Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 43 of 221
Found at i:12053744 original size:44 final size:44
Alignment explanation
Indices: 12053696--12053791 Score: 156
Period size: 44 Copynumber: 2.2 Consensus size: 44
12053686 ATATCTCAAG
*
12053696 GTCCATGTTTATAACATGGCAATTAAGGAAGAATTGACGGAAAA
1 GTCCATGTTTATAACATGGCAATTAAGAAAGAATTGACGGAAAA
* *
12053740 GTCCATGTTTATAACGTGGCAATTAAGAAAGAATTGATGGAAAA
1 GTCCATGTTTATAACATGGCAATTAAGAAAGAATTGACGGAAAA
12053784 GTACCATG
1 GT-CCATG
12053792 GTTGATCAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
44 43 0.90
45 5 0.10
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (44 bp):
GTCCATGTTTATAACATGGCAATTAAGAAAGAATTGACGGAAAA
Found at i:12053869 original size:50 final size:50
Alignment explanation
Indices: 12053809--12054057 Score: 338
Period size: 50 Copynumber: 5.0 Consensus size: 50
12053799 AATGTCAACA
*
12053809 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCAC
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAC
* * *
12053859 CAAGATGAGAGGTCCCATATAAGACCATGTCTGGGACATGGCGTTGGCAC
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAC
* *
12053909 CGAGATGAGAGGTCCCATGAAAGACCATGTTTGGGACATGGCATTGGCAC
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAC
* * *
12053959 CGAGATGAGAGGTCCTC-CGTAAGACCATGTCTGGGACATGGCATGGGCAT
1 CGAGATGAGAGGTCC-CATGTAAGACCATGTCTGGGACATGGCATTGGCAC
* * ** * * *
12054009 CGATATAAGAACTCCCATGTAAGACCATATCTGGGATATGGTATTGGCA
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
12054058 GTACAGGAAA
Statistics
Matches: 176, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
49 1 0.01
50 174 0.99
51 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.21
Consensus pattern (50 bp):
CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAC
Found at i:12060873 original size:9 final size:9
Alignment explanation
Indices: 12060858--12060889 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
12060848 TTTTATATAT
12060858 TTATGTAAG
1 TTATGTAAG
*
12060867 CTATGTAAG
1 TTATGTAAG
12060876 TTATGTAAG
1 TTATGTAAG
12060885 TTATG
1 TTATG
12060890 ATAATCATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.31, C:0.03, G:0.22, T:0.44
Consensus pattern (9 bp):
TTATGTAAG
Found at i:12060951 original size:13 final size:13
Alignment explanation
Indices: 12060933--12060959 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12060923 TGATTATCAT
12060933 CTTTAAATTTTAA
1 CTTTAAATTTTAA
12060946 CTTTAAATTTTAA
1 CTTTAAATTTTAA
12060959 C
1 C
12060960 CCTTTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (13 bp):
CTTTAAATTTTAA
Found at i:12065758 original size:50 final size:50
Alignment explanation
Indices: 12065644--12065886 Score: 297
Period size: 50 Copynumber: 4.8 Consensus size: 50
12065634 GATAATAACA
* * * ** * *
12065644 TGCCAAAGCCATGTCCCAGACATGGTATTACATGGGATGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACGTGGGA-CCTCTCATCTTGG
* * * *
12065695 TGCCCATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATCTTGG
* * * * *
12065745 TGCTAACGCCATGTCCCAGGCATGGTCTTACATGAGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATCTTGG
*
12065795 TGCCAACGCCATGTCCCATACATGGTCTTACGTGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATCTTGG
* * *
12065845 TGCCAACACCATGTCCCAGACATGGTCTTACATGTGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACGTGGGACCTCT
12065887 TTACCCAAAT
Statistics
Matches: 163, Mismatches: 29, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
50 132 0.81
51 31 0.19
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATCTTGG
Found at i:12065812 original size:100 final size:100
Alignment explanation
Indices: 12065644--12065886 Score: 351
Period size: 100 Copynumber: 2.4 Consensus size: 100
12065634 GATAATAACA
* * * ** * *
12065644 TGCCAAAGCCATGTCCCAGACATGGTATTACATGGGATGTTCTCATATCGGTGCCCATGCCATGT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGA-CCTCTCATATCGGTGCCAACGCCATGT
12065709 CCCAAACATGGTCTTACGGGGGACCTCTCATCTTGG
65 CCCAAACATGGTCTTACGGGGGACCTCTCATCTTGG
* * *
12065745 TGCTAACGCCATGTCCCAGGCATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACGCCATGTC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGGTGCCAACGCCATGTC
* *
12065810 CCATACATGGTCTTACGTGGGACCTCTCATCTTGG
66 CCAAACATGGTCTTACGGGGGACCTCTCATCTTGG
* *
12065845 TGCCAACACCATGTCCCAGACATGGTCTTACATGTGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCT
12065887 TTACCCAAAT
Statistics
Matches: 126, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
100 94 0.75
101 32 0.25
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (100 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGGTGCCAACGCCATGTC
CCAAACATGGTCTTACGGGGGACCTCTCATCTTGG
Found at i:12071814 original size:27 final size:27
Alignment explanation
Indices: 12071784--12071838 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
12071774 AGAGGGGACA
*
12071784 GTCGACGGTGATGTAGCAGATGGTCGG
1 GTCGACGGTGATGCAGCAGATGGTCGG
* *
12071811 GTCGATGGTGATGCAGTAGATGGTCGG
1 GTCGACGGTGATGCAGCAGATGGTCGG
12071838 G
1 G
12071839 GAAATATTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.18, C:0.13, G:0.45, T:0.24
Consensus pattern (27 bp):
GTCGACGGTGATGCAGCAGATGGTCGG
Found at i:12072051 original size:11 final size:12
Alignment explanation
Indices: 12072035--12072067 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
12072025 TCACAAAATG
12072035 ATTTCGT-GAAA
1 ATTTCGTCGAAA
12072046 ATTTCGTTCGAAA
1 ATTTCG-TCGAAA
12072059 ATTTCGTCG
1 ATTTCGTCG
12072068 TTTGGGCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 6 0.30
12 4 0.20
13 10 0.50
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.39
Consensus pattern (12 bp):
ATTTCGTCGAAA
Found at i:12072763 original size:56 final size:51
Alignment explanation
Indices: 12072667--12072814 Score: 192
Period size: 56 Copynumber: 2.8 Consensus size: 51
12072657 ATTTGGGTAA
*
12072667 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC--GAG---ATG
*
12072723 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCGAGATG
* * *
12072773 AGAGGTCCC-CGTAAGACCATGTGTGGGACATGGCTTTGGCAT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
12072815 GTTATGATCA
Statistics
Matches: 86, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
49 29 0.34
50 12 0.14
53 3 0.03
55 2 0.02
56 40 0.47
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (51 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCGAGATG
Found at i:12080605 original size:41 final size:42
Alignment explanation
Indices: 12080543--12080652 Score: 154
Period size: 41 Copynumber: 2.7 Consensus size: 42
12080533 CATTGAATGT
*
12080543 AAGGGGTTACTAAGTGAAGATTCCT-CGAATCACTGATCAAA
1 AAGGGGTTGCTAAGTGAAGATTCCTCCGAATCACTGATCAAA
* *
12080584 AAGGGGTCGCTAAGTGCAGATT-CTCCGAATCACTGATCAAA
1 AAGGGGTTGCTAAGTGAAGATTCCTCCGAATCACTGATCAAA
* *
12080625 AAGGGGTTGCCAAGTGTAGATTCC-CCGA
1 AAGGGGTTGCTAAGTGAAGATTCCTCCGA
12080653 GGGGTTGCTA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
40 2 0.03
41 58 0.95
42 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (42 bp):
AAGGGGTTGCTAAGTGAAGATTCCTCCGAATCACTGATCAAA
Found at i:12080665 original size:26 final size:26
Alignment explanation
Indices: 12080626--12080678 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
12080616 CTGATCAAAA
12080626 AGGGGTTGCCAAGTGTAGATTCCCCG
1 AGGGGTTGCCAAGTGTAGATTCCCCG
* *
12080652 AGGGGTTGCTAAGTGTTGATTCCCCG
1 AGGGGTTGCCAAGTGTAGATTCCCCG
12080678 A
1 A
12080679 ATTATTGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.19, C:0.21, G:0.34, T:0.26
Consensus pattern (26 bp):
AGGGGTTGCCAAGTGTAGATTCCCCG
Found at i:12080757 original size:43 final size:42
Alignment explanation
Indices: 12080652--12080766 Score: 137
Period size: 43 Copynumber: 2.7 Consensus size: 42
12080642 AGATTCCCCG
*
12080652 AGGGGTTGCTAAGTGTTGATTCCCCGAAT-TATTGATTCTAA
1 AGGGGTTGCTAAGTGTTGATTCCCCGTATCTATTGATTCTAA
*
12080693 AGGTGGTT-CTTAAGTGTTGATTCCACCGTATCT-TTGATTGTGAA
1 AGG-GGTTGC-TAAGTGTTGATTCC-CCGTATCTATTGATTCT-AA
* *
12080737 AGGGGTTGCTATGTGCTGATTCCCCGTATC
1 AGGGGTTGCTAAGTGTTGATTCCCCGTATC
12080767 ACTGAATAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
41 4 0.06
42 25 0.39
43 28 0.44
44 7 0.11
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.37
Consensus pattern (42 bp):
AGGGGTTGCTAAGTGTTGATTCCCCGTATCTATTGATTCTAA
Found at i:12082969 original size:18 final size:18
Alignment explanation
Indices: 12082919--12082970 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 18
12082909 TCTTTCTAGT
12082919 TTATTTTT-ATTTATTAAA
1 TTATTTTTCATTT-TTAAA
12082937 TT-TTTTTC---TTT-AA
1 TTATTTTTCATTTTTAAA
12082950 TTATTTTTCATTTTTAAA
1 TTATTTTTCATTTTTAAA
12082968 TTA
1 TTA
12082971 ATTATTTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
13 4 0.14
14 8 0.29
15 1 0.04
17 8 0.29
18 7 0.25
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATTTTTCATTTTTAAA
Found at i:12088966 original size:27 final size:27
Alignment explanation
Indices: 12088936--12088999 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
12088926 TTTCATTTTT
***
12088936 ATGCAATTTAGTTTGTAGGTCCAAATC
1 ATGCAATTTAGTCCATAGGTCCAAATC
12088963 ATGCAATTTAGTCCATAGGTCCAAATC
1 ATGCAATTTAGTCCATAGGTCCAAATC
12088990 ATGCAATTTA
1 ATGCAATTTA
12089000 ACCATTTTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (27 bp):
ATGCAATTTAGTCCATAGGTCCAAATC
Found at i:12090780 original size:20 final size:20
Alignment explanation
Indices: 12090722--12090781 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
12090712 ATTTTGATGT
* *
12090722 GTTAAAATGATTTTAAATTG
1 GTTAAAATCATTTTAACTTG
* *
12090742 GTTGAAATCATTTTGACTTG
1 GTTAAAATCATTTTAACTTG
*
12090762 GTTAAAATCATTCTAACTTG
1 GTTAAAATCATTTTAACTTG
12090782 AATTTAAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.43
Consensus pattern (20 bp):
GTTAAAATCATTTTAACTTG
Found at i:12091452 original size:21 final size:21
Alignment explanation
Indices: 12091414--12091453 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12091404 AAAGTAGATA
*
12091414 TATGAGAATTAACGTCTTCCC
1 TATGAGAATTAACCTCTTCCC
12091435 TATGAG-ATTGAACCTCTTC
1 TATGAGAATT-AACCTCTTC
12091454 TCGAAGACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (21 bp):
TATGAGAATTAACCTCTTCCC
Found at i:12094088 original size:94 final size:94
Alignment explanation
Indices: 12093927--12094116 Score: 362
Period size: 94 Copynumber: 2.0 Consensus size: 94
12093917 CAAGCATACA
*
12093927 CTAAACATAATGTCGAGTCTACTTGCAATAAGATAAAGCAAAGAACCAATCATTGACCTATATAA
1 CTAAACATAATGTCGAGTCTACTTGCAATAAGATAAAGCAAAAAACCAATCATTGACCTATATAA
12093992 TTTTAAATCAACACATTTACCTACCTCAT
66 TTTTAAATCAACACATTTACCTACCTCAT
12094021 CTAAACATAATGTCGAGTCTACTTGCAATAAGATAAAGCAAAAAACCAATCATTGACCTATATAA
