTGTCACATGTA
66 GTTTGGGCTAAACCTTT-AAACCAACATCAGGTTACTTGTCCGAGCTAAACCTGTGTCACATGTA
*
20517606 TCTTCAAGTCTGCAACAAATGCTGAATCTTACTAATCATCAGTAATTAACCATATCTAATGCTCG
130 TCTTCAAGTCTGCAACAAATGCTGAATCTTACTAATCATCAGTAATTAACCACATCTAATGCTCG
** * ** * *
20517671 TCTGAGCTGAACAGATCCATTTGTGACATGTTACCTATTCGGG
195 TCCAAGCTAAACAGAT-CATTCATGACAGGTTACCTATTCAGG
* * *
20517714 CTAAACCTTTTATCTACACATCAAATAGTTTGGCCAAAGCTATAAATATACATGTCAGGTTA-AC
1 CTAAACCTTTTATCTACACATCAAATAGTTTGGCCAAAGCTATAAATACACATGTCAAGTTACCC
* * * * * *
20517778 TTTCTGAGTTAAACCTTTAAA-AAGATATCAGGTTACTTGTCTGAGCTAAACCTGTGTCACATGT
66 GTT-TGGGCTAAACCTTTAAACCA-ACATCAGGTTACTTGTCCGAGCTAAACCTGTGTCACATGT
* * * ** * * ** *
20517842 ATCTTCGAGTTTGCAACAAGTGCTGAATCTTGGTAATCATC-GATAATTAACGACATTTTTTTCT
129 ATCTTCAAGTCTGCAACAAATGCTGAATCTTACTAATCATCAG-TAATTAACCACATCTAATGCT
* *
20517906 CGTCCAAGCTAAACATAT-ATTCATGCCAGGTTACTCGTA-T-AGG
193 CGTCCAAGCTAAACAGATCATTCATGACAGGTTAC-C-TATTCAGG
* * * * *
20517949 CTAAA-CTTTTATATTGACACATCAAATAGTTTGG-CGAGGACTATATATACACATGTAAAGTTA
1 CTAAACCTTTTAT-CT-ACACATCAAATAGTTTGGCCAAAG-CTATAAATACACATGTCAAGTTA
* *
20518012 CCCGTTTGGGCTAAACCTTTAAACCAACATCAAGTTACTTGTCCGAGCTAAACCTATGTCACATG
63 CCCGTTTGGGCTAAACCTTTAAACCAACATCAGGTTACTTGTCCGAGCTAAACCTGTGTCACATG
** *
20518077 TATCTTTTAGTCAGCAACAAAT
128 TATCTTCAAGTCTGCAACAAAT
20518099 TTTAGATCTC
Statistics
Matches: 314, Mismatches: 60, Indels: 23
0.79 0.15 0.06
Matches are distributed among these distances:
234 7 0.02
235 23 0.07
236 111 0.35
237 173 0.55
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (236 bp):
CTAAACCTTTTATCTACACATCAAATAGTTTGGCCAAAGCTATAAATACACATGTCAAGTTACCC
GTTTGGGCTAAACCTTTAAACCAACATCAGGTTACTTGTCCGAGCTAAACCTGTGTCACATGTAT
CTTCAAGTCTGCAACAAATGCTGAATCTTACTAATCATCAGTAATTAACCACATCTAATGCTCGT
CCAAGCTAAACAGATCATTCATGACAGGTTACCTATTCAGG
Found at i:20519562 original size:22 final size:22
Alignment explanation
Indices: 20519519--20519559 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
20519509 CTTTAAACAA
*
20519519 AAATAATAATATCTATATAATT
1 AAATAATAATATATATATAATT
*
20519541 AAATAATATTATA-ATATAA
1 AAATAATAATATATATATAA
20519560 ATTTATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
AAATAATAATATATATATAATT
Found at i:20520206 original size:145 final size:145
Alignment explanation
Indices: 20519947--20520345 Score: 389
Period size: 145 Copynumber: 2.7 Consensus size: 145
20519937 TGAATGTATA
** * * * * *
20519947 ATGATATTATAATGTTTATTCTTT-TATTAATGAT-T-TCAAC-ATAAACCTCAAATATGTAGCT
1 ATGATATTATAATGTACATT-TTTATATTAATGATATGT-AACTTTAAACATTAAACATGTAACT
* * * *
20520008 AATTTTATGGTATATTATAATATATATAATCAACATTATAAAATTAAGGTAGATTATAAATGATA
64 AATTTTATGGTAGATTATAATA-ATATAATTAGCATTATATAATT-AGGTAGATTATAAATGATA
*
20520073 TATTACCCCATATACAACT
127 TATAACCCCATATACAACT
** * * * ** * *
20520092 ATTTTTTTATAATGTACGTTTTTATGTTTTTGATTTGTAAAC-TTAAAC-TCTAAGCATGTAACT
1 ATGATATTATAATGTACATTTTTATATTAATGATATGT-AACTTTAAACAT-TAAACATGTAACT
* * * *
20520155 AAATTTATGGTAGATTATAATAATATAATTAGCGTTATATAATTAGGTAGATTATTAATGATATC
64 AATTTTATGGTAGATTATAATAATATAATTAGCATTATATAATTAGGTAGATTATAAATGATATA
* *
20520220 TAACCCTATATACAATT
129 TAACCCCATATACAACT
* **
20520237 ATGATATTATAATGTATATTTTTATATTAATGATATGTAACTTTAAACATTAAATGTGTAACTAA
1 ATGATATTATAATGTACATTTTTATATTAATGATATGTAACTTTAAACATTAAACATGTAACTAA
* *
20520302 TTTTATGGTAGATCATAAT-ATATAAATTTGACATTATATAATTA
66 TTTTATGGTAGATTATAATAATAT-AATTAG-CATTATATAATTA
20520346 TGGTTAAGTA
Statistics
Matches: 204, Mismatches: 42, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
144 10 0.05
145 123 0.60
146 33 0.16
147 38 0.19
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.43
Consensus pattern (145 bp):
ATGATATTATAATGTACATTTTTATATTAATGATATGTAACTTTAAACATTAAACATGTAACTAA
TTTTATGGTAGATTATAATAATATAATTAGCATTATATAATTAGGTAGATTATAAATGATATATA
ACCCCATATACAACT
Found at i:20524097 original size:62 final size:63
Alignment explanation
Indices: 20523997--20524143 Score: 143
Period size: 63 Copynumber: 2.3 Consensus size: 63
20523987 TGCCACATGG
* * * ** * * * **
20523997 CCTGGGCACATGCCCATGTGCCTTGGCCGTGTGGTTTTTA-AGCACAAACAGTGAGTTACACGG
1 CCTGGCCACACGCCCGTGT-CCTTGGATGTGTGATTTTTATACCACAAACAGTGACTTACACAA
* ** * *
20524060 CCTGGGCACACGTTCGTGTCCTTGGATGTGTGATTTTTATACCTCCAACAGTGACTTACACAA
1 CCTGGCCACACGCCCGTGTCCTTGGATGTGTGATTTTTATACCACAAACAGTGACTTACACAA
20524123 CCTGGCCACACGCCCGTGTCC
1 CCTGGCCACACGCCCGTGTCC
20524144 CTGGCCGTGT
Statistics
Matches: 67, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
62 17 0.25
63 50 0.75
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (63 bp):
CCTGGCCACACGCCCGTGTCCTTGGATGTGTGATTTTTATACCACAAACAGTGACTTACACAA
Found at i:20532914 original size:122 final size:122
Alignment explanation
Indices: 20532689--20532914 Score: 380
Period size: 122 Copynumber: 1.9 Consensus size: 122
20532679 CACGACTGAG
20532689 ACACACGCCCGTGTCTCTACCCATGTAGATAAAAATAGGCTATTTGCAAAGCCAATTTGCCACCC
1 ACACACGCCCGTGTCTCTACCCATGTAGATAAAAATAGGCTATTTGCAAAGCCAATTTGCCACCC
*
20532754 TTTCCTCATGCACACCTAGCAACCAAAATGATATCATTTGTAGCGTGACCGTGTGTC
66 TTTCCTCATGCACACCTAGCAACCAAAATGATACCATTTGTAGCGTGACCGTGTGTC
* * ** * *
20532811 ACACACGCCCGTGTCTTTGCCTGTGTGGATAAAAATAGGCTATTTGTAAAGCCAATTTGCCACCC
1 ACACACGCCCGTGTCTCTACCCATGTAGATAAAAATAGGCTATTTGCAAAGCCAATTTGCCACCC
*
20532876 TTTCCTCATGCACACCTAGCAACCAAAATGGTACCATTT
66 TTTCCTCATGCACACCTAGCAACCAAAATGATACCATTT
20532915 CAATACATTC
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
122 96 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.27
Consensus pattern (122 bp):
ACACACGCCCGTGTCTCTACCCATGTAGATAAAAATAGGCTATTTGCAAAGCCAATTTGCCACCC
TTTCCTCATGCACACCTAGCAACCAAAATGATACCATTTGTAGCGTGACCGTGTGTC
Found at i:20545250 original size:18 final size:18
Alignment explanation
Indices: 20545204--20545250 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
20545194 TGAGAATTAT
*
20545204 TATATTTAAATTTAACTA
1 TATATTTAATTTTAACTA
*
20545222 TAGATTATAATTTTAA-TA
1 TATATT-TAATTTTAACTA
20545240 GTATATTTAAT
1 -TATATTTAAT
20545251 CATACATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (18 bp):
TATATTTAATTTTAACTA
Found at i:20545673 original size:11 final size:11
Alignment explanation
Indices: 20545654--20545695 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
20545644 CTACAAAGTT
*
20545654 CTTTTAAAAAA
1 CTTTAAAAAAA
20545665 CTTTAAAAAATA
1 CTTTAAAAAA-A
20545677 C--TAAAAAAA
1 CTTTAAAAAAA
20545686 CTTTAAAAAA
1 CTTTAAAAAA
20545696 TACTAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
9 2 0.07
10 7 0.26
11 16 0.59
12 2 0.07
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.29
Consensus pattern (11 bp):
CTTTAAAAAAA
Found at i:20545685 original size:21 final size:21
Alignment explanation
Indices: 20545659--20545705 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
20545649 AAGTTCTTTT
20545659 AAAAAACTTTAAAAAATACTA
1 AAAAAACTTTAAAAAATACTA
20545680 AAAAAACTTTAAAAAATACTA
1 AAAAAACTTTAAAAAATACTA
20545701 AAAAA
1 AAAAA
20545706 TCTATATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (21 bp):
AAAAAACTTTAAAAAATACTA
Found at i:20545702 original size:10 final size:10
Alignment explanation
Indices: 20545668--20545706 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
20545658 TAAAAAACTT
20545668 TAAAAAATAC
1 TAAAAAATAC
20545678 TAAAAAA-AC
1 TAAAAAATAC
20545687 TTTAAAAAATAC
1 --TAAAAAATAC
20545699 TAAAAAAT
1 TAAAAAAT
20545707 CTATATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 2 0.08
10 15 0.58
11 7 0.27
12 2 0.08
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (10 bp):
TAAAAAATAC
Found at i:20550764 original size:23 final size:23
Alignment explanation
Indices: 20550738--20550798 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
20550728 AAAACCTTCA
20550738 AAGTATCAAATTGAAAAAAATCT
1 AAGTATCAAATTGAAAAAAATCT
20550761 AAGTATCAAATTGAAAAAAATCT
