Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 16 of 297
Found at i:5240004 original size:41 final size:42
Alignment explanation
Indices: 5239916--5240018 Score: 122
Period size: 41 Copynumber: 2.5 Consensus size: 42
5239906 GGCCTTCGAG
* * *
5239916 CCTAGCAGGCTATAATGCCGGTGAAATGATATTGGGCTTCAAG
1 CCTAGCAGGCGA-AATGCCGGTGAAATGATATTGGGCTTAAAA
*
5239959 CCTAGCAGGCGAAATGCCGGTG-AATGA-ATTCGGGTTTAAAA
1 CCTAGCAGGCGAAATGCCGGTGAAATGATATT-GGGCTTAAAA
5240000 CCTAGCAGGCTG-AATGCCG
1 CCTAGCAGGC-GAAATGCCG
5240019 ATGATTTGAT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
40 3 0.06
41 29 0.54
42 11 0.20
43 11 0.20
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.22
Consensus pattern (42 bp):
CCTAGCAGGCGAAATGCCGGTGAAATGATATTGGGCTTAAAA
Found at i:5243364 original size:39 final size:39
Alignment explanation
Indices: 5243321--5243396 Score: 127
Period size: 39 Copynumber: 1.9 Consensus size: 39
5243311 ATAAAATCTT
5243321 ATTCAGTATAATCAATGGATAA-TGCTCGTTTGAGCAAGC
1 ATTCAGTATAATCAATGGA-AATTGCTCGTTTGAGCAAGC
*
5243360 ATTCAGTATAATCAATGGAAATTTCTCGTTTGAGCAA
1 ATTCAGTATAATCAATGGAAATTGCTCGTTTGAGCAA
5243397 CTATTGAGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 2 0.06
39 33 0.94
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33
Consensus pattern (39 bp):
ATTCAGTATAATCAATGGAAATTGCTCGTTTGAGCAAGC
Found at i:5243452 original size:36 final size:36
Alignment explanation
Indices: 5243338--5243628 Score: 255
Period size: 36 Copynumber: 7.9 Consensus size: 36
5243328 ATAATCAATG
* * * * *
5243338 GATAATGCTCGTTTGAGCAAGCATTCAGTATAATCAATG
1 GATATTGCTCGTTTGAGC-A-C-TTTAGTAGAATCAGTA
* * *
5243377 GAAATTTCTCGTTTGAGCAACTATTGAGTAGAATTAGTA
1 GATATTGCTCGTTTGAGC-ACT-TT-AGTAGAATCAGTA
* *
5243416 GATATTTCTCATTTGAGCACTTTAGTAGAATCAGTA
1 GATATTGCTCGTTTGAGCACTTTAGTAGAATCAGTA
* * * *
5243452 GACATTGGTCATTTGAGCACGTTAAGTAGAATCAGTA
1 GATATTGCTCGTTTGAGCAC-TTTAGTAGAATCAGTA
*
5243489 GATATTGCTCG-TTGAGCACTTTCAG-AGAATCAATA
1 GATATTGCTCGTTTGAGCACTTT-AGTAGAATCAGTA
*
5243524 GATATTGCTCGTTTGAGCACTTTAGTAGAATTAGTA
1 GATATTGCTCGTTTGAGCACTTTAGTAGAATCAGTA
* * * * *
5243560 GACATTTCTCGTTTGAGCACATTCAATAGGATCAGTA
1 GATATTGCTCGTTTGAGCAC-TTTAGTAGAATCAGTA
* * *
5243597 GATATTCCTCG-TTGAACACTTAAAGTAGAATC
1 GATATTGCTCGTTTGAGCACTT-TAGTAGAATC
5243629 GGTATTCCAT
Statistics
Matches: 210, Mismatches: 34, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
35 26 0.12
36 90 0.43
37 47 0.22
38 5 0.02
39 42 0.20
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (36 bp):
GATATTGCTCGTTTGAGCACTTTAGTAGAATCAGTA
Found at i:5243529 original size:108 final size:108
Alignment explanation
Indices: 5243414--5243617 Score: 302
Period size: 108 Copynumber: 1.9 Consensus size: 108
5243404 GTAGAATTAG
* * *
5243414 TAGATATTTCTCATTTGAGCACTTTAGTAGAATCAGTAGACATTGGTCATTTGAGCACGTT-AAG
1 TAGATATTGCTCATTTGAGCACTTTAGTAGAATCAGTAGACATTGCTCATTTGAGCACATTCAA-
* *
5243478 TAGAATCAGTAGATATTGCTCGTTGAGCACTTTCAGAGAATCAA
65 TAGAATCAGTAGATATTCCTCGTTGAACACTTTCAGAGAATCAA
* * * *
5243522 TAGATATTGCTCGTTTGAGCACTTTAGTAGAATTAGTAGACATTTCTCGTTTGAGCACATTCAAT
1 TAGATATTGCTCATTTGAGCACTTTAGTAGAATCAGTAGACATTGCTCATTTGAGCACATTCAAT
*
5243587 AGGATCAGTAGATATTCCTCGTTGAACACTT
66 AGAATCAGTAGATATTCCTCGTTGAACACTT
5243618 AAAGTAGAAT
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
108 83 0.98
109 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.35
Consensus pattern (108 bp):
TAGATATTGCTCATTTGAGCACTTTAGTAGAATCAGTAGACATTGCTCATTTGAGCACATTCAAT
AGAATCAGTAGATATTCCTCGTTGAACACTTTCAGAGAATCAA
Found at i:5246483 original size:40 final size:40
Alignment explanation
Indices: 5245546--5246477 Score: 1690
Period size: 40 Copynumber: 23.3 Consensus size: 40
5245536 AAGCCAAGTA
* * * *
5245546 CCTTCGGGATTTAACC-GGATATAGCT-ACTCTCTCGAATG
1 CCTTCGGGACTTAACCTGGATATAG-TAACTCGCACAAATG
* * * *
5245585 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
* *
5245625 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
5245665 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
5245705 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
5245745 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
5245785 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
5245825 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
5245865 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
5245905 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
5245945 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
5245985 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
5246025 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
5246065 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
5246105 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
5246145 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
5246185 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
5246225 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
5246265 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
5246305 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
5246345 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
5246385 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
* * * * *
5246425 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAACCTGGATA-TAGTAACTCGCACAAATG
5246465 CCTTCGGGACTTA
1 CCTTCGGGACTTA
5246478 GCCCGGTTAT
Statistics
Matches: 875, Mismatches: 15, Indels: 5
0.98 0.02 0.01
Matches are distributed among these distances:
39 15 0.02
40 860 0.98
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAACCTGGATATAGTAACTCGCACAAATG
Found at i:5272665 original size:42 final size:43
Alignment explanation
Indices: 5272585--5272670 Score: 129
Period size: 42 Copynumber: 2.0 Consensus size: 43
5272575 TCACTAGGAA
* *
5272585 TTATGTGATCTGAACTCTTTGAGTTGTGGTATGAGTTCATGAT
1 TTATGTGATCTGAACTCATTGAGTTGTGGTATAAGTTCATGAT
* *
5272628 TTATGTGATTTGAACTCATT-AGTTGTGGTCTAAGTTCATGAT
1 TTATGTGATCTGAACTCATTGAGTTGTGGTATAAGTTCATGAT
5272670 T
1 T
5272671 ATGAGACACA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 21 0.54
43 18 0.46
ACGTcount: A:0.22, C:0.09, G:0.23, T:0.45
Consensus pattern (43 bp):
TTATGTGATCTGAACTCATTGAGTTGTGGTATAAGTTCATGAT
Found at i:5274025 original size:47 final size:46
Alignment explanation
Indices: 5273915--5274038 Score: 135
Period size: 47 Copynumber: 2.7 Consensus size: 46
5273905 GTTATTGTGG
* * *
5273915 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAGATTATGAGA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCAGATGACGAGA
* * *
5273961 GCCAGTGTAAGACCATGTCTAGTACATGGCATCGG-CATTGA-GACGAGT
1 GCTAGTGTAAGA-CATGTCTAGGACAT-GCATCGGCCA--GATGACGAGA
*
5274009 GCTAGTGTAAGACATGTCTGGGACATGCAT
1 GCTAGTGTAAGACATGTCTAGGACATGCAT
5274039 TGGCTACGAA
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
46 15 0.23
47 26 0.40
48 22 0.34
49 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCAGATGACGAGA
Found at i:5275533 original size:49 final size:49
Alignment explanation
Indices: 5275461--5275652 Score: 197
Period size: 49 Copynumber: 3.9 Consensus size: 49
5275451 TAGCTAAAGC
*
5275461 TATCTGGTACGCATAGTAGCCTACACTTAGTACTACACATGCAACCAAT
1 TATCTGGTACACATAGTAGCCTACACTTAGTACTACACATGCAACCAAT
* ** *
5275510 TATCTGGTACACATAGTAGCCTACACTTAGTACTACACACGTGACCTAAC
1 TATCTGGTACACATAGTAGCCTACACTTAGTACTACACATGCAACC-AAT
* ** * * * *
5275560 CATCTAATACACGTAGTAGCCTGCACTTAGTACTACACACGTG-ATCGAAGT
1 TATCTGGTACACATAGTAGCCTACACTTAGTACTACACA--TGCAACCAA-T
* * * *
5275611 TATCGGGTACGCATAGTAGCCTGCAGTTAGTACTACACATGC
1 TATCTGGTACACATAGTAGCCTACACTTAGTACTACACATGC
5275653 GACCTCACAA
Statistics
Matches: 116, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
49 44 0.38
50 38 0.33
51 33 0.28
52 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (49 bp):
TATCTGGTACACATAGTAGCCTACACTTAGTACTACACATGCAACCAAT
Found at i:5275592 original size:50 final size:49
Alignment explanation
Indices: 5275472--5275603 Score: 174
Period size: 50 Copynumber: 2.7 Consensus size: 49
5275462 ATCTGGTACG
* ** ** **
5275472 CATAGTAGCCTACACTTAGTACTACACATGCAACCAATTATCTGGTACA
1 CATAGTAGCCTACACTTAGTACTACACACGTGACCAACCATCTAATACA
5275521 CATAGTAGCCTACACTTAGTACTACACACGTGACCTAACCATCTAATACA
1 CATAGTAGCCTACACTTAGTACTACACACGTGACC-AACCATCTAATACA
* *
5275571 CGTAGTAGCCTGCACTTAGTACTACACACGTGA
1 CATAGTAGCCTACACTTAGTACTACACACGTGA
5275604 TCGAAGTTAT
Statistics
Matches: 73, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
49 32 0.44
50 41 0.56
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.25
Consensus pattern (49 bp):
CATAGTAGCCTACACTTAGTACTACACACGTGACCAACCATCTAATACA
Found at i:5275657 original size:101 final size:99
Alignment explanation
Indices: 5275474--5275657 Score: 253
Period size: 101 Copynumber: 1.8 Consensus size: 99
5275464 CTGGTACGCA
*
5275474 TAGTAGCCTACACTTAGTACTACACATGCAACCAATTATCTGGTACACATAGTAGCCTACACTTA
1 TAGTAGCCTACACTTAGTACTACACATGCAACCAATTATCGGGTACACATAGTAGCCTACACTTA
*
5275539 GTACTACACACGTGACCTAACCATCTAATACACG
66 GTACTACACACGCGACCTAACCATCTAATACACG
* * * * * *
5275573 TAGTAGCCTGCACTTAGTACTACACACGTG-ATCGAAGTTATCGGGTACGCATAGTAGCCTGCAG
1 TAGTAGCCTACACTTAGTACTACACA--TGCAACCAA-TTATCGGGTACACATAGTAGCCTACAC
*
5275637 TTAGTACTACACATGCGACCT
63 TTAGTACTACACACGCGACCT
5275658 CACAATAGAT
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
99 25 0.34
100 4 0.05
101 44 0.60
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.26
Consensus pattern (99 bp):
TAGTAGCCTACACTTAGTACTACACATGCAACCAATTATCGGGTACACATAGTAGCCTACACTTA
GTACTACACACGCGACCTAACCATCTAATACACG
Found at i:5281814 original size:15 final size:15
Alignment explanation
Indices: 5281794--5281834 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
5281784 GTATCGTATT
5281794 TTGGATTTCTTTATC
1 TTGGATTTCTTTATC
*
5281809 TTGGATTTCTTCATC
1 TTGGATTTCTTTATC
5281824 TTGG-TTTCTTT
1 TTGGATTTCTTT
5281835 GTCATCTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 6 0.25
15 18 0.75
ACGTcount: A:0.10, C:0.15, G:0.15, T:0.61
Consensus pattern (15 bp):
TTGGATTTCTTTATC
Found at i:5284698 original size:140 final size:140
Alignment explanation
Indices: 5284446--5285258 Score: 858
Period size: 140 Copynumber: 6.0 Consensus size: 140
5284436 TACAACAAAA
* * * *
5284446 TAGTCCTAAGACGACACTTTTGTGGCAACACTTTCCTAAGTGTTGGGATAGACTGGCCAATATAC
1 TAGTCCTAAGACGACACTTTTGGGGTAACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATAC
* * * *
5284511 GCTTTAGCCAACTATTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAAAGCTTAAATAAGAGT
66 ACTTTGGCCAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGT
5284576 TGGCTTTGTC
131 TGGCTTTGTC
* * *
5284586 TAGTCCTAAGGCGACACTTTTGGGGTGACACTTTCGTAAGTGTTGGGATAGACTTGCCAACATAC
1 TAGTCCTAAGACGACACTTTTGGGGTAACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATAC
* ** * * * *
5284651 ACTTTCGCCAACTCTTTAAATAAAGGTTGGGATATGTATGCCTAAGGCAACACTTGAATAAGAGT
66 ACTTTGGCCAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGT
*
5284716 TGGCTTTTGTG
131 TGGC-TTTGTC
** *
5284727 TAGTCCTAAGACGACACTTTTGGGGCGACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATAT
1 TAGTCCTAAGACGACACTTTTGGGGTAACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATAC
* * * * * *
5284792 GCTTTGGCCAACTCTTTGCATAAGGGTTGCGATATGTATTCCTAAGACAACGCTTAAATAAGAGT
66 ACTTTGGCCAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGT
5284857 TGGCTTTGTC
131 TGGCTTTGTC
* * * *
5284867 CAGTCCTAAGACGACA---------T-----TTTCCTAAGTGTTAGGATAGACTTGTCGACATAC
1 TAGTCCTAAGACGACACTTTTGGGGTAACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATAC
** ** * *
5284918 TTTTTGGTGAACTTTTTGTATAAGGGTTGGGATATGCATGCTTAAGGCAACGCTTAAATAAGAGT
