Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 156 of 290
Found at i:53144906 original size:22 final size:22
Alignment explanation
Indices: 53144858--53144918 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
53144848 ATTATTCCAG
*
53144858 TTATGGCTTTGCGCCAACCTAC
1 TTATGGCTTTGTGCCAACCTAC
*
53144880 ATATGGCTTTGTGCCAACCTGA-
1 TTATGGCTTTGTGCCAACCT-AC
53144902 TTATGG-TTGTGTGCCAA
1 TTATGGCTT-TGTGCCAA
53144919 ACGTATTTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.06
22 31 0.91
23 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (22 bp):
TTATGGCTTTGTGCCAACCTAC
Found at i:53146809 original size:46 final size:45
Alignment explanation
Indices: 53146759--53146934 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 45
53146749 TGGTTGAGCA
53146759 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
53146805 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* *
53146852 TCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
53146898 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53146935 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 68 0.62
47 31 0.28
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:53146915 original size:93 final size:93
Alignment explanation
Indices: 53146756--53146926 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
53146746 GGATGGTTGA
* *
53146756 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
53146821 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* * *
53146849 GCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
53146914 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
53146927 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:53157652 original size:13 final size:13
Alignment explanation
Indices: 53157634--53157658 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53157624 TAATGGTATA
53157634 TTGAATCCATGAT
1 TTGAATCCATGAT
53157647 TTGAATCCATGA
1 TTGAATCCATGA
53157659 AAATTTAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGAATCCATGAT
Found at i:53159104 original size:47 final size:47
Alignment explanation
Indices: 53159042--53159294 Score: 382
Period size: 47 Copynumber: 5.4 Consensus size: 47
53159032 CAGCCAAGAC
53159042 AGTG-ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
53159088 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * *
53159135 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAG
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
53159182 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * *
53159229 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
53159276 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
53159295 TCCCGAAGGG
Statistics
Matches: 189, Mismatches: 17, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
46 4 0.02
47 185 0.98
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:53159469 original size:37 final size:37
Alignment explanation
Indices: 53159413--53159491 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
53159403 CCGAGCTCTA
* * *
53159413 AAGACCCGATGACTACGTGTGG-GAATTTTGTCTGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
53159450 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
53159487 AAGAC
1 AAGAC
53159492 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 36 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:53162152 original size:13 final size:13
Alignment explanation
Indices: 53162134--53162158 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53162124 TCGAACATAA
53162134 ATAGCCAAACATC
1 ATAGCCAAACATC
53162147 ATAGCCAAACAT
1 ATAGCCAAACAT
53162159 TTGGTCATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.28, G:0.08, T:0.16
Consensus pattern (13 bp):
ATAGCCAAACATC
Found at i:53164649 original size:94 final size:93
Alignment explanation
Indices: 53164480--53164701 Score: 275
Period size: 94 Copynumber: 2.4 Consensus size: 93
53164470 GTTGTTGTTG
*
53164480 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCTACATTATGAGAGCCAGTGTAAGACCATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCTACATGATGAGAGCCAGTGTAAGACCATGTC
* *
53164545 TAGGATATGGCATCGGCATTGAGACGAAA
66 TAGGACATGGCATCGAC-TTGAGACGAAA
* * * **
53164574 GCTAGTGTAAGACATGTTTGGGACATGCATCGGCTACGA-GATGATAGTTAGTGTAAGACCATGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCTAC-ATGATGAGAGCCAGTGTAAGACCATGT
* * * **
53164638 CTGGGACATGGCATTGACTTGAGATGTGA
65 CTAGGACATGGCATCGACTTGAGACGAAA
*
53164667 GCAAGTGTAAGACCATGTCTGGGACATGGCATCAG
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAG
53164702 TACCTTACCC
Statistics
Matches: 109, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
93 19 0.17
94 83 0.76
95 7 0.06
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.25
Consensus pattern (93 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCTACATGATGAGAGCCAGTGTAAGACCATGTC
TAGGACATGGCATCGACTTGAGACGAAA
Found at i:53164662 original size:47 final size:47
Alignment explanation
Indices: 53164480--53164699 Score: 225
Period size: 47 Copynumber: 4.7 Consensus size: 47
53164470 GTTGTTGTTG
* ** * *
53164480 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCTACATTATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGA-GATGATA
* * * * *
53164526 GCCAGTGTAAGACCATGTCTAGGATATGGCATCGGCATTGAGACGAAA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TTGAGATGATA
* *
53164574 GCTAGTGTAAGA-CATGTTTGGGACAT-GCATCGGCTACGAGATGATA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCT-TGAGATGATA
* * *
53164620 GTTAGTGTAAGACCATGTCTGGGACATGGCATTGACTTGAGATG-TGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGAGATGAT-A
*
53164667 GCAAGTGTAAGACCATGTCTGGGACATGGCATC
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC
53164700 AGTACCTTAC
Statistics
Matches: 143, Mismatches: 24, Indels: 13
0.79 0.13 0.07
Matches are distributed among these distances:
45 1 0.01
46 38 0.27
47 73 0.51
48 29 0.20
49 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.25
Consensus pattern (47 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGAGATGATA
Found at i:53165455 original size:42 final size:42
Alignment explanation
Indices: 53165408--53165502 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 42
53165398 GTAGGCACAC
*
53165408 GGGCGTGTA-TCTAGGCTGTGTGTGACACACGGTCTACCCCAT
1 GGGCGTGTAGT-TAGGCCGTGTGTGACACACGGTCTACCCCAT
* *
53165450 GGGCGTGTAGTTCGGCCGTGTGTGACACACGGTCTGCCCCAT
1 GGGCGTGTAGTTAGGCCGTGTGTGACACACGGTCTACCCCAT
53165492 -GGCGTGTAGTT
1 GGGCGTGTAGTT
53165503 CGACCTTGTG
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
41 11 0.22
42 37 0.76
43 1 0.02
ACGTcount: A:0.14, C:0.25, G:0.35, T:0.26
Consensus pattern (42 bp):
GGGCGTGTAGTTAGGCCGTGTGTGACACACGGTCTACCCCAT
Found at i:53165513 original size:41 final size:42
Alignment explanation
Indices: 53165425--53165513 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 42
53165415 TATCTAGGCT
*
53165425 GTGTGTGACACACGGTCTACCCCATGGGCGTGTAGTTCGGCC
1 GTGTGTGACACACGGTCTACCCCATGGGCGTGTAGTTCGACC
*
53165467 GTGTGTGACACACGGTCTGCCCCAT-GGCGTGTAGTTCGACC
1 GTGTGTGACACACGGTCTACCCCATGGGCGTGTAGTTCGACC
*
53165508 TTGTGT
1 GTGTGT
53165514 CCCCTACACG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 20 0.45
42 24 0.55
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (42 bp):
GTGTGTGACACACGGTCTACCCCATGGGCGTGTAGTTCGACC
Found at i:53172303 original size:27 final size:27
Alignment explanation
Indices: 53172265--53172578 Score: 412
Period size: 27 Copynumber: 11.6 Consensus size: 27
53172255 TTTGTTTACC
*
53172265 AAATTACCAAAATGCCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * * *
53172292 AAATCACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
53172319 AAATTACCAAAATACCCCTGGTTTGTC
1 AAATTACCAAAATACCCCTGGTTTGTA
* * **
53172346 AAATTACCAAAATACCCTTGCTTTACA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
53172373 AAATTACCAAAATACCTCTTGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * * *
53172400 AAATTACTAAAATACCCTTTGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
53172427 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
53172454 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
53172481 AAATTACCAAAATACCCTTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
53172508 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
53172535 AAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTGGTTTGTA
**
53172562 AAATTACTGAAATACCC
1 AAATTACCAAAATACCC
53172579 TCGACTTGTA
Statistics
Matches: 250, Mismatches: 37, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 250 1.00
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTGTA
Found at i:53172587 original size:27 final size:27
Alignment explanation
Indices: 53172395--53172622 Score: 117
Period size: 27 Copynumber: 8.4 Consensus size: 27
53172385 TACCTCTTGT
* * *
53172395 TTGTAAAATTACTAAAATACCCTTTG-T
1 TTGTAAAATTACTGAAATACCC-TCGAC
* ** **
53172422 TTATAAAATTACCAAAATACCC-CTGGT
1 TTGTAAAATTACTGAAATACCCTC-GAC
** * *
53172449 TTGTAAAATTACCAAAATACCC-CTAGT
1 TTGTAAAATTACTGAAATACCCTCGA-C
** * *
53172476 TTGTAAAATTACCAAAATACCCT-TAGT
1 TTGTAAAATTACTGAAATACCCTCGA-C
** * *
53172503 TTGTAAAATTACCAAAATACCC-CTAGT
1 TTGTAAAATTACTGAAATACCCTCGA-C
** *
53172530 TTGTAAAATTACCAAAATACCC-CTGAT
1 TTGTAAAATTACTGAAATACCCTC-GAC
*
53172557 TTGTGAAATTACTGAAATACCCTCGAC
1 TTGTAAAATTACTGAAATACCCTCGAC
* * *
53172584 TTGTAAAATTATTGAAATACTCTCAAC
1 TTGTAAAATTACTGAAATACCCTCGAC
53172611 TTGTAAAATTAC
1 TTGTAAAATTAC
53172623 CAAAGTACCC
Statistics
Matches: 178, Mismatches: 16, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
26 1 0.01
27 175 0.98
28 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.33
Consensus pattern (27 bp):
TTGTAAAATTACTGAAATACCCTCGAC
Found at i:53172588 original size:81 final size:81
Alignment explanation
Indices: 53172265--53172650 Score: 381
Period size: 81 Copynumber: 4.8 Consensus size: 81
53172255 TTTGTTTACC
* * * * * *
53172265 AAATTACCAAAATGCCCCTGGTTTGTAAAATCACTAAAATACCCTTGGTTTATAAAATTACCAAA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGATTTGTAAAATTACCAAA
* *
53172330 ATACCC-CTGGTTTGTC
66 ATACCCTC-GATTTGTA
* ** *
53172346 AAATTACCAAAATA-CCCTTGCTTTACAAAATTACCAAAATACCTCTTG-TTTGTAAAATTACTA
1 AAATTACCAAAATACCCCTAG-TTTGTAAAATTACCAAAATACC-CTTGATTTGTAAAATTACCA
* *
53172409 AAATACCCTTTG-TTTATA
64 AAATACCC-TCGATTTGTA
* *
53172427 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCT-AGTTTGTAAAATTACCAA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGA-TTTGTAAAATTACCAA
*
53172491 AATACCCT-TAGTTTGTA
65 AATACCCTCGA-TTTGTA
* * **
53172508 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTGTGAAATTACTGAA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGATTTGTAAAATTACCAAA
*
53172573 ATACCCTCGACTTGTA
66 ATACCCTCGATTTGTA
*** * ** * **
53172589 AAATTATTGAAATA-CTCTCAACTTGTAAAATTACCAAAGTACCCTTGATTTACAAAATTACC
1 AAATTACCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCCTTGATTTGTAAAATTACC
53172651 GTTTTACCAT
Statistics
Matches: 257, Mismatches: 36, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
80 11 0.04
81 234 0.91
82 12 0.05
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (81 bp):
AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGATTTGTAAAATTACCAAA
ATACCCTCGATTTGTA
Found at i:53172685 original size:27 final size:27
Alignment explanation
Indices: 53172562--53172687 Score: 92
