Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 136 of 187
Found at i:40740859 original size:20 final size:20
Alignment explanation
Indices: 40740834--40740880 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
40740824 ACTACCTTCA
40740834 AGCTCATTC-AGCTCAATTTT
1 AGCTCATTCGAGCTC-ATTTT
*
40740854 AGCTCA-ACGAGCTCATTTT
1 AGCTCATTCGAGCTCATTTT
40740873 AGCTCATT
1 AGCTCATT
40740881 TTAGTTGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.36
Consensus pattern (20 bp):
AGCTCATTCGAGCTCATTTT
Found at i:40742540 original size:24 final size:23
Alignment explanation
Indices: 40742486--40742563 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
40742476 GGATAATTAA
**
40742486 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
40742509 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
40742533 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
40742554 GAAATAGTAT
1 GAAATGGTAT
40742564 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:40742548 original size:21 final size:21
Alignment explanation
Indices: 40742522--40742588 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
40742512 TTGGTATTTG
40742522 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
40742543 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
40742564 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
40742587 GG
1 GG
40742589 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:40744177 original size:28 final size:29
Alignment explanation
Indices: 40744123--40744202 Score: 78
Period size: 28 Copynumber: 2.8 Consensus size: 29
40744113 GGAAAATGAA
40744123 AAAGAAAAGAGTTCAGAAAAAGAGAGAGG
1 AAAGAAAAGAGTTCAGAAAAAGAGAGAGG
* * *
40744152 AAAG-AAAGAGTTGA-AAACAAGTGAGA-A
1 AAAGAAAAGAGTTCAGAAA-AAGAGAGAGG
40744179 AAGAGAAAACGAGTT-AGAAAAAGA
1 AA-AGAAAA-GAGTTCAGAAAAAGA
40744203 AAAAGAGAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
27 5 0.12
28 18 0.43
29 11 0.26
30 8 0.19
ACGTcount: A:0.60, C:0.04, G:0.28, T:0.09
Consensus pattern (29 bp):
AAAGAAAAGAGTTCAGAAAAAGAGAGAGG
Found at i:40744205 original size:18 final size:19
Alignment explanation
Indices: 40744164--40744205 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
40744154 AGAAAGAGTT
40744164 GAAAACAAGTGAGAAAAGA
1 GAAAACAAGTGAGAAAAGA
* *
40744183 GAAAACGAGTTAGAAAA-A
1 GAAAACAAGTGAGAAAAGA
40744201 GAAAA
1 GAAAA
40744206 AGAGAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.64, C:0.05, G:0.24, T:0.07
Consensus pattern (19 bp):
GAAAACAAGTGAGAAAAGA
Found at i:40754846 original size:25 final size:25
Alignment explanation
Indices: 40754812--40754896 Score: 70
Period size: 25 Copynumber: 3.4 Consensus size: 25
40754802 CCATACAATA
*
40754812 CGCCACAAAGATGTTTTAGATAATT
1 CGCCATAAAGATGTTTTAGATAATT
**
40754837 CGCCATAAAGACT-TTACAGATAACTT
1 CGCCATAAAGA-TGTTTTAGATAA-TT
40754863 -GCCATAAA-A-GCTTTTCAGATAATT
1 CGCCATAAAGATG-TTTT-AGATAATT
*
40754887 CACCATAAAG
1 CGCCATAAAG
40754897 GCTTTACAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
24 5 0.11
25 39 0.83
26 3 0.06
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (25 bp):
CGCCATAAAGATGTTTTAGATAATT
Found at i:40754900 original size:25 final size:25
Alignment explanation
Indices: 40754829--40755075 Score: 228
Period size: 25 Copynumber: 9.9 Consensus size: 25
40754819 AAGATGTTTT
* *
40754829 AGATAATTCGCCATAAAGACTTTAC
1 AGATAATTCACCATAAAGGCTTTAC
* * *
40754854 AGATAACTT-GCCATAAAAGCTTTTC
1 AGATAA-TTCACCATAAAGGCTTTAC
40754879 AGATAATTCACCATAAAGGCTTTAC
1 AGATAATTCACCATAAAGGCTTTAC
* ** *
40754904 AAATAATTTGCCACAAAGGCTTTAC
1 AGATAATTCACCATAAAGGCTTTAC
* * *
40754929 AGATAACTCGCCACAAAGGCTTTAC
1 AGATAATTCACCATAAAGGCTTTAC
* * *
40754954 AAATAATTCACCATAGAGACTTCT-C
1 AGATAATTCACCATAAAGGCTT-TAC
*
40754979 AGATAATTCGCCATAAAGGCTTTAC
1 AGATAATTCACCATAAAGGCTTTAC
* **
40755004 AGATAACTCACCATAAAGGCTTTTT
1 AGATAATTCACCATAAAGGCTTTAC
* * * *
40755029 AGATAGTTCACCACAAAAGCTTTCC
1 AGATAATTCACCATAAAGGCTTTAC
* * *
40755054 AAATAACTCACCACAAAGGCTT
1 AGATAATTCACCATAAAGGCTT
40755076 GGTTTGGTTT
Statistics
Matches: 181, Mismatches: 37, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
24 3 0.02
25 175 0.97
26 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (25 bp):
AGATAATTCACCATAAAGGCTTTAC
Found at i:40754960 original size:75 final size:74
Alignment explanation
Indices: 40754831--40755075 Score: 292
Period size: 75 Copynumber: 3.3 Consensus size: 74
40754821 GATGTTTTAG
* * * *
40754831 ATAATTCGCCATAAAGACTTTACAGATAACTTGCCATAAAAGCTTTTCAGATAATTCACCATAAA
1 ATAATTCGCCACAAAGGCTTTACAGATAACTCGCCATAAAGGCTTTTCAGATAATTCACCATAAA
40754896 GGCTTTACAA
66 GGCTTT-CAA
* * * * *
40754906 ATAATTTGCCACAAAGGCTTTACAGATAACTCGCCACAAAGGCTTTACAAATAATTCACCATAGA
1 ATAATTCGCCACAAAGGCTTTACAGATAACTCGCCATAAAGGCTTTTCAGATAATTCACCATAAA
* *
40754971 GACTTCTCAG
66 GGCTT-TCAA
* * * * *
40754981 ATAATTCGCCATAAAGGCTTTACAGATAACTCACCATAAAGGCTTTTTAGATAGTTCACCACAAA
1 ATAATTCGCCACAAAGGCTTTACAGATAACTCGCCATAAAGGCTTTTCAGATAATTCACCATAAA
*
40755046 AGCTTTCCAA
66 GGCTTT-CAA
* *
40755056 ATAACTCACCACAAAGGCTT
1 ATAATTCGCCACAAAGGCTT
40755076 GGTTTGGTTT
Statistics
Matches: 141, Mismatches: 27, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
74 1 0.01
75 139 0.99
76 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (74 bp):
ATAATTCGCCACAAAGGCTTTACAGATAACTCGCCATAAAGGCTTTTCAGATAATTCACCATAAA
GGCTTTCAA
Found at i:40760767 original size:40 final size:39
Alignment explanation
Indices: 40760736--40760945 Score: 233
Period size: 40 Copynumber: 5.3 Consensus size: 39
40760726 GGACTAAGAT
* *
40760736 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
40760776 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
40760816 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* ** *
40760856 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGAT-ACAAATCCGGGTTAAGTC
* * * * *
40760896 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
40760935 CCGAAGGCATT
1 CCGAAGGCATT
40760946 TGAACGAGGA
Statistics
Matches: 153, Mismatches: 13, Indels: 9
0.87 0.07 0.05
Matches are distributed among these distances:
39 33 0.22
40 117 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:40760899 original size:120 final size:120
Alignment explanation
Indices: 40760683--40760945 Score: 300
Period size: 120 Copynumber: 2.2 Consensus size: 120
40760673 TTGAATGCTG
* *
40760683 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
40760747 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
40760803 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* ** * * * *
40760866 TCGTGCGAGTTGTTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGAT-ACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
40760922 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
40760946 TGAACGAGGA
Statistics
Matches: 120, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
119 38 0.32
120 73 0.61
121 9 0.08
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:40760965 original size:79 final size:80
Alignment explanation
Indices: 40760736--40760980 Score: 228
Period size: 80 Copynumber: 3.1 Consensus size: 80
40760726 GGACTAAGAT
* * * * * * * ** *
40760736 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGA-GATAC
1 CCGAAGGCATTCGTGCGAGTTACTAAA-ACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGA-GC
40760799 TAAATCCGGGTTAAGTC
64 TAAATCCGGGTTAAGTC
* * * ** ** *
40760816 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
*
40760881 AATCCGGGTTATGTC
66 AATCCGGGTTAAGTC
* * *
40760896 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
* *
40760960 TATCC-GGTTAAATC
66 AATCCGGGTTAAGTC
40760974 CCGAAGG
1 CCGAAGG
40760981 TACGTGATTT
Statistics
Matches: 138, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
78 14 0.10
79 46 0.33
80 75 0.54
81 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
AATCCGGGTTAAGTC
Found at i:40768520 original size:20 final size:19
Alignment explanation
Indices: 40768497--40768546 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
40768487 ATTTCAATTC
*
40768497 AGCTCAATTTTAGCTCAATG
1 AGCTC-ATTTTAGCACAATG
**
40768517 AGCTTGTTCTTAGCACAATG
1 AGCTCATT-TTAGCACAATG
40768537 AGCTCATTTT
1 AGCTCATTTT
40768547 TTTAGCTTAC
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (19 bp):
AGCTCATTTTAGCACAATG
Found at i:40770057 original size:13 final size:12
Alignment explanation
