Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 137 of 292
Found at i:40663917 original size:42 final size:42
Alignment explanation
Indices: 40663757--40663919 Score: 161
Period size: 42 Copynumber: 3.9 Consensus size: 42
40663747 TACCATACCA
* *
40663757 ATGCCATATCCCAGATATGGTCTTACATATCA-TCTCATATCA
1 ATGCCATATCCCAGATATGGTCTTACACAT-AGTCTCATATCG
* * * * *
40663799 ATGCCAATAGCCCAGA-ATGTTCTTACACAAAATCTCACATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACATAGTCTCATATCG
* * * *
40663841 ATGCCATATCCTAGATACGGTCTTACACGA-AGTCTCATTTTG
1 ATGCCATATCCCAGATATGGTCTTACAC-ATAGTCTCATATCG
* *
40663883 ATTCCATATCCCAAATATGGTCTTACACATAGTCTCA
1 ATGCCATATCCCAGATATGGTCTTACACATAGTCTCA
40663920 GTAACCCTAA
Statistics
Matches: 98, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
41 10 0.10
42 78 0.80
43 10 0.10
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACATAGTCTCATATCG
Found at i:40664117 original size:69 final size:69
Alignment explanation
Indices: 40664002--40664147 Score: 283
Period size: 69 Copynumber: 2.1 Consensus size: 69
40663992 ATTTTTCGAA
40664002 TACATCAATAATTTAATCACAATTCATACAATAATAAAGCATTTAAAACATAATTAAAAAATGCA
1 TACAT-AATAATTTAATCACAATTCATACAATAATAAAGCATTTAAAACATAATTAAAAAATGCA
40664067 TTATT
65 TTATT
40664072 TACATAATAATTTAATCACAATTCATACAATAATAAAGCATTTAAAACATAATTAAAAAATGCAT
1 TACATAATAATTTAATCACAATTCATACAATAATAAAGCATTTAAAACATAATTAAAAAATGCAT
40664137 TATT
66 TATT
40664141 TACATAA
1 TACATAA
40664148 GAACTTACCT
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
69 71 0.93
70 5 0.07
ACGTcount: A:0.52, C:0.12, G:0.03, T:0.33
Consensus pattern (69 bp):
TACATAATAATTTAATCACAATTCATACAATAATAAAGCATTTAAAACATAATTAAAAAATGCAT
TATT
Found at i:40664468 original size:22 final size:22
Alignment explanation
Indices: 40664443--40664484 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
40664433 CCACATTTTT
*
40664443 CATTTAATCACCCTTTTACACA
1 CATTTAATAACCCTTTTACACA
* *
40664465 CATTTTATAACCTTTTTACA
1 CATTTAATAACCCTTTTACA
40664485 AATTGGTCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.26, G:0.00, T:0.43
Consensus pattern (22 bp):
CATTTAATAACCCTTTTACACA
Found at i:40671490 original size:85 final size:84
Alignment explanation
Indices: 40671364--40671519 Score: 215
Period size: 85 Copynumber: 1.8 Consensus size: 84
40671354 TACCATACCA
* * * * *
40671364 ATGCCATATCCCAGATATGGTCTTACATGTCATCTCGTATCGATGCCAATAGCCCAGCTACGGTC
1 ATGCCATATCCCAGATACGGTCTTACACGTAATCTCATATCGATGCC-ATAGCCCAGATACGGTC
40671429 TTACACAAAATCTCTCATCG
65 TTACACAAAATCTCTCATCG
* * *
40671449 ATGCCATATCCCAGATACGGTCTTACACG-AAGTCTCATATCGATGCCATATCCTAGATATGGTC
1 ATGCCATATCCCAGATACGGTCTTACACGTAA-TCTCATATCGATGCCATAGCCCAGATACGGTC
40671513 TTACACA
65 TTACACA
40671520 TAGTCTCAGT
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
84 21 0.34
85 41 0.66
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (84 bp):
ATGCCATATCCCAGATACGGTCTTACACGTAATCTCATATCGATGCCATAGCCCAGATACGGTCT
TACACAAAATCTCTCATCG
Found at i:40671525 original size:42 final size:42
Alignment explanation
Indices: 40671364--40671527 Score: 181
Period size: 42 Copynumber: 3.9 Consensus size: 42
40671354 TACCATACCA
* ** *
40671364 ATGCCATATCCCAGATATGGTCTTACATGTCA-TCTCGTATCG
1 ATGCCATATCCCAGATACGGTCTTACACAT-AGTCTCATATCG
* * * *
40671406 ATGCCAATAGCCCAGCTACGGTCTTACACAAAATCTC-TCATCG
1 ATGCC-ATATCCCAGATACGGTCTTACACATAGTCTCAT-ATCG
40671449 ATGCCATATCCCAGATACGGTCTTACACGA-AGTCTCATATCG
1 ATGCCATATCCCAGATACGGTCTTACAC-ATAGTCTCATATCG
* *
40671491 ATGCCATATCCTAGATATGGTCTTACACATAGTCTCA
1 ATGCCATATCCCAGATACGGTCTTACACATAGTCTCA
40671528 GTAACCCTAA
Statistics
Matches: 105, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
41 1 0.01
42 70 0.67
43 34 0.32
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (42 bp):
ATGCCATATCCCAGATACGGTCTTACACATAGTCTCATATCG
Found at i:40673824 original size:21 final size:20
Alignment explanation
Indices: 40673800--40673839 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
40673790 ACTTGTATAT
*
40673800 CTATCAACAAGCATTCAAAAC
1 CTATCAACAAACA-TCAAAAC
*
40673821 CTATCATCAAACATCAAAA
1 CTATCAACAAACATCAAAA
40673840 TACATGCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.50, C:0.28, G:0.03, T:0.20
Consensus pattern (20 bp):
CTATCAACAAACATCAAAAC
Found at i:40683306 original size:40 final size:39
Alignment explanation
Indices: 40683261--40683468 Score: 202
Period size: 40 Copynumber: 5.2 Consensus size: 39
40683251 CGGAATACAA
*
40683261 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
40683301 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
40683341 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* *** *
40683381 CCGGATGTGGTCACTAGCAC-AATGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAAT-GCCTTCGGGTCTTAGC
** * * *
40683421 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
40683461 CCGGATAT
1 CCGGATAT
40683469 CATTCAATTG
Statistics
Matches: 141, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 4 0.03
40 134 0.95
41 3 0.02
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:40683401 original size:80 final size:80
Alignment explanation
Indices: 40683261--40683467 Score: 238
Period size: 80 Copynumber: 2.6 Consensus size: 80
40683251 CGGAATACAA
* * *
40683261 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAAT-
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCAC-AATG
*
40683325 GCCTTCGGGTATTAGC
65 GCCTTCGGGTATTAAC
* * **
40683341 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTGGTC-ACTAGCACAATG
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-AGAACGACTAGCACAATG
*
40683405 GCCTTCGGGTCTTAAC
65 GCCTTCGGGTATTAAC
** * ** * *
40683421 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATA
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA
40683468 TCATTCAATT
Statistics
Matches: 107, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
79 3 0.03
80 102 0.95
81 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (80 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAATGG
CCTTCGGGTATTAAC
Found at i:40685481 original size:40 final size:39
Alignment explanation
Indices: 40685417--40685604 Score: 214
Period size: 39 Copynumber: 4.8 Consensus size: 39
40685407 GCTACTCGTT
* * * ** *
40685417 CAAACGCCTTCGGGACATAGCCCGGTTATGGTAACCCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGATATCATAACTCGCA
* *
40685457 CAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGATATCATAACTCGCA
* *
40685497 CAATTGCCTTCGGGCTTAGCCCGGATATCATAGCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGATATCATAACTCGCA
* * *
40685536 CAATTGCCTTCGGGCTTAGCCCGGATATCACAATTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGATATCATAACTCGCA
* * *
40685575 CAATTGCCTTCGGGCTTTGCCCGGTTATCA
1 CAAATGCCTTCGGGCTTAGCCCGGATATCA
40685605 CTCGAACATT
Statistics
Matches: 131, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 86 0.66
40 45 0.34
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGATATCATAACTCGCA
Found at i:40685534 original size:39 final size:39
Alignment explanation
Indices: 40685453--40685605 Score: 234
Period size: 39 Copynumber: 3.9 Consensus size: 39
40685443 TATGGTAACC
* *
40685453 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
40685493 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
40685532 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
* *
40685571 CGCACAATTGCCTTCGGGCTTTGCCCGGTTATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
40685606 TCGAACATTC
Statistics
Matches: 104, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 87 0.84
40 17 0.16
ACGTcount: A:0.22, C:0.32, G:0.21, T:0.25
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:40689530 original size:40 final size:39
Alignment explanation
Indices: 40689367--40689548 Score: 129
Period size: 40 Copynumber: 4.6 Consensus size: 39
40689357 AAATTGAATG
* *
40689367 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
40689406 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
40689446 ACATCCGGGCTAAGA-CCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
40689485 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
40689524 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
40689549 CTTGGTGCGG
Statistics
Matches: 111, Mismatches: 25, Indels: 13
0.74 0.17 0.09
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 46 0.41
40 59 0.53
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:40697641 original size:40 final size:39
Alignment explanation
Indices: 40697476--40697659 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
40697466 AAATTGAATG
* * *
40697476 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
40697516 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
40697556 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
40697596 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
40697635 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
40697660 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:40697684 original size:80 final size:81
Alignment explanation
Indices: 40697516--40697704 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
40697506 GCTGGAAATT
* * * *
40697516 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
40697581 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
40697597 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
40697660 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
40697676 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
40697705 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:40704827 original size:27 final size:27
Alignment explanation
Indices: 40704693--40704833 Score: 192
Period size: 27 Copynumber: 5.2 Consensus size: 27
40704683 TGGATAAGTT
** *
40704693 GTAGAATTATCGAAATACCCCTACAAG
1 GTAGAATTATCGAAATACCCCTGTAGG
*
40704720 GTAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTATCGAAATACCCCTGTAGG
*
40704747 GTAGAATTATTGAAATACCCCTGTAGG
1 GTAGAATTATCGAAATACCCCTGTAGG
* * *
40704774 GTAGAATTACCAAAATACCCCTATAGG
1 GTAGAATTATCGAAATACCCCTGTAGG
* *
40704801 ATAGAATTATCGAAATACCCTTGTAGG
1 GTAGAATTATCGAAATACCCCTGTAGG
40704828 GTAGAA
1 GTAGAA
40704834 ATACCGAGAT
Statistics
Matches: 98, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 98 1.00
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (27 bp):
GTAGAATTATCGAAATACCCCTGTAGG
Found at i:40704863 original size:54 final size:54
Alignment explanation
Indices: 40704693--40704846 Score: 218
Period size: 54 Copynumber: 2.9 Consensus size: 54
40704683 TGGATAAGTT
** *
40704693 GTAGAATTATCGAAATACCCCTACAAGGTAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTATCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGG
* * *
40704747 GTAGAATTATTGAAATACCCCTGTAGGGTAGAATTACCAAAATACCCCTATAGG
1 GTAGAATTATCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGG
* * * *
40704801 ATAGAATTATCGAAATACCCTTGTAGGGTAGAAATACCGAGATACC
1 GTAGAATTATCGAAATACCCCTGTAGGGTAGAATTACCGAAATACC
40704847 TTGGTGGGGT
Statistics
Matches: 88, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 88 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (54 bp):
GTAGAATTATCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGG
Found at i:40704877 original size:81 final size:81
Alignment explanation
Indices: 40704705--40704866 Score: 202
Period size: 81 Copynumber: 2.0 Consensus size: 81
40704695 AGAATTATCG
* * **
40704705 AAATACCCCTACAAGG-TAGAATTACCGAAATACCCCTGTAGGGTAGAATTATTGAAATACCCCT