Period size: 27 Copynumber: 4.7 Consensus size: 27
53172552 CTGATTTGTG
**
53172562 AAATTACTGAAATACCCTCGACTTGTA
1 AAATTACTGAAATACCCTCGACTTACA
* * * **
53172589 AAATTATTGAAATACTCTCAACTTGTA
1 AAATTACTGAAATACCCTCGACTTACA
* * *
53172616 AAATTAC-CAAAGTACCCTTGATTTACA
1 AAATTACTGAAA-TACCCTCGACTTACA
* *** * *
53172643 AAATTACCGTTTTACCATCGATTTACA
1 AAATTACTGAAATACCCTCGACTTACA
53172670 AAATTACTGAAATACCCT
1 AAATTACTGAAATACCCT
53172688 TGTAGGGTTG
Statistics
Matches: 75, Mismatches: 22, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
26 3 0.04
27 72 0.96
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.33
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCGACTTACA
Found at i:53172708 original size:27 final size:27
Alignment explanation
Indices: 53172671--53172892 Score: 302
Period size: 27 Copynumber: 8.3 Consensus size: 27
53172661 CGATTTACAA
* * *
53172671 AATTACTGAAATACCCTTGTAGGGTTG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
53172698 AAATACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
53172725 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
53172752 AATTATCGCAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
53172779 AATTACCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
53172806 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
53172833 AATTACTAAAATACCTCTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
53172860 AATTACCGAGATA-CCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
53172886 AATTACC
1 AATTACC
53172893 ATTTTGCCCC
Statistics
Matches: 172, Mismatches: 23, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
26 15 0.09
27 157 0.91
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:53173578 original size:26 final size:27
Alignment explanation
Indices: 53173542--53173615 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 27
53173532 ATTCTGTTAA
* **
53173542 GTGGCTTTGCCACGTTATCTAT-TCTG
1 GTGGCTCTGCCACAATATCTATATCTG
*
53173568 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTCTGCCACAATATCTATATCTG
* * *
53173595 GTGACTCTGTCACAATTTCTA
1 GTGGCTCTGCCACAATATCTA
53173616 ATAACTGAGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
26 18 0.46
27 21 0.54
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (27 bp):
GTGGCTCTGCCACAATATCTATATCTG
Found at i:53173798 original size:31 final size:31
Alignment explanation
Indices: 53173752--53174576 Score: 1632
Period size: 31 Copynumber: 26.6 Consensus size: 31
53173742 TTGCATTCAC
53173752 ATTCTGATTTTTGATTCTGTTACCTGATACTG
1 ATTCTGA-TTTTGATTCTGTTACCTGATACTG
53173784 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53173815 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53173846 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53173877 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53173908 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53173939 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53173970 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53174001 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53174032 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53174063 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53174094 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53174125 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53174156 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53174187 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53174218 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53174249 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53174280 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53174311 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53174342 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53174373 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53174404 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53174435 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53174466 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53174497 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53174528 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
*
53174559 ATTCTGATTCTGATTCTG
1 ATTCTGATTTTGATTCTG
53174577 ATTCTGATTC
Statistics
Matches: 792, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
31 785 0.99
32 7 0.01
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.48
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:53175818 original size:28 final size:28
Alignment explanation
Indices: 53175785--53175918 Score: 196
Period size: 28 Copynumber: 4.7 Consensus size: 28
53175775 GCTTGATGAT
53175785 CCATATGAATGTGATTGGGCCTGATGGG
1 CCATATGAATGTGATTGGGCCTGATGGG
*
53175813 CCATATGAATCTGATTGGGCCTGATAGGGG
1 CCATATGAATGTGATTGGGCCTGAT--GGG
*
53175843 CCATATGAATGTGATTTGGCCTGATGGG
1 CCATATGAATGTGATTGGGCCTGATGGG
* *
53175871 CCATATGAAGGTGATTGGGCCTAATGGG
1 CCATATGAATGTGATTGGGCCTGATGGG
* *
53175899 CCATATGAACGAGATTGGGC
1 CCATATGAATGTGATTGGGC
53175919 TTAAAGGGTC
Statistics
Matches: 96, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
28 70 0.73
30 26 0.27
ACGTcount: A:0.24, C:0.16, G:0.34, T:0.27
Consensus pattern (28 bp):
CCATATGAATGTGATTGGGCCTGATGGG
Found at i:53175875 original size:58 final size:56
Alignment explanation
Indices: 53175785--53175918 Score: 196
Period size: 58 Copynumber: 2.4 Consensus size: 56
53175775 GCTTGATGAT
*
53175785 CCATATGAATGTGATTGGGCCTGATGGGCCATATGAATCTGATTGGGCCTGATAGGGG
1 CCATATGAATGTGATTGGGCCTGATGGGCCATATGAAGCTGATTGGGCCT-A-AGGGG
* * *
53175843 CCATATGAATGTGATTTGGCCTGATGGGCCATATGAAGGTGATTGGGCCTAATGGG
1 CCATATGAATGTGATTGGGCCTGATGGGCCATATGAAGCTGATTGGGCCTAAGGGG
* *
53175899 CCATATGAACGAGATTGGGC
1 CCATATGAATGTGATTGGGC
53175919 TTAAAGGGTC
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
56 21 0.30
57 1 0.01
58 47 0.68
ACGTcount: A:0.24, C:0.16, G:0.34, T:0.27
Consensus pattern (56 bp):
CCATATGAATGTGATTGGGCCTGATGGGCCATATGAAGCTGATTGGGCCTAAGGGG
Found at i:53178864 original size:27 final size:27
Alignment explanation
Indices: 53178834--53178890 Score: 62
Period size: 29 Copynumber: 2.0 Consensus size: 27
53178824 ATTTTTGATG
*
53178834 AAATGAGCTATTT-GGACTAATTTGTGA
1 AAATAAGCT-TTTAGGACTAATTTGTGA
*
53178861 AAATAAGGTTTTGAAGGACTAATTTGTGA
1 AAATAAGCTTTT--AGGACTAATTTGTGA
53178890 A
1 A
53178891 TTTAACATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 3 0.12
27 7 0.28
29 15 0.60
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (27 bp):
AAATAAGCTTTTAGGACTAATTTGTGA
Found at i:53192268 original size:26 final size:26
Alignment explanation
Indices: 53192233--53192305 Score: 137
Period size: 26 Copynumber: 2.8 Consensus size: 26
53192223 TTGTGTGCCG
*
53192233 CACATAGCTGAGACACACGCCTGTGT
1 CACATGGCTGAGACACACGCCTGTGT
53192259 CACATGGCTGAGACACACGCCTGTGT
1 CACATGGCTGAGACACACGCCTGTGT
53192285 CACATGGCTGAGACACACGCC
1 CACATGGCTGAGACACACGCC
53192306 CGTATCCCTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.26, C:0.33, G:0.25, T:0.16
Consensus pattern (26 bp):
CACATGGCTGAGACACACGCCTGTGT
Found at i:53192301 original size:13 final size:13
Alignment explanation
Indices: 53192233--53192301 Score: 57
Period size: 13 Copynumber: 5.3 Consensus size: 13
53192223 TTGTGTGCCG
*
53192233 CACATAGCTGAGA
1 CACATGGCTGAGA
* * * *
53192246 CACACGCCTGTGT
1 CACATGGCTGAGA
53192259 CACATGGCTGAGA
1 CACATGGCTGAGA
* * * *
53192272 CACACGCCTGTGT
1 CACATGGCTGAGA
53192285 CACATGGCTGAGA
1 CACATGGCTGAGA
53192298 CACA
1 CACA
53192302 CGCCCGTATC
Statistics
Matches: 39, Mismatches: 17, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.17
Consensus pattern (13 bp):
CACATGGCTGAGA
Found at i:53194377 original size:29 final size:28
Alignment explanation
Indices: 53194320--53194421 Score: 100
Period size: 29 Copynumber: 3.6 Consensus size: 28
53194310 TGCCTGTATC
*
53194320 TGGCCCATTAAGCCC-AATCA-TATTCATA
1 TGGCCCATTAGGCCCAAATCACT-TT-ATA
53194348 TGGCCCATTAGGCCCAAATCACTTGTATA
1 TGGCCCATTAGGCCCAAATCACTT-TATA
**
53194377 TGGCTGATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCAC-TTTATA
* * *
53194406 TAGACCGTTAGGCCCA
1 TGGCCCATTAGGCCCA
53194422 GTCACATTCA
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
28 14 0.23
29 44 0.71
30 4 0.06
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.27
Consensus pattern (28 bp):
TGGCCCATTAGGCCCAAATCACTTTATA
Found at i:53200204 original size:2 final size:2
Alignment explanation
Indices: 53200197--53200226 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
53200187 GAGACTAGTC
*
53200197 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53200227 CATTCTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:53202050 original size:30 final size:30
Alignment explanation
Indices: 53202016--53202076 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
53202006 TCATTAACTC
53202016 AAACTTTGGAAAAATTACAATTTTTCCCCT
1 AAACTTTGGAAAAATTACAATTTTTCCCCT
* * * * *
53202046 AAACTTTTGCATATTTACACTTTTTCCCCT
1 AAACTTTGGAAAAATTACAATTTTTCCCCT
53202076 A
1 A
53202077 GGCTCAGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTTCCCCT
Found at i:53204158 original size:28 final size:27
Alignment explanation
Indices: 53204099--53204249 Score: 221
Period size: 28 Copynumber: 5.4 Consensus size: 27
53204089 ATGTTAAGGA
* *
53204099 ACTAAGTGTGCGAATTGACTATGTAGC
1 ACTAAGTGTGCGAGTTGATTATGTAGC
53204126 ACTAAGTGTGCGAGTATGATTATGTAGC
1 ACTAAGTGTGCGAGT-TGATTATGTAGC
*
53204154 ACTAAGTGTGCGAGTTGACTATGTAGC
1 ACTAAGTGTGCGAGTTGATTATGTAGC
53204181 ACTAAGTGTGCGAGTATGATTATGTAGC
1 ACTAAGTGTGCGAGT-TGATTATGTAGC
*
53204209 ACTAAGTGTGCGAGTTGATTATATATAGC
1 ACTAAGTGTGCGAGTTGA-T-TATGTAGC
*
53204238 ACTGAGTGTGCG
1 ACTAAGTGTGCG
53204250 GACTATATAT
Statistics
Matches: 114, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
27 43 0.38
28 53 0.46
29 18 0.16
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (27 bp):
ACTAAGTGTGCGAGTTGATTATGTAGC
Found at i:53204164 original size:55 final size:55
Alignment explanation
Indices: 53204099--53204249 Score: 248
Period size: 55 Copynumber: 2.7 Consensus size: 55
53204089 ATGTTAAGGA
*
53204099 ACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTATGATTATGTAGC
1 ACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTATGATTATGTAGC
53204154 ACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTATGATTATGTAGC
1 ACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTATGATTATGTAGC
* * *
53204209 ACTAAGTGTGCGAGTTGATTATATATAGCACTGAGTGTGCG
1 ACTAAGTGTGCGAGTTGA--CTATGTAGCACTAAGTGTGCG
53204250 GACTATATAT
Statistics
Matches: 90, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
55 72 0.80
57 18 0.20
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (55 bp):
ACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTATGATTATGTAGC
Found at i:53212480 original size:40 final size:40
Alignment explanation
Indices: 53212420--53212571 Score: 216
Period size: 40 Copynumber: 3.8 Consensus size: 40
53212410 ATTTGAATGA
***
53212420 GATCCGGGCTAAGTTTCGAAGGCATTTGTGCTAGTGATTT
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
*
53212460 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTT
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
* * *
53212500 GATCCGGGCTAAGACCCGAAGGCATTTGTACGAGTTGATAT
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTT
*
53212541 -ATCCGGGCTAAGACCCGAAGGCAATTGTGCT
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGCT
53212572 TGTGGTAATA
Statistics
Matches: 102, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 97 0.95
41 5 0.05
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.28
Consensus pattern (40 bp):
GATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
Found at i:53217595 original size:32 final size:33
Alignment explanation
Indices: 53217559--53217620 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
53217549 AAACAGACTA
53217559 GGCCTGAGCCCATCAA-AGAAAT-AGTATCAAGT
1 GGCCTGAGCCCATCAACAG-AATCAGTATCAAGT
* *
53217591 GGCCTTAGCCCATTAACAGAATCAGTATCA
1 GGCCTGAGCCCATCAACAGAATCAGTATCA
53217621 GATGAAGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 17 0.65
33 9 0.35
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.21
Consensus pattern (33 bp):
GGCCTGAGCCCATCAACAGAATCAGTATCAAGT
Found at i:53221820 original size:164 final size:164
Alignment explanation
Indices: 53221546--53222037 Score: 921
Period size: 164 Copynumber: 3.0 Consensus size: 164
53221536 AATTATAGTT
* * *
53221546 TCAAGGGTCGAATATCATAAGGTGGGCTTGAAAAGGCTCAAACGATCCAAAGAAATAGTGCTTAT
1 TCAAGGGTCTAATATCATAAGGTGGGCTTGAAAAGGCTCAAACAATCCAAAGAAATAGTGCCTAT
* * * *
53221611 ATCATTTTAGATATTTATGTCTCCTAAGATTTTGCCTCAAGAAAGTTACTAAGTCAATTCTAAAG
66 ATCATTTTAGATTTTTATGTCTCCTAGGATTTCGCCTCTAGAAAGTTACTAAGTCAATTCTAAAG
53221676 ATATAAACCTTCATGCATGTTTAATCTCAAAAGA
131 ATATAAACCTTCATGCATGTTTAATCTCAAAAGA
53221710 TCAAGGGTCTAATATCATAAGGTGGGCTTGAAAAGGCTCAAACAATCCAAAGAAATAGTGCCTAT
1 TCAAGGGTCTAATATCATAAGGTGGGCTTGAAAAGGCTCAAACAATCCAAAGAAATAGTGCCTAT
53221775 ATCATTTTAGATTTTTATGTCTCCTAGGATTTCGCCTCTAGAAAGTTACTAAGTCAATTCTAAAG
66 ATCATTTTAGATTTTTATGTCTCCTAGGATTTCGCCTCTAGAAAGTTACTAAGTCAATTCTAAAG
53221840 ATATAAACCTTCATGCATGTTTAATCTCAAAAGA
131 ATATAAACCTTCATGCATGTTTAATCTCAAAAGA
53221874 TCAAGGGTCTAATATCATAAGGTGGGCTTGAAAAGGCTCAAACAATCCAAAGAAATAGTGCCTAT
1 TCAAGGGTCTAATATCATAAGGTGGGCTTGAAAAGGCTCAAACAATCCAAAGAAATAGTGCCTAT
53221939 ATCATTTTAGATTTTTATGTCTCCTAGGATTTCGCCTCTAGAAAGTTACTAAGTCAATTCTAAAG
66 ATCATTTTAGATTTTTATGTCTCCTAGGATTTCGCCTCTAGAAAGTTACTAAGTCAATTCTAAAG
53222004 ATATAAACCTTCATGCATGTTTAATCTCAAAAGA
131 ATATAAACCTTCATGCATGTTTAATCTCAAAAGA
53222038 AACTAAGTTT
Statistics
Matches: 321, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
164 321 1.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (164 bp):
TCAAGGGTCTAATATCATAAGGTGGGCTTGAAAAGGCTCAAACAATCCAAAGAAATAGTGCCTAT
ATCATTTTAGATTTTTATGTCTCCTAGGATTTCGCCTCTAGAAAGTTACTAAGTCAATTCTAAAG
ATATAAACCTTCATGCATGTTTAATCTCAAAAGA
Found at i:53225474 original size:28 final size:28
Alignment explanation
Indices: 53225434--53225491 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
53225424 GCCTAAAAAG
*
53225434 TCAATGCCCCATATGTTGAGTAATTCAA
1 TCAATGCCCCATATGTTGAATAATTCAA
53225462 TCAATGCCCCATATGTTGAATAATTCAA
1 TCAATGCCCCATATGTTGAATAATTCAA
53225490 TC
1 TC
53225492 TCCAAAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (28 bp):
TCAATGCCCCATATGTTGAATAATTCAA
Found at i:53235317 original size:40 final size:40
Alignment explanation
Indices: 53235288--53235409 Score: 156
Period size: 40 Copynumber: 3.0 Consensus size: 40
53235278 TGTAGCCGAA
* *
53235288 CTTAAAGACCTGTAGGCTATATGCTGGAATGTTATCTGGG
1 CTTAAAGACCAGTAGGCTATATGCTGGAATGTTATCCGGG
* *
53235328 CTTAAAGACCAGCAAGCTATATGCTGGAATGTTATCCGGG
1 CTTAAAGACCAGTAGGCTATATGCTGGAATGTTATCCGGG
* * * *
53235368 CTTAAAGACCCGTAGGCT-TCGTGCTAGAATGCTATCCGGG
1 CTTAAAGACCAGTAGGCTAT-ATGCTGGAATGTTATCCGGG
53235408 CT
1 CT
53235410 AGAGACCCTT
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
39 1 0.01
40 70 0.99
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.28
Consensus pattern (40 bp):
CTTAAAGACCAGTAGGCTATATGCTGGAATGTTATCCGGG
Found at i:53246655 original size:47 final size:47
Alignment explanation
Indices: 53246577--53247717 Score: 1375
Period size: 47 Copynumber: 24.6 Consensus size: 47
53246567 CCCTTCGGGA
* * * *
53246577 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * * *
53246624 CCTGTCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
53246671 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
53246720 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATT----
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * * * * *
53246763 CATATCTCATACAT--A-TTTCACATT-AGC-CATTCGACTTTAC--C
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATT-CGGC
** * * * * * *
53246804 ACAGAT-ACATATCT-CA--TACATATT--TCACATTAGCCATTCAGA
1 -CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * * * *
53246846 TTTACCACATATATGCA-TGTTCATATTCACCACATTGGACATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* * *
53246893 CTTATCACACATATGCA-TGCTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* * *
53246940 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
53246987 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
53247034 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
53247081 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
53247128 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
53247175 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
53247222 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
53247269 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
53247316 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
53247363 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
53247410 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
53247457 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
53247504 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
53247551 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
53247598 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
53247645 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
53247692 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
53247718 CACAATTATC
Statistics
Matches: 1016, Mismatches: 61, Indels: 34
0.91 0.05 0.03
Matches are distributed among these distances:
38 7 0.01
39 2 0.00
40 11 0.01
41 21 0.02
42 12 0.01
43 13 0.01
45 7 0.01
47 898 0.88
48 1 0.00
49 44 0.04
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:53246834 original size:48 final size:48
Alignment explanation
Indices: 53246763--53246854 Score: 168
Period size: 48 Copynumber: 1.9 Consensus size: 48
53246753 ATCGGCCATT
53246763 CATATCTCATACATATTTCACATTAGCCATTC-GACTTTACCACAGATA
1 CATATCTCATACATATTTCACATTAGCCATTCAGA-TTTACCACAGATA
53246811 CATATCTCATACATATTTCACATTAGCCATTCAGATTTACCACA
1 CATATCTCATACATATTTCACATTAGCCATTCAGATTTACCACA
53246855 TATATGCATG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 41 0.95
49 2 0.05
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (48 bp):
CATATCTCATACATATTTCACATTAGCCATTCAGATTTACCACAGATA
Found at i:53246949 original size:94 final size:94
Alignment explanation
Indices: 53246851--53247717 Score: 1533
Period size: 94 Copynumber: 9.2 Consensus size: 94
53246841 TCAGATTTAC
* * * * * * * *
53246851 CACATATATGCA-TGTTCATATTCACCACATTGGAC-ATTCGGCCTTATCACACATATGCA-TGC
1 CACATATATACACT-TTCACATTCATCACATCGG-CTATTAGGCCTTATCACATATATACACT-T
* * *
53246913 TCACATTCATCACATTGGCCATTCGGCCTTAT
63 TCACATTCATCACATCGGCTATTAGGCCTTAT
53246945 CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
1 CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
53247010 CATTCATCACATCGGCTATTAGGCCTTAT
66 CATTCATCACATCGGCTATTAGGCCTTAT
53247039 CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
1 CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
53247104 CATTCATCACATCGGCTATTAGGCCTTAT
66 CATTCATCACATCGGCTATTAGGCCTTAT
53247133 CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
1 CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
53247198 CATTCATCACATCGGCTATTAGGCCTTAT
66 CATTCATCACATCGGCTATTAGGCCTTAT
53247227 CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
1 CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
53247292 CATTCATCACATCGGCTATTAGGCCTTAT
66 CATTCATCACATCGGCTATTAGGCCTTAT
53247321 CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
1 CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
53247386 CATTCATCACATCGGCTATTAGGCCTTAT
66 CATTCATCACATCGGCTATTAGGCCTTAT
53247415 CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
1 CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
53247480 CATTCATCACATCGGCTATTAGGCCTTAT
66 CATTCATCACATCGGCTATTAGGCCTTAT
*
53247509 CACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCA
1 CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
*
53247574 CATTCATCACATCGGCCATTAGGCCTTAT
66 CATTCATCACATCGGCTATTAGGCCTTAT
*
53247603 CACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCA
1 CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
*
53247668 CATTCATCACATCGGCCATTAGGCCTTAT
66 CATTCATCACATCGGCTATTAGGCCTTAT
* *
53247697 CACATATATATACATTCACAT
1 CACATATATACACTTTCACAT
53247718 CACAATTATC
Statistics
Matches: 755, Mismatches: 15, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
93 1 0.00
94 752 1.00
95 2 0.00
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (94 bp):
CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
CATTCATCACATCGGCTATTAGGCCTTAT
Found at i:53247021 original size:141 final size:141
Alignment explanation
Indices: 53246851--53247717 Score: 1533
Period size: 141 Copynumber: 6.1 Consensus size: 141
53246841 TCAGATTTAC
* * * * * * * *
53246851 CACATATATGCA-TGTTCATATTCACCACATTGGAC-ATTCGGCCTTATCACACATATGCA-TGC
1 CACATATATACACT-TTCACATTCATCACATCGG-CTATTAGGCCTTATCACATATATACACT-T
* * *
53246913 TCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
63 TCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
53246978 CTATTAGGCCTTAT
128 CTATTAGGCCTTAT
53246992 CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
1 CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
53247057 CATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTA
66 CATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTA
53247122 TTAGGCCTTAT
131 TTAGGCCTTAT
53247133 CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
1 CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
53247198 CATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTA
66 CATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTA
53247263 TTAGGCCTTAT
131 TTAGGCCTTAT
53247274 CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
1 CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
53247339 CATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTA
66 CATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTA
53247404 TTAGGCCTTAT
131 TTAGGCCTTAT
53247415 CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
1 CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
*
53247480 CATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCA
66 CATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTA
53247545 TTAGGCCTTAT
131 TTAGGCCTTAT
*
53247556 CACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCA
1 CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
* *
53247621 CATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCA
66 CATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTA
53247686 TTAGGCCTTAT
131 TTAGGCCTTAT
* *
53247697 CACATATATATACATTCACAT
1 CACATATATACACTTTCACAT
53247718 CACAATTATC
Statistics
Matches: 707, Mismatches: 16, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