66 ACTTTGGCCAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGT
*
5284983 CGGCTTTGTC
131 TGGCTTTGTC
* * * * * *
5284993 GA-ACACTATGCCTACACATTT-GGGTCAACACTTTCCTAAGTGTTGGGATAGACTTGCCAACAT
1 TAGTC-CTAAGACGACACTTTTGGGGT-AACACTTTCCTAAGTGTTGGGATAGACTTGCCAACAT
**
5285056 ACACTTTGGCCAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACTTTTAAATAAGA
64 ACACTTTGGCCAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGA
*
5285121 GTCGG--TT-T-
129 GTTGGCTTTGTC
* ** * *
5285129 T-GTCC--A-A-G--AC-TAT--GCCAACACTTTCCTAAGTGTTGGGATAGACTTGTCAACATAT
1 TAGTCCTAAGACGACACTTTTGGGGTAACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATAC
* * * * *
5285184 GCTTTGGCCAACTCTTTGTATAAGAGATGGTATATGCATGCCTAAGGCAACACTTAAATAAGAGT
66 ACTTTGGCCAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGT
*
5285249 TAGCTTTGTC
131 TGGCTTTGTC
5285259 CAATAGTATG
Statistics
Matches: 567, Mismatches: 85, Indels: 52
0.81 0.12 0.07
Matches are distributed among these distances:
125 1 0.00
126 199 0.35
127 1 0.00
128 4 0.01
129 3 0.01
134 1 0.00
135 1 0.00
136 1 0.00
137 1 0.00
138 2 0.00
140 228 0.40
141 125 0.22
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (140 bp):
TAGTCCTAAGACGACACTTTTGGGGTAACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATAC
ACTTTGGCCAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGT
TGGCTTTGTC
Found at i:5284977 original size:126 final size:126
Alignment explanation
Indices: 5284754--5285260 Score: 559
Period size: 126 Copynumber: 3.9 Consensus size: 126
5284744 TTTTGGGGCG
*
5284754 ACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATATGCTTTGGCCAACTCTTTGCATAAGGGT
1 ACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATATGCTTTGGCCAACTCTTTGTATAAGGGT
* * * * * *
5284819 TGCGATATGTATTCCTAAGACAACGCTTAAATAAGAGTTGGCTTTGTCCAGTCCTAAGACG
66 TGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCCAGTCCTAAGACA
* * * * * ** *
5284880 ACATTTTCCTAAGTGTTAGGATAGACTTGTCGACATACT-TTTTGGTGAACTTTTTGTATAAGGG
1 ACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATA-TGCTTTGGCCAACTCTTTGTATAAGGG
* *
5284944 TTGGGATATGCATGCTTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCGAACACTATGCCTACA
65 TTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTC---CA--GT-CCT--A
*
5285009 CATTTGGGTCA
122 -A-----GACA
**
5285020 ACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATACACTTTGGCCAACTCTTTGTATAAGGGT
1 ACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATATGCTTTGGCCAACTCTTTGTATAAGGGT
** * * * *
5285085 TGGGATATGCATGCCTAAGGCAACTTTTAAATAAGAGTCGGTTTTGTCCAAG-ACTATGCCA
66 TGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCC-AGTCCTAAGACA
* * *
5285146 ACACTTTCCTAAGTGTTGGGATAGACTTGTCAACATATGCTTTGGCCAACTCTTTGTATAAGAGA
1 ACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATATGCTTTGGCCAACTCTTTGTATAAGGGT
* * **
5285211 TGGTATATGCATGCCTAAGGCAACACTTAAATAAGAGTTAGCTTTGTCCA
66 TGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCCA
5285261 ATAGTATGTC
Statistics
Matches: 318, Mismatches: 46, Indels: 35
0.80 0.12 0.09
Matches are distributed among these distances:
125 1 0.00
126 202 0.64
127 1 0.00
129 2 0.01
131 1 0.00
132 4 0.01
134 3 0.01
135 1 0.00
137 1 0.00
138 1 0.00
140 101 0.32
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (126 bp):
ACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATATGCTTTGGCCAACTCTTTGTATAAGGGT
TGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCCAGTCCTAAGACA
Found at i:5285117 original size:266 final size:267
Alignment explanation
Indices: 5284613--5285258 Score: 798
Period size: 266 Copynumber: 2.4 Consensus size: 267
5284603 TTTTGGGGTG
* * * ** * ** *
5284613 ACACTTTCGTAAGTGTTGGGATAGACTTGCCAACATACACTTTCGCCAACTCTTTAAATAAAGGT
1 ACACTTTCCTAAGTGTTAGGATAGACTTGTCAACATATGCTTTGGCCAACTCTTTGTATAAGGGT
* * *
5284678 TGGGATATGTATGCCTAAGGCAACACTTGAATAAGAGTTGGCTTTTGT-GTAGTCCTAAGACGAC
66 TGGGATATGCATGCCTAAGGCAACACTTAAATAAGAGTTGGC-TTTGTCGTAGACCTAAGACGAC
* * **
5284742 ACTTTTGGGGCGACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATATGCTTTGGCCAACTCT
130 ACATTTGGGGCAACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATACACTTTGGCCAACTCT
* * *
5284807 TTGCATAAGGGTTGCGATATGTATTCCTAAGACAACGCTTAAATAAGAGTTGGCTTTGTCC-AGT
195 TTGCATAAGGGTTGCGATATGCATGCCTAAGACAACGCTTAAATAAGAGTCGGCTTTGTCCAAG-
* *
5284871 CCTAAGACG
259 ACTAAGACA
* * * ** *
5284880 ACATTTTCCTAAGTGTTAGGATAGACTTGTCGACATACT-TTTTGGTGAACTTTTTGTATAAGGG
1 ACACTTTCCTAAGTGTTAGGATAGACTTGTCAACATA-TGCTTTGGCCAACTCTTTGTATAAGGG
* * * * * *
5284944 TTGGGATATGCATGCTTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCG-A-ACACTATGCCTA
65 TTGGGATATGCATGCCTAAGGCAACACTTAAATAAGAGTTGGCTTTGTCGTAGAC-CTAAGACGA
*
5285007 CACATTTGGGTCAACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATACACTTTGGCCAACTC
129 CACATTTGGGGCAACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATACACTTTGGCCAACTC
* * * ** *
5285072 TTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACTTTTAAATAAGAGTCGGTTTTGTCCAAG
194 TTTGCATAAGGGTTGCGATATGCATGCCTAAGACAACGCTTAAATAAGAGTCGGCTTTGTCCAAG
* *
5285137 ACTATGCCA
259 ACTAAGACA
* * *
5285146 ACACTTTCCTAAGTGTTGGGATAGACTTGTCAACATATGCTTTGGCCAACTCTTTGTATAAGAGA
1 ACACTTTCCTAAGTGTTAGGATAGACTTGTCAACATATGCTTTGGCCAACTCTTTGTATAAGGGT
* *
5285211 TGGTATATGCATGCCTAAGGCAACACTTAAATAAGAGTTAGCTTTGTC
66 TGGGATATGCATGCCTAAGGCAACACTTAAATAAGAGTTGGCTTTGTC
5285259 CAATAGTATG
Statistics
Matches: 319, Mismatches: 55, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
265 2 0.01
266 227 0.71
267 90 0.28
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.32
Consensus pattern (267 bp):
ACACTTTCCTAAGTGTTAGGATAGACTTGTCAACATATGCTTTGGCCAACTCTTTGTATAAGGGT
TGGGATATGCATGCCTAAGGCAACACTTAAATAAGAGTTGGCTTTGTCGTAGACCTAAGACGACA
CATTTGGGGCAACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATACACTTTGGCCAACTCTT
TGCATAAGGGTTGCGATATGCATGCCTAAGACAACGCTTAAATAAGAGTCGGCTTTGTCCAAGAC
TAAGACA
Found at i:5287439 original size:40 final size:40
Alignment explanation
Indices: 5287402--5287627 Score: 348
Period size: 40 Copynumber: 5.7 Consensus size: 40
5287392 GCTACTCGTT
* *
5287402 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
5287442 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
5287482 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
5287522 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
5287562 CAAATGCCTTCGGGACTTAACCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC-TCGCA
* *
5287603 CAAA-ACCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
5287628 CATCATTCAA
Statistics
Matches: 176, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
40 166 0.94
41 10 0.06
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:5287612 original size:120 final size:120
Alignment explanation
Indices: 5287367--5287627 Score: 350
Period size: 120 Copynumber: 2.2 Consensus size: 120
5287357 CCAAATCACG
* * ** *
5287367 TACCTTCGGAATTTAA-CCGGATATAGCTACTCGTTCAAATGCCTTCGGGACATAGCCCGGTTAT
1 TACCTTCGGGACTTAACCCGGATATAGCTACTCGCACAAATGCCTTCGGGACATAACCCGGTTAT
* *
5287431 AGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAA
66 AGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACAAA
* * *
5287486 TGCCTTCGGGACTTAACCCGGATTTAG-TAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 TACCTTCGGGACTTAACCCGGATATAGCT-ACTCGCACAAATGCCTTCGGGACATAACCCGG-TT
* *
5287550 -TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATGGTCACTTAGCACAAA
64 ATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAAC-TAGCACAAA
*
5287607 -ACCTTCGGGACTTAGCCCGGA
1 TACCTTCGGGACTTAACCCGGA
5287628 CATCATTCAA
Statistics
Matches: 124, Mismatches: 14, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
119 14 0.11
120 100 0.81
121 10 0.08
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (120 bp):
TACCTTCGGGACTTAACCCGGATATAGCTACTCGCACAAATGCCTTCGGGACATAACCCGGTTAT
AGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACAAA
Found at i:5290585 original size:66 final size:66
Alignment explanation
Indices: 5290479--5290610 Score: 255
Period size: 66 Copynumber: 2.0 Consensus size: 66
5290469 TTTTTAAAGC
*
5290479 AAATACGATGGCAGCTAGTTCGAGATCATGGGTCAGATAATTTTTCTCATGTGGCTTTAATTGTC
1 AAATACGATGGCAGCTAGTTCAAGATCATGGGTCAGATAATTTTTCTCATGTGGCTTTAATTGTC
5290544 T
66 T
5290545 AAATACGATGGCAGCTAGTTCAAGATCATGGGTCAGATAATTTTTCTCATGTGGCTTTAATTGTC
1 AAATACGATGGCAGCTAGTTCAAGATCATGGGTCAGATAATTTTTCTCATGTGGCTTTAATTGTC
5290610 T
66 T
5290611 CGACGCATAG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (66 bp):
AAATACGATGGCAGCTAGTTCAAGATCATGGGTCAGATAATTTTTCTCATGTGGCTTTAATTGTC
T
Found at i:5294982 original size:39 final size:40
Alignment explanation
Indices: 5294892--5295055 Score: 176
Period size: 40 Copynumber: 4.1 Consensus size: 40
5294882 CGGAATTTAA
** *
5294892 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
5294932 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGAC-TAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
5294971 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
5295011 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
5295051 CCGGA
1 CCGGA
5295056 CATCATTCAA
Statistics
Matches: 106, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
38 4 0.04
39 32 0.30
40 58 0.55
41 12 0.11
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:5296892 original size:35 final size:35
Alignment explanation
Indices: 5296843--5296925 Score: 139
Period size: 35 Copynumber: 2.4 Consensus size: 35
5296833 TCTGCCTTAT
* *
5296843 TCCAGCCACTGGTGCATCTGCTGTCGACCACCTGC
1 TCCAGCCACTGGTGCATCTGCCGTCCACCACCTGC
*
5296878 TCTAGCCACTGGTGCATCTGCCGTCCACCACCTGC
1 TCCAGCCACTGGTGCATCTGCCGTCCACCACCTGC
5296913 TCCAGCCACTGGT
1 TCCAGCCACTGGT
5296926 ATGTCACGGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.14, C:0.41, G:0.22, T:0.23
Consensus pattern (35 bp):
TCCAGCCACTGGTGCATCTGCCGTCCACCACCTGC
Found at i:5308836 original size:27 final size:27
Alignment explanation
Indices: 5308805--5308982 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
5308795 TAAATTGTAC
5308805 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
5308832 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * * *
5308858 ATGCACTAAGTGTGCTAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
5308886 GGCACTAAGTTTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
5308914 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
5308941 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
5308968 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
5308983 GACTCAATAT
Statistics
Matches: 125, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
27 103 0.82
28 22 0.18
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:5308973 original size:82 final size:81
Alignment explanation
Indices: 5308802--5308982 Score: 211
Period size: 82 Copynumber: 2.2 Consensus size: 81
5308792 GATTAAATTG
* *
5308802 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
*
5308867 GTGTGCTAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
5308883 TGCGGCACTAAGTTTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
5308947 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
5308965 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
5308983 GACTCAATAT
Statistics
Matches: 81, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
81 17 0.21
82 64 0.79
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:5312067 original size:108 final size:106
Alignment explanation
Indices: 5311955--5312485 Score: 334
Period size: 111 Copynumber: 4.8 Consensus size: 106
5311945 TGTAAATGGG
* * *
