Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 70 of 172
Found at i:19714783 original size:39 final size:39
Alignment explanation
Indices: 19714740--19714915 Score: 228
Period size: 39 Copynumber: 4.5 Consensus size: 39
19714730 AACATGTTTT
* *
19714740 TGAGTATTACGACATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTATGATATATGCTTGAATGTTATGTGATTATA
*
19714779 TGAGTATTATGATATATGCTTGAATGTTATGTGATCATA
1 TGAGTATTATGATATATGCTTGAATGTTATGTGATTATA
* * * * *
19714818 TGAGTAGTGTGATATGTGCTTGAACGTTATGTAATTATA
1 TGAGTATTATGATATATGCTTGAATGTTATGTGATTATA
* *
19714857 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTATGATATATGCTTGAATGTTATGTGATTATA
* *
19714896 TGTGTGA-TGTGATATATGCT
1 TGAGT-ATTATGATATATGCT
19714916 CAAAAGTGAA
Statistics
Matches: 121, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
39 120 0.99
40 1 0.01
ACGTcount: A:0.29, C:0.05, G:0.23, T:0.43
Consensus pattern (39 bp):
TGAGTATTATGATATATGCTTGAATGTTATGTGATTATA
Found at i:19714941 original size:17 final size:17
Alignment explanation
Indices: 19714921--19714956 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
19714911 ATGCTCAAAA
19714921 GTGAATATGTTTACCAT
1 GTGAATATGTTTACCAT
19714938 GTGAATATGTTTACCAT
1 GTGAATATGTTTACCAT
19714955 GT
1 GT
19714957 AAAAGAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (17 bp):
GTGAATATGTTTACCAT
Found at i:19727279 original size:114 final size:112
Alignment explanation
Indices: 19727068--19727567 Score: 278
Period size: 114 Copynumber: 4.4 Consensus size: 112
19727058 GTTTTTTGAG
*
19727068 AAGCGCCGCAAAACATCTTAACCAAAATGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGGC
1 AAGCGCCGCAAAACATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGGC
* * *
19727133 GCAAAGCGAACACACTGCTAAGGCATACTATTAGCGGCGCTTTGGGCT
66 GCAAAGCGAAAACACCGCTAAGCCATA-TATTAGCGGCGCTTTGGGCT
** * * * *
19727181 AAGCGCCGCAAAATTTCTTAACCAAAACGCAGCGTTTCTGTCTTGATGTATACTATAATTAGTGG
1 AAGCGCCGCAAAACATCTTAACCAAAACGCAGAGTTT-GGTCTTGAGGTATACTAGAATTAGTGG
* * * ***
19727246 CGCATA-CTGGAAAACGCCGCTAACTCCAT-TATTAGCGGCGCTTT-TAAT
65 CGCAAAGC--GAAAACACCGCTAA-GCCATATATTAGCGGCGCTTTGGGCT
* * * * * * ** *
19727294 AAAACGTCGCAAAATATAC-TCACCAAAATGCAGAGTTTTGTCTTGAGGTATGTTAGTATTAGTG
1 -AAGCGCCGCAAAACAT-CTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTG
* * * * ** ** * **
19727358 GTGCTTATGGGAGCATGCCGCTAAAG-AATACTATTAGCGGCGCGTTCTTAG--
64 GCGC-AAAGCGAAAACACCGCT-AAGCCATA-TATTAGCGGCGC-TT-TGGGCT
* * * * * * *
19727409 AAGCGCCACAAAATATATTAACCAAAACGCAGCGTTTAGGTCTTGATGTATAGTGGAATTAGTGG
1 AAGCGCCGCAAAACATCTTAACCAAAACGCAGAGTTT-GGTCTTGAGGTATACTAGAATTAGTGG
* * * * * * ** **
19727474 CGTCCACGAGAAATCGCCTCTAAAG-CATAGTATTAGCGGCGCTTTTTGAG
65 CG-CAAAGCGAAAACACCGCT-AAGCCATA-TATTAGCGGCGCTTTGGGCT
* * * *
19727524 AAGCGCCGGAAGATATCTTAACCAAAACGCAAAGTTTTGGTCTT
1 AAGCGCCGCAAAACATCTTAACCAAAACGCAGAG-TTTGGTCTT
19727568 AACCATGCAT
Statistics
Matches: 297, Mismatches: 70, Indels: 38
0.73 0.17 0.09
Matches are distributed among these distances:
112 2 0.01
113 71 0.24
114 118 0.40
115 98 0.33
116 8 0.03
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (112 bp):
AAGCGCCGCAAAACATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGGC
GCAAAGCGAAAACACCGCTAAGCCATATATTAGCGGCGCTTTGGGCT
Found at i:19731135 original size:7 final size:6
Alignment explanation
Indices: 19731109--19731133 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19731099 GAGAGAGAAG
19731109 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
19731134 TACGAATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:19732084 original size:9 final size:9
Alignment explanation
Indices: 19732070--19732161 Score: 130
Period size: 9 Copynumber: 10.2 Consensus size: 9
19732060 TAGTAACTAA
19732070 ATAACTTAC
1 ATAACTTAC
19732079 ATAACTTAC
1 ATAACTTAC
19732088 ATAACTTAC
1 ATAACTTAC
* * *
19732097 AAAAATTAA
1 ATAACTTAC
19732106 ATAACTTAC
1 ATAACTTAC
19732115 ATAACTTAC
1 ATAACTTAC
* *
19732124 ATAAATTAA
1 ATAACTTAC
19732133 ATAACTTAC
1 ATAACTTAC
19732142 ATAACTTAC
1 ATAACTTAC
*
19732151 ATAGCTTAC
1 ATAACTTAC
19732160 AT
1 AT
19732162 TTTATGTGTA
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 72 1.00
ACGTcount: A:0.49, C:0.17, G:0.01, T:0.33
Consensus pattern (9 bp):
ATAACTTAC
Found at i:19733788 original size:21 final size:21
Alignment explanation
Indices: 19733764--19733806 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
19733754 GGAAAGCAAC
* * *
19733764 GGCTGCAGTGAGGGAAGTAGA
1 GGCTGCAGCGAGAGAAGCAGA
19733785 GGCTGCAGCGAGAGAAGCAGA
1 GGCTGCAGCGAGAGAAGCAGA
19733806 G
1 G
19733807 CAGAGCAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.14, G:0.47, T:0.09
Consensus pattern (21 bp):
GGCTGCAGCGAGAGAAGCAGA
Found at i:19739602 original size:50 final size:49
Alignment explanation
Indices: 19739543--19740204 Score: 412
Period size: 50 Copynumber: 13.2 Consensus size: 49
19739533 TTTGCCATTA
* *
19739543 TGGCTTTAATCTTTTTAACTACAATGTCGAGGAAGCATGATTCACTGTTG
1 TGGCTTTAATCTTTTTAACTGCAATGTCG-GGAAGCAAGATTCACTGTTG
* * ** * * * **
19739593 TGGCTTTAATATGTTCCACTGCACTGCCTGGGAAGTAAGATTCGTTGTTG
1 TGGCTTTAATCTTTTTAACTGCAATGTC-GGGAAGCAAGATTCACTGTTG
* * *
19739643 TAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCATGATTCGCTGTTG
1 TGGCTTTAATCTTTTTAACTGCAATGTC-GGGAAGCAAGATTCACTGTTG
* ** ** * * * *
19739693 TGGCTTTAATCTATTCCACTGCACCGCCTGGGAGGCAAGATTCGCCGTTG
1 TGGCTTTAATCTTTTTAACTGCAATGTC-GGGAAGCAAGATTCACTGTTG
* * * * * **
19739743 TGGCTTTAATATTATTAATTGCAATGTCGAGGAAGTAGGATT-TGTCGTTG
1 TGGCTTTAATCTTTTTAACTGCAATGTCG-GGAAGCAAGATTCACT-GTTG
* ** ** * * *
19739793 TGGCTTTAATCTGTTCCACTGCACCGCCTAGGAAGTAAGATTCACTGTTG
1 TGGCTTTAATCTTTTTAACTGCAATGTC-GGGAAGCAAGATTCACTGTTG
* * * *
19739843 TAGCTTTAATCTTTTTAATTGCAATGTCGGGGAAGTATGATTCACTGTTG
1 TGGCTTTAATCTTTTTAACTGCAATGTC-GGGAAGCAAGATTCACTGTTG
* ** * * * **
19739893 TGGCTTTAATCTGTTCCACTGCACTGCCTGGGAGGCAAGATTTGCTGTTG
1 TGGCTTTAATCTTTTTAACTGCAATGTC-GGGAAGCAAGATTCACTGTTG
* * *
19739943 TAGCTTTAATCTTTTTAA-TCGCAATGTCTGGGAAGCAAGATTCACCGATG
1 TGGCTTTAATCTTTTTAACT-GCAATGTC-GGGAAGCAAGATTCACTGTTG
* * ** * * * * * *
19739993 TAGCTTTAATCTATTCCACTAC-ATCGCCTGGGGAGTAAGATTCGCTGCTG
1 TGGCTTTAATCTTTTTAACTGCAAT-GTC-GGGAAGCAAGATTCACTGTTG
* * * *
19740043 TAGCATTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATG
1 TGGCTTTAATCTTTTTAACTGCAATGTC-GGGAAGCAAGATTCACTGTTG
* ** ** * * ** **
19740093 TGGCTTTAATCTATTCCACTGCACCGCTAGAGAAATAAGATTTGCTGTTG
1 TGGCTTTAATCTTTTTAACTGCAATG-TCGGGAAGCAAGATTCACTGTTG
* * * * *
19740143 TAGCTTTAATCTTTTTAACTACAATGTCGGGGAAACAAGATTCACCGATG
1 TGGCTTTAATCTTTTTAACTGCAATGTC-GGGAAGCAAGATTCACTGTTG
19740193 TGGCTTTAATCT
1 TGGCTTTAATCT
19740205 GTTCCACTGC
Statistics
Matches: 453, Mismatches: 148, Indels: 22
0.73 0.24 0.04
Matches are distributed among these distances:
49 5 0.01
50 442 0.98
51 6 0.01
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.35
Consensus pattern (49 bp):
TGGCTTTAATCTTTTTAACTGCAATGTCGGGAAGCAAGATTCACTGTTG
Found at i:19739698 original size:100 final size:100
Alignment explanation
Indices: 19739545--19740240 Score: 869
Period size: 100 Copynumber: 7.0 Consensus size: 100
19739535 TGCCATTATG
* * * *
19739545 GCTTTAATCTTTTTAACTACAATGTCGAGGAAGCATGATTCACTGTTGTGGCTTTAATATGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACTGTTGTGGCTTTAATCTGTTCC
* *
19739610 ACTGCACTGCCTGGGAAGTAAGATTCGTTGTTGTA
66 ACTGCACCGCCTGGGAAGTAAGATTCGCTGTTGTA
* * *
19739645 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCATGATTCGCTGTTGTGGCTTTAATCTATTCC
1 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACTGTTGTGGCTTTAATCTGTTCC
* * * *
19739710 ACTGCACCGCCTGGGAGGCAAGATTCGCCGTTGTG
66 ACTGCACCGCCTGGGAAGTAAGATTCGCTGTTGTA
* * * * * * **
19739745 GCTTTAATATTATTAATTGCAATGTCGAGGAAGTAGGATT-TGTCGTTGTGGCTTTAATCTGTTC
1 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACT-GTTGTGGCTTTAATCTGTTC
* *
19739809 CACTGCACCGCCTAGGAAGTAAGATTCACTGTTGTA
65 CACTGCACCGCCTGGGAAGTAAGATTCGCTGTTGTA
* * *
19739845 GCTTTAATCTTTTTAATTGCAATGTCGGGGAAGTATGATTCACTGTTGTGGCTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACTGTTGTGGCTTTAATCTGTTCC
* * * *
19739910 ACTGCACTGCCTGGGAGGCAAGATTTGCTGTTGTA
66 ACTGCACCGCCTGGGAAGTAAGATTCGCTGTTGTA
* * * * *
19739945 GCTTTAATCTTTTTAA-TCGCAATGTCTGGGAAGCAAGATTCACCGATGTAGCTTTAATCTATTC
1 GCTTTAATCTTTTTAACT-GCAATGTCGGGGAAGCAAGATTCACTGTTGTGGCTTTAATCTGTTC
* * * *
19740009 CACTACATCGCCTGGGGAGTAAGATTCGCTGCTGTA
65 CACTGCACCGCCTGGGAAGTAAGATTCGCTGTTGTA
* * * *
19740045 GCATTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTATTCC
1 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACTGTTGTGGCTTTAATCTGTTCC
* * *
19740110 ACTGCACCG-CTAGAGAAATAAGATTTGCTGTTGTA
66 ACTGCACCGCCT-GGGAAGTAAGATTCGCTGTTGTA
* * * *
19740145 GCTTTAATCTTTTTAACTACAATGTCGGGGAAACAAGATTCACCGATGTGGCTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACTGTTGTGGCTTTAATCTGTTCC
*
19740210 ACTGCACCG-CTAGGGAAATAAGATTCGCTGT
66 ACTGCACCGCCT-GGGAAGTAAGATTCGCTGT
19740241 CTTCACCGAT
Statistics
Matches: 522, Mismatches: 69, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
99 4 0.01
100 516 0.99
101 2 0.00
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (100 bp):
GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACTGTTGTGGCTTTAATCTGTTCC
ACTGCACCGCCTGGGAAGTAAGATTCGCTGTTGTA
Found at i:19748024 original size:49 final size:49
Alignment explanation
Indices: 19747932--19748083 Score: 207
Period size: 54 Copynumber: 3.0 Consensus size: 49
19747922 GGTTCACTGT
* *
19747932 AATGGAATAGAGTTGTAATTAGTAATTCAAT-TGTTTGGTTGAATGGAATGG
1 AATGGAATAGAGCTGTAA-TAG-AATTC-TTGTGTTTGGTTGAATGGAATGG
19747983 AATGGAATAGAGCTGTAATAGAATTCTTGTGTTTGGTTGAATGGAATGGAATGG
1 AATGGAATAGAGCTGTAATAGAATTCTTGTGTTTGG-T---T-GAATGGAATGG
19748037 AATGGAATAGAGCTGTAATAGAATTCTTGTGTTTGGTTGAATGGAAT
1 AATGGAATAGAGCTGTAATAGAATTCTTGTGTTTGGTTGAATGGAAT
19748084 AGATTATAAT
Statistics
Matches: 93, Mismatches: 2, Indels: 14
0.85 0.02 0.13
Matches are distributed among these distances:
48 1 0.01
49 21 0.23
50 5 0.05
51 17 0.18
53 2 0.02
54 47 0.51
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (49 bp):
AATGGAATAGAGCTGTAATAGAATTCTTGTGTTTGGTTGAATGGAATGG
Found at i:19748054 original size:54 final size:54
Alignment explanation
Indices: 19747972--19748083 Score: 224
Period size: 54 Copynumber: 2.1 Consensus size: 54
19747962 TTGTTTGGTT
19747972 GAATGGAATGGAATGGAATAGAGCTGTAATAGAATTCTTGTGTTTGGTTGAATG
1 GAATGGAATGGAATGGAATAGAGCTGTAATAGAATTCTTGTGTTTGGTTGAATG
19748026 GAATGGAATGGAATGGAATAGAGCTGTAATAGAATTCTTGTGTTTGGTTGAATG
1 GAATGGAATGGAATGGAATAGAGCTGTAATAGAATTCTTGTGTTTGGTTGAATG
19748080 GAAT
1 GAAT
19748084 AGATTATAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (54 bp):
GAATGGAATGGAATGGAATAGAGCTGTAATAGAATTCTTGTGTTTGGTTGAATG
Found at i:19748210 original size:26 final size:25
Alignment explanation
Indices: 19748161--19748211 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
19748151 ATGATTATTT
*
19748161 TTATTGTTATTAAATTTTAATAAAA
1 TTATTGTTAATAAATTTTAATAAAA
* *
19748186 TTATTGTTAAATATATTTTATTAAAA
1 TTATTGTT-AATAAATTTTAATAAAA
19748212 AAAGAAATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (25 bp):
TTATTGTTAATAAATTTTAATAAAA
Found at i:19748282 original size:57 final size:57
Alignment explanation
Indices: 19748174--19748309 Score: 155
Period size: 57 Copynumber: 2.4 Consensus size: 57
19748164 TTGTTATTAA
* * * * * * *
19748174 ATTTTAATAAAATTATTGTTAAATATATTTTATTAAAAAAAGAAATGATTTAACCAT
1 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAAAAGAAATAATTTAACAAC
* * * * *