1 CTAAACATAATGTCGAGTCTACTTGCAATAAGATAAAGCAAAAAACCAATCATTGACCTATATAA
*
12094086 TTTTAAATCAACACATTTACCTTCCTCAT
66 TTTTAAATCAACACATTTACCTACCTCAT
12094115 CT
1 CT
12094117 TTATCAAGCT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.29
Consensus pattern (94 bp):
CTAAACATAATGTCGAGTCTACTTGCAATAAGATAAAGCAAAAAACCAATCATTGACCTATATAA
TTTTAAATCAACACATTTACCTACCTCAT
Found at i:12094986 original size:272 final size:271
Alignment explanation
Indices: 12094493--12095040 Score: 979
Period size: 272 Copynumber: 2.0 Consensus size: 271
12094483 CTCTAGGAGC
* *
12094493 TTGTTTTAAACCATATAAAGCTTTTGAAATTTTGAAAACATGGTTTGGAAATTTTAGATCTTCAA
1 TTGTTTTAAACCATATAAAGCTTTTGAAAGTTTGAAAACATGGTTTGCAAATTTTAGATCTTCAA
* **
12094558 AACTTGGTGGTTGTTCAATATATGCTTCTTTATTTACAAAACCATTTAGAAAAATACTTTTTACA
66 AACTTGGTGGTTGTTCAATAGACACTTCTTTATTTACAAAACCATTTAGAAAAATACTTTTTACA
*
12094623 TCCATTTGATATAATTTGAAGTCATTAAAGCATGCAAAATCTAAAAGCATTCTAGTGGCTTCCAT
131 TCCATTTGATATAATTTGAAGTCATTAAAGCATGCAAAAGCTAAAAGCATTCTAGTGGCTTCCAT
* *
12094688 CCTAGCTACTGGAGCATAAGTTTCATCATAATCTATTCCTTCTTCTTGAGTGTAACCTTGAGCAA
196 CCTAGCTACGGGAGCATAAGTTTCATCATAATCTATTCCTTCCTCTTGAGTGTAACCTTGAGCAA
12094753 CAAGTCTAGCA
261 CAAGTCTAGCA
*
12094764 TTGTTTTCAAACCATATAAAGCTTTTGAAAGTTTGAAAATATGGTTTGCAAATTTTAGATCTTCA
1 TTGTTTT-AAACCATATAAAGCTTTTGAAAGTTTGAAAACATGGTTTGCAAATTTTAGATCTTCA
*
12094829 AAACTTGGTGGTTGTTCAATAGACACTTCTTTATTTATAAAACCATTTAGAAAAATACTTTTTAC
65 AAACTTGGTGGTTGTTCAATAGACACTTCTTTATTTACAAAACCATTTAGAAAAATACTTTTTAC
*
12094894 TTCCATTTGATATAATTTGAAGTCATTAAAGCATGCAAAAGCTAAAAGCATTCTAGTGGCTTCCA
130 ATCCATTTGATATAATTTGAAGTCATTAAAGCATGCAAAAGCTAAAAGCATTCTAGTGGCTTCCA
12094959 TCCTAGCTACGGGAGCATAAGTTTCATCATAATCTATTCCTTCCTCTTGAGTGTAACCTTGAGCA
195 TCCTAGCTACGGGAGCATAAGTTTCATCATAATCTATTCCTTCCTCTTGAGTGTAACCTTGAGCA
*
12095024 ACAAGTCTAGCC
260 ACAAGTCTAGCA
12095036 TTGTT
1 TTGTT
12095041 CCTCACTATG
Statistics
Matches: 264, Mismatches: 12, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
271 7 0.03
272 257 0.97
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (271 bp):
TTGTTTTAAACCATATAAAGCTTTTGAAAGTTTGAAAACATGGTTTGCAAATTTTAGATCTTCAA
AACTTGGTGGTTGTTCAATAGACACTTCTTTATTTACAAAACCATTTAGAAAAATACTTTTTACA
TCCATTTGATATAATTTGAAGTCATTAAAGCATGCAAAAGCTAAAAGCATTCTAGTGGCTTCCAT
CCTAGCTACGGGAGCATAAGTTTCATCATAATCTATTCCTTCCTCTTGAGTGTAACCTTGAGCAA
CAAGTCTAGCA
Found at i:12113713 original size:39 final size:38
Alignment explanation
Indices: 12113596--12113731 Score: 119
Period size: 39 Copynumber: 3.5 Consensus size: 38
12113586 GCGTTTGGAC
* * *
12113596 AAAAAACGCCGCTAAAAATGGAACATTAGCGGCGCTTTAT
1 AAAAAACGCCGCTAAAAAT-GAGCATTAGCGG-GATTTTT
* * * * * *
12113636 GAAAATCGCCACTAAAGATTGAGCAATAGCGGCATTTTT
1 AAAAAACGCCGCTAAA-AATGAGCATTAGCGGGATTTTT
* *
12113675 AAAAAACGCCGCTAAAAATGAGCTTTAGCGGTGTTTTTT
1 AAAAAACGCCGCTAAAAATGAGCATTAGCGG-GATTTTT
* *
12113714 GAAAAACGCCGCAAAAAA
1 AAAAAACGCCGCTAAAAA
12113732 CCTAAGTCCA
Statistics
Matches: 75, Mismatches: 19, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
38 12 0.16
39 38 0.51
40 23 0.31
41 2 0.03
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (38 bp):
AAAAAACGCCGCTAAAAATGAGCATTAGCGGGATTTTT
Found at i:12113823 original size:30 final size:30
Alignment explanation
Indices: 12113787--12113843 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
12113777 GGCATTTTGG
*
12113787 AAAAGCGCCGCTAATGCTCTGGTCTTTTAT
1 AAAAGCGCCGCTAATGCTCTAGTCTTTTAT
12113817 AAAAGCGCCGCTAATGCTCTAGTCTTT
1 AAAAGCGCCGCTAATGCTCTAGTCTTT
12113844 AGCGGCGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (30 bp):
AAAAGCGCCGCTAATGCTCTAGTCTTTTAT
Found at i:12113874 original size:41 final size:41
Alignment explanation
Indices: 12113811--12113999 Score: 265
Period size: 41 Copynumber: 4.6 Consensus size: 41
12113801 TGCTCTGGTC
* * *
12113811 TTTTATAAAAGCGCCGCTAATGCTCTAGTCTTTAGCGGCGT
1 TTTTAGAAAAGCGCCGCTAATGCTCTTGCCTTTAGCGGCGT
* *
12113852 TTTTGGAAAAGCGCCGCTAATGCTCTTGCCTTTAGCGGCAT
1 TTTTAGAAAAGCGCCGCTAATGCTCTTGCCTTTAGCGGCGT
*
12113893 TTTTAAAAAAGCGCCGCTAATGCTCTTGCCTTTAGCGGCGTTT
1 TTTTAGAAAAGCGCCGCTAATGCTCTTGCCTTTAGCGGCG--T
*
12113936 TTTTAGAAAAGCGCCGCTAATGCTC-TGTTCTTTAGCGGCGT
1 TTTTAGAAAAGCGCCGCTAATGCTCTTG-CCTTTAGCGGCGT
12113977 TTTT-GCAAAAGCGCCGCTAATGC
1 TTTTAG-AAAAGCGCCGCTAATGC
12114000 AAAATACTAT
Statistics
Matches: 134, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.01
41 95 0.71
42 2 0.01
43 36 0.27
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (41 bp):
TTTTAGAAAAGCGCCGCTAATGCTCTTGCCTTTAGCGGCGT
Found at i:12113980 original size:84 final size:82
Alignment explanation
Indices: 12113811--12113999 Score: 272
Period size: 84 Copynumber: 2.3 Consensus size: 82
12113801 TGCTCTGGTC
* * *
12113811 TTTTATAAAAGCGCCGCTAATGCTCTAGTCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCT
1 TTTTAAAAAAGCGCCGCTAATGCTCTAGCCTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCT
12113876 CTTGCCTTTAGCGGCAT
66 CTTGCCTTTAGCGGCAT
*
12113893 TTTTAAAAAAGCGCCGCTAATGCTCTTGCCTTTAGCGGCGTTTTTTTAGAAAAGCGCCGCTAATG
1 TTTTAAAAAAGCGCCGCTAATGCTCTAGCCTTTAGCGGCG--TTTTTAGAAAAGCGCCGCTAATG
* *
12113958 CTC-TGTTCTTTAGCGGCGT
64 CTCTTG-CCTTTAGCGGCAT
**
12113977 TTTTGCAAAAGCGCCGCTAATGC
1 TTTTAAAAAAGCGCCGCTAATGC
12114000 AAAATACTAT
Statistics
Matches: 96, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
82 37 0.39
83 2 0.02
84 57 0.59
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (82 bp):
TTTTAAAAAAGCGCCGCTAATGCTCTAGCCTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCT
CTTGCCTTTAGCGGCAT
Found at i:12114120 original size:17 final size:19
Alignment explanation
Indices: 12114083--12114121 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
12114073 TAAATTTTTT
12114083 ATAGAATTAATTATATAAA
1 ATAGAATTAATTATATAAA
*
12114102 ATAGTATTAATT-T-TAAA
1 ATAGAATTAATTATATAAA
12114119 ATA
1 ATA
12114122 TTAAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 1 0.05
19 11 0.58
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
ATAGAATTAATTATATAAA
Found at i:12114258 original size:7 final size:7
Alignment explanation
Indices: 12114246--12114275 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
12114236 ATGAATTTAA
12114246 GGATTAT
1 GGATTAT
12114253 GGATTAT
1 GGATTAT
12114260 GGATTAT
1 GGATTAT
12114267 GGATTAT
1 GGATTAT
12114274 GG
1 GG
12114276 TTTAAGGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.33, T:0.40
Consensus pattern (7 bp):
GGATTAT
Found at i:12114260 original size:22 final size:22
Alignment explanation
Indices: 12114219--12114275 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
12114209 GAGTTACTAT
* *
12114219 TTTAAGGTTTAGGGAGTATGAA
1 TTTAAGGATTATGGAGTATGAA
* *
12114241 TTTAAGGATTATGGATTATGGA
1 TTTAAGGATTATGGAGTATGAA
*
12114263 -TTATGGATTATGG
1 TTTAAGGATTATGG
12114276 TTTAAGGGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 12 0.40
22 18 0.60
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.40
Consensus pattern (22 bp):
TTTAAGGATTATGGAGTATGAA
Found at i:12114318 original size:15 final size:15
Alignment explanation
Indices: 12114295--12114346 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
12114285 TAGAATTTAA
*
12114295 GGTTTAGGGGTTATG
1 GGTTAAGGGGTTATG
* *
12114310 GGTTAAGGGTTTAAG
1 GGTTAAGGGGTTATG
*
12114325 GGTT-AGAGGTTATGG
1 GGTTAAGGGGTTAT-G
12114340 GGTTAAG
1 GGTTAAG
12114347 AGTTAGGGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
14 6 0.21
15 21 0.72
16 2 0.07
ACGTcount: A:0.21, C:0.00, G:0.44, T:0.35
Consensus pattern (15 bp):
GGTTAAGGGGTTATG
Found at i:12114327 original size:22 final size:22
Alignment explanation
Indices: 12114274--12114352 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 22
12114264 TATGGATTAT
**
12114274 GGTTTAAGGGTTAGAATTTAA-
1 GGTTTAAGGGTTAGAGGTTAAG
*
12114295 GGTTTAGGGGTTATG-GGTTAAG
1 GGTTTAAGGGTTA-GAGGTTAAG
*
12114317 GGTTTAAGGGTTAGAGGTTATG
1 GGTTTAAGGGTTAGAGGTTAAG
* *
12114339 GGGTTAAGAGTTAG
1 GGTTTAAGGGTTAG
12114353 GGATTCAAGG
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
21 17 0.35
22 31 0.65
ACGTcount: A:0.25, C:0.00, G:0.39, T:0.35
Consensus pattern (22 bp):
GGTTTAAGGGTTAGAGGTTAAG
Found at i:12120634 original size:20 final size:20
Alignment explanation
Indices: 12120609--12120654 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
12120599 AAAATAAAAT
12120609 AAAATAAA-A-TATTTGTCATA
1 AAAATAAATATTATTTG--ATA
12120629 AAAATAAATATTATTTGATA
1 AAAATAAATATTATTTGATA
12120649 AAAATA
1 AAAATA
12120655 TGTATTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 17 0.71
21 1 0.04
22 6 0.25
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (20 bp):
AAAATAAATATTATTTGATA
Found at i:12120733 original size:44 final size:44
Alignment explanation
Indices: 12120663--12120788 Score: 159
Period size: 43 Copynumber: 2.9 Consensus size: 44
12120653 TATGTATTTT
* * *
12120663 TAAAGGTT-ATGTTTTTAGCGGAGTTTGTGGGAAAAAGCGCCAC
1 TAAAGGTTAAGGTCTTTAGCGGCGTTTGTGGGAAAAAGCGCCAC
* * *
12120706 TAAAGGTTAAGGTCTTTAGCGGCGTTTGT-AGAAAAAGCGTCGC
1 TAAAGGTTAAGGTCTTTAGCGGCGTTTGTGGGAAAAAGCGCCAC
* *
12120749 TAAAAGTCAAGGTCTTTAGCGGCGTTTGTGGG-AAAAGCGC
1 TAAAGGTTAAGGTCTTTAGCGGCGTTTGTGGGAAAAAGCGC
12120789 AGCTAAAAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
43 53 0.75
44 18 0.25
ACGTcount: A:0.28, C:0.13, G:0.31, T:0.28
Consensus pattern (44 bp):
TAAAGGTTAAGGTCTTTAGCGGCGTTTGTGGGAAAAAGCGCCAC
Found at i:12120794 original size:43 final size:44
Alignment explanation
Indices: 12120676--12120870 Score: 159
Period size: 43 Copynumber: 4.5 Consensus size: 44
12120666 AGGTTATGTT
* * *
12120676 TTTAGCGGAGTTTGTGGGAAAAAGCGCCA-CTAAAGGTTAAGGTC
1 TTTAGCGGCGTTTGTGGG-AAAAGCGCCAGCTAAAAGTCAAGGTC
* * *
12120720 TTTAGCGGCGTTTGTAGAAAAAGCGTC-GCTAAAAGTCAAGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCAGCTAAAAGTCAAGGTC
** * *
12120763 TTTAGCGGCGTTTGTGGGAAAAGCG-CAGCTAAAAAACATGATC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCAGCTAAAAGTCAAGGTC
* * * * * *
12120806 TTTCGCGACGTTTAT-GCAGAAAGCGCC-GCT-AAAGAACATGGTC
1 TTTAGCGGCGTTTGTGGGA-AAAGCGCCAGCTAAAAG-TCAAGGTC
*
12120849 TTTAGCGGCGTTTATGGAGAAA
1 TTTAGCGGCGTTTGTGG-GAAA
12120871 GTGTCGCTAA
Statistics
Matches: 123, Mismatches: 21, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
42 6 0.05
43 97 0.79
44 19 0.15
45 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (44 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCAGCTAAAAGTCAAGGTC
Found at i:12120871 original size:43 final size:43
Alignment explanation
Indices: 12120716--12120904 Score: 184
Period size: 43 Copynumber: 4.4 Consensus size: 43
12120706 TAAAGGTTAA
* * * * * *
12120716 GGTCTTTAGCGGCGTTTGTAGAAAAAGCGTCGCTAAA-AGTCAA
1 GGTCTTTAGCGGCGTTTATGGAGAAAGCGCCGCTAAAGA-ACAT
* * *
12120759 GGTCTTTAGCGGCGTTTGTGG-GAAAAGCGCAGCTAAAAAACAT