1 AAATACCCCTA-TAGGATAGAATTACCGAAATACCCCTGTAGGGTAGAAATACCGAAATACCCCT
*
40704769 GTAGGGTAGAATTACCA
65 GTAGGGTAAAATTACCA
* * * *
40704786 AAATACCCCTATAGGATAGAATTATCGAAATACCCTTGTAGGGTAGAAATACCGAGATA-CCTTG
1 AAATACCCCTATAGGATAGAATTACCGAAATACCCCTGTAGGGTAGAAATACCGAAATACCCCT-
*
40704850 GTGGGGTAAAATTACCA
65 GTAGGGTAAAATTACCA
40704867 TTTTGCCCCT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
80 6 0.09
81 63 0.91
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (81 bp):
AAATACCCCTATAGGATAGAATTACCGAAATACCCCTGTAGGGTAGAAATACCGAAATACCCCTG
TAGGGTAAAATTACCA
Found at i:40711302 original size:42 final size:42
Alignment explanation
Indices: 40711191--40711344 Score: 166
Period size: 42 Copynumber: 3.6 Consensus size: 42
40711181 TACCACATCA
* * *** *
40711191 ATGCCATATTCCAGATATGATCTTACATGGGATCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACATAAAATCTCATATCG
* * * *
40711233 ATACCAATAGCCCAGCTATGGCCTTACATAAAATCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACATAAAATCTCATATCG
* *
40711276 ATGCCATATCCCAGATATGGTCTTACACAAAGTCTCATAAT-G
1 ATGCCATATCCCAGATATGGTCTTACATAAAATCTCAT-ATCG
*
40711318 ATGCCATATCCTAGATATGGTCTTACA
1 ATGCCATATCCCAGATATGGTCTTACA
40711345 CATATTCTCG
Statistics
Matches: 93, Mismatches: 17, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
42 59 0.63
43 34 0.37
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACATAAAATCTCATATCG
Found at i:40717801 original size:32 final size:32
Alignment explanation
Indices: 40717765--40717825 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
40717755 AGAAAGTTAG
40717765 AGTAATACGTGACTACTTGAAGGCCACCTTAA
1 AGTAATACGTGACTACTTGAAGGCCACCTTAA
* *
40717797 AGTAATTCGTGACTGCTTGAAGGCCACCT
1 AGTAATACGTGACTACTTGAAGGCCACCT
40717826 CAAATTGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (32 bp):
AGTAATACGTGACTACTTGAAGGCCACCTTAA
Found at i:40719632 original size:46 final size:46
Alignment explanation
Indices: 40719496--40719671 Score: 192
Period size: 46 Copynumber: 3.8 Consensus size: 46
40719486 TCACTTGTGT
* * * * * **
40719496 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGACAA
* * *
40719542 GAGCCAATGTAAGACCATGTCTGGGACATGGCATCAACATCGAGACAA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGACCTCGAGACAA
* * *
40719590 GTGCTAGTGTAAGACATGTCTGGGATATGCATCGACCTCGAGACATA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGACA-A
*
40719637 -AGCCAGTGCAAGACATGTCTGGGACATGCATCGAC
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGAC
40719672 ACAGTTATGT
Statistics
Matches: 107, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
46 58 0.54
47 28 0.26
48 21 0.20
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGACAA
Found at i:40719690 original size:94 final size:94
Alignment explanation
Indices: 40719491--40719768 Score: 248
Period size: 94 Copynumber: 2.9 Consensus size: 94
40719481 TTGTGTCACT
* * * *
40719491 TGTGTGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-A-ATATGAGAGCCAATGTAA
1 TGTGAGAGCTAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGA-AT-AGAGCCAGTGTAA
40719554 GACCATGTCTGGGACATGGCATCAACATCGA
64 GACCATGTCTGGGACATGGCATCAACATCGA
** * * *
40719585 -GACAAGTGCTAGTGTAAGACATGTCTGGGATATGCATCGACCTCGAGACATA-AGCCAGTGCAA
1 TG-TGAGAGCTAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGA-ATAGAGCCAGTGTAA
*
40719648 GA-CATGTCTGGGACAT-GCATCGACACAGT-TA
64 GACCATGTCTGGGACATGGCATC-A-ACA-TCGA
* * * * * *
40719679 TGTGAGAGCTAGTGTAAGGCCATGTCCGGGACATGGCATC-AGTCTTGAAGAGTATAGCCAGTGT
1 TGTGAGAGCTAGTGTAA-GACATGTCTGGGACAT-GCATCGA-CCTCG-AGAATAGAGCCAGTGT
*
40719743 AAGAGCATGTCTGGGACATGGCATCA
62 AAGACCATGTCTGGGACATGGCATCA
40719769 TTCCTTACCC
Statistics
Matches: 149, Mismatches: 21, Indels: 24
0.77 0.11 0.12
Matches are distributed among these distances:
92 5 0.03
93 16 0.11
94 62 0.42
95 18 0.12
96 13 0.09
97 15 0.10
98 15 0.10
99 5 0.03
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (94 bp):
TGTGAGAGCTAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGAATAGAGCCAGTGTAAGA
CCATGTCTGGGACATGGCATCAACATCGA
Found at i:40721408 original size:31 final size:31
Alignment explanation
Indices: 40721367--40721432 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
40721357 CCTTTTCATA
*
40721367 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
40721398 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
40721429 TTTC
1 TTTC
40721433 TATAAACGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:40721676 original size:24 final size:23
Alignment explanation
Indices: 40721645--40721812 Score: 219
Period size: 24 Copynumber: 7.1 Consensus size: 23
40721635 CCTAGCCTCT
*
40721645 TTTAGTAACTGGGGCAGAAGCCC
1 TTTAGTAACTGGGGCATAAGCCC
*
40721668 TTTTTGTAACTGGGGCATAAGCCC
1 -TTTAGTAACTGGGGCATAAGCCC
* * *
40721692 TTTTGATCACTAGGGCATAAGCCC
1 TTTAG-TAACTGGGGCATAAGCCC
*
40721716 TTTAATAACTGGGGCATAAGCCC
1 TTTAGTAACTGGGGCATAAGCCC
*
40721739 TTTTGATAACTGGGGCATAAGCCCC
1 TTTAG-TAACTGGGGCATAAG-CCC
*
40721764 TTTAATAACTGGGGCATAAGCCC
1 TTTAGTAACTGGGGCATAAGCCC
*
40721787 TTTAATAACTGGGGCATAAGCCC
1 TTTAGTAACTGGGGCATAAGCCC
40721810 TTT
1 TTT
40721813 TGCACTTCCT
Statistics
Matches: 129, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
23 53 0.41
24 70 0.54
25 6 0.05
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (23 bp):
TTTAGTAACTGGGGCATAAGCCC
Found at i:40721737 original size:71 final size:72
Alignment explanation
Indices: 40721645--40721813 Score: 270
Period size: 71 Copynumber: 2.4 Consensus size: 72
40721635 CCTAGCCTCT
* * * * *
40721645 TTTAGTAACTGGGGCAGAAGCCCTTTTTG-TAACTGGGGCATAAGCCCTTTTGATCACTAGGGCA
1 TTTAATAACTGGGGCATAAGCCCTTTTTGATAACTGGGGCATAAGCCCCTTTAATAACTAGGGCA
40721709 TAAGCCC
66 TAAGCCC
*
40721716 TTTAATAACTGGGGCATAAGCCC-TTTTGATAACTGGGGCATAAGCCCCTTTAATAACTGGGGCA
1 TTTAATAACTGGGGCATAAGCCCTTTTTGATAACTGGGGCATAAGCCCCTTTAATAACTAGGGCA
40721780 TAAGCCC
66 TAAGCCC
40721787 TTTAATAACTGGGGCATAAGCCCTTTT
1 TTTAATAACTGGGGCATAAGCCCTTTT
40721814 GCACTTCCTC
Statistics
Matches: 90, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
70 5 0.06
71 82 0.91
72 3 0.03
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (72 bp):
TTTAATAACTGGGGCATAAGCCCTTTTTGATAACTGGGGCATAAGCCCCTTTAATAACTAGGGCA
TAAGCCC
Found at i:40721739 original size:47 final size:47
Alignment explanation
Indices: 40721624--40721812 Score: 249
Period size: 47 Copynumber: 4.0 Consensus size: 47
40721614 GCTTTATCAT
* * *
40721624 ATAACTGGAGGCCT-AGCCTCTTTT-AGTAACTGGGGCAGAAGCCCTTTTT
1 ATAACTGG-GGCATAAGCC-CTTTTGA-TAACTGGGGCATAAGCCC-TTTA
* * *
40721673 GTAACTGGGGCATAAGCCCTTTTGATCACTAGGGCATAAGCCCTTTA
1 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTA
40721720 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCCTTTA
1 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAG-CCCTTTA
*
40721768 ATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCCTTT
1 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTT
40721813 TGCACTTCCT
Statistics
Matches: 127, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
46 6 0.05
47 59 0.46
48 50 0.39
49 12 0.09
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (47 bp):
ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTA
Found at i:40721885 original size:9 final size:9
Alignment explanation
Indices: 40721871--40721927 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
40721861 ATCTCATGTG
40721871 CATATCATA
1 CATATCATA
*
40721880 CATATCATGTG
1 CATATCA--TA
40721891 CATATCATA
1 CATATCATA
* *
40721900 CATGTCATGTG
1 CATATCA--TA
40721911 CATATCATA
1 CATATCATA
40721920 CATATCAT
1 CATATCAT
40721928 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:40721887 original size:20 final size:20
Alignment explanation
Indices: 40721859--40721929 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
40721849 GCATTTATGA
*
40721859 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
40721879 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
40721899 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
40721919 ACATATCATGT
1 ACATATCATGT
40721930 TTATCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:40721894 original size:11 final size:11
Alignment explanation
Indices: 40721864--40721918 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
40721854 TATGAACATC
40721864 TCATGTGCATA
1 TCATGTGCATA
*
40721875 TCA--TACATA
1 TCATGTGCATA
40721884 TCATGTGCATA
1 TCATGTGCATA
* *
40721895 TCA--TACATG
1 TCATGTGCATA
40721904 TCATGTGCATA
1 TCATGTGCATA
40721915 TCAT
1 TCAT
40721919 ACATATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:40722008 original size:25 final size:25
Alignment explanation
Indices: 40721966--40722015 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
40721956 ATATATAAAC
* * *
40721966 CCTAGGGGTATAATGGTCACTTTCA
1 CCTAGGGGCAAAACGGTCACTTTCA
*
40721991 CCTAGGGGCAAAACGGTCATTTTCA
1 CCTAGGGGCAAAACGGTCACTTTCA
40722016 TGTTATAAGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCACTTTCA
Found at i:40722390 original size:23 final size:24
Alignment explanation
Indices: 40722280--40722492 Score: 290
Period size: 24 Copynumber: 9.0 Consensus size: 24
40722270 GCTTTATCAT
*
40722280 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* * *
40722305 GTAACTGGGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTA
* *
40722329 GTAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
* *
40722353 ATCACTAGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
40722376 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
40722400 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
40722424 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
40722447 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
40722470 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
40722493 GTATTTCCTC
Statistics
Matches: 171, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
23 65 0.38
24 95 0.56
25 11 0.06
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:40722393 original size:71 final size:70
Alignment explanation
Indices: 40722301--40722493 Score: 314
Period size: 71 Copynumber: 2.7 Consensus size: 70
40722291 CCTAGCCTCT
* * *
40722301 TTTAGTAACTGGGGCAAAAGCCCTTTTTGTAACTGGGGCATAAGCCCTTTTGATCACTAGGGCAT
1 TTTAATAACTGGGGCATAAGCCC-TTTTGTAACTGGGGCATAAGCCCTTTTGATAACTAGGGCAT
40722366 AAGCCC
65 AAGCCC
*
40722372 TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCAT
1 TTTAATAACTGGGGCATAAGCCCTTTTG-TAACTGGGGCATAAGCCCTTTTGATAACTAGGGCAT
40722437 AAGCCC
65 AAGCCC
**
40722443 TTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTTG
1 TTTAATAACTGGGGCATAAGCCCTTTTGTAACTGGGGCATAAGCCCTTTTG
40722494 TATTTCCTCC
Statistics
Matches: 115, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
70 28 0.24
71 87 0.76
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.29
Consensus pattern (70 bp):
TTTAATAACTGGGGCATAAGCCCTTTTGTAACTGGGGCATAAGCCCTTTTGATAACTAGGGCATA
AGCCC
Found at i:40722564 original size:9 final size:9
Alignment explanation
Indices: 40722550--40722606 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
40722540 ATCTCATGTG
40722550 CATATCATA
1 CATATCATA
*
40722559 CATATCATGTG
1 CATATCA--TA
40722570 CATATCATA
1 CATATCATA
* *
40722579 CATGTCATGTG
1 CATATCA--TA
40722590 CATATCATA
1 CATATCATA
40722599 CATATCAT
1 CATATCAT
40722607 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:40722566 original size:20 final size:20
Alignment explanation
Indices: 40722538--40722608 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
40722528 GCATTTATGA
*