5311955 TCTATCCCAACATTTTTAACGTTGTCTTAGATAGGTCAATCCCAACCTTTTCTAAAAGTTGCTTT
1 TCTATCCCAACATTTTTAACGTTG-CTTAGAAAGGTCTATCCCAACCTTTT-TAAAAGTTGCCTT
* * * *
5312020 AGACAAGATCTATTCCAACCTTTTGGAGGTTACCTTAGACGA-A
64 AGACAAG-TCTATCCCAACCTTTTGAAGGTTACCTTAAACAAGA
* * ** * *
5312063 TCTATCCCAACCTTTTTAAGGTTGCTTTAGACAA-GTCTATCGTAACCTTTTTTTAAGGTTGCCT
1 TCTATCCCAACATTTTTAACGTTGC-TTAGA-AAGGTCTATCCCAACC-TTTTTAAAAGTTGCCT
* * *
5312127 TAAACAAGTCTATCCCAACCCTTTTTTAAGGTTGCCTTAAACAAGA
63 TAGACAAGTCTATCCCAA-CC-TTTTGAAGGTTACCTTAAACAAGA
* * * *
5312173 TCTATCCCAACCTTTTTTAAATGTTGCCTTAGACAAGGTCTATCTCAACATTTTTAAAAGGTTGC
1 TCTATCCCAA-CATTTTT-AACGTTG-CTTAGA-AAGGTCTATCCCAACCTTTTTAAAA-GTTGC
* * * * * *
5312238 CTTAGATAAGGTCTATCCCAACCTTTTTTAAAGGTTGCCCTAGACAAGG
61 CTTAGACAA-GTCTATCCCAACC--TTTTGAAGGTTACCTTAAACAAGA
* * * * * * *
5312287 TCTA-CACCAACCTATTTAAGGTTGCTTTAG-ACGATTCTATCCCAATCTTTTTTAAAGGTTGCC
1 TCTATC-CCAACATTTTTAACGTTGC-TTAGAAAG-GTCTATCCCAA-CCTTTTTAAAAGTTGCC
* * * * * * * * * *
5312350 TTAGACAAGGTTTATCGCAACTTTTTTTAAATGTTGCCTTAGATATGG
62 TTAGACAA-GTCTATCCCAAC--CTTTTGAAGGTTACCTTAAACAAGA
* * * ** *
5312398 TCTATCCCAACTTTTTTTAAAGGTTATCTTAGACTGGTCTATCCCAACCTTTTT-AAGGTTGCCT
1 TCTATCCCAAC-ATTTTT-AACGTT-GCTTAGAAAGGTCTATCCCAACCTTTTTAAAAGTTGCCT
* *
5312462 TAGACAGGTCTATCACAACCTTTT
63 TAGACAAGTCTATCCCAACCTTTT
5312486 TCAAAGGTTG
Statistics
Matches: 343, Mismatches: 56, Indels: 48
0.77 0.13 0.11
Matches are distributed among these distances:
107 10 0.03
108 59 0.17
109 22 0.06
110 23 0.07
111 85 0.25
112 51 0.15
113 51 0.15
114 42 0.12
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (106 bp):
TCTATCCCAACATTTTTAACGTTGCTTAGAAAGGTCTATCCCAACCTTTTTAAAAGTTGCCTTAG
ACAAGTCTATCCCAACCTTTTGAAGGTTACCTTAAACAAGA
Found at i:5312543 original size:38 final size:38
Alignment explanation
Indices: 5311814--5312531 Score: 568
Period size: 38 Copynumber: 19.6 Consensus size: 38
5311804 GAGACAAATA
* * *
5311814 TCTATCCCGACC-TTTTT-AAGTTTGCCTTAGAC-GGG
1 TCTATCCCAACCTTTTTTAAAGGTTGCCTTAGACTAGG
* *
5311849 TTTATCCTAA-CTTTTTT-AAGGTTGCCTTAGAC-AGG
1 TCTATCCCAACCTTTTTTAAAGGTTGCCTTAGACTAGG
* * * * **
5311884 TTTATCCCAA-TTTTTTTTAA-GTTGCCTTGGAAAAGG
1 TCTATCCCAACCTTTTTTAAAGGTTGCCTTAGACTAGG
** * * *
5311920 TCTATCTTAA-CTTTTTT-AAGGTTG-TTGTA-AATGGG
1 TCTATCCCAACCTTTTTTAAAGGTTGCCT-TAGACTAGG
* * *
5311955 TCTATCCCAA-CATTTTT-AACGTTGTCTTAGA-TAGG
1 TCTATCCCAACCTTTTTTAAAGGTTGCCTTAGACTAGG
* * * * * *
5311990 TCAATCCCAACCTTTTCTAAAAGTTGCTTTAGACAAGA
1 TCTATCCCAACCTTTTTTAAAGGTTGCCTTAGACTAGG
* ** * * *
5312028 TCTATTCCAACC--TTTTGGAGGTTACCTTAGACGA-A
1 TCTATCCCAACCTTTTTTAAAGGTTGCCTTAGACTAGG
* *
5312063 TCTATCCCAACC-TTTTT-AAGGTTGCTTTAGAC-AAG
1 TCTATCCCAACCTTTTTTAAAGGTTGCCTTAGACTAGG
** * * *
5312098 TCTATCGTAACCTTTTTTTAAGGTTGCCTTAAAC-AAG
1 TCTATCCCAACCTTTTTTAAAGGTTGCCTTAGACTAGG
* * *
5312135 TCTATCCCAACCCTTTTTT-AAGGTTGCCTTAAACAAGA
1 TCTATCCCAA-CCTTTTTTAAAGGTTGCCTTAGACTAGG
* *
5312173 TCTATCCCAACCTTTTTTAAATGTTGCCTTAGACAAGG
1 TCTATCCCAACCTTTTTTAAAGGTTGCCTTAGACTAGG
* * *
5312211 TCTATCTCAACATTTTTAAAAGGTTGCCTTAGA-TAAGG
1 TCTATCCCAACCTTTTTTAAAGGTTGCCTTAGACT-AGG
* *
5312249 TCTATCCCAACCTTTTTTAAAGGTTGCCCTAGACAAGG
1 TCTATCCCAACCTTTTTTAAAGGTTGCCTTAGACTAGG
* * * *
5312287 TCTA-CACCAACC-TATTT-AAGGTTGCTTTAGACGA-T
1 TCTATC-CCAACCTTTTTTAAAGGTTGCCTTAGACTAGG
* *
5312322 TCTATCCCAATCTTTTTTAAAGGTTGCCTTAGACAAGG
1 TCTATCCCAACCTTTTTTAAAGGTTGCCTTAGACTAGG
* * * *
5312360 TTTATCGCAACTTTTTTTAAATGTTGCCTTAGA-TATGG
1 TCTATCCCAACCTTTTTTAAAGGTTGCCTTAGACTA-GG
* **
5312398 TCTATCCCAACTTTTTTTAAAGGTTATCTTAGACT-GG
1 TCTATCCCAACCTTTTTTAAAGGTTGCCTTAGACTAGG
5312435 TCTATCCCAACC-TTTTT-AAGGTTGCCTTAGAC-AGG
1 TCTATCCCAACCTTTTTTAAAGGTTGCCTTAGACTAGG
* *
5312470 TCTATCACAACCTTTTTCAAAGGTTGGCCTT-GACTAGG
1 TCTATCCCAACCTTTTTTAAAGGTT-GCCTTAGACTAGG
*
5312508 TCTATCGCAACCTTTTTTAAAGGT
1 TCTATCCCAACCTTTTTTAAAGGT
5312532 CGGCATTGAC
Statistics
Matches: 558, Mismatches: 94, Indels: 59
0.78 0.13 0.08
Matches are distributed among these distances:
34 2 0.00
35 163 0.29
36 82 0.15
37 101 0.18
38 209 0.37
39 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (38 bp):
TCTATCCCAACCTTTTTTAAAGGTTGCCTTAGACTAGG
Found at i:5312554 original size:38 final size:38
Alignment explanation
Indices: 5312471--5312557 Score: 111
Period size: 38 Copynumber: 2.3 Consensus size: 38
5312461 TTAGACAGGT
* * * * *
5312471 CTATCACAACCTTTTTCAAAGGTTGGCCTTGACTAGGT
1 CTATCGCAACCTTTTTCAAAGGTCGGCATTGACTAAGA
*
5312509 CTATCGCAACCTTTTTTAAAGGTCGGCATTGACTAAGA
1 CTATCGCAACCTTTTTCAAAGGTCGGCATTGACTAAGA
*
5312547 CTTTCGCAACC
1 CTATCGCAACC
5312558 CTTCAATAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (38 bp):
CTATCGCAACCTTTTTCAAAGGTCGGCATTGACTAAGA
Found at i:5313280 original size:43 final size:45
Alignment explanation
Indices: 5313212--5313343 Score: 180
Period size: 43 Copynumber: 3.0 Consensus size: 45
5313202 CGAAATGTGG
* * *
5313212 TATTCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAAATGA-
1 TATTCGGGCTTTGAGCCTAGTAGGCTATAATGCCGGTGAAATGAT
* *
5313256 TA-TCGGGCTTTGAGCTTAGTAGGCTATGATGCCGGTGAAAT-AT
1 TATTCGGGCTTTGAGCCTAGTAGGCTATAATGCCGGTGAAATGAT
*
5313299 TATTCGAGCCTTTGAGCCTAGTAGGCTATAATGCCGGTGAAATGA
1 TATTCG-GGCTTTGAGCCTAGTAGGCTATAATGCCGGTGAAATGA
5313344 AATGTTATGT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
42 1 0.01
43 36 0.47
44 5 0.07
45 33 0.43
46 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (45 bp):
TATTCGGGCTTTGAGCCTAGTAGGCTATAATGCCGGTGAAATGAT
Found at i:5313325 original size:45 final size:43
Alignment explanation
Indices: 5313226--5313343 Score: 166
Period size: 45 Copynumber: 2.7 Consensus size: 43
5313216 CGGGCTTCGG
* *
5313226 GCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGGCTTTGA
1 GCCTAGTAGGCTATAATGCCGGTGAAATGATATCGGCCTTTGA
* *
5313269 GCTTAGTAGGCTATGATGCCGGTGAAAT-ATTATTCGAGCCTTTGA
1 GCCTAGTAGGCTATAATGCCGGTGAAATGA-TA-TCG-GCCTTTGA
5313314 GCCTAGTAGGCTATAATGCCGGTGAAATGA
1 GCCTAGTAGGCTATAATGCCGGTGAAATGA
5313344 AATGTTATGT
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
42 1 0.02
43 27 0.42
44 3 0.05
45 33 0.51
46 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (43 bp):
GCCTAGTAGGCTATAATGCCGGTGAAATGATATCGGCCTTTGA
Found at i:5313672 original size:38 final size:38
Alignment explanation
Indices: 5313640--5313772 Score: 169
Period size: 38 Copynumber: 3.5 Consensus size: 38
5313630 GCAGGCTATA
*
5313640 TGCTAGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
1 TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
*
5313678 TGCTGGTAA-TATATCTGGGTTAAATCCCGCAGGCTTCG
1 TGCTGG-AATTATATCCGGGTTAAATCCCGCAGGCTTCG
* * * * *
5313716 TGCTGGTATTATATCCGGGTTACATTCCGCAGGCCTAG
1 TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
* *
5313754 TGCTGGTATTATATTCGGG
1 TGCTGGAATTATATCCGGG
5313773 CCTTTGAGCC
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
37 1 0.01
38 81 0.96
39 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.32
Consensus pattern (38 bp):
TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
Found at i:5313815 original size:45 final size:45
Alignment explanation
Indices: 5313765--5313981 Score: 291
Period size: 45 Copynumber: 4.9 Consensus size: 45
5313755 GCTGGTATTA
* * *
5313765 TATTCGGGCCTTTGAGCCTAGCAGGCTATTATGCCAGTGAGACAC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
*
5313810 TATTCGGGCCTTTGGGCCTAGCAGGCTATAATGCCGGTGAGATAC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
*
5313855 TATTCGGGCCTTTGGGCCTAGCAGGCTATAATGCCGGTGAGATAC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
* *
5313900 TATTCGGG-CTTTCGAGCCTAGCAGGCTATAATGCCGATGAAATGA-
1 TATTCGGGCCTTT-GAGCCTAGCAGGCTATAATGCCGGTGAGAT-AC
* * *
5313945 TA-TCGGGCC-TCGATCCTAGCAGGC-AAAATGCCGGTGA
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
5313982 TTTGAGAAAA
Statistics
Matches: 158, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
42 11 0.07
43 12 0.08
44 10 0.06
45 124 0.78
46 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (45 bp):
TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
Found at i:5317569 original size:3 final size:3
Alignment explanation
Indices: 5317561--5317599 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
5317551 ATTGTAATGC
5317561 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5317600 CATAAATTGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5317964 original size:22 final size:21
Alignment explanation
Indices: 5317938--5318000 Score: 56
Period size: 22 Copynumber: 3.0 Consensus size: 21
5317928 ACTCATTGAG
5317938 TTGTGGTCTGAGTTCATGATT
1 TTGTGGTCTGAGTTCATGATT
* * ** *
5317959 TATGTGATTTGAACTCATGA-G
1 T-TGTGGTCTGAGTTCATGATT
*
5317980 TTGTGGCCTGAGTTCATGATT
1 TTGTGGTCTGAGTTCATGATT
5318001 ACGAGACACT
Statistics
Matches: 29, Mismatches: 11, Indels: 4
0.66 0.25 0.09
Matches are distributed among these distances:
20 13 0.45
21 2 0.07
22 14 0.48
ACGTcount: A:0.19, C:0.11, G:0.27, T:0.43
Consensus pattern (21 bp):
TTGTGGTCTGAGTTCATGATT
Found at i:5317992 original size:42 final size:43
Alignment explanation
Indices: 5317915--5318000 Score: 138
Period size: 42 Copynumber: 2.0 Consensus size: 43
5317905 CCACTAGGAA
*
5317915 TTATGTGATCTAAACTCATTGAGTTGTGGTCTGAGTTCATGAT
1 TTATGTGATCTAAACTCATTGAGTTGTGGCCTGAGTTCATGAT
* *
5317958 TTATGTGATTTGAACTCA-TGAGTTGTGGCCTGAGTTCATGAT
1 TTATGTGATCTAAACTCATTGAGTTGTGGCCTGAGTTCATGAT
5318000 T
1 T
5318001 ACGAGACACT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 24 0.60
43 16 0.40
ACGTcount: A:0.22, C:0.12, G:0.24, T:0.42
Consensus pattern (43 bp):
TTATGTGATCTAAACTCATTGAGTTGTGGCCTGAGTTCATGAT
Found at i:5321305 original size:20 final size:18
Alignment explanation
Indices: 5321280--5321318 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
5321270 GAAGTTTATA
*
5321280 AAATAGGTTGTAAATGTGTG
1 AAATA-GTTGAAAAT-TGTG
5321300 AAATAGTTGAAAATTGTG
1 AAATAGTTGAAAATTGTG
5321318 A
1 A
5321319 GTTGCTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 8 0.44
20 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.26, T:0.33
Consensus pattern (18 bp):
AAATAGTTGAAAATTGTG
Found at i:5321857 original size:48 final size:48
Alignment explanation
Indices: 5321783--5322149 Score: 474
Period size: 48 Copynumber: 7.6 Consensus size: 48
5321773 TATATGTGCT
*
5321783 AGTGTAAGACCATGTCTGGGAAATGGCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCC
*
5321831 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCC
*
5321879 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCC
* *** * * *
5321927 AGTGTAAGACCATGTCTGGGACATGGCATTGGCGTTGA-TATGTGTGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-CACATTATGAGAGCC
*
5321975 AGTGTAAGACCATGTCTGGGATATGGCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCC
* * *
5322023 AGTGTAAGACCATGTCTGGGATATGGCATCGG---CATTGAGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATT---ATGAGAGCC
* * * * *
5322071 AGTGTAAGGCCATGTTTGGGACATGGCATCGGCCTCGA-CATGTGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC-ATTATGAGAGCC
*
5322119 AGTGTAAGACCATGTTTGGGACATGGCATCG
1 AGTGTAAGACCATGTCTGGGACATGGCATCG
5322150 ATAATTTACC
Statistics
Matches: 282, Mismatches: 28, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
45 4 0.01
47 1 0.00
48 274 0.97
49 1 0.00
51 1 0.00
52 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCC
Found at i:5328071 original size:20 final size:18
Alignment explanation
Indices: 5328031--5328074 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
5328021 TGTGGGTAGG
*
5328031 CCGTGTGGTCTCACACGC
1 CCGTGTGGTCTCACACAC
*
5328049 CCGTGTGGCTCTGGACACAC
1 CCGTGTGG-TCT-CACACAC
5328069 CCGTGT
1 CCGTGT