140 1 0.00
141 704 1.00
142 2 0.00
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (141 bp):
CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCA
CATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTA
TTAGGCCTTAT
Found at i:53253332 original size:50 final size:50
Alignment explanation
Indices: 53253274--53253372 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 50
53253264 ATAATAAAAT
53253274 AATTATTTATATCTCAAATTTTGTGGTCCCGAAACCTCTGTTCCAACTAA
1 AATTATTTATATCTCAAATTTTGTGGTCCCGAAACCTCTGTTCCAACTAA
* *
53253324 AATTATTTATATCTCATATTTTGTGGTCTCGAAACCTCTGTTCCAACTA
1 AATTATTTATATCTCAAATTTTGTGGTCCCGAAACCTCTGTTCCAACTA
53253373 GACCCAATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.40
Consensus pattern (50 bp):
AATTATTTATATCTCAAATTTTGTGGTCCCGAAACCTCTGTTCCAACTAA
Found at i:53253896 original size:114 final size:114
Alignment explanation
Indices: 53253690--53253937 Score: 372
Period size: 114 Copynumber: 2.2 Consensus size: 114
53253680 AACAATGTGT
* *
53253690 GTGGGCCTAAGCCCAGTACAATTTCACTTGGGTCTCAACCCTTATCAAAATCAACTGGGCCTAGC
1 GTGGGCCTAAGCCCAGTACAATTTCACTTGGGTCTCAACCCTCATCAAAATCAACTGAGCCTAGC
*
53253755 CCAATCTCAATATCAGTAATAGCTGGGCCTAG-CCTATTAACAGAATCAG
66 CCAATCTCAATATCAGTAACAGCTGGGCCTAGTCC-ATTAACAGAATCAG
* * * * *
53253804 GTGTGCCTAAGCCCAGTACAATTTCACTTGGTTCTCAGCCCTCATCAGAATCAATTGAGCCTAGC
1 GTGGGCCTAAGCCCAGTACAATTTCACTTGGGTCTCAACCCTCATCAAAATCAACTGAGCCTAGC
* * *
53253869 CCATTCTCAATATCAGTAACAGTTGGGCCTAGTCCATTAACAGAATTAG
66 CCAATCTCAATATCAGTAACAGCTGGGCCTAGTCCATTAACAGAATCAG
*
53253918 GTGGGCCTAAGCCTAGTACA
1 GTGGGCCTAAGCCCAGTACA
53253938 GAATCAGTAT
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
114 118 0.98
115 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.26
Consensus pattern (114 bp):
GTGGGCCTAAGCCCAGTACAATTTCACTTGGGTCTCAACCCTCATCAAAATCAACTGAGCCTAGC
CCAATCTCAATATCAGTAACAGCTGGGCCTAGTCCATTAACAGAATCAG
Found at i:53254119 original size:22 final size:22
Alignment explanation
Indices: 53254094--53254142 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
53254084 AACAGGACAG
*
53254094 CTCAACGCCGTACATAGGACGA
1 CTCAACACCGTACATAGGACGA
* *
53254116 CTCAACACCGTAGATAGGGCGA
1 CTCAACACCGTACATAGGACGA
53254138 CTCAA
1 CTCAA
53254143 AGCCATAGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.31, G:0.22, T:0.14
Consensus pattern (22 bp):
CTCAACACCGTACATAGGACGA
Found at i:53254151 original size:22 final size:22
Alignment explanation
Indices: 53254107--53254158 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
53254097 AACGCCGTAC
*
53254107 ATAGGACGACTCAACACCGTAG
1 ATAGGACGACTCAACACCATAG
*
53254129 ATAGGGCGACTCAA-AGCCATAG
1 ATAGGACGACTCAACA-CCATAG
*
53254151 ACAGGACG
1 ATAGGACG
53254159 GCTAAAGGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.37, C:0.25, G:0.27, T:0.12
Consensus pattern (22 bp):
ATAGGACGACTCAACACCATAG
Found at i:53254711 original size:17 final size:19
Alignment explanation
Indices: 53254689--53254730 Score: 70
Period size: 17 Copynumber: 2.3 Consensus size: 19
53254679 ATCCGTGTAG
53254689 GGCCCACA-AGCCCAT-TA
1 GGCCCACACAGCCCATCTA
53254706 GGCCCACACAGCCCATCTA
1 GGCCCACACAGCCCATCTA
53254725 GGCCCA
1 GGCCCA
53254731 ACGTGGCCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 8 0.35
18 7 0.30
19 8 0.35
ACGTcount: A:0.26, C:0.45, G:0.19, T:0.10
Consensus pattern (19 bp):
GGCCCACACAGCCCATCTA
Found at i:53258366 original size:18 final size:17
Alignment explanation
Indices: 53258333--53258366 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
53258323 TTACCCGTGT
*
53258333 AGGGCCCATAAGCCCAC
1 AGGGCCCACAAGCCCAC
53258350 AGGGCCCACACAGCCCA
1 AGGGCCCACA-AGCCCA
53258367 TTTCGGCCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.44, G:0.24, T:0.03
Consensus pattern (17 bp):
AGGGCCCACAAGCCCAC
Found at i:53258979 original size:23 final size:23
Alignment explanation
Indices: 53258951--53258997 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
53258941 ACAAAGAGAG
* * *
53258951 AAAGAGGGCAAAACTAGTCGTGA
1 AAAGAGGGAAAAAATAGCCGTGA
53258974 AAAGAGGGAAAAAATAGCCGTGA
1 AAAGAGGGAAAAAATAGCCGTGA
53258997 A
1 A
53258998 CCCTAACAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.49, C:0.11, G:0.30, T:0.11
Consensus pattern (23 bp):
AAAGAGGGAAAAAATAGCCGTGA
Found at i:53261609 original size:91 final size:91
Alignment explanation
Indices: 53261454--53261635 Score: 328
Period size: 91 Copynumber: 2.0 Consensus size: 91
53261444 CCATACAGGT
53261454 AATGCCTCCAAATCTTCAGTGCGAATATCACCGCTGCCGACTCCAAGTCATGCGCCCAGTAGTTC
1 AATGCCTCCAAATCTTCAGTGCGAATATCACCGCTGCCGACTCCAAGTCATGCGCCCAGTAGTTC
*
53261519 ACTTCATGCGTCTTAAGCTAACGAGA
66 ACTTCATGAGTCTTAAGCTAACGAGA
* * *
53261545 AATGCCTTCAAATCTTCAGTGCGAATATCACCGCTGTCGATTCCAAGTCATGCGCCCAGTAGTTC
1 AATGCCTCCAAATCTTCAGTGCGAATATCACCGCTGCCGACTCCAAGTCATGCGCCCAGTAGTTC
53261610 ACTTCATGAGTCTTAAGCTAACGAGA
66 ACTTCATGAGTCTTAAGCTAACGAGA
53261636 CGCATATGCT
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 87 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.26
Consensus pattern (91 bp):
AATGCCTCCAAATCTTCAGTGCGAATATCACCGCTGCCGACTCCAAGTCATGCGCCCAGTAGTTC
ACTTCATGAGTCTTAAGCTAACGAGA
Found at i:53264052 original size:55 final size:55
Alignment explanation
Indices: 53263968--53264076 Score: 209
Period size: 55 Copynumber: 2.0 Consensus size: 55
53263958 AAAAGAGTTA
*
53263968 CCGATCTTGAGATATTTGAAGTATTGTGGGGCTGAGTCAAAATGACTACTAGATT
1 CCGATCTTGAGATATTTGAAGGATTGTGGGGCTGAGTCAAAATGACTACTAGATT
53264023 CCGATCTTGAGATATTTGAAGGATTGTGGGGCTGAGTCAAAATGACTACTAGAT
1 CCGATCTTGAGATATTTGAAGGATTGTGGGGCTGAGTCAAAATGACTACTAGAT
53264077 GCACTGTCCG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (55 bp):
CCGATCTTGAGATATTTGAAGGATTGTGGGGCTGAGTCAAAATGACTACTAGATT
Found at i:53264995 original size:40 final size:40
Alignment explanation
Indices: 53264938--53265127 Score: 247
Period size: 40 Copynumber: 4.8 Consensus size: 40
53264928 ATTTGAATAC
* * * *
53264938 ATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTTT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGATGA-TAT
*
53264978 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGATGATAT
*
53265018 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGATGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGATGATAT
* * * *
53265058 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGATGATAT
* * *
53265098 ACCCGGGTTAAGACCCGAAGGCAGTTGTGC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
53265128 TTGTGGTTAT
Statistics
Matches: 136, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 133 0.98
41 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGATGATAT
Found at i:53265071 original size:80 final size:80
Alignment explanation
Indices: 53264938--53265127 Score: 274
Period size: 80 Copynumber: 2.4 Consensus size: 80
53264928 ATTTGAATAC
* * * *
53264938 ATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCATT
*
53265003 TGTGCAAGTTGATAT
66 CGTGCAAGTTGATAT
53265018 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGATGA-TATATCCGGGCTAAGACCCGAAGGCAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGATTATATCCGGGCTAAGACCCGAAGGCAT
* *
53265082 TCGTGCGAGTTGCTAT
65 TCGTGCAAGTTGATAT
* * *
53265098 ACCCGGGTTAAGACCCGAAGGCAGTTGTGC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
53265128 TTGTGGTTAT
Statistics
Matches: 99, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
80 96 0.97
81 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCATT
CGTGCAAGTTGATAT
Found at i:53266867 original size:28 final size:28
Alignment explanation
Indices: 53266827--53266979 Score: 198
Period size: 28 Copynumber: 5.5 Consensus size: 28
53266817 ACTCGATATT
* *
53266827 TCGCACACTAAGTGCCGTACCCAATGTC
1 TCGCACACTAAGTGCCATACTCAATGTC
* **
53266855 TCGCACACTAAGTGTCATGTTCAATGTC
1 TCGCACACTAAGTGCCATACTCAATGTC
* *
53266883 TCGCACACTAAGTGCCATGCTCGATGTC
1 TCGCACACTAAGTGCCATACTCAATGTC
* * *
53266911 TCACACACTAAGTGCCACAATCAATGTC
1 TCGCACACTAAGTGCCATACTCAATGTC
* *
53266939 TCGCAAACTAAGTGCCATAATCAATGTC
1 TCGCACACTAAGTGCCATACTCAATGTC
53266967 TCGCACACTAAGT
1 TCGCACACTAAGT
53266980 ACCGTACTGT
Statistics
Matches: 108, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 108 1.00
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (28 bp):
TCGCACACTAAGTGCCATACTCAATGTC
Found at i:53267506 original size:17 final size:18
Alignment explanation
Indices: 53267479--53267512 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
53267469 TTTGACTCGA
*
53267479 TTTTTGATGATTTTTACG
1 TTTTTGATGATTGTTACG
53267497 TTTTTG-TGATTGTTAC
1 TTTTTGATGATTGTTAC
53267513 TTTGAGTACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.15, C:0.06, G:0.18, T:0.62
Consensus pattern (18 bp):
TTTTTGATGATTGTTACG
Found at i:53268793 original size:31 final size:31
Alignment explanation
Indices: 53268758--53268820 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
53268748 CTTATTAAGT
*
53268758 GAATATGATAGGCTAATTTACTCAAGTTGAC
1 GAATAAGATAGGCTAATTTACTCAAGTTGAC
53268789 GAATAAGATAGGCTAATTTACTCAAGTTGAC
1 GAATAAGATAGGCTAATTTACTCAAGTTGAC
53268820 G
1 G
53268821 GAATGTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (31 bp):
GAATAAGATAGGCTAATTTACTCAAGTTGAC
Found at i:53269137 original size:37 final size:37
Alignment explanation
Indices: 53269074--53269179 Score: 108
Period size: 37 Copynumber: 2.9 Consensus size: 37
53269064 ACATATGAGT
* ** *
53269074 ACGTGTAAGACCATAGCTAAGCTATGGCATCGTAAT-
1 ACGTGTAAGACCATAGTTGGGATATGGCATCGTAATG
* *
53269110 AGTGTGTAAGACCATAGTTGGGATATGGCATCGTGATG
1 A-CGTGTAAGACCATAGTTGGGATATGGCATCGTAATG
* *
53269148 ACATGTAAGACCAT-GTCTGGGACATGGCATCG
1 ACGTGTAAGACCATAGT-TGGGATATGGCATCG
53269180 ATATGAGATC
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
36 3 0.05
37 54 0.93
38 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.25
Consensus pattern (37 bp):
ACGTGTAAGACCATAGTTGGGATATGGCATCGTAATG
Found at i:53269209 original size:42 final size:42
Alignment explanation
Indices: 53269113--53269442 Score: 162
Period size: 42 Copynumber: 7.7 Consensus size: 42
53269103 TCGTAATAGT
*
53269113 GTGTAAGACCATAGT-TGGGATATGGCATCG---TGATGA-CA-
1 GTGTAAGACCATA-TCTGGGACATGGCATCGATATGA-GATCAC
* *
53269151 -TGTAAGACCATGTCTGGGACATGGCATCGATATGAGATCAT
1 GTGTAAGACCATATCTGGGACATGGCATCGATATGAGATCAC
* * *
53269192 GTGTAAGTCCATATCTGGGATATGGCATCAGCATCGATATGAGATCCC
1 GTGTAAGACCATATCTGGG--A---CAT-GGCATCGATATGAGATCAC
* *
53269240 GTGTAAGACCATATCTGGGATATGGCATCAGCATCGATATGAGATTAC
1 GTGTAAGACCATATCTGGG--A---CAT-GGCATCGATATGAGATCAC
* * * * * **
53269288 GTGTAAGACTATATCTAGGATATGGCTTCGGTATGAGATTTC
1 GTGTAAGACCATATCTGGGACATGGCATCGATATGAGATCAC
* * * * * **
53269330 GTGTAAGATCGTGTCTGGG--ATGCAGCATCGGTATGTGATTTC
1 GTGTAAGACCATATCTGGGACATG--GCATCGATATGAGATCAC
* ** *
53269372 GTATAAGACCATGCCTGGGACATGGCATCGATGTGAGA-CATC
1 GTGTAAGACCATATCTGGGACATGGCATCGATATGAGATCA-C
*
53269414 ATGTAAGACCATAGT-T-GGACTATGGCATC
1 GTGTAAGACCATA-TCTGGGAC-ATGGCATC
53269443 AAGTAAACGA
Statistics
Matches: 235, Mismatches: 37, Indels: 36
0.76 0.12 0.12
Matches are distributed among these distances:
36 1 0.00
37 25 0.11
39 2 0.01
40 8 0.03
41 4 0.02
42 107 0.46
43 2 0.01
44 4 0.02
46 1 0.00
47 3 0.01
48 78 0.33
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (42 bp):
GTGTAAGACCATATCTGGGACATGGCATCGATATGAGATCAC
Found at i:53269229 original size:48 final size:48