1 GGTCTTTAGCGGCGTTTATGGAG-AAAGCGCCGCTAAAGAACAT
* * * *
12120802 GATCTTTCGCGACGTTTATGCAGAAAGCGCCGCTAAAGAACAT
1 GGTCTTTAGCGGCGTTTATGGAGAAAGCGCCGCTAAAGAACAT
* *
12120845 GGTCTTTAGCGGCGTTTATGGAGAAAGTGTCGCTAAAGAACAT
1 GGTCTTTAGCGGCGTTTATGGAGAAAGCGCCGCTAAAGAACAT
** *
12120888 GACCTTTAGCGGTGTTT
1 GGTCTTTAGCGGCGTTT
12120905 TTAAAAATAA
Statistics
Matches: 121, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
43 119 0.98
44 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.26
Consensus pattern (43 bp):
GGTCTTTAGCGGCGTTTATGGAGAAAGCGCCGCTAAAGAACAT
Found at i:12121451 original size:28 final size:28
Alignment explanation
Indices: 12121382--12121452 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
12121372 TAAAATAAAA
* * * *
12121382 AATTTAATCATATTAAATATTGAAATTG
1 AATTTTATCATTTTAAATATTAAAATAG
* *
12121410 AATTATA-AATTTTTAAATATTAAAATAG
1 AATTTTATCA-TTTTAAATATTAAAATAG
12121438 AATTTTATCATTTTA
1 AATTTTATCATTTTA
12121453 TTAACTAATG
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
27 1 0.03
28 31 0.94
29 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (28 bp):
AATTTTATCATTTTAAATATTAAAATAG
Found at i:12122383 original size:20 final size:20
Alignment explanation
Indices: 12122350--12122389 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
12122340 CCAACCCTCA
*
12122350 AAACTTTTTATTTTCCCCCT
1 AAACTTTTTATTTTCACCCT
12122370 AAAC-TTTTATTTTTCACCCT
1 AAACTTTTTA-TTTTCACCCT
12122390 TTACCCCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.50
Consensus pattern (20 bp):
AAACTTTTTATTTTCACCCT
Found at i:12132513 original size:87 final size:88
Alignment explanation
Indices: 12132399--12132572 Score: 273
Period size: 87 Copynumber: 2.0 Consensus size: 88
12132389 GTCTTTCCTT
* *
12132399 TTTTTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCATCAAAAA-ACCCTC-AAACTTC
1 TTTTTTCTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAAAATT-
12132462 TTCAAAAAAAGCAATTAAACCCCTA
65 TTC-AAAAAAGCAATTAAACCCCTA
*
12132487 TTTTTTCTT-CACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAAAATTT
1 TTTTTTCTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAAAATTT
*
12132551 TCAAAAAAGCAATTAATCCCCT
66 TCAAAAAAGCAATTAAACCCCT
12132573 GCTCTTATTA
Statistics
Matches: 80, Mismatches: 4, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
87 58 0.73
88 17 0.21
89 5 0.06
ACGTcount: A:0.38, C:0.22, G:0.07, T:0.32
Consensus pattern (88 bp):
TTTTTTCTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAAAATTT
TCAAAAAAGCAATTAAACCCCTA
Found at i:12132603 original size:13 final size:13
Alignment explanation
Indices: 12132585--12132612 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12132575 TCTTATTAAA
12132585 AATTAGAAAAAAT
1 AATTAGAAAAAAT
12132598 AATTAGAAAAAAT
1 AATTAGAAAAAAT
12132611 AA
1 AA
12132613 AAAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (13 bp):
AATTAGAAAAAAT
Found at i:12132633 original size:18 final size:19
Alignment explanation
Indices: 12132612--12132659 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
12132602 AGAAAAAATA
12132612 AAAAATAATAAATTTT-AG
1 AAAAATAATAAATTTTAAG
* * *
12132630 AAAATTATTAAATTTTAAT
1 AAAAATAATAAATTTTAAG
12132649 AAAAAT-ATAAA
1 AAAAATAATAAA
12132660 AATTAAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAAATAATAAATTTTAAG
Found at i:12132947 original size:19 final size:19
Alignment explanation
Indices: 12132923--12132993 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
12132913 TTTCTATATA
12132923 TTTTATATTTTTTTACGAT
1 TTTTATATTTTTTTACGAT
**** *
12132942 TTTTATAAAAATTTACAAT
1 TTTTATATTTTTTTACGAT
*
12132961 TTTTTTATATTTTTTACGAT
1 TTTTATAT-TTTTTTACGAT
12132981 TTTTATATTTTTT
1 TTTTATATTTTTT
12132994 CTAATTATTA
Statistics
Matches: 39, Mismatches: 12, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
19 25 0.64
20 14 0.36
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.66
Consensus pattern (19 bp):
TTTTATATTTTTTTACGAT
Found at i:12132948 original size:46 final size:47
Alignment explanation
Indices: 12132856--12132956 Score: 125
Period size: 46 Copynumber: 2.1 Consensus size: 47
12132846 TTTTTTTACG
*
12132856 AAATTTATATTTCTTTAAATTTTTTATAATTTTCTTACGACTTTATAA
1 AAATTTATATTTC-TTAAATATTTTATAATTTTCTTACGACTTTATAA
* * * *
12132904 AATTTTATATTTC-TATATATTTTAT-ATTTTTTTACGATTTTTATAA
1 AAATTTATATTTCTTAAATATTTTATAATTTTCTTACGA-CTTTATAA
12132950 AAATTTA
1 AAATTTA
12132957 CAATTTTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
45 11 0.24
46 23 0.50
48 12 0.26
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (47 bp):
AAATTTATATTTCTTAAATATTTTATAATTTTCTTACGACTTTATAA
Found at i:12132976 original size:20 final size:18
Alignment explanation
Indices: 12132923--12132993 Score: 61
Period size: 18 Copynumber: 3.7 Consensus size: 18
12132913 TTTCTATATA
*
12132923 TTTTATATTTTTTTACGAT
1 TTTTATA-TTTTTTACAAT
***
12132942 TTTTATAAAAATTTACAATTT
1 TTTTAT-ATTTTTTACAA--T
*
12132963 TTTTATATTTTTTACGAT
1 TTTTATATTTTTTACAAT
12132981 TTTTATATTTTTT
1 TTTTATATTTTTT
12132994 CTAATTATTA
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
18 14 0.34
19 12 0.29
20 8 0.20
21 7 0.17
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTTATATTTTTTACAAT
Found at i:12133187 original size:88 final size:89
Alignment explanation
Indices: 12133095--12133267 Score: 253
Period size: 89 Copynumber: 2.0 Consensus size: 89
12133085 TAATAAAAGC
* *
12133095 AGGGGCTTAATTGCTTTTTTT-AAATA-AATTGAGGGTCTTTTTT-TATGCATTTTGAAAGTTCA
1 AGGGGCTTAATTGCTTTTTTTGAAA-AGAATTGAGGG-CTTTTTTCGATGCATTTTAAAAGTTCA
*
12133157 AGTACCCAATTGAGTGCAAAAAAAAT
64 AGTACCCAAATGAGTGCAAAAAAAAT
**
12133183 AGGGGCTTAATTGCTTTTTTTGAAAAGGTTTGAGGGCTTTTTTCGATGCATTTTAAAAGTTCAAG
1 AGGGGCTTAATTGCTTTTTTTGAAAAGAATTGAGGGCTTTTTTCGATGCATTTTAAAAGTTCAAG
*
12133248 TACCCAAATGATTGCAAAAA
66 TACCCAAATGAGTGCAAAAA
12133268 GAAAAGAAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
88 29 0.38
89 47 0.62
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.38
Consensus pattern (89 bp):
AGGGGCTTAATTGCTTTTTTTGAAAAGAATTGAGGGCTTTTTTCGATGCATTTTAAAAGTTCAAG
TACCCAAATGAGTGCAAAAAAAAT
Found at i:12133753 original size:27 final size:26
Alignment explanation
Indices: 12133713--12133763 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
12133703 ATAAAAGCTA
**
12133713 TAAATATTTTAAATGTTAATAAAAAAT
1 TAAATATTAAAAAT-TTAATAAAAAAT
*
12133740 TAAATATTAAAAATTTATTAAAAA
1 TAAATATTAAAAATTTAATAAAAA
12133764 TTAGAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 9 0.43
27 12 0.57
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (26 bp):
TAAATATTAAAAATTTAATAAAAAAT
Found at i:12133781 original size:8 final size:8
Alignment explanation
Indices: 12133770--12133805 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
12133760 AAAATTAGAA
12133770 AAAAATAT
1 AAAAATAT
12133778 AAAAATAGT
1 AAAAATA-T
12133787 AAAAAATAT
1 -AAAAATAT
12133796 AAAAATAT
1 AAAAATAT
12133804 AA
1 AA
12133806 TATTTTAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 17 0.65
9 2 0.08
10 7 0.27
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (8 bp):
AAAAATAT
Found at i:12133781 original size:18 final size:18
Alignment explanation
Indices: 12133758--12133802 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
12133748 AAAAATTTAT
12133758 TAAAAATTAGAAAAAAATA
1 TAAAAA-TAGAAAAAAATA
*
12133777 TAAAAATAGTAAAAAATA
1 TAAAAATAGAAAAAAATA
12133795 TAAAAATA
1 TAAAAATA
12133803 TAATATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (18 bp):
TAAAAATAGAAAAAAATA
Found at i:12134091 original size:27 final size:27
Alignment explanation
Indices: 12134039--12134091 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
12134029 GACATTATTA
**
12134039 TATTTTTCATAAATTTTAATTTTTTTG
1 TATTTTTCATAAATTTTAATAATTTTG
*
12134066 TATTTTT-ATTAAATTTTGATAATTTT
1 TATTTTTCA-TAAATTTTAATAATTTT
12134092 TTCTAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 1 0.05
27 21 0.95
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (27 bp):
TATTTTTCATAAATTTTAATAATTTTG
Found at i:12134111 original size:29 final size:31
Alignment explanation
Indices: 12134070--12134127 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
12134060 TTTTTGTATT
12134070 TTTATTAAATTTTGATAA-TTTTTTCTAAAA
1 TTTATTAAATTTTGATAATTTTTTTCTAAAA
* *
12134100 TTTATT-ATTTTTTATAATTTTTTTCTAA
1 TTTATTAAATTTTGATAATTTTTTTCTAA
12134128 TTTTTAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (31 bp):
TTTATTAAATTTTGATAATTTTTTTCTAAAA
Found at i:12134286 original size:89 final size:89
Alignment explanation
Indices: 12134136--12134352 Score: 312
Period size: 89 Copynumber: 2.4 Consensus size: 89
12134126 AATTTTTAAT
* * * * *
12134136 AAGAGTAGGGGATTAATTGCTTTTTTGAAAAATTTTAAGGGTCTTTTTGATCCATTTTGAAAGTT
1 AAGAGAAGGGGCTTAATTGCTTTTTTGAAAAAGTTTAAGGGCCTTTTTGATACATTTTGAAAGTT
12134201 CAAGTACCCAATTGAGTG-AAAAA
66 CAAGTACCCAATTGAGTGCAAAAA
* *
12134224 AAGAGAAGGGGCTTAATTGCTTTTCTTGAAGAAGTTTGAGGGCCTTTTTGATACATTTTGAAAGT
1 AAGAGAAGGGGCTTAATTGCTTTT-TTGAAAAAGTTTAAGGGCCTTTTTGATACATTTTGAAAGT
* *
12134289 TCAAGTGCTCAATTGAGTGCAAAAA
65 TCAAGTACCCAATTGAGTGCAAAAA
12134314 AAGA-AGAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTAA
1 AAGAGA-AGGGGCTTAATTGC-TTTTTTGAAAAAGTTTAA
12134353 AGACTTTTTA
Statistics
Matches: 114, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
88 22 0.19
89 53 0.46
90 35 0.31
91 4 0.04
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.35
Consensus pattern (89 bp):
AAGAGAAGGGGCTTAATTGCTTTTTTGAAAAAGTTTAAGGGCCTTTTTGATACATTTTGAAAGTT
CAAGTACCCAATTGAGTGCAAAAA
Found at i:12135599 original size:18 final size:17
Alignment explanation
Indices: 12135576--12135609 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12135566 TTAGTCTCTC
12135576 TTTCTTTCTTCCTTTTTT
1 TTTCTTT-TTCCTTTTTT
*
12135594 TTTCTTTTTTCTTTTT
1 TTTCTTTTTCCTTTTT
12135610 AAATTTAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTCTTTTTCCTTTTTT
Found at i:12140433 original size:44 final size:45
Alignment explanation
Indices: 12140335--12140447 Score: 147
Period size: 44 Copynumber: 2.5 Consensus size: 45
12140325 AAGTGCTGCA
**
12140335 ATAGTATCTTTCAACTAAGGTCTTGATTCATTCACATTTAATGCC
1 ATAGTATCTTTCAACTAAGGTCTTGACCCATTCACATTTAATGCC
* * * **
12140380 ATAGCATCTTTCAACTAGGGTCTT-ACCCGTTCAGGTTTAATGCC
1 ATAGTATCTTTCAACTAAGGTCTTGACCCATTCACATTTAATGCC
*
12140424 ATAGTATCTTTCAACTATGGTCTT
1 ATAGTATCTTTCAACTAAGGTCTT
12140448 TCTCATTTCA
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
44 37 0.63
45 22 0.37
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (45 bp):
ATAGTATCTTTCAACTAAGGTCTTGACCCATTCACATTTAATGCC
Found at i:12140477 original size:45 final size:45
Alignment explanation
Indices: 12140335--12140495 Score: 152
Period size: 45 Copynumber: 3.6 Consensus size: 45
