Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 124 of 343
Found at i:41470894 original size:54 final size:55
Alignment explanation
Indices: 41470776--41470895 Score: 215
Period size: 54 Copynumber: 2.2 Consensus size: 55
41470766 ATCTTATTAA
41470776 TATTATTATTTGGTTTTGGGTTGTAATAAGGCCATTTTTAATTATTTTTCTGGGAT
1 TATT-TTATTTGGTTTTGGGTTGTAATAAGGCCATTTTTAATTATTTTTCTGGGAT
*
41470832 TATATTATTTGGTTTTGGGTTGTAATAAGGCCA-TTTTAATTATTTTTCTGGGAT
1 TATTTTATTTGGTTTTGGGTTGTAATAAGGCCATTTTTAATTATTTTTCTGGGAT
41470886 TATTTTATTT
1 TATTTTATTT
41470896 TATACCCTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
54 30 0.48
55 29 0.47
56 3 0.05
ACGTcount: A:0.22, C:0.05, G:0.18, T:0.55
Consensus pattern (55 bp):
TATTTTATTTGGTTTTGGGTTGTAATAAGGCCATTTTTAATTATTTTTCTGGGAT
Found at i:41473888 original size:88 final size:92
Alignment explanation
Indices: 41473778--41473944 Score: 263
Period size: 88 Copynumber: 1.9 Consensus size: 92
41473768 CCCCCATAAG
* *
41473778 CGAACTCGAACTCAACTCAACGAGCTC-AGGCGTTCGCATCCATAAGTGAACTC-GACTCAACTC
1 CGAACTCGAACTCAACTCAACGAGCTCGA-ACATTCGCATCCATAAGTGAACTCGGACTCAACTC
41473841 AACGA-TTC-GATGCCTATTACATCTCA
65 AACGAGTTCGGATGCCTATTACATCTCA
*
41473867 CGAACTCG-ACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGAACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
41473931 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
41473945 TCAATCATCC
Statistics
Matches: 71, Mismatches: 3, Indels: 6
0.89 0.04 0.08
Matches are distributed among these distances:
88 39 0.55
89 24 0.34
90 3 0.04
91 5 0.07
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.22
Consensus pattern (92 bp):
CGAACTCGAACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTATTACATCTCA
Found at i:41473939 original size:46 final size:46
Alignment explanation
Indices: 41473771--41473939 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
41473761 ATGTAACCCC
* * *
41473771 CCATAAGCGAACTCGAACTCAACTCAACGAGCTC-AGGCGTTCGCAT
1 CCATAAGCGAACTCG-ACTCAACTCAACGAGTTCGAGACATTCGCAT
* * *
41473817 CCATAAGTGAACTCGACTCAACTCAACGA-TTCGATGCCTATT-ACAT
1 CCATAAGCGAACTCGACTCAACTCAACGAGTTCGA-GAC-ATTCGCAT
*
41473863 -C-TCA-CGAACTCGACTCAACTCAACGAGTTCGA-ACATTCGCAT
1 CCATAAGCGAACTCGACTCAACTCAACGAGTTCGAGACATTCGCAT
*
41473905 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
1 CCATAAGCGAACTC-GACTCAACTCAACGAGTTCG
41473940 GATGCTCAAT
Statistics
Matches: 103, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
41 3 0.03
42 4 0.04
43 22 0.21
44 11 0.11
45 22 0.21
46 39 0.38
47 2 0.02
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGACTCAACTCAACGAGTTCGAGACATTCGCAT
Found at i:41473960 original size:46 final size:45
Alignment explanation
Indices: 41473774--41473960 Score: 122
Period size: 46 Copynumber: 4.2 Consensus size: 45
41473764 TAACCCCCCA
* * * * *
41473774 TAAGCGAACTCGAACTCAACTCAACGAGCTCAGG-CGTTC-GCATCC
1 TAAGTGAACTCG-ACTCAACTCAACGAGTTC-GGATGCTCATCATCC
41473819 ATAAGTGAACTCGACTCAACTCAACGA-TTC-GATGC-CTATTACAT-C
1 -TAAGTGAACTCGACTCAACTCAACGAGTTCGGATGCTC-A-T-CATCC
* * * *** *
41473864 TCA-CGAACTCGACTCAACTCAACGAGTTCGAACATTC-GCATCC
1 TAAGTGAACTCGACTCAACTCAACGAGTTCGGATGCTCATCATCC
41473907 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAATCATCC
1 -TAAGTGAACTC-GACTCAACTCAACGAGTTCGGATGCTC-ATCATCC
41473955 T-AGTGA
1 TAAGTGA
41473961 CATGTCACTT
Statistics
Matches: 108, Mismatches: 19, Indels: 28
0.70 0.12 0.18
Matches are distributed among these distances:
42 5 0.05
43 23 0.21
44 9 0.08
45 22 0.20
46 43 0.40
47 1 0.01
48 5 0.05
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.22
Consensus pattern (45 bp):
TAAGTGAACTCGACTCAACTCAACGAGTTCGGATGCTCATCATCC
Found at i:41475631 original size:27 final size:27
Alignment explanation
Indices: 41475595--41476019 Score: 589
Period size: 27 Copynumber: 15.7 Consensus size: 27
41475585 TACTGAAATG
* * *
41475595 CCCTCAATTTGTAAAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* * *
41475622 CCCACGATTTACAAAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
41475649 CCCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
** * *
41475676 CCCTTAATTTACAGAATTACCATCTTA
1 CCCTCGATTTATAGAATTACCATTTTA
41475703 CCCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
