Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397255.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_44.0, whole genome shotgun sequence
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: 14367614
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 51264 characters in sequence are not A, C, G, or T
File 22 of 31
Found at i:10539545 original size:27 final size:26
Alignment explanation
Indices: 10539482--10539545 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 26
10539472 AGTATGTATC
**
10539482 AACTATATTTTTCAACATGTGTGCAAT
1 AACTATA-TTTTCAACATACGTGCAAT
* * *
10539509 AATTAAATTTTCAACATAACGTGTAAT
1 AACTATATTTTCAACAT-ACGTGCAAT
10539536 AACTATATTT
1 AACTATATTT
10539546 AATAACTAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
26 10 0.34
27 19 0.66
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (26 bp):
AACTATATTTTCAACATACGTGCAAT
Found at i:10539681 original size:27 final size:26
Alignment explanation
Indices: 10539611--10539689 Score: 86
Period size: 27 Copynumber: 3.0 Consensus size: 26
10539601 ATAACTTTAC
* * *
10539611 TTTTCAACATGCATGTAATAATCAAA
1 TTTTCAACATGCATGTAACAATTATA
* **
10539637 TTTTCAATATGGTGTGTAACAATTATA
1 TTTTCAACAT-GCATGTAACAATTATA
10539664 TTTTCAACATAGCATGTAACAATTAT
1 TTTTCAACAT-GCATGTAACAATTAT
10539690 TTCAAACATG
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
26 9 0.21
27 33 0.79
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (26 bp):
TTTTCAACATGCATGTAACAATTATA
Found at i:10539719 original size:52 final size:52
Alignment explanation
Indices: 10539611--10539719 Score: 114
Period size: 52 Copynumber: 2.1 Consensus size: 52
10539601 ATAACTTTAC
* * * * *
10539611 TTTTCAACATGCATGTAATAATCAAATTTTCAATATGGTGTGTAACAATTATA
1 TTTTCAACATGCATGTAACAAT-AAATTTTCAACATGGTGTATAACAACTAAA
* *
10539664 TTTTCAACATAGCATGTAACAAT-TA-TTTCAAACATGGTGTATAATAACTAAA
1 TTTTCAACAT-GCATGTAACAATAAATTTTC-AACATGGTGTATAACAACTAAA
10539716 TTTT
1 TTTT
10539720 AAAATATGGT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
51 4 0.09
52 22 0.47
53 10 0.21
54 11 0.23
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (52 bp):
TTTTCAACATGCATGTAACAATAAATTTTCAACATGGTGTATAACAACTAAA
Found at i:10544917 original size:89 final size:86
Alignment explanation
Indices: 10544763--10544941 Score: 268
Period size: 89 Copynumber: 2.0 Consensus size: 86
10544753 AAGAGTTCAC
* * *
10544763 AAAGATTGTTACTTTTCAAGCATACAGCCAATCTAAAGAGGAATATACATTTCGGTAAGGGTAGA
1 AAAGATTGTTACTTTTCAAGCATACAGCAAATCTAAAGAGGAATATACATTTCAGTAAGGCTAGA
*
10544828 ATTAAACTATGCAAATGTTTTT
66 ATT-AACTATGCAAATGCTTTT
*
10544850 AAAGATTGTTACTTTTTTCAAGCATACAGCAAATCTAAAGAGGAATATACGTTTCAGTAAGGCTA
1 AAAGATTGTTAC--TTTTCAAGCATACAGCAAATCTAAAGAGGAATATACATTTCAGTAAGGCTA
* *
10544915 GAATTAACTGTGCACATGCTTTT
64 GAATTAACTATGCAAATGCTTTT
10544938 AAAG
1 AAAG
10544942 GCAATGGACT
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
87 12 0.14
88 19 0.23
89 52 0.63
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.32
Consensus pattern (86 bp):
AAAGATTGTTACTTTTCAAGCATACAGCAAATCTAAAGAGGAATATACATTTCAGTAAGGCTAGA
ATTAACTATGCAAATGCTTTT
Found at i:10548157 original size:2 final size:2
Alignment explanation
Indices: 10548150--10548177 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10548140 TTAGATATGA
10548150 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
10548178 GCTTTGTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10552248 original size:263 final size:263
Alignment explanation
Indices: 10551773--10552298 Score: 748
Period size: 263 Copynumber: 2.0 Consensus size: 263
10551763 TCGTTCAAAG
* *
10551773 AAATGGTTATTGAGGAAAATACTCGTATGATATTGTGAAGTCAAAAGATCAAGAGCACAGAGGTC
1 AAATGGTTACTGAGGAAAATACTCGTATGATATTGCGAAGTCAAAAGATCAAGAGCACAGAGGTC
* * * *
10551838 ATTAAAAATCAGATAATGAAGGTGGGTAGCACTAAAATAAAGACTCTGAGAGGGAAAGTGACAAG
66 ATTAAAAATCAAATAATGAAGGTGGATAGCACCAAAACAAAGACTCTGAGAGGGAAAGTGACAAG
* * *
10551903 AAAAAACAAAAATAATCAGGGCATGGTTTCGGCCAAAATCTCTATTCCATATGAGGGGATGTATT
131 AAAAAACAAAAATAATCAGGGCATGGTTTCGGCCAAAATCTCTATTCCAGAGGAAGGGATGTATT
* * * * * *
10551968 AGGTGGAAACCAGCTCTATTGGTAGACT-TAGGGAAATGACGCCATGCATGGTTATTCAAAGAAA
196 AGGTGAAAACCAGCTCTATTGGTAGACTCAAGAG-AAGGACGCCATGCATGATCATTCAAAGAAA
10552032 TCTT
260 TCTT
* * * *
10552036 AAATGGTTACTGAGGAGAATACTCTTATGATATTGCGAAGTCAAAAGATCGAGAGCATAGAGGTC
1 AAATGGTTACTGAGGAAAATACTCGTATGATATTGCGAAGTCAAAAGATCAAGAGCACAGAGGTC
* * * * *
10552101 GTTGAAAATCAAATAATGAAGGTGGATAGCACCAAAACAAAGACTTTGAGAGGGAAGGTGACAGG
66 ATTAAAAATCAAATAATGAAGGTGGATAGCACCAAAACAAAGACTCTGAGAGGGAAAGTGACAAG
* * ** * *
10552166 AAACAACAAAAATAATCATGGCATGGTTTTTGCCAAAATCTTTATTCTAGAGGAAGGGATGTATT
131 AAAAAACAAAAATAATCAGGGCATGGTTTCGGCCAAAATCTCTATTCCAGAGGAAGGGATGTATT
* *
10552231 GGGTGAAAACTAGCTCTATTGGTAGACTCAAGAGAAGGACGCCATGCATGATCATTCAAAGAAAT
196 AGGTGAAAACCAGCTCTATTGGTAGACTCAAGAGAAGGACGCCATGCATGATCATTCAAAGAAAT
10552296 CTT
261 CTT
10552299 GCAAATGAAG
Statistics
Matches: 230, Mismatches: 32, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
263 227 0.99
264 3 0.01
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (263 bp):
AAATGGTTACTGAGGAAAATACTCGTATGATATTGCGAAGTCAAAAGATCAAGAGCACAGAGGTC
ATTAAAAATCAAATAATGAAGGTGGATAGCACCAAAACAAAGACTCTGAGAGGGAAAGTGACAAG
AAAAAACAAAAATAATCAGGGCATGGTTTCGGCCAAAATCTCTATTCCAGAGGAAGGGATGTATT
AGGTGAAAACCAGCTCTATTGGTAGACTCAAGAGAAGGACGCCATGCATGATCATTCAAAGAAAT
CTT
Found at i:10561834 original size:21 final size:21
Alignment explanation
Indices: 10561823--10561877 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
10561813 ATGGCATCAA
* *
10561823 TTTTTGTCATGAAAGCATTTG
1 TTTTTGTCATGAAGGCATTAG
*
10561844 TCTTTGTCATGAAGGCATTAG
1 TTTTTGTCATGAAGGCATTAG
10561865 TTTTTGTCATGAA
1 TTTTTGTCATGAA
10561878 TTTCATGAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.45
Consensus pattern (21 bp):
TTTTTGTCATGAAGGCATTAG
Found at i:10569723 original size:2 final size:2
Alignment explanation
Indices: 10569718--10569742 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10569708 CTACTATTTC
10569718 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
10569743 CCTGTAAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10573763 original size:15 final size:16
Alignment explanation
Indices: 10573743--10573776 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
10573733 TTATGGCAAG
*
10573743 AATTAATACT-ATAAT
1 AATTAATAATAATAAT
10573758 AATTAATAATAATAAT
1 AATTAATAATAATAAT
10573774 AAT
1 AAT
10573777 ATGCAAGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
AATTAATAATAATAAT
Found at i:10575628 original size:29 final size:29
Alignment explanation
Indices: 10575595--10575661 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
10575585 AATCTCTTAA
10575595 ATTATTTTAAAAAATTTAAATAAATTCTT
1 ATTATTTTAAAAAATTTAAATAAATTCTT
** * * *
10575624 ATTATTTTATTATATTTAATTAAATTTTT
1 ATTATTTTAAAAAATTTAAATAAATTCTT
*
10575653 ATAATTTTA
1 ATTATTTTA
10575662 TTTTGATCCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (29 bp):
ATTATTTTAAAAAATTTAAATAAATTCTT
Found at i:10575662 original size:29 final size:29
Alignment explanation
Indices: 10575608--10575663 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
10575598 ATTTTAAAAA
*
10575608 ATTTAAATAAATTCTTATTATTTTATTAT
1 ATTTAAATAAATTCTTATAATTTTATTAT
* *
10575637 ATTTAATTAAATTTTTATAATTTTATT
1 ATTTAAATAAATTCTTATAATTTTATT
10575664 TTGATCCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (29 bp):
ATTTAAATAAATTCTTATAATTTTATTAT
Found at i:10579808 original size:18 final size:18
Alignment explanation
Indices: 10579762--10579797 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
10579752 AATTTTTTTT
*
10579762 AAATAAT-ATCATAATTA
1 AAATAATAATAATAATTA
10579779 AAATAATAATAATAATTA
1 AAATAATAATAATAATTA
10579797 A
1 A
10579798 TAAATTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAATAATAATAATTA
Found at i:10584217 original size:60 final size:62
Alignment explanation
Indices: 10584122--10584243 Score: 203
Period size: 60 Copynumber: 2.0 Consensus size: 62
10584112 TTGTGTGATC
* *
10584122 ATGCTATTTTTTCTTTTTTTGAAAGGCAAGCTTTTTAATTAAGAAGATAAGAAGGGGTTGTT
1 ATGCTATTTTTTCTTTTTTTGAAAGGCAAACTTTTTAATTAAGAAGATAAGAAAGGGTTGTT
*
10584184 ATGCTA-TTTTT-TTTTTTTGAAAGGTAAACTTTTTAATTAAGAAGATAAGAAAGGGTTGTT
1 ATGCTATTTTTTCTTTTTTTGAAAGGCAAACTTTTTAATTAAGAAGATAAGAAAGGGTTGTT
10584244 TACCTTACAT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
60 46 0.81
61 5 0.09
62 6 0.11
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (62 bp):
ATGCTATTTTTTCTTTTTTTGAAAGGCAAACTTTTTAATTAAGAAGATAAGAAAGGGTTGTT
Found at i:10585092 original size:52 final size:51