12140325 AAGTGCTGCA
* ** *
12140335 ATAGTATCTTTCAACTAAGGTCTTGAT-TCA-TTCACATTTAATGCC
1 ATAGTATCTTTCAACTATGGTCTT--TCTCAGTTCAGGTATAATGCC
* * * * *
12140380 ATAGCATCTTTCAACTAGGGTCTTAC-CCGTTCAGGTTTAATGCC
1 ATAGTATCTTTCAACTATGGTCTTTCTCAGTTCAGGTATAATGCC
*
12140424 ATAGTATCTTTCAACTATGGTCTTTCTCATTTCAGGTATAATG-C
1 ATAGTATCTTTCAACTATGGTCTTTCTCAGTTCAGGTATAATGCC
*
12140468 ACT-GATATCTTTCAACCATGGTCTTTCT
1 A-TAG-TATCTTTCAACTATGGTCTTTCT
12140496 TGTTTCTCAA
Statistics
Matches: 98, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
43 1 0.01
44 39 0.40
45 58 0.59
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.40
Consensus pattern (45 bp):
ATAGTATCTTTCAACTATGGTCTTTCTCAGTTCAGGTATAATGCC
Found at i:12142891 original size:142 final size:144
Alignment explanation
Indices: 12142704--12143005 Score: 335
Period size: 142 Copynumber: 2.1 Consensus size: 144
12142694 AGATAAAATG
* * * *
12142704 TTTTTCTATAAAAGTCCAGGTAATTCCCTGTAAAACCCCAAGTTTTTGCTTTTACTAGGGAAAAG
1 TTTTCCTATAAAA--CCAGGTAATTCCCTGTAAAACCCCAAGTTTTTCCTTTTACTAGGAAAAAA
** * * * * * * *
12142769 TTTAAAATTAATTCTAGAAAA-TGAAGAAAATTAAAGGAAATTAAAAAGACAAAATGATTTTTCC
64 AGTAAAACTAATTCTAAAAAAGAGAAAAAAAATAAAGAAAATTAAAAAGA-AAAATGACTTTTCC
* *
12142833 -TATAAAGACCTAA-GC
128 ACATAAAAACCTAAGGC
* * ** *
12142848 TTTTCCTATAAAACCAGTTAA-TCCCTTGTAAAACCTCGGGTTTTTCCTTTTATTAGGAAAAAAA
1 TTTTCCTATAAAACCAGGTAATTCCC-TGTAAAACCCCAAGTTTTTCCTTTTACTAGGAAAAAAA
*
12142912 GTAAAACTAATTCTAAAAAAGAGAAAAAAAATAAAGAAAATTAAAAAGATAAATGACTTTTCCAC
65 GTAAAACTAATTCTAAAAAAGAGAAAAAAAATAAAGAAAATTAAAAAGAAAAATGACTTTTCCAC
12142977 ATAAAAACCTAAGGC
130 ATAAAAACCTAAGGC
12142992 -TTTCCATATAAAAC
1 TTTTCC-TATAAAAC
12143006 TCAAGTTTTT
Statistics
Matches: 132, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
141 4 0.03
142 66 0.50
143 40 0.30
144 22 0.17
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (144 bp):
TTTTCCTATAAAACCAGGTAATTCCCTGTAAAACCCCAAGTTTTTCCTTTTACTAGGAAAAAAAG
TAAAACTAATTCTAAAAAAGAGAAAAAAAATAAAGAAAATTAAAAAGAAAAATGACTTTTCCACA
TAAAAACCTAAGGC
Found at i:12147093 original size:46 final size:46
Alignment explanation
Indices: 12147026--12147195 Score: 216
Period size: 46 Copynumber: 3.7 Consensus size: 46
12147016 TAATATTCCT
* * * *
12147026 GTATTCTCGAGTCTGCAACATATGCAGGAACTCGGACCCTAATCAC
1 GTATTCTCGAGTCCGCAACATATGCAGGAGCTTGGAACCTAATCAC
* * *
12147072 GTATTCTCGAGTCTGCAACATATGCAAGAGCTTGGAACCTAATCAT
1 GTATTCTCGAGTCCGCAACATATGCAGGAGCTTGGAACCTAATCAC
* * *
12147118 GTATTCTCGAGTCCGTAACATATGTAGGAGCTTGGAACCTATTC-C
1 GTATTCTCGAGTCCGCAACATATGCAGGAGCTTGGAACCTAATCAC
* *
12147163 TGTAATCTCGAGTCCACAACATATGCAGGAGCT
1 -GTATTCTCGAGTCCGCAACATATGCAGGAGCT
12147196 CAAAACTTGG
Statistics
Matches: 108, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
46 108 1.00
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (46 bp):
GTATTCTCGAGTCCGCAACATATGCAGGAGCTTGGAACCTAATCAC
Found at i:12149128 original size:25 final size:25
Alignment explanation
Indices: 12149097--12149148 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
12149087 AGACAAGGAA
*
12149097 AATGATGGGAGTGAGGAGATGGATG
1 AATGATGGGAGTGAGGAGATGAATG
12149122 AATGATGGGAGTGAGGAGATGAATG
1 AATGATGGGAGTGAGGAGATGAATG
12149147 AA
1 AA
12149149 GAGGACGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.00, G:0.44, T:0.19
Consensus pattern (25 bp):
AATGATGGGAGTGAGGAGATGAATG
Found at i:12159211 original size:9 final size:9
Alignment explanation
Indices: 12159195--12159261 Score: 82
Period size: 9 Copynumber: 7.4 Consensus size: 9
12159185 GTTAAATGAA
12159195 TCGAGTTAT
1 TCGAGTTAT
*
12159204 TTGAGTTAAT
1 TCGAGTT-AT
*
12159214 T-GGGTTAT
1 TCGAGTTAT
*
12159222 TCGAGTTAA
1 TCGAGTTAT
12159231 TCGAGTTAT
1 TCGAGTTAT
*
12159240 TCGAGTTAA
1 TCGAGTTAT
12159249 TCGAGTTAT
1 TCGAGTTAT
12159258 TCGA
1 TCGA
12159262 ATCAACTCGA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
8 3 0.06
9 43 0.88
10 3 0.06
ACGTcount: A:0.25, C:0.09, G:0.24, T:0.42
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:12159222 original size:18 final size:18
Alignment explanation
Indices: 12159193--12159261 Score: 111
Period size: 18 Copynumber: 3.8 Consensus size: 18
12159183 GAGTTAAATG
*
12159193 AATCGAGTTATTTGAGTT
1 AATCGAGTTATTCGAGTT
* *
12159211 AATTGGGTTATTCGAGTT
1 AATCGAGTTATTCGAGTT
12159229 AATCGAGTTATTCGAGTT
1 AATCGAGTTATTCGAGTT
12159247 AATCGAGTTATTCGA
1 AATCGAGTTATTCGA
12159262 ATCAACTCGA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.41
Consensus pattern (18 bp):
AATCGAGTTATTCGAGTT
Found at i:12159330 original size:9 final size:9
Alignment explanation
Indices: 12159315--12159351 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
12159305 TAATTTTTTG
12159315 AATTCGAAT
1 AATTCGAAT
*
12159324 AACTCGAAT
1 AATTCGAAT
12159333 AATTCGAAT
1 AATTCGAAT
12159342 AATTCGAAT
1 AATTCGAAT
12159351 A
1 A
12159352 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:12159565 original size:30 final size:31
Alignment explanation
Indices: 12159530--12159589 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
12159520 AAACCTTTTA
* *
12159530 TTTTCCCCCAAAATTTTTA-CTCCTTCCCAC
1 TTTTCCCCCAAAACTTTTATCCCCTTCCCAC
*
12159560 TTTTCCCCTAAAACTTTTATCCCCTTCCCA
1 TTTTCCCCCAAAACTTTTATCCCCTTCCCA
12159590 TCCCACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTATCCCCTTCCCAC
Found at i:12163617 original size:533 final size:533
Alignment explanation
Indices: 12162611--12163675 Score: 2130
Period size: 533 Copynumber: 2.0 Consensus size: 533
12162601 AAATGGGATG
12162611 GTTTTTACAAACTTGGGCCATAATGTGCCTGCAACAAAAGAAAATAACAGTTAAGTAAACTTATT
1 GTTTTTACAAACTTGGGCCATAATGTGCCTGCAACAAAAGAAAATAACAGTTAAGTAAACTTATT
12162676 GAAGAAACCAAACAAAGGGATTAAAAACAAATTAAATGAATAAAATAATGCAGGAAAGAAATATT
66 GAAGAAACCAAACAAAGGGATTAAAAACAAATTAAATGAATAAAATAATGCAGGAAAGAAATATT
12162741 AACCAGCTCAAAAAATGATGGAATTTTTATCTCGAATTATAGGAGCTCCGAAGTACTGCTTTAAT
131 AACCAGCTCAAAAAATGATGGAATTTTTATCTCGAATTATAGGAGCTCCGAAGTACTGCTTTAAT
12162806 CGTTGGCCGTTGACTTTGAAAGTAGAACCAGTCTTGTTGTCTTTAATTGCCACAGCTCCATGAGA
196 CGTTGGCCGTTGACTTTGAAAGTAGAACCAGTCTTGTTGTCTTTAATTGCCACAGCTCCATGAGA
12162871 ATAGACATACACTATCTCGAATGGGCTAAACCAACGAGATTTTAATTTGCTAGGAAACAATTATA
261 ATAGACATACACTATCTCGAATGGGCTAAACCAACGAGATTTTAATTTGCTAGGAAACAATTATA
12162936 GCCTGGACTTAAATAACAAGACTTGTTGTTCAGGTGCAAATTGCTATTGCAAAATCTTGTTGTCA
326 GCCTGGACTTAAATAACAAGACTTGTTGTTCAGGTGCAAATTGCTATTGCAAAATCTTGTTGTCA
12163001 TGCCATCGTTTAGTATTTTCTTTGTACATCTTGGCATTCTCATAAGCTTGTGCTCTAAATTCTTC
391 TGCCATCGTTTAGTATTTTCTTTGTACATCTTGGCATTCTCATAAGCTTGTGCTCTAAATTCTTC
12163066 CATCTCATTTAACAAAACAGGCGATTAATACCAGCAAGACTCCAATCCATATTCAATTTCTTAAT
456 CATCTCATTTAACAAAACAGGCGATTAATACCAGCAAGACTCCAATCCATATTCAATTTCTTAAT
12163131 TGCCCAATATGTT
521 TGCCCAATATGTT
12163144 GTTTTTACAAACTTGGGCCATAATGTGCCTGCAACAAAAGAAAATAACAGTTAAGTAAACTTATT
1 GTTTTTACAAACTTGGGCCATAATGTGCCTGCAACAAAAGAAAATAACAGTTAAGTAAACTTATT
12163209 GAAGAAACCAAACAAAGGGATTAAAAACAAATTAAATGAATAAAATAATGCAGGAAAGAAATATT
66 GAAGAAACCAAACAAAGGGATTAAAAACAAATTAAATGAATAAAATAATGCAGGAAAGAAATATT
12163274 AACCAGCTCAAAAAATGATGGAATTTTTATCTCGAATTATAGGAGCTCCGAAGTACTGCTTTAAT
131 AACCAGCTCAAAAAATGATGGAATTTTTATCTCGAATTATAGGAGCTCCGAAGTACTGCTTTAAT
12163339 CGTTGGCCGTTGACTTTGAAAGTAGAACCAGTCTTGTTGTCTTTAATTGCCACAGCTCCATGAGA
196 CGTTGGCCGTTGACTTTGAAAGTAGAACCAGTCTTGTTGTCTTTAATTGCCACAGCTCCATGAGA
12163404 ATAGACATACACTATCTCGAATGGGCTAAACCAACGAGATTTTAATTTGCTAGGAAACAATTATA
261 ATAGACATACACTATCTCGAATGGGCTAAACCAACGAGATTTTAATTTGCTAGGAAACAATTATA
12163469 GCCTGGACTTAAATAACAAGACTTGTTGTTCAGGTGCAAATTGCTATTGCAAAATCTTGTTGTCA
326 GCCTGGACTTAAATAACAAGACTTGTTGTTCAGGTGCAAATTGCTATTGCAAAATCTTGTTGTCA
12163534 TGCCATCGTTTAGTATTTTCTTTGTACATCTTGGCATTCTCATAAGCTTGTGCTCTAAATTCTTC
391 TGCCATCGTTTAGTATTTTCTTTGTACATCTTGGCATTCTCATAAGCTTGTGCTCTAAATTCTTC
12163599 CATCTCATTTAACAAAACAGGCGATTAATACCAGCAAGACTCCAATCCATATTCAATTTCTTAAT
456 CATCTCATTTAACAAAACAGGCGATTAATACCAGCAAGACTCCAATCCATATTCAATTTCTTAAT
12163664 TGCCCAATATGT
521 TGCCCAATATGT
12163676 CTTATGTTCA
Statistics
Matches: 532, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
533 532 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (533 bp):
GTTTTTACAAACTTGGGCCATAATGTGCCTGCAACAAAAGAAAATAACAGTTAAGTAAACTTATT
GAAGAAACCAAACAAAGGGATTAAAAACAAATTAAATGAATAAAATAATGCAGGAAAGAAATATT
AACCAGCTCAAAAAATGATGGAATTTTTATCTCGAATTATAGGAGCTCCGAAGTACTGCTTTAAT
CGTTGGCCGTTGACTTTGAAAGTAGAACCAGTCTTGTTGTCTTTAATTGCCACAGCTCCATGAGA
ATAGACATACACTATCTCGAATGGGCTAAACCAACGAGATTTTAATTTGCTAGGAAACAATTATA
GCCTGGACTTAAATAACAAGACTTGTTGTTCAGGTGCAAATTGCTATTGCAAAATCTTGTTGTCA
TGCCATCGTTTAGTATTTTCTTTGTACATCTTGGCATTCTCATAAGCTTGTGCTCTAAATTCTTC
CATCTCATTTAACAAAACAGGCGATTAATACCAGCAAGACTCCAATCCATATTCAATTTCTTAAT
TGCCCAATATGTT
Found at i:12170175 original size:17 final size:17
Alignment explanation
Indices: 12170155--12170189 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
12170145 ATGCATAATC
*
12170155 ACAGTTCATTCAATATA
1 ACAGTTCATACAATATA
12170172 ACAGTTCATACAATATA
1 ACAGTTCATACAATATA
12170189 A
1 A
12170190 TAATTCATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (17 bp):
ACAGTTCATACAATATA
Found at i:12170196 original size:17 final size:17
Alignment explanation
Indices: 12170159--12170197 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
12170149 ATAATCACAG
* *
12170159 TTCATTCAATATAACAG
1 TTCATACAATATAACAA
*
12170176 TTCATACAATATAATAA
1 TTCATACAATATAACAA
12170193 TTCAT
1 TTCAT
12170198 CCATACCACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (17 bp):
TTCATACAATATAACAA
Found at i:12171196 original size:28 final size:29
Alignment explanation
Indices: 12171140--12171210 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 29
12171130 CGTATATGCA
* *
12171140 TATATATTATATATAATCAAGACCTACACC
1 TATATATTATATATAATCAAAACCCACA-C
*
12171170 TATATATTATAT-TTA-CAAAACCCACAC
1 TATATATTATATATAATCAAAACCCACAC
12171197 -ATATATTATATATA
1 TATATATTATATATA
12171211 TACATACCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 11 0.31
27 2 0.06
28 9 0.25
29 2 0.06
30 12 0.33
ACGTcount: A:0.45, C:0.17, G:0.01, T:0.37
Consensus pattern (29 bp):
TATATATTATATATAATCAAAACCCACAC
Found at i:12171214 original size:28 final size:30
Alignment explanation
Indices: 12171140--12171214 Score: 88
Period size: 28 Copynumber: 2.6 Consensus size: 30
12171130 CGTATATGCA
* *
12171140 TATATATTATATATA-ATCAAGACCTACACC
1 TATATATTATATATATA-CAAAACCCACACC
12171170 TATATATTATAT-T-TACAAAACCCACA-C
1 TATATATTATATATATACAAAACCCACACC
12171197 -ATATATTATATATATACA
1 TATATATTATATATATACA
12171215 TACCTTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 11 0.28
27 2 0.05
28 13 0.32
29 2 0.05
30 12 0.30
ACGTcount: A:0.45, C:0.17, G:0.01, T:0.36
Consensus pattern (30 bp):
TATATATTATATATATACAAAACCCACACC