19748231 ATTTTAACATAATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAAC
1 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAAAAGAAATAATTTAACAAC
19748288 ATTCTTAATATAATTATTATTA
1 ATT-TTAATATAATTATTATTA
19748310 TATGAATTAA
Statistics
Matches: 65, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
57 48 0.74
58 17 0.26
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (57 bp):
ATTTTAATATAATTATTATTAAATATAATTTAATAAAAAAAGAAATAATTTAACAAC
Found at i:19752959 original size:23 final size:23
Alignment explanation
Indices: 19752933--19752985 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
19752923 CAAATTCTCC
*
19752933 ATGTAAAGAAGCATAACACAAAA
1 ATGTAAAGAAACATAACACAAAA
* *
19752956 ATGTTAAGAAACATGACACAAAA
1 ATGTAAAGAAACATAACACAAAA
*
19752979 GTGTAAA
1 ATGTAAA
19752986 CCAAGTGCGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.57, C:0.11, G:0.15, T:0.17
Consensus pattern (23 bp):
ATGTAAAGAAACATAACACAAAA
Found at i:19753344 original size:32 final size:32
Alignment explanation
Indices: 19753306--19753371 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
19753296 AATGGGTCAG
19753306 AAATAGCGGCTACCCAAGCAATGCTTGCTTAC
1 AAATAGCGGCTACCCAAGCAATGCTTGCTTAC
19753338 AAATAGCGGCTACCCAAGCAATGCTTGCTTAC
1 AAATAGCGGCTACCCAAGCAATGCTTGCTTAC
19753370 AA
1 AA
19753372 CTATCTCTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.21
Consensus pattern (32 bp):
AAATAGCGGCTACCCAAGCAATGCTTGCTTAC
Found at i:19772438 original size:39 final size:37
Alignment explanation
Indices: 19772375--19772455 Score: 99
Period size: 39 Copynumber: 2.1 Consensus size: 37
19772365 CTCACAAGAC
* * *
19772375 TTTTCTTTTTTTTTTAACTTGATTTTTTTGCTCATTTTT
1 TTTTTTTTTTTTTTTAACTCGATTTTTTT--TCACTTTT
**
19772414 TTTTTTTTTTTTTTTTGCTCGATTTTTTTTCACTTTT
1 TTTTTTTTTTTTTTTAACTCGATTTTTTTTCACTTTT
19772451 TTTTT
1 TTTTT
19772456 GAATTTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 12 0.32
39 25 0.68
ACGTcount: A:0.07, C:0.10, G:0.05, T:0.78
Consensus pattern (37 bp):
TTTTTTTTTTTTTTTAACTCGATTTTTTTTCACTTTT
Found at i:19772450 original size:26 final size:26
Alignment explanation
Indices: 19772381--19772456 Score: 82
Period size: 26 Copynumber: 2.8 Consensus size: 26
19772371 AGACTTTTCT
19772381 TTTTTTTTTAACTTGATTTTTTTGCTCA
1 TTTTTTTTTAACTT--TTTTTTTGCTCA
***
19772409 TTTTTTTTTTTTTTTTTTTTTGCTCGA
1 TTTTTTTTTAACTTTTTTTTTGCTC-A
*
19772436 -TTTTTTTTCACTTTTTTTTTG
1 TTTTTTTTTAACTTTTTTTTTG
19772457 AATTTTTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 29 0.71
27 1 0.02
28 11 0.27
ACGTcount: A:0.08, C:0.09, G:0.07, T:0.76
Consensus pattern (26 bp):
TTTTTTTTTAACTTTTTTTTTGCTCA
Found at i:19772463 original size:39 final size:39
Alignment explanation
Indices: 19772380--19772466 Score: 97
Period size: 39 Copynumber: 2.2 Consensus size: 39
19772370 AAGACTTTTC
* *
19772380 TTTTTTTTTTAACTTGATTTTTTTGCTCATTTTTTTTT-T
1 TTTTTTTTTTAACTCGATTTTTTT-CTCATTTTTTTTTAA
**
19772419 TTTTTTTTTTTGCTCGATTTTTTT-TCACTTTTTTTTTGAA
1 TTTTTTTTTTAACTCGATTTTTTTCTCA-TTTTTTTTT-AA
19772459 TTTTTTTT
1 TTTTTTTT
19772467 CAATCAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
37 3 0.07
38 9 0.22
39 21 0.51
40 8 0.20
ACGTcount: A:0.09, C:0.08, G:0.06, T:0.77
Consensus pattern (39 bp):
TTTTTTTTTTAACTCGATTTTTTTCTCATTTTTTTTTAA
Found at i:19774528 original size:20 final size:20
Alignment explanation
Indices: 19774488--19774539 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
19774478 ACCAATAAAA
19774488 TAAATGAGCTGAATTGTAGC
1 TAAATGAGCTGAATTGTAGC
19774508 TAAATTGAGCTCG-ATTG-AGC
1 TAAA-TGAGCT-GAATTGTAGC
19774528 TGAAATGAGCTG
1 T-AAATGAGCTG
19774540 GTCGGAGCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 1 0.03
20 14 0.48
21 13 0.45
22 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.29
Consensus pattern (20 bp):
TAAATGAGCTGAATTGTAGC
Found at i:19780820 original size:51 final size:50
Alignment explanation
Indices: 19780763--19780905 Score: 189
Period size: 51 Copynumber: 2.8 Consensus size: 50
19780753 AAAGTGATGG
19780763 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGCT-TCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAG-TAT-GA
* * *
19780814 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGT-ATGA
* * * *
19780865 TCACATGTGTAGTACCATGTGTAGGCTACTATGTGAACCGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGG
19780906 TATCAATAAT
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
50 1 0.01
51 79 0.98
52 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTATGA
Found at i:19781182 original size:16 final size:16
Alignment explanation
Indices: 19781161--19781192 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
19781151 TGATTGAAAG
*
19781161 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
19781177 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
19781193 GCAACAAAAC
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:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:19790669 original size:16 final size:17
Alignment explanation
Indices: 19790644--19790678 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
19790634 TTTTTTTCAA
19790644 TCATCCCTCATCC-CTC
1 TCATCCCTCATCCTCTC
*
19790660 TCATCTCTCATCCTCTC
1 TCATCCCTCATCCTCTC
19790677 TC
1 TC
19790679 TCAACTCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.11, C:0.51, G:0.00, T:0.37
Consensus pattern (17 bp):
TCATCCCTCATCCTCTC
Found at i:19794613 original size:830 final size:830
Alignment explanation
Indices: 19793015--19794670 Score: 3312
Period size: 830 Copynumber: 2.0 Consensus size: 830
19793005 TAATCTCCAT
19793015 TATATGTATACCAAAACCGAATTCGTATACACCTAATTATTTATACTTAAATCACTTCCAAAGGT
1 TATATGTATACCAAAACCGAATTCGTATACACCTAATTATTTATACTTAAATCACTTCCAAAGGT
19793080 TTATATTTCATTTCCTTACAAAATAAATATTTCATATCCTATTTTATACTTATATACTATCAATT
66 TTATATTTCATTTCCTTACAAAATAAATATTTCATATCCTATTTTATACTTATATACTATCAATT
19793145 AAAATTAACCCGTGCATAACATTCATTTATATAATATATATCATGAAATGCTATACCACAACAAA
131 AAAATTAACCCGTGCATAACATTCATTTATATAATATATATCATGAAATGCTATACCACAACAAA
19793210 AATATGCATAATCTATAATTCAAACCAAAACCGAGCAAAGCAAACTAATTAAGCCATATTCGCAT
196 AATATGCATAATCTATAATTCAAACCAAAACCGAGCAAAGCAAACTAATTAAGCCATATTCGCAT
19793275 GGCTTTAATACTTACACATTTAAATTTAAACAAAGTTCGAACCGACATACATGCCATAATCAAAA
261 GGCTTTAATACTTACACATTTAAATTTAAACAAAGTTCGAACCGACATACATGCCATAATCAAAA
19793340 TTAAGTTTCAACTTATAAAATACCGTAGTTATTTGATAGTGTGACAAACTTTGTTGACGAATCTT
326 TTAAGTTTCAACTTATAAAATACCGTAGTTATTTGATAGTGTGACAAACTTTGTTGACGAATCTT
19793405 CGAGCTCGTAACAACCTCCAAAATCTACAAAACAAAAGTAAACAAAAATAGAAAGTAAGCTACCT
391 CGAGCTCGTAACAACCTCCAAAATCTACAAAACAAAAGTAAACAAAAATAGAAAGTAAGCTACCT
19793470 TAGCTTAGTAAGTCTTTAGCAATTCATAAATAAAATATGAATCATATAATTCCTTAAATAAATTT
456 TAGCTTAGTAAGTCTTTAGCAATTCATAAATAAAATATGAATCATATAATTCCTTAAATAAATTT
19793535 ACTAAACTGCAATTACCATTTATGAATACTATCGAAACTTTTATTAACCTCAAGACCTTTTATTC
521 ACTAAACTGCAATTACCATTTATGAATACTATCGAAACTTTTATTAACCTCAAGACCTTTTATTC
19793600 ATAACAATTAAACATGATATAAACTTACAAATTTGTGCCTACCATTCGCACATAACCGAATATGT
586 ATAACAATTAAACATGATATAAACTTACAAATTTGTGCCTACCATTCGCACATAACCGAATATGT
19793665 ATACTCATCGAATACATATATATACATCAATATCCTTTATTTTATTTACATTCAATCAATGTACT
651 ATACTCATCGAATACATATATATACATCAATATCCTTTATTTTATTTACATTCAATCAATGTACT
19793730 TACCTAATATCAAATAAGATATAAATAACACATACCTGATTATTATAATATCATAATCCATTTGT
716 TACCTAATATCAAATAAGATATAAATAACACATACCTGATTATTATAATATCATAATCCATTTGT
19793795 TGTTATATTGACAAAAAACTTACTAAACACACATTTTAAAATGATTATGA
781 TGTTATATTGACAAAAAACTTACTAAACACACATTTTAAAATGATTATGA
19793845 TATATGTATACCAAAACCGAATTCGTATACACCTAATTATTTATACTTAAATCACTTCCAAAGGT
1 TATATGTATACCAAAACCGAATTCGTATACACCTAATTATTTATACTTAAATCACTTCCAAAGGT
19793910 TTATATTTCATTTCCTTACAAAATAAATATTTCATATCCTATTTTATACTTATATACTATCAATT
66 TTATATTTCATTTCCTTACAAAATAAATATTTCATATCCTATTTTATACTTATATACTATCAATT
19793975 AAAATTAACCCGTGCATAACATTCATTTATATAATATATATCATGAAATGCTATACCACAACAAA
131 AAAATTAACCCGTGCATAACATTCATTTATATAATATATATCATGAAATGCTATACCACAACAAA
19794040 AATATGCATAATCTATAATTCAAACCAAAACCGAGCAAAGCAAACTAATTAAGCCATATTCGCAT
196 AATATGCATAATCTATAATTCAAACCAAAACCGAGCAAAGCAAACTAATTAAGCCATATTCGCAT
19794105 GGCTTTAATACTTACACATTTAAATTTAAACAAAGTTCGAACCGACATACATGCCATAATCAAAA
261 GGCTTTAATACTTACACATTTAAATTTAAACAAAGTTCGAACCGACATACATGCCATAATCAAAA
19794170 TTAAGTTTCAACTTATAAAATACCGTAGTTATTTGATAGTGTGACAAACTTTGTTGACGAATCTT
326 TTAAGTTTCAACTTATAAAATACCGTAGTTATTTGATAGTGTGACAAACTTTGTTGACGAATCTT
19794235 CGAGCTCGTAACAACCTCCAAAATCTACAAAACAAAAGTAAACAAAAATAGAAAGTAAGCTACCT
391 CGAGCTCGTAACAACCTCCAAAATCTACAAAACAAAAGTAAACAAAAATAGAAAGTAAGCTACCT
19794300 TAGCTTAGTAAGTCTTTAGCAATTCATAAATAAAATATGAATCATATAATTCCTTAAATAAATTT
456 TAGCTTAGTAAGTCTTTAGCAATTCATAAATAAAATATGAATCATATAATTCCTTAAATAAATTT
19794365 ACTAAACTGCAATTACCATTTATGAATACTATCGAAACTTTTATTAACCTCAAGACCTTTTATTC
521 ACTAAACTGCAATTACCATTTATGAATACTATCGAAACTTTTATTAACCTCAAGACCTTTTATTC
19794430 ATAACAATTAAACATGATATAAACTTACAAATTTGTGCCTACCATTCGCACATAACCGAATATGT
586 ATAACAATTAAACATGATATAAACTTACAAATTTGTGCCTACCATTCGCACATAACCGAATATGT
19794495 ATACTCATCGAATACATATATATACATCAATATCCTTTATTTTATTTACATTCAATCAATGTACT
651 ATACTCATCGAATACATATATATACATCAATATCCTTTATTTTATTTACATTCAATCAATGTACT
19794560 TACCTAATATCAAATAAGATATAAATAACACATACCTGATTATTATAATATCATAATCCATTTGT
716 TACCTAATATCAAATAAGATATAAATAACACATACCTGATTATTATAATATCATAATCCATTTGT
19794625 TGTTATATTGACAAAAAACTTACTAAACACACATTTTAAAATGATT
781 TGTTATATTGACAAAAAACTTACTAAACACACATTTTAAAATGATT
19794671 CACCGGCATG
Statistics
Matches: 826, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
830 826 1.00
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.33
Consensus pattern (830 bp):
TATATGTATACCAAAACCGAATTCGTATACACCTAATTATTTATACTTAAATCACTTCCAAAGGT
TTATATTTCATTTCCTTACAAAATAAATATTTCATATCCTATTTTATACTTATATACTATCAATT
AAAATTAACCCGTGCATAACATTCATTTATATAATATATATCATGAAATGCTATACCACAACAAA
AATATGCATAATCTATAATTCAAACCAAAACCGAGCAAAGCAAACTAATTAAGCCATATTCGCAT
GGCTTTAATACTTACACATTTAAATTTAAACAAAGTTCGAACCGACATACATGCCATAATCAAAA
TTAAGTTTCAACTTATAAAATACCGTAGTTATTTGATAGTGTGACAAACTTTGTTGACGAATCTT
CGAGCTCGTAACAACCTCCAAAATCTACAAAACAAAAGTAAACAAAAATAGAAAGTAAGCTACCT
TAGCTTAGTAAGTCTTTAGCAATTCATAAATAAAATATGAATCATATAATTCCTTAAATAAATTT
ACTAAACTGCAATTACCATTTATGAATACTATCGAAACTTTTATTAACCTCAAGACCTTTTATTC
ATAACAATTAAACATGATATAAACTTACAAATTTGTGCCTACCATTCGCACATAACCGAATATGT
ATACTCATCGAATACATATATATACATCAATATCCTTTATTTTATTTACATTCAATCAATGTACT
TACCTAATATCAAATAAGATATAAATAACACATACCTGATTATTATAATATCATAATCCATTTGT
TGTTATATTGACAAAAAACTTACTAAACACACATTTTAAAATGATTATGA
Found at i:19794763 original size:41 final size:41
Alignment explanation
Indices: 19794718--19794816 Score: 146
Period size: 41 Copynumber: 2.4 Consensus size: 41
19794708 AGAACATCGA
* *
19794718 CATTAAGCTTGCTAGATGTAAAGTCTGAAATATTTCACCAG
1 CATTAAGCTTGCTAGACGTAAAGTCTGAAATATTTCAACAG
* *
19794759 CATTAAGCCTGCTAGACGTAAAGTCTGAAATATTTCAACGG
1 CATTAAGCTTGCTAGACGTAAAGTCTGAAATATTTCAACAG
19794800 CATTAAG-TCTGCTAGAC
1 CATTAAGCT-TGCTAGAC
19794817 ACAGAGTCTG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (41 bp):
CATTAAGCTTGCTAGACGTAAAGTCTGAAATATTTCAACAG
Found at i:19794825 original size:41 final size:41
Alignment explanation
Indices: 19794718--19794828 Score: 132
Period size: 41 Copynumber: 2.7 Consensus size: 41
19794708 AGAACATCGA
* *** *
19794718 CATTAAGCTTGCTAGATGTAAAGTCTGAAATATTTCACCAG
1 CATTAAGCCTGCTAGACACAAAGTCTGAAATATTTCAACAG
** *
19794759 CATTAAGCCTGCTAGACGTAAAGTCTGAAATATTTCAACGG
1 CATTAAGCCTGCTAGACACAAAGTCTGAAATATTTCAACAG
* *
19794800 CATTAAGTCTGCTAGACACAGAGTCTGAA
1 CATTAAGCCTGCTAGACACAAAGTCTGAA
19794829 TAACTCATAT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (41 bp):