Indices: 40770039--40770074 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
40770029 GTAAGTTTTG
40770039 AAAAAAATTCAA
1 AAAAAAATTCAA
*
40770051 AAAAAAATTTGAA
1 AAAAAAA-TTCAA
40770064 AAAAAAATTCA
1 AAAAAAATTCA
40770075 TGTTGTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.72, C:0.06, G:0.03, T:0.19
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:40774122 original size:20 final size:21
Alignment explanation
Indices: 40774092--40774142 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
40774082 AATTTAACTT
40774092 AGTTCAGCTCACTCGAGCTCA
1 AGTTCAGCTCACTCGAGCTCA
*
40774113 AGTT-AGCTCATTCGAGCTCA
1 AGTTCAGCTCACTCGAGCTCA
40774133 A-TTCAGCTCA
1 AGTTCAGCTCA
40774143 ATCTTAACCC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 2 0.07
20 22 0.79
21 4 0.14
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27
Consensus pattern (21 bp):
AGTTCAGCTCACTCGAGCTCA
Found at i:40774865 original size:22 final size:21
Alignment explanation
Indices: 40774836--40774883 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
40774826 AAGCATGAAC
*
40774836 TGAA-ATTTTAATGATTTAGTG
1 TGAACATTTTAATGAATT-GTG
* *
40774857 TGAACATTTTTATTAATTGTG
1 TGAACATTTTAATGAATTGTG
40774878 TGAACA
1 TGAACA
40774884 CATAGATGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (21 bp):
TGAACATTTTAATGAATTGTG
Found at i:40776299 original size:20 final size:20
Alignment explanation
Indices: 40776274--40776319 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
40776264 CAACTTAATT
*
40776274 TTAGCTCAATGAGCTCGTTC
1 TTAGCTCAATGAGCTCATTC
*
40776294 TTAGCTCAATGAGCTCATTT
1 TTAGCTCAATGAGCTCATTC
40776314 TTAGCT
1 TTAGCT
40776320 TACTTTAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCAATGAGCTCATTC
Found at i:40790245 original size:19 final size:19
Alignment explanation
Indices: 40790217--40790263 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
40790207 GCGAAAATAC
*
40790217 AAAAGAAAAGAAAAATGAAA
1 AAAAG-AAAGAAAAATCAAA
*
40790237 AAAAGAAAGAAAATTCAAA
1 AAAAGAAAGAAAAATCAAA
*
40790256 AAATGAAA
1 AAAAGAAA
40790264 ATGAAAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.77, C:0.02, G:0.13, T:0.09
Consensus pattern (19 bp):
AAAAGAAAGAAAAATCAAA
Found at i:40790265 original size:33 final size:32
Alignment explanation
Indices: 40790228--40790304 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 32
40790218 AAAGAAAAGA
40790228 AAAATGAAAAAAAGAAAGAAAATTCAAAAA-ATG
1 AAAATGAAAAAAAGAAAGAAAA--CAAAAAGATG
* *
40790261 AAAATGAAAAGAAAGCAAGAAAAGAAAAAGATG
1 AAAATGAAAA-AAAGAAAGAAAACAAAAAGATG
*
40790294 AAAAAGAAAAA
1 AAAATGAAAAA
40790305 GTGAGTGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
32 6 0.15
33 22 0.56
34 11 0.28
ACGTcount: A:0.74, C:0.03, G:0.16, T:0.08
Consensus pattern (32 bp):
AAAATGAAAAAAAGAAAGAAAACAAAAAGATG
Found at i:40795150 original size:20 final size:19
Alignment explanation
Indices: 40795127--40795191 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
40795117 AAGCTCAAAC
40795127 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
40795147 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
40795167 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
40795187 GAGCT
1 GAGCT
40795192 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:40795955 original size:20 final size:19
Alignment explanation
Indices: 40795932--40795996 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
40795922 AAGCTCAAAC
40795932 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
40795952 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
40795972 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
40795992 GAGCT
1 GAGCT
40795997 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:40804598 original size:18 final size:17
Alignment explanation
Indices: 40804573--40804606 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
40804563 AAATAAAAGT
40804573 AAAGTATAAAAAGTATA
1 AAAGTATAAAAAGTATA
*
40804590 AAAGATATAACAAGTAT
1 AAAG-TATAAAAAGTAT
40804607 TATATATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.62, C:0.03, G:0.12, T:0.24
Consensus pattern (17 bp):
AAAGTATAAAAAGTATA
Found at i:40805690 original size:17 final size:17
Alignment explanation
Indices: 40805631--40805695 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 17
40805621 AATTAAGTCA
*
40805631 ATAATTAATTTTTGAAA-
1 ATAATTAATTATT-AAAT
*
40805648 AAAATTAATTATTAAAT
1 ATAATTAATTATTAAAT
* *
40805665 ATAAATAATTAGTTTAAT
1 ATAATTAATTA-TTAAAT
40805683 -TAATTAATT-TTAA
1 ATAATTAATTATTAA
40805696 TTGAATAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
15 3 0.08
16 3 0.08
17 28 0.72
18 5 0.13
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
ATAATTAATTATTAAAT
Found at i:40805760 original size:16 final size:16
Alignment explanation
Indices: 40805741--40805774 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40805731 ATATTTTAGC
40805741 TTTATCGTATTAAAAT
1 TTTATCGTATTAAAAT
* *
40805757 TTTATTGTATTAGAAT
1 TTTATCGTATTAAAAT
40805773 TT
1 TT
40805775 GTGTAAACGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (16 bp):
TTTATCGTATTAAAAT
Found at i:40808394 original size:9 final size:9
Alignment explanation
Indices: 40808380--40808404 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
40808370 AGGATTCATC
40808380 AACTCGATT
1 AACTCGATT
40808389 AACTCGATT
1 AACTCGATT
40808398 AACTCGA
1 AACTCGA
40808405 ACTTTTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (9 bp):
AACTCGATT
Found at i:40808697 original size:27 final size:27
Alignment explanation
Indices: 40808665--40808841 Score: 210
Period size: 27 Copynumber: 6.6 Consensus size: 27
40808655 TACGCCACTA
* * *
40808665 AAAGGCTTTTATTTCATATTACGCTAC
1 AAAGGCTTTTCTTTCATATTATGCCAC
40808692 AAAGGCTTTTCTTTCATATTATGCCAC
1 AAAGGCTTTTCTTTCATATTATGCCAC
* * * *
40808719 AAAGTCTTTCCTTTTATATTATGCTAC
1 AAAGGCTTTTCTTTCATATTATGCCAC
* * **
40808746 AAAGTCTTTCCTTTCATATTACACCAC
1 AAAGGCTTTTCTTTCATATTATGCCAC
*
40808773 AAAGGCTTTTATTTCATATTATGCCAC
1 AAAGGCTTTTCTTTCATATTATGCCAC
*** *
40808800 AAATTATTTTCTTTCATATTATGCCAT
1 AAAGGCTTTTCTTTCATATTATGCCAC
40808827 AAAGGCTTTTCTTTC
1 AAAGGCTTTTCTTTC
40808842 CTAACATGTT
Statistics
Matches: 126, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 126 1.00
ACGTcount: A:0.28, C:0.20, G:0.08, T:0.44
Consensus pattern (27 bp):
AAAGGCTTTTCTTTCATATTATGCCAC
Found at i:40808777 original size:81 final size:81
Alignment explanation
Indices: 40808665--40808841 Score: 237
Period size: 81 Copynumber: 2.2 Consensus size: 81
40808655 TACGCCACTA
** * * * *
40808665 AAAGGCTTTTATTTCATATTACGCTACAAAGGCTTTTCTTTCATATTATGCCACAAAGTCTTTCC
1 AAAGGCTTTCCTTTCATATTACACCACAAAGGCTTTTATTTCATATTATGCCACAAAGTATTTCC
* *
40808730 TTTTATATTATGCTAC
66 TTTCATATTATGCCAC
* * *
40808746 AAAGTCTTTCCTTTCATATTACACCACAAAGGCTTTTATTTCATATTATGCCACAAATTATTTTC
1 AAAGGCTTTCCTTTCATATTACACCACAAAGGCTTTTATTTCATATTATGCCACAAAGTATTTCC
*
40808811 TTTCATATTATGCCAT
66 TTTCATATTATGCCAC
*
40808827 AAAGGCTTTTCTTTC
1 AAAGGCTTTCCTTTC
40808842 CTAACATGTT
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.28, C:0.20, G:0.08, T:0.44
Consensus pattern (81 bp):
AAAGGCTTTCCTTTCATATTACACCACAAAGGCTTTTATTTCATATTATGCCACAAAGTATTTCC
TTTCATATTATGCCAC
Found at i:40810539 original size:4 final size:4
Alignment explanation
Indices: 40810530--40810556 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
40810520 AAGTTTTATT
40810530 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
40810557 TTACTTAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:40810575 original size:26 final size:26
Alignment explanation
Indices: 40810524--40810576 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
40810514 GTTGTAAAGT
* *
40810524 TTTATTTTTATTTATTTATTTATTTA
1 TTTATTTTTACTTATTTAATTATTTA
40810550 TTTATTTTTACTTAGTTTAATT-TTTA
1 TTTATTTTTACTTA-TTTAATTATTTA
40810576 T
1 T
40810577 GTAAATATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (26 bp):
TTTATTTTTACTTATTTAATTATTTA
Found at i:40819033 original size:50 final size:52
Alignment explanation
Indices: 40818975--40819093 Score: 170
Period size: 50 Copynumber: 2.3 Consensus size: 52
40818965 TTAATAAAGT
* * **
40818975 CATGCATTATGTAACTCTCATGTTAG-TTAAGTTTGCATCA-TAAATTATGA
1 CATGCATTATGTAACTCCCATGTTAGCTAAAGTTTGCATCATTAAATTAACA
*
40819025 CATGCATTATGTAACTCCCATGTTAGCTAAAGTTTGCATCATTAAATTAACT
1 CATGCATTATGTAACTCCCATGTTAGCTAAAGTTTGCATCATTAAATTAACA
*
40819077 CATGCATTAAGTAACTC