Alignment explanation
Indices: 10584967--10585311 Score: 232
Period size: 52 Copynumber: 6.5 Consensus size: 51
10584957 ATTGAAATCC
*
10584967 TTTT-TTGAGTTTTCCCACCACTTTGGTGAAAACT-AAGAAATTTTGTTTAGAAAC
1 TTTTCTTGAGTTTTCCCACCACTTTGGT-AAAA-TAAAG-AA-TTT-TTTAGAAAT
* *
10585021 TTTTCTTGAGTTTTTCCACCACTTTGACTAAAATAAAGAATTTTTTAGAAAT
1 TTTTCTTGAGTTTTCCCACCACTTTG-GTAAAATAAAGAATTTTTTAGAAAT
* * * * * *
10585073 TTTTCTTGAGCTTTCCCACCACTCTGGTGAAACACAA-AACTTTTTAAAAAT
1 TTTTCTTGAGTTTTCCCACCACTTTGGTAAAATA-AAGAATTTTTTAGAAAT
* * *
10585124 CTTTTCTTGAGTTTTGCCACCACTTTGGTGAAAA-CAAGAATTTTTTAAAAAAAT
1 -TTTTCTTGAGTTTTCCCACCACTTTGGT-AAAATAAAGAATTTTTT--AGAAAT
* * * * * * *
10585178 TTTAC-TGAAATTTTAATCCCAACACTTTAGTGAAATCCAAGAATTTTTTCAGAAAC
1 TTTTCTTG--AGTTT--TCCCACCACTTTGGTAAAAT-AAAGAATTTTTT-AGAAAT
* * ** * * *
10585234 TTTTCTTGAGTTTTACCAACACTTTGAAAAAATAAAAAAATTTCTAGAAAT
1 TTTTCTTGAGTTTTCCCACCACTTTGGTAAAATAAAGAATTTTTTAGAAAT
* * * *
10585285 TTTTGTTTAGTTTTCCCTCAACTTTGG
1 TTTTCTTGAGTTTTCCCACCACTTTGG
10585312 CGAAAACCAT
Statistics
Matches: 230, Mismatches: 45, Indels: 35
0.74 0.15 0.11
Matches are distributed among these distances:
51 44 0.19
52 75 0.33
53 25 0.11
54 17 0.07
55 34 0.15
56 21 0.09
57 14 0.06
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (51 bp):
TTTTCTTGAGTTTTCCCACCACTTTGGTAAAATAAAGAATTTTTTAGAAAT
Found at i:10586103 original size:2 final size:2
Alignment explanation
Indices: 10586098--10586124 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10586088 AGTACTTCAT
10586098 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
10586125 TGCATTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10586459 original size:23 final size:25
Alignment explanation
Indices: 10586418--10586470 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
10586408 TCTAATTTCA
*
10586418 TATTTTTCATTTTCATCTTTA-AAT
1 TATTTTTCATATTCATCTTTATAAT
* *
10586442 TATTTTT-ATATTCCTCTTTATGAT
1 TATTTTTCATATTCATCTTTATAAT
10586466 TATTT
1 TATTT
10586471 GAAATTATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.23, C:0.11, G:0.02, T:0.64
Consensus pattern (25 bp):
TATTTTTCATATTCATCTTTATAAT
Found at i:10594418 original size:63 final size:63
Alignment explanation
Indices: 10594329--10594454 Score: 146
Period size: 63 Copynumber: 2.0 Consensus size: 63
10594319 TGAGATTTGG
* * * * *
10594329 TGCATTTTGATTGTTGTTATTAGAGTTTATCTGTTTTGCAATAACATGTAACTTTTTAAACAT
1 TGCATTTTGATCGTTGTTATCAGAGTTTATCTGTTTTGCAACAACATGCAACTTGTTAAACAT
* * * * *
10594392 TGCATTTTGATCGCTT-TTATCGGAGTTTGTTTGTTTTGCGACAATATGCAACTTGTTAAACAT
1 TGCATTTTGATCG-TTGTTATCAGAGTTTATCTGTTTTGCAACAACATGCAACTTGTTAAACAT
10594455 ATAAGTTTGA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
63 50 0.96
64 2 0.04
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.47
Consensus pattern (63 bp):
TGCATTTTGATCGTTGTTATCAGAGTTTATCTGTTTTGCAACAACATGCAACTTGTTAAACAT
Found at i:10598028 original size:42 final size:42
Alignment explanation
Indices: 10597978--10598061 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
10597968 GAGGTGAATG
10597978 GTTAAGAAACCTCTTAATAGATATTCCATTAGGAATGAAACT
1 GTTAAGAAACCTCTTAATAGATATTCCATTAGGAATGAAACT
10598020 GTTAAGAAACCTCTTAATAGATATTCCATTAGGAATGAAACT
1 GTTAAGAAACCTCTTAATAGATATTCCATTAGGAATGAAACT
10598062 AACACCTTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (42 bp):
GTTAAGAAACCTCTTAATAGATATTCCATTAGGAATGAAACT
Found at i:10599171 original size:46 final size:46
Alignment explanation
Indices: 10599104--10599196 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
10599094 CATATAAGTT
* *
10599104 TATTTTTTCTCAATCTTTAGTAGTTGAAACAGTATTAATGATTGAG
1 TATTTTTTCTCAACCTTTAGTAGTTGAAACAGTATAAATGATTGAG
*
10599150 TATTTTTTCTCAACCTTTAGTAGTTGAAACAGTCTAAATGATTGAG
1 TATTTTTTCTCAACCTTTAGTAGTTGAAACAGTATAAATGATTGAG
10599196 T
1 T
10599197 CTGTTAATCT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (46 bp):
TATTTTTTCTCAACCTTTAGTAGTTGAAACAGTATAAATGATTGAG
Found at i:10603122 original size:24 final size:24
Alignment explanation
Indices: 10603088--10603143 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
10603078 AAAAAAGAAC
* *
10603088 AAAAAGA-AAAGGAAAAGAGAAAT
1 AAAAAGAGAAAGGAAAAAACAAAT
*
10603111 AAAAAGAGAAAGGAAAAAACAAGT
1 AAAAAGAGAAAGGAAAAAACAAAT
10603135 AAAAAGAGA
1 AAAAAGAGA
10603144 CCTCTATGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 7 0.24
24 22 0.76
ACGTcount: A:0.73, C:0.02, G:0.21, T:0.04
Consensus pattern (24 bp):
AAAAAGAGAAAGGAAAAAACAAAT
Found at i:10603636 original size:20 final size:20
Alignment explanation
Indices: 10603611--10603651 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
10603601 ATATCCTCAA
* *
10603611 CTTCTCTGGTAATTCTACTC
1 CTTCTCTAGTAATTATACTC
10603631 CTTCTCTAGTAATTATACTC
1 CTTCTCTAGTAATTATACTC
10603651 C
1 C
10603652 CTCTTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.29, G:0.07, T:0.44
Consensus pattern (20 bp):
CTTCTCTAGTAATTATACTC
Found at i:10616205 original size:116 final size:116
Alignment explanation
Indices: 10616001--10616232 Score: 410
Period size: 116 Copynumber: 2.0 Consensus size: 116
10615991 TCACATTGGT
*
10616001 AGTGAACAAACAAGGGAAGTTATGTGAATATGGCAAACGGACTGACCAAAGGTGGCAATGGAGAA
1 AGTGAACAAACAAGGGAAGGTATGTGAATATGGCAAACGGACTGACCAAAGGTGGCAATGGAGAA
* * *
10616066 TTGAGTTAAGAAGGCAACTGTTTGGTTGAGAATTTGAACAATGGACAAGAC
66 TTGAGTTAAGAAGACAACTGTTTGGTTGAGAATTTAAAAAATGGACAAGAC
* *
10616117 AGTGAACAAACAAGGGAAGGTATGTGAATATGGCAAATGGACTGACCAAGGGTGGCAATGGAGAA
1 AGTGAACAAACAAGGGAAGGTATGTGAATATGGCAAACGGACTGACCAAAGGTGGCAATGGAGAA
10616182 TTGAGTTAAGAAGACAACTGTTTGGTTGAGAATTTAAAAAATGGACAAGAC
66 TTGAGTTAAGAAGACAACTGTTTGGTTGAGAATTTAAAAAATGGACAAGAC
10616233 TCTGGAGTTT
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
116 110 1.00
ACGTcount: A:0.40, C:0.10, G:0.29, T:0.21
Consensus pattern (116 bp):
AGTGAACAAACAAGGGAAGGTATGTGAATATGGCAAACGGACTGACCAAAGGTGGCAATGGAGAA
TTGAGTTAAGAAGACAACTGTTTGGTTGAGAATTTAAAAAATGGACAAGAC
Found at i:10617053 original size:38 final size:38
Alignment explanation
Indices: 10617000--10617077 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
10616990 TTGTTTAATA
*
10617000 GGAAGAGTTTTATCTTGCAAAGGAATCCTAGCTTGATT
1 GGAAGAGTTTCATCTTGCAAAGGAATCCTAGCTTGATT
*
10617038 GGAAGAGTTTCATCTTGCAAAGGAATCCTAGTTTGATT
1 GGAAGAGTTTCATCTTGCAAAGGAATCCTAGCTTGATT
10617076 GG
1 GG
10617078 GATGTCGAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (38 bp):
GGAAGAGTTTCATCTTGCAAAGGAATCCTAGCTTGATT
Found at i:10619710 original size:28 final size:28
Alignment explanation
Indices: 10619679--10619732 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
10619669 AATTTTTTTA
10619679 TAAAATTTGAGATT-TTT-AATTGAAAAAT
1 TAAAATTT-A-ATTCTTTGAATTGAAAAAT
10619707 TAAAATTTAATTCTTTGAATTGAAAA
1 TAAAATTTAATTCTTTGAATTGAAAA
10619733 GATACATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 3 0.12
27 4 0.17
28 17 0.71
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (28 bp):
TAAAATTTAATTCTTTGAATTGAAAAAT
Found at i:10621716 original size:21 final size:20
Alignment explanation
Indices: 10621687--10621727 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
10621677 NNNNNNNNNN
*
10621687 TAAAGTAAATAAATATAAAAT
1 TAAAATAAATAAATA-AAAAT
*
10621708 TAAAATAAATTAATAAAAAT
1 TAAAATAAATAAATAAAAAT
10621728 AAACTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (20 bp):
TAAAATAAATAAATAAAAAT
Found at i:10621748 original size:16 final size:18
Alignment explanation
Indices: 10621701--10621750 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
10621691 GTAAATAAAT
* *
10621701 ATAAAATTAAAATAAATTA
1 ATAAAAATAAACT-AATTA
10621720 ATAAAAATAAACTAATT-
1 ATAAAAATAAACTAATTA
10621737 ATAAAAAT-AACTAA
1 ATAAAAATAAACTAA
10621751 ACTATAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 6 0.21
17 8 0.28
18 4 0.14
19 11 0.38
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (18 bp):
ATAAAAATAAACTAATTA
Found at i:10621756 original size:17 final size:17
Alignment explanation
Indices: 10621720--10621757 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
10621710 AAATAAATTA
*
10621720 ATAAAAATAAACTAATT
1 ATAAAAATAAACTAACT
10621737 ATAAAAAT-AACTAAACT
1 ATAAAAATAAACT-AACT
10621754 ATAA
1 ATAA
10621758 TTAAAAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAAAATAAACTAACT
Found at i:10622241 original size:32 final size:32
Alignment explanation
Indices: 10622170--10622252 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 32
10622160 TAGAAGGGCT
** ***
10622170 AAACTATAAAATTTTTTAA-AAAATAAAGGTA
1 AAACTATAAAATTTTAAAACAAAATAAAAACA
10622201 AAACTATAAAATTTTAAAACAAAATAAAAACA
1 AAACTATAAAATTTTAAAACAAAATAAAAACA