CATTAAGCCTGCTAGACACAAAGTCTGAAATATTTCAACAG
Found at i:19796270 original size:66 final size:66
Alignment explanation
Indices: 19796164--19796297 Score: 250
Period size: 66 Copynumber: 2.0 Consensus size: 66
19796154 GACCAATACA
* *
19796164 TTCTATAATCTCATACGGTCTAATAAATCTCGGACTCAATTTGCCTTTACGACTAAATCTGAGTA
1 TTCTATAATCTCATACAGTCCAATAAATCTCGGACTCAATTTGCCTTTACGACTAAATCTGAGTA
19796229 T
66 T
19796230 TTCTATAATCTCATACAGTCCAATAAATCTCGGACTCAATTTGCCTTTACGACTAAATCTGAGTA
1 TTCTATAATCTCATACAGTCCAATAAATCTCGGACTCAATTTGCCTTTACGACTAAATCTGAGTA
19796295 T
66 T
19796296 TT
1 TT
19796298 TCTTCCATGG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.37
Consensus pattern (66 bp):
TTCTATAATCTCATACAGTCCAATAAATCTCGGACTCAATTTGCCTTTACGACTAAATCTGAGTA
T
Found at i:19805350 original size:21 final size:20
Alignment explanation
Indices: 19805326--19805375 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 20
19805316 GCGGTGGCAA
19805326 TGAGATTAATTACTATAATGG
1 TGAGATTAA-TACTATAATGG
*
19805347 TGAGATTGAATACTGTAATGG
1 TGAGATT-AATACTATAATGG
19805368 TGAGATTA
1 TGAGATTA
19805376 GAAACAACGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 1 0.04
21 24 0.89
22 2 0.07
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (20 bp):
TGAGATTAATACTATAATGG
Found at i:19805628 original size:15 final size:15
Alignment explanation
Indices: 19805604--19805645 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
19805594 TTAAACTATA
19805604 TAAAATTAAATATTAT
1 TAAAA-TAAATATTAT
* *
19805620 TAAAATAAAAAGTAT
1 TAAAATAAATATTAT
19805635 T-AAATAAATAT
1 TAAAATAAATAT
19805646 AATGATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 8 0.36
15 9 0.41
16 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (15 bp):
TAAAATAAATATTAT
Found at i:19806188 original size:23 final size:23
Alignment explanation
Indices: 19806141--19806219 Score: 126
Period size: 23 Copynumber: 3.5 Consensus size: 23
19806131 AAAAATAATA
*
19806141 AATAATAAAACATATTA--AAAT
1 AATAATAAAAGATATTATCAAAT
19806162 AATAATAAAAGATATTATCAAAT
1 AATAATAAAAGATATTATCAAAT
*
19806185 AATAATAAAAGACATTATCAAAT
1 AATAATAAAAGATATTATCAAAT
19806208 AATAATAAAAGA
1 AATAATAAAAGA
19806220 CATTGAAATT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
21 16 0.30
23 38 0.70
ACGTcount: A:0.65, C:0.05, G:0.04, T:0.27
Consensus pattern (23 bp):
AATAATAAAAGATATTATCAAAT
Found at i:19807831 original size:29 final size:29
Alignment explanation
Indices: 19807768--19807834 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
19807758 CGATTTCGCG
* * *
19807768 AAAAACGGACCATTTCGGTAAATAATTAC
1 AAAAAGGGCCCATTTCGGTAAATAATTAA
* *
19807797 ATAAAGGGCCCATTTCGGTAAAT-TTTGAA
1 AAAAAGGGCCCATTTCGGTAAATAATT-AA
19807826 AAAAAGGGC
1 AAAAAGGGC
19807835 TTTTTTTGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
28 2 0.06
29 29 0.94
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (29 bp):
AAAAAGGGCCCATTTCGGTAAATAATTAA
Found at i:19808993 original size:22 final size:22
Alignment explanation
Indices: 19808967--19809018 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
19808957 TTATTCAATT
19808967 TATTT-TTTATTATATATATAAA
1 TATTTGTTTATT-TATATATAAA
* *
19808989 TATTTGTTTATTTATATTTATA
1 TATTTGTTTATTTATATATAAA
19809011 TATTTGTT
1 TATTTGTT
19809019 CGCTTACATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (22 bp):
TATTTGTTTATTTATATATAAA
Found at i:19809412 original size:27 final size:27
Alignment explanation
Indices: 19809356--19809412 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
19809346 ATTTTTTAAT
*
19809356 AATTATAACAAAATTAAAAAATAGACA
1 AATTATAACAAAATTAAAAAATAGAAA
*
19809383 AATTAT-ACAAAATATTAAAAATTA-AAA
1 AATTATAAC-AAA-ATTAAAAAATAGAAA
19809410 AAT
1 AAT
19809413 ACGTCCATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 2 0.08
27 14 0.54
28 10 0.38
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (27 bp):
AATTATAACAAAATTAAAAAATAGAAA
Found at i:19816013 original size:50 final size:53
Alignment explanation
Indices: 19815902--19816016 Score: 146
Period size: 56 Copynumber: 2.2 Consensus size: 53
19815892 ATTTGAGTAA
* * *
19815902 AGAGATCCCATGTAAGACCATGTCTGGGATATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCA-CGAG--TATG
*
19815958 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C-CGAG-ATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCACGAGTATG
19816008 AGAGGTCCC
1 AGAGGTCCC
19816017 GAGTATCCTT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
50 12 0.22
53 3 0.05
55 1 0.02
56 39 0.71
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.23
Consensus pattern (53 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCACGAGTATG
Found at i:19816111 original size:18 final size:18
Alignment explanation
Indices: 19816088--19816125 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
19816078 TGTAGGTAAA
19816088 AGCCTAATAGACAAGTTC
1 AGCCTAATAGACAAGTTC
19816106 AGCCTAATAGACAAGTTC
1 AGCCTAATAGACAAGTTC
19816124 AG
1 AG
19816126 GTGAGTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (18 bp):
AGCCTAATAGACAAGTTC
Found at i:19822289 original size:24 final size:24
Alignment explanation
Indices: 19822253--19822313 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
19822243 TACTTGAAGG
* *
19822253 GACCCTCATGAGGGTGTAAGAGTA
1 GACCCTTAGGAGGGTGTAAGAGTA
* *
19822277 GACCCTTAGGAGGGTGTGAGAGTC
1 GACCCTTAGGAGGGTGTAAGAGTA
*
19822301 GCACCTTTAGGAG
1 G-ACCCTTAGGAG
19822314 CATTTAGCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
24 21 0.68
25 10 0.32
ACGTcount: A:0.25, C:0.18, G:0.36, T:0.21
Consensus pattern (24 bp):
GACCCTTAGGAGGGTGTAAGAGTA
Found at i:19825928 original size:10 final size:9
Alignment explanation
Indices: 19825906--19825980 Score: 60
Period size: 10 Copynumber: 7.4 Consensus size: 9
19825896 AGTCCCCAAA
19825906 TTATTATTTT
1 TTATT-TTTT
19825916 TTATTTTTCT
1 TTATTTTT-T
19825926 TTATTTATTT
1 TTATTT-TTT
19825936 TTATTTATTT
1 TTATTT-TTT
* *
19825946 TGATTTTGAT
1 TTATTTT-TT
19825956 TTATTTATTAT
1 TTATTT-TT-T
19825967 TTATATTTTT
1 TTAT-TTTTT
19825977 TTAT
1 TTAT
19825981 GCTTTAGGAA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
9 4 0.07
10 39 0.71
11 10 0.18
12 2 0.04
ACGTcount: A:0.20, C:0.01, G:0.03, T:0.76
Consensus pattern (9 bp):
TTATTTTTT
Found at i:19825940 original size:30 final size:31
Alignment explanation
Indices: 19825906--19825977 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
19825896 AGTCCCCAAA
**
19825906 TTATTATTTTTTATTTTTCTTTATTTATT-T
1 TTATTATTTTTTATTTTGATTTATTTATTAT
*
19825936 TTATT-TATTTTGATTTTGATTTATTTATTAT
1 TTATTAT-TTTTTATTTTGATTTATTTATTAT
19825967 TTA-TATTTTTT
1 TTATTATTTTTT
19825978 TATGCTTTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
29 1 0.03
30 29 0.83
31 5 0.14
ACGTcount: A:0.19, C:0.01, G:0.03, T:0.76
Consensus pattern (31 bp):
TTATTATTTTTTATTTTGATTTATTTATTAT
Found at i:19827028 original size:25 final size:25
Alignment explanation
Indices: 19826992--19827065 Score: 79
Period size: 25 Copynumber: 3.1 Consensus size: 25
19826982 ATTAATATCC
19826992 AAAT-AAGTAATAAATAATAAAATA
1 AAATAAAGTAATAAATAATAAAATA
19827016 AAATAAAGTAATAAATAAAGTAAAA-A
1 AAATAAAGTAATAAAT-AA-TAAAATA
*
19827042 TAA-AAA-TAATAAAT-A-AAAATA
1 AAATAAAGTAATAAATAATAAAATA
19827063 AAA
1 AAA
19827066 ATTGGGTTGC
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
20 4 0.09
21 3 0.07
22 1 0.02
24 12 0.27
25 14 0.32
26 5 0.11
27 5 0.11
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (25 bp):
AAATAAAGTAATAAATAATAAAATA
Found at i:19827056 original size:24 final size:24
Alignment explanation
Indices: 19827007--19827067 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
19826997 AGTAATAAAT
*
19827007 AATAAAAT-AAAAT-AAAGTAATA
1 AATAAAATAAAAATAAAAATAATA
*
19827029 AATAAAGTAAAAATAAAAATAATA
1 AATAAAATAAAAATAAAAATAATA
19827053 AATAAAAATAAAAAT
1 AAT-AAAATAAAAAT
19827068 TGGGTTGCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.21
23 5 0.15
24 11 0.33
25 10 0.30
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.21
Consensus pattern (24 bp):
AATAAAATAAAAATAAAAATAATA
Found at i:19827060 original size:13 final size:13
Alignment explanation
Indices: 19826999--19827067 Score: 67
Period size: 12 Copynumber: 5.6 Consensus size: 13
19826989 TCCAAATAAG
*
19826999 TAATAAATAATAA
1 TAATAAATAAAAA
*
19827012 -AATAAA-ATAAAG
1 TAATAAATA-AAAA
*
19827024 TAATAAAT-AAAG
1 TAATAAATAAAAA
19827036 TAA-AAATAAAAA
1 TAATAAATAAAAA
19827048 TAATAAATAAAAA
1 TAATAAATAAAAA
19827061 TAA-AAAT
1 TAATAAAT
19827068 TGGGTTGCCT
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
11 5 0.10
12 25 0.52
13 18 0.38
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (13 bp):
TAATAAATAAAAA
Found at i:19831721 original size:11 final size:9
Alignment explanation
Indices: 19831691--19831716 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
19831681 TAAAAACACA
19831691 AACTAAAAT
1 AACTAAAAT
19831700 AACTAAAAT
1 AACTAAAAT
19831709 AACTAAAA
1 AACTAAAA
19831717 AATAATGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (9 bp):
AACTAAAAT
Found at i:19832536 original size:156 final size:155
Alignment explanation
Indices: 19832317--19832692 Score: 432
Period size: 156 Copynumber: 2.4 Consensus size: 155
19832307 TGCCACTGTG
* * * *
19832317 GATCAATCATTTGCGGCGCTTTTTGGAAAATGCCGCAAAAAAGTTGAGCAAAACGACGCCATTTC
1 GATCAAGCATTAGCGGCG-TTTTTGGAAAATGCCGCAAAAAAGTTGAGCAAAATGACGTCATTT-
* * * **
19832382 CT-TTTCGAGCTTTAGTGGCATTAGTGGCACTTTTTAACAAACGCCGCAATAGATTGAGAATTAA
64 CTGTTTCGAGCTTTAGTGGCATTAGTGACACTTTATAACAAACACCGCAATAGATAAAGAATTAA
*
19832446 CAACGCTTTTTGTTAAACAACGCAAAA
129 CAACGCTTTTTGATAAACAACGCAAAA
* * * *
19832473 GATCAAGCATTAGCGGCGTTTGTTGGAAAACGCCGCAAAAAAGTTAAGCAAAATGACATCATTTT
1 GATCAAGCATTAGCGGCGTTT-TTGGAAAATGCCGCAAAAAAGTTGAGCAAAATGACGTCATTTC
* * * *
19832538 TGTTTTGAGCTTTAGTGGCATTAGTGACACTTTATAACAAATACCGCGATAGATAAAGAATTAGC
65 TGTTTCGAGCTTTAGTGGCATTAGTGACACTTTATAACAAACACCGCAATAGATAAAGAATTAAC
*** * **
19832603 GGTGCTTTTTGATAAACACCGCTGAA
130 AACGCTTTTTGATAAACAACGCAAAA
* * * * *
19832629 GATCAAGCAATAACAATGC-TTTTTGTAAAATGCCGTAAAAAAGTTGAGCAAAATGACGTCATTT
1 GATCAAGCATTAGC--GGCGTTTTTGGAAAATGCCGCAAAAAAGTTGAGCAAAATGACGTCATTT
19832693 TTTGCTGAAC
Statistics
Matches: 184, Mismatches: 32, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
155 4 0.02
156 175 0.95
157 3 0.02
158 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (155 bp):
GATCAAGCATTAGCGGCGTTTTTGGAAAATGCCGCAAAAAAGTTGAGCAAAATGACGTCATTTCT
GTTTCGAGCTTTAGTGGCATTAGTGACACTTTATAACAAACACCGCAATAGATAAAGAATTAACA
ACGCTTTTTGATAAACAACGCAAAA
Found at i:19832737 original size:14 final size:14
Alignment explanation
Indices: 19832707--19832768 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
19832697 CTGAACTTTT
19832707 TTTAGGGTTTATA-G
1 TTTAGGGTTTA-AGG
19832721 TTTAGGGTTTAAGG
1 TTTAGGGTTTAAGG
** *
19832735 TTTAGTATTTAATG
1 TTTAGGGTTTAAGG
** *
19832749 TTTAATGTTTATGG
1 TTTAGGGTTTAAGG
19832763 TTTAGG
1 TTTAGG
19832769 TTTTTAGGGT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
13 1 0.03
14 37 0.97
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.52
Consensus pattern (14 bp):
TTTAGGGTTTAAGG
Found at i:19832872 original size:14 final size:14
Alignment explanation
Indices: 19832807--19832873 Score: 57
Period size: 14 Copynumber: 4.8 Consensus size: 14
19832797 TATTTTTGGA
* *
19832807 TTAGAGTTTTGAGT
1 TTAGAGTTTAGGGT
*
19832821 TTAAAGTTTAGGGT
1 TTAGAGTTTAGGGT
*
19832835 TTAAAGTTT-GGAGT
1 TTAGAGTTTAGG-GT
*
19832849 TT-GGGATTTAGGGT
1 TTAGAG-TTTAGGGT
19832863 TTAGAGTTTAG
1 TTAGAGTTTAG