Found at i:12175023 original size:9 final size:9
Alignment explanation
Indices: 12175006--12175050 Score: 63
Period size: 9 Copynumber: 5.0 Consensus size: 9
12174996 ACCGAAGAAA
*
12175006 CATCATCCT
1 CATCGTCCT
12175015 CATCGTCCT
1 CATCGTCCT
*
12175024 CATCGTCTT
1 CATCGTCCT
12175033 CATCGTCCT
1 CATCGTCCT
*
12175042 CATCATCCT
1 CATCGTCCT
12175051 TTTTGCAACC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.16, C:0.42, G:0.07, T:0.36
Consensus pattern (9 bp):
CATCGTCCT
Found at i:12177220 original size:12 final size:10
Alignment explanation
Indices: 12177202--12177270 Score: 50
Period size: 10 Copynumber: 6.7 Consensus size: 10
12177192 TGTATTAAAA
12177202 TTATATA-AT
1 TTATATATAT
12177211 CTTATATATAT
1 -TTATATATAT
*
12177222 TTATATACAT
1 TTATATATAT
* *
12177232 ATATATTTAT
1 TTATATATAT
* * *
12177242 ATACAATAAAT
1 TTA-TATATAT
12177253 CTTATATATAT
1 -TTATATATAT
12177264 TTATATA
1 TTATATA
12177271 CATGTATCTA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
10 33 0.72
11 11 0.24
12 2 0.04
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (10 bp):
TTATATATAT
Found at i:12177235 original size:16 final size:16
Alignment explanation
Indices: 12177214--12177260 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
12177204 ATATAATCTT
12177214 ATATATATTTATATAC
1 ATATATATTTATATAC
12177230 ATATATATTTATATAC
1 ATATATATTTATATAC
*
12177246 A-ATAAATCTTATATA
1 ATATATAT-TTATATA
12177261 TATTTATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 5 0.17
16 24 0.83
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATATATTTATATAC
Found at i:12184576 original size:2 final size:2
Alignment explanation
Indices: 12184569--12184593 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12184559 GAGCTTGTCA
12184569 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12184594 AACAGCCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12185325 original size:24 final size:23
Alignment explanation
Indices: 12185276--12185325 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
12185266 TACTAAGTAA
*
12185276 TATTTATTATGTAAAATATGTAT
1 TATTTATTATGTAAAATATATAT
* * *
12185299 TATTTATTTATTTAAAATTTATTT
1 TATTTA-TTATGTAAAATATATAT
12185323 TAT
1 TAT
12185326 AATTTAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
TATTTATTATGTAAAATATATAT
Found at i:12186643 original size:15 final size:16
Alignment explanation
Indices: 12186617--12186646 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12186607 ATTAGTTAGT
12186617 TTTAAGTTTTGTTTTG
1 TTTAAGTTTTGTTTTG
12186633 TTTAA-TTTTGTTTT
1 TTTAAGTTTTGTTTT
12186647 ACTTTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.73
Consensus pattern (16 bp):
TTTAAGTTTTGTTTTG
Found at i:12189614 original size:3 final size:3
Alignment explanation
Indices: 12189606--12189647 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
12189596 AATCTACCCA
12189606 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
12189648 GTCTCAACTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:12190892 original size:25 final size:25
Alignment explanation
Indices: 12190842--12190892 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
12190832 TATTGATAAC
*
12190842 TTAATATATAGATAATATATACATT
1 TTAATATATAGATAATATATAAATT
* *
12190867 TTAATAT-TATATATTATTATAAATT
1 TTAATATATAGATAATA-TATAAATT
12190892 T
1 T
12190893 ATTTTTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (25 bp):
TTAATATATAGATAATATATAAATT
Found at i:12209288 original size:26 final size:26
Alignment explanation
Indices: 12209242--12209342 Score: 125
Period size: 26 Copynumber: 3.9 Consensus size: 26
12209232 TCTCATCTCA
* *
12209242 ATTTTACCCTAG-TAAAATTTTAACG
1 ATTTTACCCCAGATAAAATTTTAATG
* *
12209267 ATTTTACCCCCGATAAAATTTTGATG
1 ATTTTACCCCAGATAAAATTTTAATG
*
12209293 ATTTTACCCTTAG-TAAAATTTTAATG
1 ATTTTACCC-CAGATAAAATTTTAATG
*
12209319 ATTTTACCCTAGATAAAATTTTAA
1 ATTTTACCCCAGATAAAATTTTAA
12209343 GAAAATTCGT
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
25 13 0.20
26 52 0.79
27 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.42
Consensus pattern (26 bp):
ATTTTACCCCAGATAAAATTTTAATG
Found at i:12209313 original size:52 final size:51
Alignment explanation
Indices: 12209242--12209340 Score: 162
Period size: 52 Copynumber: 1.9 Consensus size: 51
12209232 TCTCATCTCA
*
12209242 ATTTTACCCTAGTAAAATTTTAACGATTTTACCCCCGATAAAATTTTGATG
1 ATTTTACCCTAGTAAAATTTTAACGATTTTACCCCAGATAAAATTTTGATG
* *
12209293 ATTTTACCCTTAGTAAAATTTTAATGATTTTACCCTAGATAAAATTTT
1 ATTTTACCC-TAGTAAAATTTTAACGATTTTACCCCAGATAAAATTTT
12209341 AAGAAAATTC
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 9 0.20
52 35 0.80
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.42
Consensus pattern (51 bp):
ATTTTACCCTAGTAAAATTTTAACGATTTTACCCCAGATAAAATTTTGATG
Found at i:12216467 original size:24 final size:24
Alignment explanation
Indices: 12216440--12216490 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
12216430 TAGAAAAGAA
*
12216440 GACTTATTCTTCCTTAACACAAGG
1 GACTCATTCTTCCTTAACACAAGG
12216464 GACTCATTCTTCCTTAACACAAGG
1 GACTCATTCTTCCTTAACACAAGG
12216488 GAC
1 GAC
12216491 GACAACCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.29
Consensus pattern (24 bp):
GACTCATTCTTCCTTAACACAAGG
Found at i:12217763 original size:25 final size:25
Alignment explanation
Indices: 12217729--12217777 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
12217719 ACTCTTTTAC
12217729 TTACTACTTATTACTTATACGACCG
1 TTACTACTTATTACTTATACGACCG
12217754 TTACTACTTATTACTTATACGACC
1 TTACTACTTATTACTTATACGACC
12217778 ATGTATGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.41
Consensus pattern (25 bp):
TTACTACTTATTACTTATACGACCG
Found at i:12218590 original size:9 final size:9
Alignment explanation
Indices: 12218572--12218615 Score: 79
Period size: 9 Copynumber: 4.9 Consensus size: 9
12218562 ATAGGTTTAA
12218572 GTTAAATTG
1 GTTAAATTG
*
12218581 GTTGAATTG
1 GTTAAATTG
12218590 GTTAAATTG
1 GTTAAATTG
12218599 GTTAAATTG
1 GTTAAATTG
12218608 GTTAAATT
1 GTTAAATT
12218616 TCAAGTTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (9 bp):
GTTAAATTG
Found at i:12222480 original size:44 final size:43
Alignment explanation
Indices: 12222418--12222504 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 43
12222408 GCAGCCTGCT
*
12222418 TCAGTTAAAAGCATAATTGTTTTGCTCATCGGACTATTTCAAA
1 TCAGTTAAAAGCATAATTGTTTCGCTCATCGGACTATTTCAAA
*
12222461 TCAGTTAAAAAGCTTAATTGTTTCGCTCATCGGACTATTTCAAA
1 TCAGTT-AAAAGCATAATTGTTTCGCTCATCGGACTATTTCAAA
12222505 CAACAGGTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 6 0.15
44 35 0.85
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (43 bp):
TCAGTTAAAAGCATAATTGTTTCGCTCATCGGACTATTTCAAA
Found at i:12236003 original size:15 final size:15
Alignment explanation
Indices: 12235983--12236012 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12235973 CATATTCAAA
*
12235983 CCATCATTTTACCTT
1 CCATCATTCTACCTT
12235998 CCATCATTCTACCTT
1 CCATCATTCTACCTT
12236013 ATCAAGCCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.37, G:0.00, T:0.43
Consensus pattern (15 bp):
CCATCATTCTACCTT
Found at i:12236752 original size:25 final size:25
Alignment explanation
Indices: 12236724--12236804 Score: 96
Period size: 25 Copynumber: 3.3 Consensus size: 25
12236714 GTATGTTCCC
12236724 ACGAGCTAGAAATCGGTAAGCTCAT
1 ACGAGCTAGAAATCGGTAAGCTCAT
12236749 ACGAGCT-GAGAATCGGTAAGCTC-T
1 ACGAGCTAGA-AATCGGTAAGCTCAT
* *
12236773 CATGAACTA-AAATCGGTAAGCTCAT
1 -ACGAGCTAGAAATCGGTAAGCTCAT
*
12236798 ACCAGCT
1 ACGAGCT
12236805 GTGGTGTGTC
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
24 20 0.43
25 27 0.57
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (25 bp):
ACGAGCTAGAAATCGGTAAGCTCAT
Found at i:12245593 original size:2 final size:2
Alignment explanation
Indices: 12245586--12245649 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
12245576 ACATATCTAC
12245586 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
12245628 GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA
12245650 TGGAAGGACT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:12247320 original size:43 final size:42
Alignment explanation
Indices: 12247231--12247526 Score: 384
Period size: 42 Copynumber: 7.0 Consensus size: 42
12247221 GCGCTTACAT
12247231 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
* *
12247273 AAAAAAACGCCACTAAAGATCATGTTCTTTAGCAGCGCTTAG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
*
12247315 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCCTAG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
12247357 AAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
1 -AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA-G
* * *
12247401 AAAAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTCGG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT-AG
** * * *
12247444 AGGAAAACGCCTCTAAA-AGTAATGTTCTATAGCGGCGCTT-G
1 AAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTAG
**
12247485 TTCAAAAACGCCGCTAAA-AGT-AGTGTTCTTTAGCGGCGCTTA
1 -AAAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTTA
12247527 TTTCACAAAC
Statistics
Matches: 226, Mismatches: 21, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
41 2 0.01
42 113 0.50
43 110 0.49
44 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
Found at i:12247539 original size:85 final size:85
Alignment explanation
Indices: 12247231--12247526 Score: 386
Period size: 85 Copynumber: 3.5 Consensus size: 85
12247221 GCGCTTACAT
12247231 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG-AAAAAAACGCCACTAAAGATCA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAAACGCCACTAAAGATCA
*
12247295 TGTTCTTTAGCAGCGCTTAG
66 TGTTCTTTAGCGGCGCTTAG
* *
12247315 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCCTAGAAAAAAAACGCCGCTAAAGATCA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAAACGCCACTAAAGATCA
12247380 TGTTCTTTAGCGGCGCTTAGG
66 TGTTCTTTAGCGGCGCTTA-G
* * * * ** * *
12247401 AAAAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTCGGAGGAAAACGCCTCTAAA-AGTA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAAACGCCACTAAAGA-TC
*
12247465 ATGTTCTATAGCGGCGCTT-G
65 ATGTTCTTTAGCGGCGCTTAG
**
12247485 TTCAAAAACGCCGCTAAA-AGT-AGTGTTCTTTAGCGGCGCTTA
1 -AAAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTTA
12247527 TTTCACAAAC
Statistics
Matches: 188, Mismatches: 18, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
84 44 0.23
85 72 0.38
86 72 0.38
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (85 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAAACGCCACTAAAGATCA
TGTTCTTTAGCGGCGCTTAG
Found at i:12247961 original size:12 final size:12
Alignment explanation