* * *
10622233 AAATTATAAATTTTTGAAAC
1 AAACTATAAAATTTTAAAAC
10622253 TTTTGAGGAT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 17 0.40
32 26 0.60
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (32 bp):
AAACTATAAAATTTTAAAACAAAATAAAAACA
Found at i:10638270 original size:8 final size:8
Alignment explanation
Indices: 10638234--10638412 Score: 50
Period size: 7 Copynumber: 23.0 Consensus size: 8
10638224 ATCTCTTAAA
10638234 TATATTTT
1 TATATTTT
*
10638242 TA-A-TGT
1 TATATTTT
*
10638248 TATA-TAT
1 TATATTTT
10638255 TATATTTT
1 TATATTTT
10638263 TAT-TTTT
1 TATATTTT
*
10638270 TATTATGATCT
1 TA-TAT--TTT
*
10638281 TATATATT
1 TATATTTT
10638289 T-TATTTT
1 TATATTTT
10638296 TAT-TTTT
1 TATATTTT
10638303 ATATTAATTTT
1 -TA-T-ATTTT
*
10638314 TATATTATA
1 TATATT-TT
10638323 TATTATATTT
1 TA-TAT-TTT
10638333 TA-ATTTT
1 TATATTTT
10638340 T-T-TTTACT
1 TATATTT--T
*
10638348 TATA-TTA
1 TATATTTT
*
10638355 TATAAATTT
1 TAT-ATTTT
10638364 TA-ATTTT
1 TATATTTT
10638371 T-TATTTT
1 TATATTTT
10638378 TATA---T
1 TATATTTT
*
10638383 TATATATT
1 TATATTTT
10638391 T-TATTTT
1 TATATTTT
*
10638398 AATATTTT
1 TATATTTT
10638406 T-TATTTT
1 TATATTTT
10638413 AATCATAATA
Statistics
Matches: 129, Mismatches: 15, Indels: 55
0.65 0.08 0.28
Matches are distributed among these distances:
5 5 0.04
6 7 0.05
7 53 0.41
8 31 0.24
9 13 0.10
10 11 0.09
11 9 0.07
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (8 bp):
TATATTTT
Found at i:10638331 original size:71 final size:76
Alignment explanation
Indices: 10638234--10638415 Score: 221
Period size: 71 Copynumber: 2.4 Consensus size: 76
10638224 ATCTCTTAAA
* * *
10638234 TATATTTTTAATGTTATATATTATATTTTTATTTTTTATTA-TGATCTTATAT-ATTTT-A-TTT
1 TATATTTTT-ATATTATATATTATATTTTAATTTTTTATTACTGATATTATATAATTTTAATTTT
10638295 TTATTTTTATAT
65 TTATTTTTATAT
* *
10638307 TA-ATTTTTATATTATATATTATATTTTAATTTTTTTTTACTTATATTATATAAATTTTAATTTT
1 TATATTTTTATATTATATATTATATTTTAATTTTTTATTACTGATATTATAT-AATTTTAATTTT
10638371 TTATTTTTATAT
65 TTATTTTTATAT
* * *
10638383 TATATATTTTATTTTAATATTTTTTATTTTAAT
1 TATAT-TTTTATATT-ATATATTATATTTTAAT
10638416 CATAATATTA
Statistics
Matches: 93, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
71 28 0.30
72 15 0.16
73 2 0.02
74 5 0.05
75 1 0.01
76 17 0.18
77 2 0.02
78 8 0.09
79 15 0.16
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (76 bp):
TATATTTTTATATTATATATTATATTTTAATTTTTTATTACTGATATTATATAATTTTAATTTTT
TATTTTTATAT
Found at i:10638378 original size:64 final size:69
Alignment explanation
Indices: 10638236--10638409 Score: 198
Period size: 64 Copynumber: 2.6 Consensus size: 69
10638226 CTCTTAAATA
* * * * * *
10638236 TATTTTTAATGTTATATATTATATTTTTATTTTTTATTATGATCTTATATATTTTATTTTTATTT
1 TATTTTT-ATATTATATATTATATTTTAATTTTTT-TTATGATCTTATATATATAAATTTTATAT
10638301 TTATAT
64 TTATAT
10638307 TAATTTTTATATTATATATTATATTTTAATTTTTTTT-T-A-CTTATATTATATAAATTTTA-AT
1 T-ATTTTTATATTATATATTATATTTTAATTTTTTTTATGATCTTATA-TATATAAATTTTATAT
10638368 TT-T-T
64 TTATAT
* *
10638372 TATTTTTATATTATATATTTTATTTTAATATTTTTTAT
1 TATTTTTATATTATATATTATATTTTAATTTTTTTTAT
10638410 TTTAATCATA
Statistics
Matches: 92, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
64 33 0.36
65 3 0.03
66 1 0.01
67 9 0.10
68 11 0.12
69 1 0.01
70 2 0.02
71 26 0.28
72 6 0.07
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (69 bp):
TATTTTTATATTATATATTATATTTTAATTTTTTTTATGATCTTATATATATAAATTTTATATTT
ATAT
Found at i:10638386 original size:28 final size:27
Alignment explanation
Indices: 10638355--10638410 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
10638345 ACTTATATTA
*
10638355 TATAAATTTTAATTTT-TTATTTTTATAT
1 TATAAATTTT-ATTTTAATATTTTT-TAT
*
10638383 TATATATTTTATTTTAATATTTTTTAT
1 TATAAATTTTATTTTAATATTTTTTAT
10638410 T
1 T
10638411 TTAATCATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 9 0.36
28 16 0.64
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (27 bp):
TATAAATTTTATTTTAATATTTTTTAT
Found at i:10638413 original size:15 final size:15
Alignment explanation
Indices: 10638374--10638415 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
10638364 TAATTTTTTA
*
10638374 TTTTTATATT-ATAT
1 TTTTTATTTTAATAT
*
10638388 ATTTTATTTTAATAT
1 TTTTTATTTTAATAT
10638403 TTTTTATTTTAAT
1 TTTTTATTTTAAT
10638416 CATAATATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTATTTTAATAT
Found at i:10639462 original size:14 final size:14
Alignment explanation
Indices: 10639403--10639468 Score: 55
Period size: 14 Copynumber: 4.7 Consensus size: 14
10639393 TATATAAGTT
*
10639403 ATATGTTAATATTA
1 ATATATTAATATTA
*
10639417 ATATA-TAATTATAA
1 ATATATTAA-TATTA
* *
10639431 ATATCTT-ATATCTT
1 ATATATTAATAT-TA
10639445 ATATATTAATATTA
1 ATATATTAATATTA
*
10639459 ATATAATAAT
1 ATATATTAAT
10639469 TACACCTATA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
13 6 0.15
14 29 0.73
15 5 0.12
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (14 bp):
ATATATTAATATTA
Found at i:10641635 original size:101 final size:98
Alignment explanation
Indices: 10641523--10641710 Score: 259
Period size: 101 Copynumber: 1.9 Consensus size: 98
10641513 AAAACTATTA
* * * * * *
10641523 AAAAAATAGAAGACCCAATAATAGAATATCAAAATATAAATTTTTTTTTGTTTTTACAAAGATTA
1 AAAAAAGAGAAGACCCAACAACAAAATATCAAAACATAAA-ATTTTTTTGTTTTTACAAAGATT-
*
10641588 AGAGAAAAAAAATTTAAAATTCAAAACTACATTCAG
64 A-AGAAAAAAAATCTAAAATTCAAAACTACATTCAG
* * *
10641624 AAAAAAGAGAAGACTCAACAACAAAATATCCAAACCTAAAATTTTTTTGTTTTTACAAAGATTAA
1 AAAAAAGAGAAGACCCAACAACAAAATATCAAAACATAAAATTTTTTTGTTTTTACAAAGATTAA
10641689 GAAAAAAAATCTAAAATTCAAA
66 GAAAAAAAATCTAAAATTCAAA
10641711 TTGCATTCAG
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
98 22 0.29
99 1 0.01
100 22 0.29
101 32 0.42
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.28
Consensus pattern (98 bp):
AAAAAAGAGAAGACCCAACAACAAAATATCAAAACATAAAATTTTTTTGTTTTTACAAAGATTAA
GAAAAAAAATCTAAAATTCAAAACTACATTCAG
Found at i:10652999 original size:20 final size:20
Alignment explanation
Indices: 10652974--10653012 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
10652964 ATTGCTTAGG
10652974 AGTATAGTTATTTGAAATTT
1 AGTATAGTTATTTGAAATTT
10652994 AGTATAGTTATTTGAAATT
1 AGTATAGTTATTTGAAATT
10653013 CTGTGTCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (20 bp):
AGTATAGTTATTTGAAATTT
Found at i:10658269 original size:24 final size:24
Alignment explanation
Indices: 10658228--10658292 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 24
10658218 CCCGCCGGGA
*
10658228 GGCG-CGCGCGGCGCCCGCACG-AGC
1 GGCGCCGCGC-GCGGCCGC-CGCAGC
*
10658252 GGCGCCGC-CGACGGCCGCCGCGGC
1 GGCGCCGCGCG-CGGCCGCCGCAGC
10658276 GGCGCCGCGCGCGGCCG
1 GGCGCCGCGCGCGGCCG
10658293 GCACCCGCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
23 3 0.09
24 27 0.77
25 5 0.14
ACGTcount: A:0.05, C:0.48, G:0.48, T:0.00
Consensus pattern (24 bp):
GGCGCCGCGCGCGGCCGCCGCAGC
Found at i:10658290 original size:15 final size:16
Alignment explanation
Indices: 10658265--10658304 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
10658255 GCCGCCGACG
10658265 GCCGC-CGCGG-CGGC
1 GCCGCGCGCGGCCGGC
10658279 GCCGCGCGCGGCCGGC
1 GCCGCGCGCGGCCGGC
*
10658295 ACC-CGCGCGG
1 GCCGCGCGCGG
10658305 GGCCATGCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 5 0.22
15 12 0.52
16 6 0.26
ACGTcount: A:0.03, C:0.50, G:0.47, T:0.00
Consensus pattern (16 bp):
GCCGCGCGCGGCCGGC
Found at i:10658433 original size:3 final size:3
Alignment explanation
Indices: 10658427--10658477 Score: 50
Period size: 3 Copynumber: 16.3 Consensus size: 3
10658417 GACGCGCCGC
* *
10658427 CGG CGG CGG CGG CCGG -GG CGG CGCG CGC CGG CGCG CGG CGG CGC CGG
1 CGG CGG CGG CGG -CGG CGG CGG CG-G CGG CGG CG-G CGG CGG CGG CGG
10658474 CGG C
1 CGG C
10658478 TCGACGGGCG
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 2 0.05
3 29 0.73
4 9 0.22
ACGTcount: A:0.00, C:0.41, G:0.59, T:0.00
Consensus pattern (3 bp):
CGG
Found at i:10658448 original size:15 final size:16
Alignment explanation
Indices: 10658408--10658477 Score: 67
Period size: 16 Copynumber: 4.4 Consensus size: 16
10658398 CCGGGCGCCG
*
10658408 CGGCGGCGG-GACGCGC
1 CGGCGGCGGCGGCG-GC
*
10658424 CGCCGGCGGCGGCGGC
1 CGGCGGCGGCGGCGGC
10658440 CGG-GGCGGC-GCGCGC
1 CGGCGGCGGCGGCG-GC
10658455 CGGCGCGCGGCGGC-GC
1 CGGCG-GCGGCGGCGGC
10658471 CGGCGGC
1 CGGCGGC
10658478 TCGACGGGCG
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
14 3 0.07
15 13 0.28
16 20 0.43
17 8 0.17
18 2 0.04
ACGTcount: A:0.01, C:0.41, G:0.57, T:0.00
Consensus pattern (16 bp):
CGGCGGCGGCGGCGGC
Found at i:10658460 original size:10 final size:10
Alignment explanation
Indices: 10658427--10658477 Score: 63