19832874 TATTTAAGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
13 3 0.07
14 36 0.84
15 4 0.09
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (14 bp):
TTAGAGTTTAGGGT
Found at i:19832878 original size:21 final size:21
Alignment explanation
Indices: 19832819--19832879 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
19832809 AGAGTTTTGA
* * **
19832819 GTTTAAAGTTTAGGGTTTAAA
1 GTTTAGAGTTTAGGATTTAGG
* *
19832840 GTTTGGAGTTTGGGATTTAGG
1 GTTTAGAGTTTAGGATTTAGG
*
19832861 GTTTAGAGTTTAGTATTTA
1 GTTTAGAGTTTAGGATTTA
19832880 AGATTCTTTT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (21 bp):
GTTTAGAGTTTAGGATTTAGG
Found at i:19832884 original size:28 final size:28
Alignment explanation
Indices: 19832811--19832884 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 28
19832801 TTTGGATTAG
*
19832811 AGTTTTGAGTTTAA-AGTTTAGGGTTTAA
1 AGTTTGGAGTTTAAGA-TTTAGGGTTTAA
** *
19832839 AGTTTGGAGTTTGGGATTTAGGGTTTAG
1 AGTTTGGAGTTTAAGATTTAGGGTTTAA
*
19832867 AGTTTAGTA-TTTAAGATT
1 AGTTT-GGAGTTTAAGATT
19832885 CTTTTTAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
28 34 0.92
29 3 0.08
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (28 bp):
AGTTTGGAGTTTAAGATTTAGGGTTTAA
Found at i:19833026 original size:7 final size:7
Alignment explanation
Indices: 19833014--19833116 Score: 82
Period size: 7 Copynumber: 14.4 Consensus size: 7
19833004 TTAGTGTATA
19833014 GGTTTAG
1 GGTTTAG
19833021 GGTTTAAG
1 GGTTT-AG
19833029 GG-TTATG
1 GGTTTA-G
*
19833036 GGCTTAG
1 GGTTTAG
19833043 GGTTTAG
1 GGTTTAG
19833050 GGTTTAG
1 GGTTTAG
* *
19833057 GATTTAA
1 GGTTTAG
* *
19833064 AGTTTAT
1 GGTTTAG
19833071 GGTTTAG
1 GGTTTAG
*
19833078 GGTTTACA
1 GGTTTA-G
* *
19833086 TGCTTAG
1 GGTTTAG
*
19833093 GGTTTAT
1 GGTTTAG
19833100 GGTTTAG
1 GGTTTAG
*
19833107 TGTTTAG
1 GGTTTAG
19833114 GGT
1 GGT
19833117 CCGATTTTAA
Statistics
Matches: 74, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
6 1 0.01
7 62 0.84
8 11 0.15
ACGTcount: A:0.18, C:0.03, G:0.35, T:0.44
Consensus pattern (7 bp):
GGTTTAG
Found at i:19833103 original size:22 final size:20
Alignment explanation
Indices: 19833046--19833105 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 20
19833036 GGCTTAGGGT
*
19833046 TTAGGGTTTAGGATTTAAAGT
1 TTAGGGTTTAGG-TTTAAAGC
* *
19833067 TTATGGTTTAGGGTTTACATGC
1 TTAGGGTTTA-GGTTTA-AAGC
19833089 TTAGGGTTTATGGTTTA
1 TTAGGGTTTA-GGTTTA
19833106 GTGTTTAGGG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 13 0.41
22 19 0.59
ACGTcount: A:0.22, C:0.03, G:0.28, T:0.47
Consensus pattern (20 bp):
TTAGGGTTTAGGTTTAAAGC
Found at i:19833106 original size:29 final size:28
Alignment explanation
Indices: 19832988--19833112 Score: 87
Period size: 29 Copynumber: 4.4 Consensus size: 28
19832978 AGTGTTAAGA
* * *
19832988 GTTTAGTGTTTACA-GATTAGTGTATA-G
1 GTTTAGGGTTTACATG-TTAGGGTTTATG
* * *
19833015 GTTTAGGGTTTA-AGGGTTATGGGCTTAGG
1 GTTTAGGGTTTACA-TGTTA-GGGTTTATG
* **
19833044 GTTTAGGGTTTAGGAT-TTAAAGTTTATG
1 GTTTAGGGTTTA-CATGTTAGGGTTTATG
19833072 GTTTAGGGTTTACATGCTTAGGGTTTATG
1 GTTTAGGGTTTACATG-TTAGGGTTTATG
*
19833101 GTTTAGTGTTTA
1 GTTTAGGGTTTA
19833113 GGGTCCGATT
Statistics
Matches: 77, Mismatches: 13, Indels: 14
0.74 0.12 0.13
Matches are distributed among these distances:
26 1 0.01
27 16 0.21
28 22 0.29
29 37 0.48
31 1 0.01
ACGTcount: A:0.21, C:0.03, G:0.31, T:0.45
Consensus pattern (28 bp):
GTTTAGGGTTTACATGTTAGGGTTTATG
Found at i:19833717 original size:21 final size:22
Alignment explanation
Indices: 19833672--19833717 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
19833662 AAAATTATCA
*
19833672 TAAATATTATATTTCTAAAATT
1 TAAATATTAAATTTCTAAAATT
19833694 TAAAT-TTAAATTT-TAAAATCT
1 TAAATATTAAATTTCTAAAAT-T
19833715 TAA
1 TAA
19833718 TTTGCAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 11 0.50
22 5 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAATATTAAATTTCTAAAATT
Found at i:19836279 original size:28 final size:29
Alignment explanation
Indices: 19836241--19836426 Score: 126
Period size: 28 Copynumber: 5.9 Consensus size: 29
19836231 GTTTACTAGG
19836241 TTTAATGTGAATAAATTATCAATTTTTGA
1 TTTAATGTGAATAAATTATCAATTTTTGA
*
19836270 TTTAAT-TGAATAAATTATGTTTGATTAGTTTATTCGA
1 TTTAATGTGAATAAATTA----TCA--A-TTT-TT-GA
* *
19836307 TTTAATGTGAATAAATTATCGATTTTTTA
1 TTTAATGTGAATAAATTATCAATTTTTGA
*
19836336 TTTAAT-TGAATAAATTATGTTTGATTAGTTTATTTGA
1 TTTAATGTGAATAAATTA----TCA--A--TT-TTTGA
* *
19836373 TTTTATGTGAATAAATTATCAATTTTTTA
1 TTTAATGTGAATAAATTATCAATTTTTGA
*
19836402 TTTAAT-TGAATAAATTATCGATTTT
1 TTTAATGTGAATAAATTATCAATTTT
19836427 ATATTTGATT
Statistics
Matches: 125, Mismatches: 12, Indels: 41
0.70 0.07 0.23
Matches are distributed among these distances:
28 40 0.32
29 22 0.18
30 4 0.03
31 3 0.02
32 5 0.04
34 5 0.04
35 3 0.02
36 4 0.03
37 17 0.14
38 22 0.18
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.52
Consensus pattern (29 bp):
TTTAATGTGAATAAATTATCAATTTTTGA
Found at i:19836291 original size:66 final size:66
Alignment explanation
Indices: 19836200--19836419 Score: 361
Period size: 66 Copynumber: 3.3 Consensus size: 66
19836190 ACTTTATATA
* *
19836200 TTTGA-TTAATTGAATAAATTATGTTTGATTAGTTTACTAGGTTTAATGTGAATAAATTATCAAT
1 TTTGATTTAATTGAATAAATTATGTTTGATTAGTTTATTAGATTTAATGTGAATAAATTATCAAT
19836264 T
66 T
* *
19836265 TTTGATTTAATTGAATAAATTATGTTTGATTAGTTTATTCGATTTAATGTGAATAAATTATCGAT
1 TTTGATTTAATTGAATAAATTATGTTTGATTAGTTTATTAGATTTAATGTGAATAAATTATCAAT
19836330 T
66 T
* * *
19836331 TTTTATTTAATTGAATAAATTATGTTTGATTAGTTTATTTGATTTTATGTGAATAAATTATCAAT
1 TTTGATTTAATTGAATAAATTATGTTTGATTAGTTTATTAGATTTAATGTGAATAAATTATCAAT
19836396 T
66 T
*
19836397 TTTTATTTAATTGAATAAATTAT
1 TTTGATTTAATTGAATAAATTAT
19836420 CGATTTTATA
Statistics
Matches: 146, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
65 5 0.03
66 141 0.97
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (66 bp):
TTTGATTTAATTGAATAAATTATGTTTGATTAGTTTATTAGATTTAATGTGAATAAATTATCAAT
T
Found at i:19836321 original size:38 final size:36
Alignment explanation
Indices: 19836266--19836391 Score: 142
Period size: 38 Copynumber: 3.6 Consensus size: 36
19836256 TTATCAATTT
19836266 TTGATTTAATTGAATAAATTATGTTTGATTAGTTTA
1 TTGATTTAATTGAATAAATTATGTTTGATTAGTTTA
*
19836302 TTCGATTTAATGTGAATAAATTA---TCGA-T--TTT-
1 TT-GATTTAAT-TGAATAAATTATGTTTGATTAGTTTA
19836333 TT-ATTTAATTGAATAAATTATGTTTGATTAGTTTA
1 TTGATTTAATTGAATAAATTATGTTTGATTAGTTTA
*
19836368 TTTGATTTTATGTGAATAAATTAT
1 -TTGATTTAAT-TGAATAAATTAT
19836392 CAATTTTTTA
Statistics
Matches: 75, Mismatches: 3, Indels: 22
0.75 0.03 0.22
Matches are distributed among these distances:
28 11 0.15
29 7 0.09
31 5 0.07
32 4 0.05
34 4 0.05
35 3 0.04
36 4 0.05
37 14 0.19
38 23 0.31
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (36 bp):
TTGATTTAATTGAATAAATTATGTTTGATTAGTTTA
Found at i:19836648 original size:9 final size:9
Alignment explanation
Indices: 19836634--19836841 Score: 149
Period size: 9 Copynumber: 23.0 Consensus size: 9
19836624 ATATCTCAAT
19836634 CATAACTTA
1 CATAACTTA
*
19836643 CATAACTCA
1 CATAACTTA
19836652 CATAACTTA
1 CATAACTTA
19836661 CATAACTTA
1 CATAACTTA
*
19836670 CATAACTCA
1 CATAACTTA
*
19836679 CAT-ACATA
1 CATAACTTA
*
19836687 CATAATTTA
1 CATAACTTA
19836696 -ATAACTTA
1 CATAACTTA
* *
19836704 TATATATCATA
1 CATA-A-CTTA
*
19836715 TCGTAACTTA
1 -CATAACTTA
*
19836725 CATAACTCA
1 CATAACTTA
19836734 CATAACTTA
1 CATAACTTA
19836743 -ATAACGTATA
1 CATAAC-T-TA
* * *
19836753 TATATCATA
1 CATAACTTA
19836762 TCATAACTTA
1 -CATAACTTA
*
19836772 CATAACTCA
1 CATAACTTA
*
19836781 AATAACTTA
1 CATAACTTA
*
19836790 TATAACTTA
1 CATAACTTA
19836799 CATAA--TA
1 CATAACTTA
*
19836806 CATAA-ATA
1 CATAACTTA
* * *
19836814 TATATCATA
1 CATAACTTA
19836823 TCATAACTTA
1 -CATAACTTA
19836833 CATAACTTA
1 CATAACTTA
19836842 ATTATACTTA
Statistics
Matches: 157, Mismatches: 30, Indels: 24
0.74 0.14 0.11
Matches are distributed among these distances:
7 7 0.04
8 23 0.15
9 99 0.63
10 18 0.11
11 8 0.05
12 2 0.01
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.34
Consensus pattern (9 bp):
CATAACTTA
Found at i:19839770 original size:15 final size:14
Alignment explanation
Indices: 19839746--19839776 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
19839736 TATTGTAAGA
19839746 ATATTTTTAACATT
1 ATATTTTTAACATT
19839760 ATATCTTTTAACATT
1 ATAT-TTTTAACATT
19839775 AT
1 AT
19839777 TGTAAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (14 bp):
ATATTTTTAACATT
Found at i:19852612 original size:21 final size:21
Alignment explanation
Indices: 19852588--19852631 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
19852578 GACCAGTGAA
19852588 AGCTGCTTAAAGAGTATGTAT
1 AGCTGCTTAAAGAGTATGTAT
19852609 AGCTGCTTAAAGAGTATGTAT
1 AGCTGCTTAAAGAGTATGTAT
19852630 AG
1 AG
19852632 GTCTTCTTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.09, G:0.25, T:0.32
Consensus pattern (21 bp):
AGCTGCTTAAAGAGTATGTAT
Found at i:19854707 original size:182 final size:180
Alignment explanation
Indices: 19854359--19854713 Score: 557
Period size: 182 Copynumber: 2.0 Consensus size: 180
19854349 GTCACCAAGT
* **
19854359 GTCGCCCGCTAGAAATATTGAATGTGATTATCAAGGAGTTAGATTTTGAGCTAGAAGTCGCACAT
1 GTCGCCCGCTAGAAATATTGAATGCGATTATCAAGGAGTTAGATTTTGAGCTAGAACCCGCACAT
* * *
19854424 TTTTTCTTAAATTCTCTATATGCGGATCTCACTAAGTTCTCCCGAACTTATAAGTTTTCTACTTA
66 TTTTTCATAAATTCTCTATATGCGAATCTCACTAAGTTCTCCCAAACTTATAAGTTTTCTACTTA
* *
19854489 AATGCAGGTTAGTTAAAGATTCAGAAATCAAGAAGGACTAAGCCAAAAGG
131 AATGCAGGTTAGTTAAAGACTCAGAAATCAAGAAGGACCAAGCCAAAAGG
*
19854539 GTCGCCCGCTAGAAATATTGAATGCGATTATCAAGGAGTTAGATTTTGAGCTAGACCCCGCACAT
1 GTCGCCCGCTAGAAATATTGAATGCGATTATCAAGGAGTTAGATTTTGAGCTAGAACCCGCACA-
* * *
19854604 TTTTTTCCATAAATTCTCTATATGCGAATCTCACTAAGTTTTCCCAAACTTTTAAGTTTTCTTCT
65 TTTTTT-CATAAATTCTCTATATGCGAATCTCACTAAGTTCTCCCAAACTTATAAGTTTTCTACT
* * *
19854669 TAAATGTAGGTTAGTTAAAGACTCAGGAATCGAGAAGGACCAAGC
129 TAAATGCAGGTTAGTTAAAGACTCAGAAATCAAGAAGGACCAAGC
19854714 TAGACTTTGA
Statistics
Matches: 158, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
180 60 0.38
181 6 0.04
182 92 0.58
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (180 bp):
GTCGCCCGCTAGAAATATTGAATGCGATTATCAAGGAGTTAGATTTTGAGCTAGAACCCGCACAT
TTTTTCATAAATTCTCTATATGCGAATCTCACTAAGTTCTCCCAAACTTATAAGTTTTCTACTTA
AATGCAGGTTAGTTAAAGACTCAGAAATCAAGAAGGACCAAGCCAAAAGG
Found at i:19855041 original size:6 final size:6
Alignment explanation
Indices: 19855026--19855213 Score: 324
Period size: 6 Copynumber: 31.5 Consensus size: 6
19855016 CTTTATATTG
19855026 ATTT-T ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT
* * * *
19855073 ATTTAT ATTTAT ATTTAT ATTTAT GTTTAT GTTTAT GTTTAT GTTTAT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT
*
19855121 GTTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT
19855169 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATT
19855214 ACTTTAGTTT
Statistics
Matches: 180, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
5 4 0.02
6 176 0.98
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (6 bp):
ATTTAT
Found at i:19866938 original size:6 final size:7
Alignment explanation
Indices: 19866921--19866947 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
19866911 CAGGTATTCC
19866921 AAAAAAG
1 AAAAAAG
19866928 AAAAAAG
1 AAAAAAG
19866935 AAAAAAG
1 AAAAAAG
19866942 AAAAAA
1 AAAAAA
19866948 AATAAGATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:19874626 original size:47 final size:47
Alignment explanation
Indices: 19874555--19874971 Score: 573
Period size: 47 Copynumber: 8.6 Consensus size: 47