1 AAGTATCAAATTGAAAAAAATCT
*
20550784 AAGTATCAAAGTGAA
1 AAGTATCAAATTGAA
20550799 CATTGAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.56, C:0.08, G:0.11, T:0.25
Consensus pattern (23 bp):
AAGTATCAAATTGAAAAAAATCT
Found at i:20559723 original size:422 final size:422
Alignment explanation
Indices: 20558909--20559988 Score: 2133
Period size: 422 Copynumber: 2.6 Consensus size: 422
20558899 CAGTGGTTTC
*
20558909 AGGGTGGCCGGCCATAGTAGTTTAGGAGACAAAAATTTTAGTTTAGGTGAATTAGGTGAACTTAT
1 AGGGTGGCCGGCCATAGTAGTTTA--AGAGAAAAATTTTAGTTTAGGTGAATTAGGTGAACTTAT
20558974 TTGACTTGAAATATTATAATAAAGAAAAGATGATATCATACTTCATCTTCCCCATTTTTTTCAAT
64 TTGACTTGAAATATTATAATAAAGAAAAGATGATATCATACTTCATCTTCCCCATTTTTTTCAAT
20559039 CAAAATTTACTGCAAAGAGAAGGGTTTTTGAAGCTTTAAAATTCAGCAACTCATTACTCACACAA
129 CAAAATTTACTGCAAAGAGAAGGGTTTTTGAAGCTTTAAAATTCAGCAACTCATTACTCACACAA
20559104 GTAAGTGATTTTCTTAAAAAATTTTGTACTTTTGGAGTCCCTGATGTTATAGCATTATTATATAG
194 GTAAGTGATTTTCTTAAAAAATTTTGTACTTTTGGAGTCCCTGATGTTATAGCATTATTATATAG
20559169 ATACATGAAAATTTTGATGAATTAATTTTATCGATTGTGAGCCCAATTGTGAAAAAGGACTAAAT
259 ATACATGAAAATTTTGATGAATTAATTTTATCGATTGTGAGCCCAATTGTGAAAAAGGACTAAAT
20559234 CGCATAAAGTGCAAAAGTCCAAATTAGATAGAAAAGAGTGTTAAATTGTCATGGACTAATTTTGG
324 CGCATAAAGTGCAAAAGTCCAAATTAGATAGAAAAGAGTGTTAAATTGTCATGGACTAATTTTGG
20559299 AGGCTTTTAAAGGGAAATTAAACCCTTAAAAACA
389 AGGCTTTTAAAGGGAAATTAAACCCTTAAAAACA
20559333 AGGGTGGCCGGCCATAGTAGTTTAAGAGAAAAATTTTAGTTTAGGTGAATTAGGTGAACTTATTT
1 AGGGTGGCCGGCCATAGTAGTTTAAGAGAAAAATTTTAGTTTAGGTGAATTAGGTGAACTTATTT
20559398 GACTTGAAATATTATAATAAAGAAAAGATGATATCATACTTCATCTTCCCCATTTTTTTCAATCA
66 GACTTGAAATATTATAATAAAGAAAAGATGATATCATACTTCATCTTCCCCATTTTTTTCAATCA
20559463 AAATTTACTGCAAAGAGAAGGGTTTTTGAAGCTTTAAAATTCAGCAACTCATTACTCACACAAGT
131 AAATTTACTGCAAAGAGAAGGGTTTTTGAAGCTTTAAAATTCAGCAACTCATTACTCACACAAGT
20559528 AAGTGATTTTCTTAAAAAATTTTGTACTTTTGGAGTCCCTGATGTTATAGCATTATTATATAGAT
196 AAGTGATTTTCTTAAAAAATTTTGTACTTTTGGAGTCCCTGATGTTATAGCATTATTATATAGAT
20559593 ACATGAAAATTTTGATGAATTAATTTTATCGATTGTGAGCCCAATTGTGAAAAAGGACTAAATCG
261 ACATGAAAATTTTGATGAATTAATTTTATCGATTGTGAGCCCAATTGTGAAAAAGGACTAAATCG
20559658 CATAAAGTGCAAAAGTCCAAATTAGATAGAAAAGAGTGTTAAATTGTCATGGACTAATTTTGGAG
326 CATAAAGTGCAAAAGTCCAAATTAGATAGAAAAGAGTGTTAAATTGTCATGGACTAATTTTGGAG
20559723 GCTTTTAAAGGGAAATTAAACCCTTAAAAACA
391 GCTTTTAAAGGGAAATTAAACCCTTAAAAACA
20559755 AGGGTGGCCGGCCATAGTAGTTTAAGAGAAAAATTTTAGTTTAGGTGAATTAGGTGAACTTATTT
1 AGGGTGGCCGGCCATAGTAGTTTAAGAGAAAAATTTTAGTTTAGGTGAATTAGGTGAACTTATTT
20559820 GACTTGAAATATTATAATAAAGAAAAGATGATATCATACTTCATCTTCCCCATTTTTTTCAATCA
66 GACTTGAAATATTATAATAAAGAAAAGATGATATCATACTTCATCTTCCCCATTTTTTTCAATCA
20559885 AAATTTACTGCAAAGAGAAGGGTTTTTGAAGCTTTAAAATTCAGCAACTCATTACTCACACAAGT
131 AAATTTACTGCAAAGAGAAGGGTTTTTGAAGCTTTAAAATTCAGCAACTCATTACTCACACAAGT
20559950 AAGTGATTTTCTTAAAAAATTTTGTACTTTTGGAGTCCC
196 AAGTGATTTTCTTAAAAAATTTTGTACTTTTGGAGTCCC
20559989 CTTTGCATGG
Statistics
Matches: 655, Mismatches: 1, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
422 631 0.96
424 24 0.04
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (422 bp):
AGGGTGGCCGGCCATAGTAGTTTAAGAGAAAAATTTTAGTTTAGGTGAATTAGGTGAACTTATTT
GACTTGAAATATTATAATAAAGAAAAGATGATATCATACTTCATCTTCCCCATTTTTTTCAATCA
AAATTTACTGCAAAGAGAAGGGTTTTTGAAGCTTTAAAATTCAGCAACTCATTACTCACACAAGT
AAGTGATTTTCTTAAAAAATTTTGTACTTTTGGAGTCCCTGATGTTATAGCATTATTATATAGAT
ACATGAAAATTTTGATGAATTAATTTTATCGATTGTGAGCCCAATTGTGAAAAAGGACTAAATCG
CATAAAGTGCAAAAGTCCAAATTAGATAGAAAAGAGTGTTAAATTGTCATGGACTAATTTTGGAG
GCTTTTAAAGGGAAATTAAACCCTTAAAAACA
Found at i:20561919 original size:28 final size:28
Alignment explanation
Indices: 20561879--20561933 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
20561869 GACACAGGCG
20561879 TGTCCAGGCCGTGTGAGGAATACGGGCA
1 TGTCCAGGCCGTGTGAGGAATACGGGCA
20561907 TGTCCAGGCCGTGTGAGGAATACGGGC
1 TGTCCAGGCCGTGTGAGGAATACGGGC
20561934 TAAGGACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.20, C:0.22, G:0.40, T:0.18
Consensus pattern (28 bp):
TGTCCAGGCCGTGTGAGGAATACGGGCA
Found at i:20571047 original size:55 final size:55
Alignment explanation
Indices: 20570956--20571083 Score: 148
Period size: 55 Copynumber: 2.3 Consensus size: 55
20570946 GGTCGTGGGT
* ** *
20570956 AAACCTGCCAAAACAACACGGGCGTGCGACACGCCCGTGCCTAGAAACCGTGGCC
1 AAACCTGTCAAATTAACACGGGCATGCGACACGCCCGTGCCTAGAAACCGTGGCC
* * * * * *
20571011 AAACCTGTCAAATTAACACGGTCATGCGCCATGCCCGTGTCTAGAACCCGTGGTC
1 AAACCTGTCAAATTAACACGGGCATGCGACACGCCCGTGCCTAGAAACCGTGGCC
* *
20571066 GAACCTGTCAGATTAACA
1 AAACCTGTCAAATTAACA
20571084 TGGGAGGGGG
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 61 1.00
ACGTcount: A:0.29, C:0.32, G:0.23, T:0.16
Consensus pattern (55 bp):
AAACCTGTCAAATTAACACGGGCATGCGACACGCCCGTGCCTAGAAACCGTGGCC
Found at i:20578065 original size:42 final size:42
Alignment explanation
Indices: 20578018--20578103 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
20578008 TTAAGCGGAG
20578018 TTGATCGAACGCCTAGAAATAGGGTTACGAGATTTTACCGAA
1 TTGATCGAACGCCTAGAAATAGGGTTACGAGATTTTACCGAA
20578060 TTGATCGAACGCCTAGAAATAGGGTTACGAGATTTTACCGAA
1 TTGATCGAACGCCTAGAAATAGGGTTACGAGATTTTACCGAA
20578102 TT
1 TT
20578104 AGGGTGAAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (42 bp):
TTGATCGAACGCCTAGAAATAGGGTTACGAGATTTTACCGAA
Found at i:20583696 original size:31 final size:31
Alignment explanation
Indices: 20583658--20583716 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
20583648 GACAATATGC
20583658 AAGCCATAATGCAGCAGTTGTGCAAACATCA
1 AAGCCATAATGCAGCAGTTGTGCAAACATCA
*
20583689 AAGCCATAATGCAGCAGTTGTGCCAACA
1 AAGCCATAATGCAGCAGTTGTGCAAACA
20583717 CTTCCACATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (31 bp):
AAGCCATAATGCAGCAGTTGTGCAAACATCA
Found at i:20583803 original size:17 final size:17
Alignment explanation
Indices: 20583781--20583825 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
20583771 TGACTCCTCC
20583781 TATTTATTTTTTATTAT
1 TATTTATTTTTTATTAT
*
20583798 TATTTATTCTTTTTTTAT
1 TATTTATT-TTTTATTAT
20583816 T-TTTATTTTT
1 TATTTATTTTT
20583826 ATTTTTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 3 0.12
17 14 0.54
18 9 0.35
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (17 bp):
TATTTATTTTTTATTAT
Found at i:20583811 original size:21 final size:20
Alignment explanation
Indices: 20583783--20583831 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
20583773 ACTCCTCCTA
20583783 TTTA-TTTTTTATTATTATT
1 TTTATTTTTTTATTATTATT
* *
20583802 TATTCTTTTTTTATTTTTATT
1 T-TTATTTTTTTATTATTATT
20583823 TTTATTTTT
1 TTTATTTTT
20583832 CTTTTAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 9 0.36
21 15 0.60
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTATTTTTTTATTATTATT
Found at i:20583818 original size:6 final size:6
Alignment explanation
Indices: 20583794--20583847 Score: 56
Period size: 6 Copynumber: 9.0 Consensus size: 6
20583784 TTATTTTTTA
* * *
20583794 TTATTAT TTATTC TT-TTT TTATTT TTATTT TTATTT TTCTTT TAATTT
1 TTATT-T TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
*
20583842 TCATTT
1 TTATTT
20583848 CAATTTTATT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
5 4 0.10
6 31 0.77
7 5 0.12
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (6 bp):
TTATTT
Found at i:20588224 original size:40 final size:41
Alignment explanation
Indices: 20588081--20588227 Score: 145
Period size: 40 Copynumber: 3.6 Consensus size: 41
20588071 CGAGCTTCGG
*
20588081 GCCTAGCAGGCTATAATGCCGGTGAAATG-ATATCGGGCTTCAA
1 GCCTAGCAGGCTA-AATGCCGGTG-AATGAAT-TCGGGCTTAAA
* * * * *
20588124 GCCTAGCAGGCGAAATGCCAGTGAATGAGTTCAGACTTAAA
1 GCCTAGCAGGCTAAATGCCGGTGAATGAATTCGGGCTTAAA
* *** *
20588165 GTCTAGCAGGCTTCGTGCCGGTG-ATGAATTCGGGTTTAAA
1 GCCTAGCAGGCTAAATGCCGGTGAATGAATTCGGGCTTAAA
*
20588205 ACCTAGCAGGCTAAATGCCGGTG