Period size: 9 Copynumber: 5.4 Consensus size: 10
10658417 GACGCGCCGC
10658427 CGGCG-GCGG
1 CGGCGCGCGG
*
10658436 CGGC-CGGGG
1 CGGCGCGCGG
*
10658445 CGGCGCGCGC
1 CGGCGCGCGG
10658455 CGGCGCGCGG
1 CGGCGCGCGG
10658465 CGGCGC-CGG
1 CGGCGCGCGG
10658474 CGGC
1 CGGC
10658478 TCGACGGGCG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
9 18 0.50
10 18 0.50
ACGTcount: A:0.00, C:0.41, G:0.59, T:0.00
Consensus pattern (10 bp):
CGGCGCGCGG
Found at i:10658512 original size:43 final size:39
Alignment explanation
Indices: 10658419--10658513 Score: 95
Period size: 43 Copynumber: 2.4 Consensus size: 39
10658409 GGCGGCGGGA
* *
10658419 CGCGCCGCCGGCGGCGGCGGCCGGGGCGGCGCGCGCCGG
1 CGCGCGGCCGGCGCCGGCGGCCGGGGCGGCGCGCGCCGG
*
10658458 CGCGCGG-CGGCGCCGGCGGCTCGACGGGCGCGCCGCGCGCGGG
1 CGCGCGGCCGGCGCCGGCGGC-CG--GGGCG-G-CGCGCGCCGG
*
10658501 CTCG-GGCCGGCGC
1 CGCGCGGCCGGCGC
10658514 GCCGCCGCCG
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
38 12 0.26
39 8 0.17
41 5 0.11
42 3 0.07
43 18 0.39
ACGTcount: A:0.01, C:0.43, G:0.54, T:0.02
Consensus pattern (39 bp):
CGCGCGGCCGGCGCCGGCGGCCGGGGCGGCGCGCGCCGG
Found at i:10658527 original size:16 final size:16
Alignment explanation
Indices: 10658508--10658539 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10658498 GGGCTCGGGC
10658508 CGGCGCGCCGCCGCCG
1 CGGCGCGCCGCCGCCG
*
10658524 CGGCGCGCGGCCGCCG
1 CGGCGCGCCGCCGCCG
10658540 GGGGGGGGCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.53, G:0.47, T:0.00
Consensus pattern (16 bp):
CGGCGCGCCGCCGCCG
Found at i:10658579 original size:17 final size:17
Alignment explanation
Indices: 10658557--10658597 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
10658547 GCGGGGGGGG
10658557 GCCGGCGGGCCGGCCGC
1 GCCGGCGGGCCGGCCGC
* *
10658574 GCCGGCGGGGCGGCGGC
1 GCCGGCGGGCCGGCCGC
*
10658591 GGCGGCG
1 GCCGGCG
10658598 AGATGAGCAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.00, C:0.39, G:0.61, T:0.00
Consensus pattern (17 bp):
GCCGGCGGGCCGGCCGC
Found at i:10661220 original size:17 final size:17
Alignment explanation
Indices: 10661182--10661224 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
10661172 TAGCATCAAT
* *
10661182 ACAAAAAATAAAGGGAA
1 ACAAAGAATAAAAGGAA
*
10661199 A-AAAGAATAAAAGTAA
1 ACAAAGAATAAAAGGAA
10661215 ACAAAGAATA
1 ACAAAGAATA
10661225 TGAAAACCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.72, C:0.05, G:0.14, T:0.09
Consensus pattern (17 bp):
ACAAAGAATAAAAGGAA
Found at i:10663228 original size:27 final size:26
Alignment explanation
Indices: 10663169--10663228 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
10663159 AAAAATATCT
*** *
10663169 TAATAAATTAATTTTTTATTAATTAG
1 TAATAAATTAATAAATTATTAATTAA
10663195 TATATAAATTAATAAATTATTAATTAAA
1 TA-ATAAATTAATAAATTATTAATT-AA
10663223 TAATAA
1 TAATAA
10663229 TAATTAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 2 0.07
27 23 0.82
28 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
TAATAAATTAATAAATTATTAATTAA
Found at i:10666873 original size:3 final size:3
Alignment explanation
Indices: 10666865--10666893 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
10666855 TTTAGATTCT
10666865 TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
10666894 TGAACCAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:10668015 original size:12 final size:12
Alignment explanation
Indices: 10667998--10668022 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10667988 TGCCTGTATA
10667998 TGCAAGCAACAT
1 TGCAAGCAACAT
10668010 TGCAAGCAACAT
1 TGCAAGCAACAT
10668022 T
1 T
10668023 TGCAGATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TGCAAGCAACAT
Found at i:10670407 original size:79 final size:81
Alignment explanation
Indices: 10670229--10670521 Score: 249
Period size: 82 Copynumber: 3.6 Consensus size: 81
10670219 ACCGGCTTTT
* * * * * * * * * * *
10670229 TTGGAAGATGAAGTAATCTTTGAGACAAAATCATTAATGACAACCATATAATAATATAAGTTATA
1 TTGGAAGAAGTAGTAATCTTTTAAAGAAAATCATTAATGACGACCAAATAA-GATAGAAGATATT
** **
10670294 TATATTATGTACATTTC
65 TATAAGACCTACATTTC
*
10670311 TTGGAAGAAGTAGTAATCGTTTAAAGAAAATCATTAATGACGACCAAATAA-ATCAGAA-ATATT
1 TTGGAAGAAGTAGTAATCTTTTAAAGAAAATCATTAATGACGACCAAATAAGAT-AGAAGATATT
* *
10670374 T-T-AGCAACCTGC-TTTT
65 TATAAG--ACCTACATTTC
* * * * *
10670390 TTGGAAGAAATAGTAATCTTTTAAACAACAA-CATTAATGAC-AACAAATAATGATATAAGTTAT
1 TTGGAAGAAGTAGTAATCTTTTAAAGAA-AATCATTAATGACGACCAAATAA-GATAGAAGATAT
**
10670453 TTATAAGATGTACATTTC
64 TTATAAGACCTACATTTC
*
10670471 TTGGAAGAAGTAGTAATCTTTTAAAGAAGATCATTAATGACGACCAAATAA
1 TTGGAAGAAGTAGTAATCTTTTAAAGAAAATCATTAATGACGACCAAATAA
10670522 TAATTTGAGT
Statistics
Matches: 168, Mismatches: 31, Indels: 24
0.75 0.14 0.11
Matches are distributed among these distances:
78 8 0.05
79 42 0.25
80 22 0.13
81 43 0.26
82 53 0.32
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.32
Consensus pattern (81 bp):
TTGGAAGAAGTAGTAATCTTTTAAAGAAAATCATTAATGACGACCAAATAAGATAGAAGATATTT
ATAAGACCTACATTTC
Found at i:10670496 original size:160 final size:161
Alignment explanation
Indices: 10670199--10670521 Score: 490
Period size: 160 Copynumber: 2.0 Consensus size: 161
10670189 TGAAGCTTCC
* * *
10670199 AAATCTGAAATACTTTAGCAACCGGCTTTTTTGGAAGATGAAGTAATCTTTGAGACAAAATCATT
1 AAATCAGAAATACTTTAGCAACCGGCTTTTTTGGAAGATAAAGTAATCTTTGAAACAAAATCATT
* **
10670264 AATGACAACCATATAATAATATAAGTTATATATATTATGTACATTTCTTGGAAGAAGTAGTAATC
66 AATGACAACCAAATAATAATATAAGTTATATATAAGATGTACATTTCTTGGAAGAAGTAGTAATC
10670329 GTTTAAAGAAAATCATTAATGACGACCAAAT
131 GTTTAAAGAAAATCATTAATGACGACCAAAT
* * *
10670360 AAATCAGAAATATTTTAGCAACCTGCTTTTTTGGAAGA-AATAGTAATCTTTTAAACAACAA-CA
1 AAATCAGAAATACTTTAGCAACCGGCTTTTTTGGAAGATAA-AGTAATCTTTGAAACAA-AATCA
* *
10670423 TTAATGACAA-CAAATAATGATATAAGTTATTTATAAGATGTACATTTCTTGGAAGAAGTAGTAA
64 TTAATGACAACCAAATAATAATATAAGTTATATATAAGATGTACATTTCTTGGAAGAAGTAGTAA
* *
10670487 TCTTTTAAAGAAGATCATTAATGACGACCAAAT
129 TCGTTTAAAGAAAATCATTAATGACGACCAAAT
10670520 AA
1 AA
10670522 TAATTTGAGT
Statistics
Matches: 147, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
160 83 0.56
161 62 0.42
162 2 0.01
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (161 bp):
AAATCAGAAATACTTTAGCAACCGGCTTTTTTGGAAGATAAAGTAATCTTTGAAACAAAATCATT
AATGACAACCAAATAATAATATAAGTTATATATAAGATGTACATTTCTTGGAAGAAGTAGTAATC
GTTTAAAGAAAATCATTAATGACGACCAAAT
Found at i:10687289 original size:18 final size:18
Alignment explanation
Indices: 10687268--10687302 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
10687258 CCACCACCAC
10687268 CACCAAAACCACCATAAT
1 CACCAAAACCACCATAAT
*
10687286 CACCAAATCCACCATAA
1 CACCAAAACCACCATAA
10687303 CCATCATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.40, G:0.00, T:0.11
Consensus pattern (18 bp):
CACCAAAACCACCATAAT
Found at i:10695831 original size:13 final size:13
Alignment explanation
Indices: 10695813--10695837 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10695803 TGCAACAACA
10695813 AAAAATAAAAAAT
1 AAAAATAAAAAAT
10695826 AAAAATAAAAAA
1 AAAAATAAAAAA
10695838 AAACTTACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:10712603 original size:47 final size:47
Alignment explanation
Indices: 10712549--10712641 Score: 123
Period size: 47 Copynumber: 2.0 Consensus size: 47
10712539 TTTTATTTTT
* ** *
10712549 AATCAAATACGTCTCTATAATTAATGGTTAATTAATTATTCTAAGTC
1 AATCAAATAAGTCTCTATAATTAATACTTAACTAATTATTCTAAGTC
* * *
10712596 AATCAAATAAGTTTCTGTAATTAATACTTAACTAATTATTTTAAGT
1 AATCAAATAAGTCTCTATAATTAATACTTAACTAATTATTCTAAGT
10712642 TAATGTGAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
47 39 1.00
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.42
Consensus pattern (47 bp):
AATCAAATAAGTCTCTATAATTAATACTTAACTAATTATTCTAAGTC
Found at i:10712735 original size:20 final size:21
Alignment explanation
Indices: 10712710--10712749 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
10712700 TATTAATCAT
10712710 ATAAATTTATTTAA-TTTAAA
1 ATAAATTTATTTAACTTTAAA
*
10712730 ATAAATTTTTTTAACTTTAA
1 ATAAATTTATTTAACTTTAA
10712750 CTTTTCAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
ATAAATTTATTTAACTTTAAA
Found at i:10717056 original size:35 final size:35
Alignment explanation
Indices: 10717015--10717084 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
10717005 TATATTACAG
*
10717015 CCAAAATAGATTTCCAGAATGTTCAAGGAAATTGA
1 CCAAAATAGATTTCAAGAATGTTCAAGGAAATTGA
*
10717050 CCAAAATAGATTTCAAGAATGTTCAGGGAAATTGA
1 CCAAAATAGATTTCAAGAATGTTCAAGGAAATTGA
10717085 GGGATGATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.26
Consensus pattern (35 bp):
CCAAAATAGATTTCAAGAATGTTCAAGGAAATTGA