19874545 CCCTTCGGGA
* * * * * *
19874555 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
19874602 CCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
19874649 CTTATCACATATATACACTTTCACATTCATCGCATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19874696 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19874743 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGG---------C--C-ATTAGGC
*
19874802 CTTATCACATATATACACTTTCACATTCATCACATCGGCCAGTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
19874849 CTTATCACATATATATACACTTTCACATTCATCACATTGTCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
19874898 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
19874945 CTTATCACATATATACAGTTTCACATT
1 CTTATCACATATATACACTTTCACATT
19874972 TATTCAAATA
Statistics
Matches: 334, Mismatches: 22, Indels: 28
0.87 0.06 0.07
Matches are distributed among these distances:
47 242 0.72
48 1 0.00
49 43 0.13
50 1 0.00
56 1 0.00
58 1 0.00
59 45 0.13
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:19874799 original size:59 final size:59
Alignment explanation
Indices: 19874723--19874842 Score: 231
Period size: 59 Copynumber: 2.0 Consensus size: 59
19874713 CTTTCACATT
19874723 CATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGC
1 CATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGC
*
19874782 CATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGC
1 CATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGC
19874841 CA
1 CA
19874843 GTAGGCCTTA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.29, C:0.32, G:0.10, T:0.29
Consensus pattern (59 bp):
CATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGC
Found at i:19874804 original size:106 final size:101
Alignment explanation
Indices: 19874669--19874971 Score: 431
Period size: 106 Copynumber: 3.0 Consensus size: 101
19874659 ATATACACTT
19874669 TCACATTCATCGCATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
1 TCACA-TCATC-CATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
19874734 CCATTAGGCCTTATCACATATATACACTTTCACATTCA
64 CCATTAGGCCTTATCACATATATACACTTTCACATTCA
19874772 TCACATCGGCCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACAT
1 TCACAT----CATC-CATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACAT
*
19874837 CGGCCAGTAGGCCTTATCACATATATATACACTTTCACATTCA
61 CGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCA
* *
19874880 TCACAT--T--GTC--C-ATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCC
1 TCACATCATCCATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCC
* *
19874938 ATTAGGTCTTATCACATATATACAGTTTCACATT
66 ATTAGGCCTTATCACATATATACACTTTCACATT
19874972 TATTCAAATA
Statistics
Matches: 187, Mismatches: 7, Indels: 21
0.87 0.03 0.10
Matches are distributed among these distances:
94 18 0.10
96 59 0.32
97 1 0.01
99 2 0.01
102 2 0.01
103 5 0.03
106 73 0.39
108 27 0.14
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (101 bp):
TCACATCATCCATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCC
ATTAGGCCTTATCACATATATACACTTTCACATTCA
Found at i:19874937 original size:202 final size:200
Alignment explanation
Indices: 19874599--19874971 Score: 647
Period size: 202 Copynumber: 1.9 Consensus size: 200
19874589 TTGGCCACTC
*
19874599 GGCCCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
1 GGCCCTATCACATATATACACTTTCACATTCATCACATCGGCCAGTAGGCCTTATCACATATATA
* *
19874664 CACTTTCACATTCATCGCATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
66 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
19874729 ATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATCACATCGGC
131 ATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATCACATCGGC
19874794 TATTA
196 TATTA
*
19874799 GGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCAGTAGGCCTTATCACATATATA
1 GGCCCTATCACATATATACACTTTCACATTCATCACATCGGCCAGTAGGCCTTATCAC--ATATA
* * *
19874864 TACACTTTCACATTCATCACATTGTCCATTCGGCCTTATCACATATATACACTTTCACATTCATC
64 TACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATC
* *
19874929 ACATCGGCCATTAGGTCTTATCACATATATACAGTTTCACATT
129 ACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATT
19874972 TATTCAAATA
Statistics
Matches: 162, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
200 56 0.35
202 106 0.65
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (200 bp):
GGCCCTATCACATATATACACTTTCACATTCATCACATCGGCCAGTAGGCCTTATCACATATATA
CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
ATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATCACATCGGC
TATTA
Found at i:19874939 original size:155 final size:153
Alignment explanation
Indices: 19874629--19874939 Score: 541
Period size: 155 Copynumber: 2.0 Consensus size: 153
19874619 CTTTCACATT
* * *
19874629 CATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCGCATCGGCTATTAG
1 CATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCAGTAG
19874694 GCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
66 GCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
19874759 ACTTTCACATTCATCACATCGGC
131 ACTTTCACATTCATCACATCGGC
*
19874782 CATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCAGTAG
1 CATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCAGTAG
* * *
19874847 GCCTTATCACATATATATACACTTTCACATTCATCACATTGTCCATTCGGCCTTATCACATATAT
66 GCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT
19874912 ACACTTTCACATTCATCACATCGGC
129 ACACTTTCACATTCATCACATCGGC
19874937 CAT
1 CAT
19874940 TAGGTCTTAT
Statistics
Matches: 149, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
153 71 0.48
155 78 0.52
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (153 bp):
CATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCAGTAG
GCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGC
Found at i:19880631 original size:27 final size:27
Alignment explanation
Indices: 19880600--19880777 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
19880590 TAAATTGTAC
19880600 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
19880627 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
19880653 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
19880681 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
19880709 AGCACTAAGTGTGCGATTTGATTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
19880736 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
19880763 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
19880778 GACTCAATAT
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 108 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:19880714 original size:82 final size:81
Alignment explanation
Indices: 19880601--19880756 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
19880591 AAATTGTACA
*
19880601 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTA-GCACTAAGTG
19880665 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
19880682 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTG
*
19880747 TGCGAGTTGA
65 TGCGAATTGA
19880757 TTATATAGCA
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 15 0.22
82 52 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:19880768 original size:82 final size:81
Alignment explanation
Indices: 19880597--19880777 Score: 238
Period size: 82 Copynumber: 2.2 Consensus size: 81
19880587 GATTAAATTG
*
19880597 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
19880662 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
19880678 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGAT-GCACT
* **
19880742 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
19880760 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
19880778 GACTCAATAT
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
81 18 0.21
82 67 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
GTGTGCGAATTGACCA
Found at i:19888804 original size:27 final size:27
Alignment explanation
Indices: 19888773--19888950 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
19888763 TAAATTGTAC
19888773 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
19888800 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
19888826 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
19888854 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
19888882 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
19888909 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
19888936 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
19888951 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:19888887 original size:82 final size:81
Alignment explanation
Indices: 19888774--19888929 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
19888764 AAATTGTACA
* *
19888774 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
19888838 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
19888855 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
19888920 TGCGAGTTGA
65 TGCGAATTGA
19888930 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:19888941 original size:82 final size:81
Alignment explanation
Indices: 19888770--19888950 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
19888760 GATTAAATTG
* *
19888770 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
19888835 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
19888851 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
19888915 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
19888933 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
19888951 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:19892728 original size:27 final size:25
Alignment explanation
Indices: 19892698--19892747 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
19892688 AATACAAAGA
19892698 GCAACAATAATCACAATCACATATTAT
1 GCAACAATAATCA-AATCA-ATATTAT
*
19892725 GCAACACTAATCAAATCAATATT
1 GCAACAATAATCAAATCAATATT
19892748 CCAAAACCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 5 0.23
27 12 0.55
ACGTcount: A:0.48, C:0.22, G:0.04, T:0.26
Consensus pattern (25 bp):
GCAACAATAATCAAATCAATATTAT
Found at i:19893407 original size:3 final size:3
Alignment explanation
Indices: 19893399--19893459 Score: 59
Period size: 3 Copynumber: 20.3 Consensus size: 3
19893389 TACTAATACA
* * * * * * *
19893399 AAT AAT AAT ACT AAT AAT TAT AAT AAC AGT AAC ATT AAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19893447 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
19893460 TTTAAAAGAA
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19894424 original size:6 final size:6
Alignment explanation
Indices: 19894415--19894464 Score: 55
Period size: 6 Copynumber: 8.0 Consensus size: 6
19894405 AAAAGCATGT
** *
19894415 GAAAAA GAAAAA GAAATT GAAAAA GAAAAA GAAAACA AAAGAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAA-A GAA-AAA GAAAAA
19894465 AGTGATTGAG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
6 28 0.78
7 6 0.17
8 2 0.06
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (6 bp):
GAAAAA
Found at i:19894424 original size:18 final size:18
Alignment explanation
Indices: 19894414--19894448 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
19894404 AAAAAGCATG
19894414 TGAAAAAGAAAAAGAAAT
1 TGAAAAAGAAAAAGAAAT
19894432 TGAAAAAGAAAAAGAAA
1 TGAAAAAGAAAAAGAAA
19894449 ACAAAAGAAA
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:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (18 bp):
TGAAAAAGAAAAAGAAAT
Found at i:19897066 original size:51 final size:51
Alignment explanation
Indices: 19897005--19897195 Score: 219