1 GCCTAGCAGGCTAAATGCCGGTG
20588228 TTTTGATAAA
Statistics
Matches: 82, Mismatches: 21, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
40 31 0.38
41 29 0.35
42 10 0.12
43 12 0.15
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.23
Consensus pattern (41 bp):
GCCTAGCAGGCTAAATGCCGGTGAATGAATTCGGGCTTAAA
Found at i:20589982 original size:29 final size:29
Alignment explanation
Indices: 20589940--20589998 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
20589930 ACATTTAGTG
20589940 GTATCAGAGCATGGTTTAGTCAATTCTCA
1 GTATCAGAGCATGGTTTAGTCAATTCTCA
*
20589969 GTATCAGAGCATGGTTTAGTCGATTCTCA
1 GTATCAGAGCATGGTTTAGTCAATTCTCA
20589998 G
1 G
20589999 ACTAACCTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (29 bp):
GTATCAGAGCATGGTTTAGTCAATTCTCA
Found at i:20595112 original size:40 final size:40
Alignment explanation
Indices: 20595038--20595179 Score: 207
Period size: 40 Copynumber: 3.6 Consensus size: 40
20595028 AACCCAAGTA
* * *
20595038 CCTTCGGGATTTAG-CCAGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
*
20595077 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
20595117 CCTTTGAGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
20595157 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
20595180 CATTCGAATA
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 12 0.13
40 79 0.86
41 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:20597102 original size:39 final size:39
Alignment explanation
Indices: 20597048--20597126 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
20597038 GGATTAAGTG
20597048 TTAGTTAATGAGTTAGTTATATGGAGATAAATAACCGTA
1 TTAGTTAATGAGTTAGTTATATGGAGATAAATAACCGTA
* * *
20597087 TTAGTTAATGAGTTAGTTATATGGTGATACATAGCCGTA
1 TTAGTTAATGAGTTAGTTATATGGAGATAAATAACCGTA
20597126 T
1 T
20597127 GTTTATATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (39 bp):
TTAGTTAATGAGTTAGTTATATGGAGATAAATAACCGTA
Found at i:20597963 original size:43 final size:43
Alignment explanation
Indices: 20597905--20598075 Score: 227
Period size: 43 Copynumber: 4.0 Consensus size: 43
20597895 TATCGAAATG
*
20597905 TGATATTCGAGCTTCGGGCCTAGCAGGCTGTAATGCCGGTGAAA
1 TGATA-TCGAGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAAA
* *
20597949 TGATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAGA
1 TGATATCGAGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAAA
* * *
20597992 TAATATCGAGCCTCGGGCGTAGCAGGCTATAATGCCGGTGAAA
1 TGATATCGAGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAAA
* ** * *
20598035 TGATATCGGGCTTCAAGCCTAGCAGGCGA-AATGCCAGTGAA
1 TGATATCGAGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAA
20598076 TGAGTTCAGA
Statistics
Matches: 111, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
42 11 0.10
43 95 0.86
44 5 0.05
ACGTcount: A:0.25, C:0.21, G:0.32, T:0.22
Consensus pattern (43 bp):
TGATATCGAGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAAA
Found at i:20598056 original size:86 final size:85
Alignment explanation
Indices: 20597911--20598074 Score: 256
Period size: 86 Copynumber: 1.9 Consensus size: 85
20597901 AATGTGATAT
* * **
20597911 TCGAGCTTCGGGCCTAGCAGGCTGTAATGCCGGTGAAATGATATCGGGCTTCGGGCCTAGCAGGC
1 TCGAGCCTCGGGCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGGCTTCAAGCCTAGCAGGC
* *
20597976 TATAATGCCGGTGAGATAATA
66 GA-AATGCCAGTGAGATAATA
*
20597997 TCGAGCCTCGGGCGTAGCAGGCTATAATGCCGGTGAAATGATATCGGGCTTCAAGCCTAGCAGGC
1 TCGAGCCTCGGGCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGGCTTCAAGCCTAGCAGGC
20598062 GAAATGCCAGTGA
66 GAAATGCCAGTGA
20598075 ATGAGTTCAG
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
85 10 0.14
86 61 0.86
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.21
Consensus pattern (85 bp):
TCGAGCCTCGGGCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGGCTTCAAGCCTAGCAGGC
GAAATGCCAGTGAGATAATA
Found at i:20598151 original size:40 final size:41
Alignment explanation
Indices: 20597922--20598154 Score: 159
Period size: 43 Copynumber: 5.6 Consensus size: 41
20597912 CGAGCTTCGG
* ***
20597922 GCCTAGCAGGCTGTAATGCCGGTGAAATG-ATATCGGGCTTCGG
1 GCCTAGCAGGCT-AAATGCCGGTG-AATGAAT-TCGGGCTTAAA
* * ***
20597965 GCCTAGCAGGCTATAATGCCGGTGAGAT-AATATCGAGCCTCGG
1 GCCTAGCAGGCTA-AATGCCGGTGA-ATGAAT-TCGGGCTTAAA
* *
20598008 GCGTAGCAGGCTATAATGCCGGTGAAATG-ATATCGGGCTTCAA
1 GCCTAGCAGGCTA-AATGCCGGTG-AATGAAT-TCGGGCTTAAA
* * * * *
20598051 GCCTAGCAGGCGAAATGCCAGTGAATGAGTTCAGACTTAAA
1 GCCTAGCAGGCTAAATGCCGGTGAATGAATTCGGGCTTAAA
* *** *
20598092 GTCTAGCAGGCTTCGTGCCGGTG-ATGAATTCGGGTTTAAA
1 GCCTAGCAGGCTAAATGCCGGTGAATGAATTCGGGCTTAAA
*
20598132 ACCTAGCAGGCTAAATGCCGGTG
1 GCCTAGCAGGCTAAATGCCGGTG
20598155 TTTTGATAAA
Statistics
Matches: 154, Mismatches: 30, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
40 31 0.20
41 29 0.19
42 11 0.07
43 82 0.53
44 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.23
Consensus pattern (41 bp):
GCCTAGCAGGCTAAATGCCGGTGAATGAATTCGGGCTTAAA
Found at i:20599782 original size:51 final size:51
Alignment explanation
Indices: 20599722--20599827 Score: 185
Period size: 51 Copynumber: 2.1 Consensus size: 51
20599712 AGCACGATTA
*
20599722 ATGGATAAAACACGCGTATATGAAAAGTTTAAAATTGATCAAAAAAAATTG
1 ATGGATAAAACACGCGTATATGAAAAGTATAAAATTGATCAAAAAAAATTG
* *
20599773 ATGGATAAAACACGCGTGTATGAAAAGTATAAAATTGATCAAAAAAAATTT
1 ATGGATAAAACACGCGTATATGAAAAGTATAAAATTGATCAAAAAAAATTG
20599824 ATGG
1 ATGG
20599828 CCTAGTTTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.25
Consensus pattern (51 bp):
ATGGATAAAACACGCGTATATGAAAAGTATAAAATTGATCAAAAAAAATTG
Found at i:20602870 original size:8 final size:8
Alignment explanation
Indices: 20602832--20602870 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
20602822 ATGACCAAAT
*
20602832 TGCCCTCA
1 TGCCCTTA
*
20602840 TGCCCTCA
1 TGCCCTTA
20602848 TGCCCTTA
1 TGCCCTTA
20602856 TGCCCTTA
1 TGCCCTTA
20602864 TGCCCTT
1 TGCCCTT
20602871 TCTTTAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.10, C:0.44, G:0.13, T:0.33
Consensus pattern (8 bp):
TGCCCTTA
Found at i:20611181 original size:50 final size:52
Alignment explanation
Indices: 20611106--20611210 Score: 169
Period size: 50 Copynumber: 2.1 Consensus size: 52
20611096 CACAAGTTTA
* * *
20611106 TTTCATACTAACTCTTATTCTTTTATCAATGAATTATATTTGTATA-A-AAT
1 TTTCATACTAACGCATATTCTTTTATAAATGAATTATATTTGTATATATAAT
20611156 TTTCATACTAACGCATATTCTTTTATAAATGAATTATATTTGTATATATAAT
1 TTTCATACTAACGCATATTCTTTTATAAATGAATTATATTTGTATATATAAT
20611208 TTT
1 TTT
20611211 TTTATATTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
50 43 0.86
51 1 0.02
52 6 0.12
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.50
Consensus pattern (52 bp):
TTTCATACTAACGCATATTCTTTTATAAATGAATTATATTTGTATATATAAT
Found at i:20611552 original size:26 final size:26
Alignment explanation
Indices: 20611522--20611572 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
20611512 AGTGATTTGT
20611522 TTTATATTCTAATGTTAATTTCTTAA
1 TTTATATTCTAATGTTAATTTCTTAA
* *
20611548 TTTATATTTTGATGTTAATTTCTTA
1 TTTATATTCTAATGTTAATTTCTTA
20611573 TATCCCATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (26 bp):
TTTATATTCTAATGTTAATTTCTTAA
Found at i:20614264 original size:22 final size:22
Alignment explanation
Indices: 20614208--20614264 Score: 62
Period size: 26 Copynumber: 2.5 Consensus size: 22
20614198 ATGGTACAAA
20614208 TTGATT-TATAAATCATGATTT
1 TTGATTCTATAAATCATGATTT
*
20614229 TTTATTCCATCTATAAATCATGATTT
1 TTGA-T---TCTATAAATCATGATTT
20614255 TTGATTCTAT
1 TTGATTCTAT
20614265 GTTAGTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
21 3 0.10
22 6 0.21
25 2 0.07
26 18 0.62
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.53
Consensus pattern (22 bp):
TTGATTCTATAAATCATGATTT
Found at i:20617512 original size:25 final size:24
Alignment explanation
Indices: 20617404--20617518 Score: 94