40722538 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
40722558 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
40722578 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
40722598 ACATATCATGT
1 ACATATCATGT
40722609 TTATCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:40722573 original size:11 final size:11
Alignment explanation
Indices: 40722543--40722597 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
40722533 TATGAACATC
40722543 TCATGTGCATA
1 TCATGTGCATA
*
40722554 TCA--TACATA
1 TCATGTGCATA
40722563 TCATGTGCATA
1 TCATGTGCATA
* *
40722574 TCA--TACATG
1 TCATGTGCATA
40722583 TCATGTGCATA
1 TCATGTGCATA
40722594 TCAT
1 TCAT
40722598 ACATATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:40722687 original size:25 final size:24
Alignment explanation
Indices: 40722645--40722692 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
40722635 ATATATAAAC
* * *
40722645 CCTAGGGGTATAATGGTCACTTTTA
1 CCTAGGGGCAAAACGGTCA-TTTTA
40722670 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
40722693 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (24 bp):
CCTAGGGGCAAAACGGTCATTTTA
Found at i:40723914 original size:27 final size:27
Alignment explanation
Indices: 40723837--40723916 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
40723827 TCATACGGAA
40723837 CATA-AGGGCATATT-C-GTCATTTTAC
1 CATACAGGGC-TATTACGGTCATTTTAC
* *
40723862 CATACAGGGGTATTACGGTCACTTTAC
1 CATACAGGGCTATTACGGTCATTTTAC
* *
40723889 CCTACAAGGGCT-TTACGGTCTTTTTAC
1 CATAC-AGGGCTATTACGGTCATTTTAC
40723916 C
1 C
40723917 TTTTAGGGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
25 8 0.18
26 5 0.11
27 27 0.60
28 5 0.11
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.34
Consensus pattern (27 bp):
CATACAGGGCTATTACGGTCATTTTAC
Found at i:40724000 original size:27 final size:27
Alignment explanation
Indices: 40723923--40724199 Score: 152
Period size: 27 Copynumber: 10.2 Consensus size: 27
40723913 TACCTTTTAG
* **
40723923 GGGTATTTTAGTCATTTTATCCTAC-AA
1 GGGTATTTTAGTAATTTTAT-AAACTAA
* * * * *
40723950 GGGTGTTTTGGTAAATCTACAAACTAA
1 GGGTATTTTAGTAATTTTATAAACTAA
* *
40723977 GGGTATTTTAGTAATTTTGTAAACCAA
1 GGGTATTTTAGTAATTTTATAAACTAA
* * *
40724004 TGGTATTTCTA-TAATTTTTAAAAAGTCAA
1 GGGTATTT-TAGTAA-TTTTATAAACT-AA
* * *
40724033 GGGTATTTCT-GTAACTTTGTAAA-TCA
1 GGGTATTT-TAGTAATTTTATAAACTAA
* * * *
40724059 GGAGTATTTTGGTAATTTTACAAATTGA
1 GG-GTATTTTAGTAATTTTATAAACTAA
** * * * *
40724087 GGGTATTTCGGTAATTTCACAAGCCAA
1 GGGTATTTTAGTAATTTTATAAACTAA
* *
40724114 GGGTATTTTGGTAATTTTACAAACT-A
1 GGGTATTTTAGTAATTTTATAAACTAA
* * *
40724140 GGGTTATTTTGGTAATTTTACAAACCAA
1 GGG-TATTTTAGTAATTTTATAAACTAA
*
40724168 GGGTATTTTAGTAATTTTGTAAA-TAGA
1 GGGTATTTTAGTAATTTTATAAACTA-A
40724195 GGGTA
1 GGGTA
40724200 AAATAGTAAT
Statistics
Matches: 195, Mismatches: 44, Indels: 22
0.75 0.17 0.08
Matches are distributed among these distances:
26 11 0.06
27 147 0.75
28 23 0.12
29 14 0.07
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.40
Consensus pattern (27 bp):
GGGTATTTTAGTAATTTTATAAACTAA
Found at i:40724120 original size:54 final size:54
Alignment explanation
Indices: 40724062--40724199 Score: 188
Period size: 54 Copynumber: 2.6 Consensus size: 54
40724052 TAAATCAGGA
*
40724062 GTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAGCCAAGG
1 GTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAGG
* * *
40724116 GTATTTTGGTAATTTTACAAACT-AGGGTTATTTTGGTAATTTTACAAACCAAGG
1 GTATTTTGGTAATTTTACAAATTGAGGG-TATTTCGGTAATTTCACAAACCAAGG
* ** *
40724170 GTATTTTAGTAATTTTGTAAATAGAGGGTA
1 GTATTTTGGTAATTTTACAAATTGAGGGTA
40724200 AAATAGTAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
53 4 0.05
54 65 0.89
55 4 0.05
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (54 bp):
GTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAGG
Found at i:40724171 original size:81 final size:80
Alignment explanation
Indices: 40723947--40724184 Score: 223
Period size: 81 Copynumber: 2.9 Consensus size: 80
40723937 TTTTATCCTA
* * * * ** *
40723947 CAAGGGTGTTTTGGTAAATCTACAAACTAAGGGTATTTTAGTAATTTTGTAAACCAATGGTATTT
1 CAAGGGTATTTTGGTAATTTTACAAACT-AGGGTATTTTGGTAATTTTACAAACCAAGGGTATTT
*
40724012 CTA-TAATTTTTAAAAAGT
65 C-AGTAA--TTTAAAAAGC
* ***
40724030 CAAGGGTATTTCT-GTAACTTTGTA-AATC-AGGAGTATTTTGGTAATTTTACAAATTGAGGGTA
1 CAAGGGTATTT-TGGTAA-TTT-TACAAACTAGG-GTATTTTGGTAATTTTACAAACCAAGGGTA
* * *
40724092 TTTCGGTAATTTCACAAGC
62 TTTCAGTAATTTAAAAAGC
40724111 CAAGGGTATTTTGGTAATTTTACAAACTAGGGTTATTTTGGTAATTTTACAAACCAAGGGTATTT
1 CAAGGGTATTTTGGTAATTTTACAAACTAGGG-TATTTTGGTAATTTTACAAACCAAGGGTATTT
*
40724176 TAGTAATTT
65 CAGTAATTT
40724185 TGTAAATAGA
Statistics
Matches: 125, Mismatches: 21, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
79 2 0.02
80 8 0.06
81 61 0.49
82 3 0.02
83 44 0.35
84 5 0.04
85 2 0.02
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (80 bp):
CAAGGGTATTTTGGTAATTTTACAAACTAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTC
AGTAATTTAAAAAGC
Found at i:40724206 original size:27 final size:27
Alignment explanation
Indices: 40724177--40724379 Score: 209
Period size: 27 Copynumber: 7.6 Consensus size: 27
40724167 AGGGTATTTT
* *
40724177 AGTAATTTTGTAAATAGAGGGTAAAAT
1 AGTAATTCTGTAAATAGAGGGTAAAAC
40724204 AGTAATTCTGTAAATCA-AGGGTAAAAC
1 AGTAATTCTGTAAAT-AGAGGGTAAAAC
* *
40724231 AGTAATTCTATAAATCA-AGGGTAAAAT
1 AGTAATTCTGTAAAT-AGAGGGTAAAAC
* *
40724258 AGTAATTCAGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATAGAGGGTAAAAC
* * *
40724285 GGTAATTCTGTAAGTCGAGGGTAAAAC
1 AGTAATTCTGTAAATAGAGGGTAAAAC
*
40724312 -GATAATTATGTAAATCAG-GGGTAAAAC
1 AG-TAATTCTGTAAAT-AGAGGGTAAAAC
* * *
40724339 GGTAATTATGTAAATCG-GGGTAAAAC
1 AGTAATTCTGTAAATAGAGGGTAAAAC
*
40724365 GGTAATTCTGTAAAT
1 AGTAATTCTGTAAAT
40724380 CGGAGGTACT
Statistics
Matches: 155, Mismatches: 16, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
26 25 0.16
27 127 0.82
28 3 0.02
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (27 bp):
AGTAATTCTGTAAATAGAGGGTAAAAC
Found at i:40724209 original size:54 final size:54
Alignment explanation
Indices: 40724062--40724264 Score: 133
Period size: 54 Copynumber: 3.8 Consensus size: 54
40724052 TAAATCAGGA
* * * ** * * *
40724062 GTATTTTGGTAATTTTACAAATTGAGGGT-ATTTCGGTAATTTCACAAGCCAAGG
1 GTATTTTAGTAATTTTATAAATAGAGGGTAAAAT-AGTAATTTTACAAACCAAGG
* * * *** *
40724116 GTATTTTGGTAATTTTACAAACTAG-GGTTATTTTGGTAATTTTACAAACCAAGG
1 GTATTTTAGTAATTTTATAAA-TAGAGGGTAAAATAGTAATTTTACAAACCAAGG
* * ** *
40724170 GTATTTTAGTAATTTTGTAAATAGAGGGTAAAATAGTAATTCTGTAAATCAAGG
1 GTATTTTAGTAATTTTATAAATAGAGGGTAAAATAGTAATTTTACAAACCAAGG
**** *
40724224 GTAAAACAGTAATTCTATAAATCA-AGGGTAAAATAGTAATT
1 GTATTTTAGTAATTTTATAAAT-AGAGGGTAAAATAGTAATT
40724265 CAGTAAATCG
Statistics
Matches: 122, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
53 3 0.02
54 113 0.93
55 6 0.05
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.36
Consensus pattern (54 bp):
GTATTTTAGTAATTTTATAAATAGAGGGTAAAATAGTAATTTTACAAACCAAGG
Found at i:40724236 original size:81 final size:81
Alignment explanation
Indices: 40724151--40724380 Score: 223
Period size: 81 Copynumber: 2.9 Consensus size: 81
40724141 GGTTATTTTG
* *** ** *
40724151 GTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAATAGAGGGTAAAATAGTAATTCTGTA
1 GTAATTCTACAAACCAAGGGTAAAATAGTAATTCAGTAAATAGAGGGTAAAACAGTAATTCTGTA
40724216 AATCAAGGGTAAAACA
66 AATCAAGGGTAAAACA
* * * *
40724232 GTAATTCTATAAATCAAGGGTAAAATAGTAATTCAGTAAATCGAGGGTAAAACGGTAATTCTGTA
1 GTAATTCTACAAACCAAGGGTAAAATAGTAATTCAGTAAATAGAGGGTAAAACAGTAATTCTGTA
* *
40724297 AGTCGAGGGTAAAAC-
66 AATCAAGGGTAAAACA
* ** * * ** * *
40724312 GATAATTATGTAAATCAGGGGTAAAACGGTAATT-ATGTAAATCG-GGGTAAAACGGTAATTCTG
1 G-TAATTCTACAAACCAAGGGTAAAATAGTAATTCA-GTAAATAGAGGGTAAAACAGTAATTCTG
40724375 TAAATC
64 TAAATC
40724381 GGAGGTACTT
Statistics
Matches: 128, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
80 26 0.20
81 102 0.80
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.29
Consensus pattern (81 bp):
GTAATTCTACAAACCAAGGGTAAAATAGTAATTCAGTAAATAGAGGGTAAAACAGTAATTCTGTA
AATCAAGGGTAAAACA
Found at i:40724265 original size:54 final size:54
Alignment explanation
Indices: 40724177--40724380 Score: 234
Period size: 54 Copynumber: 3.8 Consensus size: 54
40724167 AGGGTATTTT
*
40724177 AGTAATTTTGTAAAT-AGAGGGTAAAATAGTAATTCTGTAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCA-AGGGTAAAATAGTAATTCTGTAAATCAAGGGTAAAAC
* * *
40724231 AGTAATTCTATAAATCAAGGGTAAAATAGTAATTCAGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTGTAAATCAAGGGTAAAAC
* * * * * *
40724285 GGTAATTCTGTAAGTCGAGGGTAAAA-CGATAATTATGTAAATCAGGGGTAAAAC
1 AGTAATTCTGTAAATCAAGGGTAAAATAG-TAATTCTGTAAATCAAGGGTAAAAC
* * * **
40724339 GGTAATTATGTAAATC-GGGGTAAAACGGTAATTCTGTAAATC
1 AGTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTGTAAATC
40724381 GGAGGTACTT
Statistics
Matches: 129, Mismatches: 18, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
53 22 0.17
54 106 0.82
55 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (54 bp):
AGTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTGTAAATCAAGGGTAAAAC
Found at i:40724413 original size:27 final size:27
Alignment explanation
Indices: 40724376--40724481 Score: 119
Period size: 27 Copynumber: 4.0 Consensus size: 27
40724366 GTAATTCTGT
*
40724376 AAATCGGAGGTACTTT-GGTAATTTTAC
1 AAATCGAAGGTA-TTTCGGTAATTTTAC
* *
40724403 AAGTCGAAGGTATTTCGGTAAATTTAC
1 AAATCGAAGGTATTTCGGTAATTTTAC
* *
40724430 AAATCGAGGGTATTTCAGT-ATTTTAC
1 AAATCGAAGGTATTTCGGTAATTTTAC
*
40724456 AAA-CTAAGGGTATTTCGGTAATTTTA
1 AAATCGAA-GGTATTTCGGTAATTTTA
40724482 GTAAACTAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
25 2 0.03
26 22 0.33
27 42 0.64
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.37
Consensus pattern (27 bp):
AAATCGAAGGTATTTCGGTAATTTTAC
Found at i:40724465 original size:26 final size:28
Alignment explanation
Indices: 40724411--40724490 Score: 78
Period size: 26 Copynumber: 3.0 Consensus size: 28
40724401 ACAAGTCGAA
* * *
40724411 GGTATTTCGGTAAATTTA-CAAA-TCGAG
1 GGTATTTCAGTAATTTTAGCAAACT-AAG
40724438 GGTATTTCAGT-ATTTTA-CAAACTAAG
1 GGTATTTCAGTAATTTTAGCAAACTAAG
* *
40724464 GGTATTTCGGTAATTTTAGTAAACTAA
1 GGTATTTCAGTAATTTTAGCAAACTAA
40724491 AGTATTCTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
26 21 0.47
27 17 0.38
28 7 0.16
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.38
Consensus pattern (28 bp):
GGTATTTCAGTAATTTTAGCAAACTAAG
Found at i:40724495 original size:27 final size:26
Alignment explanation
Indices: 40724439--40724496 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
40724429 CAAATCGAGG
*
40724439 GTATTTCAGTATTTTACAAACTAAGG
1 GTATTTCAGTATTTTACAAACTAAGA
* *
40724465 GTATTTCGGTAATTTTAGTAAACTAA-A
1 GTATTTCAGT-ATTTTA-CAAACTAAGA
40724492 GTATT
1 GTATT
40724497 CTAAACAGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 9 0.33
27 11 0.41
28 7 0.26
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (26 bp):
GTATTTCAGTATTTTACAAACTAAGA
Found at i:40727316 original size:31 final size:31
Alignment explanation
Indices: 40727275--40727340 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
40727265 CCTTTTCATA
*
40727275 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
40727306 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
40727337 TTTC
1 TTTC
40727341 TATAAACGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:40727642 original size:23 final size:24
Alignment explanation