Indices: 12247944--12247983 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
12247934 TTTTGAACTT
*
12247944 CTGCTTCTATTG
1 CTGCTTCTATCG
*
12247956 CTGCTTCTCTCG
1 CTGCTTCTATCG
*
12247968 CTGCTTCTCTCG
1 CTGCTTCTATCG
12247980 CTGC
1 CTGC
12247984 GGCCTCTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.03, C:0.38, G:0.17, T:0.42
Consensus pattern (12 bp):
CTGCTTCTATCG
Found at i:12247994 original size:21 final size:21
Alignment explanation
Indices: 12247968--12248036 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
12247958 GCTTCTCTCG
*
12247968 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
*
12247989 CTGCTTCTCTCGCTGTAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* * *
12248010 CTGCTTCCCTCGCTGCCGCAT
1 CTGCTTCTCTCGCTGCAGCCT
12248031 CTGCTT
1 CTGCTT
12248037 TAAGTTGCTG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.03, C:0.42, G:0.20, T:0.35
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:12250108 original size:40 final size:39
Alignment explanation
Indices: 12250063--12250141 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
12250053 TTGGGATTTA
* *
12250063 GGGAAATTAAATCGGGGAAACTGGGGGAATAAGAATTGGG
1 GGGAAATGAAATCGGGG-AACTGGGGGAATAAGAAATGGG
* *
12250103 GGGAAATGAAATCGGGGAATTGGGGGAATACGAAATGGG
1 GGGAAATGAAATCGGGGAACTGGGGGAATAAGAAATGGG
12250142 AAATTAGGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
39 19 0.54
40 16 0.46
ACGTcount: A:0.37, C:0.05, G:0.42, T:0.16
Consensus pattern (39 bp):
GGGAAATGAAATCGGGGAACTGGGGGAATAAGAAATGGG
Found at i:12250146 original size:23 final size:24
Alignment explanation
Indices: 12250096--12250146 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
12250086 GGGGAATAAG
* *
12250096 AATTGGGGGGAAATGAAATCGGGG
1 AATTGGGGGGAAACGAAATCGGGA
12250120 AATT-GGGGGAATACGAAAT-GGGA
1 AATTGGGGGGAA-ACGAAATCGGGA
12250143 AATT
1 AATT
12250147 AGGGAATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.37, C:0.04, G:0.39, T:0.20
Consensus pattern (24 bp):
AATTGGGGGGAAACGAAATCGGGA
Found at i:12250714 original size:22 final size:22
Alignment explanation
Indices: 12250680--12250732 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
12250670 ATAGGCCTCT
12250680 AACTTT-AACCCGTAACCTTTA
1 AACTTTAAACCCGTAACCTTTA
12250701 AACTTTAAACCCGTAACCTTTA
1 AACTTTAAACCCGTAACCTTTA
12250723 AACTTTAAAC
1 AACTTTAAAC
12250733 TCTTAAACCC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 6 0.19
22 25 0.81
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (22 bp):
AACTTTAAACCCGTAACCTTTA
Found at i:12250738 original size:15 final size:14
Alignment explanation
Indices: 12250693--12250769 Score: 55
Period size: 15 Copynumber: 5.3 Consensus size: 14
12250683 TTTAACCCGT
12250693 AACCTTTAAACTTTA
1 AACC-TTAAACTTTA
* *
12250708 AACCCGTAACCTTTA
1 AA-CCTTAAACTTTA
*
12250723 AACTTTAAACTCTTA
1 AACCTTAAACT-TTA
* **
12250738 AACCCTAAACTACA
1 AACCTTAAACTTTA
* *
12250752 AACCTTACACTCTA
1 AACCTTAAACTTTA
12250766 AACC
1 AACC
12250770 CATAACCTTA
Statistics
Matches: 47, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
14 21 0.45
15 24 0.51
16 2 0.04
ACGTcount: A:0.40, C:0.30, G:0.01, T:0.29
Consensus pattern (14 bp):
AACCTTAAACTTTA
Found at i:12250754 original size:29 final size:30
Alignment explanation
Indices: 12250696--12250770 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 30
12250686 AACCCGTAAC
* **
12250696 CTTTAAACT-TTAAACCCGTAACCTTTAAA
1 CTTTAAACTCTTAAACCCGTAAACTACAAA
12250725 CTTTAAACTCTTAAACCC-TAAACTACAAA
1 CTTTAAACTCTTAAACCCGTAAACTACAAA
* *
12250754 CCTTACACTC-TAAACCC
1 CTTTAAACTCTTAAACCC
12250771 ATAACCTTAC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
28 7 0.17
29 25 0.62
30 8 0.20
ACGTcount: A:0.39, C:0.31, G:0.01, T:0.29
Consensus pattern (30 bp):
CTTTAAACTCTTAAACCCGTAAACTACAAA
Found at i:12250766 original size:21 final size:21
Alignment explanation
Indices: 12250742--12250789 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
12250732 CTCTTAAACC
12250742 CTAAACTACA-AACCTTACACT
1 CTAAAC-ACATAACCTTACACT
*
12250763 CTAAACCCATAACCTTACACT
1 CTAAACACATAACCTTACACT
*
12250784 CAAAAC
1 CTAAAC
12250790 CATGCATTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (21 bp):
CTAAACACATAACCTTACACT
Found at i:12251783 original size:259 final size:261
Alignment explanation
Indices: 12251320--12251851 Score: 851
Period size: 259 Copynumber: 2.0 Consensus size: 261
12251310 TATTTTGCTT
12251320 TTTTGCGGCGTTTTAACGTCAGCACCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTTT
1 TTTTGCGGCGTTTTAACGTCAGCACCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTTT
*
12251385 TGGTTCAGATATTTTGCGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACAAAA
66 TGGTTCAGATATTTTACGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACAAAA
12251450 CACTGCGTTTTGTTAAGATACGTTGCGGCGCTTGATCCAAAGCGCCGCTAAAGTTATTCTTTAAC
131 CACTGCGTTTTGTTAAGATACGTTGCGGCGCTTGATCCAAAGCGCCGCTAAAGTTATTCTTTAAC
* *
12251515 GGTGTTTTCTAGTAAGCGCCAC-TAA-TATA-ATCAAAATTAAAACTACGCATTTTAGTTAAGAT
196 GGCGTTTTCTAGTAAGCGCCACATAAGTATACATCAAAATTAAAACTACGCATTTTAGTAAAGAT
12251577 A
261 A
* *
12251578 CTTTTGCGGCGTTTTAACGTTAGCGCCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTT
1 -TTTTGCGGCGTTTTAACGTCAGCACCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTT
* *
12251643 TTGGTTCAGATTTTTTACGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACCAA
65 TTGGTTCAGATATTTTACGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACAAA
* * *
12251708 ACACTGCGTTTTGTTAAGATATGTTGCGGTGCTTTG-GCTC-AAGCGCCGCTAAA-TCTATTCTT
130 ACACTGCGTTTTGTTAAGATACGTTGCGGCGC-TTGATC-CAAAGCGCCGCTAAAGT-TATTCTT
*
12251770 TAACGGCGTTTTCTAGTAAGCGCCACTAATATAAGTATACATCAAAATTAAAACTACGCGTTTTA
192 TAACGGCGTTTTCTAGTAAGCGCCAC----ATAAGTATACATCAAAATTAAAACTACGCATTTTA
12251835 GTAAAGATA
253 GTAAAGATA
12251844 TTTTGCGG
1 TTTTGCGG
12251852 TGCTTTCTAC
Statistics
Matches: 252, Mismatches: 11, Indels: 14
0.91 0.04 0.05
Matches are distributed among these distances:
258 1 0.00
259 200 0.79
260 4 0.02
264 3 0.01
265 12 0.05
266 32 0.13
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (261 bp):
TTTTGCGGCGTTTTAACGTCAGCACCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTTT
TGGTTCAGATATTTTACGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACAAAA
CACTGCGTTTTGTTAAGATACGTTGCGGCGCTTGATCCAAAGCGCCGCTAAAGTTATTCTTTAAC
GGCGTTTTCTAGTAAGCGCCACATAAGTATACATCAAAATTAAAACTACGCATTTTAGTAAAGAT
A
Found at i:12252151 original size:114 final size:112
Alignment explanation
Indices: 12251910--12252191 Score: 287
Period size: 113 Copynumber: 2.5 Consensus size: 112
12251900 GCATATCACA
* * * * * * ** *
12251910 AAGCGCCACTAAATCTAGGATAAATCAACAAAAAAAATGATGCATTTTGGTTAAGATATTTTGCG
1 AAGCGCCACTAATTCTAGGATACATCAAC-ATAAAAATGATGCGTTTTGGTTAGGAGAAATTACG
* *
12251975 CCGCATATCGCAAAACGCCGCTAAGACGCTTTTGCGGCGTTTTTTGAG
65 CCGCATATCGCAAAACGCCGCTAAGACACTTTAGCGGCGTTTTTTGAG
12252023 AAGCGCCACTAATTCTAGGATACATCAACACTAAAAATGATGCGTTTTGGTTAGGAGAAATTACG
1 AAGCGCCACTAATTCTAGGATACATCAACA-TAAAAATGATGCGTTTTGGTTAGGAGAAATTACG
* * * * * * * *
12252088 GCGCGTTGTTGTAAAATGCTGCTAAGACACTTTAGCGGCGTGTTTTT-TG
65 CCGC-ATATCGCAAAACGCCGCTAAGACACTTTAGCGGCGT-TTTTTGAG
* * * * * * *
12252137 AAGCGCCACTAATTCTTGCATACATAAAGATGAAAATGTTGCGTTTTGGATAGGA
1 AAGCGCCACTAATTCTAGGATACATCAACATAAAAATGATGCGTTTTGGTTAGGA
12252192 TATTTTGCGG
Statistics
Matches: 140, Mismatches: 26, Indels: 6
0.81 0.15 0.03
Matches are distributed among these distances:
112 1 0.01
113 79 0.56
114 55 0.39
115 5 0.04
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (112 bp):
AAGCGCCACTAATTCTAGGATACATCAACATAAAAATGATGCGTTTTGGTTAGGAGAAATTACGC
CGCATATCGCAAAACGCCGCTAAGACACTTTAGCGGCGTTTTTTGAG
Found at i:12264441 original size:33 final size:34
Alignment explanation
Indices: 12264387--12264469 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 34
12264377 GACATAAAGC
* *
12264387 TTAAC-TTATAATTCAATAATTTAGATTTAATAG
1 TTAACTTTATAATTTAATAATTTAGATTTAATAA
12264420 TTAACTTTATAATTTAA-AATTTAGATTTAATAA
1 TTAACTTTATAATTTAATAATTTAGATTTAATAA
* *
12264453 TGAACTTCATAATTTAA
1 TTAACTTTATAATTTAA
12264470 GTATTAAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 35 0.78
34 10 0.22
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (34 bp):
TTAACTTTATAATTTAATAATTTAGATTTAATAA
Found at i:12274782 original size:17 final size:17
Alignment explanation
Indices: 12274760--12274805 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
12274750 CCAAAAACTA
12274760 CGAGCTCACCAAATGTG
1 CGAGCTCACCAAATGTG
*
12274777 CGAGCTCGCCAAATGTG
1 CGAGCTCACCAAATGTG
*
12274794 GGAGCTCACCAA
1 CGAGCTCACCAA
12274806 GATCGTGAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.15
Consensus pattern (17 bp):
CGAGCTCACCAAATGTG
Found at i:12274838 original size:17 final size:17
Alignment explanation
Indices: 12274795--12274839 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
12274785 CCAAATGTGG
*
12274795 GAGCTCACCAAGATCGT
1 GAGCTCACCAACATCGT
* *
12274812 GAACTCACCAACATTGT
1 GAGCTCACCAACATCGT
*
12274829 GAGCTTACCAA
1 GAGCTCACCAA
12274840 GCAAGAGAGC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (17 bp):
GAGCTCACCAACATCGT
Found at i:12281902 original size:17 final size:18
Alignment explanation
Indices: 12281880--12282027 Score: 77
Period size: 17 Copynumber: 8.8 Consensus size: 18
12281870 AACTGCGAAC
* *
12281880 TGCGAGCTCCCCAAATG-
1 TGCGAGCTCACCAAAAGA
12281897 TGCGAGCTCACCAAAAGA
1 TGCGAGCTCACCAAAAGA
*
12281915 TGCGAGCTCACC--ATGA
1 TGCGAGCTCACCAAAAGA
* *
12281931 CTACGAGCTCACC-AGA-A
1 -TGCGAGCTCACCAAAAGA
* *
12281948 T---AACTCACCAAAAAA
1 TGCGAGCTCACCAAAAGA
** *
12281963 TATGAGCTCACCAAATG-
1 TGCGAGCTCACCAAAAGA
12281980 TGCGAGCTCACC--AAGA
1 TGCGAGCTCACCAAAAGA
* * *
12281996 TCGCGAGCTTACCAACA-C
1 T-GCGAGCTCACCAAAAGA
12282014 TGCGAGCTCACCAA
1 TGCGAGCTCACCAA
12282028 GCATGAGAGT
Statistics
Matches: 101, Mismatches: 18, Indels: 24
0.71 0.13 0.17
Matches are distributed among these distances:
13 7 0.07
14 2 0.02
15 4 0.04
16 5 0.05
17 59 0.58
18 23 0.23
19 1 0.01
ACGTcount: A:0.34, C:0.32, G:0.19, T:0.16
Consensus pattern (18 bp):
TGCGAGCTCACCAAAAGA
Found at i:12285401 original size:34 final size:34
Alignment explanation
Indices: 12285358--12285425 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
12285348 AAATGGTTGT
12285358 GGTTCACAATCTGGGGATAGCAGAGCTTTCCAAA
1 GGTTCACAATCTGGGGATAGCAGAGCTTTCCAAA
12285392 GGTTCACAATCTGGGGATAGCAGAGCTTTCCAAA
1 GGTTCACAATCTGGGGATAGCAGAGCTTTCCAAA
12285426 CAACGAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (34 bp):
GGTTCACAATCTGGGGATAGCAGAGCTTTCCAAA
Found at i:12289932 original size:54 final size:54
Alignment explanation
Indices: 12289873--12289988 Score: 144
Period size: 54 Copynumber: 2.1 Consensus size: 54