Alignment explanation
Indices: 53269174--53269313 Score: 226
Period size: 48 Copynumber: 2.9 Consensus size: 48
53269164 CTGGGACATG
* *
53269174 GCATCGATATGAGATCATGTGTAAGTCCATATCTGGGATATGGCATCA
1 GCATCGATATGAGATCACGTGTAAGACCATATCTGGGATATGGCATCA
*
53269222 GCATCGATATGAGATCCCGTGTAAGACCATATCTGGGATATGGCATCA
1 GCATCGATATGAGATCACGTGTAAGACCATATCTGGGATATGGCATCA
* * *
53269270 GCATCGATATGAGATTACGTGTAAGACTATATCTAGGATATGGC
1 GCATCGATATGAGATCACGTGTAAGACCATATCTGGGATATGGC
53269314 TTCGGTATGA
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 85 1.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (48 bp):
GCATCGATATGAGATCACGTGTAAGACCATATCTGGGATATGGCATCA
Found at i:53276396 original size:28 final size:28
Alignment explanation
Indices: 53276323--53276397 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
53276313 TATATATATG
* * *
53276323 TGGCACATAGTGTGCGAAATATTCAGAA
1 TGGCACTTAGTGTGCGAGATATTAAGAA
* *
53276351 TGACACTTGGTGTGCGAGATATTAAGTAA
1 TGGCACTTAGTGTGCGAGATATTAAG-AA
53276380 -GGCACTTAGTGTGCGAGA
1 TGGCACTTAGTGTGCGAGA
53276398 CAGCGAAGAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 37 0.95
29 2 0.05
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (28 bp):
TGGCACTTAGTGTGCGAGATATTAAGAA
Found at i:53278907 original size:46 final size:47
Alignment explanation
Indices: 53278801--53278922 Score: 147
Period size: 46 Copynumber: 2.6 Consensus size: 47
53278791 TGTCTTCGAC
** * *
53278801 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCC--A-ATATATCTAAT
* *
53278851 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCC-ATATATCTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
*
53278897 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
53278923 CTGTCCTGTC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
46 34 0.53
50 30 0.47
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (47 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
Found at i:53283668 original size:26 final size:26
Alignment explanation
Indices: 53283639--53283720 Score: 80
Period size: 26 Copynumber: 3.1 Consensus size: 26
53283629 ATCTTTAATG
*
53283639 ATAATAATATATAGATAAAAT-GTAT
1 ATAATAATATATAGATAAAATAATAT
* *
53283664 AATAATAATAATTTGTGA-AAAATAATAT
1 -ATAATAAT-ATAT-AGATAAAATAATAT
53283692 ATAATAATATATA-ATAAAATAATTAT
1 ATAATAATATATAGATAAAATAA-TAT
53283718 ATA
1 ATA
53283721 CAATATAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
24 1 0.02
25 7 0.15
26 17 0.37
27 16 0.35
28 5 0.11
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (26 bp):
ATAATAATATATAGATAAAATAATAT
Found at i:53283712 original size:12 final size:10
Alignment explanation
Indices: 53283684--53283725 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
53283674 ATTTGTGAAA
53283684 AATAATATAT
1 AATAATATAT
53283694 AATAATATAT
1 AATAATATAT
53283704 AATAA-A-AT
1 AATAATATAT
* *
53283712 AATTATATAC
1 AATAATATAT
53283722 AATA
1 AATA
53283726 TAAAAATAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
8 6 0.22
9 2 0.07
10 19 0.70
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (10 bp):
AATAATATAT
Found at i:53283771 original size:16 final size:16
Alignment explanation
Indices: 53283743--53283782 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
53283733 AAGGTTAAGA
53283743 ATAAAATAAATAACAAT
1 ATAAAA-AAATAACAAT
*
53283760 ATAAAAAAATAATAAT
1 ATAAAAAAATAACAAT
53283776 A-AAAAAA
1 ATAAAAAA
53283783 TATATATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.27
16 10 0.45
17 6 0.27
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (16 bp):
ATAAAAAAATAACAAT
Found at i:53300678 original size:46 final size:45
Alignment explanation
Indices: 53300583--53300753 Score: 168
Period size: 46 Copynumber: 3.7 Consensus size: 45
53300573 TCTCGTAGCT
* * * *
53300583 GATGCATGTCCCAAACATGTCTTACACTGGCT-TACATCTCGAGGTC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTCT-C-TCTCAATGTC
*
53300629 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTCTC-TCTCAATGTC
* * *
53300675 GATGCCATGTCCCAGGCATGGTCATACACTAGCTCTC-AT-AATGTGATC
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCTCTCAA--TG-TC
*
53300723 GATGCATGTGCCAGACATGTCTTACACTAGC
1 GATGCATGTCCCAGACATGTCTTACACTAGC
53300754 ACACAAATGA
Statistics
Matches: 106, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
45 2 0.02
46 55 0.52
47 28 0.26
48 21 0.20
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTCTCTCTCAATGTC
Found at i:53304493 original size:27 final size:27
Alignment explanation
Indices: 53304385--53304502 Score: 121
Period size: 27 Copynumber: 4.4 Consensus size: 27
53304375 GGATAAGTTA
*
53304385 TAGAATTACCGAAATACCTCTT-TAGGA
1 TAGAATTACCGAAATACC-CTTGTAGGG
** * *
53304412 TAGAATTATGGAAATACCCTTATAAGG
1 TAGAATTACCGAAATACCCTTGTAGGG
* *
53304439 TAGAAATACCGAAATACCCCTGTAGGG
1 TAGAATTACCGAAATACCCTTGTAGGG
* * *
53304466 TAGAATTACTGAGATACCCTTGTGGGG
1 TAGAATTACCGAAATACCCTTGTAGGG
*
53304493 TAAAATTACC
1 TAGAATTACC
53304503 ATTTTGCCCC
Statistics
Matches: 73, Mismatches: 17, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
26 3 0.04
27 70 0.96
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.27
Consensus pattern (27 bp):
TAGAATTACCGAAATACCCTTGTAGGG
Found at i:53305091 original size:103 final size:103
Alignment explanation
Indices: 53304912--53305116 Score: 401
Period size: 103 Copynumber: 2.0 Consensus size: 103
53304902 TTTGGTAAAA
*
53304912 AGACTAGGTAAGTACTTTTGATTACTTGGTAAACGTTAGAATGAGAACGAAACCTTAGCAATAGG
1 AGACTAGGTAAGTACTTTTGATTACTTGGTAAACGTTAGAATGAGAACGAAACCTTAGCAATAGC
53304977 TAATAATTACTGAAATACCCTTATGCATGAAAAATTAT
66 TAATAATTACTGAAATACCCTTATGCATGAAAAATTAT
53305015 AGACTAGGTAAGTACTTTTGATTACTTGGTAAACGTTAGAATGAGAACGAAACCTTAGCAATAGC
1 AGACTAGGTAAGTACTTTTGATTACTTGGTAAACGTTAGAATGAGAACGAAACCTTAGCAATAGC
53305080 TAATAATTACTGAAATACCCTTATGCATGAAAAATTA
66 TAATAATTACTGAAATACCCTTATGCATGAAAAATTA
53305117 CGATTTTACC
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 101 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (103 bp):
AGACTAGGTAAGTACTTTTGATTACTTGGTAAACGTTAGAATGAGAACGAAACCTTAGCAATAGC
TAATAATTACTGAAATACCCTTATGCATGAAAAATTAT
Found at i:53305376 original size:26 final size:27
Alignment explanation
Indices: 53305347--53305406 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
53305337 CCACATATAT
*
53305347 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
53305373 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
53305400 ATATCTG
1 ATATCTG
53305407 GCAGGCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:53308955 original size:31 final size:31
Alignment explanation
Indices: 53308920--53308983 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
53308910 CCTTTTCATA
53308920 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
53308951 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
53308982 TT
1 TT
53308984 ACTATAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:53309263 original size:26 final size:25
Alignment explanation
Indices: 53309191--53309274 Score: 100
Period size: 26 Copynumber: 3.4 Consensus size: 25
53309181 CTGAAGCCCT
*
53309191 AGCCTCTTTTAAT-AACTGGGGC-AA
1 AGCC-CTTTTGATAAACTGGGGCAAA
*
53309215 AGCCCTTTTGATAAACTGCGGCAAA
1 AGCCCTTTTGATAAACTGGGGCAAA
* *
53309240 AGCCATTTTCGGTAAACTGGGGCAAA
1 AGCCCTTTT-GATAAACTGGGGCAAA
53309266 AGCCCTTTT
1 AGCCCTTTT
53309275 TGCACTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
23 7 0.14
24 12 0.24
25 10 0.20
26 22 0.43
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (25 bp):
AGCCCTTTTGATAAACTGGGGCAAA
Found at i:53309357 original size:19 final size:20
Alignment explanation
Indices: 53309322--53309367 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 20
53309312 TTATGAATAC
53309322 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
53309342 ATCATGTGCA-ATCATACAT
1 ATCATGTGCATATCATACAT
53309361 ATCATGT
1 ATCATGT
53309368 ATATCAGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.35
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:53311956 original size:39 final size:39
Alignment explanation
Indices: 53311901--53312078 Score: 225
Period size: 39 Copynumber: 4.6 Consensus size: 39
53311891 TTCCAACCCA
* *
53311901 AATGCCTTCGGAACTTAGCCCGGATATAACATCAACACG
1 AATGCCTTCGGGACTTAGCCCGGATATAATATCAACACG
* * *
53311940 AATGCCTTCGGGACTTAGCCCAGATATAATATCAGCATG
1 AATGCCTTCGGGACTTAGCCCGGATATAATATCAACACG
* *
53311979 AATGCCTTCGGAACTTAGCCCGGATATAATACCAACACG
1 AATGCCTTCGGGACTTAGCCCGGATATAATATCAACACG
* *
53312018 AATGCCTTCGGGACTTAGCCTGGATATAA-ATCTCACAC-
1 AATGCCTTCGGGACTTAGCCCGGATATAATATC-AACACG
* * *
53312056 AAGGCCTGCGGGTCTTAGCCCGG
1 AATGCCTTCGGGACTTAGCCCGG
53312079 TTAAAATCCT
Statistics
Matches: 120, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
38 21 0.17
39 99 0.82
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.22
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAGCCCGGATATAATATCAACACG
Found at i:53312030 original size:78 final size:78
Alignment explanation
Indices: 53311901--53312046 Score: 256
Period size: 78 Copynumber: 1.9 Consensus size: 78
53311891 TTCCAACCCA
*
53311901 AATGCCTTCGGAACTTAGCCCGGATATAACATCAACACGAATGCCTTCGGGACTTAGCCCAGATA
1 AATGCCTTCGGAACTTAGCCCGGATATAACACCAACACGAATGCCTTCGGGACTTAGCCCAGATA
53311966 TAATATCAGCATG
66 TAATATCAGCATG
* **
53311979 AATGCCTTCGGAACTTAGCCCGGATATAATACCAACACGAATGCCTTCGGGACTTAGCCTGGATA
1 AATGCCTTCGGAACTTAGCCCGGATATAACACCAACACGAATGCCTTCGGGACTTAGCCCAGATA
53312044 TAA
66 TAA
53312047 ATCTCACACA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 64 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (78 bp):
AATGCCTTCGGAACTTAGCCCGGATATAACACCAACACGAATGCCTTCGGGACTTAGCCCAGATA
TAATATCAGCATG
Found at i:53326079 original size:39 final size:39
Alignment explanation
Indices: 53326036--53326209 Score: 147
Period size: 40 Copynumber: 4.4 Consensus size: 39
53326026 CCTACGGGAA
* * *
53326036 TTTAAACCCGGTATAATACCAACTCGTAGCCTGCGGGTC
1 TTTAAGCCCGGTATAATACCAACACGAAGCCTGCGGGTC
* * *
53326075 TTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGGTC
1 TTTAAGCCCGG-TATAATACCAACACGAAGCCTGCGGGTC
* * * * *
53326115 TTTAAGCCCGG-ATAACATTCTAC-CATATAGCCTACGGGTC
1 TTTAAGCCCGGTATAATA-CCAACAC-GA-AGCCTGCGGGTC
* * * *
53326155 TTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCAGGTC
1 TTTAAGCCCGG-TATAATACCAACACGAAGCCTGCGGGTC
53326195 TTTAAGCCCGG-ATAA
1 TTTAAGCCCGGTATAA
53326210 CATTCCTCAA
Statistics
Matches: 104, Mismatches: 24, Indels: 15
0.73 0.17 0.10
Matches are distributed among these distances:
38 7 0.07
39 13 0.12
40 77 0.74
41 3 0.03
42 4 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (39 bp):
TTTAAGCCCGGTATAATACCAACACGAAGCCTGCGGGTC
Found at i:53326157 original size:80 final size:80
Alignment explanation
Indices: 53326062--53326214 Score: 288
Period size: 80 Copynumber: 1.9 Consensus size: 80
53326052 TACCAACTCG
* *
53326062 TAGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGA
1 TAGCCTACGGGTCTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCAGGTCTTTAAGCCCGGA
53326127 TAACATTCTACCATA
66 TAACATTCTACCATA
53326142 TAGCCTACGGGTCTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCAGGTCTTTAAGCCCGGA
1 TAGCCTACGGGTCTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCAGGTCTTTAAGCCCGGA
53326207 TAACATTC
66 TAACATTC
53326215 CTCAAGTATC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 71 1.00