Indices: 40727546--40727744 Score: 269
Period size: 24 Copynumber: 8.4 Consensus size: 24
40727536 CTGAAGGCCT
* * *
40727546 AGCCTCTTTTAGTAACTAGGGCAAA
1 AGCC-CTTTTAATAACTGGGGCATA
**
40727571 AGCCCTTTTTGTAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
* * *
40727595 AGCCCTTTTGATCACTAGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
40727619 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
40727642 AGCCCTTTTGATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
* *
40727666 AGCCCTTTTGATAACTGAGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
40727690 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
40727713 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
40727736 AGCCCTTTT
1 AGCCCTTTT
40727745 GCACTTCCTC
Statistics
Matches: 158, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
23 64 0.41
24 90 0.57
25 4 0.03
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:40727645 original size:71 final size:70
Alignment explanation
Indices: 40727553--40727745 Score: 298
Period size: 71 Copynumber: 2.7 Consensus size: 70
40727543 CCTAGCCTCT
* * * *
40727553 TTTAGTAACTAGGGCAAAAGCCCTTTTTGTAACTGGGGCATAAGCCCTTTTGATCACT-AGGGCA
1 TTTAATAACTGGGGCATAAGCCC-TTTTGTAACTGGGGCATAAGCCCTTTTGATAACTGA-GGCA
40727617 TAAGCCC
64 TAAGCCC
40727624 TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGAGGCAT
1 TTTAATAACTGGGGCATAAGCCCTTTTG-TAACTGGGGCATAAGCCCTTTTGATAACTGAGGCAT
40727689 AAGCCC
65 AAGCCC
**
40727695 TTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTTG
1 TTTAATAACTGGGGCATAAGCCCTTTTGTAACTGGGGCATAAGCCCTTTTG
40727746 CACTTCCTCC
Statistics
Matches: 114, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
70 28 0.25
71 85 0.75
72 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.29
Consensus pattern (70 bp):
TTTAATAACTGGGGCATAAGCCCTTTTGTAACTGGGGCATAAGCCCTTTTGATAACTGAGGCATA
AGCCC
Found at i:40727816 original size:9 final size:9
Alignment explanation
Indices: 40727802--40727858 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
40727792 ATCTCATGTG
40727802 CATATCATA
1 CATATCATA
*
40727811 CATATCATGTG
1 CATATCA--TA
40727822 CATATCATA
1 CATATCATA
* *
40727831 CATGTCATGTG
1 CATATCA--TA
40727842 CATATCATA
1 CATATCATA
40727851 CATATCAT
1 CATATCAT
40727859 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:40727818 original size:20 final size:20
Alignment explanation
Indices: 40727790--40727860 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
40727780 GCATTTATGA
*
40727790 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
40727810 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
40727830 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
40727850 ACATATCATGT
1 ACATATCATGT
40727861 TTATCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:40727825 original size:11 final size:11
Alignment explanation
Indices: 40727795--40727849 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
40727785 TATGAACATC
40727795 TCATGTGCATA
1 TCATGTGCATA
*
40727806 TCA--TACATA
1 TCATGTGCATA
40727815 TCATGTGCATA
1 TCATGTGCATA
* *
40727826 TCA--TACATG
1 TCATGTGCATA
40727835 TCATGTGCATA
1 TCATGTGCATA
40727846 TCAT
1 TCAT
40727850 ACATATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:40728261 original size:24 final size:23
Alignment explanation
Indices: 40728230--40728419 Score: 238
Period size: 24 Copynumber: 8.1 Consensus size: 23
40728220 CCTAGCCTCT
*
40728230 TTTAGTAACTGGGGCAAAAGCCC
1 TTTAGTAACTGGGGCATAAGCCC
*
40728253 TTTTTGTAACTGGGGCATAAGCCC
1 -TTTAGTAACTGGGGCATAAGCCC
* * *
40728277 TTTTGATCACTAGGGCATAAGCCC
1 TTTAG-TAACTGGGGCATAAGCCC
*
40728301 TTTAATAACTGGGGCATAAGCCC
1 TTTAGTAACTGGGGCATAAGCCC
*
40728324 TTTTGATAACTGGGGCATAAGCCC
1 TTTAG-TAACTGGGGCATAAGCCC
*
40728348 TTTTGATAACTGGGGCATAAGCCC
1 TTTAG-TAACTGGGGCATAAGCCC
* *
40728372 TTCAATAACTGGGGCATAAGCCC
1 TTTAGTAACTGGGGCATAAGCCC
*
40728395 TTTAATAACT-GGGCATAAGCCC
1 TTTAGTAACTGGGGCATAAGCCC
40728417 TTT
1 TTT
40728420 TGCACTTCCT
Statistics
Matches: 150, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.10
23 51 0.34
24 84 0.56
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (23 bp):
TTTAGTAACTGGGGCATAAGCCC
Found at i:40728322 original size:71 final size:70
Alignment explanation
Indices: 40728230--40728421 Score: 296
Period size: 71 Copynumber: 2.7 Consensus size: 70
40728220 CCTAGCCTCT
* * *
40728230 TTTAGTAACTGGGGCAAAAGCCCTTTTTGTAACTGGGGCATAAGCCCTTTTGATCACTAGGGCAT
1 TTTAATAACTGGGGCATAAGCCC-TTTTGTAACTGGGGCATAAGCCCTTTTGATAACTAGGGCAT
40728295 AAGCCC
65 AAGCCC
*
40728301 TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCAT
1 TTTAATAACTGGGGCATAAGCCCTTTTG-TAACTGGGGCATAAGCCCTTTTGATAACTAGGGCAT
40728366 AAGCCC
65 AAGCCC
* **
40728372 TTCAATAACTGGGGCATAAGCCCTTTAATAACT-GGGCATAAGCCCTTTTG
1 TTTAATAACTGGGGCATAAGCCCTTTTGTAACTGGGGCATAAGCCCTTTTG
40728422 CACTTCCTCC
Statistics
Matches: 113, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
69 17 0.15
70 10 0.09
71 86 0.76
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (70 bp):
TTTAATAACTGGGGCATAAGCCCTTTTGTAACTGGGGCATAAGCCCTTTTGATAACTAGGGCATA
AGCCC
Found at i:40728324 original size:47 final size:48
Alignment explanation
Indices: 40728209--40728421 Score: 276
Period size: 47 Copynumber: 4.5 Consensus size: 48
40728199 GCTTTATCAT
* * *
40728209 ATAACTGGAGGCCT-AGCCTCTTTT-AGTAACTGGGGCAAAAGCCCTTTTT
1 ATAACTGG-GGCATAAGCC-CTTTTGA-TAACTGGGGCATAAGCCCTTTTA
* * *
40728258 GTAACTGGGGCATAAGCCCTTTTGATCACTAGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTA
*
40728305 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTA
**
40728353 ATAACTGGGGCATAAGCCC-TTCAATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTA
40728399 ATAACT-GGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
40728422 CACTTCCTCC
Statistics
Matches: 145, Mismatches: 15, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
45 12 0.08
46 11 0.08
47 64 0.44
48 46 0.32
49 12 0.08
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTA
Found at i:40728494 original size:20 final size:20
Alignment explanation
Indices: 40728466--40728536 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
40728456 GCATTTATGA
* *
40728466 ACATCTCATGTGTATATCAT
1 ACATATCATGTGCATATCAT
40728486 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
40728506 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
40728526 ACATATCATGT
1 ACATATCATGT
40728537 TTATCAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:40728612 original size:25 final size:24
Alignment explanation
Indices: 40728573--40728620 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
40728563 ATATATAAAC
* *
40728573 CCTAGGGGTATAATGGTCACTTTTA
1 CCTAGGGGCAAAATGGTCA-TTTTA
40728598 CCTAGGGGCAAAATGGTCATTTT
1 CCTAGGGGCAAAATGGTCATTTT
40728621 CATGTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (24 bp):
CCTAGGGGCAAAATGGTCATTTTA
Found at i:40728996 original size:23 final size:24
Alignment explanation
Indices: 40728886--40729098 Score: 272
Period size: 24 Copynumber: 9.0 Consensus size: 24
40728876 GCTTTATCAT
*
40728886 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* * * *
40728911 GTAACTAGGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTA
* *
40728935 GTAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
* *
40728959 ATCACTAGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
40728982 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
40729006 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
40729030 ATAACTGGGGCATAAGCAC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
40729053 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
40729076 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
40729099 GCACTTCCTC
Statistics
Matches: 167, Mismatches: 18, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
23 64 0.38
24 93 0.56
25 10 0.06
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:40728999 original size:71 final size:70
Alignment explanation
Indices: 40728907--40729099 Score: 296
Period size: 71 Copynumber: 2.7 Consensus size: 70
40728897 CCTAGCCTCT
* * * *
40728907 TTTAGTAACTAGGGCAAAAGCCCTTTTTGTAACTGGGGCATAAGCCCTTTTGATCACTAGGGCAT
1 TTTAATAACTGGGGCATAAGCCC-TTTTGTAACTGGGGCATAAGCCCTTTTGATAACTAGGGCAT
*
40728972 AAGCCC
65 AAGCAC
*
40728978 TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCAT
1 TTTAATAACTGGGGCATAAGCCCTTTTG-TAACTGGGGCATAAGCCCTTTTGATAACTAGGGCAT
40729043 AAGCAC
65 AAGCAC
**
40729049 TTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTTG
1 TTTAATAACTGGGGCATAAGCCCTTTTGTAACTGGGGCATAAGCCCTTTTG
40729100 CACTTCCTCC
Statistics
Matches: 113, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
70 28 0.25
71 85 0.75
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (70 bp):
TTTAATAACTGGGGCATAAGCCCTTTTGTAACTGGGGCATAAGCCCTTTTGATAACTAGGGCATA
AGCAC
Found at i:40729170 original size:9 final size:9
Alignment explanation
Indices: 40729156--40729212 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
40729146 ATCTCATGTG
40729156 CATATCATA
1 CATATCATA
*
40729165 CATATCATGTG
1 CATATCA--TA
40729176 CATATCATA
1 CATATCATA
* *
40729185 CATGTCATGTG
1 CATATCA--TA
40729196 CATATCATA
1 CATATCATA
40729205 CATATCAT
1 CATATCAT
40729213 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:40729172 original size:20 final size:20
Alignment explanation
Indices: 40729144--40729214 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
40729134 GCATTTATGA
*
40729144 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
40729164 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
40729184 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
40729204 ACATATCATGT
1 ACATATCATGT
40729215 TTATCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:40729179 original size:11 final size:11
Alignment explanation
Indices: 40729149--40729203 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
40729139 TATGAACATC
40729149 TCATGTGCATA
1 TCATGTGCATA
*
40729160 TCA--TACATA
1 TCATGTGCATA
40729169 TCATGTGCATA
1 TCATGTGCATA
* *
40729180 TCA--TACATG
1 TCATGTGCATA
40729189 TCATGTGCATA
1 TCATGTGCATA
40729200 TCAT
1 TCAT
40729204 ACATATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:40729222 original size:678 final size:679
Alignment explanation
Indices: 40727361--40729356 Score: 3811
Period size: 677 Copynumber: 2.9 Consensus size: 679
40727351 ATGGCCCATA
*
40727361 GGCCCATTTCAATATCACATATAATGTCAATGAAAGAATGCAAACCCATTTGGGGAGACTACTCA
1 GGCCCATTTCAATATCACATATAATGTCAATGAAATAATGCAAACCCATTTGGGGAGACTACTCA
40727426 ACCCACCATCCGCTACTCTCCACCCGTACCAACCAACACACCATGTGGGGATTAACTCAACCCAC
66 ACCCACCATCCGCTACTCTCCACCCGTACCAACCAACACACCATGTGGGGATTAACTCAACCCAC
*
40727491 CCCGCCATAACTCTCCACTGGCAGCATAGCTGCTTTATCATATAACTGAAGGCCTAGCCTCTTTT
131 CCCGCCATAACTCTCCACTGGCAGCATAGCTGCTTTATCATATAACTGGAGGCCTAGCCTCTTTT
40727556 AGTAACTAGGGCAAAAGCCCTTTTTGTAACTGGGGCATAAGCCCTTTTGATCACTAGGGCATAAG
196 AGTAACTAGGGCAAAAGCCCTTTTTGTAACTGGGGCATAAGCCCTTTTGATCACTAGGGCATAAG
*
40727621 CCCTTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGAGG
261 CCCTTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGG
40727686 CATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTTGCACTT
326 CATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTTGCACTT
40727751 CCTCCATCCATATAAAAACCCAACCCAATGCATTTATGAACATCTCATGTGCATATCATACATAT
391 CCTCCATCCATATAAAAACCCAACCCAATGCATTTATGAACATCTCATGTGCATATCATACATAT
40727816 CATGTGCATATCATACATGTCATGTGCATATCATACATATCATGTTTATCAAAATCCCATGCATT