5328075 CATCAACCCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.36
19 3 0.14
20 11 0.50
ACGTcount: A:0.11, C:0.36, G:0.30, T:0.23
Consensus pattern (18 bp):
CCGTGTGGTCTCACACAC
Found at i:5329856 original size:40 final size:40
Alignment explanation
Indices: 5329812--5330103 Score: 394
Period size: 40 Copynumber: 7.3 Consensus size: 40
5329802 GGACTAAGAT
*
5329812 CCGAAGGCATTTGTGCGAGATACAAATTTCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
5329852 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
5329892 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
5329932 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
* *
5329972 CCGAAGGCCTTTGTGCGAGATACTAAA-TCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
* * ** * *
5330012 CCGAAGGCATTCGTGCGAGTTGTTAAA-TCCGGGTTATGTC
1 CCGAAGGCATTTGTGCGAGAT-ACAAATTCCGGGTTAAGCC
* * * * * *
5330052 CCGAAGGCA-TTGTGTGAGTTACTAAA-ACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
5330091 CCGAAGGCATTTG
1 CCGAAGGCATTTG
5330104 AACGAGGAGC
Statistics
Matches: 233, Mismatches: 15, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
39 32 0.14
40 198 0.85
41 3 0.01
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
Found at i:5330121 original size:79 final size:80
Alignment explanation
Indices: 5329879--5330136 Score: 222
Period size: 80 Copynumber: 3.2 Consensus size: 80
5329869 AGATACAAAT
* * * *
5329879 TCCGGGTTAAGCCCCGAAGG-CATTTGTGCGAGATAC-AAATTCCGGGTTAAGCCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCCA-TTGTGCGAGATACTAAA-ACCGGGCTAAGTCCCGAAGGCAT
* ** *
5329942 TTGTGCGA-GATAC-AAA
64 TCGAACGAGGA-GCTAAA
* * * *
5329958 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 -TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
5330023 CGTGCGAGTTGTTAAA
65 CGAACGAGGAGCTAAA
* * * * *
5330039 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
5330103 GAACGAGGAGCTATA
66 GAACGAGGAGCTAAA
*
5330118 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
5330137 TACGTGATTT
Statistics
Matches: 150, Mismatches: 24, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
78 14 0.09
79 49 0.33
80 80 0.53
81 7 0.05
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGGAGCTAAA
Found at i:5334410 original size:27 final size:27
Alignment explanation
Indices: 5334379--5334556 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
5334369 TAAATTGTAC
*
5334379 AGCACTAAGTGTTCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
5334406 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
5334432 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
5334460 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
5334488 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
5334515 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
5334542 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
5334557 GACTCAATAT
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 105 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:5334493 original size:82 final size:81
Alignment explanation
Indices: 5334380--5334535 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
5334370 AAATTGTACA
* * *
5334380 GCACTAAGTGTTCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
5334444 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
5334461 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
5334526 TGCGAGTTGA
65 TGCGAATTGA
5334536 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 14 0.21
82 51 0.77
83 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:5334547 original size:82 final size:81
Alignment explanation
Indices: 5334376--5334556 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
5334366 GATTAAATTG
* * *
5334376 TACAGCACTAAGTGTTCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
5334441 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
5334457 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
5334521 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
5334539 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
5334557 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 17 0.20
82 66 0.80
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:5342263 original size:56 final size:56
Alignment explanation
Indices: 5342177--5342288 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
5342167 TAGTCCCAGG
* *
5342177 TACAAGCTCAATACCAAACTCTACCTCCCGAACATGTGGTAAACCCGGTAATTCTT
1 TACAAGCTCAATACCAAACTCTACCTCCCGAACAGGTGGTAAACCCAGTAATTCTT
*
5342233 TACAAGCTCAATACGAAACTCTACCTCCCGAACAGGTGGTAAACCCAGTAATTCTT
1 TACAAGCTCAATACCAAACTCTACCTCCCGAACAGGTGGTAAACCCAGTAATTCTT
5342289 CCGGAAAAAC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.24
Consensus pattern (56 bp):
TACAAGCTCAATACCAAACTCTACCTCCCGAACAGGTGGTAAACCCAGTAATTCTT
Found at i:5345680 original size:40 final size:40
Alignment explanation
Indices: 5345582--5345844 Score: 309
Period size: 40 Copynumber: 6.6 Consensus size: 40
5345572 TCCTCGTTCA
* * * ** *
5345582 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
5345621 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
5345661 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
5345701 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
5345741 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
5345781 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
5345821 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
5345845 CAGCATTCAA
Statistics
Matches: 199, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
39 37 0.19
40 154 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:5353740 original size:27 final size:27
Alignment explanation
Indices: 5353658--5353740 Score: 78
Period size: 27 Copynumber: 3.1 Consensus size: 27
5353648 GTGTACTCTA
* *
5353658 AAAGGAATGCCTTTGTGCCATATTTTG
1 AAAGGAATGCCTTTGTGGCATATCTTG
* * * **
5353685 AAAAGAATGTCTTTGTAGTGTA-CTTTG
1 AAAGGAATGCCTTTGTGGCATATC-TTG
*
5353712 AAAGGAATGCCTTTGTGGCATATCCTG
1 AAAGGAATGCCTTTGTGGCATATCTTG
5353739 AA
1 AA
5353741 TGGATTGCTT
Statistics
Matches: 41, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
27 40 0.98
28 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (27 bp):
AAAGGAATGCCTTTGTGGCATATCTTG
Found at i:5354024 original size:26 final size:26
Alignment explanation
Indices: 5353984--5354035 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
5353974 TTTTCACTGC
*
5353984 GTAGGTGTTCGCCTATGAATTGTGAT
1 GTAGGTGTTCACCTATGAATTGTGAT
*
5354010 GTAGGTGTTCACCTATGAATTTTGAT
1 GTAGGTGTTCACCTATGAATTGTGAT
5354036 TGTGTACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.27, T:0.40
Consensus pattern (26 bp):
GTAGGTGTTCACCTATGAATTGTGAT
Found at i:5357190 original size:58 final size:58
Alignment explanation
Indices: 5357100--5357216 Score: 207
Period size: 58 Copynumber: 2.0 Consensus size: 58
5357090 AGTGATTCTT
*
5357100 TCTTGGTTAATATGACCAAGTCTCAAATGTTAAAAGTACGCCTTATTAGAGTGAGAAG
1 TCTTGGTTAACATGACCAAGTCTCAAATGTTAAAAGTACGCCTTATTAGAGTGAGAAG
* *
5357158 TCTTGGTTAACATGACCAAGTCTGAAATGTTAAAGGTACGCCTTATTAGAGTGAGAAG
1 TCTTGGTTAACATGACCAAGTCTCAAATGTTAAAAGTACGCCTTATTAGAGTGAGAAG
5357216 T
1 T
5357217 TTTAAGTTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (58 bp):
TCTTGGTTAACATGACCAAGTCTCAAATGTTAAAAGTACGCCTTATTAGAGTGAGAAG
Found at i:5358976 original size:22 final size:23
Alignment explanation
Indices: 5358938--5358995 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 23
5358928 CATTCCAAAT
*
5358938 CATCCATTA-AACATTCAACTAAA
1 CATCCATTATAA-GTTCAACTAAA
* *
5358961 CAT-CATTATAAGTTCACCTATA
1 CATCCATTATAAGTTCAACTAAA
5358983 CATGCCATTATAA
1 CAT-CCATTATAA
5358996 CCTTGGCCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 16 0.55
23 5 0.17
24 8 0.28
ACGTcount: A:0.41, C:0.24, G:0.03, T:0.31
Consensus pattern (23 bp):
CATCCATTATAAGTTCAACTAAA
Found at i:5363441 original size:16 final size:17
Alignment explanation
Indices: 5363415--5363446 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5363405 TTTAATTAGA
5363415 TAAATTAATTTTCTAAT
1 TAAATTAATTTTCTAAT
5363432 TAAA-TAATTTTCTAA
1 TAAATTAATTTTCTAA
5363447 ACCAAATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAATTAATTTTCTAAT
Found at i:5376261 original size:5 final size:5
Alignment explanation
Indices: 5376251--5376284 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
5376241 TTGCATACCC
* *
5376251 ATCCA ATCCA ATCCA ATGCA ATGCA ATCCA ATCC
1 ATCCA ATCCA ATCCA ATCCA ATCCA ATCCA ATCC
5376285 TCACGGTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.38, C:0.35, G:0.06, T:0.21
Consensus pattern (5 bp):
ATCCA
Found at i:5376520 original size:10 final size:10
Alignment explanation
Indices: 5376505--5376533 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
5376495 TCTCTCCCTC
5376505 CCTCCCTCTA
1 CCTCCCTCTA
5376515 CCTCCCTCTA
1 CCTCCCTCTA
5376525 CCTCCCTCT
1 CCTCCCTCT
5376534 CTCTCTCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.07, C:0.62, G:0.00, T:0.31
Consensus pattern (10 bp):
CCTCCCTCTA
Found at i:5376537 original size:2 final size:2
Alignment explanation
Indices: 5376530--5377326 Score: 1576
Period size: 2 Copynumber: 398.5 Consensus size: 2
5376520 CTCTACCTCC
5376530 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5376572 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5376614 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5376656 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5376698 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5376740 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5376782 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5376824 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5376866 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5376908 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5376950 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5376992 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5377034 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5377076 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5377118 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5377160 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5377202 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5377244 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* *
5377286 CC CC CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
5377327 ATAAGTGAGT
Statistics
Matches: 793, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 793 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5379426 original size:27 final size:26
Alignment explanation
Indices: 5379396--5379477 Score: 89
Period size: 25 Copynumber: 3.2 Consensus size: 26
5379386 ACAAAATCAA
5379396 GAAGCACTC-TCTCGAGCCATATAACAG
1 GAAGC-CTCATCT-GAGCCATATAACAG
*
5379423 GAAG-CTCATGTGAGCCATATAACAG
1 GAAGCCTCATCTGAGCCATATAACAG
* * *
5379448 GAAG-CTCATGTGAGCCATGTAACAA
1 GAAGCCTCATCTGAGCCATATAACAG
5379473 GAAGC
1 GAAGC
5379478 TTATCCGGTC
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
25 44 0.88
26 2 0.04
27 4 0.08
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.18
Consensus pattern (26 bp):
GAAGCCTCATCTGAGCCATATAACAG
Found at i:5379438 original size:25 final size:25
Alignment explanation
Indices: 5379409--5379478 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
5379399 GCACTCTCTC
5379409 GAGCCATATAACAGGAAGCTCATGT
1 GAGCCATATAACAGGAAGCTCATGT
5379434 GAGCCATATAACAGGAAGCTCATGT
1 GAGCCATATAACAGGAAGCTCATGT
* *
5379459 GAGCCATGTAACAAGAAGCT
1 GAGCCATATAACAGGAAGCT
5379479 TATCCGGTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.19