Found at i:10731531 original size:2 final size:2
Alignment explanation
Indices: 10731524--10731559 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
10731514 TTGCTTCATG
10731524 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10731560 TGCGTCAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10734558 original size:2 final size:2
Alignment explanation
Indices: 10734553--10734589 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
10734543 ACACACACAC
10734553 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
10734590 GTCCAATATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10735768 original size:2 final size:2
Alignment explanation
Indices: 10735725--10735749 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10735715 AGAGTGTGCC
10735725 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
10735750 CCTTTCCAAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10745712 original size:19 final size:20
Alignment explanation
Indices: 10745684--10745731 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
10745674 GAATTTCTCT
10745684 CTCTTTTTTT-TTTTT-TTG
1 CTCTTTTTTTCTTTTTCTTG
*
10745702 CTCTGTTTTTTCTTTTTCTTT
1 CTCT-TTTTTTCTTTTTCTTG
10745723 CTCTTTTTT
1 CTCTTTTTT
10745732 CTTCTGCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 4 0.15
19 6 0.23
20 10 0.38
21 6 0.23
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (20 bp):
CTCTTTTTTTCTTTTTCTTG
Found at i:10745732 original size:19 final size:19
Alignment explanation
Indices: 10745677--10745734 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 19
10745667 CTTTCCAGAA
*
10745677 TTTCTCTCTCTTTTTT-TT
1 TTTCTTTCTCTTTTTTCTT
10745695 TTT-TTTGCTCTGTTTTTTCTT
1 TTTCTTT-CTC--TTTTTTCTT
10745716 TTTCTTTCTCTTTTTTCTT
1 TTTCTTTCTCTTTTTTCTT
10745735 CTGCTTTGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
17 2 0.06
18 6 0.18
19 9 0.26
20 6 0.18
21 8 0.24
22 3 0.09
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (19 bp):
TTTCTTTCTCTTTTTTCTT
Found at i:10746938 original size:15 final size:16
Alignment explanation
Indices: 10746910--10746972 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
10746900 GCGCGCGGGC
10746910 GGCGCGGGCGCCGCGG
1 GGCGCGGGCGCCGCGG
* *
10746926 GGCGGGGGC-CCGCGCT
1 GGCGCGGGCGCCGCG-G
**
10746942 GGCGCCGGGCGGGGCGG
1 GGCG-CGGGCGCCGCGG
10746959 GGCGC-GGCGCCGCG
1 GGCGCGGGCGCCGCG
10746973 CGGGGGGCGG
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
15 12 0.33
16 13 0.36
17 8 0.22
18 3 0.08
ACGTcount: A:0.00, C:0.37, G:0.62, T:0.02
Consensus pattern (16 bp):
GGCGCGGGCGCCGCGG
Found at i:10746967 original size:22 final size:23
Alignment explanation
Indices: 10746937--10746997 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
10746927 GCGGGGGCCC
10746937 GCGCTGGCGCCGG-GCGGGGCGGG
1 GCGC-GGCGCCGGCGCGGGGCGGG
*
10746960 GCGCGGCGCCGCGCGGGGGGCGGG
1 GCGCGGCGCCG-GCGCGGGGCGGG
*
10746984 GCGGGGC-CCGGCGC
1 GCGCGGCGCCGGCGC
10746998 CGGGTGGGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 10 0.30
23 8 0.24
24 15 0.45
ACGTcount: A:0.00, C:0.34, G:0.64, T:0.02
Consensus pattern (23 bp):
GCGCGGCGCCGGCGCGGGGCGGG
Found at i:10747169 original size:91 final size:91
Alignment explanation
Indices: 10747062--10747229 Score: 211
Period size: 91 Copynumber: 1.8 Consensus size: 91
10747052 CGGGCCCGAC
* *
10747062 GGCGCGCGGGCGCGGCGCGGGTGC-GCCGCG-GGCGGCCGCGCGGGC-CGCCGGGCGGCGG-GCG
1 GGCGCGCGGGCGCGGCGCGGGCGCGGCCGCGCGG-GGCCGCGCGGGCGCGCC-GGCGCCGGCGCG
10747123 GGTGGGCGGGCGCGGCCGCGGGGTCGTGCT
64 GGT-GGC-GGCGCGGCCGCGGGGTCGTGCT
* * *
10747153 GGCGCGCGGTGC-CGGCGCGGGCGCGGCGGCGCGGGGCCGCGGGGGCGCGCCGGCGCCGGCGTGG
1 GGCGCGCGG-GCGCGGCGCGGGCGCGGCCGCGCGGGGCCGCGCGGGCGCGCCGGCGCCGGCGCGG
10747217 GTGGCGGCGCGGC
65 GTGGCGGCGCGGC
10747230 GCCGGGCGCG
Statistics
Matches: 67, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
91 28 0.42
92 28 0.42
93 11 0.16
ACGTcount: A:0.00, C:0.35, G:0.61, T:0.05
Consensus pattern (91 bp):
GGCGCGCGGGCGCGGCGCGGGCGCGGCCGCGCGGGGCCGCGCGGGCGCGCCGGCGCCGGCGCGGG
TGGCGGCGCGGCCGCGGGGTCGTGCT
Found at i:10747180 original size:24 final size:24
Alignment explanation
Indices: 10747156--10747208 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
10747146 TCGTGCTGGC
*
10747156 GCGCGGTGCCGGCGCGGGCGCGGCG
1 GCGCGGGGCC-GCGCGGGCGCGGCG
* *
10747181 GCGCGGGGCCGCGGGGGCGCGCCG
1 GCGCGGGGCCGCGCGGGCGCGGCG
10747205 GCGC
1 GCGC
10747209 CGGCGTGGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.00, C:0.38, G:0.60, T:0.02
Consensus pattern (24 bp):
GCGCGGGGCCGCGCGGGCGCGGCG
Found at i:10748521 original size:34 final size:32
Alignment explanation
Indices: 10748455--10748539 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 32
10748445 CGCGCCCCGG
10748455 GGCGCGCGGCGGGCGCCCGCCCGCCGGCGGCC
1 GGCGCGCGGCGGGCGCCCGCCCGCCGGCGGCC
* * *
10748487 GGCGCCGCGGCGGGGGCGCCGCCCGCGGGTGGCC
1 GGCG-CGCGGCGGGCGC-CCGCCCGCCGGCGGCC
10748521 -GCGCG-GTGTCGGGCGCCCG
1 GGCGCGCG-G-CGGGCGCCCG
10748540 GCGGGCCCCG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
31 1 0.02
32 10 0.22
33 20 0.44
34 14 0.31
ACGTcount: A:0.00, C:0.44, G:0.53, T:0.04
Consensus pattern (32 bp):
GGCGCGCGGCGGGCGCCCGCCCGCCGGCGGCC
Found at i:10748676 original size:16 final size:15
Alignment explanation
Indices: 10748655--10748698 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
10748645 GCCCGCGTCC
10748655 GCGGCGGCCGCCGCG
1 GCGGCGGCCGCCGCG
*
10748670 GCTGGCGGCCGTCGCG
1 GC-GGCGGCCGCCGCG
10748686 GCGG-GGCCGCCGC
1 GCGGCGGCCGCCGC
10748699 CGGGTCGGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 8 0.31
15 4 0.15
16 14 0.54
ACGTcount: A:0.00, C:0.43, G:0.52, T:0.05
Consensus pattern (15 bp):
GCGGCGGCCGCCGCG
Found at i:10748775 original size:23 final size:24
Alignment explanation
Indices: 10748715--10748783 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
10748705 GGCTGCTCCC
** *
10748715 TGCGCGCATCCGCCGGGCGGCCCG
1 TGCGCGCGCCCGCCCGGCGGCCCG
*
10748739 TGCGCGCGCCCGCCCGGCGGCCTG
1 TGCGCGCGCCCGCCCGGCGGCCCG
*
10748763 -GCGCGC-CCTCGCCCGGGGGCC
1 TGCGCGCGCC-CGCCCGGCGGCC
10748784 GGGGCCGGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
22 2 0.05
23 17 0.44
24 20 0.51
ACGTcount: A:0.01, C:0.49, G:0.42, T:0.07
Consensus pattern (24 bp):
TGCGCGCGCCCGCCCGGCGGCCCG
Found at i:10748823 original size:7 final size:7
Alignment explanation
Indices: 10748775--10748826 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
10748765 GCGCCCTCGC
*
10748775 CCGGGGG
1 CCGGGCG
10748782 CCGGG-G
1 CCGGGCG
10748788 CCGGGGCG
1 CC-GGGCG
*
10748796 CCCGGCG
1 CCGGGCG
*
10748803 CCGGACGG
1 CCGGGC-G
10748811 CCGGGCG
1 CCGGGCG
10748818 CCGGGCG
1 CCGGGCG
10748825 CC
1 CC
10748827 CCGGGCCCCC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
6 3 0.08
7 26 0.68
8 9 0.24
ACGTcount: A:0.02, C:0.42, G:0.56, T:0.00
Consensus pattern (7 bp):
CCGGGCG
Found at i:10748889 original size:36 final size:34
Alignment explanation
Indices: 10748808--10748894 Score: 92
Period size: 35 Copynumber: 2.6 Consensus size: 34
10748798 CGGCGCCGGA
10748808 CGGCCGG-GCGC-CGGGCG-CC-CCGGGCCCCCG
1 CGGCCGGCGCGCGCGGGCGCCCGCCGGGCCCCCG
*
10748838 CGGCCGGCGCGCGCGGCGCGCCCGCCGGGGCCCCG
1 CGGCCGGCGCGCGCGG-GCGCCCGCCGGGCCCCCG
* * *
10748873 TGGGCGGGGCGTCGCGGGCGCC
1 CGGCCGGCGCG-CGCGGGCGCC
10748895 GCGGCCGCGC
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
30 7 0.15
31 4 0.09
32 3 0.06
33 3 0.06
34 2 0.04
35 23 0.49
36 5 0.11
ACGTcount: A:0.00, C:0.47, G:0.51, T:0.02
Consensus pattern (34 bp):
CGGCCGGCGCGCGCGGGCGCCCGCCGGGCCCCCG
Found at i:10760095 original size:8 final size:9
Alignment explanation
Indices: 10760080--10760127 Score: 52
Period size: 8 Copynumber: 5.8 Consensus size: 9
10760070 TTATTTAATT
10760080 TAAA-ATAA
1 TAAATATAA
10760088 -AAATATAA
1 TAAATATAA
10760096 -AAAT-TAA
1 TAAATATAA
10760103 TTAAATATAA
1 -TAAATATAA
10760113 TAAA-ATAA
1 TAAATATAA
10760121 TAAATAT
1 TAAATAT
10760128 TTATTCAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
7 6 0.17
8 16 0.46
9 10 0.29
10 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
TAAATATAA
Found at i:10760102 original size:25 final size:26
Alignment explanation
Indices: 10760074--10760125 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 26
10760064 AAAAAATTAT
10760074 TTAATTTAAA-ATAA-AAATATAA-AAA
1 TTAA-TTAAATATAATAAA-ATAATAAA
10760099 TTAATTAAATATAATAAAATAATAAA
1 TTAATTAAATATAATAAAATAATAAA
10760125 T
1 T
10760126 ATTTATTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 5 0.21
25 12 0.50
26 7 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
TTAATTAAATATAATAAAATAATAAA
Found at i:10760110 original size:17 final size:17