Period size: 51 Copynumber: 3.8 Consensus size: 51
19896995 TCGGTTCACA
* *
19897005 TAGTAGCCTGCACATAGTACTATACATGTGACCATCACTATCTGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACG
* * * * * *
19897056 TATTAGCCTGCACATAGTACTACACACGTGATCGA--AGCAATCCGATACGCA
1 TAGTAGCCTGCACATAGTACTACACATGTGA-CCATCA-CTATCCGATACACG
* * *
19897107 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCGGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACC-ATCACTATCCGATACACG
*
19897157 TAGTAGCCTGCACATAGTACTACACATGTTACCATCACT
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACT
19897196 TTCACTTTCA
Statistics
Matches: 115, Mismatches: 19, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
49 4 0.03
50 41 0.36
51 67 0.58
52 2 0.02
53 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACG
Found at i:19897211 original size:101 final size:102
Alignment explanation
Indices: 19896999--19897182 Score: 273
Period size: 102 Copynumber: 1.8 Consensus size: 102
19896989 ATGATATCGG
* * * *
19896999 TTCACATAGTAGCCTGCACATAGTACTATACATGTGACCATCACTATCTGATACACGTATTAGCC
1 TTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCGGATACACGTAGTAGCC
*
19897064 TGCACATAGTACTACACACGTGATCGAAGCAATCCGA
66 TGCACATAGTACTACACACGTGATCCAAGCAATCCGA
* * *
19897101 TACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCGGGTACACGTAGTAGC
1 TTCACATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCGGATACACGTAGTAGC
19897164 CTGCACATAGTACTACACA
65 CTGCACATAGTACTACACA
19897183 TGTTACCATC
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
101 34 0.46
102 36 0.49
103 4 0.05
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (102 bp):
TTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCGGATACACGTAGTAGCC
TGCACATAGTACTACACACGTGATCCAAGCAATCCGA
Found at i:19910430 original size:40 final size:39
Alignment explanation
Indices: 19910375--19910515 Score: 176
Period size: 40 Copynumber: 3.6 Consensus size: 39
19910365 ACTCAGATAA
* * * *
19910375 GGGCACCAAAGTGCAATCAGGAGCACCAAAGTGCAAACAG
1 GGGCACCGAAGTGCAATCAGG-GTACCGAAGTACAAACAG
*
19910415 GGGCACCGATGTGCAATCAGGGTACCGAAGTACAAACAG
1 GGGCACCGAAGTGCAATCAGGGTACCGAAGTACAAACAG
* * *
19910454 GGGCATCGATGTGCAATCAAGGGTACCGAAGTACAAACAA
1 GGGCACCGAAGTGCAATC-AGGGTACCGAAGTACAAACAG
19910494 GGGCA-CGTAAGTGCAATCAGGG
1 GGGCACCG-AAGTGCAATCAGGG
19910516 CATAATTTAC
Statistics
Matches: 91, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
39 38 0.42
40 53 0.58
ACGTcount: A:0.35, C:0.22, G:0.30, T:0.12
Consensus pattern (39 bp):
GGGCACCGAAGTGCAATCAGGGTACCGAAGTACAAACAG
Found at i:19910436 original size:20 final size:20
Alignment explanation
Indices: 19910375--19910515 Score: 124
Period size: 20 Copynumber: 7.1 Consensus size: 20
19910365 ACTCAGATAA
*
19910375 GGGCACCAAAGTGCAATCAG
1 GGGCACCGAAGTGCAATCAG
* * *
19910395 GAGCACCAAAGTGCAAACAG
1 GGGCACCGAAGTGCAATCAG
*
19910415 GGGCACCGATGTGCAATCA-
1 GGGCACCGAAGTGCAATCAG
* * *
19910434 GGGTACCGAAGTACAAACAG
1 GGGCACCGAAGTGCAATCAG
* * *
19910454 GGGCATCGATGTGCAATCAA
1 GGGCACCGAAGTGCAATCAG
* * * *
19910474 GGGTACCGAAGTACAAACAA
1 GGGCACCGAAGTGCAATCAG
19910494 GGGCA-CGTAAGTGCAATCAG
1 GGGCACCG-AAGTGCAATCAG
19910514 GG
1 GG
19910516 CATAATTTAC
Statistics
Matches: 94, Mismatches: 25, Indels: 4
0.76 0.20 0.03
Matches are distributed among these distances:
19 17 0.18
20 77 0.82
ACGTcount: A:0.35, C:0.22, G:0.30, T:0.12
Consensus pattern (20 bp):
GGGCACCGAAGTGCAATCAG
Found at i:19915869 original size:20 final size:20
Alignment explanation
Indices: 19915841--19915924 Score: 53
Period size: 20 Copynumber: 4.2 Consensus size: 20
19915831 AGATGCACAA
*
19915841 CAGGGGCACCAAAGTGCAAT
1 CAGGAGCACCAAAGTGCAAT
* *
19915861 CAGGAGCA-CAAATGTACTAT
1 CAGGAGCACCAAA-GTGCAAT
* * * *
19915881 TAGGAGCACCGAACTGCAAA
1 CAGGAGCACCAAAGTGCAAT
* * * *
19915901 CAGGGGCACCGATGAGCAAT
1 CAGGAGCACCAAAGTGCAAT
19915921 CAGG
1 CAGG
19915925 TGTATTGAAG
Statistics
Matches: 47, Mismatches: 15, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
19 4 0.09
20 40 0.85
21 3 0.06
ACGTcount: A:0.36, C:0.24, G:0.29, T:0.12
Consensus pattern (20 bp):
CAGGAGCACCAAAGTGCAAT
Found at i:19915960 original size:40 final size:39
Alignment explanation
Indices: 19915916--19916008 Score: 116
Period size: 40 Copynumber: 2.3 Consensus size: 39
19915906 GCACCGATGA
* *
19915916 GCAATCAGGTGTATTGAAGTACAAAC-AGGTACATGTAAGT
1 GCAATCAGG-GTATCGAAGTACAAACAAGG-ACACGTAAGT
* *
19915956 GCAATCAGGGGTACCGAAGTACAAACAAGGGCACGTAAGT
1 GCAATCA-GGGTATCGAAGTACAAACAAGGACACGTAAGT
19915996 GCAATCAGGGTAT
1 GCAATCAGGGTAT
19916009 AATTTACGTA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
39 5 0.11
40 36 0.78
41 5 0.11
ACGTcount: A:0.37, C:0.16, G:0.28, T:0.19
Consensus pattern (39 bp):
GCAATCAGGGTATCGAAGTACAAACAAGGACACGTAAGT
Found at i:19915975 original size:20 final size:20
Alignment explanation
Indices: 19915950--19916005 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
19915940 ACAGGTACAT
*
19915950 GTAAGTGCAATCAGGGGTACC
1 GTAAGTGCAATCAGGGGCA-C
* * *
19915971 G-AAGTACAAACAAGGGCAC
1 GTAAGTGCAATCAGGGGCAC
19915990 GTAAGTGCAATCAGGG
1 GTAAGTGCAATCAGGG
19916006 TATAATTTAC
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.36, C:0.18, G:0.32, T:0.14
Consensus pattern (20 bp):
GTAAGTGCAATCAGGGGCAC
Found at i:19917227 original size:11 final size:11
Alignment explanation
Indices: 19917211--19917252 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
19917201 TTAAAACACT
*
19917211 AGAAAAGTAAA
1 AGAAAACTAAA
*
19917222 AGAAAACTAAG
1 AGAAAACTAAA
*
19917233 AGAAACCTAAA
1 AGAAAACTAAA
19917244 AG-AAACTAA
1 AGAAAACTAA
19917253 TGCTAAAACT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
10 6 0.23
11 20 0.77
ACGTcount: A:0.67, C:0.10, G:0.14, T:0.10
Consensus pattern (11 bp):
AGAAAACTAAA
Found at i:19917265 original size:22 final size:22
Alignment explanation
Indices: 19917211--19917252 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
19917201 TTAAAACACT
*
19917211 AGAAAAGTAAAAGAAAACTAAG
1 AGAAAACTAAAAGAAAACTAAG
*
19917233 AGAAACCTAAAAG-AAACTAA
1 AGAAAACTAAAAGAAAACTAA
19917253 TGCTAAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.67, C:0.10, G:0.14, T:0.10
Consensus pattern (22 bp):
AGAAAACTAAAAGAAAACTAAG
Found at i:19920066 original size:40 final size:40
Alignment explanation
Indices: 19919979--19920088 Score: 123
Period size: 40 Copynumber: 2.8 Consensus size: 40
19919969 AGATAGATCG
* * *
19919979 AACACACCAGACAGAAGCTCATAAGAGCTGATCCAACTGA
1 AACACGCCAAACAGAAGCTCATAAGAGCTGATCCAACTAA
*** * * *
19920019 TGTACGCCAAACAGAAGCTCATAAGTGCTGGTCCACCTAA
1 AACACGCCAAACAGAAGCTCATAAGAGCTGATCCAACTAA
*
19920059 AACACGCC-AATAGAAGCTCATAAGAGCTGA
1 AACACGCCAAACAGAAGCTCATAAGAGCTGA
19920089 ATAGAAGCTC
Statistics
Matches: 55, Mismatches: 15, Indels: 1
0.77 0.21 0.01
Matches are distributed among these distances:
39 19 0.35
40 36 0.65
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.15
Consensus pattern (40 bp):
AACACGCCAAACAGAAGCTCATAAGAGCTGATCCAACTAA
Found at i:19928603 original size:17 final size:16
Alignment explanation
Indices: 19928581--19928612 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
19928571 GCAAGCAATC
19928581 GATTAAACAACAAAGAA
1 GATTAAACAA-AAAGAA
19928598 GATTAAACAAAAAGA
1 GATTAAACAAAAAGA
19928613 TGAAGGAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.66, C:0.09, G:0.12, T:0.12
Consensus pattern (16 bp):
GATTAAACAAAAAGAA
Found at i:19936730 original size:21 final size:21
Alignment explanation
Indices: 19936704--19936767 Score: 110
Period size: 21 Copynumber: 3.0 Consensus size: 21
19936694 GAAACACGCC
19936704 AACAGAAGCTCATAAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
*
19936725 AACAGAAGCTCATAAGAGCTT
1 AACAGAAGCTCATAAGAGCTA
*
19936746 AACAGAAGCTCATAAAAGCTA
1 AACAGAAGCTCATAAGAGCTA
19936767 A
1 A
19936768 TCCACCTGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.48, C:0.19, G:0.17, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTA
Found at i:19948052 original size:25 final size:25
Alignment explanation
Indices: 19948018--19948087 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
19948008 CAGGCCCATT
* *
19948018 TTCACAGCTCGTGTAAGCATTTTGA
1 TTCACAGCTCGTGTGAGCATTCTGA
* * *
19948043 TTCATAGCTCTTGTGAGCGTTCTGA
1 TTCACAGCTCGTGTGAGCATTCTGA
19948068 TTCACAGCTCGTGTGAGCAT
1 TTCACAGCTCGTGTGAGCAT
19948088 ACATGTAAAG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (25 bp):
TTCACAGCTCGTGTGAGCATTCTGA
Found at i:19954780 original size:28 final size:28
Alignment explanation
Indices: 19954748--19954833 Score: 145
Period size: 28 Copynumber: 3.0 Consensus size: 28
19954738 AAAAGTACAA
*
19954748 TGTGGGCCTTAGCCCATTACAGTAACAG
1 TGTGGGCCTTAGCCCAATACAGTAACAG
*
19954776 TGTGGGCCTTAGCCCAATACAGTAACAA
1 TGTGGGCCTTAGCCCAATACAGTAACAG
19954804 TGTGGGCCTTAGCCCAATACAGTAATCAG
1 TGTGGGCCTTAGCCCAATACAGTAA-CAG
19954833 T
1 T
19954834 ACAATGCAGT
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 51 0.94
29 3 0.06
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.24
Consensus pattern (28 bp):
TGTGGGCCTTAGCCCAATACAGTAACAG
Found at i:19955144 original size:27 final size:27
Alignment explanation
Indices: 19955113--19955562 Score: 335
Period size: 27 Copynumber: 16.7 Consensus size: 27
19955103 TCATCTCCTA
**
19955113 GGGGTATAACGGTCATTTTACCTTTTG
1 GGGGTATTTCGGTCATTTTACCTTTTG
* ** **
19955140 AGGGTATTTCTATCATTTTACAC-TTCA
1 GGGGTATTTCGGTCATTTTAC-CTTTTG
* * *
19955167 GAGGTATTCCGGTCATTTTACCCTTTG
1 GGGGTATTTCGGTCATTTTACCTTTTG
* * * * *
19955194 GGTGTACTTCGATCATTTTACCCTTCG
1 GGGGTATTTCGGTCATTTTACCTTTTG
* *
19955221 GGGGTATTTCGATCATTTTACCCTTTG
1 GGGGTATTTCGGTCATTTTACCTTTTG
**
19955248 GGGGTATTTTAGTCATTTTACCTTTTG
1 GGGGTATTTCGGTCATTTTACCTTTTG
*
19955275 GGGGTATTTCAGTCATTTTACCTTTTG
1 GGGGTATTTCGGTCATTTTACCTTTTG
*** * *
19955302 GGGGTATTTTTTTCATTTTACCCTATG
1 GGGGTATTTCGGTCATTTTACCTTTTG
* ** * * *
19955329 GGGATATTTTAGTCATTTCACCCTTCG
1 GGGGTATTTCGGTCATTTTACCTTTTG
* * * *
19955356 AGGGTATTTCGATCATTTTACCCTTCG
1 GGGGTATTTCGGTCATTTTACCTTTTG
* ** *
19955383 AGGGTATTTTAGTCATTTTACCTTTCG
1 GGGGTATTTCGGTCATTTTACCTTTTG
* *
19955410 GGGGTATTTCAGTCATTTTACCTTTTA
1 GGGGTATTTCGGTCATTTTACCTTTTG
* * * **
19955437 GGGGCATTTCAGTCATTTTACCCTTCA
1 GGGGTATTTCGGTCATTTTACCTTTTG
* ** * *
19955464 AGGGTATTTCAATCATTTTACCCTTCG
1 GGGGTATTTCGGTCATTTTACCTTTTG
* * *
19955491 GGGGTATTTCGATCATTTTACCCTTCG
1 GGGGTATTTCGGTCATTTTACCTTTTG
* * * *
19955518 AGGGTATTTCGATCATTTTACCCTTCG
1 GGGGTATTTCGGTCATTTTACCTTTTG
* * *
19955545 AGAGTATTTCAGTCATTT
1 GGGGTATTTCGGTCATTT
19955563 GCCCACAAAT
Statistics
Matches: 355, Mismatches: 66, Indels: 4
0.84 0.16 0.01
Matches are distributed among these distances:
26 1 0.00
27 353 0.99
28 1 0.00
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (27 bp):
GGGGTATTTCGGTCATTTTACCTTTTG
Found at i:19955173 original size:54 final size:54
Alignment explanation
Indices: 19955124--19955562 Score: 428
Period size: 54 Copynumber: 8.1 Consensus size: 54
19955114 GGGTATAACG
* * * * * * *
19955124 GTCATTTTACCTTTTGAGGGTATTTCTATCATTTTACACTTCAGAGGTATTCCG
1 GTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCAGGGGTATTTCA
* * *
19955178 GTCATTTTACCCTTTG-GGTGTACTTCGATCATTTTACCCTTCGGGGGTATTTC-
1 GTCATTTTACCCTTCGAGG-GTATTTCGATCATTTTACCCTTCAGGGGTATTTCA
* * * * **
19955231 GATCATTTTACCCTTTGGGGGTATTT-TAGTCATTTTACCTTTTGGGGGTATTTCA
1 G-TCATTTTACCCTTCGAGGGTATTTCGA-TCATTTTACCCTTCAGGGGTATTTCA
* * * *** *
19955286 GTCATTTTACCTTTTGGGGGTATTTTTTTCATTTTACCC-T-ATGGGGATATTTTA
1 GTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCA-GGGG-TATTTCA