Consensus pattern (25 bp):
GAGCCATATAACAGGAAGCTCATGT
Found at i:5379606 original size:25 final size:25
Alignment explanation
Indices: 5379552--5379610 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
5379542 GCAACCCCGA
*
5379552 AGAGCTAT-TATTAGGAAGCTTCGG
1 AGAGCCATATATTAGGAAGCTTCGG
*
5379576 ATAGCCATATATTAGGAAG-TTCAGG
1 AGAGCCATATATTAGGAAGCTTC-GG
*
5379601 CGAGCCATAT
1 AGAGCCATAT
5379611 CAGGAAGCTC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 9 0.31
25 20 0.69
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.27
Consensus pattern (25 bp):
AGAGCCATATATTAGGAAGCTTCGG
Found at i:5392002 original size:20 final size:20
Alignment explanation
Indices: 5391959--5391998 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
5391949 TATTATATAG
5391959 TTAATTAAGGTTTTAATTAA
1 TTAATTAAGGTTTTAATTAA
5391979 TTAATTAA-GTTTT-ATTAA
1 TTAATTAAGGTTTTAATTAA
5391997 TT
1 TT
5391999 TTAAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.35
19 5 0.25
20 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
TTAATTAAGGTTTTAATTAA
Found at i:5393524 original size:21 final size:21
Alignment explanation
Indices: 5393500--5393540 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5393490 TTAAAACTTT
* *
5393500 TCTTCATAATAAATCTAAATA
1 TCTTCAAAATAAATATAAATA
*
5393521 TCTTTAAAATAAATATAAAT
1 TCTTCAAAATAAATATAAAT
5393541 TTTAAAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (21 bp):
TCTTCAAAATAAATATAAATA
Found at i:5399076 original size:39 final size:39
Alignment explanation
Indices: 5399022--5399101 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
5399012 TAGGGATCCT
5399022 AAGGATTAAAAATATAAATAATAGAGCATGTAAAACGTG
1 AAGGATTAAAAATATAAATAATAGAGCATGTAAAACGTG
*
5399061 AAGGATTAAGAATATAAATAATAGAGCATGTAAAACGTG
1 AAGGATTAAAAATATAAATAATAGAGCATGTAAAACGTG
5399100 AA
1 AA
5399102 ATCTATCAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.54, C:0.05, G:0.19, T:0.23
Consensus pattern (39 bp):
AAGGATTAAAAATATAAATAATAGAGCATGTAAAACGTG
Found at i:5401468 original size:269 final size:269
Alignment explanation
Indices: 5400986--5401523 Score: 916
Period size: 269 Copynumber: 2.0 Consensus size: 269
5400976 TCCAAACTTC
* *
5400986 AGCTGCTAAGAGATCAACCCCTTTCAATCTCAAAAATTCAATCGCACTATTTCTTCGTAATTCCT
1 AGCTGCTAAGAGATCAACCCCTTTCAATCTCAAAAATTCAATCGCACCATTTCTCCGTAATTCCT
* * * *
5401051 TTATTAGATCCTGTCGAACAGTAGGTGCCGATACTGTAGCAAAAGTAATTTTCGCAACACACTAA
66 TTATTAGAGCCCGTCGAACAGTAGGTGCAGATACTGTAGCAAAAGTAATTTCCGCAACACACTAA
*
5401116 AGAGCATCAGCGATAGCTCAAAGTAAATTTGAATCACCTACTCCCTCATTATTACCTTGCTCAAC
131 AGAGCATCAGCGATAGCTCAAAGTAAATTTGAATCACCTACTCCCTCATTATTACCTCGCTCAAC
* * *
5401181 ATTAGGTTGTTGAGCACTAGCTGGGTTAAAATTCAGCGTTACTGATTCAGTTTCCTCACAATCCT
196 ATTAGGTTGTTAAGCACTAGCTAGGTTAAAATTCAGCATTACTGATTCAGTTTCCTCACAATCCT
5401246 CAGTATAAT
261 CAGTATAAT
*
5401255 AGCTGCTAAGAGATCAACCCCTTTCAATCTCAAAAATTCAATCGCACCATTTCTCCGTAATTTCT
1 AGCTGCTAAGAGATCAACCCCTTTCAATCTCAAAAATTCAATCGCACCATTTCTCCGTAATTCCT
*
5401320 TTATTAGAGCCCGTCGAACAGTAGGTGTCAG-TACTGTAGCAGAAGTAATTTCCGCAACACACTA
66 TTATTAGAGCCCGTCGAACAGTAGGTG-CAGATACTGTAGCAAAAGTAATTTCCGCAACACACTA
* *
5401384 AAGAGCATCAGCGATAGCTCGAAGTAAATTTGAATCACCTACTCCCTCATTATTAGCTCGCTCAA
130 AAGAGCATCAGCGATAGCTCAAAGTAAATTTGAATCACCTACTCCCTCATTATTACCTCGCTCAA
* *
5401449 CATTAGGTTGTTAAGCACTAGCTAGGTTAACATTCAGCATTACTGATTCAGTTTCCTTACAATCC
195 CATTAGGTTGTTAAGCACTAGCTAGGTTAAAATTCAGCATTACTGATTCAGTTTCCTCACAATCC
5401514 TCAGTATAAT
260 TCAGTATAAT
5401524 CATCGCTAGA
Statistics
Matches: 252, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
269 250 0.99
270 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (269 bp):
AGCTGCTAAGAGATCAACCCCTTTCAATCTCAAAAATTCAATCGCACCATTTCTCCGTAATTCCT
TTATTAGAGCCCGTCGAACAGTAGGTGCAGATACTGTAGCAAAAGTAATTTCCGCAACACACTAA
AGAGCATCAGCGATAGCTCAAAGTAAATTTGAATCACCTACTCCCTCATTATTACCTCGCTCAAC
ATTAGGTTGTTAAGCACTAGCTAGGTTAAAATTCAGCATTACTGATTCAGTTTCCTCACAATCCT
CAGTATAAT
Found at i:5404412 original size:27 final size:27
Alignment explanation
Indices: 5404358--5404412 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
5404348 ATATATGAAT
*
5404358 TCATTTCAATATCCATATCACATTTCA
1 TCATTTCAATATCCATATCACATCTCA
* *
5404385 TCATTTC-ATATTCCATTTCCCATCTCA
1 TCATTTCAATA-TCCATATCACATCTCA
5404412 T
1 T
5404413 ATTCATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 3 0.12
27 21 0.88
ACGTcount: A:0.27, C:0.29, G:0.00, T:0.44
Consensus pattern (27 bp):
TCATTTCAATATCCATATCACATCTCA
Found at i:5404421 original size:18 final size:19
Alignment explanation
Indices: 5404390--5404426 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
5404380 TTTCATCATT
5404390 TCATATTCCATTTCCCATC
1 TCATATTCCATTTCCCATC
*
5404409 TCATATT-CATTTCTCATC
1 TCATATTCCATTTCCCATC
5404427 ATTGTCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.22, C:0.32, G:0.00, T:0.46
Consensus pattern (19 bp):
TCATATTCCATTTCCCATC
Found at i:5408908 original size:5 final size:5
Alignment explanation
Indices: 5408898--5408923 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5408888 GAGGCCCATT
5408898 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
5408924 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:5410758 original size:24 final size:24
Alignment explanation
Indices: 5410731--5410787 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
5410721 TGCTCCGTTC
*
5410731 TGTTCTGTTCTGTT-TGAATTGCAT
1 TGTTCTGCTCTGTTCTG-ATTGCAT
* * *
5410755 TGTTTTGCTCTGTTCTGTTTGCCT
1 TGTTCTGCTCTGTTCTGATTGCAT
5410779 TGTTCTGCT
1 TGTTCTGCT
5410788 GTACTACCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.05, C:0.18, G:0.21, T:0.56
Consensus pattern (24 bp):
TGTTCTGCTCTGTTCTGATTGCAT
Found at i:5413398 original size:15 final size:15
Alignment explanation
Indices: 5413373--5413407 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
5413363 GACTCTATTT
*
5413373 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
5413387 TAATTAATATTAAGA
1 TAATTAATATTAAGA
5413402 TAATTA
1 TAATTA
5413408 TTAATGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:5413624 original size:43 final size:42
Alignment explanation
Indices: 5413561--5413645 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 42
5413551 CATCTTTTTC
5413561 TGTAGACACTCTCTCCCCAAAAGTCTAGGCTTTTGTTCTTCT
1 TGTAGACACTCTCTCCCCAAAAGTCTAGGCTTTTGTTCTTCT
* * * *
5413603 NTGTAGACCCTCTTTCTCCAAAATTCTAGGCTTTTGTTCTTCT
1 -TGTAGACACTCTCTCCCCAAAAGTCTAGGCTTTTGTTCTTCT
5413646 CATATTTCCT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.18, C:0.27, G:0.13, T:0.41
Consensus pattern (42 bp):
TGTAGACACTCTCTCCCCAAAAGTCTAGGCTTTTGTTCTTCT
Found at i:5421334 original size:6 final size:7
Alignment explanation
Indices: 5421317--5421342 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5421307 TTATTTTTAA
5421317 AAAAATT
1 AAAAATT
5421324 AAAAATT
1 AAAAATT
5421331 AAAAATT
1 AAAAATT
5421338 AAAAA
1 AAAAA
5421343 AATATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAAATT
Found at i:5423129 original size:199 final size:201
Alignment explanation
Indices: 5422782--5423181 Score: 750
Period size: 199 Copynumber: 2.0 Consensus size: 201
5422772 TTTAAATGGT
5422782 GTTATACAGTCAATGCCACAATACACATACATGATACAATTATATGAGAGCACACACTTAAAACA
1 GTTATACAGTCAATGCCACAATACACATACATGATACAATTATATGAGAGCACACACTTAAAACA
*
5422847 CACTAGATTTTGGCGCGCCCAAGATGTCGGTGAAAAACAAACTTTGATTGAAATAGTAAAATGAA
66 CACTAGATTTTGGCGCGCCCAAGATGTCGGTGAAAAACAAACTTTGATTGAAATAATAAAATGAA
5422912 AACTATAATGTGTTAAGTTCAAACCAATGTGT-A-TTTTTTTTTATAAAGAAGATATAAAAAGAT
131 AACTATAATGTGTTAAGTTCAAACCAATGTGTAACTTTTTTTTTATAAAGAAGATATAAAAAGAT
5422975 GAACTC
196 GAACTC
*
5422981 GTTATACAGTCAATGCCACAATACACATACATGATACAATTATATGAGAGCACACACTTAAAATA
1 GTTATACAGTCAATGCCACAATACACATACATGATACAATTATATGAGAGCACACACTTAAAACA
5423046 CACTAGATTTTGGCGCGCCCAAGATGTCGGTGAAAAACAAACTTTGATTGAAATAATAAAATGAA
66 CACTAGATTTTGGCGCGCCCAAGATGTCGGTGAAAAACAAACTTTGATTGAAATAATAAAATGAA
* *
5423111 AACTATAATGTTTTAAGTTCAAATCAATGTGTAACTTTTTTTTTATAAAGAAGATATAAAAAGAT
131 AACTATAATGTGTTAAGTTCAAACCAATGTGTAACTTTTTTTTTATAAAGAAGATATAAAAAGAT
5423176 GAACTC
196 GAACTC
5423182 TCTCAAAATA
Statistics
Matches: 195, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
199 158 0.81
200 1 0.01
201 36 0.18
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (201 bp):
GTTATACAGTCAATGCCACAATACACATACATGATACAATTATATGAGAGCACACACTTAAAACA
CACTAGATTTTGGCGCGCCCAAGATGTCGGTGAAAAACAAACTTTGATTGAAATAATAAAATGAA
AACTATAATGTGTTAAGTTCAAACCAATGTGTAACTTTTTTTTTATAAAGAAGATATAAAAAGAT
GAACTC
Found at i:5423504 original size:26 final size:27
Alignment explanation
Indices: 5423463--5423515 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
5423453 TGAAAATAGA
* *
5423463 AAAAATACAATTGGAAAAA-TAGGAAG
1 AAAAATAAAATAGGAAAAAGTAGGAAG
5423489 AAAAATAAAATAGGAAAAAGTAGGAAG
1 AAAAATAAAATAGGAAAAAGTAGGAAG
5423516 TTATATGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.64, C:0.02, G:0.21, T:0.13
Consensus pattern (27 bp):
AAAAATAAAATAGGAAAAAGTAGGAAG
Found at i:5425330 original size:62 final size:62
Alignment explanation
Indices: 5425233--5425350 Score: 209
Period size: 62 Copynumber: 1.9 Consensus size: 62
5425223 AATTTCCTAG
**
5425233 AATTCTTAACGATTAGAAGATATTTGCGTATGGTGTACCAATTAATAAGCTTAATGTGTTAT
1 AATTCTTAACGATTAGAAGATATTTGCACATGGTGTACCAATTAATAAGCTTAATGTGTTAT
*
5425295 AATTCTTAACGATTAGAAGATATTTGCACATGGTGTACCAATTAATGAGCTTAATG
1 AATTCTTAACGATTAGAAGATATTTGCACATGGTGTACCAATTAATAAGCTTAATG
5425351 AGTGTTATGT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (62 bp):
AATTCTTAACGATTAGAAGATATTTGCACATGGTGTACCAATTAATAAGCTTAATGTGTTAT
Found at i:5427715 original size:23 final size:23
Alignment explanation
Indices: 5427684--5427729 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5427674 TTATTAACAT
* *
5427684 TGTTCGTGAACATGTTCGTTTAA
1 TGTTCGTGAACATATTCGATTAA
*
5427707 TGTTTGTGAACATATTCGATTAA
1 TGTTCGTGAACATATTCGATTAA
5427730 GTTAAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (23 bp):
TGTTCGTGAACATATTCGATTAA
Found at i:5427922 original size:48 final size:48
Alignment explanation
Indices: 5427859--5427956 Score: 151
Period size: 48 Copynumber: 2.0 Consensus size: 48
5427849 ACAAACTGAA
* * *
5427859 CACGAATAAATTTAAAAATAAACAAGTGAACATGAATAGAAGTTTATT
1 CACGAATAAACTTAAAAATAAAAAAATGAACATGAATAGAAGTTTATT
* *
5427907 CACGAATAAACTTAAAAATAAAAAAATGAACATGAATAGAGGTTTGTT
1 CACGAATAAACTTAAAAATAAAAAAATGAACATGAATAGAAGTTTATT
5427955 CA
1 CA
5427957 TTCAAATTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.52, C:0.09, G:0.13, T:0.26
Consensus pattern (48 bp):
CACGAATAAACTTAAAAATAAAAAAATGAACATGAATAGAAGTTTATT
Found at i:5430013 original size:38 final size:36
Alignment explanation
Indices: 5429906--5430026 Score: 145
Period size: 38 Copynumber: 3.3 Consensus size: 36
5429896 CTACCTTCAT
* ** *
5429906 CCGATTTGCTTCCTTGTTTCTTTGCTTTTTTTTCTG
1 CCGATTTGCTCCCCAGTTTCTTTTCTTTTTTTTCTG
*
5429942 CCGATTTGCT-CCCAGTTTATTTTCTTTTCTTTTCTG
1 CCGATTTGCTCCCCAGTTTCTTTTCTTTT-TTTTCTG
* *
5429978 CCGATTTGCTCCCCCCGTTTCTTTTCTTTCTTTTTCGG
1 CCGATTTGCT-CCCCAGTTTCTTTTCTTT-TTTTTCTG
5430016 CCGATTTGCTC
1 CCGATTTGCTC
5430027 AATTTTTGCC
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
35 14 0.19
36 27 0.36
37 1 0.01
38 31 0.42
39 1 0.01
ACGTcount: A:0.05, C:0.28, G:0.13, T:0.54
Consensus pattern (36 bp):
CCGATTTGCTCCCCAGTTTCTTTTCTTTTTTTTCTG
Found at i:5431132 original size:69 final size:69
Alignment explanation
Indices: 5431048--5431186 Score: 199
Period size: 69 Copynumber: 2.0 Consensus size: 69
5431038 TTTGTTGGTT
*
5431048 TGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAAATGTTATT-AGTTTGTTAGTGAGTAGAAGAT