12289863 TACTCAGTGA
** * * *
12289873 GTTACACGGGC-AGAGACATGGGCTGGGACATGGCTGTGTGTCTCTAGTTCGAAT
1 GTTACACGGGCAAG-GACACAGACTGGGACATGACTGTGTGTCCCTAGTTCGAAT
* * *
12289927 GTTACACGGGCAAGGACACAGACTGGGACATGACTGTGTGTCCCTATTTTGATT
1 GTTACACGGGCAAGGACACAGACTGGGACATGACTGTGTGTCCCTAGTTCGAAT
12289981 GTTACACG
1 GTTACACG
12289989 ACCTAATACA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 51 0.96
55 2 0.04
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.27
Consensus pattern (54 bp):
GTTACACGGGCAAGGACACAGACTGGGACATGACTGTGTGTCCCTAGTTCGAAT
Found at i:12296335 original size:19 final size:19
Alignment explanation
Indices: 12296293--12296333 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
12296283 AGAAAAAGTC
12296293 AAAAGTAAGAACGAGAAGA
1 AAAAGTAAGAACGAGAAGA
12296312 AAAAGTACAGAAC-A-AAGA
1 AAAAGTA-AGAACGAGAAGA
12296330 AAAA
1 AAAA
12296334 AGCATTGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.68, C:0.07, G:0.20, T:0.05
Consensus pattern (19 bp):
AAAAGTAAGAACGAGAAGA
Found at i:12296378 original size:23 final size:24
Alignment explanation
Indices: 12296349--12296397 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
12296339 TGTGACTGAG
*
12296349 AAAAAAGT-A-AAAAGTCAAGTGAA
1 AAAAAAGTCATAAAAGT-AAGAGAA
12296372 AAAAAAGTCATAAAAGTAAGAGAA
1 AAAAAAGTCATAAAAGTAAGAGAA
12296396 AA
1 AA
12296398 CTCAGTCATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 8 0.35
24 9 0.39
25 6 0.26
ACGTcount: A:0.67, C:0.04, G:0.16, T:0.12
Consensus pattern (24 bp):
AAAAAAGTCATAAAAGTAAGAGAA
Found at i:12313917 original size:43 final size:42
Alignment explanation
Indices: 12313870--12314133 Score: 153
Period size: 43 Copynumber: 6.2 Consensus size: 42
12313860 ACTTCAGAGT
* *
12313870 GATAAGATCTGTGCTTTTGATCTACTCCACTATTGCTTAGGGA
1 GATAAGAT-TGTGCTTTCGATCTACTCCACTACTGCTTAGGGA
* * * * *
12313913 GATAAGA-TCTACAATCTTCGACCTACTCCACTGCTGCTCAGGGA
1 GATAAGATTGTGC--T-TTCGATCTACTCCACTACTGCTTAGGGA
* * *
12313957 GATAAG--GGTGCTTTCGATCTGCTCCATTACTG-TGTAGGGA
1 GATAAGATTGTGCTTTCGATCTACTCCACTACTGCT-TAGGGA
* * * * * ** *
12313997 GATAAGA-TCTACAATCTTCAACCTACTCCGCTGTTGCTCAGGGA
1 GATAAGATTGTGC--T-TTCGATCTACTCCACTACTGCTTAGGGA
* * *
12314041 GATAAGGTTGGTGCTTTCGATCTGCTCCACTACTGCTTAGAGA
1 GATAAGATT-GTGCTTTCGATCTACTCCACTACTGCTTAGGGA
* * * * *
12314084 GATAAGATTGGTTTCTTTTG-TCTGCTTCACTACTGTTTAGGGA
1 GATAAGATT-G-TGCTTTCGATCTACTCCACTACTGCTTAGGGA
12314127 GATAAGA
1 GATAAGA
12314134 CTTGATGCGA
Statistics
Matches: 166, Mismatches: 43, Indels: 24
0.71 0.18 0.10
Matches are distributed among these distances:
39 1 0.01
40 27 0.16
41 6 0.04
43 68 0.41
44 60 0.36
45 2 0.01
46 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (42 bp):
GATAAGATTGTGCTTTCGATCTACTCCACTACTGCTTAGGGA
Found at i:12313939 original size:44 final size:44
Alignment explanation
Indices: 12313891--12314046 Score: 142
Period size: 44 Copynumber: 3.6 Consensus size: 44
12313881 TGCTTTTGAT
* *
12313891 CTACTCCACTATTGCTTAGGGAGATAAGATCTACAATCTTCGAC
1 CTACTCCACTACTGCTCAGGGAGATAAGATCTACAATCTTCGAC
* ** * *
12313935 CTACTCCACTGCTGCTCAGGGAGATAAG-GGTGC--T-TTCGAT
1 CTACTCCACTACTGCTCAGGGAGATAAGATCTACAATCTTCGAC
* * * *
12313975 CTGCTCCATTACTG-TGTAGGGAGATAAGATCTACAATCTTCAAC
1 CTACTCCACTACTGCT-CAGGGAGATAAGATCTACAATCTTCGAC
* **
12314019 CTACTCCGCTGTTGCTCAGGGAGATAAG
1 CTACTCCACTACTGCTCAGGGAGATAAG
12314047 GTTGGTGCTT
Statistics
Matches: 84, Mismatches: 22, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
39 1 0.01
40 27 0.32
41 3 0.04
43 3 0.04
44 49 0.58
45 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (44 bp):
CTACTCCACTACTGCTCAGGGAGATAAGATCTACAATCTTCGAC
Found at i:12313982 original size:84 final size:86
Alignment explanation
Indices: 12313880--12314091 Score: 313
Period size: 84 Copynumber: 2.5 Consensus size: 86
12313870 GATAAGATCT
* * * *
12313880 GTGCTTTTGATCTACTCCACTATTGCTTAGGGAGATAAGATCTACAATCTTCGACCTACTCCACT
1 GTGCTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACT
12313945 GCTGCTCAGGGAGATAA-G-G
66 GCTGCTCAGGGAGATAAGGTG
* *
12313964 GTGCTTTCGATCTGCTCCATTACTG-TGTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGC
1 GTGCTTTCGATCTGCTCCACTACTGCT-TAGGGAGATAAGATCTACAATCTTCAACCTACTCCAC
*
12314028 TGTTGCTCAGGGAGATAAGGTTG
65 TGCTGCTCAGGGAGATAAGG-TG
*
12314051 GTGCTTTCGATCTGCTCCACTACTGCTTAGAGAGATAAGAT
1 GTGCTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGAT
12314092 TGGTTTCTTT
Statistics
Matches: 114, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
83 1 0.01
84 73 0.64
85 1 0.01
87 38 0.33
88 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (86 bp):
GTGCTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACT
GCTGCTCAGGGAGATAAGGTG
Found at i:12336084 original size:21 final size:21
Alignment explanation
Indices: 12336054--12336133 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
12336044 AAAAGCTAAC
*
12336054 AAAATGCCACAAAGGCCTTAT
1 AAAATACCACAAAGGCCTTAT
* * * *
12336075 TAAATACCACAGAGG-CTAACA
1 AAAATACCACAAAGGCCTTA-T
*
12336096 AAAATACCACAAAGGCCATAT
1 AAAATACCACAAAGGCCTTAT
*
12336117 CAAAATACCACATAGGC
1 -AAAATACCACAAAGGC
12336134 TAACAGAATG
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
20 3 0.07
21 25 0.56
22 17 0.38
ACGTcount: A:0.47, C:0.25, G:0.12, T:0.15
Consensus pattern (21 bp):
AAAATACCACAAAGGCCTTAT
Found at i:12336106 original size:42 final size:43
Alignment explanation
Indices: 12336048--12336166 Score: 154
Period size: 42 Copynumber: 2.8 Consensus size: 43
12336038 TGCCATAAAA
* * *
12336048 GCTAAC-AAAATGCCACAAAGGCCTTAT-TAAATACCACAGAG
1 GCTAACAAAAATACCACAAAGGCCATATCAAAATACCACAGAG
*
12336089 GCTAACAAAAATACCACAAAGGCCATATCAAAATACCACATAG
1 GCTAACAAAAATACCACAAAGGCCATATCAAAATACCACAGAG
* **
12336132 GCTAAC-AGAATGTCACAAAGGCCATATCAAAATAC
1 GCTAACAAAAATACCACAAAGGCCATATCAAAATAC
12336167 TCTATAAAAG
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
41 6 0.09
42 45 0.65
43 18 0.26
ACGTcount: A:0.47, C:0.24, G:0.13, T:0.16
Consensus pattern (43 bp):
GCTAACAAAAATACCACAAAGGCCATATCAAAATACCACAGAG
Found at i:12341462 original size:13 final size:13
Alignment explanation
Indices: 12341444--12341489 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
12341434 TCTGATACTC
*
12341444 TGTTTTCAAGATA
1 TGTTTTAAAGATA
* * *
12341457 TGTTTTTAGGTTA
1 TGTTTTAAAGATA
12341470 TGTTTTAAAGATA
1 TGTTTTAAAGATA
12341483 TGTTTTA
1 TGTTTTA
12341490 CACGTGCTCC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.26, C:0.02, G:0.17, T:0.54
Consensus pattern (13 bp):
TGTTTTAAAGATA
Found at i:12348888 original size:659 final size:658
Alignment explanation
Indices: 12347632--12348955 Score: 2235
Period size: 659 Copynumber: 2.0 Consensus size: 658
12347622 TTTCTTGATG
* * *
12347632 ACGTCCATCTAAGTCAACCAGAAACTACTCTATATTTGAACTATGTTTCTTATTTTAATAAGGTT
1 ACGTCCATCTAAGTCAACAAGAAAATACTCTATATTTGAACTATGTTTCTTATATTAATAAGGTT
* * * *
12347697 ATGATTAAGAATTATAGGCTTGGACACCCTAATATTTACTATTTAGACTTTTGTTACCTAATTTA
66 ATGATTAAGAATTATAGGCTTGGAAACCCTAATATTTACTATTTAGACATTTGCTACCTAATCTA
*
12347762 TTTAAGAATAAAAATCCTTCATATTACTGTGAATTTTGTGAATTGGCTAAACATCATCGGTCATT
131 TTTAAGAATAAAAATCCTTCATATTACTGTGAAATTTGTGAATTGGCTAAACATCATCGGTCATT
* *
12347827 CTTTCTACCTCAAAAATATAAGACTTCCAAACCTTTTTTTTTTAATTCATAGTGATGTTTGGGGA
196 CTTTCCACCTCAAAAATATAAGACTTCCAAACCTTTTTTTTTTAATTCATAGTGATGTATGGGGA
*
12347892 CATTCAATAATCTCAAATTTTTCAGGCAAATGTTGGCTTGTCACATTTATTGATGATCATACTCA
261 CATTCAATAATCTCAAATTTTTCAGGAAAATGTTGGCTTGTCACATTTATTGATGATCATACTCA
* *
12347957 CATTTATTAAGTGTTTTACTAAAAGATAAGTCTGAAGTTAAATTGTGTTTTAATCGTTTTATGCC
326 CATTTATTAAGTGTTTTACTAAAAGATAAGTCTGAAGTTAAAATGTGTTTCAATCGTTTTATGCC
*
12348022 ACGGAGGAAACACAATTTGGTGTGAAAATCAAAATATTTTGGAGTGACAATAGAGAGGAATTTTT
391 ACGGAGGAAACACAATTTGGAGTGAAAATCAAAATATTTTGGAGTGACAATAGAGAGGAATTTTT
* *
12348087 TTGTAACCAATTAGCAATTTTCTTAACCAAACATGGAATAGTCCATCAAAGCTCTTGTATAAATA
456 TGGTAACCAATTAGCAATTTTCTTAACCAAACATGGAATAGTCCATCAAAGCTCTTGTACAAATA
12348152 CACCACAACAAAATGGAATTGCAGAAAGGAAAAATCGCCATATTTTGGAAGCAACTAGAGCCTTA
521 CACCACAACAAAATGGAATTGCAGAAAGGAAAAATCGCCATATTTTGGAAGCAACTAGAGCCTTA
* *
12348217 ATGTTCACTAGTCATGTACCATATTATCTTTGGGGAGAGGC-TTTTTTAACGGCCACATATATTA
586 ATGTTCACTAGTCAGGTACCATATTATCTTTGGGGAGAGGCTTTTTTTAACAGCCACATATATTA
12348281 TTAATAGA
651 TTAATAGA
* *
12348289 ACGTCCATCTAAGTCAACAAGAAAATACTCTATATTTGAACTCTGTTTCTTATATTGATAAGGTT
1 ACGTCCATCTAAGTCAACAAGAAAATACTCTATATTTGAACTATGTTTCTTATATTAATAAGGTT
* * *
12348354 ATGATTAAGAATTATAGGCTTGGAAACCCTAATTTTTAGTATTTAGGCATTTGCTACCTAATCTA
66 ATGATTAAGAATTATAGGCTTGGAAACCCTAATATTTACTATTTAGACATTTGCTACCTAATCTA
12348419 TTTAAGAATAAAAATCCTTCATATTACTGTGAAATTTGTGAATTGGCTAAACATCATCGGTCATT
131 TTTAAGAATAAAAATCCTTCATATTACTGTGAAATTTGTGAATTGGCTAAACATCATCGGTCATT
12348484 CTTTCCACCTCAAAAATATAAGACTTCCAAACC-TTTTTTTTTAATTCATAGTGATGTATGGGGA
196 CTTTCCACCTCAAAAATATAAGACTTCCAAACCTTTTTTTTTTAATTCATAGTGATGTATGGGGA
*
12348548 CATTCAATAATCTCAAATTTTTCAGGAAAATGTTGGCTTGTCACATTTATTGATGATTATACTCA
261 CATTCAATAATCTCAAATTTTTCAGGAAAATGTTGGCTTGTCACATTTATTGATGATCATACTCA
* * *
12348613 CATTTATTAAGTTTTTTTTTATTAAAAGATAAGTCTG-AGTTAAAAATGTGTTTCAATCTTTTTA
326 CATTTATTAAG---TGTTTTACTAAAAGATAAGTCTGAAGTT-AAAATGTGTTTCAATCGTTTTA
* * *
12348677 TGCTATGGAGGAAACACAATTTGGAGTGAAAATCAAAATATTTTGGAGTGACAATAGAGGGGAAT
387 TGCCACGGAGGAAACACAATTTGGAGTGAAAATCAAAATATTTTGGAGTGACAATAGAGAGGAAT
* *
12348742 TTTTTGGTAACCAATTAGGAATTTTCTTAATCAAACATGGAATAGTCCATCAAAGCTCTTGTACA
452 TTTTTGGTAACCAATTAGCAATTTTCTTAACCAAACATGGAATAGTCCATCAAAGCTCTTGTACA
*
12348807 AATACACCACAACAAAATGGAATTGCAGAAAGGAAAAA-C-CACAGTATTTTGGAAGTAACTAGA
517 AATACACCACAACAAAATGGAATTGCAGAAAGGAAAAATCGC-CA-TATTTTGGAAGCAACTAGA
* *
12348870 GCCTTAATGTTCACTAGTCAGGTACCATGTTATCTTTGGGGAGAGGCTTTTTTTAACAGCTACAT
580 GCCTTAATGTTCACTAGTCAGGTACCATATTATCTTTGGGGAGAGGCTTTTTTTAACAGCCACAT
*
12348935 ATCTTATTAATAGA
645 ATATTATTAATAGA
12348949 ACGTCCA
1 ACGTCCA
12348956 GTAAGATTAT
Statistics
Matches: 624, Mismatches: 36, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
656 104 0.17
657 215 0.34
658 7 0.01
659 263 0.42
660 35 0.06
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (658 bp):
ACGTCCATCTAAGTCAACAAGAAAATACTCTATATTTGAACTATGTTTCTTATATTAATAAGGTT
ATGATTAAGAATTATAGGCTTGGAAACCCTAATATTTACTATTTAGACATTTGCTACCTAATCTA
TTTAAGAATAAAAATCCTTCATATTACTGTGAAATTTGTGAATTGGCTAAACATCATCGGTCATT
CTTTCCACCTCAAAAATATAAGACTTCCAAACCTTTTTTTTTTAATTCATAGTGATGTATGGGGA
CATTCAATAATCTCAAATTTTTCAGGAAAATGTTGGCTTGTCACATTTATTGATGATCATACTCA
CATTTATTAAGTGTTTTACTAAAAGATAAGTCTGAAGTTAAAATGTGTTTCAATCGTTTTATGCC
ACGGAGGAAACACAATTTGGAGTGAAAATCAAAATATTTTGGAGTGACAATAGAGAGGAATTTTT
TGGTAACCAATTAGCAATTTTCTTAACCAAACATGGAATAGTCCATCAAAGCTCTTGTACAAATA
CACCACAACAAAATGGAATTGCAGAAAGGAAAAATCGCCATATTTTGGAAGCAACTAGAGCCTTA