1 CATGCATTATGTAACTC
40819094 ATTTGTTCAT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 25 0.41
51 13 0.21
52 23 0.38
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.37
Consensus pattern (52 bp):
CATGCATTATGTAACTCCCATGTTAGCTAAAGTTTGCATCATTAAATTAACA
Found at i:40824340 original size:52 final size:51
Alignment explanation
Indices: 40824211--40824342 Score: 169
Period size: 50 Copynumber: 2.6 Consensus size: 51
40824201 ATGTGTTATG
* * * **
40824211 CATTTAATAAAGTCAAGCATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAGTTAAGTTTGCAT
* *
40824262 CA-TAAATTATGACATGCATTATGTAACTCCCATGTTAGTTAAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAGTT-AAGTTTGCAT
40824313 CATTAAATTAAGTCATGCATT-TAGTAACTC
1 CATTAAATTAAGTCATGCATTAT-GTAACTC
40824343 ATTTGTTCAT
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
50 31 0.45
51 15 0.22
52 23 0.33
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (51 bp):
CATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAGTTAAGTTTGCAT
Found at i:40834712 original size:18 final size:19
Alignment explanation
Indices: 40834679--40834720 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
40834669 ATATTTCCCG
*
40834679 CAAAAAAAGTAGAAAAAGT
1 CAAAAAAAGTAGAAAAAGA
*
40834698 CAAAAAAATTA-AAAAAGA
1 CAAAAAAAGTAGAAAAAGA
40834716 CAAAA
1 CAAAA
40834721 TCAAGAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.74, C:0.07, G:0.10, T:0.10
Consensus pattern (19 bp):
CAAAAAAAGTAGAAAAAGA
Found at i:40835353 original size:21 final size:20
Alignment explanation
Indices: 40835328--40835369 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
40835318 TCAATCGAGT
40835328 TCAATTCAGCTCAATTTTAGC
1 TCAA-TCAGCTCAATTTTAGC
* *
40835349 TCAATGAGCTCATTTTTAGC
1 TCAATCAGCTCAATTTTAGC
40835369 T
1 T
40835370 TACTTTAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (20 bp):
TCAATCAGCTCAATTTTAGC
Found at i:40840333 original size:32 final size:32
Alignment explanation
Indices: 40840297--40840360 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
40840287 CGCATTCCTC
40840297 TATCATTTGGTATCAGATTTTGGGCATTTTGG
1 TATCATTTGGTATCAGATTTTGGGCATTTTGG
*
40840329 TATCATTTGGTATCAGATTTTGGGCGTTTTGG
1 TATCATTTGGTATCAGATTTTGGGCATTTTGG
40840361 AAACCCTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.17, C:0.09, G:0.27, T:0.47
Consensus pattern (32 bp):
TATCATTTGGTATCAGATTTTGGGCATTTTGG
Found at i:40842828 original size:11 final size:10
Alignment explanation
Indices: 40842803--40842863 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
40842793 ACCAATAAAA
40842803 TAAA-TGAGC
1 TAAATTGAGC
*
40842812 TGAATTGTAGC
1 TAAATTG-AGC
40842823 TAAATTGAGC
1 TAAATTGAGC
**
40842833 TCGATTGAGC
1 TAAATTGAGC
40842843 TGAAA-TGAGC
1 T-AAATTGAGC
*
40842853 TCAATTGAGC
1 TAAATTGAGC
40842863 T
1 T
40842864 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:40842864 original size:20 final size:20
Alignment explanation
Indices: 40842804--40842864 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
40842794 CCAATAAAAT
*
40842804 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
40842824 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
40842845 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
40842865 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:40844952 original size:18 final size:18
Alignment explanation
Indices: 40844931--40844965 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
40844921 TTTTTCTTTT
40844931 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
40844949 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
40844966 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:40844962 original size:6 final size:6
Alignment explanation
Indices: 40844953--40845057 Score: 52
Period size: 6 Copynumber: 17.2 Consensus size: 6
40844943 TCAATCTCAA
* * * ** **
40844953 TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTC TCACTAT TTTGAT
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCT-T TTTCTT
* ** * *
40845005 TT-CTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
40845051 TTTCTT T
1 TTTCTT T
40845058 CAATTTCTTT
Statistics
Matches: 69, Mismatches: 25, Indels: 10
0.66 0.24 0.10
Matches are distributed among these distances:
5 7 0.10
6 49 0.71
7 10 0.14
8 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.04, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:40845070 original size:6 final size:6
Alignment explanation
Indices: 40845004--40845057 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
40844994 ACTATTTTGA
* ** * *
40845004 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
40845051 TTTCTT T
1 TTTCTT T
40845058 CAATTTCTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.04, C:0.15, G:0.06, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:40846151 original size:13 final size:13
Alignment explanation
Indices: 40846135--40846160 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40846125 TTTTTTTCGA
40846135 TTTTTTTGAATTT
1 TTTTTTTGAATTT
40846148 TTTTTTTGAATTT
1 TTTTTTTGAATTT
40846161 CTTCTCTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (13 bp):
TTTTTTTGAATTT
Found at i:40849258 original size:12 final size:12
Alignment explanation
Indices: 40849241--40849281 Score: 68
Period size: 11 Copynumber: 3.6 Consensus size: 12
40849231 TCAGATTTTG
40849241 TTTTTTTTTGAA
1 TTTTTTTTTGAA
40849253 -TTTTTTTTGAA
1 TTTTTTTTTGAA
40849264 TTTTTTTTTG-A
1 TTTTTTTTTGAA
40849275 TTTTTTT
1 TTTTTTT
40849282 AAACTTACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.12, C:0.00, G:0.07, T:0.80
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:40849528 original size:29 final size:29
Alignment explanation
Indices: 40849495--40849554 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
40849485 AAGGATTCAA
* * *
40849495 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTAATGGATATAAAGTTTATGT
*
40849524 AGATGGATTAATGGATATAAAGTTTTTGT
1 AGATGGATTAATGGATATAAAGTTTATGT
40849553 AG
1 AG
40849555 GTTTGGTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.00, G:0.28, T:0.40
Consensus pattern (29 bp):
AGATGGATTAATGGATATAAAGTTTATGT
Found at i:40850812 original size:10 final size:10
Alignment explanation
Indices: 40850796--40850853 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
40850786 CAACTCCGAC
40850796 CAGCTCAATT
1 CAGCTCAATT
* *
40850806 GAGCTCATTT
1 CAGCTCAATT
40850816 CAGCTCAA-T
1 CAGCTCAATT
40850825 CGAGCTCAATT
1 C-AGCTCAATT
*
40850836 TAGCTACAATT
1 CAGCT-CAATT
40850847 CAGCTCA
1 CAGCTCA
40850854 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:40850819 original size:20 final size:20
Alignment explanation
Indices: 40850796--40850856 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
40850786 CAACTCCGAC
40850796 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
40850816 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
40850837 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
40850857 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:40856560 original size:20 final size:19
Alignment explanation
Indices: 40856535--40856620 Score: 61
Period size: 20 Copynumber: 4.5 Consensus size: 19
40856525 ATGAAAATAC
40856535 AAAAGAAAAGAAAAATGAGA
1 AAAAGAAAAGAAAAA-GAGA
* * *
40856555 AAAAGAGAGGAAAAATGA-T
1 AAAAGAAAAGAAAAA-GAGA
*
40856574 AAAAGAAAATGAGAAA-AG-
1 AAAAGAAAA-GAAAAAGAGA
* *
40856592 ACAAGAAAAGAGAAAGAAGA
1 AAAAGAAAAGAAAAAG-AGA
40856612 AAAAGAAAA
1 AAAAGAAAA
40856621 AGATTGTGAA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
17 6 0.11
18 9 0.17
19 9 0.17
20 29 0.55
ACGTcount: A:0.72, C:0.01, G:0.22, T:0.05
Consensus pattern (19 bp):
AAAAGAAAAGAAAAAGAGA
Found at i:40856612 original size:32 final size:32
Alignment explanation
Indices: 40856535--40856623 Score: 82
Period size: 32 Copynumber: 2.9 Consensus size: 32
40856525 ATGAAAATAC
* *
40856535 AAAAGA-AAAG-A-AAAATGAGAAAAAGAGAGG
1 AAAAGAGAAAGAAGAAAATGAG-AAAAGACAAG
40856565 AAAA-ATGATAA-AAGAAAATGAGAAAAGACAAG
1 AAAAGA-GA-AAGAAGAAAATGAGAAAAGACAAG
*
40856597 AAAAGAGAAAGAAGAAAAAGA-AAAAGA
1 AAAAGAGAAAGAAGAAAATGAGAAAAGA
40856624 TTGTGAAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
29 1 0.02
30 4 0.08
31 9 0.18
32 26 0.53
33 9 0.18
ACGTcount: A:0.72, C:0.01, G:0.22, T:0.04
Consensus pattern (32 bp):
AAAAGAGAAAGAAGAAAATGAGAAAAGACAAG
Found at i:40856617 original size:6 final size:6
Alignment explanation