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (80 bp):
TAGCCTACGGGTCTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCAGGTCTTTAAGCCCGGA
TAACATTCTACCATA
Found at i:53326215 original size:40 final size:40
Alignment explanation
Indices: 53326063--53326208 Score: 215
Period size: 40 Copynumber: 3.6 Consensus size: 40
53326053 ACCAACTCGT
53326063 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGA
1 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGA
* * *
53326103 AGCCTGCGGGTCTTTAAGCCCGGATA-ACATTCTACCA-TA
1 AGCCTGCGGGTCTTTAAGCCCGGATACA-ATTCCAGCACGA
*
53326142 TAGCCTACGGGTCTTTAAGCCCGGATACAATTCCAGCACGA
1 -AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGA
*
53326183 AGCCTGCAGGTCTTTAAGCCCGGATA
1 AGCCTGCGGGTCTTTAAGCCCGGATA
53326209 ACATTCCTCA
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
39 2 0.02
40 89 0.96
41 2 0.02
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGA
Found at i:53327642 original size:24 final size:24
Alignment explanation
Indices: 53327610--53327655 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
53327600 ATCATCTCAA
53327610 TTATGCATAAATTTTCAAGAATAG
1 TTATGCATAAATTTTCAAGAATAG
*
53327634 TTATGCATAATTTTTCAAGAAT
1 TTATGCATAAATTTTCAAGAAT
53327656 GGCATAGTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (24 bp):
TTATGCATAAATTTTCAAGAATAG
Found at i:53340666 original size:7 final size:7
Alignment explanation
Indices: 53340637--53340676 Score: 50
Period size: 6 Copynumber: 6.1 Consensus size: 7
53340627 TTAGAAAGAA
53340637 AAGAAAG
1 AAGAAAG
53340644 AA-AAAG
1 AAGAAAG
53340650 AA-AAAG
1 AAGAAAG
53340656 -AGAAAG
1 AAGAAAG
53340662 AAGAAAG
1 AAGAAAG
*
53340669 GAGAAAG
1 AAGAAAG
53340676 A
1 A
53340677 CGCACGACCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 1 0.03
6 14 0.48
7 14 0.48
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (7 bp):
AAGAAAG
Found at i:53350962 original size:139 final size:138
Alignment explanation
Indices: 53350694--53351109 Score: 494
Period size: 139 Copynumber: 3.0 Consensus size: 138
53350684 TCCTAAGACG
* * * * *
53350694 ACACTTTTGGGCTGACACTTTCTTAAGTGTTGGAATAGACTTGCCGATATACGTTTTGGTCAATT
1 ACACTTTTGGGCTG-CACTTTCCTAAGTGTTGGAATGGACTTGCCGACATACGTTTTGGCCAACT
* * *
53350759 CTTTGTATAAGGGTAGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTGGCTTTGTCCAA
65 CTTTGTATAAGGCT-GGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTTTCCAA
53350824 CACTATGCCA
129 CACTATGCCA
* * *
53350834 ACACTTTTGGGTTGCACTTTCCTAAGTGTTGGAATGGACTTGTCGACATACGCTTTGGCCAACTC
1 ACACTTTTGGGCTGCACTTTCCTAAGTGTTGGAATGGACTTGCCGACATACGTTTTGGCCAACTC
*
53350899 TTTGTATAATGGCTGGGATATGCATGCCTAAGGCAATGCTTAAATAAGAGTCGGCTTTTTCCAAC
66 TTTGTATAA-GGCTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTTTCCAAC
* *
53350964 ACTATGTCG
130 ACTATGCCA
** * * * * *
53350973 ACACTTTTGGGCCAACACATTCCTAAGTCTTGGGATAGG-CTTGCCAACATACATTTTGGCCAAC
1 ACACTTTTGGG-CTGCACTTTCCTAAGTGTTGGAAT-GGACTTGCCGACATACGTTTTGGCCAAC
* * * * * * *
53351037 TCTTTTTATAAGGGGTTGAGAAATGTATGCCTAAGGCAACACTTAAATAAGAGTCAGCTTTGTT-
64 TCTTTGTATAA--GGCTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTT-TTC
53351101 CAACACTAT
126 CAACACTAT
53351110 AACGACTTCT
Statistics
Matches: 238, Mismatches: 33, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
139 119 0.50
140 65 0.27
141 52 0.22
142 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (138 bp):
ACACTTTTGGGCTGCACTTTCCTAAGTGTTGGAATGGACTTGCCGACATACGTTTTGGCCAACTC
TTTGTATAAGGCTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTTTCCAACA
CTATGCCA
Found at i:53351729 original size:35 final size:35
Alignment explanation
Indices: 53351682--53351995 Score: 260
Period size: 35 Copynumber: 9.0 Consensus size: 35
53351672 CAACCCACCT
* *
53351682 CCCCAACCTTTTTAAGTTTGCCTTAGACGACTCTA
1 CCCCAACCTTTTTAAGGTTGCCTTAGACGAGTCTA
* * * * *
53351717 GCCCAATCTTTTTAA-GTTCGTCTTAGATG-GTGTA
1 CCCCAACCTTTTTAAGGTT-GCCTTAGACGAGTCTA
* * **
53351751 CCCCAATCTTTTTCAGGTTGCCTTAGACGAGTCCG
1 CCCCAACCTTTTTAAGGTTGCCTTAGACGAGTCTA
* * *
53351786 CCCTAACTTTTTTAAGGTTGCCTTAAAC-AGGTCTA
1 CCCCAACCTTTTTAAGGTTGCCTTAGACGA-GTCTA
* * * *
53351821 TCCCGACCTTTTTATGGTTGCCTTAGACGGGTCTA
1 CCCCAACCTTTTTAAGGTTGCCTTAGACGAGTCTA
* * **
53351856 CCCCGACCCTTTTAAGGTTGCCTTAGGTGAGTCTA
1 CCCCAACCTTTTTAAGGTTGCCTTAGACGAGTCTA
** * * ** *
53351891 TGCCAACATTTTTATGGTTGTTTTAAAC-AGGTCTA
1 CCCCAACCTTTTTAAGGTTGCCTTAGACGA-GTCTA
* *
53351926 CCCTAACCTCTTTT-AGGTTGCCTTAGAAGAGTCTA
1 CCCCAACCT-TTTTAAGGTTGCCTTAGACGAGTCTA
* *
53351961 CCCCAACCTTTTTTAGGTTGCCTTAGACGGGTCTA
1 CCCCAACCTTTTTAAGGTTGCCTTAGACGAGTCTA
53351996 TCCTAACATT
Statistics
Matches: 213, Mismatches: 57, Indels: 18
0.74 0.20 0.06
Matches are distributed among these distances:
34 32 0.15
35 176 0.83
36 5 0.02
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (35 bp):
CCCCAACCTTTTTAAGGTTGCCTTAGACGAGTCTA
Found at i:53351904 original size:105 final size:105
Alignment explanation
Indices: 53351749--53352008 Score: 301
Period size: 105 Copynumber: 2.5 Consensus size: 105
53351739 TTAGATGGTG
* * * *** *
53351749 TACCCCAATCTTTTTCAGGTTGCCTTAGACGAGTCCGCCCTAACTTTTTTAAGGTTGCCTTAAAC
1 TACCCCAACCCTTTTAAGGTTGCCTTAGACGAGTCTATCCTAACATTTTTAAGGTTGCCTTAAAC
* * *
53351814 AGGTCTATCCC-GACCT-TTTTATGGTTGCCTTAGACGGGTC
66 AGGTCTA-CCCTAACCTCTTTTA-GGTTGCCTTAGAAGAGTC
* ** * **
53351854 TACCCCGACCCTTTTAAGGTTGCCTTAGGTGAGTCTATGCC-AACATTTTTATGGTTGTTTTAAA
1 TACCCCAACCCTTTTAAGGTTGCCTTAGACGAGTCTAT-CCTAACATTTTTAAGGTTGCCTTAAA
53351918 CAGGTCTACCCTAACCTCTTTTAGGTTGCCTTAGAAGAGTC
65 CAGGTCTACCCTAACCTCTTTTAGGTTGCCTTAGAAGAGTC
* * *
53351959 TACCCCAACCTTTTTTAGGTTGCCTTAGACGGGTCTATCCTAACATTTTT
1 TACCCCAACCCTTTTAAGGTTGCCTTAGACGAGTCTATCCTAACATTTTT
53352009 TTAGTCGAGT
Statistics
Matches: 129, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
104 5 0.04
105 117 0.91
106 7 0.05
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (105 bp):
TACCCCAACCCTTTTAAGGTTGCCTTAGACGAGTCTATCCTAACATTTTTAAGGTTGCCTTAAAC
AGGTCTACCCTAACCTCTTTTAGGTTGCCTTAGAAGAGTC
Found at i:53352223 original size:35 final size:35
Alignment explanation
Indices: 53352146--53352223 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 35
53352136 TTTTATTTTG
* * * *
53352146 ACCTTTTTTTGTGTCGTTGATTTCTTCCTATTCCG
1 ACCTTTTTTTGGGTCATTGATTTCCTCCTATTCCA
* *
53352181 ACC-TTTTTTGGGTCATTTATTTCCTCTTATTCCA
1 ACCTTTTTTTGGGTCATTGATTTCCTCCTATTCCA
53352215 ACCTTTTTT
1 ACCTTTTTT
53352224 AAAGGTCGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
34 28 0.78
35 8 0.22
ACGTcount: A:0.12, C:0.23, G:0.10, T:0.55
Consensus pattern (35 bp):
ACCTTTTTTTGGGTCATTGATTTCCTCCTATTCCA
Found at i:53353286 original size:22 final size:21
Alignment explanation
Indices: 53353258--53353308 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
53353248 TTTAAAACAA
53353258 TAATTATGTTTTA-AAATACTAT
1 TAATTAT-TTTTACAAA-ACTAT
53353280 TAATTA-TTTTACAAAACTAT
1 TAATTATTTTTACAAAACTAT
53353300 TCAATTATT
1 T-AATTATT
53353309 AAACTACTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 11 0.42
21 8 0.31
22 7 0.27
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (21 bp):
TAATTATTTTTACAAAACTAT
Found at i:53353298 original size:20 final size:21
Alignment explanation
Indices: 53353266--53353308 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
53353256 AATAATTATG
53353266 TTTTAAAATACTATT-AATTA
1 TTTTAAAATACTATTCAATTA
53353286 TTTTACAAA-ACTATTCAATTA
1 TTTTA-AAATACTATTCAATTA
53353307 TT
1 TT
53353309 AAACTACTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTAAAATACTATTCAATTA
Found at i:53353307 original size:21 final size:20
Alignment explanation
Indices: 53353266--53353337 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 20
53353256 AATAATTATG
53353266 TTTTAAAATACTATTAATTA
1 TTTTAAAATACTATTAATTA
53353286 TTTTACAAA-ACTATTCAATTA
1 TTTTA-AAATACTATT-AATTA
*
53353307 --TTAAACTACTATT-ATT-
1 TTTTAAAATACTATTAATTA
**
53353323 TTTTACCATACTATT
1 TTTTAAAATACTATT
53353338 TAAAAAAGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
17 3 0.07
18 12 0.28
19 9 0.21
20 11 0.26
21 8 0.19
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTTAAAATACTATTAATTA
Found at i:53354166 original size:28 final size:28
Alignment explanation
Indices: 53354099--53354156 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
53354089 CTCAGGATCA
*
53354099 AAATAA-TATATCAGTTTAAATATTATT
1 AAATAATTAAATCAGTTTAAATATTATT
* *
53354126 TAATAATTAAATCATTTTAAATATTATT
1 AAATAATTAAATCAGTTTAAATATTATT
53354154 AAA
1 AAA
53354157 ATCATTAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (28 bp):
AAATAATTAAATCAGTTTAAATATTATT
Found at i:53359394 original size:29 final size:29
Alignment explanation
Indices: 53359355--53359433 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
53359345 CTTAATAATC
*
53359355 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
* *
53359385 AACTCGCACAGTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
* *
53359414 AGCCCGCACACTTAATGCCA
1 AACCCGCACACTTAGTGCCA
53359434 ATCTCACAAC
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
28 3 0.07
29 35 0.85
30 3 0.07
ACGTcount: A:0.29, C:0.32, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:53369264 original size:29 final size:27
Alignment explanation
Indices: 53369246--53369315 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
53369236 ATATTAAGTC
53369246 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
53369273 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
53369301 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
53369316 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:53369309 original size:28 final size:28
Alignment explanation
Indices: 53369246--53369343 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
53369236 ATATTAAGTC
*
53369246 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
53369273 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
53369301 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
53369330 CGCACACTTAGTGC
1 CGCACACTTAGTGC
53369344 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:53373296 original size:30 final size:30
Alignment explanation
Indices: 53373262--53373321 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
53373252 TAATTTAGGA
53373262 TCTAAATTTAACTCCTTAATTACCCAATAT
1 TCTAAATTTAACTCCTTAATTACCCAATAT
53373292 TCTAAATTTAACTCCTTAATTACCCAATAT
1 TCTAAATTTAACTCCTTAATTACCCAATAT
53373322 GCTTTCCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (30 bp):
TCTAAATTTAACTCCTTAATTACCCAATAT
Found at i:53377511 original size:53 final size:54
Alignment explanation
Indices: 53377448--53377655 Score: 240
Period size: 53 Copynumber: 3.9 Consensus size: 54
53377438 TTTCCTTTTT
* * * * * *
53377448 GAACTTACCATTGCCATGTCTTGACATGGCCTTACGTGGTATCCTTGCCTTAT-
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATA
* * **
53377501 GAACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATA
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCC-TTGCCTTATA
* * *
53377555 GTAACTCATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATA
1 G-AACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATA
* * *
53377610 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTT
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTT
53377656 ATCTTACCAA
Statistics
Matches: 134, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
52 2 0.01
53 44 0.33