Period size: 24 Copynumber: 4.8 Consensus size: 24
20617394 GACTCACCAT
* *
20617404 AGCTCAAAAGAGCTTACTGCTTTC
1 AGCTCAATAGAGCTTACTGTTTTC
* * * *
20617428 AGCTTATTGGAGCTTACCT-ATTT-
1 AGCTCAATAGAGCTTA-CTGTTTTC
20617451 AGCTCGAA-AGAGCTTACTGTTTTC
1 AGCTC-AATAGAGCTTACTGTTTTC
*
20617475 AGCTTAATAGAGCTTACTGTTTATC
1 AGCTCAATAGAGCTTACTGTTT-TC
*
20617500 AGCTCAGA-GGAGCTTACTG
1 AGCTCA-ATAGAGCTTACTG
20617519 ACCATGACTC
Statistics
Matches: 72, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
22 2 0.03
23 16 0.22
24 34 0.47
25 19 0.26
26 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (24 bp):
AGCTCAATAGAGCTTACTGTTTTC
Found at i:20633036 original size:15 final size:15
Alignment explanation
Indices: 20633004--20633032 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20632994 ATTTTCAGTG
20633004 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
20633019 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
20633033 ATTTTTGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:20634209 original size:43 final size:43
Alignment explanation
Indices: 20634161--20634319 Score: 139
Period size: 43 Copynumber: 3.7 Consensus size: 43
20634151 ATAGGATTTC
* * **
20634161 CGATATGTG-TTCTCGTGTAATACCATGTCTAGGATGTTGGCAT
1 CGATATGTGATT-TCGAGTAAGACCATGTCTAGGACATTGGCAT
*
20634204 CGATATGTGATTTCGAGTAAGACCATGTCTGGGACATTGGCAT
1 CGATATGTGATTTCGAGTAAGACCATGTCTAGGACATTGGCAT
* * *
20634247 CG-TAATTGTGA-TTCGTGTAAGACCCTGTCT-GCGACAGTGGCAT
1 CGAT-A-TGTGATTTCGAGTAAGACCATGTCTAG-GACATTGGCAT
* * *
20634290 CGACATGTGATTAC-ATGTAAGACCACGTCT
1 CGATATGTGATTTCGA-GTAAGACCATGTCT
20634320 GGGGCGTTGG
Statistics
Matches: 96, Mismatches: 13, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
42 7 0.07
43 82 0.85
44 7 0.07
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (43 bp):
CGATATGTGATTTCGAGTAAGACCATGTCTAGGACATTGGCAT
Found at i:20638985 original size:43 final size:43
Alignment explanation
Indices: 20638932--20639076 Score: 134
Period size: 43 Copynumber: 3.4 Consensus size: 43
20638922 ACTGAGAAGT
*
20638932 TCTGAGACATTGGCATCGATATGTGATTTCGAGTAAGACCATG
1 TCTGGGACATTGGCATCGATATGTGATTTCGAGTAAGACCATG
* *
20638975 TCTGGGACATTGGCATCG-TAATTGTGA-TTCGTGTAAGACCCTG
1 TCTGGGACATTGGCATCGAT-A-TGTGATTTCGAGTAAGACCATG
* * ** * * *
20639018 TCTGCGACAGTGGCATCGACGTGTGATTAC-ATGTAATACCACG
1 TCTGGGACATTGGCATCGATATGTGATTTCGA-GTAAGACCATG
* *
20639061 TCTAGGACGTTGGCAT
1 TCTGGGACATTGGCAT
20639077 TGTACGATAT
Statistics
Matches: 81, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
42 6 0.07
43 70 0.86
44 5 0.06
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (43 bp):
TCTGGGACATTGGCATCGATATGTGATTTCGAGTAAGACCATG
Found at i:20646456 original size:33 final size:33
Alignment explanation
Indices: 20646413--20646509 Score: 109
Period size: 33 Copynumber: 3.1 Consensus size: 33
20646403 NTTTTTTATA
20646413 ATTATTTTAAAATTAATTTGTTAGTAATTTAGG
1 ATTATTTTAAAATTAATTTGTTAGTAATTTAGG
* *
20646446 ATTATGTTAAAATT-TTTTG-T-GT--TTGTA--
1 ATTATTTTAAAATTAATTTGTTAGTAATT-TAGG
*
20646473 ATTATTTTAAAATTAATTTATTAGTAATTTAGG
1 ATTATTTTAAAATTAATTTGTTAGTAATTTAGG
20646506 ATTA
1 ATTA
20646510 AATTATAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
27 13 0.25
28 5 0.10
29 3 0.06
30 4 0.08
31 3 0.06
32 6 0.12
33 17 0.33
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (33 bp):
ATTATTTTAAAATTAATTTGTTAGTAATTTAGG
Found at i:20646526 original size:60 final size:60
Alignment explanation
Indices: 20646411--20646529 Score: 186
Period size: 60 Copynumber: 2.0 Consensus size: 60
20646401 NNNTTTTTTA
* ** *
20646411 TAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTAAAATTTTTTGTGTTTG
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAATTAAAATTTGTTGTGTTTG
20646471 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAATTATAAA-TTGTTGTGTTT
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAATTA-AAATTTGTTGTGTTT
20646530 AGTTTAGTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
60 51 0.94
61 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (60 bp):
TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAATTAAAATTTGTTGTGTTTG
Found at i:20649437 original size:28 final size:28
Alignment explanation
Indices: 20649383--20649440 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 28
20649373 TATAGGGGTT
20649383 TTCACACGGCCTGACACACGCCCGTGTCC
1 TTCACACGGCCTGA-ACACGCCCGTGTCC
*
20649412 TTCACACGGCCATG-ACACGCTCGTGTCC
1 TTCACACGGCC-TGAACACGCCCGTGTCC
20649440 T
1 T
20649441 AACCCATGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 14 0.52
29 11 0.41
30 2 0.07
ACGTcount: A:0.17, C:0.41, G:0.21, T:0.21
Consensus pattern (28 bp):
TTCACACGGCCTGAACACGCCCGTGTCC
Found at i:20650555 original size:68 final size:68
Alignment explanation
Indices: 20650426--20650559 Score: 205
Period size: 68 Copynumber: 2.0 Consensus size: 68
20650416 GTGAATCTTA
* *
20650426 CTTCTGAGATGGATCAATCAGCTTCCTTGGAGTAACTCCTTAATCCCTATTCTGTACCTCCCTTT
1 CTTCTGAGATGGATCAATCAGCTTCCTTGGAGTAACTCCTTAATCACTATTCTCTACCTCCCTTT
20650491 TAG
66 TAG
* * * **
20650494 CTTCTGAGATGGATCAATCGGCTTCCTTGGAGTAATTCCTTACTCACTATTCTCTGTCTCCCTTT
1 CTTCTGAGATGGATCAATCAGCTTCCTTGGAGTAACTCCTTAATCACTATTCTCTACCTCCCTTT
20650559 T
66 T
20650560 CTTCCTCCTC
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 59 1.00
ACGTcount: A:0.19, C:0.28, G:0.15, T:0.39
Consensus pattern (68 bp):
CTTCTGAGATGGATCAATCAGCTTCCTTGGAGTAACTCCTTAATCACTATTCTCTACCTCCCTTT
TAG
Found at i:20654848 original size:55 final size:55
Alignment explanation
Indices: 20654706--20654849 Score: 146
Period size: 55 Copynumber: 2.6 Consensus size: 55
20654696 TGCAAGCCCC
* ** * * *
20654706 AACGCTCGTGTTAATTTAACAAGTTCGACCACGGGTGTTCCACACGGGCGTGTCA
1 AACGCCCGTGTTGTTTTAACAGGTTCGACCACGGGTCTTCCACACGGGCATGTCA
* * * * *
20654761 AACTCCCGTGTTGTTTTAACAGGTTCGCCCACGGTTCTTCCACCCGGGCATGTCG
1 AACGCCCGTGTTGTTTTAACAGGTTCGACCACGGGTCTTCCACACGGGCATGTCA
* **
20654816 CACGCCCGTGTTGTTTTGGCAGGCTT-GACCACGG
1 AACGCCCGTGTTGTTTTAACAGG-TTCGACCACGG
20654850 CCATATCGCA
Statistics
Matches: 72, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
55 70 0.97
56 2 0.03
ACGTcount: A:0.17, C:0.29, G:0.26, T:0.27
Consensus pattern (55 bp):
AACGCCCGTGTTGTTTTAACAGGTTCGACCACGGGTCTTCCACACGGGCATGTCA
Found at i:20655156 original size:47 final size:47
Alignment explanation
Indices: 20655087--20655182 Score: 147
Period size: 47 Copynumber: 2.0 Consensus size: 47
20655077 CGACTTACCT
** * * *
20655087 CTCCAGTGAATGGTGATGGTGGTTTGAGAAGTTTATACTCCTCATTC
1 CTCCAGTGAATGGCCATGGTGGTTTGAAAAGTTTATACTACTAATTC
20655134 CTCCAGTGAATGGCCATGGTGGTTTGAAAAGTTTATACTACTAATTC
1 CTCCAGTGAATGGCCATGGTGGTTTGAAAAGTTTATACTACTAATTC
20655181 CT
1 CT
20655183 GCTATCAATC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (47 bp):
CTCCAGTGAATGGCCATGGTGGTTTGAAAAGTTTATACTACTAATTC
Found at i:20660099 original size:47 final size:49
Alignment explanation
Indices: 20660029--20660294 Score: 204
Period size: 47 Copynumber: 5.7 Consensus size: 49
20660019 GTAAGGTGCT
* * * *
20660029 GATGCCATATCCTAGACACGGTCTTACACTAGCTCAT-ATCTCAT-GTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATCTCATAGCC
* * *
20660076 AATGCCATGTCCCAGACATGGTCTTACACT-GACT-ATCATCTCGTAACC
1 GATGCCATGTCCCAGACATGGTCTTACACTAG-CTCATCATCTCATAGCC
* * * * * *
20660124 GATG-CATGTCCCAAACAT-GTCTTACACTGGCTTA-CGTCT-TTAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATCTCATA-GCC
* *
20660170 GATG-CATGTCCCAGACAT-GTCTTACACTAGCAC-TCGTCTCGAT-GCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATCTC-ATAGCC
* * * *
20660216 GATGCCATGTCCCAGACATGGTCTTACACTAGCTC-TCATAAT-GTGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCAT-CTCATAGCC
*
20660264 GATG-CATGTCCTAGACAT-GTCTTACACTAGC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGC
20660295 CCACAATAAC