456 CATGTGCATATCATACATGTCATGTGCATATCATACATATCATGTTTATCAAAATCCCATGCATT
40727881 AAGTTCATATATAAACCCTAGGGGTATAATGGTCACTTTTACCTAGGGG-AAAACGGTCATTTTC
521 AAGTTCATATATAAACCCTAGGGGTATAATGGTCACTTTTACCTAGGGGCAAAACGGTCATTTTC
40727945 ATGTTATAAGGGTAATCTTGTAATTCTACCAAAAATTAGGG-TTCCATGTTCATTAACGATTACT
586 ATGTTATAAGGGTAATCTTGTAATTCTACCAAAAATTAGGGTTTCCATGTTCATTAACGATTACT
40728009 AACAATTCATGGGTGCAAATAGTGATTCT
651 AACAATTCATGGGTGCAAATAGTGATTCT
40728038 GGCCCATTTCAATATCACATATAATGTCAATGAAATAATGCAAACCCATTTGGGGAGACTACTCA
1 GGCCCATTTCAATATCACATATAATGTCAATGAAATAATGCAAACCCATTTGGGGAGACTACTCA
40728103 ACCCACCATCCGCTACTCTCCACCCGTACCAACCAACACACCATGTGGGGATTAACTCAACCCAC
66 ACCCACCATCCGCTACTCTCCACCCGTACCAACCAACACACCATGTGGGGATTAACTCAACCCAC
40728168 CCCGCCATAACTCTCCACTGGCAGCATAGCTGCTTTATCATATAACTGGAGGCCTAGCCTCTTTT
131 CCCGCCATAACTCTCCACTGGCAGCATAGCTGCTTTATCATATAACTGGAGGCCTAGCCTCTTTT
*
40728233 AGTAACTGGGGCAAAAGCCCTTTTTGTAACTGGGGCATAAGCCCTTTTGATCACTAGGGCATAAG
196 AGTAACTAGGGCAAAAGCCCTTTTTGTAACTGGGGCATAAGCCCTTTTGATCACTAGGGCATAAG
40728298 CCCTTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGG
261 CCCTTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGG
*
40728363 CATAAGCCCTTCAATAACTGGGGCATAAGCCCTTTAATAACT-GGGCATAAGCCCTTTTGCACTT
326 CATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTTGCACTT
*
40728427 CCTCCATCCATATAAAAACCCAACCCAATGCATTTATGAACATCTCATGTGTATATCATACATAT
391 CCTCCATCCATATAAAAACCCAACCCAATGCATTTATGAACATCTCATGTGCATATCATACATAT
40728492 CATGTGCATATCATACATGTCATGTGCATATCATACATATCATGTTTATCAAAATCCCATGCATT
456 CATGTGCATATCATACATGTCATGTGCATATCATACATATCATGTTTATCAAAATCCCATGCATT
*
40728557 AAGTTCATATATAAACCCTAGGGGTATAATGGTCACTTTTACCTAGGGGCAAAATGGTCATTTTC
521 AAGTTCATATATAAACCCTAGGGGTATAATGGTCACTTTTACCTAGGGGCAAAACGGTCATTTTC
40728622 ATGTTATAAGGGTAATCTTGTAATTCTACCAAAAATTAGGGTTTCCATGTTCATTAACGATTACT
586 ATGTTATAAGGGTAATCTTGTAATTCTACCAAAAATTAGGGTTTCCATGTTCATTAACGATTACT
40728687 AACAATTCATGGGTGCAAATAGTGATTCT
651 AACAATTCATGGGTGCAAATAGTGATTCT
40728716 GGCCCATTTCAATATCACATATAATGTCAATGAAATAATGCAAACCCATTTGGGGAGACTACTCA
1 GGCCCATTTCAATATCACATATAATGTCAATGAAATAATGCAAACCCATTTGGGGAGACTACTCA
40728781 ACCCACCATCCGCTACTCTCCACCCGTACCAACCAACACACCATGT-GGGATTAACTCAACCCAC
66 ACCCACCATCCGCTACTCTCCACCCGTACCAACCAACACACCATGTGGGGATTAACTCAACCCAC
40728845 CCCGCCATAACTCTCCACTGGCAGCATAGCTGCTTTATCATATAACTGGAGGCCTAGCCTCTTTT
131 CCCGCCATAACTCTCCACTGGCAGCATAGCTGCTTTATCATATAACTGGAGGCCTAGCCTCTTTT
40728910 AGTAACTAGGGCAAAAGCCCTTTTTGTAACTGGGGCATAAGCCCTTTTGATCACTAGGGCATAAG
196 AGTAACTAGGGCAAAAGCCCTTTTTGTAACTGGGGCATAAGCCCTTTTGATCACTAGGGCATAAG
40728975 CCCTTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGG
261 CCCTTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGG
*
40729040 CATAAGCACTTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTTGCACTT
326 CATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTTGCACTT
40729105 CCTCCATCCATATAAAAACCCAACCCAATGCATTTATGAACATCTCATGTGCATATCATACATAT
391 CCTCCATCCATATAAAAACCCAACCCAATGCATTTATGAACATCTCATGTGCATATCATACATAT
40729170 CATGTGCATATCATACATGTCATGTGCATATCATACATATCATGTTTATCAAAATCCCATGCATT
456 CATGTGCATATCATACATGTCATGTGCATATCATACATATCATGTTTATCAAAATCCCATGCATT
*
40729235 AAGTTCATATATAAACCCTAGGGGTATAATGGTCACTTTTACCTAGGGGCAAAACGGTCATTTCC
521 AAGTTCATATATAAACCCTAGGGGTATAATGGTCACTTTTACCTAGGGGCAAAACGGTCATTTTC
* * ** *
40729300 ATATTATAAGGGTAATATCATAATTTTACCAAAAATTAGGGATTTTTCCATGTTCAT
586 ATGTTATAAGGGTAATCTTGTAATTCTACCAAAAATTAGGG---TTTCCATGTTCAT
40729357 CATCAGTTAC
Statistics
Matches: 1295, Mismatches: 18, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
676 200 0.15
677 669 0.52
678 413 0.32
681 13 0.01
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (679 bp):
GGCCCATTTCAATATCACATATAATGTCAATGAAATAATGCAAACCCATTTGGGGAGACTACTCA
ACCCACCATCCGCTACTCTCCACCCGTACCAACCAACACACCATGTGGGGATTAACTCAACCCAC
CCCGCCATAACTCTCCACTGGCAGCATAGCTGCTTTATCATATAACTGGAGGCCTAGCCTCTTTT
AGTAACTAGGGCAAAAGCCCTTTTTGTAACTGGGGCATAAGCCCTTTTGATCACTAGGGCATAAG
CCCTTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGG
CATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTTGCACTT
CCTCCATCCATATAAAAACCCAACCCAATGCATTTATGAACATCTCATGTGCATATCATACATAT
CATGTGCATATCATACATGTCATGTGCATATCATACATATCATGTTTATCAAAATCCCATGCATT
AAGTTCATATATAAACCCTAGGGGTATAATGGTCACTTTTACCTAGGGGCAAAACGGTCATTTTC
ATGTTATAAGGGTAATCTTGTAATTCTACCAAAAATTAGGGTTTCCATGTTCATTAACGATTACT
AACAATTCATGGGTGCAAATAGTGATTCT
Found at i:40730521 original size:27 final size:27
Alignment explanation
Indices: 40730459--40730523 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
40730449 GGGCATATTC
*
40730459 GTCATTTTACCATACAGGGGTATTATG
1 GTCATTTTACCATACAGGGGTATTACG
* *
40730486 GTCACTTTACCCTACAGGGGCT-TTACG
1 GTCATTTTACCATACAGGGG-TATTACG
*
40730513 GTCTTTTTACC
1 GTCATTTTACC
40730524 TTTTAGGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (27 bp):
GTCATTTTACCATACAGGGGTATTACG
Found at i:40730607 original size:27 final size:27
Alignment explanation
Indices: 40730554--40730792 Score: 187
Period size: 27 Copynumber: 8.8 Consensus size: 27
40730544 TTTCATCCTA
* * *
40730554 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* **
40730581 CAAGGGTATTTTAGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* * * * *
40730608 CAATGGTATCTCT-ATAATTTTTAGAAAGT
1 CAAGGGTAT-TTTGGTAA-TTTTACAAA-C
* * ** *
40730637 TAAGGGTATTTCT-GTAACTTTGTAAAT
1 CAAGGGTATTT-TGGTAATTTTACAAAC
*
40730664 C-AGGAGTATTTTGGTAATTTTACAAAT
1 CAAGG-GTATTTTGGTAATTTTACAAAC
** * * *
40730691 TGAGGGTATTTCGGTAATTTCACAAGC
1 CAAGGGTATTTTGGTAATTTTACAAAC
40730718 CAAGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* *
40730745 TAGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
*
40730772 CAAGGGTATTTTAGTAATTTT
1 CAAGGGTATTTTGGTAATTTT
40730793 GTAAATCGAG
Statistics
Matches: 167, Mismatches: 38, Indels: 14
0.76 0.17 0.06
Matches are distributed among these distances:
26 4 0.02
27 133 0.80
28 19 0.11
29 11 0.07
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAC
Found at i:40730727 original size:54 final size:54
Alignment explanation
Indices: 40730669--40730806 Score: 188
Period size: 54 Copynumber: 2.6 Consensus size: 54
40730659 TAAATCAGGA
*
40730669 GTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAGCCAAGG
1 GTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAGG
* * *
40730723 GTATTTTGGTAATTTTACAAACT-AGGGGTATTTTGGTAATTTTACAAACCAAGG
1 GTATTTTGGTAATTTTACAAATTGA-GGGTATTTCGGTAATTTCACAAACCAAGG
* ** *
40730777 GTATTTTAGTAATTTTGTAAATCGAGGGTA
1 GTATTTTGGTAATTTTACAAATTGAGGGTA
40730807 AAACAGTAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
53 1 0.01
54 71 0.97
55 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (54 bp):
GTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAGG
Found at i:40730814 original size:27 final size:27
Alignment explanation
Indices: 40730784--40730993 Score: 226
Period size: 27 Copynumber: 7.7 Consensus size: 27
40730774 AGGGTATTTT
*
40730784 AGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
40730811 AGTAATTCTGTAATTCAAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * *
40730838 AGTAATTCTATAAATCAAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
40730865 AGTAATTCAGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * *
40730892 GGTTATTCTGTAAGTCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
40730919 -GATAATTATGTAAAT-TAGGGGTAAAAC
1 AG-TAATTCTGTAAATCGA-GGGTAAAAC
* * *
40730946 GGTAATTATGTAAATCGGGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
40730973 GGTAATTCTATAAATCAGAGG
1 AGTAATTCTGTAAATC-GAGG
40730994 TACTTTGGTA
Statistics
Matches: 155, Mismatches: 23, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
26 2 0.01
27 149 0.96
28 4 0.03
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (27 bp):
AGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:40730833 original size:81 final size:81
Alignment explanation
Indices: 40730758--40730981 Score: 218
Period size: 81 Copynumber: 2.8 Consensus size: 81
40730748 GGGTATTTTG
* *** **
40730758 GTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTA
1 GTAATTCTACAAACCAAGGGTAAAATAGTAATTCAGTAAATCGAGGGTAAAACAGTAATTCTGTA
*
40730823 ATTCAAGGGTAAAACA
66 AGTCAAGGGTAAAACA
* * * *
40730839 GTAATTCTATAAATCAAGGGTAAAATAGTAATTCAGTAAATCGAGGGTAAAACGGTTATTCTGTA
1 GTAATTCTACAAACCAAGGGTAAAATAGTAATTCAGTAAATCGAGGGTAAAACAGTAATTCTGTA
*
40730904 AGTCGAGGGTAAAAC-
66 AGTCAAGGGTAAAACA
* ** ** * ** * *
40730919 GATAATTATGTAAATTAGGGGTAAAACGGTAATT-ATGTAAATCGGGGGTAAAACGGTAATTCT
1 G-TAATTCTACAAACCAAGGGTAAAATAGTAATTCA-GTAAATCGAGGGTAAAACAGTAATTCT
40730982 ATAAATCAGA
Statistics
Matches: 121, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
80 2 0.02
81 119 0.98
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (81 bp):
GTAATTCTACAAACCAAGGGTAAAATAGTAATTCAGTAAATCGAGGGTAAAACAGTAATTCTGTA
AGTCAAGGGTAAAACA
Found at i:40731021 original size:27 final size:27
Alignment explanation
Indices: 40730972--40731090 Score: 118
Period size: 27 Copynumber: 4.4 Consensus size: 27
40730962 GGGGGTAAAA
* *
40730972 CGGTAATTCTATAAATC-AGAGGTACTTT
1 CGGTAATTTTACAAATCGA-AGGTA-TTT
*
40731000 -GGTAATTTTACAAGTCGAAGGTATTT
1 CGGTAATTTTACAAATCGAAGGTATTT
* *
40731026 CGGTAAATTTACAAATCGAGGGTATTT
1 CGGTAATTTTACAAATCGAAGGTATTT
* * *
40731053 CAGTATTTTTACAAA-CTAAGGGTATTT
1 CGGTAATTTTACAAATCGAA-GGTATTT
40731080 CGGTAATTTTA
1 CGGTAATTTTA
40731091 GTAAACTAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
26 5 0.07
27 69 0.92
28 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (27 bp):
CGGTAATTTTACAAATCGAAGGTATTT
Found at i:40731104 original size:27 final size:27
Alignment explanation
Indices: 40731001--40731105 Score: 72
Period size: 27 Copynumber: 3.9 Consensus size: 27
40730991 AGGTACTTTG
* * *
40731001 GTAATTTTACAAGTCGAAG-GTATTTCG
1 GTAATTTTACAA-ACTAAGAGTATTTCA
* * *
40731028 GTAAATTTACAAA-TCGAGGGTATTTCA
1 GTAATTTTACAAACT-AAGAGTATTTCA
* * *
40731055 GTATTTTTACAAACTAAGGGTATTTCG
1 GTAATTTTACAAACTAAGAGTATTTCA
*
40731082 GTAATTTTAGTAAACTAA-AGTATT
1 GTAATTTTA-CAAACTAAGAGTATT
40731106 CTAAACAGGG
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
26 2 0.03
27 52 0.84
28 8 0.13
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (27 bp):
GTAATTTTACAAACTAAGAGTATTTCA
Found at i:40737082 original size:12 final size:12
Alignment explanation
Indices: 40737065--40737098 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
40737055 CTACCTAGTT
*
40737065 TTGAGCATGGCC
1 TTGAGCACGGCC
40737077 TTGAGCACGGCC
1 TTGAGCACGGCC
40737089 TTGAGCACGG
1 TTGAGCACGG
40737099 GCATGTTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.26, G:0.35, T:0.21
Consensus pattern (12 bp):
TTGAGCACGGCC
Found at i:40740363 original size:40 final size:41
Alignment explanation
Indices: 40740319--40740408 Score: 96
Period size: 40 Copynumber: 2.3 Consensus size: 41
40740309 TACAATGATG
* *
40740319 TTTGACGATA-AATCAGCTATTTGTGGCACTTAGTCTGCGA
1 TTTGACGATAGAATCAGCTATATATGGCACTTAGTCTGCGA
** * * *
40740359 TTTGAC-ATAGCTTCGGCTATATATGGCACTTAGTGTGTGA
1 TTTGACGATAGAATCAGCTATATATGGCACTTAGTCTGCGA
40740399 TTTGA-GATAG
1 TTTGACGATAG
40740409 CTTCGGCTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
39 3 0.07
40 38 0.93
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.37
Consensus pattern (41 bp):
TTTGACGATAGAATCAGCTATATATGGCACTTAGTCTGCGA
Found at i:40740409 original size:40 final size:40
Alignment explanation
Indices: 40740342--40740436 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 40