54 42 0.31
55 44 0.33
56 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (54 bp):
GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATA
Found at i:53377584 original size:55 final size:53
Alignment explanation
Indices: 53377459--53377647 Score: 227
Period size: 55 Copynumber: 3.5 Consensus size: 53
53377449 AACTTACCAT
* * * * *
53377459 TGCCATGTCTTGACATGGCCTTACGTGGTATCCTTGCCTTAT-GAACTCACCAT
1 TGCCATGCCTTGACATGGTCTTACATGGTA-CCTTGCCTTATAGAACTCATCAA
* *
53377512 TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
1 TGCCATGCCTTGACATGGTCTTACATGGTACC-TTGCCTTATAG-AACTCATCAA
* * * *
53377567 TGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAA
1 TGCCATGCCTTGACATGGTCTTACATG-GTACCTTGCCTTATAGAACTCATCAA
*
53377621 TGCCATGCCTTGGCATGGTCTTACATG
1 TGCCATGCCTTGACATGGTCTTACATG
53377648 ATATCCTTAT
Statistics
Matches: 117, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
52 2 0.02
53 34 0.29
54 35 0.30
55 44 0.38
56 2 0.02
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (53 bp):
TGCCATGCCTTGACATGGTCTTACATGGTACCTTGCCTTATAGAACTCATCAA
Found at i:53377782 original size:95 final size:95
Alignment explanation
Indices: 53377683--53377888 Score: 412
Period size: 95 Copynumber: 2.2 Consensus size: 95
53377673 TTTCCAAACC
53377683 TGGTCTTACATGGTATCCTTGTCTTAGTGCTAATTCCACATCTTGATGTGGTCTTACATAGAGTC
1 TGGTCTTACATGGTATCCTTGTCTTAGTGCTAATTCCACATCTTGATGTGGTCTTACATAGAGTC
53377748 CTTAATCAATGCCGATGCCATGTCTTGACA
66 CTTAATCAATGCCGATGCCATGTCTTGACA
53377778 TGGTCTTACATGGTATCCTTGTCTTAGTGCTAATTCCACATCTTGATGTGGTCTTACATAGAGTC
1 TGGTCTTACATGGTATCCTTGTCTTAGTGCTAATTCCACATCTTGATGTGGTCTTACATAGAGTC
53377843 CTTAATCAATGCCGATGCCATGTCTTGACA
66 CTTAATCAATGCCGATGCCATGTCTTGACA
53377873 TGGTCTTACATGGTAT
1 TGGTCTTACATGGTAT
53377889 TCTTAACCAT
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 111 1.00
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.37
Consensus pattern (95 bp):
TGGTCTTACATGGTATCCTTGTCTTAGTGCTAATTCCACATCTTGATGTGGTCTTACATAGAGTC
CTTAATCAATGCCGATGCCATGTCTTGACA
Found at i:53377845 original size:48 final size:48
Alignment explanation
Indices: 53377683--53377838 Score: 174
Period size: 48 Copynumber: 3.3 Consensus size: 48
53377673 TTTCCAAACC
*
53377683 TGGTCTTACATGGTATCCTTGTCTTAGTGCTAATTCCACATCTTGATG
1 TGGTCTTACATAGTATCCTTGTCTTAGTGCTAATTCCACATCTTGATG
* * ** * ** **
53377731 TGGTCTTACATAG-AGTCCTTAATC--AATGCCGATGCCATGTCTTGACA
1 TGGTCTTACATAGTA-TCCTT-GTCTTAGTGCTAATTCCACATCTTGATG
*
53377778 TGGTCTTACATGGTATCCTTGTCTTAGTGCTAATTCCACATCTTGATG
1 TGGTCTTACATAGTATCCTTGTCTTAGTGCTAATTCCACATCTTGATG
53377826 TGGTCTTACATAG
1 TGGTCTTACATAG
53377839 AGTCCTTAAT
Statistics
Matches: 82, Mismatches: 21, Indels: 10
0.73 0.19 0.09
Matches are distributed among these distances:
46 2 0.02
47 33 0.40
48 45 0.55
49 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (48 bp):
TGGTCTTACATAGTATCCTTGTCTTAGTGCTAATTCCACATCTTGATG
Found at i:53377894 original size:47 final size:47
Alignment explanation
Indices: 53377731--53377883 Score: 175
Period size: 47 Copynumber: 3.2 Consensus size: 47
53377721 CATCTTGATG
53377731 TGGTCTTACATAGAGTCCTTAATCAATGCCGATGCCATGTCTTGACA
1 TGGTCTTACATAGAGTCCTTAATCAATGCCGATGCCATGTCTTGACA
* * * ** * ** **
53377778 TGGTCTTACATGGTA-TCCTT-GTCTTAGTGCTAATTCCACATCTTGATG
1 TGGTCTTACATAG-AGTCCTTAATC--AATGCCGATGCCATGTCTTGACA
53377826 TGGTCTTACATAGAGTCCTTAATCAATGCCGATGCCATGTCTTGACA
1 TGGTCTTACATAGAGTCCTTAATCAATGCCGATGCCATGTCTTGACA
53377873 TGGTCTTACAT
1 TGGTCTTACAT
53377884 GGTATTCTTA
Statistics
Matches: 81, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
46 2 0.02
47 44 0.54
48 33 0.41
49 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (47 bp):
TGGTCTTACATAGAGTCCTTAATCAATGCCGATGCCATGTCTTGACA
Found at i:53377963 original size:43 final size:43
Alignment explanation
Indices: 53377898--53377980 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
53377888 TTCTTAACCA
* *
53377898 TCAATTCCTCCTTAAATGCCATGTTATGAA-CATGGACTTTCCG
1 TCAATTCCTCCTTAAATGCCATGGTA-CAACCATGGACTTTCCG
* * *
53377941 TCAATTCTTCCTTAATTTCCATGGTACAACCATGGACTTT
1 TCAATTCCTCCTTAAATGCCATGGTACAACCATGGACTTT
53377981 AAGATATCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 2 0.06
43 32 0.94
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.37
Consensus pattern (43 bp):
TCAATTCCTCCTTAAATGCCATGGTACAACCATGGACTTTCCG
Found at i:53379829 original size:49 final size:49
Alignment explanation
Indices: 53379664--53379884 Score: 237
Period size: 49 Copynumber: 4.4 Consensus size: 49
53379654 GAGGTCACAT
* * * * * *
53379664 GTGTAGTACTAAGTGCAGGCTACTATGCGTACTCGAAAACTGTGATCACGT
1 GTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAA-T-TGGTCACGC
* * ** *
53379715 GTGTAGTACTAAGTGCAAGCTACTACGTGTA-TCAGATGGTTAGGTCACGT
1 GTGTAGTACTAAGTGCAGGCTACTACGTGTACT-GGATAATT-GGTCACGC
* *
53379765 GTGTACTATTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCACGC
1 GTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCACGC
* * *
53379814 GTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCAC
1 GTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCACGC
* *
53379863 GTGTAGTACTATGCGCAGGCTA
1 GTGTAGTACTAAGTGCAGGCTA
53379885 GTATGCGTAC
Statistics
Matches: 145, Mismatches: 22, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
49 72 0.50
50 42 0.29
51 31 0.21
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.29
Consensus pattern (49 bp):
GTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCACGC
Found at i:53383727 original size:49 final size:48
Alignment explanation
Indices: 53383597--53383741 Score: 191
Period size: 49 Copynumber: 2.9 Consensus size: 48
53383587 TCTATTGTGA
* *
53383597 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTA-CC--AGATTGT
* * * * *
53383648 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATTG-T
53383697 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGAT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGAT
53383742 AGCTTCGGCT
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
48 4 0.05
49 41 0.51
50 2 0.02
51 34 0.42
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (48 bp):
GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATTGT
Found at i:53387323 original size:17 final size:17
Alignment explanation
Indices: 53387301--53387337 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
53387291 ACTAATATGG
53387301 TAGTACTTGGGCATATT
1 TAGTACTTGGGCATATT
53387318 TAGTACTTGGGCATATT
1 TAGTACTTGGGCATATT
53387335 TAG
1 TAG
53387338 GCAATAGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.41
Consensus pattern (17 bp):
TAGTACTTGGGCATATT
Found at i:53393008 original size:40 final size:40
Alignment explanation
Indices: 53392944--53393032 Score: 135
Period size: 40 Copynumber: 2.2 Consensus size: 40
53392934 ATCAGACGAT
* *
53392944 TTATTCAT-TTGACTTAATCTGTAGAAATCCCTATGTTATA
1 TTATT-ATCTTGACTTAATCCGTAGAAATCCCTAAGTTATA
*
53392984 TTATTATCTTGACTTGATCCGTAGAAATCCCTAAGTTATA
1 TTATTATCTTGACTTAATCCGTAGAAATCCCTAAGTTATA
53393024 TTATTATCT
1 TTATTATCT
53393033 CGAAACTAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 2 0.04
40 43 0.96
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (40 bp):
TTATTATCTTGACTTAATCCGTAGAAATCCCTAAGTTATA
Found at i:53401945 original size:46 final size:46
Alignment explanation
Indices: 53401878--53402052 Score: 314
Period size: 46 Copynumber: 3.8 Consensus size: 46
53401868 TGTAACCCGC
* * * *
53401878 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
53401924 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
53401970 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
53402016 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
53402053 TGCTCAACCA
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 125 1.00
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:53406701 original size:20 final size:20
Alignment explanation
Indices: 53406676--53406727 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
53406666 CGAGTAAGGG
53406676 ACACGGGCGTGTCCCAAAGC
1 ACACGGGCGTGTCCCAAAGC
* *
53406696 ACACGGGCATTTCCCAAAGC
1 ACACGGGCGTGTCCCAAAGC
*
53406716 ACACGGGTGTGT
1 ACACGGGCGTGT
53406728 GCATTGCCTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.31, G:0.29, T:0.15
Consensus pattern (20 bp):
ACACGGGCGTGTCCCAAAGC
Found at i:53411557 original size:28 final size:29
Alignment explanation
Indices: 53411526--53411586 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
53411516 TTTGGGTTGG
53411526 ATGGGCCAGAAAAATGAG-ATTGGGCCTA
1 ATGGGCCAGAAAAATGAGAATTGGGCCTA
* * * *
53411554 ATGGGCCATAAGAATGTGAATTGGGCCTG
1 ATGGGCCAGAAAAATGAGAATTGGGCCTA
53411583 ATGG
1 ATGG
53411587 ACTATATGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.31, C:0.13, G:0.34, T:0.21
Consensus pattern (29 bp):
ATGGGCCAGAAAAATGAGAATTGGGCCTA
Found at i:53411586 original size:29 final size:28
Alignment explanation
Indices: 53411525--53411649 Score: 85
Period size: 29 Copynumber: 4.4 Consensus size: 28
53411515 GTTTGGGTTG
* *
53411525 GATGGGCCAGAAAAATGAGATTGGGCCT
1 GATGGGCCATAAGAATGAGATTGGGCCT
* *
53411553 AATGGGCCATAAGAATGTGAATTGGGCCT
1 GATGGGCCATAAGAATGAG-ATTGGGCCT
* * * *
53411582 GATGGACTATATGAACGTGA-ATTAGG-CT
1 GATGGGCCATAAGAA--TGAGATTGGGCCT
*
53411610 GGATAGGCCATATA-AATGAGATTGGGCCT
1 -GATGGGCCATA-AGAATGAGATTGGGCCT
* *
53411639 AATGGACCATA
1 GATGGGCCATA
53411650 TGCATGCATA
Statistics
Matches: 72, Mismatches: 18, Indels: 14
0.69 0.17 0.13
Matches are distributed among these distances:
27 3 0.04
28 30 0.42
29 37 0.51
31 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Consensus pattern (28 bp):
GATGGGCCATAAGAATGAGATTGGGCCT
Found at i:53430220 original size:43 final size:45
Alignment explanation
Indices: 53430171--53430296 Score: 161
Period size: 43 Copynumber: 2.9 Consensus size: 45
53430161 GATTACCGAG
* *
53430171 ATGTGATTACCTGTAAGACCATGTTTGGGACATTGGCATTG-TAT
1 ATGTGATTACGTGTAAGACCATGTTTGGGACATTGGCATCGTTAT
* * * *
53430215 -TGTGATTACGTGTAAGACCATGTCTGGGATAATGGTATCGTTAT
1 ATGTGATTACGTGTAAGACCATGTTTGGGACATTGGCATCGTTAT
*
53430259 ATG-G-TTTCGTGTAAGACCATGTTTGGGACATTGGCATC
1 ATGTGATTACGTGTAAGACCATGTTTGGGACATTGGCATC
53430297 AACAAGTGAT
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
43 63 0.91
44 4 0.06
45 2 0.03
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (45 bp):
ATGTGATTACGTGTAAGACCATGTTTGGGACATTGGCATCGTTAT
Found at i:53432693 original size:26 final size:26
Alignment explanation
Indices: 53432657--53432710 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
53432647 CATTTATTGG
* *
53432657 TATCAGAGCTACGGTTTAGTCAATTT
1 TATCAGAGCTACGATTTAATCAATTT
*
53432683 TATCAGAGCTACGATTTAATCGATTT
1 TATCAGAGCTACGATTTAATCAATTT
53432709 TA
1 TA
53432711 GGACTAACGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.39
Consensus pattern (26 bp):
TATCAGAGCTACGATTTAATCAATTT
Found at i:53444483 original size:63 final size:67
Alignment explanation
Indices: 53444341--53444488 Score: 157
Period size: 63 Copynumber: 2.3 Consensus size: 67
53444331 GAGTGCACAT
* * **
53444341 CATGTGTACAAGAGAGCTACGAGATACTATGTAGTAGCTAGGTCACATGTGTGATACGGGATGTA
1 CATGTGTACAAGAGAGCTACGAGATACAATGTAG-AGCTAGGTCACATGGGTGATACAAGATGTA
53444406 TCC
65 TCC
* *
53444409 CATGTAG-ACAAGAGAGCTATGAGATA-AAT-T-G-GCTAGGTCACATGGGTGGTACTAAG-TGT
1 CATGT-GTACAAGAGAGCTACGAGATACAATGTAGAGCTAGGTCACATGGGTGATAC-AAGATGT
53444468 -TCAC