Statistics
Matches: 181, Mismatches: 25, Indels: 27
0.78 0.11 0.12
Matches are distributed among these distances:
45 2 0.01
46 73 0.40
47 77 0.43
48 28 0.15
49 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (49 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATCTCATAGCC
Found at i:20660174 original size:46 final size:45
Alignment explanation
Indices: 20660081--20660294 Score: 191
Period size: 46 Copynumber: 4.6 Consensus size: 45
20660071 ATGTCAATGC
* * *
20660081 CATGTCCCAGACATGGTCTTACACT-GACTATCATCTCGTA-ACCGATG
1 CATGTCCCAGACAT-GTCTTACACTAG-CT-TCGTCTC-TAGGCTGATG
* * *
20660128 CATGTCCCAAACATGTCTTACACTGGCTTACGTCTTTAGGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCTT-CGTCTCTAGGCTGATG
* * * *
20660174 CATGTCCCAGACATGTCTTACACTAGCACTCGTCTCGATGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGC-TTCGTCTCTAGGCTGATG
* * *
20660220 CCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGT-GGCTGATG
1 -CATGTCCCAGACAT-GTCTTACACTAGCT-TCGT-CTCTAGGCTGATG
*
20660268 CATGTCCTAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
20660295 CCACAATAAC
Statistics
Matches: 139, Mismatches: 20, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
45 3 0.02
46 71 0.51
47 42 0.30
48 22 0.16
49 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (45 bp):
CATGTCCCAGACATGTCTTACACTAGCTTCGTCTCTAGGCTGATG
Found at i:20664488 original size:46 final size:45
Alignment explanation
Indices: 20664431--20664601 Score: 182
Period size: 46 Copynumber: 3.7 Consensus size: 45
20664421 TCTCGTAGCC
* *
20664431 GATGCATGTCCTAGACATGTCTTACACTGGCTTACGTCTTGAGGCA
1 GATGCATGTCCTAGACATGTCTTACACTAGCTT-CGTCTTGAGGCT
* * * *
20664477 GATGCATGTCCTATACATGTCTTACACTAGCACTCGTCTCGATGCT
1 GATGCATGTCCTAGACATGTCTTACACTAGC-TTCGTCTTGAGGCT
* * * * *
20664523 GATGCCATGTCCCAGACATGGTCTTTCACTAGCTCTCATAC-TGTGGTT
1 GATG-CATGTCCTAGACAT-GTCTTACACTAGCT-TCGT-CTTGAGGCT
20664571 GATGCATGTCCTAGACATGTCTTACACTAGC
1 GATGCATGTCCTAGACATGTCTTACACTAGC
20664602 CCACATTAAC
Statistics
Matches: 103, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
46 54 0.52
47 26 0.25
48 22 0.21
49 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (45 bp):
GATGCATGTCCTAGACATGTCTTACACTAGCTTCGTCTTGAGGCT
Found at i:20674115 original size:13 final size:13
Alignment explanation
Indices: 20674075--20674115 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
20674065 AAAGCACGAT
*
20674075 TCACTCGGGCATG
1 TCACACGGGCATG
*
20674088 TCACACGAGCATG
1 TCACACGGGCATG
*
20674101 TCACACGGGCGTG
1 TCACACGGGCATG
20674114 TC
1 TC
20674116 CCTGCCAAGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.20, C:0.32, G:0.29, T:0.20
Consensus pattern (13 bp):
TCACACGGGCATG
Found at i:20682144 original size:47 final size:46
Alignment explanation
Indices: 20682070--20682237 Score: 168
Period size: 47 Copynumber: 3.7 Consensus size: 46
20682060 GTAAGGTTCT
* * * *
20682070 GATGGCATGTCCTAGACACGGTCTTACACTAGCTCATATCTCATGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCAC-TATCTCATGTC
* *
20682117 GATGCCATGTCCCTGACATGGTCTTACACTA--ACTA--TCATCTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCACTATCTCATGTC
* * * *
20682159 GATG-CATGTCCCAAATAT-GTCTTACACTAGCACTTGTCTCGATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCAC-TATCTC-ATGTC
*
20682205 GATGCCATGTCCCAGACATGGTCTTATACTAGC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGC
20682238 TCTCATAATG
Statistics
Matches: 98, Mismatches: 15, Indels: 15
0.77 0.12 0.12
Matches are distributed among these distances:
40 11 0.11
41 11 0.11
42 12 0.12
43 1 0.01
44 2 0.02
45 3 0.03
46 7 0.07
47 39 0.40
48 12 0.12
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.30
Consensus pattern (46 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCACTATCTCATGTC
Found at i:20682184 original size:40 final size:42
Alignment explanation
Indices: 20682110--20682187 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 42
20682100 AGCTCATATC
* **
20682110 TCATGTCGATGCCATGTCCCTGACATGGTCTTACACTAACTA
1 TCATCTCGATGCCATGTCCCAAACATGGTCTTACACTAACTA
*
20682152 TCATCTCGATG-CATGTCCCAAATAT-GTCTTACACTA
1 TCATCTCGATGCCATGTCCCAAACATGGTCTTACACTA
20682188 GCACTTGTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 11 0.34
41 11 0.34
42 10 0.31
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.32
Consensus pattern (42 bp):
TCATCTCGATGCCATGTCCCAAACATGGTCTTACACTAACTA
Found at i:20687507 original size:16 final size:16
Alignment explanation
Indices: 20687486--20687516 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
20687476 GCAAAAGTTG
20687486 AGTTCTAGTAGCTAAT
1 AGTTCTAGTAGCTAAT
20687502 AGTTCTAGTAGCTAA
1 AGTTCTAGTAGCTAA
20687517 AGGTATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (16 bp):
AGTTCTAGTAGCTAAT
Found at i:20693923 original size:30 final size:29
Alignment explanation
Indices: 20693876--20693943 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 29
20693866 GCCTCAAGTA
*
20693876 GCCAAAGCTAGTTAAATCGCACACTTAGT
1 GCCAAAGCTAGTTAAATCACACACTTAGT
20693905 GCCAAAGCTAGTTTAAATCACACACTTAGT
1 GCCAAAGCTAG-TTAAATCACACACTTAGT
20693935 GCCAAAGCT
1 GCCAAAGCT
20693944 TCCGATTCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 11 0.30
30 26 0.70
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (29 bp):
GCCAAAGCTAGTTAAATCACACACTTAGT
Found at i:20694983 original size:12 final size:12
Alignment explanation
Indices: 20694963--20694994 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
20694953 CAAAGTTGTC
20694963 CACACGGGTAGA
1 CACACGGGTAGA
*
20694975 CACATGGGTAGA
1 CACACGGGTAGA
20694987 CACACGGG
1 CACACGGG
20694995 CATGTGTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.31, C:0.25, G:0.34, T:0.09
Consensus pattern (12 bp):
CACACGGGTAGA
Found at i:20696381 original size:6 final size:6
Alignment explanation
Indices: 20696370--20696403 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
20696360 TTCTGTAATT
* *
20696370 TGAATC TGAATC TGGATC TGAATT TGAATC TGAA
1 TGAATC TGAATC TGAATC TGAATC TGAATC TGAA
20696404 ACTGTACCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (6 bp):
TGAATC
Found at i:20696941 original size:5 final size:5
Alignment explanation
Indices: 20696924--20697176 Score: 427
Period size: 5 Copynumber: 50.0 Consensus size: 5
20696914 ATAAAGAATA
* * *
20696924 ATATT ATTATA ATATA ATATA ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT A-TATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
20696975 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
20697025 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
20697075 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
*
20697125 ATATT ATATT ATATT ATTATT ATATT AT-TAT ATTATT ATATT ATAAT
1 ATATT ATATT ATATT A-TATT ATATT ATAT-T A-TATT ATATT ATATT
20697172 ATATT
1 ATATT
20697177 TTTATCATTA
Statistics
Matches: 239, Mismatches: 4, Indels: 10
0.94 0.02 0.04
Matches are distributed among these distances:
4 1 0.00
5 225 0.94
6 12 0.05
7 1 0.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:20697268 original size:16 final size:16
Alignment explanation
Indices: 20697247--20697277 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
20697237 AATAGGGGAA
20697247 AGAAAGAAAGAAAAAC
1 AGAAAGAAAGAAAAAC
20697263 AGAAAGAAAGAAAAA
1 AGAAAGAAAGAAAAA
20697278 GGAAAGGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.00
Consensus pattern (16 bp):
AGAAAGAAAGAAAAAC
Found at i:20698211 original size:56 final size:55
Alignment explanation
Indices: 20698144--20698308 Score: 233
Period size: 56 Copynumber: 2.9 Consensus size: 55
20698134 TGAGTATAGT
*
20698144 GATTGGTAGTATTCTGCATAAGTTGTGGACTATCGTAGCTCTGTGTGAGCATCGAG
1 GATTGGTAGTATTCTGCATATGTTGTGGACTA-CGTAGCTCTGTGTGAGCATCGAG
* *
20698200 GATTGGTAGTATT-TCGCATATGTTATGGACTACCGTAGCTCTGTGTGAGCATCTAG