Alignment explanation
Indices: 10760080--10760127 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
10760070 TTATTTAATT
10760080 TAAAATAA-AAATATAA
1 TAAAATAATAAATATAA
*
10760096 -AAATTAATTAAATATAA
1 TAAAATAA-TAAATATAA
10760113 TAAAATAATAAATAT
1 TAAAATAATAAATAT
10760128 TTATTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 6 0.22
17 15 0.56
18 6 0.22
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAATAATAAATATAA
Found at i:10760145 original size:21 final size:21
Alignment explanation
Indices: 10760121--10760185 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 21
10760111 AATAAAATAA
10760121 TAAATATTTATTCAAAAATTT
1 TAAATATTTATTCAAAAATTT
10760142 TAAATAATTTA---AAAATTATTT
1 TAAAT-ATTTATTCAAAA--ATTT
*
10760163 TAAATTTTTACCTTCAAAAATTT
1 TAAATATTTA--TTCAAAAATTT
10760186 ATTTAAAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 14
0.70 0.02 0.28
Matches are distributed among these distances:
19 4 0.11
20 4 0.11
21 14 0.40
22 5 0.14
23 4 0.11
25 4 0.11
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (21 bp):
TAAATATTTATTCAAAAATTT
Found at i:10760955 original size:4 final size:4
Alignment explanation
Indices: 10760946--10760976 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
10760936 ACACTTCCAT
10760946 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
10760977 TATATCTGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:10772407 original size:18 final size:19
Alignment explanation
Indices: 10772386--10772473 Score: 51
Period size: 18 Copynumber: 4.7 Consensus size: 19
10772376 TTGTTAATGA
10772386 AATTTTATATT-ATAATTT
1 AATTTTATATTCATAATTT
*
10772404 AATTTTAT-TTCAGTGA-TT
1 AATTTTATATTCA-TAATTT
* ** **
10772422 AATTTTTTTAAATTGTTAATGA
1 AA---TTTTATATTCATAATTT
10772444 AATTTTATATT-ATAATTT
1 AATTTTATATTCATAATTT
10772462 AATTTTAT-TTCA
1 AATTTTATATTCA
10772474 AAAGAAGTTA
Statistics
Matches: 51, Mismatches: 11, Indels: 16
0.65 0.14 0.21
Matches are distributed among these distances:
17 4 0.08
18 26 0.51
19 10 0.20
21 7 0.14
22 4 0.08
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (19 bp):
AATTTTATATTCATAATTT
Found at i:10775183 original size:2 final size:2
Alignment explanation
Indices: 10775176--10775202 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10775166 TTTCTTATGA
10775176 AT 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 AT A
10775203 ATGTTGTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10786467 original size:30 final size:27
Alignment explanation
Indices: 10786394--10786467 Score: 76
Period size: 30 Copynumber: 2.6 Consensus size: 27
10786384 ATAGAGAAAT
10786394 TTAAATAAATTTTTATTTTTTATTACA
1 TTAAATAAATTTTTATTTTTTATTACA
* * **
10786421 TTCAATCAAATATTTATATTTTTATTTTAGG
1 TTAAAT-AAAT-TTT-TATTTTT-TATTACA
10786452 TTAAATAAATTTTTAT
1 TTAAATAAATTTTTAT
10786468 GACTTGTTAG
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
27 5 0.13
28 7 0.18
29 6 0.16
30 11 0.29
31 9 0.24
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (27 bp):
TTAAATAAATTTTTATTTTTTATTACA
Found at i:10789434 original size:61 final size:62
Alignment explanation
Indices: 10789357--10789494 Score: 161
Period size: 61 Copynumber: 2.2 Consensus size: 62
10789347 TTTTGGCTCG
*
10789357 GAGCATTTTGTCTTGTAAGAATCAAACAGTGCATTCCCAAAAAGTCAATTC-TTTGCCTCCA
1 GAGCATTTTGTTTTGTAAGAATCAAACAGTGCATTCCCAAAAAGTCAATTCTTTTGCCTCCA
* ** * ** * * *
10789418 GAGTATTTTGTTTTGTAAGAATTGATCAGTGCATTCTTAATAAGTCGATTCTTTTTGCCTCTA
1 GAGCATTTTGTTTTGTAAGAATCAAACAGTGCATTCCCAAAAAGTCAATTC-TTTTGCCTCCA
*
10789481 GAGCATTCTGTTTT
1 GAGCATTTTGTTTT
10789495 CGAGGAATCA
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
61 42 0.67
63 21 0.33
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (62 bp):
GAGCATTTTGTTTTGTAAGAATCAAACAGTGCATTCCCAAAAAGTCAATTCTTTTGCCTCCA
Found at i:10791550 original size:36 final size:37
Alignment explanation
Indices: 10791477--10791557 Score: 130
Period size: 36 Copynumber: 2.2 Consensus size: 37
10791467 TCTAATATAT
*
10791477 GAAAATCCAATAACTCATTTAAAGGGTTAGAAAAAGA
1 GAAAATCTAATAACTCATTTAAAGGGTTAGAAAAAGA
10791514 GAAAATCTAATAACTCA-TTAAAGGGTTA-AAAGAAGA
1 GAAAATCTAATAACTCATTTAAAGGGTTAGAAA-AAGA
10791550 GAAAATCT
1 GAAAATCT
10791558 TGTATAATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
35 3 0.07
36 23 0.55
37 16 0.38
ACGTcount: A:0.52, C:0.10, G:0.16, T:0.22
Consensus pattern (37 bp):
GAAAATCTAATAACTCATTTAAAGGGTTAGAAAAAGA
Found at i:10792783 original size:101 final size:98
Alignment explanation
Indices: 10792603--10792790 Score: 268
Period size: 101 Copynumber: 1.9 Consensus size: 98
10792593 AAATAGTATC
**
10792603 TAAATACAATTTGAATTTTAGATTTTTTTTCTTAATCTTTGTAAAAACAAGGAAATTCTAGATTT
1 TAAATACAATTTGAATTTTAGATTTTTTTTCTTAATCTTTGTAAAAACAAAAAAATTCTAGATTT
* * * *
10792668 TGATATAGTGTTGTTGGGTCTTCTGTTTTTTTT
66 CGATATACTATTGTTAGGTCTTCTGTTTTTTTT
* *
10792701 TAAATACAGTTTTGAATTTTAGATTTTTTTTCTCTTAATCTTTGTAAGAACAAAAAAATTCTAGA
1 TAAATACA-ATTTGAATTTTAGA-TTTTTTT-TCTTAATCTTTGTAAAAACAAAAAAATTCTAGA
*
10792766 TTTCGATATTCTATTGTTAGGTCTT
63 TTTCGATATACTATTGTTAGGTCTT
10792791 TCATTTTTTT
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
98 8 0.10
99 13 0.17
100 7 0.09
101 50 0.64
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.49
Consensus pattern (98 bp):
TAAATACAATTTGAATTTTAGATTTTTTTTCTTAATCTTTGTAAAAACAAAAAAATTCTAGATTT
CGATATACTATTGTTAGGTCTTCTGTTTTTTTT
Found at i:10800626 original size:16 final size:17
Alignment explanation
Indices: 10800589--10800626 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
10800579 CAAAAGAAAA
10800589 AAATTATATTATTTTAT
1 AAATTATATTATTTTAT
*
10800606 -CATTATATT-TTTTAT
1 AAATTATATTATTTTAT
10800621 AAATTA
1 AAATTA
10800627 AGATAGAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 3
0.78 0.09 0.13
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
AAATTATATTATTTTAT
Found at i:10807028 original size:58 final size:58
Alignment explanation
Indices: 10806964--10807080 Score: 198
Period size: 58 Copynumber: 2.0 Consensus size: 58
10806954 CTTCGAAGGA
10806964 AACCACAAATGAAGATGGAATAATAGAACTTTTCTTCACAAAAACTAGAATTCTTGCC
1 AACCACAAATGAAGATGGAATAATAGAACTTTTCTTCACAAAAACTAGAATTCTTGCC
* * * *
10807022 AACCACAAATGAAGATGGAATAATATAACTTTTTTTCACAATAATTAGAATTCTTGCC
1 AACCACAAATGAAGATGGAATAATAGAACTTTTCTTCACAAAAACTAGAATTCTTGCC
10807080 A
1 A
10807081 TATCGATCCT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (58 bp):
AACCACAAATGAAGATGGAATAATAGAACTTTTCTTCACAAAAACTAGAATTCTTGCC
Found at i:10808067 original size:20 final size:20
Alignment explanation
Indices: 10808029--10808066 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10808019 CACGCCTCTT
10808029 TCTTCCTCTTTTTCTTTTTC
1 TCTTCCTCTTTTTCTTTTTC
*
10808049 TCTTTCTCTTTTT-TTTTT
1 TCTTCCTCTTTTTCTTTTT
10808067 TTTTTTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (20 bp):
TCTTCCTCTTTTTCTTTTTC
Found at i:10815583 original size:22 final size:21
Alignment explanation
Indices: 10815558--10815626 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
10815548 TATTTTTATT
10815558 TTTATTTTTAATATATTAAAAA
1 TTTATTTTTAA-ATATTAAAAA
* * * *
10815580 TTTATAATTAAAATTTTAAATA
1 TTTAT-TTTTAAATATTAAAAA
*
10815602 TTGTATTTTTAAA-ATTAAAAT
1 TT-TATTTTTAAATATTAAAAA
10815623 TTTA
1 TTTA
10815627 ATTTAATTTC
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
20 2 0.06
21 7 0.19
22 20 0.56
23 7 0.19
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (21 bp):
TTTATTTTTAAATATTAAAAA
Found at i:10815625 original size:14 final size:14
Alignment explanation
Indices: 10815572--10815627 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
10815562 TTTTTAATAT
* *
10815572 ATTAAAAATTTATA
1 ATTAAAATTTTAAA
10815586 ATTAAAATTTTAAA
1 ATTAAAATTTTAAA
** *
10815600 TATTGTATTTTTAAA
1 -ATTAAAATTTTAAA
10815615 ATTAAAATTTTAA
1 ATTAAAATTTTAA
10815628 TTTAATTTCT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
14 22 0.67
15 11 0.33
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
ATTAAAATTTTAAA
Found at i:10815646 original size:26 final size:29
Alignment explanation
Indices: 10815588--10815646 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 29
10815578 AATTTATAAT
* * *
10815588 TAAAATTTTAAATATTGTATTTTTAAAAT
1 TAAAATTTTAAATATTGAATTTCTAAAAA
10815617 TAAAATTTT-AAT-TT-AATTTCTAAAAA
1 TAAAATTTTAAATATTGAATTTCTAAAAA
10815643 TAAA
1 TAAA
10815647 GTATTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 13 0.48
27 2 0.07
28 3 0.11
29 9 0.33
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (29 bp):
TAAAATTTTAAATATTGAATTTCTAAAAA
Found at i:10816233 original size:22 final size:20
Alignment explanation