1 TGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAAATGTTATTGA-TTTGTTAGTCAGTAGAAGAT
5431112 GAAAC
65 GAAAC
* * * * * *
5431117 TGTTCTGGCAGTTGTTTTGATTGTCTGCTGGAAATTGTTCTTGATTTGTTAGTCAGTAGAATATG
1 TGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAAATGTTATTGATTTGTTAGTCAGTAGAAGATG
5431182 AAAC
66 AAAC
5431186 T
1 T
5431187 AGAACTTGAT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
69 61 0.98
70 1 0.02
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.42
Consensus pattern (69 bp):
TGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAAATGTTATTGATTTGTTAGTCAGTAGAAGATG
AAAC
Found at i:5432415 original size:37 final size:37
Alignment explanation
Indices: 5432372--5432460 Score: 151
Period size: 37 Copynumber: 2.4 Consensus size: 37
5432362 ATCATAAATA
*
5432372 AATAAACTAATCAATGTTCAAACTTTGAACATGCTTT
1 AATAAACTAATCAATGTTAAAACTTTGAACATGCTTT
*
5432409 ATTAAACTAATCAATGTTAAAACTTTGAACATGCTTT
1 AATAAACTAATCAATGTTAAAACTTTGAACATGCTTT
*
5432446 AATGAACTAATCAAT
1 AATAAACTAATCAAT
5432461 ATATTTATAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.35
Consensus pattern (37 bp):
AATAAACTAATCAATGTTAAAACTTTGAACATGCTTT
Found at i:5432543 original size:33 final size:33
Alignment explanation
Indices: 5432506--5432578 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
5432496 AAACTTGTAG
* *
5432506 TATACATATACCAACAATTAATTTTAGGTCAAT
1 TATACATACACCAACAATTAATTTTACGTCAAT
5432539 TATACATACACCAACAATTAATTTTACGTCAAT
1 TATACATACACCAACAATTAATTTTACGTCAAT
5432572 TATACAT
1 TATACAT
5432579 GCTTTAATGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.36
Consensus pattern (33 bp):
TATACATACACCAACAATTAATTTTACGTCAAT
Found at i:5432596 original size:138 final size:138
Alignment explanation
Indices: 5432437--5432722 Score: 529
Period size: 138 Copynumber: 2.1 Consensus size: 138
5432427 AAAACTTTGA
5432437 ACATGCTTTAATGAACTAATCAATATATTTATACGAAATTAAATGTCATAAAAGTTTTAAAACTT
1 ACATGCTTTAATGAACTAATCAATATATTTATACGAAATTAAATGTCATAAAAGTTTTAAAACTT
*
5432502 GTAGT-ATACATATACCAACAATTAATTTTAGGTCAATTATACATACACCAACAATTAATTTTAC
66 G-AATCATACATATACCAACAATTAATTTTAGGTCAATTATACATACACCAACAATTAATTTTAC
5432566 GTCAATTAT
130 GTCAATTAT
*
5432575 ACATGCTTTAATGAACTAATCAATATATTTATACGAAATTAAATGTTATAAAAGTTTTAAAACTT
1 ACATGCTTTAATGAACTAATCAATATATTTATACGAAATTAAATGTCATAAAAGTTTTAAAACTT
*
5432640 GAATCATACATATACCAACAATTAATTTTAGGTCAATTATACATACACCAACAATTAATTTTAGG
66 GAATCATACATATACCAACAATTAATTTTAGGTCAATTATACATACACCAACAATTAATTTTACG
5432705 TCAATTAT
131 TCAATTAT
5432713 ACATGCTTTA
1 ACATGCTTTA
5432723 TAATTTCTTT
Statistics
Matches: 144, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
137 2 0.01
138 142 0.99
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (138 bp):
ACATGCTTTAATGAACTAATCAATATATTTATACGAAATTAAATGTCATAAAAGTTTTAAAACTT
GAATCATACATATACCAACAATTAATTTTAGGTCAATTATACATACACCAACAATTAATTTTACG
TCAATTAT
Found at i:5432682 original size:33 final size:33
Alignment explanation
Indices: 5432645--5432716 Score: 135
Period size: 33 Copynumber: 2.2 Consensus size: 33
5432635 AACTTGAATC
*
5432645 ATACATATACCAACAATTAATTTTAGGTCAATT
1 ATACATACACCAACAATTAATTTTAGGTCAATT
5432678 ATACATACACCAACAATTAATTTTAGGTCAATT
1 ATACATACACCAACAATTAATTTTAGGTCAATT
5432711 ATACAT
1 ATACAT
5432717 GCTTTATAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.35
Consensus pattern (33 bp):
ATACATACACCAACAATTAATTTTAGGTCAATT
Found at i:5435928 original size:91 final size:91
Alignment explanation
Indices: 5435781--5435988 Score: 335
Period size: 91 Copynumber: 2.3 Consensus size: 91
5435771 TTGATTTTAG
* *
5435781 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
5435846 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
*
5435873 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
5435938 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
5435964 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
5435989 GTTATAATTA
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 92 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:5435957 original size:26 final size:28
Alignment explanation
Indices: 5435903--5435963 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
5435893 TATTATCAAG
* *
5435903 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
5435931 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
5435957 AATTATA
1 AATTATA
5435964 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:5435963 original size:44 final size:43
Alignment explanation
Indices: 5435821--5435963 Score: 121
Period size: 44 Copynumber: 3.2 Consensus size: 43
5435811 GAATTTTATG
* *
5435821 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
5435865 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
5435912 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
5435956 AAATTATA
1 AAATTATA
5435964 CAAATTCATA
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 12 0.16
46 11 0.14
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:5436166 original size:25 final size:26
Alignment explanation
Indices: 5436138--5436192 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
5436128 TTATTAAATT
*
5436138 ATATATTTTAATTATAA-TATATTTA
1 ATATATTTTAATAATAATTATATTTA
*
5436163 ATATA-TTTAATAATAATTATGTTTA
1 ATATATTTTAATAATAATTATATTTA
5436188 A-ATAT
1 ATATAT
5436193 GATTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATTTTAATAATAATTATATTTA
Found at i:5436414 original size:45 final size:44
Alignment explanation
Indices: 5436314--5436424 Score: 124
Period size: 45 Copynumber: 2.6 Consensus size: 44
5436304 TTTTCCATTA
5436314 TGCTATTACACCTCTATTCC--T---TTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * * ***
5436353 TACTATTACGCTTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
5436398 TGCTATTACACCTCTATTCCATTACAT
1 TGCTATTACACCTCTATTCCATTACAT
5436425 CTCTAATCCA
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
39 17 0.30
41 1 0.02
44 14 0.25
45 25 0.44
ACGTcount: A:0.31, C:0.28, G:0.05, T:0.36
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:5436423 original size:16 final size:16
Alignment explanation
Indices: 5436404--5436455 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
5436394 GATTTGCTAT
* *
5436404 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
*
5436420 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
5436436 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
5436452 TACA
1 TACA
5436456 GCGAACCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:5437003 original size:21 final size:21
Alignment explanation
Indices: 5436969--5437022 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
5436959 AATTAATATT
*
5436969 TAAAATTA-TAAAAAAAATCA
1 TAAAAATATTAAAAAAAATCA
* * **
5436989 TAAAAGTATTAAAAAATATTT
1 TAAAAATATTAAAAAAAATCA
5437010 TAAAAATATTAAA
1 TAAAAATATTAAA
5437023 CATATTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
TAAAAATATTAAAAAAAATCA
Found at i:5437021 original size:9 final size:10
Alignment explanation
Indices: 5436989--5437035 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
5436979 AAAAAAATCA
*
5436989 TAAAAGTATT
1 TAAAAATATT
*
5436999 AAAAAATATTT
1 TAAAAATA-TT
5437010 TAAAAATA-T
1 TAAAAATATT
*
5437019 TAAACATATT
1 TAAAAATATT
5437029 TAAAAAT
1 TAAAAAT
5437036 TATCAAAATC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
9 8 0.27
10 13 0.43
11 9 0.30
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (10 bp):
TAAAAATATT
Found at i:5438360 original size:22 final size:20
Alignment explanation
Indices: 5438313--5438366 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
5438303 TATTAAATCA
5438313 TTATAATATTTTACATTTTT
1 TTATAATATTTTACATTTTT
*
5438333 TAATAAT-TGTTTACAATTTTTT
1 TTATAATAT-TTTAC-A-TTTTT
5438355 TTATAA-ATTTTA
1 TTATAATATTTTA
5438367 TAGCTTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
19 1 0.04
20 11 0.39
21 5 0.18
22 11 0.39
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (20 bp):
TTATAATATTTTACATTTTT
Found at i:5449007 original size:39 final size:39
Alignment explanation
Indices: 5448912--5449173 Score: 302
Period size: 39 Copynumber: 6.6 Consensus size: 39
5448902 TTGAATGCTG
*
5448912 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* *
5448950 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
* *
5448991 TTCGGGCTAAGCCCGAAGGCATTTGTGCTAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
*
5449030 TCCGGGCTAAGCCCGAAGGCATTAGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
* *
5449069 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
* *
5449108 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACTATAA
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-TACTA-AT
*
5449149 T-CGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAG-CCCGAAGGCATTTG
5449174 AACGAGGAGC
Statistics
Matches: 198, Mismatches: 18, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
39 126 0.64
40 57 0.29
41 14 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:5451093 original size:93 final size:93
Alignment explanation
Indices: 5450934--5451105 Score: 301
Period size: 93 Copynumber: 1.8 Consensus size: 93
5450924 CGCCCATAAG
* *
5450934 CGAACTCGGACTCAACTCAACGAGCTTGGGCATTCGCATCCATGAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
5450999 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
5451027 CGAACTCGGACTCAACTCAACGAG-TTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTT-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
5451091 AACGAGTTCGGATGC
65 AACGAGTTCGGATGC
5451106 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:5451102 original size:46 final size:46
Alignment explanation
Indices: 5450927--5451102 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
5450917 TGTAACCCGC
* *
5450927 CCATAAGCGAACTCGGACTCAACTCAACGAGCTT-GGGCATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAG-TTCGGACATTTGCAT
* * * *
5450973 CCATGAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
*
5451023 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
*
5451066 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
5451103 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 12, Indels: 16
0.80 0.09 0.12
Matches are distributed among these distances:
43 6 0.05
44 2 0.02
45 4 0.04
46 60 0.55
47 29 0.26
48 2 0.02
49 2 0.02
50 5 0.05
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:5453537 original size:30 final size:30
Alignment explanation
Indices: 5453493--5453581 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
5453483 CAAAGATAAC
5453493 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
5453522 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * *
5453552 AAGAGATCCA-AGATAAAGAAACCCAAGATA
1 AAGAAAACCAGA-ATAAAGAAATCCAAGATA
5453582 CGATACTATG
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 10 0.20
30 38 0.76
31 2 0.04
ACGTcount: A:0.58, C:0.16, G:0.16, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:5453541 original size:15 final size:15
Alignment explanation
Indices: 5453493--5453572 Score: 85
Period size: 15 Copynumber: 5.4 Consensus size: 15
5453483 CAAAGATAAC
*
5453493 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
5453507 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
5453522 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
5453537 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
*
5453552 AAGAGATCCA-AGATA
1 AAGAAATCCAGA-ATA
5453567 AAGAAA
1 AAGAAA
5453573 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
14 10 0.18
15 44 0.80
16 1 0.02