1 GATTGGTAGTATTCT-GCATATGTTGTGGACTA-CGTAGCTCTGTGTGAGCATCGAG
* * *
20698256 GATTGGTAGTATTCCGCATATGTTGTGGACTACTGTAGCTCTGTATGATCATC
1 GATTGGTAGTATTCTGCATATGTTGTGGACTAC-GTAGCTCTGTGTGAGCATC
20698309 AAAGCATACA
Statistics
Matches: 98, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
55 2 0.02
56 96 0.98
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.36
Consensus pattern (55 bp):
GATTGGTAGTATTCTGCATATGTTGTGGACTACGTAGCTCTGTGTGAGCATCGAG
Found at i:20704715 original size:22 final size:23
Alignment explanation
Indices: 20704690--20704738 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
20704680 ATGTTTTTAC
20704690 TTTTATTCTAT-TTTAAGAC-TATT
1 TTTTATT-TATCTTTAAG-CTTATT
*
20704713 TTTTATTTTTCTTTAAGCTTATT
1 TTTTATTTATCTTTAAGCTTATT
20704736 TTT
1 TTT
20704739 ATTAGGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.20, C:0.08, G:0.04, T:0.67
Consensus pattern (23 bp):
TTTTATTTATCTTTAAGCTTATT
Found at i:20710771 original size:21 final size:21
Alignment explanation
Indices: 20710747--20710791 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
20710737 TTCTAGGTCG
*
20710747 TCTTCTTTTCTT-TCTTATTTT
1 TCTTCTTTTATTAT-TTATTTT
20710768 TCTTCTTTTATTATTTATTTT
1 TCTTCTTTTATTATTTATTTT
20710789 TCT
1 TCT
20710792 CCATAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.76
Consensus pattern (21 bp):
TCTTCTTTTATTATTTATTTT
Found at i:20720829 original size:19 final size:19
Alignment explanation
Indices: 20720805--20720842 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
20720795 GGCCGAAGAT
20720805 GAATGTGAAAGTGTATGTA
1 GAATGTGAAAGTGTATGTA
20720824 GAATGTGAAAGTGTATGTA
1 GAATGTGAAAGTGTATGTA
20720843 TGTGATAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.32, T:0.32
Consensus pattern (19 bp):
GAATGTGAAAGTGTATGTA
Found at i:20720886 original size:150 final size:150
Alignment explanation
Indices: 20720674--20720951 Score: 556
Period size: 150 Copynumber: 1.9 Consensus size: 150
20720664 CCAATGTGAT
20720674 GAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGT
1 GAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGT
20720739 ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAAGA
66 ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAAGA
20720804 TGAATGTGAAAGTGTATGTA
131 TGAATGTGAAAGTGTATGTA
20720824 GAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGT
1 GAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGT
20720889 ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAA
66 ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAA
20720952 TGGCCAATGT
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
150 128 1.00
ACGTcount: A:0.33, C:0.07, G:0.32, T:0.28
Consensus pattern (150 bp):
GAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGT
ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAAGA
TGAATGTGAAAGTGTATGTA
Found at i:20721133 original size:47 final size:47
Alignment explanation
Indices: 20720622--20721121 Score: 804
Period size: 47 Copynumber: 10.4 Consensus size: 47
20720612 ATTTTGTTAC
20720622 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAAAGTGTATG--TATGTGATAAGGCCGAATGGCCAATGT
20720671 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGT
20720718 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGT
** *
20720765 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAAGATGAATGTGAAAGT
1 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCG-A-ATG---GCCAATGT
20720817 GTATGTAGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGT
1 G-A--T-GAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGT
20720868 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGT
20720915 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGT
20720962 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGT
20721009 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGT
* * * * *
20721056 GATGAATGTGAAAGTATATATATATGATAAGGCCGAATGGTCAATGG
1 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGT
*
20721103 GATGGAA-GTGGAAGTGTAT
1 GAT-GAATGTGAAAGTGTAT
20721122 AACTGTGATA
Statistics
Matches: 428, Mismatches: 13, Indels: 22
0.92 0.03 0.05
Matches are distributed among these distances:
47 349 0.82
48 5 0.01
49 23 0.05
50 1 0.00
51 6 0.01
52 6 0.01
53 1 0.00
54 3 0.01
55 2 0.00
56 32 0.07
ACGTcount: A:0.33, C:0.07, G:0.32, T:0.28
Consensus pattern (47 bp):
GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGT
Found at i:20724075 original size:16 final size:16
Alignment explanation
Indices: 20724049--20724086 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
20724039 TTCATTATCC
20724049 ATCATATGGCCGATTAT
1 ATCA-ATGGCCGATTAT
20724066 ATCAATGGCCGATTAT
1 ATCAATGGCCGATTAT
20724082 ATCAA
1 ATCAA
20724087 ATAAAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (16 bp):
ATCAATGGCCGATTAT
Found at i:20724996 original size:42 final size:44
Alignment explanation
Indices: 20724893--20724998 Score: 119
Period size: 44 Copynumber: 2.5 Consensus size: 44
20724883 ATGTGTTTTT
* *
20724893 GTGTAAGACCACATCTGGGACGTTGGCATCGACTTATGATTTAC
1 GTGTAAGACCATATCTGGGACATTGGCATCGACTTATGATTTAC
* * *
20724937 GTGTAGGACCATGTCTGGGACATTTGCATCGTA-TT-TGATTT-C
1 GTGTAAGACCATATCTGGGACATTGGCATCG-ACTTATGATTTAC
* *
20724979 GTGTAAGTCCCTATCTGGGA
1 GTGTAAGACCATATCTGGGA
20724999 TAGTGGTATT
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
42 17 0.33
43 6 0.12
44 28 0.54
45 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (44 bp):
GTGTAAGACCATATCTGGGACATTGGCATCGACTTATGATTTAC
Found at i:20728092 original size:71 final size:71
Alignment explanation
Indices: 20728009--20728159 Score: 284
Period size: 71 Copynumber: 2.1 Consensus size: 71
20727999 GAATATACAT
**
20728009 TACCAAAAGATACTTAATTAACAACAAGGGTCAACCCTATACATGCCATTATCAAAATTCAACTA
1 TACCAAAAGATACAAAATTAACAACAAGGGTCAACCCTATACATGCCATTATCAAAATTCAACTA
20728074 AAAGAG
66 AAAGAG
20728080 TACCAAAAGATACAAAATTAACAACAAGGGTCAACCCTATACATGCCATTATCAAAATTCAACTA
1 TACCAAAAGATACAAAATTAACAACAAGGGTCAACCCTATACATGCCATTATCAAAATTCAACTA
20728145 AAAGAG
66 AAAGAG
20728151 TACCAAAAG
1 TACCAAAAG
20728160 GGCTTAGATA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
71 78 1.00
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.21
Consensus pattern (71 bp):
TACCAAAAGATACAAAATTAACAACAAGGGTCAACCCTATACATGCCATTATCAAAATTCAACTA
AAAGAG
Found at i:20728632 original size:40 final size:40
Alignment explanation
Indices: 20728569--20728774 Score: 315
Period size: 40 Copynumber: 5.2 Consensus size: 40
20728559 AACCCAAGTA
* * *
20728569 CCTTCGGGATTTAG-TCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
20728608 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
20728648 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
20728688 CCTTCGAGACTTAGCCCGGATATATTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
20728728 CCTTCGAGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
20728768 CCTTCGG
1 CCTTCGG
20728775 ATCTTAGTCC
Statistics
Matches: 153, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
39 13 0.08
40 140 0.92
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:20729089 original size:48 final size:48
Alignment explanation
Indices: 20729029--20729124 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
20729019 TATATCACCG
20729029 TTTATTTGTTATGCTTATATGTCATGACATAATCAAATCATAAACTAA
1 TTTATTTGTTATGCTTATATGTCATGACATAATCAAATCATAAACTAA
*
20729077 TTTATTTTTTATGCTTATATGTCATGACATAATCAAATCATAAACTAA
1 TTTATTTGTTATGCTTATATGTCATGACATAATCAAATCATAAACTAA
20729125 GTTCCATTAC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (48 bp):
TTTATTTGTTATGCTTATATGTCATGACATAATCAAATCATAAACTAA
Found at i:20729516 original size:42 final size:42
Alignment explanation
Indices: 20729454--20729536 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
20729444 GACTTAACCC