* *
19955340 GTCATTTCACCCTTCGAGGGTATTTCGATCATTTTACCCTTC-GAGGGTATTTTA
1 GTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCAG-GGGTATTTCA
* * * * *
19955394 GTCATTTTACCTTTCGGGGGTATTTC-AGTCATTTTACCTTTTAGGGGCATTTCA
1 GTCATTTTACCCTTCGAGGGTATTTCGA-TCATTTTACCCTTCAGGGGTATTTCA
* * *
19955448 GTCATTTTACCCTTCAAGGGTATTTCAATCATTTTACCCTTCGGGGGTATTTC-
1 GTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCAGGGGTATTTCA
*
19955501 GATCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTC-GAGAGTATTTCA
1 G-TCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCAG-GGGTATTTCA
19955556 GTCATTT
1 GTCATTT
19955563 GCCCACAAAT
Statistics
Matches: 328, Mismatches: 40, Indels: 34
0.82 0.10 0.08
Matches are distributed among these distances:
53 12 0.04
54 305 0.93
55 11 0.03
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (54 bp):
GTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCAGGGGTATTTCA
Found at i:19955236 original size:81 final size:79
Alignment explanation
Indices: 19955125--19955562 Score: 447
Period size: 81 Copynumber: 5.4 Consensus size: 79
19955115 GGTATAACGG
* * * * * *
19955125 TCATTTTACCTTTTGAGGGTATTTCTATCATTTTACACTTCAGAGGTATTCCGGTCATTTTACCC
1 TCATTTTACCCTTCGAGGGTATTTCTATCATTTTAC-CTTCGGGGGTATTTCAGTCATTTTACCC
*
19955190 TTTGGGTGTACTTCGA
65 TTTGGG-GTATTTCGA
* * * * *
19955206 TCATTTTACCCTTCGGGGGTATTTCGATCATTTTACCCTTTGGGGGTATTTTAGTCATTTTACCT
1 TCATTTTACCCTTCGAGGGTATTTCTATCATTTTA-CCTTCGGGGGTATTTCAGTCATTTTACCC
19955271 TTTGGGGGTATTTC-A
65 TTT-GGGGTATTTCGA
* * * * * * * *
19955286 GTCATTTTACCTTTTGGGGGTATTTTTTTCATTTTACCCTAT-GGGGATATTTTAGTCATTTCAC
1 -TCATTTTACCCTTCGAGGGTATTTCTATCATTTTA-CCT-TCGGGGGTATTTCAGTCATTTTAC
*
19955350 CCTTCGAGGGTATTTCGA
63 CCTTTG-GGGTATTTCGA
19955368 TCATTTTACCCTTCGAGGGTATTT-TAGTCATTTTACCTTTCGGGGGTATTTCAGTCATTTTACC
1 TCATTTTACCCTTCGAGGGTATTTCTA-TCATTTTACC-TTCGGGGGTATTTCAGTCATTTTACC
* *
19955432 TTTTAGGGGCATTTC-A
64 CTTT-GGGGTATTTCGA
* *
19955448 GTCATTTTACCCTTCAAGGGTATTTCAATCATTTTACCCTTCGGGGGTATTTC-GATCATTTTAC
1 -TCATTTTACCCTTCGAGGGTATTTCTATCATTTTA-CCTTCGGGGGTATTTCAG-TCATTTTAC
*
19955512 CCTTCGAGGGTATTTCGA
63 CCTTTG-GGGTATTTCGA
*
19955530 TCATTTTACCCTTCGAGAGTATTTC-AGTCATTT
1 TCATTTTACCCTTCGAGGGTATTTCTA-TCATTT
19955563 GCCCACAAAT
Statistics
Matches: 302, Mismatches: 38, Indels: 34
0.81 0.10 0.09
Matches are distributed among these distances:
80 10 0.03
81 281 0.93
82 11 0.04
ACGTcount: A:0.18, C:0.19, G:0.18, T:0.45
Consensus pattern (79 bp):
TCATTTTACCCTTCGAGGGTATTTCTATCATTTTACCTTCGGGGGTATTTCAGTCATTTTACCCT
TTGGGGTATTTCGA
Found at i:19961336 original size:22 final size:22
Alignment explanation
Indices: 19961310--19961354 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
19961300 AGATCAACAC
19961310 AAATAT-AATCACATACATATCA
1 AAATATCAATCACAT-CATATCA
*
19961332 AAATATCAATCTCATCATATCA
1 AAATATCAATCACATCATATCA
19961354 A
1 A
19961355 TCATCATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (22 bp):
AAATATCAATCACATCATATCA
Found at i:19963458 original size:51 final size:50
Alignment explanation
Indices: 19963289--19963622 Score: 391
Period size: 51 Copynumber: 6.6 Consensus size: 50
19963279 TCGATACACA
*
19963289 TAGTAGCCTTCACATAGTACTACACACGTGATCAAG-TTTTACGGTTCACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAAGATTTT-CGGTTCACG
* * * *
19963339 TAGTAGCCTTCATATAGTACTACACACGTGATCAAGCTTTACGGTTCACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAAGATTTTCGGTTCACG
* * *
19963389 TAGTAGCCTTCACATAGTACTACACACGTGACCAAAGATTTTTGGTACACA
1 TAGTAGCCTTCACATAGTACTACACACGTGACC-AAGATTTTCGGTTCACG
* * ** *
19963440 TAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAAGATTT-TCGGTTCACG
* * * * *
19963491 TAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACA
1 TAGTAGCCTTCACATAGTACTACACACGTGACC-AAGATTTTCGGTTCACG
* * * ** *
19963542 TTGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAAGATTT-TCGGTTCACG
*
19963593 TAGTAGCCTTCACACAGTACTACACACGTG
1 TAGTAGCCTTCACATAGTACTACACACGTG
19963623 TTCATCGATA
Statistics
Matches: 237, Mismatches: 42, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
50 83 0.35
51 151 0.64
52 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (50 bp):
TAGTAGCCTTCACATAGTACTACACACGTGACCAAGATTTTCGGTTCACG
Found at i:19963516 original size:102 final size:101
Alignment explanation
Indices: 19963279--19963622 Score: 489
Period size: 102 Copynumber: 3.4 Consensus size: 101
19963269 CTTTTATCAT
* * * * * *
19963279 TCGATACACATAGTAGCCTTCACATAGTACTACACACGTGATC-AAGTTTTACGGTTCACGTAGT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGTTTT-CGGTACACATAGT
* * *
19963343 AGCCTTCA-TATAGTACTACACACGTGATCAAGC-TTTA
65 AGCCTTCACT-TAGTACTACACATGTGA-CCATCATTTA
* * *
19963380 -CGGTTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGATTTTTGGTACACATAGT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAG-TTTTCGGTACACATAGT
19963444 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
65 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* *
19963481 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTGT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAG-TTTTCGGTACACATAGT
19963546 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
65 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
19963583 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTG
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTG
19963623 TTCATCGATA
Statistics
Matches: 222, Mismatches: 16, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
100 41 0.18
101 41 0.18
102 140 0.63
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (101 bp):
TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGTTTTCGGTACACATAGTA
GCCTTCACTTAGTACTACACATGTGACCATCATTTA
Found at i:19968252 original size:41 final size:41
Alignment explanation
Indices: 19968204--19968445 Score: 247
Period size: 41 Copynumber: 5.9 Consensus size: 41
19968194 GATTCAGAAT
* *
19968204 TACCAAAGT-CTAAATAGAGGCACATATGTGCAATTCAGGGG
1 TACCAAAGTAC-AAATAGGGGCACGTATGTGCAATTCAGGGG
* * * * *
19968245 TAACAAAGTACAAACAGGGGCATC-TATGTCCAATTCACGTG
1 TACCAAAGTACAAATAGGGGCA-CGTATGTGCAATTCAGGGG
* * * *
19968286 TACCGAAGTAAAAATAGGGGCACGTATGTGCAATTTAGTGG
1 TACCAAAGTACAAATAGGGGCACGTATGTGCAATTCAGGGG
* *
19968327 TACCAAAGTACAAATAGGGGCACGTATGTACAATTCAGGCG
1 TACCAAAGTACAAATAGGGGCACGTATGTGCAATTCAGGGG
** * *
19968368 TACGGAAGTACAAATAGGGGCACGTATGTGCATTTTAGGGG
1 TACCAAAGTACAAATAGGGGCACGTATGTGCAATTCAGGGG
* * **
19968409 TACCGAAGT-CGAAATAGTGGCGTGTATGTGCAATTCA
1 TACCAAAGTAC-AAATAGGGGCACGTATGTGCAATTCA
19968446 TCATTATTAT
Statistics
Matches: 164, Mismatches: 33, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
40 2 0.01
41 160 0.98
42 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (41 bp):
TACCAAAGTACAAATAGGGGCACGTATGTGCAATTCAGGGG
Found at i:19968424 original size:82 final size:82
Alignment explanation
Indices: 19968215--19968445 Score: 277
Period size: 82 Copynumber: 2.8 Consensus size: 82
19968205 ACCAAAGTCT
* * * * * *
19968215 AAATAGAGGCACATATGTGCAATTCAGGGGTAACAAAGTACAAACAGGGGCATC-TATGTCCAAT
1 AAATAGGGGCACGTATGTGCAATTTAGGGGTACCAAAGTACAAATAGGGGCA-CGTATGTACAAT
*
19968279 TCACGTGTACCGAAGTAA
65 TCACGCGTACCGAAGTAA
*
19968297 AAATAGGGGCACGTATGTGCAATTTAGTGGTACCAAAGTACAAATAGGGGCACGTATGTACAATT
1 AAATAGGGGCACGTATGTGCAATTTAGGGGTACCAAAGTACAAATAGGGGCACGTATGTACAATT
* * *
19968362 CAGGCGTACGGAAGTAC
66 CACGCGTACCGAAGTAA
* * * ** *
19968379 AAATAGGGGCACGTATGTGCATTTTAGGGGTACCGAAGT-CGAAATAGTGGCGTGTATGTGCAAT
1 AAATAGGGGCACGTATGTGCAATTTAGGGGTACCAAAGTAC-AAATAGGGGCACGTATGTACAAT
19968443 TCA
65 TCA
19968446 TCATTATTAT
Statistics
Matches: 129, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
81 2 0.02
82 127 0.98
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (82 bp):
AAATAGGGGCACGTATGTGCAATTTAGGGGTACCAAAGTACAAATAGGGGCACGTATGTACAATT
CACGCGTACCGAAGTAA
Found at i:19968424 original size:123 final size:123
Alignment explanation
Indices: 19968204--19968443 Score: 288
Period size: 123 Copynumber: 2.0 Consensus size: 123
19968194 GATTCAGAAT
* *
19968204 TACCAAAGTCTAAATAGAGGCACATATGTGCAATTCAGGGGTAACAAAGTACAAACAGGGGCATC
1 TACCAAAGTCTAAATAGAGGCACATATGTACAATTCAGGCGTAACAAAGTACAAACAGGGGCATC
*
19968269 TATGTCCAATTCACGTGTACCGAAGTAAAAATAGGGGCACGTATGTGCAATTTAGTGG
66 TATGTCCAATTCACGGGTACCGAAGTAAAAATAGGGGCACGTATGTGCAATTTAGTGG
* * * *
19968327 TACCAAAGTAC-AAATAGGGGCACGTATGTACAATTCAGGCGT-ACGGAAGTACAAATAGGGGCA
1 TACCAAAGT-CTAAATAGAGGCACATATGTACAATTCAGGCGTAAC-AAAGTACAAACAGGGGCA
* * * * ** * **
19968390 -CGTATGTGCATTTTAGGGGTACCGAAGTCGAAATAGTGGCGTGTATGTGCAATT
64 TC-TATGTCCAATTCACGGGTACCGAAGTAAAAATAGGGGCACGTATGTGCAATT
19968444 CATCATTATT
Statistics
Matches: 98, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
122 3 0.03
123 94 0.96
124 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (123 bp):
TACCAAAGTCTAAATAGAGGCACATATGTACAATTCAGGCGTAACAAAGTACAAACAGGGGCATC
TATGTCCAATTCACGGGTACCGAAGTAAAAATAGGGGCACGTATGTGCAATTTAGTGG
Found at i:19972235 original size:25 final size:25
Alignment explanation
Indices: 19972209--19972325 Score: 130
Period size: 25 Copynumber: 4.7 Consensus size: 25
19972199 GATACTCCAC
*
19972209 AGCTCGTGTGAGCATACCGACTTAC
1 AGCTCGTGTGAGCATACCGACTTAT
* *
19972234 AGCTCGTGTGAGCATATCAACTTAT
1 AGCTCGTGTGAGCATACCGACTTAT
* * * *
19972259 AGCTTGTGAGAGCATATCG-GTCTAT
1 AGCTCGTGTGAGCATACCGACT-TAT
19972284 AGCTCGTGTGAGCATACCGA-TTCAT
1 AGCTCGTGTGAGCATACCGACTT-AT
*
19972309 AGCTCGTATGAGCATAC
1 AGCTCGTGTGAGCATAC
19972326 ATGTACAAGA
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
24 2 0.03
25 76 0.97
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (25 bp):
AGCTCGTGTGAGCATACCGACTTAT
Found at i:19976155 original size:40 final size:40
Alignment explanation
Indices: 19976072--19976413 Score: 442
Period size: 40 Copynumber: 8.6 Consensus size: 40
19976062 TTGAATGCTG
* * * * * *
19976072 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
19976112 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
19976152 TCCGGGTTAAGT-CCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
19976191 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
19976231 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
19976271 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
19976311 TCCGGGTTATGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
19976351 TCCGGGTTATA-TCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTA-AGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * * *
19976390 ACCAGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
19976414 TGAACGAGGA
Statistics
Matches: 273, Mismatches: 24, Indels: 11
0.89 0.08 0.04
Matches are distributed among these distances:
39 67 0.25
40 198 0.73
41 8 0.03
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:19976330 original size:120 final size:119
Alignment explanation
Indices: 19976072--19976413 Score: 449
Period size: 119 Copynumber: 2.9 Consensus size: 119
19976062 TTGAATGCTG
* * * * * * * *
19976072 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGATTAAGAT-CCGAAGGCCT
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGG-CA
*
19976135 TTGTGCGAGATACTAAATCCGGGTTAAGT-CCGAAGGCATTCGTGCGAGTTATTAAA
63 TTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
19976191 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT-
**
19976256 GTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
65 GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
19976311 TCCGGGTTATGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATA-TCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTA-AGTCCCGAAGGCATT