ATGTTCACTAGTCAGGTACCATATTATCTTTGGGGAGAGGCTTTTTTTAACAGCCACATATATTA
TTAATAGA
Found at i:12351925 original size:20 final size:20
Alignment explanation
Indices: 12351900--12351939 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
12351890 GCAATTATAC
12351900 CAAATCAATTCATATTTCAT
1 CAAATCAATTCATATTTCAT
*
12351920 CAAATCATTTCATATTTCAT
1 CAAATCAATTCATATTTCAT
12351940 TTCAATCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (20 bp):
CAAATCAATTCATATTTCAT
Found at i:12352260 original size:42 final size:42
Alignment explanation
Indices: 12352173--12352363 Score: 127
Period size: 42 Copynumber: 4.5 Consensus size: 42
12352163 AATTATGCCA
* ** * * * *
12352173 GCACATAAGTGCATCATCGGACGTATCAAAAAAAATATA-TCG
1 GCACATAAGTGCATCATTGGATATACCAAAGATATTATACT-G
12352215 GCACATAAGTGCATCATTGGATATACCAAAGATATTATACTG
1 GCACATAAGTGCATCATTGGATATACCAAAGATATTATACTG
** * ** **
12352257 GCACGCGAAGTGCATCATTGGATAAACTGAAG-TAATTATGTTG
1 GCAC-ATAAGTGCATCATTGGATATACCAAAGAT-ATTATACTG
* *** *
12352300 GCACGTAAGTGCATCATCAAATATACCGAAA-ATATTATACTA
1 GCACATAAGTGCATCATTGGATATACC-AAAGATATTATACTG
* *
12352342 GCACACATAGTGCATCAATGGA
1 GCACATA-AGTGCATCATTGGA
12352364 CAAACTGAAG
Statistics
Matches: 112, Mismatches: 31, Indels: 11
0.73 0.20 0.07
Matches are distributed among these distances:
42 65 0.58
43 47 0.42
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (42 bp):
GCACATAAGTGCATCATTGGATATACCAAAGATATTATACTG
Found at i:12352274 original size:43 final size:42
Alignment explanation
Indices: 12352221--12352363 Score: 128
Period size: 43 Copynumber: 3.4 Consensus size: 42
12352211 ATCGGCACAT
12352221 AAGTGCATCATTGGATATACCAAAGATATTATACTGGCACGC
1 AAGTGCATCATTGGATATACCAAAGATATTATACTGGCACGC
* ** ** *
12352263 GAAGTGCATCATTGGATAAACTGAAG-TAATTATGTTGGCACGT
1 -AAGTGCATCATTGGATATACCAAAGAT-ATTATACTGGCACGC
*** * *
12352306 AAGTGCATCATCAAATATACCGAAA-ATATTATACTAGCACAC
1 AAGTGCATCATTGGATATACC-AAAGATATTATACTGGCACGC
*
12352348 ATAGTGCATCAATGGA
1 A-AGTGCATCATTGGA
12352364 CAAACTGAAG
Statistics
Matches: 75, Mismatches: 21, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
42 28 0.37
43 47 0.63
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (42 bp):
AAGTGCATCATTGGATATACCAAAGATATTATACTGGCACGC
Found at i:12352309 original size:85 final size:85
Alignment explanation
Indices: 12352214--12352375 Score: 220
Period size: 85 Copynumber: 1.9 Consensus size: 85
12352204 AAAATATATC
*** * * *
12352214 GGCACATAAGTGCATCATTGGATATACC-AAAGATATTATACTGGCACGCGA-AGTGCATCATTG
1 GGCACATAAGTGCATCATCAAATATACCGAAA-ATATTATACTAGCACAC-ATAGTGCATCAATG
*
12352277 GATAAACTGAAGTAATTATGTT
64 GACAAACTGAAGTAATTATGTT
*
12352299 GGCACGTAAGTGCATCATCAAATATACCGAAAATATTATACTAGCACACATAGTGCATCAATGGA
1 GGCACATAAGTGCATCATCAAATATACCGAAAATATTATACTAGCACACATAGTGCATCAATGGA
12352364 CAAACTGAAGTA
66 CAAACTGAAGTA
12352376 TAGCTTATAC
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
84 1 0.01
85 63 0.94
86 3 0.04
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.25
Consensus pattern (85 bp):
GGCACATAAGTGCATCATCAAATATACCGAAAATATTATACTAGCACACATAGTGCATCAATGGA
CAAACTGAAGTAATTATGTT
Found at i:12353926 original size:85 final size:85
Alignment explanation
Indices: 12353808--12354092 Score: 401
Period size: 85 Copynumber: 3.4 Consensus size: 85
12353798 TTATTAACTC
* * * * * *
12353808 TAAAGATGGTTGCTAAGTGCTGATTTCACCGTATCTTTGATTGTGAAAGGGGTTGCCATCTGCTG
1 TAAAGGTGGTTGCTAAGTGTTGATTCCACCGTATCTTTGATTGTGAAAGGGGTTGCTATATGATG
*
12353873 ATTCCCTGTATCACTGAATA
66 ATTCCCCGTATCACTGAATA
* *
12353893 TAAAGGTGGTTGCTAAGTGTTGGTTCCATCGTATCTTTGATTGTGAAAGGGGTTGCTATATGATG
1 TAAAGGTGGTTGCTAAGTGTTGATTCCACCGTATCTTTGATTGTGAAAGGGGTTGCTATATGATG
*
12353958 ATTCCCCATATCACTGAATA
66 ATTCCCCGTATCACTGAATA
* * * * *
12353978 TAAAGGTGGTTGCTAAGTATTGATTCCGCTGTATCTTTGATTGTGAAAGGGGTTGCTATGTGTTG
1 TAAAGGTGGTTGCTAAGTGTTGATTCCACCGTATCTTTGATTGTGAAAGGGGTTGCTATATGATG
*
12354043 ATTCCCCGTATCGCTGAAT-
66 ATTCCCCGTATCACTGAATA
* *
12354062 TTAAGGTGGTTGCTAAGTGTTGAATCCACCG
1 TAAAGGTGGTTGCTAAGTGTTGATTCCACCG
12354093 AGTAACGGAT
Statistics
Matches: 176, Mismatches: 24, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
84 26 0.15
85 150 0.85
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (85 bp):
TAAAGGTGGTTGCTAAGTGTTGATTCCACCGTATCTTTGATTGTGAAAGGGGTTGCTATATGATG
ATTCCCCGTATCACTGAATA
Found at i:12353949 original size:43 final size:42
Alignment explanation
Indices: 12353815--12354084 Score: 210
Period size: 43 Copynumber: 6.4 Consensus size: 42
12353805 CTCTAAAGAT
* *
12353815 GGTTGCTAAGTGCTGATTTCACCGTATCTTTGATTGTGAAAGG
1 GGTTGCTAAGTGTTGA-TTCCCCGTATCTTTGATTGTGAAAGG
* ** * * ** * *
12353858 GGTTGCCATCTGCTGATTCCCTGTATCACTGAATAT-AAAGG
1 GGTTGCTAAGTGTTGATTCCCCGTATCTTTGATTGTGAAAGG
* *
12353899 TGGTTGCTAAGTGTTGGTTCCATCGTATCTTTGATTGTGAAAGG
1 -GGTTGCTAAGTGTTGATTCC-CCGTATCTTTGATTGTGAAAGG
* * ** * *
12353943 GGTTGCTATA-TGATGATTCCCCATATCACTGAATAT-AAAGG
1 GGTTGCTA-AGTGTTGATTCCCCGTATCTTTGATTGTGAAAGG
* *
12353984 TGGTTGCTAAGTATTGATTCCGCTGTATCTTTGATTGTGAAAGG
1 -GGTTGCTAAGTGTTGATTCC-CCGTATCTTTGATTGTGAAAGG
* **
12354028 GGTTGCTATGTGTTGATTCCCCGTATCGCTGAATT-T--AAGG
1 GGTTGCTAAGTGTTGATTCCCCGTATCTTTG-ATTGTGAAAGG
12354068 TGGTTGCTAAGTGTTGA
1 -GGTTGCTAAGTGTTGA
12354085 ATCCACCGAG
Statistics
Matches: 175, Mismatches: 42, Indels: 22
0.73 0.18 0.09
Matches are distributed among these distances:
40 4 0.02
41 26 0.15
42 64 0.37
43 70 0.40
44 11 0.06
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.37
Consensus pattern (42 bp):
GGTTGCTAAGTGTTGATTCCCCGTATCTTTGATTGTGAAAGG
Found at i:12364950 original size:214 final size:214
Alignment explanation
Indices: 12364555--12364979 Score: 518
Period size: 214 Copynumber: 2.0 Consensus size: 214
12364545 ATTATGATGT
** * *
12364555 TAGGAACTGCTCCTATCTCAAGTGCCCCTTAAAGAGTAGCCCTAGTAGAGTTGAAGTAGTTGAAA
1 TAGGAACAACTCCTATCTCAAGTGCCCCTTAAAGAATAGCCCTAGTAGAGTTGAAGTAGTTAAAA
* * * * * * * *
12364620 ACTCAGCTACAATAACTATAGGACAAGGGTTTCATCAGACCAAGTGTTTCACTTTGGGGTGCGCC
66 ACTAAACTACAAGAACTATAGGACAAGGGGTTCATCAGACCAAATGTTTCACCTTAGGGTGCACC
* * * **
12364685 AATACTATTCATTAAAAAGAATGATGGGACTCTTTGGTTATGTATTGATTACAAGAAGCTAAA-A
131 AATACTATTCATTAAAAAGAAGGATAGGACTCTTTGGTTATGTACTGATTACAAGAAAATAAACA
*
12364749 TAGGTAACCATAAAGAATGC
196 -AGGTAACCACAAAGAATGC
*
12364769 TAGGAACAACTCCTATCTCAAGTGCGCCTTATAA-AATAGCCCTAGTAGAGTTGAA-TGAGTTAA
1 TAGGAACAACTCCTATCTCAAGTGCCCCTTA-AAGAATAGCCCTAGTAGAGTTGAAGT-AGTTAA
* * * * *
12364832 AAACTAAACTATAAGAACTGTTGGATAAGGGGTTCATTAGACCAAATGTTTCACCTTAGGGTGCA
64 AAACTAAACTACAAGAACTATAGGACAAGGGGTTCATCAGACCAAATGTTTCACCTTAGGGTGCA
* * * *
12364897 CCAATGCTATTCGTTAAGAAGAAGGATAGGAC-CTTTCGG-TAGTGTACTGATTACAGGAAAATA
129 CCAATACTATTCATTAAAAAGAAGGATAGGACTCTTT-GGTTA-TGTACTGATTACAAGAAAATA
12364960 AACAAGGTAACCACAAAGAA
192 AACAAGGTAACCACAAAGAA
12364980 CAAGTATCTG
Statistics
Matches: 178, Mismatches: 28, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
213 7 0.04
214 168 0.94
215 3 0.02
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (214 bp):
TAGGAACAACTCCTATCTCAAGTGCCCCTTAAAGAATAGCCCTAGTAGAGTTGAAGTAGTTAAAA
ACTAAACTACAAGAACTATAGGACAAGGGGTTCATCAGACCAAATGTTTCACCTTAGGGTGCACC
AATACTATTCATTAAAAAGAAGGATAGGACTCTTTGGTTATGTACTGATTACAAGAAAATAAACA
AGGTAACCACAAAGAATGC
Found at i:12370744 original size:27 final size:27
Alignment explanation
Indices: 12370714--12370789 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
12370704 AAGATAGTGA
* *
12370714 ATCATTGCTTTGAGTAAGGCCCCACAG
1 ATCATTACTTTGAGCAAGGCCCCACAG
*
12370741 ATCATTACTTTGGGCAAGGCCCCACAG
1 ATCATTACTTTGAGCAAGGCCCCACAG
* *
12370768 ATCATTACTTTAAGCAATGCCC
1 ATCATTACTTTGAGCAAGGCCC
12370790 AGCAGATGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (27 bp):
ATCATTACTTTGAGCAAGGCCCCACAG
Found at i:12374874 original size:14 final size:14
Alignment explanation
Indices: 12374855--12374886 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
12374845 TATACGTGCA
*
12374855 TGTGGCCTAGTAAT
1 TGTGGCCAAGTAAT
12374869 TGTGGCCAAGTAAT
1 TGTGGCCAAGTAAT
12374883 TGTG
1 TGTG
12374887 ACCCTTCAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.22, C:0.12, G:0.31, T:0.34
Consensus pattern (14 bp):
TGTGGCCAAGTAAT
Found at i:12393095 original size:20 final size:20
Alignment explanation
Indices: 12393070--12393112 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
12393060 ATTAGAATAT
12393070 ATAAAAAAGTAAAAATAAAG
1 ATAAAAAAGTAAAAATAAAG
12393090 ATAAAAAAGTAAAAATAAAG
1 ATAAAAAAGTAAAAATAAAG
12393110 ATA
1 ATA
12393113 TCTGTCCCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.16
Consensus pattern (20 bp):
ATAAAAAAGTAAAAATAAAG
Found at i:12397813 original size:4 final size:4
Alignment explanation
Indices: 12397804--12397829 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
12397794 AAAAAAGAAG
12397804 AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AA
12397830 TGTTATGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:12399834 original size:20 final size:20
Alignment explanation
Indices: 12399809--12399848 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12399799 TTAATATGAA
* *
12399809 ATTCTTTTATTTAGTATTTT
1 ATTCTTCTATTTAATATTTT
12399829 ATTCTTCTATTTAATATTTT
1 ATTCTTCTATTTAATATTTT
12399849 TTTACTTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.68
Consensus pattern (20 bp):
ATTCTTCTATTTAATATTTT
Found at i:12410249 original size:16 final size:16
Alignment explanation
Indices: 12410228--12410261 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
12410218 CTCGGTCCTT
12410228 TCCCTCTGTCTTTTGG
1 TCCCTCTGTCTTTTGG
12410244 TCCCTCTGTCTTTTGG
1 TCCCTCTGTCTTTTGG
12410260 TC
1 TC
12410262 ACAAGTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.32, G:0.18, T:0.50
Consensus pattern (16 bp):
TCCCTCTGTCTTTTGG
Found at i:12411519 original size:22 final size:19
Alignment explanation
Indices: 12411494--12411535 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
12411484 TGATAATCAT
12411494 TAATATATAATTATATCTATTA
1 TAATATAT-ATTA-AT-TATTA
12411516 TAATATATATTAATTATTA
1 TAATATATATTAATTATTA
12411535 T
1 T
12411536 CAACTTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 4 0.20
22 8 0.40
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATATATATTAATTATTA
Found at i:12412285 original size:25 final size:24
Alignment explanation
Indices: 12412256--12412311 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 24
12412246 TTTCTCCTAA
*
12412256 ATTTTAATTTTATTTAATTATTTAAT
1 ATTTTAA-TTTATTGAATTA-TTAAT
12412282 -TTTTCAATTTATTGAATTATTAAT
1 ATTTT-AATTTATTGAATTATTAAT
12412306 ATTTTA
1 ATTTTA
12412312 TACTAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 6 0.22
25 19 0.70
26 2 0.07
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (24 bp):
ATTTTAATTTATTGAATTATTAAT
Done.