40740332 CAGCTATTTG
*
40740342 TGGCACTTAGTCTGCGATTTGACATAGCTTCGGCTATATA
1 TGGCACTTAGTGTGCGATTTGACATAGCTTCGGCTATATA
* * *
40740382 TGGCACTTAGTGTGTGATTTGAGATAGCTTCGGCTATGTA
1 TGGCACTTAGTGTGCGATTTGACATAGCTTCGGCTATATA
* *
40740422 CGACACTTAGTGTGC
1 TGGCACTTAGTGTGC
40740437 AAGATATCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (40 bp):
TGGCACTTAGTGTGCGATTTGACATAGCTTCGGCTATATA
Found at i:40748547 original size:39 final size:39
Alignment explanation
Indices: 40748503--40748626 Score: 176
Period size: 39 Copynumber: 3.2 Consensus size: 39
40748493 TATGAGATTG
* *
40748503 AAAATATTCAGACATGAGGTCCGCAGGCTATATGCTGGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
* *
40748542 AAAATATCCGGACATGAGATCCGCAGGCTATATGCTAGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
* * **
40748581 AATATATCCGGACTTGAGGTCCGCAGGCTACGTGCTGGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
40748620 AAAATAT
1 AAAATAT
40748627 TCGGGTTAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 74 1.00
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (39 bp):
AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
Found at i:40753868 original size:20 final size:21
Alignment explanation
Indices: 40753845--40753887 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
40753835 ATAAGCATGT
*
40753845 ATTTTG-ATGTTTGATGATAG
1 ATTTTGAATGCTTGATGATAG
*
40753865 ATTTTGAATGCTTGTTGATAG
1 ATTTTGAATGCTTGATGATAG
40753886 AT
1 AT
40753888 ATACAAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.26, C:0.02, G:0.23, T:0.49
Consensus pattern (21 bp):
ATTTTGAATGCTTGATGATAG
Found at i:40759091 original size:42 final size:42
Alignment explanation
Indices: 40759044--40759207 Score: 181
Period size: 42 Copynumber: 3.9 Consensus size: 42
40759034 TTAGGGTTAC
*
40759044 TGAGACTATGTGTAAGACCATATCTAGGATATGGCATCGATA
1 TGAGACTATGTGTAAGACCATATCTGGGATATGGCATCGATA
40759086 TGAGACT-TCGTGTAAGACCATATCTGGGATATGGCATCGATGA
1 TGAGACTAT-GTGTAAGACCATATCTGGGATATGGCATCGAT-A
* * * * * *
40759129 -GAGATTTTGTGTAAGATCGTAGCTGGGCTATTGGCATCGATA
1 TGAGACTATGTGTAAGACCATATCTGGGATA-TGGCATCGATA
* **
40759171 CGAGA-TGACATGTAAGACCATATCTGGGATATGGCAT
1 TGAGACT-ATGTGTAAGACCATATCTGGGATATGGCAT
40759208 TGGTATGGTA
Statistics
Matches: 103, Mismatches: 13, Indels: 12
0.80 0.10 0.09
Matches are distributed among these distances:
41 1 0.01
42 69 0.67
43 33 0.32
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (42 bp):
TGAGACTATGTGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:40777822 original size:40 final size:39
Alignment explanation
Indices: 40777741--40777958 Score: 235
Period size: 40 Copynumber: 5.5 Consensus size: 39
40777731 AAGCCAAGTA
* * * *
40777741 CCTTCGGGATTTA-ACCGGATATAGCT-ATTCGCTCAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAATG
*
40777779 CCTTCGGGACATAGCCCGGATATAGTAACTCGCATCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCA-CAATG
* *
40777819 CCTTCGGGACTTAGCCCGGATATAATAACTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCAC-AATG
* * *
40777859 CCTTCGGGACTTAGCCCAGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCAC-AATG
* * *
40777899 CCTGCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACT--CGCACAATG
40777940 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
40777959 TTATCATCCA
Statistics
Matches: 155, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
38 12 0.08
39 16 0.10
40 101 0.65
41 22 0.14
42 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAATG
Found at i:40785022 original size:40 final size:39
Alignment explanation
Indices: 40784874--40785024 Score: 243
Period size: 38 Copynumber: 3.9 Consensus size: 39
40784864 GAATGTGCGA
*
40784874 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGC-AATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
40784912 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAG-T
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
*
40784950 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
* *
40784989 GTGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCG
1 GTGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCG
40785025 GGTTACCATA
Statistics
Matches: 105, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
38 71 0.68
39 17 0.16
40 17 0.16
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.24
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
Found at i:40785040 original size:40 final size:39
Alignment explanation
Indices: 40784875--40785055 Score: 240
Period size: 38 Copynumber: 4.6 Consensus size: 39
40784865 AATGTGCGAG
* *
40784875 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGC-AATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
40784913 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAG-TA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
40784951 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
40784990 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
40785030 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
40785056 GTTTGAACGA
Statistics
Matches: 128, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
38 70 0.55
39 17 0.13
40 41 0.32
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:40785076 original size:80 final size:77
Alignment explanation
Indices: 40784881--40785079 Score: 204
Period size: 76 Copynumber: 2.6 Consensus size: 77
40784871 CGAGTGATAT
** * *
40784881 CCGGGCTAAGCCCGAAGGCAATTGTGC-AATTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTG
1 CCGGGCTAAGCCCGAAGGCAATTGAACGAGTAGTGATATCCGGGCTAAGCCCGAAGGCAATTGTG
** *
40784945 CGAGTATGATAT
66 CGAGTACCATAA
** * * *
40784957 CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCAATTGAACGAGTAGTGATATCCGGGCTAAG-CCCGAAGGCAATTGT
*
40785022 GCGGGTTACCATAA
65 GCGAG-TACCATAA
* **
40785036 CCGGGCTATGTCCCGAAGGCGTTTGAACGAGTAGCT-ATATCCGG
1 CCGGGCTAAG-CCCGAAGGCAATTGAACGAGTAG-TGATATCCGG
40785080 ATAAACTCCG
Statistics
Matches: 105, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
76 27 0.26
77 19 0.18
78 18 0.17
79 14 0.13
80 26 0.25
81 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (77 bp):
CCGGGCTAAGCCCGAAGGCAATTGAACGAGTAGTGATATCCGGGCTAAGCCCGAAGGCAATTGTG
CGAGTACCATAA
Found at i:40791543 original size:25 final size:25
Alignment explanation
Indices: 40791514--40791561 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
40791504 TTATAATATG
* * *
40791514 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
40791539 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
40791562 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:40791630 original size:20 final size:20
Alignment explanation
Indices: 40791605--40791663 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
40791595 TAAATATGGT
40791605 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
40791625 ATGTATGATACGCACATGAT
1 ATGTATGATATGCACATGAA
40791645 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
40791664 GGTAATCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:40791793 original size:24 final size:24
Alignment explanation
Indices: 40791714--40791831 Score: 154
Period size: 23 Copynumber: 5.0 Consensus size: 24
40791704 GAGGAAGTGA
40791714 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
*
40791737 CAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
40791760 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
40791784 GAAAGGGCTT-TGGCCCCAGTTATT
1 AAAAGGGCTTAT-GCCCCAGTTATT
*
40791808 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
40791832 ATGATAAAGC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
23 44 0.52
24 30 0.35
25 11 0.13
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:40792058 original size:31 final size:31
Alignment explanation
Indices: 40792023--40792086 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
40792013 CGTTTACAGT
40792023 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
40792054 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
40792085 AA
1 AA
40792087 TATGAAAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:40797320 original size:93 final size:93
Alignment explanation
Indices: 40797161--40797332 Score: 267
Period size: 93 Copynumber: 1.8 Consensus size: 93
40797151 CGCCCATAAG
*** *
40797161 CGAACTCGAACTCAACTCAACGAGCTTGGGTGTTCGCATCCATGAGTGAACTCGGACTCAACTCA
1 CGAACTCGAACTCAACTCAACGAGCTTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
40797226 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
40797254 CGAACTCCG-ACTCAACTCAACGAG-TTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACT
1 CGAACT-CGAACTCAACTCAACGAGCTT-GGACATTCGCATCCATAAGTGAACTCGGACTCAACT
40797317 CAACGAGTTCGGATGC
64 CAACGAGTTCGGATGC
40797333 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
92 2 0.03
93 68 0.94
94 2 0.03
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (93 bp):
CGAACTCGAACTCAACTCAACGAGCTTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:40797329 original size:46 final size:46
Alignment explanation
Indices: 40797154--40797329 Score: 171
Period size: 46 Copynumber: 3.8 Consensus size: 46
40797144 TGTAACCCGC
* *** *
40797154 CCATAAGCGAACTCGAACTCAACTCAACGAGCTT-GGGTGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAG-TTCGGACATTTGCAT
* * * *
40797200 CCATGAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
* *
40797250 -C-TCA-CGAACTCCGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
*
40797293 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
40797330 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 17, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 4 0.04
46 58 0.55
47 28 0.27
48 2 0.02
49 1 0.01
50 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:40797348 original size:46 final size:46
Alignment explanation
Indices: 40797162--40797348 Score: 124
Period size: 46 Copynumber: 4.0 Consensus size: 46
40797152 GCCCATAAGC
* * * *
40797162 GAACTCGAACTCAACTCAACGAGCTT-GGGTGTTC--GCATCCATGAGT
1 GAACTCGGACTCAACTCAACGAG-TTCGGATGCTCAACCATCC--GAGT
*
40797208 GAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATCTC-A-C
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATC-CGAGT
* * * *
40797255 GAACTCCGACTCAACTCAACGAGTTCGGACAT-TTGCATCCAT--AAGT
1 GAACTCGGACTCAACTCAACGAGTTCGG--ATGCT-CAACCATCCGAGT
40797301 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCGAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCGAGT
40797347 GA
1 GA
40797349 CATGTCACTT
Statistics
Matches: 111, Mismatches: 12, Indels: 36
0.70 0.08 0.23
Matches are distributed among these distances:
44 8 0.07
45 5 0.05
46 58 0.52
47 30 0.27
48 1 0.01
49 3 0.03
50 5 0.05
51 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCGAGT
Found at i:40804306 original size:59 final size:57
Alignment explanation
Indices: 40804222--40804352 Score: 210
Period size: 59 Copynumber: 2.3 Consensus size: 57
40804212 AAAATTGTAC
*
40804222 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGTCTGATTATATAGCACTAAGTGTGCGAGCTGAAAATATAT
*
40804279 AGCACTAAGTGTGCGAG-CTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATGT
1 AGCACTAAGTGTGCGAGTCTG---ATTATATAGCACTAAGTGTGCGAGCTGAAAATATAT
40804338 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
40804353 GATTCACTAT
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
56 2 0.03
57 17 0.25
59 50 0.72
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.27
Consensus pattern (57 bp):
AGCACTAAGTGTGCGAGTCTGATTATATAGCACTAAGTGTGCGAGCTGAAAATATAT