* * * * *
19976375 GTGTGAGTTACTAAAACCAGGCTATGTCCCGAAGGCATT
65 GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
19976414 TGAACGAGGA
Statistics
Matches: 198, Mismatches: 20, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
118 4 0.02
119 100 0.51
120 93 0.47
121 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTG
TGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:19983544 original size:40 final size:40
Alignment explanation
Indices: 19983461--19983748 Score: 420
Period size: 40 Copynumber: 7.2 Consensus size: 40
19983451 TTGAATGCTG
* * * * * *
19983461 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
19983501 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
19983541 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
19983581 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
19983621 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
19983661 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
19983701 TCCGGGTTAAGT-CCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
19983740 TCCGGGTTA
1 TCCGGGTTA
19983749 TAAGGCATTG
Statistics
Matches: 230, Mismatches: 15, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
39 36 0.16
40 186 0.81
41 8 0.03
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:19985630 original size:20 final size:19
Alignment explanation
Indices: 19985601--19985674 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 19
19985591 AGCTAATAAC
19985601 GAGCTCAATGAGCTTAATT
1 GAGCTCAATGAGCTTAATT
* * *
19985620 GAGCTCGAATGCGCTGACTT
1 GAGCTC-AATGAGCTTAATT
19985640 GAGCTCCAATGAGC-TAACTT
1 GAGCT-CAATGAGCTTAA-TT
19985660 GAGCTCAAATGAGCT
1 GAGCTC-AATGAGCT
19985675 CAATCACATG
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
19 8 0.18
20 35 0.80
21 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (19 bp):
GAGCTCAATGAGCTTAATT
Found at i:19985654 original size:10 final size:9
Alignment explanation
Indices: 19985601--19985678 Score: 50
Period size: 10 Copynumber: 8.0 Consensus size: 9
19985591 AGCTAATAAC
19985601 GAGCTCAAT
1 GAGCTCAAT
*
19985610 GAGCTTAATT
1 GAGCTCAA-T
19985620 GAGCTCGAAT
1 GAGCTC-AAT
* * *
19985630 GCGCTGACTT
1 GAGCTCA-AT
19985640 GAGCTCCAAT
1 GAGCT-CAAT
19985650 GAGCT-AACTT
1 GAGCTCAA--T
19985660 GAGCTCAAAT
1 GAGCTC-AAT
19985670 GAGCTCAAT
1 GAGCTCAAT
19985679 CACATGAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
8 2 0.04
9 11 0.21
10 35 0.66
11 3 0.06
12 2 0.04
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (9 bp):
GAGCTCAAT
Found at i:19989933 original size:20 final size:21
Alignment explanation
Indices: 19989910--19989955 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
19989900 AGTTCAATTC
19989910 AGCTCAACT-TTAGCTCAATG
1 AGCTCAACTCTTAGCTCAATG
**
19989930 AGCTC-GTTCTTAGCTCAATG
1 AGCTCAACTCTTAGCTCAATG
19989950 AGCTCA
1 AGCTCA
19989956 TTTTTAGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (21 bp):
AGCTCAACTCTTAGCTCAATG
Found at i:19989962 original size:20 final size:20
Alignment explanation
Indices: 19989918--19989964 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
19989908 TCAGCTCAAC
*
19989918 TTTAGCTCAATGAGCTCGTT
1 TTTAGCTCAATGAGCTCATT
*
19989938 CTTAGCTCAATGAGCTCATT
1 TTTAGCTCAATGAGCTCATT
19989958 TTTAGCT
1 TTTAGCT
19989965 TACTTTAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (20 bp):
TTTAGCTCAATGAGCTCATT
Found at i:19991214 original size:15 final size:16
Alignment explanation
Indices: 19991194--19991226 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
19991184 CTCCATCAAT
19991194 TACCTT-TTTCTATTC
1 TACCTTGTTTCTATTC
19991209 TACCTTGTTTCTATTC
1 TACCTTGTTTCTATTC
19991225 TA
1 TA
19991227 AACTGAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.15, C:0.24, G:0.03, T:0.58
Consensus pattern (16 bp):
TACCTTGTTTCTATTC
Found at i:19997665 original size:19 final size:19
Alignment explanation
Indices: 19997607--19997665 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
19997597 CATCTCAATG
* * *
19997607 CACAAAGTGCATATTAAGA
1 CACAAAGTGCATCTTGACA
** * *
19997626 CACAAAGTTAATCCTGGCA
1 CACAAAGTGCATCTTGACA
19997645 CACAAAGTGCATCTTGACA
1 CACAAAGTGCATCTTGACA
19997664 CA
1 CA
19997666 TAAGTGCAAA
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (19 bp):
CACAAAGTGCATCTTGACA
Found at i:19999158 original size:49 final size:49
Alignment explanation
Indices: 19999105--19999214 Score: 211
Period size: 49 Copynumber: 2.2 Consensus size: 49
19999095 CCATCCTGAA
*
19999105 TGGCCCAACAACAATGACTTTCACTATTCTTACATTTTACCATCCTAGG
1 TGGCCCAACAACAATAACTTTCACTATTCTTACATTTTACCATCCTAGG
19999154 TGGCCCAACAACAATAACTTTCACTATTCTTACATTTTACCATCCTAGG
1 TGGCCCAACAACAATAACTTTCACTATTCTTACATTTTACCATCCTAGG
19999203 TGGCCCAACAAC
1 TGGCCCAACAAC
19999215 GATCGGATGG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 60 1.00
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (49 bp):
TGGCCCAACAACAATAACTTTCACTATTCTTACATTTTACCATCCTAGG
Found at i:20007258 original size:20 final size:20
Alignment explanation
Indices: 20007233--20007271 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
20007223 GCTACTCATA
20007233 TTTTCA-AAAACTTATCAGAG
1 TTTTCAGAAAACTTA-CAGAG
*
20007253 TTTTCAGAACACTTACAGA
1 TTTTCAGAAAACTTACAGA
20007272 ATTAGCGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (20 bp):
TTTTCAGAAAACTTACAGAG
Found at i:20008078 original size:23 final size:25
Alignment explanation
Indices: 20008027--20008078 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 25
20008017 AATCCTACCA
*
20008027 ACCAACCTCTACACACCATATCCGT
1 ACCAACCTCTACACACCATAGCCGT
20008052 -CCAACC-CTACACACCAT-GCCGT
1 ACCAACCTCTACACACCATAGCCGT
20008074 ACCAA
1 ACCAA
20008079 AATGCGGCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 4 0.16
23 15 0.60
24 6 0.24
ACGTcount: A:0.33, C:0.46, G:0.06, T:0.15
Consensus pattern (25 bp):
ACCAACCTCTACACACCATAGCCGT
Found at i:20010870 original size:21 final size:20
Alignment explanation
Indices: 20010829--20010870 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
20010819 CCTGTTATCC
*
20010829 AATAAAAACCTAAGATTCCT
1 AATAAAAACCTAAAATTCCT
20010849 AATAATAAACC-AAAATTACCT
1 AATAA-AAACCTAAAATT-CCT
20010870 A
1 A
20010871 TCCGATTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.55, C:0.19, G:0.02, T:0.24
Consensus pattern (20 bp):
AATAAAAACCTAAAATTCCT
Found at i:20013719 original size:21 final size:21
Alignment explanation
Indices: 20013678--20013721 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
20013668 ACGACCTAAT
*
20013678 TAAATAAAAAGGATAATTAAA
1 TAAATAAAAAGGATAAATAAA
*
20013699 TAAAT-AAAATGATACAATAAA
1 TAAATAAAAAGGATA-AATAAA
20013720 TA
1 TA
20013722 CTAAAGATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (21 bp):
TAAATAAAAAGGATAAATAAA
Found at i:20021091 original size:19 final size:18
Alignment explanation
Indices: 20021055--20021094 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
20021045 TTTCCACTCG
*
20021055 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
20021073 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
20021092 TTT
1 TTT
20021095 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:20022170 original size:14 final size:14
Alignment explanation
Indices: 20022151--20022204 Score: 101
Period size: 14 Copynumber: 3.9 Consensus size: 14
20022141 ACTAGCTCTC
20022151 TTTTTTTTCACAAT
1 TTTTTTTTCACAAT
20022165 TTTTTTTTCACAAT
1 TTTTTTTTCACAAT
20022179 TTTTTTTTCA-AAT
1 TTTTTTTTCACAAT
20022192 TTTTTTTTCACAA
1 TTTTTTTTCACAA
20022205 CTTGATATCC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.33
14 26 0.67
ACGTcount: A:0.22, C:0.13, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTTTTTCACAAT
Found at i:20022182 original size:27 final size:27
Alignment explanation
Indices: 20022151--20022204 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
20022141 ACTAGCTCTC
20022151 TTTTTTTTCACAATTTTTTTTTCACAAT
1 TTTTTTTTCA-AATTTTTTTTTCACAAT
20022179 TTTTTTTTCAAATTTTTTTTTCACAA
1 TTTTTTTTCAAATTTTTTTTTCACAA
20022205 CTTGATATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 16 0.62
28 10 0.38
ACGTcount: A:0.22, C:0.13, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTTTTTTCAAATTTTTTTTTCACAAT
Found at i:20022262 original size:13 final size:13
Alignment explanation
Indices: 20022244--20022292 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
20022234 GAAACTAGTA
20022244 TTTTTTTCGAATT
1 TTTTTTTCGAATT
*
20022257 TTTTTTTTGAATAT
1 TTTTTTTCGAAT-T
* *
20022271 ATTTTTT-GAGTT
1 TTTTTTTCGAATT
20022283 TTTTTTTCGA
1 TTTTTTTCGA
20022293 GAAACTACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 7 0.23
13 16 0.53
14 7 0.23
ACGTcount: A:0.16, C:0.04, G:0.10, T:0.69
Consensus pattern (13 bp):
TTTTTTTCGAATT
Found at i:20029568 original size:13 final size:13
Alignment explanation
Indices: 20029550--20029616 Score: 68
Period size: 13 Copynumber: 5.2 Consensus size: 13
20029540 TCTCTTCTTC
20029550 TTCTTTTCTTTTT
1 TTCTTTTCTTTTT
20029563 TTCTTTT-TTTTT
1 TTCTTTTCTTTTT
20029575 CTTCTTGTTC--TTT
1 -TTCTT-TTCTTTTT
* *
20029588 TTATTTTCTCTTT
1 TTCTTTTCTTTTT
20029601 TTCTTTTCTCTTTT
1 TTCTTTTCT-TTTT
20029615 TT
1 TT
20029617 TCACGAGCAT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
11 3 0.07
12 9 0.20
13 26 0.58
14 7 0.16
ACGTcount: A:0.01, C:0.16, G:0.01, T:0.81
Consensus pattern (13 bp):
TTCTTTTCTTTTT
Found at i:20029578 original size:32 final size:33
Alignment explanation
Indices: 20029542--20029609 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 33
20029532 GTGCATATTC
*
20029542 TCTTCTTCTTCTTTTCT-TTTTTTCTTTTT-TTT
1 TCTTCTTCTTCTTTT-TATTTTCTCTTTTTCTTT
*
20029574 TCTTCTTGTTCTTTTTATTTTCTCTTTTTCTTT
1 TCTTCTTCTTCTTTTTATTTTCTCTTTTTCTTT
20029607 TCT
1 TCT
20029610 CTTTTTTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 1 0.03
32 25 0.78
33 6 0.19
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.78
Consensus pattern (33 bp):
TCTTCTTCTTCTTTTTATTTTCTCTTTTTCTTT
Found at i:20029585 original size:19 final size:20
Alignment explanation
Indices: 20029553--20029607 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 20
20029543 CTTCTTCTTC
20029553 TTTTCTT-TTTTTCTTTTT-
1 TTTTCTTCTTTTTCTTTTTA
*
20029571 TTTTCTTCTTGTTCTTTTTA
1 TTTTCTTCTTTTTCTTTTTA
20029591 TTTTC-TCTTTTTCTTTT
1 TTTTCTTCTTTTTCTTTT
20029608 CTCTTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 7 0.21
19 21 0.64
20 5 0.15
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.82
Consensus pattern (20 bp):
TTTTCTTCTTTTTCTTTTTA
Found at i:20029615 original size:8 final size:7
Alignment explanation
Indices: 20029547--20029616 Score: 52
Period size: 7 Copynumber: 9.3 Consensus size: 7
20029537 TATTCTCTTC
20029547 TTCTTCTT
1 TTCTT-TT
20029555 TTCTTTTT
1 TTC-TTTT
20029563 TTCTTTT
1 TTCTTTT
*
20029570 TT-TTTC
1 TTCTTTT
20029576 TTCTTGTT
1 TTCTT-TT
*
20029584 CTTTTTATT
1 -TTCTT-TT
20029593 TTCTCTTT
1 TTCT-TTT
20029601 TTCTTTT
1 TTCTTTT
*
20029608 CTCTTTT
1 TTCTTTT
20029615 TT
1 TT
20029617 TCACGAGCAT
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
6 5 0.10
7 18 0.36
8 18 0.36
9 9 0.18
ACGTcount: A:0.01, C:0.17, G:0.01, T:0.80
Consensus pattern (7 bp):
TTCTTTT
Found at i:20050128 original size:14 final size:14
Alignment explanation
Indices: 20050109--20050136 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20050099 CTTCAAGGAA
20050109 TGATAAATTAATAT
1 TGATAAATTAATAT
20050123 TGATAAATTAATAT
1 TGATAAATTAATAT
20050137 AAGTCATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
TGATAAATTAATAT
Done.