Indices: 10816177--10816233 Score: 53
Period size: 23 Copynumber: 2.8 Consensus size: 20
10816167 AATATAGATG
10816177 TAAA-ATAATAAAAATTTAT
1 TAAATATAATAAAAATTTAT
* * *
10816196 TTAATTTAAAATAAAATTATAAT
1 TAAATATAATA-AAAATT-T-AT
10816219 TAAATATAATAAAAA
1 TAAATATAATAAAAA
10816234 ATTAAAAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
19 3 0.11
20 4 0.14
21 6 0.21
22 5 0.18
23 10 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAATATAATAAAAATTTAT
Found at i:10817560 original size:2 final size:2
Alignment explanation
Indices: 10817553--10817581 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10817543 AGCTTTTGAA
10817553 AT AT 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 AT AT A
10817582 CTTTGATGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10819204 original size:2 final size:2
Alignment explanation
Indices: 10819197--10819226 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10819187 TTAATTACTC
10819197 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10819227 CATTCAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10825462 original size:85 final size:85
Alignment explanation
Indices: 10825353--10825510 Score: 237
Period size: 85 Copynumber: 1.9 Consensus size: 85
10825343 GTTATGTTTG
* * * *
10825353 TTGGTTTTCCAACAGACATAATTATTTTTCATATAAACAT-AGCTGAATTATTTTTCAAATAAAC
1 TTGGTTTTCCAACAGACATAATTATTTTTCAAACAAACATAATC-GAATTATTTTTCAAACAAAC
10825417 TTAACTGTTTTGTTCTATCTA
65 TTAACTGTTTTGTTCTATCTA
* * *
10825438 TTGGTTTTCCAATAGATATAATTATTTTTCAAACAAACATAATCGAATTATTTTTCAAACAGACT
1 TTGGTTTTCCAACAGACATAATTATTTTTCAAACAAACATAATCGAATTATTTTTCAAACAAACT
10825503 TAACTGTT
66 TAACTGTT
10825511 CCGTCTTATT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
85 63 0.97
86 2 0.03
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (85 bp):
TTGGTTTTCCAACAGACATAATTATTTTTCAAACAAACATAATCGAATTATTTTTCAAACAAACT
TAACTGTTTTGTTCTATCTA
Found at i:10826305 original size:16 final size:16
Alignment explanation
Indices: 10826284--10826319 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
10826274 CTCAACAGAG
10826284 AAAAGAAATTGAACTT
1 AAAAGAAATTGAACTT
10826300 AAAAGAAATTGAACTT
1 AAAAGAAATTGAACTT
10826316 AAAA
1 AAAA
10826320 CTTCTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.61, C:0.06, G:0.11, T:0.22
Consensus pattern (16 bp):
AAAAGAAATTGAACTT
Found at i:10828103 original size:24 final size:24
Alignment explanation
Indices: 10828058--10828116 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
10828048 TTTTTTATTA
* *
10828058 ATCTTGATTATATAAAAAGAAATT
1 ATCTTGAGTATATAAAAAGAAAGT
* *
10828082 ATCTTGAGTATATAAGAGGAAAGT
1 ATCTTGAGTATATAAAAAGAAAGT
*
10828106 ATTTTGAGTAT
1 ATCTTGAGTAT
10828117 TTAATCTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.42, C:0.03, G:0.17, T:0.37
Consensus pattern (24 bp):
ATCTTGAGTATATAAAAAGAAAGT
Found at i:10832950 original size:21 final size:21
Alignment explanation
Indices: 10832921--10832964 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
10832911 AGTTATGTCT
*
10832921 ATTAGTTTTCCAACAAACATA
1 ATTAGTTTTCAAACAAACATA
*
10832942 ATTATTTTTCAAACAAACATA
1 ATTAGTTTTCAAACAAACATA
10832963 AT
1 AT
10832965 CAAATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.45, C:0.16, G:0.02, T:0.36
Consensus pattern (21 bp):
ATTAGTTTTCAAACAAACATA
Found at i:10832970 original size:26 final size:26
Alignment explanation
Indices: 10832941--10832991 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
10832931 CAACAAACAT
10832941 AATTATTTTTCAAACAAACATAATCA
1 AATTATTTTTCAAACAAACATAATCA
*
10832967 AATTATTTTTCAAACAAACTTAATC
1 AATTATTTTTCAAACAAACATAATC
10832992 GTTTTGTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (26 bp):
AATTATTTTTCAAACAAACATAATCA
Found at i:10833693 original size:17 final size:16
Alignment explanation
Indices: 10833668--10833725 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
10833658 TAAGATATTT
*
10833668 AAATCTGAAATGATTC
1 AAATTTGAAATGATTC
**
10833684 AAAATTTGAAAAAATTC
1 -AAATTTGAAATGATTC
* * *
10833701 ATATTCGAAATGAGTC
1 AAATTTGAAATGATTC
10833717 AAATTTGAA
1 AAATTTGAA
10833726 CATATTTGAA
Statistics
Matches: 31, Mismatches: 10, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
16 18 0.58
17 13 0.42
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.31
Consensus pattern (16 bp):
AAATTTGAAATGATTC
Found at i:10842016 original size:2 final size:2
Alignment explanation
Indices: 10842009--10842037 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10841999 TGAGACCTTC
10842009 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
10842038 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:10852104 original size:14 final size:13
Alignment explanation
Indices: 10852081--10852153 Score: 62
Period size: 14 Copynumber: 5.5 Consensus size: 13
10852071 ATGTTATAAT
*
10852081 TAAAACAAAAATA
1 TAAAATAAAAATA
10852094 TGAAAATAAAATATA
1 T-AAAATAAAA-ATA
10852109 TAAAATAAAAATCA
1 TAAAATAAAAAT-A
*
10852123 -AAAATTAAAATA
1 TAAAATAAAAATA
10852135 -AAATATAAAAGAT-
1 TAAA-ATAAAA-ATA
10852148 TAAAAT
1 TAAAAT
10852154 TTATATCAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
12 4 0.08
13 20 0.39
14 23 0.45
15 4 0.08
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (13 bp):
TAAAATAAAAATA
Found at i:10852127 original size:7 final size:6
Alignment explanation
Indices: 10852082--10852144 Score: 54
Period size: 6 Copynumber: 9.5 Consensus size: 6
10852072 TGTTATAATT
* *
10852082 AAAACA AAAATA TGAAAATA AAATATA TAAAATA AAAATCA AAAATT AAAATA
1 AAAATA AAAATA --AAAATA AAA-ATA -AAAATA AAAAT-A AAAATA AAAATA
10852135 AAATATA AAA
1 AAA-ATA AAA
10852145 GATTAAAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
6 21 0.44
7 18 0.38
8 9 0.19
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.21
Consensus pattern (6 bp):
AAAATA
Found at i:10852151 original size:20 final size:18
Alignment explanation
Indices: 10852096--10852153 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 18
10852086 CAAAAATATG
10852096 AAAATAAAATATATAAAATA
1 AAAATAAAA-AT-TAAAATA
10852116 AAAATCAAAAATTAAAATA
1 AAAAT-AAAAATTAAAATA
10852135 AAATATAAAAGATTAAAAT
1 AAA-ATAAAA-ATTAAAAT
10852154 TTATATCAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 14 0.40
20 17 0.49
21 4 0.11
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (18 bp):
AAAATAAAAATTAAAATA
Found at i:10852153 original size:33 final size:35
Alignment explanation
Indices: 10852078--10852153 Score: 106
Period size: 33 Copynumber: 2.3 Consensus size: 35
10852068 ATAATGTTAT
10852078 AATTAAAA-CAAAAATATGAAAATAAAATATATAA
1 AATTAAAATCAAAAATATGAAAATAAAATATATAA
*
10852112 AATAAAAATCAAAAAT-T-AAAATAAAATATA-AA
1 AATTAAAATCAAAAATATGAAAATAAAATATATAA
10852144 AGATTAAAAT
1 A-ATTAAAAT
10852154 TTATATCAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
32 3 0.08
33 20 0.53
34 8 0.21
35 7 0.18
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (35 bp):
AATTAAAATCAAAAATATGAAAATAAAATATATAA
Found at i:10852174 original size:46 final size:41
Alignment explanation
Indices: 10852124--10852236 Score: 127
Period size: 46 Copynumber: 2.6 Consensus size: 41
10852114 TAAAAATCAA
* **
10852124 AAATTAAAATAAAATATAAAAGATTAAAATTTATATCAAGTAAAAT
1 AAATTAAAATAAAATATATAAGATTAAAAAGTATAT----T-AAAT
* *
10852170 AAATTAAAATAAAATATATAATATAAAAAAGTATATTAAAT
1 AAATTAAAATAAAATATATAAGATTAAAAAGTATATTAAAT
*
10852211 AAATAAAAATAAAATATATAAGATTA
1 AAATTAAAATAAAATATATAAGATTA
10852237 TAATAATAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
41 27 0.46
42 1 0.02
46 31 0.53
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (41 bp):
AAATTAAAATAAAATATATAAGATTAAAAAGTATATTAAAT
Found at i:10852522 original size:15 final size:15
Alignment explanation
Indices: 10852478--10852549 Score: 72
Period size: 15 Copynumber: 4.8 Consensus size: 15
10852468 TTATTTTCCT
* * *
10852478 TGCAATGACATTGCT
1 TGCAATCACATTACC
* *
10852493 TGCAAGCATATTACC
1 TGCAATCACATTACC
*
10852508 TACAATCACATTACC
1 TGCAATCACATTACC
*
10852523 TGCAATCATATTACC
1 TGCAATCACATTACC
*
10852538 TGTAATCACATT
1 TGCAATCACATT
10852550 GCATTGTAAA
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.32
Consensus pattern (15 bp):
TGCAATCACATTACC
Found at i:10852527 original size:30 final size:30
Alignment explanation
Indices: 10852493--10852549 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
10852483 TGACATTGCT
10852493 TGCAAGCATATTACCTACAATCACATTACC
1 TGCAAGCATATTACCTACAATCACATTACC
* **
10852523 TGCAATCATATTACCTGTAATCACATT
1 TGCAAGCATATTACCTACAATCACATT
10852550 GCATTGTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.35, C:0.26, G:0.07, T:0.32