Found at i:40804310 original size:30 final size:30
Alignment explanation
Indices: 40804192--40804352 Score: 206
Period size: 29 Copynumber: 5.5 Consensus size: 30
40804182 GACAAGATTG
* * * * *
40804192 GCACTAAGTGTGCGGGTTTTAAAATTGTACA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
*
40804223 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
40804251 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
40804280 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
40804310 GCACTAAGTGTGCGAGCTGAAAA-TATGTA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
40804339 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
40804353 GATTCACTAT
Statistics
Matches: 120, Mismatches: 6, Indels: 10
0.88 0.04 0.07
Matches are distributed among these distances:
27 2 0.02
28 22 0.18
29 48 0.40
30 30 0.25
31 18 0.15
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:40812200 original size:59 final size:57
Alignment explanation
Indices: 40812116--40812246 Score: 210
Period size: 59 Copynumber: 2.3 Consensus size: 57
40812106 AAAATTGTAC
*
40812116 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGTCTGATTATATAGCACTAAGTGTGCGAGCTGAAAATATAT
*
40812173 AGCACTAAGTGTGCGAG-CTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATGT
1 AGCACTAAGTGTGCGAGTCTG---ATTATATAGCACTAAGTGTGCGAGCTGAAAATATAT
40812232 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
40812247 GATTCACTAT
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
56 2 0.03
57 17 0.25
59 50 0.72
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.27
Consensus pattern (57 bp):
AGCACTAAGTGTGCGAGTCTGATTATATAGCACTAAGTGTGCGAGCTGAAAATATAT
Found at i:40812204 original size:30 final size:30
Alignment explanation
Indices: 40812086--40812246 Score: 206
Period size: 29 Copynumber: 5.5 Consensus size: 30
40812076 GACAAGATTG
* * * * *
40812086 GCACTAAGTGTGCGGGTTTTAAAATTGTACA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
*
40812117 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
40812145 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
40812174 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
40812204 GCACTAAGTGTGCGAGCTGAAAA-TATGTA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
40812233 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
40812247 GATTCACTAT
Statistics
Matches: 120, Mismatches: 6, Indels: 10
0.88 0.04 0.07
Matches are distributed among these distances:
27 2 0.02
28 22 0.18
29 48 0.40
30 30 0.25
31 18 0.15
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:40824303 original size:38 final size:38
Alignment explanation
Indices: 40824252--40824451 Score: 276
Period size: 38 Copynumber: 5.3 Consensus size: 38
40824242 ATATTTGATG
40824252 TATATCCGGGTTAAATCCCGAAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGAAGGCTTCGTGCTGGTAT
* * *
40824290 TATATCCGGGTTAAATCTCGCAGGCTTCGTGCTAGTAT
1 TATATCCGGGTTAAATCCCGAAGGCTTCGTGCTGGTAT
* * *
40824328 TATATCCGGGTTAAATCTCGTAGGCTTCGTGCTGGTAA
1 TATATCCGGGTTAAATCCCGAAGGCTTCGTGCTGGTAT
* *
40824366 TATGTCCGGGTTAAATCCC-ACAGGCTTCATGCTGGTAT
1 TATATCCGGGTTAAATCCCGA-AGGCTTCGTGCTGGTAT
* * *
40824404 TATATCCGGGTTAAATCCCGTAGGCCTAGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGAAGGCTTCGTGCTGGTAT
*
40824442 TATATTCGGG
1 TATATCCGGG
40824452 CCTTTGAGCC
Statistics
Matches: 143, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
38 143 1.00
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (38 bp):
TATATCCGGGTTAAATCCCGAAGGCTTCGTGCTGGTAT
Found at i:40827936 original size:40 final size:40
Alignment explanation
Indices: 40827887--40828021 Score: 261
Period size: 40 Copynumber: 3.4 Consensus size: 40
40827877 CGGATGTAAC
*
40827887 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
40827927 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
40827967 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
40828007 AACCCGCACGAATGC
1 AACCCGCACGAATGC
40828022 TATGCACATA
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 94 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (40 bp):
AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:40831004 original size:39 final size:39
Alignment explanation
Indices: 40830957--40831139 Score: 240
Period size: 39 Copynumber: 4.6 Consensus size: 39
40830947 AATGTTCGAG
40830957 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
40830996 TGATATCCGGGCTAAGCCCGAAGGCAATTGGGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
40831035 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* ** *
40831074 TGATATCCGGGTTAAGTCCCGAAGGCCTTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
40831114 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
40831140 GTTTGAACGA
Statistics
Matches: 126, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
39 88 0.70
40 38 0.30
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:40839030 original size:39 final size:39
Alignment explanation
Indices: 40838983--40839203 Score: 318
Period size: 39 Copynumber: 5.6 Consensus size: 39
40838973 AATGTTCGAG
40838983 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
40839022 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
40839061 TGATATCCGGGCTAAGCCCGAAGGCAATTG-GCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
40839099 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* ** *
40839138 TGATATCCGGGTTAAGTCCCGAAGGCCTTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
40839178 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
40839204 GTTTGAACGA
Statistics
Matches: 165, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
38 38 0.23
39 89 0.54
40 38 0.23
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:40839115 original size:116 final size:118
Alignment explanation
Indices: 40838983--40839203 Score: 329
Period size: 116 Copynumber: 1.9 Consensus size: 118
40838973 AATGTTCGAG
* *
40838983 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTATGATATCCGGGCTAAGTCCCGAAGGC
** *
40839047 AATTGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGCAATTGGCGAGTTA
66 AATTGTGCGAGTTACCATAACCGGGCTAAGTCCCGAAGGCAATTGGCGAGTTA
* *
40839099 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGTTAAGTCCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTATGATATCCGGGCTAAGTCCCGAAGGC
** * *
40839164 CTTTGTGCGGGTTACCATAACCGGGCTATGTCCCGAAGGC
66 AATTGTGCGAGTTACCATAACCGGGCTAAGTCCCGAAGGC
40839204 GTTTGAACGA
Statistics
Matches: 92, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
116 51 0.55
117 32 0.35
118 9 0.10
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.23
Consensus pattern (118 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTATGATATCCGGGCTAAGTCCCGAAGGC
AATTGTGCGAGTTACCATAACCGGGCTAAGTCCCGAAGGCAATTGGCGAGTTA
Found at i:40839120 original size:77 final size:78
Alignment explanation
Indices: 40838983--40839203 Score: 318
Period size: 77 Copynumber: 2.8 Consensus size: 78
40838973 AATGTTCGAG
40838983 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCA
* *
40839048 ATTGTGCGAGTTA
66 ATTGTGCAAATTA
40839061 TGATATCCGGGCTAAGCCCGAAGGCAATTG-GCGAGTTATGATATCCGGGCTAAGCCCGAAGGCA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCA
*
40839125 ATTGTGCAAATTG
66 ATTGTGCAAATTA
* ** * ** * *
40839138 TGATATCCGGGTTAAGTCCCGAAGGCCTTTGTGCGGGTTACCATAACCGGGCTATGTCCCGAAGG
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGG
40839203 C
64 C
40839204 GTTTGAACGA
Statistics
Matches: 129, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
77 59 0.46
78 42 0.33
79 19 0.15
80 9 0.07
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.23
Consensus pattern (78 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCA
ATTGTGCAAATTA
Found at i:40842472 original size:42 final size:42
Alignment explanation
Indices: 40842351--40842472 Score: 138
Period size: 43 Copynumber: 2.9 Consensus size: 42
40842341 TATCGTACCA
* * * *
40842351 ATGCCATATCCTAGATATGGTCTTACATGTAATCTCGTATCG
1 ATGCCATACCCCAGATATGGTCTTACACGTAATCTCATATCG
* * *
40842393 ATTCCAATAGCCCAGCTATGGTCTTACACG-AAGTCTCATATCG
1 ATGCC-ATACCCCAGATATGGTCTTACACGTAA-TCTCATATCG
* *
40842436 ATGCCATACCCCAGATATAGTCTTGCACGTAATCTCA
1 ATGCCATACCCCAGATATGGTCTTACACGTAATCTCA
40842473 GTAACCCTAA
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
42 31 0.47
43 35 0.53
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (42 bp):
ATGCCATACCCCAGATATGGTCTTACACGTAATCTCATATCG
Found at i:40850192 original size:19 final size:20
Alignment explanation
Indices: 40850157--40850194 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40850147 TGTATTTTAT
40850157 TATATTATGATTTTATAACA
1 TATATTATGATTTTATAACA
*
40850177 TATATTATTA-TTTATAAC
1 TATATTATGATTTTATAAC
40850195 CTTTATAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (20 bp):
TATATTATGATTTTATAACA
Found at i:40854284 original size:15 final size:15
Alignment explanation
Indices: 40854266--40854296 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
40854256 AATAATGTTA
40854266 TAACTCAAACTTCTT
1 TAACTCAAACTTCTT
40854281 TAACTCAAACTTCTT
1 TAACTCAAACTTCTT
40854296 T
1 T
40854297 GCAGGAGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (15 bp):
TAACTCAAACTTCTT
Found at i:40855595 original size:9 final size:9
Alignment explanation
Indices: 40855581--40855648 Score: 66
Period size: 9 Copynumber: 7.3 Consensus size: 9
40855571 TTATTATTCA
40855581 TTTCTTTAT
1 TTTCTTTAT
40855590 TTTCTTTA-
1 TTTCTTTAT
40855598 TTTCATTTAT
1 TTTC-TTTAT
**
40855608 TAGCTTTAT
1 TTTCTTTAT
40855617 TTTCTTTATT
1 TTTCTTTA-T
*
40855627 TATTATTTAT
1 T-TTCTTTAT
*
40855637 TCTCTTTAT
1 TTTCTTTAT
40855646 TTT
1 TTT
40855649 ATTCTCAGTT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
8 4 0.09
9 31 0.66
10 6 0.13
11 6 0.13
ACGTcount: A:0.16, C:0.10, G:0.01, T:0.72
Consensus pattern (9 bp):
TTTCTTTAT
Found at i:40855644 original size:16 final size:14
Alignment explanation
Indices: 40855552--40855654 Score: 54
Period size: 14 Copynumber: 7.3 Consensus size: 14
40855542 CCCCTTATAG
40855552 TCTCTTTCATTTTAT
1 TCTCTTT-ATTTTAT
*
40855567 T-TCATTATTATTCAT
1 TCTCTTTATT-TT-AT
*
40855582 T-TCTTTATTTTCT
1 TCTCTTTATTTTAT
*
40855595 T-TATTTCA-TTTAT
1 TCTCTTT-ATTTTAT
** *
40855608 TAGCTTTATTTTCT
1 TCTCTTTATTTTAT
*
40855622 T-TATTTATTATTTAT
1 TCTCTTTA-T-TTTAT
40855637 TCTCTTTATTTTAT
1 TCTCTTTATTTTAT
40855651 TCTC
1 TCTC
40855655 AGTTTACTCT
Statistics
Matches: 68, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
13 19 0.28
14 27 0.40
15 17 0.25
16 5 0.07
ACGTcount: A:0.17, C:0.14, G:0.01, T:0.68
Consensus pattern (14 bp):
TCTCTTTATTTTAT
Found at i:40855650 original size:18 final size:17
Alignment explanation
Indices: 40855562--40855651 Score: 67
Period size: 18 Copynumber: 5.1 Consensus size: 17
40855552 TCTCTTTCAT
*
40855562 TTTATTTCATTA--TTA
1 TTTATTTCTTTATTTTA
* *
40855577 TTCATTTCTTTATTTTC
1 TTTATTTCTTTATTTTA
***
40855594 TTTATTTCATTTATTAGC
1 TTTATTTC-TTTATTTTA
40855612 TTTATTTTCTTTATTTATTA
1 TTTA-TTTCTTTA-TT-TTA
40855632 TTTATTCTCTTTATTTTA
1 TTTATT-TCTTTATTTTA
40855650 TT
1 TT
40855652 CTCAGTTTAC
Statistics
Matches: 59, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
15 10 0.17
17 9 0.15
18 20 0.34
19 10 0.17
20 10 0.17
ACGTcount: A:0.19, C:0.10, G:0.01, T:0.70
Consensus pattern (17 bp):
TTTATTTCTTTATTTTA
Found at i:40858810 original size:42 final size:42
Alignment explanation
Indices: 40858764--40858845 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
40858754 TAAGTTGAGA