ACGTcount: A:0.60, C:0.14, G:0.16, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:5453577 original size:15 final size:15
Alignment explanation
Indices: 5453504--5453581 Score: 88
Period size: 15 Copynumber: 5.2 Consensus size: 15
5453494 AGAAAACCGA
5453504 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
5453519 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
5453533 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
*
5453548 AATAAAGAGATCCAAG
1 -ATAAAGAAATCCAAG
*
5453564 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
5453579 ATA
1 ATA
5453582 CGATACTATG
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
14 4 0.07
15 46 0.85
16 4 0.07
ACGTcount: A:0.58, C:0.15, G:0.15, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:5456657 original size:46 final size:46
Alignment explanation
Indices: 5456494--5456712 Score: 219
Period size: 46 Copynumber: 4.7 Consensus size: 46
5456484 TGTAACCCGC
* * * * * *
5456494 CCATAAGAGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCAT
** * * * * *
5456540 TTATGAGTGAACTCGGACTCAACTGAACAAGTTCGGATGACTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC--A-GAC-ATTTGCAT
* * *
5456590 -C-TCA-CGAACTCGGACTCAACTCAATGAGTTCAGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCAT
5456633 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCAT
* *
5456679 CGATAAGTGAACTCGGAATCAACTCAACGAGTTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
5456713 GGATGCTCAA
Statistics
Matches: 140, Mismatches: 26, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
43 6 0.04
44 4 0.03
45 3 0.02
46 96 0.69
47 23 0.16
48 2 0.01
49 2 0.01
50 4 0.03
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCAT
Found at i:5457306 original size:48 final size:49
Alignment explanation
Indices: 5457235--5457330 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 49
5457225 TTTTCTTATG
5457235 TTTTATGACATGCTGATCATTTTTCCCTT-CTATGGCAACATCAAATTA
1 TTTTATGACATGCTGATCATTTTTCCCTTGCTATGGCAACATCAAATTA
*
5457283 TTTTATGACATGTTGATCATTTTTCCCTTGCTATGGCAACATCAAATT
1 TTTTATGACATGCTGATCATTTTTCCCTTGCTATGGCAACATCAAATT
5457331 CTCACTCTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 28 0.61
49 18 0.39
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (49 bp):
TTTTATGACATGCTGATCATTTTTCCCTTGCTATGGCAACATCAAATTA
Found at i:5461241 original size:12 final size:12
Alignment explanation
Indices: 5461224--5461248 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5461214 ACAACATATA
5461224 TTCAGAAAAATC
1 TTCAGAAAAATC
5461236 TTCAGAAAAATC
1 TTCAGAAAAATC
5461248 T
1 T
5461249 GATATCTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (12 bp):
TTCAGAAAAATC
Found at i:5462111 original size:66 final size:66
Alignment explanation
Indices: 5462023--5462147 Score: 180
Period size: 66 Copynumber: 1.9 Consensus size: 66
5462013 GGACACTCCC
* *
5462023 GTGCTGCAGGCCGTGTTCGACCTCGTGTAATTCATAT-ACTTGAGCACACGGCCATGCCATAAGT
1 GTGCTGCAGGCCATGTTCGACCTCGTGTAACTC-TATGACTTGAGCACACGGCCATGCCATAAGT
5462087 CA
65 CA
* * * *
5462089 GTGCTGCAGGTCATGTTTGACCTCGTGTGACTCTCTGACTTGAGCACACGGCCATGCCA
1 GTGCTGCAGGCCATGTTCGACCTCGTGTAACTCTATGACTTGAGCACACGGCCATGCCA
5462148 CATGCCTGTG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 2 0.04
66 50 0.96
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.26
Consensus pattern (66 bp):
GTGCTGCAGGCCATGTTCGACCTCGTGTAACTCTATGACTTGAGCACACGGCCATGCCATAAGTC
A
Found at i:5463231 original size:14 final size:15
Alignment explanation
Indices: 5463207--5463239 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5463197 TATCATCACC
5463207 TCATGTTTTCATATA
1 TCATGTTTTCATATA
*
5463222 TCAT-TTTTCATGTA
1 TCATGTTTTCATATA
5463236 TCAT
1 TCAT
5463240 CATTTACTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.24, C:0.15, G:0.06, T:0.55
Consensus pattern (15 bp):
TCATGTTTTCATATA
Found at i:5472855 original size:20 final size:20
Alignment explanation
Indices: 5472832--5472975 Score: 51
Period size: 20 Copynumber: 7.2 Consensus size: 20
5472822 AAGGGTATGT
5472832 AAGTGCATTCAGGGGTACCA
1 AAGTGCATTCAGGGGTACCA
* ** *
5472852 AAGTACAAACAGGGGCA-CA
1 AAGTGCATTCAGGGGTACCA
* *
5472871 TATA-TGCATTTAGGGGTACCG
1 -A-AGTGCATTCAGGGGTACCA
* * * ***
5472892 AAGTACAATCAGGGGCATTT
1 AAGTGCATTCAGGGGTACCA
* *
5472912 ATGTGCATTCAGGAGTACCA
1 AAGTGCATTCAGGGGTACCA
* * **
5472932 AAGTACAAGT-AGGGGTACGT
1 AAGTGC-ATTCAGGGGTACCA
* * *
5472952 ATGTGCATTCAGGGTTACTA
1 AAGTGCATTCAGGGGTACCA
5472972 AAGT
1 AAGT
5472976 ACAATCAAGG
Statistics
Matches: 80, Mismatches: 38, Indels: 12
0.62 0.29 0.09
Matches are distributed among these distances:
19 5 0.06
20 71 0.89
21 4 0.05
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.24
Consensus pattern (20 bp):
AAGTGCATTCAGGGGTACCA
Found at i:5472879 original size:40 final size:40
Alignment explanation
Indices: 5472834--5473042 Score: 202
Period size: 40 Copynumber: 5.2 Consensus size: 40
5472824 GGGTATGTAA
5472834 GTGCATTCAGGGGTACCAAAGTACAAACAGGGGCACATAT
1 GTGCATTCAGGGGTACCAAAGTACAAACAGGGGCACATAT
* * * * **
5472874 ATGCATTTAGGGGTACCGAAGTACAATCAGGGGCATTTAT
1 GTGCATTCAGGGGTACCAAAGTACAAACAGGGGCACATAT
* ** * *
5472914 GTGCATTCAGGAGTACCAAAGTACAAGTAGGGGTACGTAT
1 GTGCATTCAGGGGTACCAAAGTACAAACAGGGGCACATAT
* * * * *
5472954 GTGCATTCAGGGTTACTAAAGTACAATCAAGGGCACATTT
1 GTGCATTCAGGGGTACCAAAGTACAAACAGGGGCACATAT
* * * ** * * *
5472994 GTGCATTTAAGGCTACCGCACTACAAACAGGGCCACACAT
1 GTGCATTCAGGGGTACCAAAGTACAAACAGGGGCACATAT
5473034 GTGCATTCA
1 GTGCATTCA
5473043 TTCAATAATT
Statistics
Matches: 132, Mismatches: 37, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
40 132 1.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (40 bp):
GTGCATTCAGGGGTACCAAAGTACAAACAGGGGCACATAT
Found at i:5473037 original size:120 final size:120
Alignment explanation
Indices: 5472824--5473042 Score: 285
Period size: 120 Copynumber: 1.8 Consensus size: 120
5472814 GTATAAACAA
* * * *
5472824 GGGTATGTAAGTGCATTCAGGGGTACCAAAGTACAAACAGGGGCACATATATGCATTTAGGGGTA
1 GGGTACGTAAGTGCATTCAGGGGTACCAAAGTACAAACAAGGGCACATATATGCATTTAAGGCTA
* * * ***
5472889 CCGAAGTACAATCAGGGGCATTTATGTGCATTCAGGAGTACCAAAGTACAAGTAG
66 CCGAACTACAAACAGGGCCACACATGTGCATTCAGGAGTACCAAAGTACAAGTAG
* * * * * *
5472944 GGGTACGTATGTGCATTCAGGGTTACTAAAGTACAATCAAGGGCACATTTGTGCATTTAAGGCTA
1 GGGTACGTAAGTGCATTCAGGGGTACCAAAGTACAAACAAGGGCACATATATGCATTTAAGGCTA
*
5473009 CCGCACTACAAACAGGGCCACACATGTGCATTCA
66 CCGAACTACAAACAGGGCCACACATGTGCATTCA
5473043 TTCAATAATT
Statistics
Matches: 82, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
120 82 1.00
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (120 bp):
GGGTACGTAAGTGCATTCAGGGGTACCAAAGTACAAACAAGGGCACATATATGCATTTAAGGCTA
CCGAACTACAAACAGGGCCACACATGTGCATTCAGGAGTACCAAAGTACAAGTAG
Found at i:5476395 original size:233 final size:232
Alignment explanation
Indices: 5475989--5476439 Score: 848
Period size: 233 Copynumber: 1.9 Consensus size: 232
5475979 TGGTAGAAGT
*
5475989 AAATAGATCTTGTTACGAGGATTTCAAAAATGTAAAAATCATTAAAAAGGGGCTAGAACAGACTT
1 AAATAGATCTTGTTACGAGGATTTCAAAAATGTAAAAATCATTAAAAAAGGGCTAGAACAGACTT
5476054 ACAATCGAGCTTGGAATCTTGCAAAACCCTAGCCATGGTTTCTTCATGTAAAATTCAGCCAAGGA
66 ACAATCGAGCTTGGAATCTTGCAAAACCCTAGCCATGGTTTCTTCATGTAAAATTCAGCCAAGGA
*
5476119 AGAAGATGGAAAAGAAATTGTGGCTTTTATTTTGTTTATTAAGTCATTTAATTACTAAATGACCA
131 AAAAGATGGAAAAGAAATTGTGGCTTTTATTTTGTTTATTAAGTCATTTAATTACTAAATGACCA
5476184 AAATGCCCCTAAATTAAAATTAAAATTAAGTCATGTA
196 AAATGCCCCTAAATTAAAATTAAAATTAAGTCATGTA
* *
5476221 AAATAGATCTTGTTACGAGGATTTCAAAAATGTAAAAATCATTAAAAAAAGGGCTGGAACGGACT
1 AAATAGATCTTGTTACGAGGATTTCAAAAATGTAAAAATCATT-AAAAAAGGGCTAGAACAGACT
5476286 TACAATCGAGCTTGGAATCTTGCAAAACCCTAGCCATGGTTTCTTCATGTAAAATTCAGCCAAGG
65 TACAATCGAGCTTGGAATCTTGCAAAACCCTAGCCATGGTTTCTTCATGTAAAATTCAGCCAAGG
*
5476351 AAAAAGATGGACAAGAAATTGTGGCTTTTATTTTGTTTATTAAGTCATTTAATTACTAAATGACC
130 AAAAAGATGGAAAAGAAATTGTGGCTTTTATTTTGTTTATTAAGTCATTTAATTACTAAATGACC
5476416 AAAATGCCCCTAAATTAAAATTAA
195 AAAATGCCCCTAAATTAAAATTAA
5476440 TCTATTTCAC
Statistics
Matches: 213, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
232 43 0.20
233 170 0.80
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (232 bp):
AAATAGATCTTGTTACGAGGATTTCAAAAATGTAAAAATCATTAAAAAAGGGCTAGAACAGACTT
ACAATCGAGCTTGGAATCTTGCAAAACCCTAGCCATGGTTTCTTCATGTAAAATTCAGCCAAGGA
AAAAGATGGAAAAGAAATTGTGGCTTTTATTTTGTTTATTAAGTCATTTAATTACTAAATGACCA
AAATGCCCCTAAATTAAAATTAAAATTAAGTCATGTA
Found at i:5477740 original size:12 final size:12
Alignment explanation
Indices: 5477723--5477747 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5477713 AGCACGTGAC
5477723 ATTTCCCGTCAA
1 ATTTCCCGTCAA
5477735 ATTTCCCGTCAA
1 ATTTCCCGTCAA
5477747 A
1 A
5477748 CACACGAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.32, G:0.08, T:0.32
Consensus pattern (12 bp):
ATTTCCCGTCAA
Found at i:5479708 original size:48 final size:48
Alignment explanation
Indices: 5479621--5479849 Score: 307
Period size: 48 Copynumber: 4.8 Consensus size: 48
5479611 TCTCATATTG
* ****
5479621 ATGCCATGTCCCAGGCATGGTCTTACACAAAATCACATATCGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
** * * * *
5479669 ACCCCA-GATCCTAGATATGGTCTTATATGGGATCACATATTGATGCCA
1 ATGCCATG-TCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
*
5479717 ATGCCATGTCCCAGACATGGTCTTACATGGGACCACATATCGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
* *
5479765 ATGCCATGTCCTAGACATGGTCTTACATAGGATCACATATCGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
*
5479813 ATGCCATGTCCCAAACATGGTCTTACATGGGATCACA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACA
5479850 ATGCCATAGC
Statistics
Matches: 155, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
47 1 0.01
48 153 0.99
49 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
Found at i:5479870 original size:37 final size:37
Alignment explanation
Indices: 5479829--5479913 Score: 118
Period size: 37 Copynumber: 2.3 Consensus size: 37
5479819 TGTCCCAAAC
5479829 ATGGTCTTACATGGGATCACAATGCCATAGCCTAG-CT
1 ATGGTCTTACATGGGATCACAATGCCATAGCC-AGACT
** * *
5479866 ATGGTCTTACATGTTATTACAATGCCATAGCCCGACT
1 ATGGTCTTACATGGGATCACAATGCCATAGCCAGACT
5479903 ATGGTCTTACA
1 ATGGTCTTACA
5479914 CTTATGATCG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 1 0.02
37 42 0.98
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (37 bp):
ATGGTCTTACATGGGATCACAATGCCATAGCCAGACT
Found at i:5482887 original size:40 final size:40
Alignment explanation
Indices: 5482793--5483017 Score: 231
Period size: 40 Copynumber: 5.6 Consensus size: 40
5482783 TATTCGAATG
* *
5482793 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTA-GCGACT
* * * * * *
5482834 ATAACCGGACTAAGATCCGAAGGCATTCGTACGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAG-CGACT
* *
5482874 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGCGACT
* * *
5482914 ATATCTGGGCTAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGCGACT
* * *
5482954 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
* *
5482994 ACATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
5483018 CTTGCGCAAG
Statistics
Matches: 154, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
39 1 0.01
40 124 0.81
41 28 0.18
42 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGCGACT
Found at i:5482973 original size:80 final size:80
Alignment explanation
Indices: 5482793--5483017 Score: 281
Period size: 80 Copynumber: 2.8 Consensus size: 80
5482783 TATTCGAATG
* * * *
5482793 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-GTGACTATATCCGGGCTAAGACCCGAAGGC
*
5482858 ATTCGTACGAGTTGCT
65 ATTCGTACGAGTCGCT
* * * * *