Indices: 40856564--40856623 Score: 50
Period size: 7 Copynumber: 9.3 Consensus size: 6
40856554 AAAAAGAGAG
* *
40856564 GAAAAA TGATAAAA GAAAAT GAGAAAA G-ACAA GAAAAGA GAAAGAA GAAAAA
1 GAAAAA -GA-AAAA GAAAAA GA-AAAA GAAAAA GAAAA-A GAAA-AA GAAAAA
40856616 GAAAAA GA
1 GAAAAA GA
40856624 TTGTGAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
5 4 0.09
6 17 0.39
7 18 0.41
8 5 0.11
ACGTcount: A:0.72, C:0.02, G:0.22, T:0.05
Consensus pattern (6 bp):
GAAAAA
Found at i:40860393 original size:4 final size:4
Alignment explanation
Indices: 40860375--40860408 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
40860365 TATAAAAATT
40860375 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
40860409 AATAAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:40861820 original size:23 final size:22
Alignment explanation
Indices: 40861768--40861820 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
40861758 TCCTCGTCTT
*
40861768 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
40861790 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
40861813 TTTCTTTT
1 TTTCTTTT
40861821 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:40866541 original size:21 final size:21
Alignment explanation
Indices: 40866512--40866551 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
40866502 GCTGGAACCT
40866512 TCCTTGAAGCTTC-TTGAACG
1 TCCTTGAAGCTTCGTTGAACG
40866532 TCCTTGGAAGCTTCGTTGAA
1 TCCTT-GAAGCTTCGTTGAA
40866552 GTTTCCAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 8 0.44
22 5 0.28
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.35
Consensus pattern (21 bp):
TCCTTGAAGCTTCGTTGAACG
Found at i:40867351 original size:36 final size:36
Alignment explanation
Indices: 40867303--40867373 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
40867293 TATCAGTATC
*
40867303 GGCATTCGGTAGAAGATGGTTGAGACACATGATTGA
1 GGCATTCCGTAGAAGATGGTTGAGACACATGATTGA
40867339 GGCATTCCGTAGAAGATGGTTGAGACACATGATTG
1 GGCATTCCGTAGAAGATGGTTGAGACACATGATTG
40867374 GGAAAAAGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.30, C:0.13, G:0.32, T:0.25
Consensus pattern (36 bp):
GGCATTCCGTAGAAGATGGTTGAGACACATGATTGA
Found at i:40867494 original size:46 final size:46
Alignment explanation
Indices: 40867444--40867611 Score: 189
Period size: 46 Copynumber: 3.6 Consensus size: 46
40867434 TGGTTGAGCA
* * *
40867444 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGTAAACG
* * *
40867490 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGTAA--A--CG
* * *
40867537 TCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATTTGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGTAAACG
*
40867583 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
40867612 GTTTATGGGC
Statistics
Matches: 102, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 57 0.56
47 28 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGTAAACG
Found at i:40867600 original size:93 final size:93
Alignment explanation
Indices: 40867441--40867613 Score: 283
Period size: 93 Copynumber: 1.9 Consensus size: 93
40867431 GGATGGTTGA
* * *
40867441 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGTCCGAACTCGTTGAGT
40867506 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*** *
40867534 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATTTGAACGTCCGAGCTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGTCCGAACTCGTTGAGT
40867599 TGAGTCCGAGTTCGT
66 TGAGTCCGAGTTCGT
40867614 TTATGGGCGG
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:40869329 original size:24 final size:24
Alignment explanation
Indices: 40869283--40869329 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
40869273 CACTTTTTCC
* *
40869283 TTTCTTTTTTTCATTTTTCTTTTT
1 TTTCTCTTTTTCATCTTTCTTTTT
40869307 TTTCTCTTTTTCAATCTTT-TTTT
1 TTTCTCTTTTTC-ATCTTTCTTTT
40869330 CTTATACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (24 bp):
TTTCTCTTTTTCATCTTTCTTTTT
Found at i:40869623 original size:20 final size:21
Alignment explanation
Indices: 40869600--40869640 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
40869590 CATCAGTTCA
*
40869600 TTTGAGCTCG-ATTCAGCTTG
1 TTTGAGCTAGAATTCAGCTTG
40869620 TTTGAGCTAGAATTCAGCTTG
1 TTTGAGCTAGAATTCAGCTTG
40869641 ATTCAGCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (21 bp):
TTTGAGCTAGAATTCAGCTTG
Found at i:40869701 original size:12 final size:11
Alignment explanation
Indices: 40869670--40869703 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
40869660 CATTCTAATA
40869670 AATTAAGTTTT
1 AATTAAGTTTT
*
40869681 AATTCAGTTTAT
1 AATTAAGTTT-T
40869693 AATTAAGTTTT
1 AATTAAGTTTT
40869704 CTACAGCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.53
Consensus pattern (11 bp):
AATTAAGTTTT
Found at i:40873548 original size:9 final size:9
Alignment explanation
Indices: 40873534--40873567 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
40873524 TGATTTGCTG
40873534 ATTAGTTAA
1 ATTAGTTAA
40873543 ATTAGTTAA
1 ATTAGTTAA
40873552 ATTAGTTAA
1 ATTAGTTAA
40873561 ATTAGTT
1 ATTAGTT
40873568 TTAACAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (9 bp):
ATTAGTTAA
Found at i:40873844 original size:18 final size:17
Alignment explanation
Indices: 40873823--40873856 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40873813 TAATTTTTAA
40873823 ATGTGTCTAAATTAATTC
1 ATGTG-CTAAATTAATTC
*
40873841 ATGTGCTGAATTAATT
1 ATGTGCTAAATTAATT
40873857 TGTGTGTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (17 bp):
ATGTGCTAAATTAATTC
Found at i:40873957 original size:24 final size:24
Alignment explanation
Indices: 40873930--40873984 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
40873920 GCCTGGACAG
*
40873930 ATTTAATGAGCTGCTGGTTGACGA
1 ATTTAATGAGCTGCTGGTGGACGA
*
40873954 ATTTAATGAGTTGCTGGTGGACGA
1 ATTTAATGAGCTGCTGGTGGACGA
40873978 ATTTAAT
1 ATTTAAT
40873985 ATGTCCTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.27, C:0.09, G:0.27, T:0.36
Consensus pattern (24 bp):
ATTTAATGAGCTGCTGGTGGACGA
Found at i:40874939 original size:20 final size:21
Alignment explanation
Indices: 40874904--40874961 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
40874894 CCTAGCTCAT
*
40874904 TTCCAGCTCA-TCGAGCTCCG
1 TTCCAGCTCATTTGAGCTCCG
40874924 -TCCAGCTCATTTGAGCT-CG
1 TTCCAGCTCATTTGAGCTCCG
* *
40874943 TTTCAGCTCGTTTGAGCTC
1 TTCCAGCTCATTTGAGCTC
40874962 AACCGAGCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 11 0.34
20 21 0.66
ACGTcount: A:0.14, C:0.33, G:0.21, T:0.33
Consensus pattern (21 bp):
TTCCAGCTCATTTGAGCTCCG
Found at i:40877454 original size:42 final size:42
Alignment explanation
Indices: 40877392--40877488 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
40877382 AGATTATGAG
* * *
40877392 AGAAAATGAGAGGATTTTGAATGAAATCGAGAGAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
*
40877434 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAATAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
*
40877476 AG-AAATGAAAGAA
1 AGAAAATGAGAGAA
40877489 AAAGAAAAGG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 10 0.20
42 40 0.80
ACGTcount: A:0.57, C:0.04, G:0.24, T:0.15
Consensus pattern (42 bp):
AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
Found at i:40877524 original size:18 final size:18
Alignment explanation
Indices: 40877503--40877554 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
40877493 AAAAGGAGGT
40877503 TGAGAGTGAAAAAGAAAA
1 TGAGAGTGAAAAAGAAAA
* ***
40877521 TGAGATTGAAAAAGAGTT
1 TGAGAGTGAAAAAGAAAA
*
40877539 TGAGAGAGAAAAAGAA
1 TGAGAGTGAAAAAGAA
40877555 TGTGAACAAG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.29, T:0.15
Consensus pattern (18 bp):
TGAGAGTGAAAAAGAAAA
Found at i:40877583 original size:18 final size:19
Alignment explanation
Indices: 40877547--40877585 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
40877537 TTTGAGAGAG
*
40877547 AAAAAGAATGTGAACAAGA
1 AAAAAGAATGTGAAAAAGA
*
40877566 AAAAAGAGTG-GAAAAAGA
1 AAAAAGAATGTGAAAAAGA
40877584 AA
1 AA
40877586 TTAAGATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.08
Consensus pattern (19 bp):
AAAAAGAATGTGAAAAAGA
Found at i:40880505 original size:15 final size:15
Alignment explanation
Indices: 40880459--40880506 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
40880449 AAACCTACAA
*
40880459 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
40880474 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