*
20729454 CTAACCACATTCTGCTGAAAATCCTTTGAATTTCTACTAGCT
1 CTAACCACATTCTGCCGAAAATCCTTTGAATTTCTACTAGCT
20729496 CTAACCACATTCTGCCGAAAATCCTTTGAATTTCTACTAGC
1 CTAACCACATTCTGCCGAAAATCCTTTGAATTTCTACTAGC
20729537 ACACACACAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.29, C:0.28, G:0.10, T:0.34
Consensus pattern (42 bp):
CTAACCACATTCTGCCGAAAATCCTTTGAATTTCTACTAGCT
Found at i:20733958 original size:13 final size:13
Alignment explanation
Indices: 20733940--20733965 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20733930 ATATTATAAT
20733940 TATTTTATGTTAA
1 TATTTTATGTTAA
20733953 TATTTTATGTTAA
1 TATTTTATGTTAA
20733966 AAATAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TATTTTATGTTAA
Found at i:20735527 original size:40 final size:40
Alignment explanation
Indices: 20735472--20735613 Score: 241
Period size: 40 Copynumber: 3.6 Consensus size: 40
20735462 TATTCGGATG
20735472 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTTGCT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTTGCT
*
20735512 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTTGCT
*
20735552 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTTGCT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTTGCT
* *
20735592 ATATCC-GGCTAATTCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
20735614 TACTTGGGTT
Statistics
Matches: 98, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
39 15 0.15
40 83 0.85
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTTGCT
Found at i:20749473 original size:55 final size:54
Alignment explanation
Indices: 20749353--20749537 Score: 210
Period size: 55 Copynumber: 3.4 Consensus size: 54
20749343 GTTCCATGTT
* * * *
20749353 TTGACATGGTCTTACGTGGTATCCTTGCCTTAT-GAACTCACCATTGCCATGCC
1 TTGACATGGTCTTACATGGTATCTTTGCCTTATAGAACTTACCAATGCCATGCC
* ** * * *
20749406 TTGGCATGGTCTTACATGGGCTCTTTGCCTTATAGTAATTTATCAATGCCATGTC
1 TTGACATGGTCTTACATGGTATCTTTGCCTTATAG-AACTTACCAATGCCATGCC
* * * *
20749461 TTGACATGGTCTTACATGATTTCTTTGCCTTGTAGAACTTACCAATGTCATGCC
1 TTGACATGGTCTTACATGGTATCTTTGCCTTATAGAACTTACCAATGCCATGCC
* *
20749515 TTGGCATGGTCTTACTTGGTATC
1 TTGACATGGTCTTACATGGTATC
20749538 CTTAAACCCT
Statistics
Matches: 107, Mismatches: 23, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
53 28 0.26
54 35 0.33
55 44 0.41
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (54 bp):
TTGACATGGTCTTACATGGTATCTTTGCCTTATAGAACTTACCAATGCCATGCC
Found at i:20753493 original size:39 final size:39
Alignment explanation
Indices: 20753450--20753528 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
20753440 ACCAAGGGTT
*
20753450 AGATCATACAAAGCAGCAATTACCAGTAGCTTTGACCTA
1 AGATCATACAAAGCAGCAATTACCAGTAACTTTGACCTA
*
20753489 AGATCATACAGAGCAGCAATTACCAGTAACTTTGACCTA
1 AGATCATACAAAGCAGCAATTACCAGTAACTTTGACCTA
20753528 A
1 A
20753529 CAACAATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.23
Consensus pattern (39 bp):
AGATCATACAAAGCAGCAATTACCAGTAACTTTGACCTA
Found at i:20754704 original size:26 final size:28
Alignment explanation
Indices: 20754675--20754730 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 28
20754665 AAAAAAAATT
*
20754675 AAAA-CTCTTGTAAAATAAAA-CTCA-AG
1 AAAATCTCTTG-AAAAGAAAACCTCAGAG
*
20754701 AAAATTTCTTGAAAAGAAAACCTCAGAG
1 AAAATCTCTTGAAAAGAAAACCTCAGAG
20754729 AA
1 AA
20754731 TTTATTAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 12 0.48
27 9 0.36
28 4 0.16
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.21
Consensus pattern (28 bp):
AAAATCTCTTGAAAAGAAAACCTCAGAG
Found at i:20763187 original size:24 final size:24
Alignment explanation
Indices: 20763155--20763200 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
20763145 TCTACCTGTT
20763155 GAGTCTACTGAGTTTGTGATTAAA
1 GAGTCTACTGAGTTTGTGATTAAA
20763179 GAGTCTACTGAGTTTGTGATTA
1 GAGTCTACTGAGTTTGTGATTA
20763201 GAGTGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.39
Consensus pattern (24 bp):
GAGTCTACTGAGTTTGTGATTAAA
Found at i:20769864 original size:48 final size:48
Alignment explanation
Indices: 20769808--20769903 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
20769798 TAATCGAATT
20769808 TGATCTGAGTTATATTTTAATCGGTAATACCTTGTAACCC-ACTTCCGG
1 TGATCTGAGTTATATTTTAATCGGTAATACCTTGTAACCCTA-TTCCGG
20769856 TGATCTGAGTTATATTTTAATCGGTAATACCTTGTAACCCTATTCCGG
1 TGATCTGAGTTATATTTTAATCGGTAATACCTTGTAACCCTATTCCGG
20769904 CGACAAAAGT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 46 0.98
49 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.39
Consensus pattern (48 bp):
TGATCTGAGTTATATTTTAATCGGTAATACCTTGTAACCCTATTCCGG
Found at i:20770105 original size:21 final size:22
Alignment explanation
Indices: 20770054--20770105 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
20770044 ATAATATTAA
*
20770054 TATATT-TTCTTAAATAATATG
1 TATATTATTATTAAATAATATG
*
20770075 TTTAATTTATTATTAAAT-ATATG
1 TAT-A-TTATTATTAAATAATATG
20770098 TATATTAT
1 TATATTAT
20770106 AATATTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
21 6 0.24
22 2 0.08
23 9 0.36
24 8 0.32
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (22 bp):
TATATTATTATTAAATAATATG
Found at i:20770111 original size:23 final size:24
Alignment explanation
Indices: 20770063--20770112 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
20770053 ATATATTTTC
* *
20770063 TTAAATAATATGTTTAATTTATTA
1 TTAAATAATATGTATAATTTAATA
20770087 TTAAAT-ATATGTAT-ATTATAATA
1 TTAAATAATATGTATAATT-TAATA
20770110 TTA
1 TTA
20770113 TTTATACACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 3 0.13
23 14 0.61
24 6 0.26
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (24 bp):
TTAAATAATATGTATAATTTAATA
Found at i:20770172 original size:19 final size:19
Alignment explanation
Indices: 20770148--20770215 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 19
20770138 CGCACACTTG
20770148 TTATTTAAGGATTAATTGC
1 TTATTTAAGGATTAATTGC
*** *
20770167 TTATTTAATCCTTCACTTTTTG-
1 TTATTTAAGGATT-A---ATTGC
20770189 TTATTTAAGGATTAATTGC
1 TTATTTAAGGATTAATTGC
20770208 TTATTTAA
1 TTATTTAA
20770216 TCCTTCACTT
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
18 3 0.08
19 18 0.50
20 1 0.03
21 1 0.03
22 10 0.28
23 3 0.08
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.53
Consensus pattern (19 bp):
TTATTTAAGGATTAATTGC
Found at i:20770192 original size:41 final size:41
Alignment explanation
Indices: 20770145--20770228 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
20770135 TACCGCACAC
20770145 TTGTTATTTAAGGATTAATTGCTTATTTAATCCTTCACTTT
1 TTGTTATTTAAGGATTAATTGCTTATTTAATCCTTCACTTT
20770186 TTGTTATTTAAGGATTAATTGCTTATTTAATCCTTCACTTT
1 TTGTTATTTAAGGATTAATTGCTTATTTAATCCTTCACTTT
20770227 TT
1 TT
20770229 CTTTAATCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.55
Consensus pattern (41 bp):
TTGTTATTTAAGGATTAATTGCTTATTTAATCCTTCACTTT
Found at i:20778242 original size:22 final size:22
Alignment explanation
Indices: 20778211--20778260 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
20778201 AGTCAACAAA
*
20778211 ACGGCCCAAC-ACGTTAGACAGG
1 ACGGCTCAACGACG-TAGACAGG
*
20778233 ACGGCTCAACGTCGTAGACAGG
1 ACGGCTCAACGACGTAGACAGG
20778255 ACGGCT
1 ACGGCT
20778261 AAAGGCCGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.28, C:0.30, G:0.30, T:0.12
Consensus pattern (22 bp):
ACGGCTCAACGACGTAGACAGG
Found at i:20778270 original size:22 final size:22
Alignment explanation
Indices: 20778225--20778270 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
20778215 CCCAACACGT
* *
20778225 TAGACAGGACGGCTCAACGTCG
1 TAGACAGGACGGCTAAACGCCG
*
20778247 TAGACAGGACGGCTAAAGGCCG
1 TAGACAGGACGGCTAAACGCCG
20778269 TA
1 TA
20778271 AATATCGCAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.24, G:0.33, T:0.13
Consensus pattern (22 bp):
TAGACAGGACGGCTAAACGCCG
Found at i:20778376 original size:21 final size:21