64 ATC-C
53444472 CATGTGTACAAGAGAGC
1 CATGTGTACAAGAGAGC
53444489 CAAATTATAT
Statistics
Matches: 70, Mismatches: 6, Indels: 13
0.79 0.07 0.15
Matches are distributed among these distances:
62 3 0.04
63 38 0.54
64 1 0.01
65 1 0.01
66 1 0.01
67 2 0.03
68 23 0.33
69 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (67 bp):
CATGTGTACAAGAGAGCTACGAGATACAATGTAGAGCTAGGTCACATGGGTGATACAAGATGTAT
CC
Found at i:53446811 original size:73 final size:73
Alignment explanation
Indices: 53446692--53446833 Score: 275
Period size: 73 Copynumber: 1.9 Consensus size: 73
53446682 ATCACAATGG
*
53446692 GATTTTCAGCAGAGGTCTTGGAAGATCTAGTCCTTTTGCGAGATGTAGACATTTTTCTCGAAGAA
1 GATTTTCAGCACAGGTCTTGGAAGATCTAGTCCTTTTGCGAGATGTAGACATTTTTCTCGAAGAA
53446757 TAAGTTGT
66 TAAGTTGT
53446765 GATTTTCAGCACAGGTCTTGGAAGATCTAGTCCTTTTGCGAGATGTAGACATTTTTCTCGAAGAA
1 GATTTTCAGCACAGGTCTTGGAAGATCTAGTCCTTTTGCGAGATGTAGACATTTTTCTCGAAGAA
53446830 TAAG
66 TAAG
53446834 AAAAAAATTG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.35
Consensus pattern (73 bp):
GATTTTCAGCACAGGTCTTGGAAGATCTAGTCCTTTTGCGAGATGTAGACATTTTTCTCGAAGAA
TAAGTTGT
Found at i:53455232 original size:12 final size:13
Alignment explanation
Indices: 53455200--53455232 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
53455190 ACTTACTAGT
53455200 ATTTAATTCTATA
1 ATTTAATTCTATA
53455213 ATTT-ATTCTA-A
1 ATTTAATTCTATA
53455224 ATTTAATTC
1 ATTTAATTC
53455233 AACTTACACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.26
12 10 0.53
13 4 0.21
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTTAATTCTATA
Found at i:53455608 original size:49 final size:49
Alignment explanation
Indices: 53455536--53455759 Score: 272
Period size: 49 Copynumber: 4.5 Consensus size: 49
53455526 CTAGTACGCA
* *
53455536 TAGTAGCCTGTACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGATACACG
* * ** *
53455585 TAGTAGCCTGCACTTAGTACTACACATGTGACTTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGAC-CAATTATCCGATACACG
* * * * * *
53455635 TAGTAG-CTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCCG
1 TAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TTATCCGATAC-ACG
*
53455686 -AGTAGCCTGCACTTAGTACTATACATGCGACCAATTATCCGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGATACACG
53455734 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
53455760 CATGACCTCA
Statistics
Matches: 147, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
48 2 0.01
49 88 0.60
50 34 0.23
51 23 0.16
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGATACACG
Found at i:53455681 original size:100 final size:98
Alignment explanation
Indices: 53455536--53455760 Score: 292
Period size: 100 Copynumber: 2.3 Consensus size: 98
53455526 CTAGTACGCA
* *
53455536 TAGTAGCCTGTACTTAGTACTACACATGCGACCAATTATCCGGTAC-ACGTAGTAGCCTGCACTT
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACGACG-AGTAGCCTGCACTT
* * *
53455600 AGTACTACACATGTGACTTAACCATCTGATACACG
65 AGTACTACACATGCGAC-CAACCATCCGATACACG
* * * *
53455635 TAGTAG-CTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCCGAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCCGGTACGACGAGTAGCCTGCACT
* **
53455699 TAGTACTATACATGCGACCAATTATCCGATACACG
64 TAGTACTACACATGCGACCAACCATCCGATACACG
53455734 TAGTAGCCTGCACTTAGTACTACACAC
1 TAGTAGCCTGCACTTAGTACTACACAC
53455761 ATGACCTCAC
Statistics
Matches: 110, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
98 21 0.19
99 28 0.25
100 59 0.54
101 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (98 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACGACGAGTAGCCTGCACTTA
GTACTACACATGCGACCAACCATCCGATACACG
Found at i:53456569 original size:59 final size:59
Alignment explanation
Indices: 53456498--53456621 Score: 230
Period size: 59 Copynumber: 2.1 Consensus size: 59
53456488 CCGACTAAGC
* *
53456498 CCAAAATCAGGATGTTACGTTTCTCCCCCCTCTAGGGATTTTCATCCCTAAAAATCTTA
1 CCAAAATCAGGATGTTACATTTCTCCCCCCTCTAGGGATTTTCATCCCCAAAAATCTTA
53456557 CCAAAATCAGGATGTTACATTTCTCCCCCCTCTAGGGATTTTCATCCCCAAAAATCTTA
1 CCAAAATCAGGATGTTACATTTCTCCCCCCTCTAGGGATTTTCATCCCCAAAAATCTTA
53456616 CCAAAA
1 CCAAAA
53456622 AAGTGGTTTT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (59 bp):
CCAAAATCAGGATGTTACATTTCTCCCCCCTCTAGGGATTTTCATCCCCAAAAATCTTA
Found at i:53465527 original size:16 final size:16
Alignment explanation
Indices: 53465506--53465546 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
53465496 GTAGATCGAC
* *
53465506 AAAAGCTGAAATGTCG
1 AAAAGCCGAAATGCCG
53465522 AAAAGCCGAAATGCCG
1 AAAAGCCGAAATGCCG
53465538 AAAAGCCGA
1 AAAAGCCGA
53465547 TAGTTTGGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.46, C:0.20, G:0.24, T:0.10
Consensus pattern (16 bp):
AAAAGCCGAAATGCCG
Found at i:53465791 original size:28 final size:29
Alignment explanation
Indices: 53465760--53465906 Score: 149
Period size: 29 Copynumber: 5.2 Consensus size: 29
53465750 GTGAGCATGA
* *
53465760 ATAT-AATGTGATTTGGGCCAAATGGGCC
1 ATATGAATGTGAATTGGGCCTAATGGGCC
*
53465788 ATAT-AA-ATGATATTGGGCCTAATGGGCC
1 ATATGAATGTGA-ATTGGGCCTAATGGGCC
* *
53465816 ATATGAATGTGAATTGGGCTTGATGGGCC
1 ATATGAATGTGAATTGGGCCTAATGGGCC
* **
53465845 ATATGAACGTGAATTGGGCCGGATGGGCC
1 ATATGAATGTGAATTGGGCCTAATGGGCC
* ** *
53465874 ATATAAATAAG-ATTGGGCCTAGTGGGCC
1 ATATGAATGTGAATTGGGCCTAATGGGCC
53465902 ATATG
1 ATATG
53465907 CATATATGTA
Statistics
Matches: 99, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
27 3 0.03
28 43 0.43
29 50 0.51
30 3 0.03
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.27
Consensus pattern (29 bp):
ATATGAATGTGAATTGGGCCTAATGGGCC
Found at i:53473616 original size:29 final size:29
Alignment explanation
Indices: 53473541--53473692 Score: 134
Period size: 29 Copynumber: 5.3 Consensus size: 29
53473531 GTGAGCATGA
* *
53473541 ATAT-AATGTGATTTGGGCCGGATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
* * *
53473569 ATAT-ATATG-GGATTGGGCCTAATAGGCC
1 ATATGA-ATGTGAATTGGGCCTGATGGGCC
53473597 ATATGAATGTGAATTGGGCCTGATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
* ** * *
53473626 ACATGAACCTGAATTGAGCCGGATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
* *
53473655 ATATAAATGAG-ATTGGGCCT-AGTGGGCC
1 ATATGAATGTGAATTGGGCCTGA-TGGGCC
*
53473683 ATATGCATGT
1 ATATGAATGT
53473693 ATGTAGGGGT
Statistics
Matches: 97, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
27 1 0.01
28 46 0.47
29 50 0.52
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
ATATGAATGTGAATTGGGCCTGATGGGCC
Found at i:53476265 original size:29 final size:30
Alignment explanation
Indices: 53476226--53476304 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
53476216 CTTAATAATC
53476226 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
53476256 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
53476285 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
53476305 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:53485478 original size:29 final size:29
Alignment explanation
Indices: 53485415--53485482 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
53485405 TAATCAACCG
53485415 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
53485444 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
53485473 CGCACACTTA
1 CGCACACTTA
53485483 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:53485594 original size:174 final size:174
Alignment explanation
Indices: 53485304--53485631 Score: 620
Period size: 174 Copynumber: 1.9 Consensus size: 174
53485294 AACTCAAGGT
*
53485304 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
53485369 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
53485434 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
53485478 ACTTACCTTTTCCGCTGTCCAAAATTGACTTGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
53485543 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
*
53485608 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
53485632 TGTACAATTT
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 150 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:53485623 original size:29 final size:30
Alignment explanation
Indices: 53485584--53485662 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
53485574 CTTAATAATC
53485584 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
53485614 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
53485643 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
53485663 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:53488515 original size:17 final size:17
Alignment explanation
Indices: 53488493--53488526 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
53488483 ACACGGGAAA
53488493 ATAAAGCTTAGTAAGCT
1 ATAAAGCTTAGTAAGCT
53488510 ATAAAGCTTAGTAAGCT
1 ATAAAGCTTAGTAAGCT
53488527 TGTATACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (17 bp):
ATAAAGCTTAGTAAGCT
Found at i:53490929 original size:16 final size:18
Alignment explanation
Indices: 53490894--53490930 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
53490884 AGTGGTCCTT
*
53490894 ATGCAATTTCTAATCTAA
1 ATGCAATTTCTAACCTAA
53490912 ATGCAATTT-T-ACCTAA
1 ATGCAATTTCTAACCTAA
53490928 ATG
1 ATG
53490931 TATGAATGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 1 0.06
18 9 0.50
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (18 bp):
ATGCAATTTCTAACCTAA
Found at i:53492376 original size:19 final size:17
Alignment explanation
Indices: 53492343--53492389 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
53492333 ATTTCATGTC
53492343 TAAAATTACTATTTAAG
1 TAAAATTACTATTTAAG
*
53492360 TAAAATTCACTTATTTAAA
1 TAAAATT-AC-TATTTAAG
53492379 TAATAATTACT
1 TAA-AATTACT
53492390 CGAGATAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 7 0.27
18 3 0.12
19 12 0.46
20 4 0.15
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.43
Consensus pattern (17 bp):
TAAAATTACTATTTAAG
Found at i:53492799 original size:24 final size:24
Alignment explanation
Indices: 53492771--53492831 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
53492761 GGCATGATTA
53492771 AACTAATAATTCAAGCAAAAAGTT
1 AACTAATAATTCAAGCAAAAAGTT
53492795 AACTAATAATTCAAGCAAAAAGTT
1 AACTAATAATTCAAGCAAAAAGTT
*
53492819 AAGTAA-AATTCAA
1 AACTAATAATTCAA
53492832 TGAAACAGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 7 0.19
24 29 0.81
ACGTcount: A:0.56, C:0.11, G:0.08, T:0.25
Consensus pattern (24 bp):
AACTAATAATTCAAGCAAAAAGTT
Found at i:53496361 original size:45 final size:45
Alignment explanation
Indices: 53496305--53496395 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
53496295 GAACTATGTG
*
53496305 ATCTAAACTCATTGAGTTATGGTTTGAGTTCATGATATATGTGAC
1 ATCTAAACTCATTGAGTTATGGTCTGAGTTCATGATATATGTGAC
* * *
53496350 ATCTGAACTCATTGAGTTGTGGTCTGAGTTCATGATGTATGTGAC
1 ATCTAAACTCATTGAGTTATGGTCTGAGTTCATGATATATGTGAC
53496395 A
1 A
53496396 CATGTTTTGG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.38
Consensus pattern (45 bp):
ATCTAAACTCATTGAGTTATGGTCTGAGTTCATGATATATGTGAC
Found at i:53499708 original size:16 final size:16
Alignment explanation
Indices: 53499687--53499717 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
53499677 CGGTAAATCC
53499687 CGAAATGCCGAAAAGT
1 CGAAATGCCGAAAAGT
53499703 CGAAATGCCGAAAAG
1 CGAAATGCCGAAAAG
53499718 CCAAAAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.19, G:0.26, T:0.10
Consensus pattern (16 bp):
CGAAATGCCGAAAAGT
Done.