40880488 AAACTTCATATCCAT
1 AAACTTCATATCCAT
40880503 AAAC
1 AAAC
40880507 CCACCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:40885933 original size:24 final size:25
Alignment explanation
Indices: 40885880--40885933 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
40885870 AACAAATTCT
* *
40885880 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
40885905 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
40885928 TTTTTT
1 TTTTTT
40885934 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:40888199 original size:14 final size:14
Alignment explanation
Indices: 40888180--40888207 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40888170 CTAGACCGTA
40888180 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
40888194 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
40888208 CCTTTTTTTT
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:0.14, C:0.07, G:0.07, T:0.71
Consensus pattern (14 bp):
TGCAATTTTTTTTT
Found at i:40888217 original size:23 final size:24
Alignment explanation
Indices: 40888186--40888231 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
40888176 CGTATGCAAT
*
40888186 TTTTTTTTTGCAATTTTTTTTTCC
1 TTTTTTTTCGCAATTTTTTTTTCC
* *
40888210 TTTTTTTTCGGATTTTTTTTTT
1 TTTTTTTTCGCAATTTTTTTTT
40888232 TCGAAACTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.07, C:0.09, G:0.07, T:0.78
Consensus pattern (24 bp):
TTTTTTTTCGCAATTTTTTTTTCC
Found at i:40888242 original size:15 final size:15
Alignment explanation
Indices: 40888210--40888264 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
40888200 TTTTTTTTCC
* **
40888210 TTTTTTTTCGGATTT
1 TTTTTTTTCGAAACT
40888225 TTTTTTTTCGAAACT
1 TTTTTTTTCGAAACT
40888240 TTTTTTTT---AACTT
1 TTTTTTTTCGAAAC-T
40888253 TTTTTTTTCGAA
1 TTTTTTTTCGAA
40888265 GCTACGATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 3 0.09
13 9 0.27
15 20 0.61
16 1 0.03
ACGTcount: A:0.15, C:0.09, G:0.07, T:0.69
Consensus pattern (15 bp):
TTTTTTTTCGAAACT
Found at i:40888242 original size:28 final size:28
Alignment explanation
Indices: 40888211--40888264 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
40888201 TTTTTTTCCT
* *
40888211 TTTTTTTCGGATTTTTTTTTTTCGAAAC
1 TTTTTTTCGAACTTTTTTTTTTCGAAAC
**
40888239 TTTTTTTTTAACTTTTTTTTTTCGAA
1 TTTTTTTCGAACTTTTTTTTTTCGAA
40888265 GCTACGATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.15, C:0.09, G:0.07, T:0.69
Consensus pattern (28 bp):
TTTTTTTCGAACTTTTTTTTTTCGAAAC
Found at i:40892610 original size:24 final size:25
Alignment explanation
Indices: 40892557--40892610 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
40892547 AACAAATTCT
* *
40892557 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
40892582 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
40892605 TTTTTT
1 TTTTTT
40892611 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:40894876 original size:15 final size:15
Alignment explanation
Indices: 40894858--40894886 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40894848 CTAGACCGTA
40894858 TGCAATTTTTTTTTT
1 TGCAATTTTTTTTTT
40894873 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
40894887 CGAAGCTACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (15 bp):
TGCAATTTTTTTTTT
Found at i:40900480 original size:40 final size:40
Alignment explanation
Indices: 40900436--40900607 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
40900426 GGACTAAGAT
*
40900436 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACTAAA-TCCGGGTTAAGTC
*
40900476 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
* * * *
40900516 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
* * * * *
40900556 CCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
40900595 CCGAAGGCATTTG
1 CCGAAGGCATTTG
40900608 AACGAGGAGC
Statistics
Matches: 118, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
39 34 0.29
40 81 0.69
41 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:40900521 original size:80 final size:79
Alignment explanation
Indices: 40900436--40900607 Score: 220
Period size: 79 Copynumber: 2.2 Consensus size: 79
40900426 GGACTAAGAT
*
40900436 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
40900500 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
40900516 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
40900581 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
40900595 CCGAAGGCATTTG
1 CCGAAGGCATTTG
40900608 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 38 0.48
80 38 0.48
81 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:40900625 original size:79 final size:80
Alignment explanation
Indices: 40900463--40900640 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
40900453 AGATACAAAT
* * * *
40900463 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
40900528 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
40900543 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
40900607 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
40900622 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
40900641 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:40911543 original size:28 final size:28
Alignment explanation
Indices: 40911507--40911626 Score: 161
Period size: 28 Copynumber: 4.3 Consensus size: 28
40911497 CAGTAATAGT
** *
40911507 ACAGTGTGGGCCTTAGCCTGATACAGTA
1 ACAGTGTGGGCCTTAGCCCAATACAGAA
* *
40911535 ACAATGTGGGCTTTAGCCCAATACAGAA
1 ACAGTGTGGGCCTTAGCCCAATACAGAA
* *
40911563 ACCGTGTGGGCCTTAGCCCATTACA-ATA
1 ACAGTGTGGGCCTTAGCCCAATACAGA-A
40911591 ACAGTGTGGGCCTTAGCCCAATACAGAA
1 ACAGTGTGGGCCTTAGCCCAATACAGAA
40911619 ACAGTGTG
1 ACAGTGTG
40911627 ATAATGCAAC
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
27 1 0.01
28 77 0.97
29 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (28 bp):
ACAGTGTGGGCCTTAGCCCAATACAGAA
Found at i:40911578 original size:56 final size:56
Alignment explanation
Indices: 40911507--40911626 Score: 179
Period size: 56 Copynumber: 2.1 Consensus size: 56
40911497 CAGTAATAGT
* * *
40911507 ACAGTGTGGGCCTTAGCCTGA-TACAGTAACAATGTGGGCTTTAGCCCAATACAGAA
1 ACAGTGTGGGCCTTAGCC-CATTACAATAACAATGTGGGCCTTAGCCCAATACAGAA
* *
40911563 ACCGTGTGGGCCTTAGCCCATTACAATAACAGTGTGGGCCTTAGCCCAATACAGAA
1 ACAGTGTGGGCCTTAGCCCATTACAATAACAATGTGGGCCTTAGCCCAATACAGAA
40911619 ACAGTGTG
1 ACAGTGTG
40911627 ATAATGCAAC
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 1 0.02
56 56 0.98
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (56 bp):
ACAGTGTGGGCCTTAGCCCATTACAATAACAATGTGGGCCTTAGCCCAATACAGAA
Found at i:40911751 original size:26 final size:26
Alignment explanation
Indices: 40911722--40911775 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
40911712 ACACACCAAC
*
40911722 ATCGCAGC-AGAGCTGCGAGTAATAGT
1 ATCGCAGCGA-AGCTGCCAGTAATAGT
*
40911748 ATCGTAGCGAAGCTGCCAGTAATAGT
1 ATCGCAGCGAAGCTGCCAGTAATAGT
40911774 AT
1 AT
40911776 ATGTGGCGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (26 bp):
ATCGCAGCGAAGCTGCCAGTAATAGT
Found at i:40911968 original size:27 final size:26
Alignment explanation
Indices: 40911915--40911993 Score: 88
Period size: 27 Copynumber: 3.0 Consensus size: 26
40911905 ACATAAGGCC
*
40911915 ATAATGGTCATTTAATCTCCTA-GGGGT
1 ATAATGGTCATTTTA-C-CCTATGGGGT
40911942 ATAATGGTCATTTTACCCTATGAGGGT
1 ATAATGGTCATTTTACCCTATG-GGGT
***
40911969 ATTGCGGTCATTTTACCCTATGGGG
1 ATAATGGTCATTTTACCCTATGGGG
40911994 GTATTTCAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
25 4 0.09
26 5 0.11
27 37 0.80
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (26 bp):
ATAATGGTCATTTTACCCTATGGGGT
Found at i:40911995 original size:27 final size:27
Alignment explanation
Indices: 40911947--40911998 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
40911937 GGGGTATAAT
40911947 GGTCATTTTACCCTATGAGGGTATTGC
1 GGTCATTTTACCCTATGAGGGTATTGC
*
40911974 GGTCATTTTACCCTATGGGGGTATT
1 GGTCATTTTACCCTATGAGGGTATT
40911999 TCAATCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.38
Consensus pattern (27 bp):
GGTCATTTTACCCTATGAGGGTATTGC
Found at i:40912006 original size:27 final size:27
Alignment explanation
Indices: 40911949--40912010 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
40911939 GGTATAATGG
**
40911949 TCATTTTACCCTATGAGGGTATTGCGG
1 TCATTTTACCCTATGAGGGTATTGCAA
* *
40911976 TCATTTTACCCTATGGGGGTATTTCAA
1 TCATTTTACCCTATGAGGGTATTGCAA