Alignment explanation
Indices: 20778323--20778379 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
20778313 CATAAGTATC
* *
20778323 ACAGAAAGGCTAAAGCCTTAT
1 ACAGGAAGGCTACAGCCTTAT
20778344 ACAGGAAGGCTACAGCCTTAT
1 ACAGGAAGGCTACAGCCTTAT
20778365 ACAGGACA-GCTACAG
1 ACAGGA-AGGCTACAG
20778380 GCCGTACACT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 32 0.97
22 1 0.03
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.16
Consensus pattern (21 bp):
ACAGGAAGGCTACAGCCTTAT
Found at i:20779533 original size:5 final size:6
Alignment explanation
Indices: 20779515--20779594 Score: 54
Period size: 6 Copynumber: 12.0 Consensus size: 6
20779505 AATTTTCTCC
* *
20779515 TTCTTT TTCTTT TTCTTT TTCTTT CTCCCTTTT CTTCTTT ATTCATTC
1 TTCTTT TTCTTT TTCTTT TTCTTT -T-TC-TTT -TTCTTT -TTC-TTT
20779563 TTCTTAT TTCTTT TTCTATT CTT-TTT TTCTTT
1 TTCTT-T TTCTTT TTCT-TT -TTCTTT TTCTTT
20779595 ATTTTGTTTA
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
5 2 0.03
6 30 0.49
7 18 0.30
8 6 0.10
9 5 0.08
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (6 bp):
TTCTTT
Found at i:20779537 original size:12 final size:13
Alignment explanation
Indices: 20779514--20779594 Score: 60
Period size: 13 Copynumber: 6.0 Consensus size: 13
20779504 TAATTTTCTC
20779514 CTTCTTTTTCTTT
1 CTTCTTTTTCTTT
20779527 -TTCTTTTTCTTT
1 CTTCTTTTTCTTT
*
20779539 CTCCCTTTTCTTCTTT
1 CT-TC-TTT-TTCTTT
* *
20779555 ATTCATTCTTCTTAT
1 CTTC-TTTTTCTT-T
20779570 -TTCTTTTTCTATT
1 CTTCTTTTTCT-TT
20779583 CTT-TTTTTCTTT
1 CTTCTTTTTCTTT
20779595 ATTTTGTTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
12 14 0.25
13 15 0.27
14 12 0.22
15 7 0.13
16 7 0.13
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (13 bp):
CTTCTTTTTCTTT
Found at i:20779575 original size:21 final size:20
Alignment explanation
Indices: 20779543--20779597 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
20779533 TTCTTTCTCC
*
20779543 CTTTTCTTCTTTATTC-ATT
1 CTTTTTTTCTTTATTCTATT
20779562 CTTCTTATTTCTTT-TTCTATT
1 CTT-TT-TTTCTTTATTCTATT
20779583 CTTTTTTTCTTTATT
1 CTTTTTTTCTTTATT
20779598 TTGTTTAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 10 0.32
20 9 0.29
21 12 0.39
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (20 bp):
CTTTTTTTCTTTATTCTATT
Found at i:20780114 original size:21 final size:21
Alignment explanation
Indices: 20780088--20780128 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
20780078 AGCTACGGTA
20780088 TTACACATATACATATACTGC
1 TTACACATATACATATACTGC
*
20780109 TTACACGTATACATATACTG
1 TTACACATATACATATACTG
20780129 ACCTGGTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (21 bp):
TTACACATATACATATACTGC
Found at i:20780594 original size:26 final size:26
Alignment explanation
Indices: 20780565--20780672 Score: 173
Period size: 26 Copynumber: 4.2 Consensus size: 26
20780555 TGGTACAAAT
*
20780565 TGATAATGGGTTAGGTAAATGTTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
20780591 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
20780617 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
20780643 TGATAAT-GGTTAAGGTAAATGTTCCA
1 TGATAATGGGTT-AGGTAAATGTTCCA
20780669 TGAT
1 TGAT
20780673 GGGTATTTCA
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
25 4 0.05
26 72 0.95
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:20781873 original size:16 final size:15
Alignment explanation
Indices: 20781847--20781876 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
20781837 ACTAGATTGG
20781847 CAAAAGCCGAAAAGC
1 CAAAAGCCGAAAAGC
20781862 CAAAATGCCGAAAAG
1 CAAAA-GCCGAAAAG
20781877 TCGGTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.23, G:0.20, T:0.03
Consensus pattern (15 bp):
CAAAAGCCGAAAAGC
Found at i:20782145 original size:28 final size:26
Alignment explanation
Indices: 20782114--20782188 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
20782104 AAAAGTAGCT
* *
20782114 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTATTATACCCCTA-G-ATGCA
* * *
20782142 AAATTATTGTTATACCCCTAGGTGCA
1 AAATTACTATTATACCCCTAGATGCA
*
20782168 AAATTACCATTATACCCCTAG
1 AAATTACTATTATACCCCTAG
20782189 GGTTAATTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 21 0.54
27 1 0.03
28 17 0.44
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32
Consensus pattern (26 bp):
AAATTACTATTATACCCCTAGATGCA
Found at i:20782375 original size:54 final size:53
Alignment explanation
Indices: 20782293--20782433 Score: 228
Period size: 54 Copynumber: 2.6 Consensus size: 53
20782283 AGGAAGCATC
20782293 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
20782347 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
* * *
20782401 TTGGTGGCTCTGCCACAATATCTGTATCTGGTG
1 CTGGTGGCTATGCCACATTATCTG-ATCTGGTG
20782434 ACTTCGTCAC
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
53 7 0.09
54 75 0.91
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.35
Consensus pattern (53 bp):
CTGGTGGCTATGCCACATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
Found at i:20782429 original size:32 final size:27
Alignment explanation
Indices: 20782293--20782433 Score: 189
Period size: 27 Copynumber: 5.2 Consensus size: 27
20782283 AGGAAGCATC
*
20782293 CTGGTGGCTATGCCACA-ATTATCTGAT
1 CTGGTGGCTCTGCCACATA-TATCTGAT
*
20782320 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACATATATCTGAT
*
20782347 CTGGTGGCTATGCCACGAT-TATCTGAT
1 CTGGTGGCTCTGCCAC-ATATATCTGAT
*
20782374 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACATATATCTGAT
*
20782401 TTGGTGGCTCTGCCACA-ATATCTGTAT
1 CTGGTGGCTCTGCCACATATATCTG-AT
20782428 CTGGTG
1 CTGGTG
20782434 ACTTCGTCAC
Statistics
Matches: 101, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
26 9 0.09
27 89 0.88
28 3 0.03
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.35
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATATATCTGAT
Found at i:20787738 original size:26 final size:26
Alignment explanation
Indices: 20787709--20787816 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
20787699 TGGTACAAAT
20787709 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
20787735 TGATAATAGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
20787761 TGATAATGGGTTAGGCAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
20787787 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
20787813 TGAT
1 TGAT
20787817 GGGCATCTCA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:20789477 original size:27 final size:26
Alignment explanation
Indices: 20789437--20789576 Score: 163
Period size: 27 Copynumber: 5.2 Consensus size: 26
20789427 AGGAAGCGTC
*
20789437 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
20789464 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
20789491 CTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
* *
20789518 CTGGTGGCTCTGCTACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
* * *
20789545 CTGGTGGCACTGGCACAATATCTGTAT
1 CTGGTGGCTCTGCCACATTATCTG-AT
20789572 CTGGT
1 CTGGT
20789577 AACTTCGTCA
Statistics
Matches: 97, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
26 10 0.10
27 85 0.88
28 2 0.02
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:20789519 original size:54 final size:54
Alignment explanation
Indices: 20789437--20789576 Score: 221
Period size: 54 Copynumber: 2.6 Consensus size: 54
20789427 AGGAAGCGTC
20789437 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
* *
20789491 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCTACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
*
20789545 CTGGTGGC-ACTGGCACAA-TATCTGTATCTGGT
1 CTGGTGGCTA-TGCCACAATTATCTG-ATCTGGT
20789577 AACTTCGTCA
Statistics
Matches: 80, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
53 7 0.09
54 73 0.91
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
Done.