5482874 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCTGGGCTAAAACCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
* * *
5482939 TTTGTGCTAG-CGACT
66 TTCGTACGAGTCG-CT
* * *
5482954 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACCACATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGC
5483018 CTTGCGCAAG
Statistics
Matches: 122, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
79 1 0.01
80 89 0.73
81 32 0.26
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.24
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
TTCGTACGAGTCGCT
Found at i:5483007 original size:120 final size:121
Alignment explanation
Indices: 5482793--5483017 Score: 294
Period size: 120 Copynumber: 1.9 Consensus size: 121
5482783 TATTCGAATG
** * *
5482793 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCCGAAGGC
* * *
5482858 ATTCGTACGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
66 ATTCATACGAGTTGCCACATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
* * *
5482914 ATATCTGGGCTAAAACCCGAAGGCATTTGTGCTA-GCGACTATATCCGGGCTAAG-TCCCGAAGG
1 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGAT-CCGAAGG
* * *
5482977 CATTTATGCTAG-TGACCACATCCGGGCTAAGACCCGAAGGC
65 CATTCATACGAGTTG-CCACATCCGGGCTAAGACCCGAAGGC
5483018 CTTGCGCAAG
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
119 3 0.03
120 56 0.63
121 30 0.34
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.24
Consensus pattern (121 bp):
ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCCGAAGGC
ATTCATACGAGTTGCCACATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
Found at i:5488084 original size:54 final size:54
Alignment explanation
Indices: 5488022--5488133 Score: 192
Period size: 54 Copynumber: 2.1 Consensus size: 54
5488012 TGTTAAAAAT
*
5488022 AAAG-ATTAGAAATAAGTAAAATAGAAGTGAAATG-AGTAAACAAACGCTAAGGG
1 AAAGAATTAGAAATAAGTAAAATAGAAGTGAAA-GCAGTAAACAAACGCTAAGGC
5488075 AAAGAATTAGAAATAAGTAAAATAGAAGTGAAAGCAGTAAACAAACGCTAAGGC
1 AAAGAATTAGAAATAAGTAAAATAGAAGTGAAAGCAGTAAACAAACGCTAAGGC
5488129 AAAGA
1 AAAGA
5488134 GATTGAGTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
53 5 0.09
54 51 0.91
ACGTcount: A:0.56, C:0.07, G:0.21, T:0.15
Consensus pattern (54 bp):
AAAGAATTAGAAATAAGTAAAATAGAAGTGAAAGCAGTAAACAAACGCTAAGGC
Found at i:5503778 original size:17 final size:19
Alignment explanation
Indices: 5503742--5503778 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
5503732 AAAGCCCATA
5503742 ACACGACCCATGTGGGCCC
1 ACACGACCCATGTGGGCCC
*
5503761 ACACG-CCCGTGT-GGCCC
1 ACACGACCCATGTGGGCCC
5503778 A
1 A
5503779 ATAAACCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 6 0.35
19 5 0.29
ACGTcount: A:0.19, C:0.43, G:0.27, T:0.11
Consensus pattern (19 bp):
ACACGACCCATGTGGGCCC
Found at i:5505140 original size:10 final size:10
Alignment explanation
Indices: 5505127--5505156 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
5505117 AGAACAAATA
5505127 TATTCAAACT
1 TATTCAAACT
5505137 TATTCAAACT
1 TATTCAAACT
5505147 TATTCAAACT
1 TATTCAAACT
5505157 CTTGGTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (10 bp):
TATTCAAACT
Found at i:5514762 original size:10 final size:10
Alignment explanation
Indices: 5514749--5514778 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
5514739 AGAACAAATA
5514749 TATTCAAACT
1 TATTCAAACT
5514759 TATTCAAACT
1 TATTCAAACT
5514769 TATTCAAACT
1 TATTCAAACT
5514779 CTTGGTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (10 bp):
TATTCAAACT
Found at i:5519833 original size:24 final size:24
Alignment explanation
Indices: 5519776--5519912 Score: 139
Period size: 24 Copynumber: 5.7 Consensus size: 24
5519766 CCATGTTTAC
* **
5519776 CCGCACACATAGTGCCTTAGTAAT
1 CCGCACACATAGTGCCATACAAAT
* * * * * *
5519800 TCACATACATATTGACATTCAAAT
1 CCGCACACATAGTGCCATACAAAT
5519824 CCGCACACATAGTGCCATACAAAT
1 CCGCACACATAGTGCCATACAAAT
* *
5519848 CCGCACACATAGTGTCGTACAAAT
1 CCGCACACATAGTGCCATACAAAT
* *
5519872 TCGCACACATAGTGCCATTCAAAT
1 CCGCACACATAGTGCCATACAAAT
* *
5519896 TCGTACACATAGTGCCA
1 CCGCACACATAGTGCCA
5519913 AAGTCATTTC
Statistics
Matches: 91, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 91 1.00
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.24
Consensus pattern (24 bp):
CCGCACACATAGTGCCATACAAAT
Found at i:5519873 original size:72 final size:72
Alignment explanation
Indices: 5519776--5519912 Score: 184
Period size: 72 Copynumber: 1.9 Consensus size: 72
5519766 CCATGTTTAC
* ** * *
5519776 CCGCACACATAGTGCCTTAGTAATTCACATACATATTGACATTCAAATCCGCACACATAGTGCCA
1 CCGCACACATAGTGCCGTACAAATTCACACACATAGTGACATTCAAATCCGCACACATAGTGCCA
5519841 TACAAAT
66 TACAAAT
* * * * *
5519848 CCGCACACATAGTGTCGTACAAATTCGCACACATAGTGCCATTCAAATTCGTACACATAGTGCCA
1 CCGCACACATAGTGCCGTACAAATTCACACACATAGTGACATTCAAATCCGCACACATAGTGCCA
5519913 AAGTCATTTC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
72 55 1.00
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.24
Consensus pattern (72 bp):
CCGCACACATAGTGCCGTACAAATTCACACACATAGTGACATTCAAATCCGCACACATAGTGCCA
TACAAAT
Found at i:5521186 original size:15 final size:14
Alignment explanation
Indices: 5521160--5521195 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
5521150 CTTTTTCTTC
*
5521160 TTTTATTCATTCAT
1 TTTTATTAATTCAT
5521174 TTCTTATTAATTCAT
1 TT-TTATTAATTCAT
5521189 TTTTATT
1 TTTTATT
5521196 TGGATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTATTAATTCAT
Found at i:5527789 original size:27 final size:26
Alignment explanation
Indices: 5527745--5527796 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
5527735 CTCGCCGCAA
*
5527745 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
5527772 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
5527797 ACAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:5527856 original size:29 final size:27
Alignment explanation
Indices: 5527833--5527892 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
5527823 CGCCACATAT
5527833 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGGCCTAGCCACA
* * * *
5527859 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGGCCTAGCCACA
5527886 ATATCTG
1 ATATCTG
5527893 ACAGCCTCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGGCCTAGCCACA
Found at i:5533100 original size:28 final size:28
Alignment explanation
Indices: 5533037--5533253 Score: 220
Period size: 28 Copynumber: 7.4 Consensus size: 28
5533027 ATATTAAGTC
*
5533037 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
5533064 CGCACACTTAGTGCTATGTAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
5533092 CGCACACTTATTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
5533120 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
*
5533149 CGCACACTTAGCGCTCTTAGTGCTATGTAATCAAACT
1 CG--CAC--A-----CTTAGTGCTATATAATCAAACT
5533186 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
5533214 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
5533243 CGCACACTTAG
1 CGCACACTTAG
5533254 CGCCAATCTC
Statistics
Matches: 159, Mismatches: 19, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
27 21 0.13
28 88 0.55
29 23 0.14
31 3 0.02
33 2 0.01
35 3 0.02
37 7 0.04
38 12 0.08
ACGTcount: A:0.32, C:0.27, G:0.13, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:5533183 original size:94 final size:94
Alignment explanation
Indices: 5533070--5533256 Score: 365
Period size: 94 Copynumber: 2.0 Consensus size: 94
5533060 AACTCGCACA
*
5533070 CTTAGTGCTATGTAATCAAACTCGCACACTTATTGCTATATAATCAAACTCGCACACTTAGTGCT
1 CTTAGTGCTATGTAATCAAACTCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCT
5533135 GTACAATTTAAACCCGCACACTTAGCGCT
66 GTACAATTTAAACCCGCACACTTAGCGCT
5533164 CTTAGTGCTATGTAATCAAACTCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCT
1 CTTAGTGCTATGTAATCAAACTCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCT
5533229 GTACAATTTAAACCCGCACACTTAGCGC
66 GTACAATTTAAACCCGCACACTTAGCGC
5533257 CAATCTCATG
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (94 bp):
CTTAGTGCTATGTAATCAAACTCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCT
GTACAATTTAAACCCGCACACTTAGCGCT
Found at i:5537832 original size:34 final size:35
Alignment explanation
Indices: 5537784--5537868 Score: 118
Period size: 34 Copynumber: 2.5 Consensus size: 35
5537774 GCGAATACAT
*
5537784 TCTGGGCCTAAGCCCATATTAGTAACAGT-AACAG
1 TCTGGGCCTAAGCCCATATTAATAACAGTAAACAG
* * *
5537818 TCTGGGCCTTAGCCCATTTTAATATCAGTAAACAG
1 TCTGGGCCTAAGCCCATATTAATAACAGTAAACAG
*
5537853 TCTAGGCCTAAGCCCA
1 TCTGGGCCTAAGCCCA
5537869 CCTCAATACA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 25 0.57
35 19 0.43
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (35 bp):
TCTGGGCCTAAGCCCATATTAATAACAGTAAACAG
Found at i:5538304 original size:29 final size:27
Alignment explanation
Indices: 5538280--5538376 Score: 101
Period size: 27 Copynumber: 3.6 Consensus size: 27
5538270 CATCACATAG
5538280 GGGCAAAACAGTCATTTTGCCTCACAA
1 GGGCAAAACAGTCATTTTGCCTCACAA
* *
5538307 GGGCAAAATAGTCATTTTGTAC-CACAA
1 GGGCAAAACAGTCATTTTG-CCTCACAA
* * *
5538334 GGGAAAAATAGTCATTTTACC-CACAA
1 GGGCAAAACAGTCATTTTGCCTCACAA
5538360 GGG-AAATTACAGTCATT
1 GGGCAAA--ACAGTCATT
5538377 ATATCTTATA
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.05
26 9 0.15
27 48 0.79
28 1 0.02
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.25
Consensus pattern (27 bp):
GGGCAAAACAGTCATTTTGCCTCACAA
Found at i:5538319 original size:27 final size:26
Alignment explanation
Indices: 5538280--5538362 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
5538270 CATCACATAG
*
5538280 GGGCAAAACAGTCATTTTGCCTCACAA
1 GGGCAAAATAGTCATTTTGCC-CACAA
*
5538307 GGGCAAAATAGTCATTTTGTACCACAA
1 GGGCAAAATAGTCATTTTG-CCCACAA
* *
5538334 GGGAAAAATAGTCATTTTACCCACAA
1 GGGCAAAATAGTCATTTTGCCCACAA
5538360 GGG
1 GGG
5538363 AAATTACAGT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
26 9 0.18
27 40 0.80
28 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (26 bp):
GGGCAAAATAGTCATTTTGCCCACAA
Found at i:5551055 original size:45 final size:43
Alignment explanation
Indices: 5550992--5551201 Score: 133
Period size: 42 Copynumber: 4.9 Consensus size: 43
5550982 ATAAAATTCT
*
5550992 GATATGTGTTTTCATGTAAGACCACGTCTGGGACATTGGCATC
1 GATATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATC
* * * *
5551035 GATATATGTGTTTTCGTGTAAGACCACATCTAGGA-GTTAGG-GTC
1 G--ATATGTGTTTTCGTGTAAGACCACGTCTGGGACATT-GGCATC
* * * * *
5551079 GATATGTGGTTACGAGTAAGACCATGTCTGGGACATCGGCATC
1 GATATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATC
* * * * * * *
5551122 G-TATTTGATCT-GTGTAAGACC-CTATCTAGGACAGTGGCACC
1 GATATGTGTTTTCGTGTAAGACCAC-GTCTGGGACATTGGCATC
* * ** * * *
5551163 GATATGAGATAGCATGTAAGTCCACGTCTGGGACGTTGG
1 GATATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGG
5551202 TATTGTATGA
Statistics
Matches: 123, Mismatches: 35, Indels: 18
0.70 0.20 0.10
Matches are distributed among these distances:
41 23 0.19
42 40 0.33
43 23 0.19
44 6 0.05
45 31 0.25
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.30
Consensus pattern (43 bp):
GATATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATC
Found at i:5553604 original size:30 final size:30
Alignment explanation
Indices: 5553568--5553630 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
5553558 ACTTATTTTA
5553568 TTGTTAATTTTGCTATTATTTT-GAAGGCAT
1 TTGTTAATTTTGCTATTATTTTAG-AGGCAT
*
5553598 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGCTATTATTTTAGAGGCAT
5553628 TTG
1 TTG
5553631 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.22, C:0.05, G:0.17, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGCTATTATTTTAGAGGCAT
Done.