40912003 TCATTTTA
1 TCATTTTA
40912011 TTTGGTCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTATGAGGGTATTGCAA
Found at i:40912050 original size:27 final size:27
Alignment explanation
Indices: 40912019--40912237 Score: 196
Period size: 27 Copynumber: 8.1 Consensus size: 27
40912009 TATTTGGTCT
*
40912019 TTTTACCCTTCAAGGGTATTTCGATCA
1 TTTTACCCTTCGAGGGTATTTCGATCA
* *
40912046 TTTTACCTTTCGAGGGTATTTCAATCA
1 TTTTACCCTTCGAGGGTATTTCGATCA
* * *
40912073 TTTTACCTTTTGGGGGTATTTCTG-TCA
1 TTTTACCCTTCGAGGGTATTTC-GATCA
* ** *
40912100 TTTTACCTTTTAAGGGTATTTCGGTCA
1 TTTTACCCTTCGAGGGTATTTCGATCA
* *
40912127 TTTTACCCTTCGGGGGTATTTC-AGTTA
1 TTTTACCCTTCGAGGGTATTTCGA-TCA
40912154 TTTTACCCTAT-GAGGGTATTTC-AGTCA
1 TTTTACCCT-TCGAGGGTATTTCGA-TCA
** **
40912181 TTTTACTGTTC-AGGGGTATTTCGGCCA
1 TTTTACCCTTCGA-GGGTATTTCGATCA
* *
40912208 TTTTACCCTTCGGGGGTATTTCGATTA
1 TTTTACCCTTCGAGGGTATTTCGATCA
40912235 TTT
1 TTT
40912238 GCCCACAAAT
Statistics
Matches: 158, Mismatches: 26, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
26 3 0.02
27 154 0.97
28 1 0.01
ACGTcount: A:0.17, C:0.18, G:0.20, T:0.45
Consensus pattern (27 bp):
TTTTACCCTTCGAGGGTATTTCGATCA
Found at i:40912063 original size:67 final size:67
Alignment explanation
Indices: 40911946--40912077 Score: 178
Period size: 67 Copynumber: 2.0 Consensus size: 67
40911936 AGGGGTATAA
* * *
40911946 TGGTCATTTTACCCTATGAGGGTATTGCGGTCATTTTACCCTATGGGGGTATTTCAATCATTTTA
1 TGGTCATTTTACCCTATAAGGGTATTGCGATCATTTTACCCTATGAGGGTATTTCAATCATTTTA
40912011 TT
66 TT
* * *
40912013 TGGTCTTTTTACCCT-TCAAGGGTATTTCGATCATTTTA-CCTTTCGAGGGTATTTCAATCATTT
1 TGGTCATTTTACCCTAT-AAGGGTATTGCGATCATTTTACCCTAT-GAGGGTATTTCAATCATTT
40912076 TA
64 TA
40912078 CCTTTTGGGG
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
66 5 0.09
67 52 0.91
ACGTcount: A:0.20, C:0.17, G:0.18, T:0.45
Consensus pattern (67 bp):
TGGTCATTTTACCCTATAAGGGTATTGCGATCATTTTACCCTATGAGGGTATTTCAATCATTTTA
TT
Found at i:40912157 original size:81 final size:81
Alignment explanation
Indices: 40912019--40912237 Score: 289
Period size: 81 Copynumber: 2.7 Consensus size: 81
40912009 TATTTGGTCT
* * * * * * * *
40912019 TTTTACCCTTCAAGGGTATTTCGATCATTTTACCTTTCGAGGGTATTTCAATCATTTTACCTTTT
1 TTTTACCTTTCAAGGGTATTTCGGTCATTTTACCCTTCGGGGGTATTTCAGTTATTTTACCCTAT
* *
40912084 GGGGGTATTTCTGTCA
66 GAGGGTATTTCAGTCA
*
40912100 TTTTACCTTTTAAGGGTATTTCGGTCATTTTACCCTTCGGGGGTATTTCAGTTATTTTACCCTAT
1 TTTTACCTTTCAAGGGTATTTCGGTCATTTTACCCTTCGGGGGTATTTCAGTTATTTTACCCTAT
40912165 GAGGGTATTTCAGTCA
66 GAGGGTATTTCAGTCA
* *
40912181 TTTTA-CTGTTCAGGGGTATTTCGGCCATTTTACCCTTCGGGGGTATTTC-GATTATTT
1 TTTTACCT-TTCAAGGGTATTTCGGTCATTTTACCCTTCGGGGGTATTTCAG-TTATTT
40912238 GCCCACAAAT
Statistics
Matches: 122, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
80 3 0.02
81 119 0.98
ACGTcount: A:0.17, C:0.18, G:0.20, T:0.45
Consensus pattern (81 bp):
TTTTACCTTTCAAGGGTATTTCGGTCATTTTACCCTTCGGGGGTATTTCAGTTATTTTACCCTAT
GAGGGTATTTCAGTCA
Found at i:40915067 original size:10 final size:9
Alignment explanation
Indices: 40915042--40915066 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
40915032 TGCAATGATC
40915042 TAAAAAACA
1 TAAAAAACA
40915051 TAAAAAACA
1 TAAAAAACA
40915060 TAAAAAA
1 TAAAAAA
40915067 ATGAAGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (9 bp):
TAAAAAACA
Found at i:40920621 original size:17 final size:17
Alignment explanation
Indices: 40920594--40920650 Score: 56
Period size: 17 Copynumber: 3.7 Consensus size: 17
40920584 TTGCATGCCC
40920594 ATGTGGGCCCACAAGCCT
1 ATGT-GGCCCACAAGCCT
40920612 ATGTGG-CC-C-A---T
1 ATGTGGCCCACAAGCCT
40920623 ATG-GGCCCACAAGCCT
1 ATGTGGCCCACAAGCCT
40920639 ATGTGGCCCACA
1 ATGTGGCCCACA
40920651 CGGCCCAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 15
0.68 0.00 0.32
Matches are distributed among these distances:
10 2 0.06
11 6 0.19
12 1 0.03
13 1 0.03
14 1 0.03
15 1 0.03
16 6 0.19
17 10 0.31
18 4 0.12
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.18
Consensus pattern (17 bp):
ATGTGGCCCACAAGCCT
Found at i:40920627 original size:27 final size:27
Alignment explanation
Indices: 40920590--40920648 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
40920580 CATGTTGCAT
*
40920590 GCCCATGTGGGCCCACAAGCCTATGTG
1 GCCCATATGGGCCCACAAGCCTATGTG
40920617 GCCCATATGGGCCCACAAGCCTATGTG
1 GCCCATATGGGCCCACAAGCCTATGTG
40920644 GCCCA
1 GCCCA
40920649 CACGGCCCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.20, C:0.36, G:0.27, T:0.17
Consensus pattern (27 bp):
GCCCATATGGGCCCACAAGCCTATGTG
Found at i:40930093 original size:94 final size:94
Alignment explanation
Indices: 40929983--40930158 Score: 334
Period size: 94 Copynumber: 1.9 Consensus size: 94
40929973 GATAAAAAGG
*
40929983 GGATTTGATATATTCCTTATCAGATAAGGAAATATAATTTAATTATTATTTAAAAGAGTTTTAAA
1 GGATTTGATATATTCCTTATCAGATAAGAAAATATAATTTAATTATTATTTAAAAGAGTTTTAAA
40930048 TAAATAATAATTAAAATTCAAAATCAAAA
66 TAAATAATAATTAAAATTCAAAATCAAAA
*
40930077 GGATTTGATATATTCCTTATCAGATAAGAAAATATAATTTAATTATTATTTAAAAGAGTTTTAGA
1 GGATTTGATATATTCCTTATCAGATAAGAAAATATAATTTAATTATTATTTAAAAGAGTTTTAAA
40930142 TAAATAATAATTAAAAT
66 TAAATAATAATTAAAAT
40930159 AGAATTTAAT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 80 1.00
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.39
Consensus pattern (94 bp):
GGATTTGATATATTCCTTATCAGATAAGAAAATATAATTTAATTATTATTTAAAAGAGTTTTAAA
TAAATAATAATTAAAATTCAAAATCAAAA
Found at i:40945942 original size:12 final size:12
Alignment explanation
Indices: 40945925--40945960 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 12
40945915 TAGCTCTCTC
40945925 TTTTTTTCAATT
1 TTTTTTTCAATT
40945937 TTTTTTTCACAATT
1 TTTTTTT--CAATT
40945951 TTTTTTTCAA
1 TTTTTTTCAA
40945961 AATTTTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 10 0.45
14 12 0.55
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTTTTCAATT
Found at i:40945949 original size:14 final size:14
Alignment explanation
Indices: 40945932--40945967 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
40945922 CTCTTTTTTT
40945932 CAATTTTTTTTTCA
1 CAATTTTTTTTTCA
40945946 CAATTTTTTTTTCA
1 CAATTTTTTTTTCA
*
40945960 AAATTTTT
1 CAATTTTT
40945968 GATCGCATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.64
Consensus pattern (14 bp):
CAATTTTTTTTTCA
Found at i:40945966 original size:12 final size:12
Alignment explanation
Indices: 40945925--40945967 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
40945915 TAGCTCTCTC
*
40945925 TTTTTTTCAATT
1 TTTTTTTCAAAT
40945937 TTTTTTTCACAATT
1 TTTTTTTCA-AA-T
*
40945951 TTTTTTTCAAAA
1 TTTTTTTCAAAT
40945963 TTTTT
1 TTTTT
40945968 GATCGCATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 14 0.52
13 3 0.11
14 10 0.37
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTTTTCAAAT
Found at i:40952177 original size:89 final size:89
Alignment explanation
Indices: 40952026--40952219 Score: 388
Period size: 89 Copynumber: 2.2 Consensus size: 89
40952016 CCTTAGTTGT
40952026 AAGATTCGGTTTCTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTCAAAT
1 AAGATTCGGTTTCTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTCAAAT
40952091 TGCTCAAAACAGCAAAATTGGACC
66 TGCTCAAAACAGCAAAATTGGACC
40952115 AAGATTCGGTTTCTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTCAAAT
1 AAGATTCGGTTTCTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTCAAAT
40952180 TGCTCAAAACAGCAAAATTGGACC
66 TGCTCAAAACAGCAAAATTGGACC
40952204 AAGATTCGGTTTCTTG
1 AAGATTCGGTTTCTTG
40952220 ATTTTCTTGA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 105 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (89 bp):
AAGATTCGGTTTCTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTCAAAT
TGCTCAAAACAGCAAAATTGGACC
Found at i:40956930 original size:58 final size:58
Alignment explanation
Indices: 40956840--40957104 Score: 521
Period size: 58 Copynumber: 4.6 Consensus size: 58
40956830 AAAGTCATGC
40956840 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
40956898 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
40956956 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
40957014 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
*
40957072 ATTATGTAACTTTCATGTTAGTTAAATTTGCAT
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
40957105 TTCAAAACCA
Statistics
Matches: 206, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 206 1.00
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (58 bp):
ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
Found at i:40958517 original size:17 final size:18
Alignment explanation
Indices: 40958495--40958535 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
40958485 TATCAAGTTG
40958495 AAAAAAAAA-TTCGTGAA
1 AAAAAAAAATTTCGTGAA
40958512 AAAAAAAAATTTCGTGAA
1 AAAAAAAAATTTCGTGAA
40958530 AAAAAA
1 AAAAAA
40958536 GAAGAAGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.68, C:0.05, G:0.10, T:0.17
Consensus pattern (18 bp):
AAAAAAAAATTTCGTGAA
Found at i:40960480 original size:58 final size:58
Alignment explanation
Indices: 40960390--40960712 Score: 637
Period size: 58 Copynumber: 5.6 Consensus size: 58
40960380 AAAGTCATGC
40960390 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
40960448 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
40960506 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
40960564 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
40960622 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
*
40960680 ATTATGTAACTTTCATGTTAGTTAAATTTGCAT
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
40960713 TTCAAAACCA
Statistics
Matches: 264, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 264 1.00
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.45
Consensus pattern (58 bp):
ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
Found at i:40963199 original size:45 final size:45
Alignment explanation
Indices: 40963148--40963335 Score: 306
Period size: 45 Copynumber: 4.2 Consensus size: 45
40963138 TCGGCCATGG
* * *
40963148 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGG-CTAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTC-AAA
*
40963193 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
40963238 TGCTTCCTCAAATTCTTCCATGAATTATGCATAATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
40963283 TGCTTCCTCAAATTCTCCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
40963328 TGCTTCCT
1 TGCTTCCT
40963336 TAATTTCATG
Statistics
Matches: 134, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 133 0.99
46 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:40968960 original size:56 final size:56
Alignment explanation
Indices: 40968876--40968993 Score: 218
Period size: 56 Copynumber: 2.1 Consensus size: 56
40968866 TTCCAGACTC
*
40968876 TTTTTTTTTGCGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTAGGAAATT
1 TTTTTTTTTGAGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTAGGAAATT
*
40968932 TTTTTTTTTGAGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTAGGCAATT
1 TTTTTTTTTGAGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTAGGAAATT
40968988 TTTTTT
1 TTTTTT
40968994 ATTTTTTTTA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 60 1.00
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (56 bp):
TTTTTTTTTGAGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTAGGAAATT
Found at i:40969614 original size:45 final size:45
Alignment explanation
Indices: 40969565--40969672 Score: 162
Period size: 45 Copynumber: 2.4 Consensus size: 45
40969555 TCGGCCATGG
* * *
40969565 TGCTTCCTCAATTTGTTTCATAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGCCAAA
* * *
40969610 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGCCAAA
40969655 TGCTTCCTCAAATTCTTC
1 TGCTTCCTCAAATTCTTC
40969673 AAAAGGGTAG
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGCCAAA
Found at i:40969769 original size:45 final size:45
Alignment explanation
Indices: 40969720--40969824 Score: 147
Period size: 45 Copynumber: 2.3 Consensus size: 45
40969710 TCGGCCATGG
* **
40969720 TGCTTCCTCAATTTGTTTCATAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAATTTCTCCCATAAATTATGCATGATGTTGGCCAAA
* * *
40969765 TGCTTCCTCAAATTCTCCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAATTTCTCCCATAAATTATGCATGATGTTGGCCAAA
*
40969810 TGCTTCCTTAATTTC
1 TGCTTCCTCAATTTC
40969825 ATGCCGTTCA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (45 bp):
TGCTTCCTCAATTTCTCCCATAAATTATGCATGATGTTGGCCAAA
Found at i:40969799 original size:155 final size:155
Alignment explanation
Indices: 40969517--40969817 Score: 584
Period size: 155 Copynumber: 1.9 Consensus size: 155
40969507 ATAGGCAAAA
40969517 CAAAAGGGTAGCCGAATGGGCAAAATTGGAAGCCAAATTCGGCCATGGTGCTTCCTCAATTTGTT
1 CAAAAGGGTAGCCGAATGGGCAAAATTGGAAGCCAAATTCGGCCATGGTGCTTCCTCAATTTGTT
* *
40969582 TCATAAATTATGCATGATGTTGGCCAAATGCTTCCTTAAATTCTTCCATGAATTATGCATGATGT
66 TCATAAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTCCCATGAATTATGCATGATGT
40969647 TGGTCAAATGCTTCCTCAAATTCTT
131 TGGTCAAATGCTTCCTCAAATTCTT
40969672 CAAAAGGGTAGCCGAATGGGCAAAATTGGAAGCCAAATTCGGCCATGGTGCTTCCTCAATTTGTT
1 CAAAAGGGTAGCCGAATGGGCAAAATTGGAAGCCAAATTCGGCCATGGTGCTTCCTCAATTTGTT
40969737 TCATAAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTCCCATGAATTATGCATGATGT
66 TCATAAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTCCCATGAATTATGCATGATGT
40969802 TGGTCAAATGCTTCCT
131 TGGTCAAATGCTTCCT
40969818 TAATTTCATG
Statistics
Matches: 144, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
155 144 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (155 bp):
CAAAAGGGTAGCCGAATGGGCAAAATTGGAAGCCAAATTCGGCCATGGTGCTTCCTCAATTTGTT
TCATAAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTCCCATGAATTATGCATGATGT
TGGTCAAATGCTTCCTCAAATTCTT
Found at i:40970464 original size:30 final size:30
Alignment explanation
Indices: 40970430--40970526 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
40970420 AGCTCACTCC
40970430 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
40970460 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
40970490 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
40970520 TAGCTCA
1 TAGCTCA
40970527 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:40973904 original size:18 final size:18
Alignment explanation
Indices: 40973881--40973916 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
40973871 AGATTAAAAA
40973881 AATCAGA-TCACAAAGAAT
1 AATCAGATTCA-AAAGAAT
40973899 AATCAGATTCAAAAGAAT
1 AATCAGATTCAAAAGAAT
40973917 TCTAGGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.56, C:0.14, G:0.11, T:0.19
Consensus pattern (18 bp):
AATCAGATTCAAAAGAAT
Found at i:40978923 original size:23 final size:23
Alignment explanation
Indices: 40978879--40978923 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
40978869 TGAAATCGAC
40978879 ACAAGCAGAAAATTAAAAAGATTG
1 ACAAGCAGAAAA-TAAAAAGATTG
40978903 ACAAGCAAGAAAA-AAAAAGAT
1 ACAAGC-AGAAAATAAAAAGAT
40978924 AAAGTCCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 8 0.40
24 6 0.30
25 6 0.30
ACGTcount: A:0.64, C:0.09, G:0.16, T:0.11
Consensus pattern (23 bp):
ACAAGCAGAAAATAAAAAGATTG
Found at i:40988221 original size:16 final size:16
Alignment explanation
Indices: 40988193--40988225 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
40988183 TCATAGTAGG
40988193 TTTGATATTAAAAAAA
1 TTTGATATTAAAAAAA
40988209 TTTGA-ATTAAAAAAA
1 TTTGATATTAAAAAAA
40988224 TT
1 TT
40988226 CTATCAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (16 bp):
TTTGATATTAAAAAAA
Found at i:41007392 original size:29 final size:27
Alignment explanation
Indices: 41007359--41007413 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
41007349 GTGATTAAAT
41007359 AAAATCGACA-CAAGCAGAATTTAAAAGAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAA
*
41007388 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
41007414 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.33
28 2 0.08
29 10 0.42
30 4 0.17
ACGTcount: A:0.60, C:0.11, G:0.15, T:0.15
Consensus pattern (27 bp):
AAAATCGACAGCAAGAAATTAAAAGAA
Found at i:41012027 original size:19 final size:17
Alignment explanation
Indices: 41011991--41012029 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
41011981 TCAATTGCTG
41011991 ATTAGTTAAATAAATTA
1 ATTAGTTAAATAAATTA
*
41012008 ATTAGCTTAAGATTAATTA
1 ATTAG-TTAA-ATAAATTA
41012027 ATT
1 ATT
41012030 TAATAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 10 0.53
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (17 bp):
ATTAGTTAAATAAATTA
Found at i:41014312 original size:18 final size:18
Alignment explanation
Indices: 41014275--41014313 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
41014265 AACAAAAAAG
* *
41014275 AAGAAAAAGAAATTGTAA
1 AAGAAAAAGAAATCGAAA
41014293 AAGAAAAAGAAATCGAAA