Consensus pattern (30 bp):
TGCAAGCATATTACCTACAATCACATTACC
Found at i:10854782 original size:18 final size:18
Alignment explanation
Indices: 10854759--10854795 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
10854749 AAGAGAGTTC
10854759 GGTTTGTTTCTTTTAATT
1 GGTTTGTTTCTTTTAATT
10854777 GGTTTGTTTCTTTTAATT
1 GGTTTGTTTCTTTTAATT
10854795 G
1 G
10854796 AGAGAAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.05, G:0.19, T:0.65
Consensus pattern (18 bp):
GGTTTGTTTCTTTTAATT
Found at i:10855280 original size:5 final size:5
Alignment explanation
Indices: 10855265--10855299 Score: 61
Period size: 5 Copynumber: 6.8 Consensus size: 5
10855255 CAGATTGCCT
10855265 CCCTAC CCCTC CCCTC CCCTC CCCTC CCCTC CCCT
1 CCCT-C CCCTC CCCTC CCCTC CCCTC CCCTC CCCT
10855300 TTTCTTCCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.03, C:0.77, G:0.00, T:0.20
Consensus pattern (5 bp):
CCCTC
Found at i:10858974 original size:24 final size:26
Alignment explanation
Indices: 10858924--10858975 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
10858914 ATAAATATTT
*
10858924 TACTTCAAATATGTAAATAATGTTAA
1 TACTTCAAATATGTAAATAATCTTAA
10858950 TACTT-AAATATG-AAAT-ATCTATAA
1 TACTTCAAATATGTAAATAATCT-TAA
10858974 TA
1 TA
10858976 TTTCTTTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 3 0.12
24 9 0.38
25 7 0.29
26 5 0.21
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (26 bp):
TACTTCAAATATGTAAATAATCTTAA
Found at i:10862362 original size:32 final size:32
Alignment explanation
Indices: 10862321--10862393 Score: 146
Period size: 32 Copynumber: 2.3 Consensus size: 32
10862311 TTTTAACCTT
10862321 AAAAAGTTTTAAACCTTTCATTTCACATTGTC
1 AAAAAGTTTTAAACCTTTCATTTCACATTGTC
10862353 AAAAAGTTTTAAACCTTTCATTTCACATTGTC
1 AAAAAGTTTTAAACCTTTCATTTCACATTGTC
10862385 AAAAAGTTT
1 AAAAAGTTT
10862394 GTCAAGCTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (32 bp):
AAAAAGTTTTAAACCTTTCATTTCACATTGTC
Found at i:10863456 original size:67 final size:68
Alignment explanation
Indices: 10863311--10863464 Score: 168
Period size: 67 Copynumber: 2.3 Consensus size: 68
10863301 CGTGTACTGT
* * * * * * *
10863311 ATGAGATGATTAAGCA-TGCATGATAAATGCCATGATGCTATGTATATGATGTAAATTCCATATG
1 ATGAGATGA-TAAACAGTACATGATAAATGACATGATGCTATGTATATCACGTAAATTCCACATA
10863375 CCAC
65 CCAC
* * * * *
10863379 ATAAGATGATAAACAGTACATGATAAATGATATGATGCT-TGTATCTCACGTAGATTCCACATAT
1 ATGAGATGATAAACAGTACATGATAAATGACATGATGCTATGTATATCACGTAAATTCCACATAC
10863443 CAC
66 CAC
*
10863446 ATGAGATGATAAAGAGTAC
1 ATGAGATGATAAACAGTAC
10863465 TTATTGAAGA
Statistics
Matches: 71, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
67 43 0.61
68 28 0.39
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (68 bp):
ATGAGATGATAAACAGTACATGATAAATGACATGATGCTATGTATATCACGTAAATTCCACATAC
CAC
Found at i:10866513 original size:18 final size:19
Alignment explanation
Indices: 10866475--10866509 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
10866465 GTATCCTTTT
10866475 ATACAGATTAAACATGATA
1 ATACAGATTAAACATGATA
10866494 ATACA-ATT-AACATGAT
1 ATACAGATTAAACATGAT
10866510 TAATTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 3 0.19
19 5 0.31
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (19 bp):
ATACAGATTAAACATGATA
Found at i:10866876 original size:19 final size:19
Alignment explanation
Indices: 10866852--10866890 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
10866842 ATATATATAT
*
10866852 ATATATATTTGTGTCTAGC
1 ATATATATTTGTATCTAGC
*
10866871 ATATATGTTTGTATCTAGC
1 ATATATATTTGTATCTAGC
10866890 A
1 A
10866891 GATTGTGCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.46
Consensus pattern (19 bp):
ATATATATTTGTATCTAGC
Found at i:10872012 original size:4 final size:4
Alignment explanation
Indices: 10872003--10872031 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
10871993 TATTTGCTGT
10872003 TATC TATC TATC TATC TATC TATC TATC T
1 TATC TATC TATC TATC TATC TATC TATC T
10872032 CTCTCTCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:10872036 original size:2 final size:2
Alignment explanation
Indices: 10872029--10872055 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10872019 TATCTATCTA
10872029 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
10872056 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:10872060 original size:2 final size:2
Alignment explanation
Indices: 10872055--10872087 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
10872045 TCTCTCTCTC
10872055 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10872088 GTTGTTTGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10874486 original size:18 final size:18
Alignment explanation
Indices: 10874463--10874497 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
10874453 GCGACCTCGA
10874463 CCCCGGCCACGTCCACGC
1 CCCCGGCCACGTCCACGC
10874481 CCCCGGCCACGTCCACG
1 CCCCGGCCACGTCCACG
10874498 TACCGAAGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.60, G:0.23, T:0.06
Consensus pattern (18 bp):
CCCCGGCCACGTCCACGC
Found at i:10875568 original size:6 final size:6
Alignment explanation
Indices: 10875557--10875583 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
10875547 TGCTTCTATT
10875557 GTTAGG GTTAGG GTTAGG GTTAGG GTT
1 GTTAGG GTTAGG GTTAGG GTTAGG GTT
10875584 TTTTAATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.48, T:0.37
Consensus pattern (6 bp):
GTTAGG
Found at i:10876886 original size:18 final size:18
Alignment explanation
Indices: 10876862--10876922 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 18
10876852 CAGCAATATG
*
10876862 TACATCAGCATTCACATT
1 TACATCAACATTCACATT
* * *
10876880 AACATCAATATTCAAATT
1 TACATCAACATTCACATT
*
10876898 TACCTCAACATTCACATT
1 TACATCAACATTCACATT
10876916 TACATCA
1 TACATCA
10876923 TCAAAAAACT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.39, C:0.26, G:0.02, T:0.33
Consensus pattern (18 bp):
TACATCAACATTCACATT
Found at i:10877051 original size:18 final size:18
Alignment explanation
Indices: 10877030--10877078 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
10877020 CGTCAACATC
**
10877030 CACATTAACATCAATTTT
1 CACATTAACATCAAAATT
* *
10877048 CACATTCACCTCAAAATT
1 CACATTAACATCAAAATT
*
10877066 CACATTTACATCA
1 CACATTAACATCA
10877079 TTAAAAAACT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.39, C:0.29, G:0.00, T:0.33
Consensus pattern (18 bp):
CACATTAACATCAAAATT
Found at i:10877132 original size:156 final size:156
Alignment explanation
Indices: 10876844--10877142 Score: 472
Period size: 156 Copynumber: 1.9 Consensus size: 156
10876834 CAAAAACTCC
* * * * *
10876844 CCTTCTATCAGCAATATGTACATCAGCATTCACATTAACATCAATATTCAAATTTACCTCAACAT
1 CCTTCTATCAACAATATGTACATCAACATCCACATTAACATCAATATTCAAATTCACCTCAAAAT
* *
10876909 TCACATTTACATCATCAAAAAACTTACCAAGGTTAGAATCCATTGTTTACAGGGGAATTGCACGT
66 TCACATTTACATCATCAAAAAACTTACCAAGGTTAGAATCCATTGTTTACAGGGAAATTACACGT
10876974 ATTAGGTCCAAGTCAAGGTGGATTTT
131 ATTAGGTCCAAGTCAAGGTGGATTTT
* * *
10877000 CCTTCTATCAACAATATGTACGTCAACATCCACATTAACATCAATTTTCACATTCACCTCAAAAT
1 CCTTCTATCAACAATATGTACATCAACATCCACATTAACATCAATATTCAAATTCACCTCAAAAT
* * *
10877065 TCACATTTACATCATTAAAAAACTTACCAAGGTTAGAATCCATTGTTTGCAGGGAAATTACAGGT
66 TCACATTTACATCATCAAAAAACTTACCAAGGTTAGAATCCATTGTTTACAGGGAAATTACACGT
*
10877130 ATTAGGTCTAAGT
131 ATTAGGTCCAAGT
10877143 AGAGATGGAC
Statistics
Matches: 129, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
156 129 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.31
Consensus pattern (156 bp):
CCTTCTATCAACAATATGTACATCAACATCCACATTAACATCAATATTCAAATTCACCTCAAAAT
TCACATTTACATCATCAAAAAACTTACCAAGGTTAGAATCCATTGTTTACAGGGAAATTACACGT
ATTAGGTCCAAGTCAAGGTGGATTTT
Found at i:10877400 original size:29 final size:29
Alignment explanation
Indices: 10877363--10877421 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
10877353 TTGTCATCAC
** *
10877363 ATTTGTGTTATGGTGCACCATTGAGTCAT
1 ATTTGTGTTATGGTAAACCATCGAGTCAT
10877392 ATTTGTGTTATGGTAAACCATCGAGTCAT
1 ATTTGTGTTATGGTAAACCATCGAGTCAT
10877421 A
1 A
10877422 GAGAAGTCGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (29 bp):
ATTTGTGTTATGGTAAACCATCGAGTCAT
Found at i:10879405 original size:16 final size:16
Alignment explanation
Indices: 10879380--10879423 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
10879370 AAAATAAAAT
* *
10879380 TTTGAATTATTTTTAA
1 TTTGAGTTATTTTGAA
10879396 TTTGAGTTATTTTGAA
1 TTTGAGTTATTTTGAA
*
10879412 TTTGAGTCATTT
1 TTTGAGTTATTT
10879424 AAATTTAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.25, C:0.02, G:0.14, T:0.59
Consensus pattern (16 bp):
TTTGAGTTATTTTGAA
Done.