40858764 AGAATTTATTTTGATTGTGAGTTGAGGATTTTGCTTGAGGGC
1 AGAATTTATTTTGATTGTGAGTTGAGGATTTTGCTTGAGGGC
*
40858806 AGAATTTGTTTTGATTGTGAGTTGAGGATTTTGCTTGAGG
1 AGAATTTATTTTGATTGTGAGTTGAGGATTTTGCTTGAGG
40858846 ACAAGCAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.21, C:0.04, G:0.32, T:0.44
Consensus pattern (42 bp):
AGAATTTATTTTGATTGTGAGTTGAGGATTTTGCTTGAGGGC
Found at i:40862674 original size:16 final size:16
Alignment explanation
Indices: 40862655--40862686 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40862645 AATTATTTTA
40862655 TTACAAAATTTCACTT
1 TTACAAAATTTCACTT
*
40862671 TTACATAATTTCACTT
1 TTACAAAATTTCACTT
40862687 ACTCCATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (16 bp):
TTACAAAATTTCACTT
Found at i:40862972 original size:50 final size:50
Alignment explanation
Indices: 40862888--40863180 Score: 225
Period size: 50 Copynumber: 5.8 Consensus size: 50
40862878 CGAAGCTCTT
* * *
40862888 TGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATC
* * * * ** *
40862938 TAGTACTCGTAGTAGCCTGCACTTAGCACTACACACGTGATCGAAGTTAA-C
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGA-CCTA-TCAATC
* * * * * * * * *
40862989 GGGTACGCATATTAGCCTGCACTTAGTCCTACACACGTGACTTAACCATC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATC
* * **
40863039 TGATACACGTAGTATCCTGCACTTAGTACTACACACGTGGTTGAAGT-T-AAT-
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACA--T-G-TGACCTATCAATC
* * * **
40863090 GGGTACGCATAGTAGCCTGCACTTAGTACTACACATACGACCTATCAATC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATC
* * *
40863140 TGGTACACGAAGTAGCCTACACTTAGTACTACACACGTGAC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGAC
40863181 TCACAACGGA
Statistics
Matches: 183, Mismatches: 50, Indels: 20
0.72 0.20 0.08
Matches are distributed among these distances:
47 3 0.02
48 1 0.01
49 5 0.03
50 98 0.54
51 66 0.36
52 5 0.03
53 1 0.01
54 4 0.02
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (50 bp):
TGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATC
Found at i:40863058 original size:101 final size:101
Alignment explanation
Indices: 40862889--40863179 Score: 413
Period size: 101 Copynumber: 2.9 Consensus size: 101
40862879 GAAGCTCTTT
*
40862889 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCT-AGTACTCGTAGTAG
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGA-TACACGTAGTAG
*
40862953 CCTGCACTTAGCACTACACACGTGATCGAAGTTAACG
65 CCTGCACTTAGTACTACACACGTGATCGAAGTTAACG
* * * * * * * *
40862990 GGTACGCATATTAGCCTGCACTTAGTCCTACACACGTGACTTAACCATCTGATACACGTAGTATC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGATACACGTAGTAGC
* * *
40863055 CTGCACTTAGTACTACACACGTGGTTGAAGTTAATG
66 CTGCACTTAGTACTACACACGTGATCGAAGTTAACG
* * *
40863091 GGTACGCATAGTAGCCTGCACTTAGTACTACACATACGACCTATCAATCTGGTACACGAAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGATACACGTAGTAGC
*
40863156 CTACACTTAGTACTACACACGTGA
66 CTGCACTTAGTACTACACACGTGA
40863180 CTCACAACGG
Statistics
Matches: 163, Mismatches: 26, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
101 162 0.99
102 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (101 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGATACACGTAGTAGC
CTGCACTTAGTACTACACACGTGATCGAAGTTAACG
Found at i:40867589 original size:28 final size:28
Alignment explanation
Indices: 40867514--40867595 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
40867504 GATTTTAAAT
* *
40867514 AATAGCCTTTGTGGTAAGCTATGAAAAG
1 AATAGCCTTTGTGGCAAACTATGAAAAG
* *
40867542 AATAGTCATTGTGGCAAACTATGAAAAG
1 AATAGCCTTTGTGGCAAACTATGAAAAG
* * *
40867570 AATAGCCTTTGCGGCGAACTCTGAAA
1 AATAGCCTTTGTGGCAAACTATGAAA
40867596 GGGATGCCTC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.26
Consensus pattern (28 bp):
AATAGCCTTTGTGGCAAACTATGAAAAG
Found at i:40869347 original size:40 final size:40
Alignment explanation
Indices: 40869267--40869447 Score: 267
Period size: 40 Copynumber: 4.5 Consensus size: 40
40869257 ACCCAAGTTT
* * * *
40869267 CTTCGGGAT-TTAG-CCGGATATAACCACACGCCCAATTGC
1 CTTCGGG-TCTTAGCCCGGATATAACAACTCGCACAAATGC
* * *
40869306 CTTCGGGTCTTAACCCGGACATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
40869346 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
40869386 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
*
40869426 CTTCGGGGCTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
40869448 CATTCAAATG
Statistics
Matches: 129, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
38 1 0.01
39 10 0.08
40 118 0.91
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
Found at i:40876650 original size:93 final size:93
Alignment explanation
Indices: 40876538--40876708 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
40876528 GCCCATAAGT
* *
40876538 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCAGACTCAACTCAA
40876603 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
40876631 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCAGACTCAACTCAA
40876696 CGAGTTCGGATGC
66 CGAGTTCGGATGC
40876709 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:40876724 original size:46 final size:46
Alignment explanation
Indices: 40876530--40876710 Score: 224
Period size: 46 Copynumber: 3.9 Consensus size: 46
40876520 TGTAACCCGC
* * *
40876530 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* * *
40876576 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
40876626 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
*
40876669 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTC
40876711 AACCATCCTA
Statistics
Matches: 114, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 71 0.62
47 31 0.27
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:40880155 original size:40 final size:40
Alignment explanation
Indices: 40880075--40880255 Score: 258
Period size: 40 Copynumber: 4.5 Consensus size: 40
40880065 ACCCAAGTTT
* * * *
40880075 CTTCGGGAT-TTAG-CCGGATATAACCACACGCCCAATTGC
1 CTTCGGG-TCTTAGCCCGGATATAACAACTCGCACAAATGC
* * *
40880114 CTTCGGGTCTTAACCCGGACATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
*
40880154 CTTTGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
40880194 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
*
40880234 CTTCGGGGCTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
40880256 CATTCAAATG
Statistics
Matches: 127, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
38 1 0.01
39 10 0.08
40 116 0.91
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
Found at i:40886154 original size:27 final size:27
Alignment explanation
Indices: 40886098--40886155 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
40886088 GCAATCATAG
* *
40886098 AGTCCACCGGGACAATAAACATAAGGT
1 AGTCCACCGGGACAATAAAAATAAGAT
* *
40886125 AGTCCACTGGGACAGTAAAAAT-AGAAT
1 AGTCCACCGGGACAATAAAAATAAG-AT
40886152 AGTC
1 AGTC
40886156 TGTCAAAACG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.17
Consensus pattern (27 bp):
AGTCCACCGGGACAATAAAAATAAGAT
Found at i:40892996 original size:56 final size:56
Alignment explanation
Indices: 40892929--40893042 Score: 210
Period size: 56 Copynumber: 2.0 Consensus size: 56
40892919 AATGATTGAA
40892929 AAATGACAAATGATTCACTAGATTTACTCATTGGAGTATTAGGTGCTTCTTAGTTT
1 AAATGACAAATGATTCACTAGATTTACTCATTGGAGTATTAGGTGCTTCTTAGTTT
* *
40892985 AAATGACAAATGGTTCACTAGATTTACTCATTGGAGTATTATGTGCTTCTTAGTTT
1 AAATGACAAATGATTCACTAGATTTACTCATTGGAGTATTAGGTGCTTCTTAGTTT
40893041 AA
1 AA
40893043 TGATAAGTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (56 bp):
AAATGACAAATGATTCACTAGATTTACTCATTGGAGTATTAGGTGCTTCTTAGTTT
Found at i:40893146 original size:100 final size:99
Alignment explanation
Indices: 40893018--40893216 Score: 310
Period size: 100 Copynumber: 2.0 Consensus size: 99
40893008 TTACTCATTG
* * * *
40893018 GAGTATTATGTGCTTCTTAGTTTAATGATAAGTTTGATTTCA-GATTAATTTAGTCACTTTGAAT
1 GAGTATTAGGTACTTCTTAGCTTAATGATAAGTTTGATTT-AGGATTAATTTAATCACTTTGAAT
40893082 ATTTATTTAATAAAATAAATAATGATTCTAAAATA
65 ATTTATTTAATAAAATAAATAATGATTCTAAAATA
*
40893117 GAGTATTAGGTACTTTCTTAGCTTAATGATAAGTTTGATTTAGGGTTAATTTAATCACTTTGAAT
1 GAGTATTAGGTAC-TTCTTAGCTTAATGATAAGTTTGATTTAGGATTAATTTAATCACTTTGAAT
* *
40893182 ATTTATTTAATAGAATAAATAATGATTTTAAAATA
65 ATTTATTTAATAAAATAAATAATGATTCTAAAATA
40893217 AAGCTAAATT
Statistics
Matches: 91, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
99 12 0.13
100 79 0.87
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (99 bp):
GAGTATTAGGTACTTCTTAGCTTAATGATAAGTTTGATTTAGGATTAATTTAATCACTTTGAATA
TTTATTTAATAAAATAAATAATGATTCTAAAATA
Found at i:40896274 original size:12 final size:12
Alignment explanation
Indices: 40896257--40896281 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40896247 TGTGAAAAAT
40896257 AAAATAAAATAA
1 AAAATAAAATAA
40896269 AAAATAAAATAA
1 AAAATAAAATAA
40896281 A
1 A
40896282 GAACATACAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:40900673 original size:12 final size:12
Alignment explanation
Indices: 40900656--40900680 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40900646 TGTGAAAAAT
40900656 AAAATAAAATAA
1 AAAATAAAATAA
40900668 AAAATAAAATAA
1 AAAATAAAATAA
40900680 A
1 A
40900681 GAACACACAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:40907127 original size:37 final size:36
Alignment explanation
Indices: 40907077--40907163 Score: 147
Period size: 37 Copynumber: 2.3 Consensus size: 36
40907067 TACGAAGTCT
40907077 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
40907113 GTACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 -TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
40907150 TCACCCGGAACATA
1 T-ACCCGG-ACATA
40907164 TTTCCAAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
36 1 0.02
37 42 0.88
38 5 0.10
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.21
Consensus pattern (36 bp):
TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
Found at i:40907299 original size:49 final size:49
Alignment explanation
Indices: 40907232--40907399 Score: 300
Period size: 49 Copynumber: 3.4 Consensus size: 49
40907222 TTTACCACAT
*
40907232 ATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
40907281 ATATATATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
*
40907330 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
40907379 ATATATATATACATTTTCACA
1 --ATATATATACATTTTCACA
40907400 AATTTTGATA
Statistics
Matches: 115, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
49 96 0.83
51 19 0.17
ACGTcount: A:0.31, C:0.26, G:0.08, T:0.35
Consensus pattern (49 bp):
ATATATATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
Found at i:40915363 original size:21 final size:21
Alignment explanation
Indices: 40915321--40915374 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
40915311 TTCTCATTTT
* * *
40915321 CAGCAACTTCTTCTTTTTCAG
1 CAGCAACTTCCTCTTCTGCAG
40915342 C-GACAACTTCCTCTTCTGCAG
1 CAG-CAACTTCCTCTTCTGCAG
40915363 CAGCAACTTCCT
1 CAGCAACTTCCT
40915375 TCTCAACAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.20, C:0.35, G:0.11, T:0.33
Consensus pattern (21 bp):
CAGCAACTTCCTCTTCTGCAG
Found at i:40924519 original size:6 final size:6
Alignment explanation
Indices: 40924502--40924540 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
40924492 TAATTATTAG
* * *
40924502 TTTTAT TATTAT GTTTAT TTTTAT TTTTAT TTTCAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
40924541 ATTGTACTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.77
Consensus pattern (6 bp):
TTTTAT
Done.