1 AAGAAAAAGAAATCGAAA
41014311 AAG
1 AAG
41014314 TGAGAGAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.69, C:0.03, G:0.18, T:0.10
Consensus pattern (18 bp):
AAGAAAAAGAAATCGAAA
Found at i:41019823 original size:13 final size:12
Alignment explanation
Indices: 41019805--41019848 Score: 61
Period size: 13 Copynumber: 3.5 Consensus size: 12
41019795 TTGTAGATTC
41019805 AAAAAAAAATCGA
1 AAAAAAAAAT-GA
41019818 AAAAAAAAATGGA
1 AAAAAAAAAT-GA
*
41019831 AAAAAAAATTGA
1 AAAAAAAAATGA
41019843 AAAAAA
1 AAAAAA
41019849 TAATTGCATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 8 0.28
13 21 0.72
ACGTcount: A:0.80, C:0.02, G:0.09, T:0.09
Consensus pattern (12 bp):
AAAAAAAAATGA
Found at i:41019853 original size:13 final size:12
Alignment explanation
Indices: 41019805--41019854 Score: 64
Period size: 12 Copynumber: 4.0 Consensus size: 12
41019795 TTGTAGATTC
*
41019805 AAAAAAAAATCG
1 AAAAAAAAATTG
*
41019817 AAAAAAAAAATGG
1 -AAAAAAAAATTG
41019830 AAAAAAAAATTG
1 AAAAAAAAATTG
41019842 AAAAAAATAATTG
1 AAAAAAA-AATTG
41019855 CATACGGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
12 18 0.53
13 16 0.47
ACGTcount: A:0.74, C:0.02, G:0.10, T:0.14
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:41026479 original size:13 final size:12
Alignment explanation
Indices: 41026461--41026521 Score: 104
Period size: 12 Copynumber: 5.0 Consensus size: 12
41026451 TTGTAGATTC
41026461 AAAAAAAAATTG
1 AAAAAAAAATTG
*
41026473 AAAAAAAAATCG
1 AAAAAAAAATTG
41026485 AAAAAAAAATTG
1 AAAAAAAAATTG
41026497 AAAAAAAAATTTG
1 AAAAAAAAA-TTG
41026510 AAAAAAAAATTG
1 AAAAAAAAATTG
41026522 CATACGGTCT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
12 34 0.74
13 12 0.26
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:41038142 original size:22 final size:22
Alignment explanation
Indices: 41038104--41038158 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
41038094 GAATATTTAC
*
41038104 ATAAAAATTAAACTAAGTAAAA
1 ATAAAAAATAAACTAAGTAAAA
41038126 ATAAATAAATAAA-TAAGTAAAA
1 ATAAA-AAATAAACTAAGTAAAA
41038148 AT-AAAAATAAA
1 ATAAAAAATAAA
41038159 ACTTTACAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 7 0.23
21 2 0.06
22 16 0.52
23 6 0.19
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.22
Consensus pattern (22 bp):
ATAAAAAATAAACTAAGTAAAA
Found at i:41040395 original size:56 final size:55
Alignment explanation
Indices: 41040279--41040396 Score: 150
Period size: 55 Copynumber: 2.1 Consensus size: 55
41040269 TGCATGCTTT
* * * * *
41040279 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTAATTTAATTCATGTTTTGCTGCA
*
41040333 CTTTAAATGCCGTTCCATACATGG-GAACATCTAATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTAATTTAATTCATGT-TTTGCTGCA
41040389 CATTAAAT
1 CATTAAAT
41040397 CAGCAAGCAG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
54 3 0.06
55 27 0.50
56 24 0.44
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTAATTTAATTCATGTTTTGCTGCA
Found at i:41044904 original size:15 final size:15
Alignment explanation
Indices: 41044884--41044914 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
41044874 CCAACCTTCA
41044884 AATTTTACCTCAATT
1 AATTTTACCTCAATT
41044899 AATTTTACCTCAATT
1 AATTTTACCTCAATT
41044914 A
1 A
41044915 TACATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTTACCTCAATT
Found at i:41047174 original size:11 final size:11
Alignment explanation
Indices: 41047158--41047184 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
41047148 TAGAAATTAG
41047158 TTTGTGAAACT
1 TTTGTGAAACT
41047169 TTTGTGAAACT
1 TTTGTGAAACT
41047180 TTTGT
1 TTTGT
41047185 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:41055941 original size:20 final size:20
Alignment explanation
Indices: 41055916--41055970 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
41055906 ACGAGTTAAA
* *
41055916 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
41055936 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
*
41055956 TTGAGCTCAAATGAG
1 TTGAGCTCGAATGAG
41055971 TTGAACCACA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:41057432 original size:78 final size:78
Alignment explanation
Indices: 41057303--41057451 Score: 271
Period size: 78 Copynumber: 1.9 Consensus size: 78
41057293 GATTGTGCGC
* *
41057303 GGACCAAGATCGAGTTGCCAAGTCACGGGAAACTCCTACGAAAATCCTAAACAATCAGATCTGAA
1 GGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAACCCTAAACAATCAGATCTGAA
41057368 ACGAAACAGGCGT
66 ACGAAACAGGCGT
*
41057381 GGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAACCCTAAACAATTAGATCTGAA
1 GGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAACCCTAAACAATCAGATCTGAA
41057446 ACGAAA
66 ACGAAA
41057452 TAGAAAATTA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 68 1.00
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.15
Consensus pattern (78 bp):
GGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAACCCTAAACAATCAGATCTGAA
ACGAAACAGGCGT
Found at i:41066580 original size:23 final size:23
Alignment explanation
Indices: 41066550--41066615 Score: 114
Period size: 23 Copynumber: 2.9 Consensus size: 23
41066540 CTTTTTGAAC
*
41066550 CATTTCCATTTCGAACCAAATTA
1 CATTTCCATTTCGTACCAAATTA
41066573 CATTTCCATTTCGTACCAAATTA
1 CATTTCCATTTCGTACCAAATTA
*
41066596 CATTACCATTTCGTACCAAA
1 CATTTCCATTTCGTACCAAA
41066616 CCCAAACCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (23 bp):
CATTTCCATTTCGTACCAAATTA
Found at i:41066997 original size:21 final size:22
Alignment explanation
Indices: 41066972--41067030 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
41066962 AATATTCATA
41066972 CGAAATTAAAAAAAAGTGAATT
1 CGAAATTAAAAAAAAGTGAATT
**
41066994 -GAAATTTTAAAAAA---AATT
1 CGAAATTAAAAAAAAGTGAATT
41067012 CGAGAATTAAAAAAAAGTG
1 CGA-AATTAAAAAAAAGTG
41067031 TTTCGCGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 9
0.68 0.10 0.22
Matches are distributed among these distances:
18 4 0.14
19 2 0.07
20 10 0.36
21 12 0.43
ACGTcount: A:0.59, C:0.03, G:0.14, T:0.24
Consensus pattern (22 bp):
CGAAATTAAAAAAAAGTGAATT
Found at i:41071810 original size:23 final size:22
Alignment explanation
Indices: 41071759--41071810 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
41071749 CCTCGTCTTT
*
41071759 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
41071781 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
41071804 TTCTTTT
1 TTCTTTT
41071811 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:41072731 original size:55 final size:55
Alignment explanation
Indices: 41072665--41072779 Score: 230
Period size: 55 Copynumber: 2.1 Consensus size: 55
41072655 AAAAGAAAAA
41072665 ATCAAATTCTCAATGAGGTAGAATTCAATCTTGTGAGTTCTTTATCAGAGTTTAT
1 ATCAAATTCTCAATGAGGTAGAATTCAATCTTGTGAGTTCTTTATCAGAGTTTAT
41072720 ATCAAATTCTCAATGAGGTAGAATTCAATCTTGTGAGTTCTTTATCAGAGTTTAT
1 ATCAAATTCTCAATGAGGTAGAATTCAATCTTGTGAGTTCTTTATCAGAGTTTAT
41072775 ATCAA
1 ATCAA
41072780 CCAATTAGAG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 60 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (55 bp):
ATCAAATTCTCAATGAGGTAGAATTCAATCTTGTGAGTTCTTTATCAGAGTTTAT
Found at i:41085146 original size:19 final size:19
Alignment explanation
Indices: 41085122--41085202 Score: 135
Period size: 19 Copynumber: 4.2 Consensus size: 19
41085112 AATCTTTAAG
41085122 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
41085141 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
41085160 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
41085179 GACATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
41085200 GAT
1 GAT
41085203 CTTGTAATCT
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
19 50 0.86
21 8 0.14
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:41085214 original size:22 final size:21
Alignment explanation
Indices: 41085125--41085219 Score: 94
Period size: 19 Copynumber: 4.8 Consensus size: 21
41085115 CTTTAAGGAT
*
41085125 ATGCAATCTT--AGATATGAT
1 ATGCAATCTTGAAGATATGAC
*
41085144 ATGCAATCTT--AGATATGAT
1 ATGCAATCTTGAAGATATGAC
41085163 ATGCAATCTT--AGATATGAC
1 ATGCAATCTTGAAGATATGAC
41085182 ATGCAATCTTGAAGATATGATC
1 ATGCAATCTTGAAGATATGA-C
* * *
41085204 TTGTAATCTTGGAGAT
1 ATGCAATCTTGAAGAT
41085220 TTAATTTGTA
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
19 47 0.68
21 8 0.12
22 14 0.20
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.36
Consensus pattern (21 bp):
ATGCAATCTTGAAGATATGAC
Done.