41475730 CCCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
** * *
41475757 CCCTTAATTTACAGAATTACCATCTTA
1 CCCTCGATTTATAGAATTACCATTTTA
41475784 CCCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
41475811 CCCTCGATTTATAGAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
41475838 CCCTCGATTTACAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* * *
41475865 CCCTCGATTTACAGAGTTACTATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* *
41475892 CCCTCAATTTATAAAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
41475919 CCCTCGATTTATAGAATTATCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
41475946 CCCTCGATTTATAGAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* ***
41475973 CCCTCGATTTATAAAATTATTGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* *
41476000 CCCTCGATTTACAAAATTAC
1 CCCTCGATTTATAGAATTAC
41476020 TGAAATACCT
Statistics
Matches: 355, Mismatches: 43, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 355 1.00
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.40
Consensus pattern (27 bp):
CCCTCGATTTATAGAATTACCATTTTA
Found at i:41476028 original size:27 final size:27
Alignment explanation
Indices: 41475890--41476084 Score: 108
Period size: 27 Copynumber: 7.2 Consensus size: 27
41475880 GTTACTATTT
* * **
41475890 TACCCTCAATTTATAAAATTAC-CATTT
1 TACCCTCGATTTATAAAATTACTGA-AA
* * **
41475917 TACCCTCGATTTATAGAATTA-TCATTT
1 TACCCTCGATTTATAAAATTACTGA-AA
* * ***
41475944 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAAAATTACTGAAA
* ***
41475971 TACCCTCGATTTATAAAATTATTGTTT
1 TACCCTCGATTTATAAAATTACTGAAA
*
41475998 TACCCTCGATTTACAAAATTACTGAAA
1 TACCCTCGATTTATAAAATTACTGAAA
* * * * **
41476025 TACCTTTGGTTTACAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTACTGAAA
* *
41476052 CACCCTCGA-TCAGTAAAATTACTGAAA
1 TACCCTCGATTTA-TAAAATTACTGAAA
41476079 TACCCT
1 TACCCT
41476085 TGTAAGGTAG
Statistics
Matches: 138, Mismatches: 27, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
26 2 0.01
27 136 0.99
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (27 bp):
TACCCTCGATTTATAAAATTACTGAAA
Found at i:41476098 original size:27 final size:27
Alignment explanation
Indices: 41476068--41476308 Score: 257
Period size: 27 Copynumber: 9.2 Consensus size: 27
41476058 CGATCAGTAA
* *
41476068 AATTACTGAAATACCCTTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
41476095 AATTACTGAAATAACCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
**
41476122 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
41476149 AATTACTAAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
41476176 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
41476203 AAATACCGAAATACCCCTGTA--G--G
1 AATTACTGAAATACCCCTGTAGGGTAG
*
41476226 -A-TA--GAATTACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
41476249 AAATACCGAAATACCCCTGTAGGATAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * * *
41476276 AATTA-TCGAGATACCCTTGTGGGGTAA
1 AATTACT-GAAATACCCCTGTAGGGTAG
41476303 AATTAC
1 AATTAC
41476309 CATTTTGCCC
Statistics
Matches: 182, Mismatches: 22, Indels: 19
0.82 0.10 0.09
Matches are distributed among these distances:
19 13 0.07
21 3 0.02
22 1 0.01
23 2 0.01
24 1 0.01
25 3 0.02
27 159 0.87
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.25
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:41476099 original size:54 final size:54
Alignment explanation
Indices: 41476041--41476310 Score: 192
Period size: 54 Copynumber: 5.1 Consensus size: 54
41476031 TGGTTTACAA
* * * *
41476041 AATTACCAAAACACCCTCGATCA-GTAAAATTACTGAAATACCCTTGTAAGGTAG
1 AATTACCAAAATACCCTCGAT-AGGTAGAATTACTGAAATACCCCTGTAGGGTAG
** **
41476095 AATTACTGAAATAACCCT-G-TAGGGTAGAATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCAAAAT-ACCCTCGATA-GGTAGAATTACTGAAATACCCCTGTAGGGTAG
* *
41476149 AATTACTAAAATACCC-CTATAGGGTAGAATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCAAAATACCCTCGATA-GGTAGAATTACTGAAATACCCCTGTAGGGTAG
* * * *
41476203 AAATACCGAAATACCC-C--T--GTAGGA-TA--GAATTACCCCTGTAGGGTAG
1 AATTACCAAAATACCCTCGATAGGTAGAATTACTGAAATACCCCTGTAGGGTAG
* * * * * *
41476249 AAATACCGAAATACCC-CTG-TAGGATAGAATTA-TCGAGATACCCTTGTGGGGTAA
1 AATTACCAAAATACCCTC-GATAGG-TAGAATTACT-GAAATACCCCTGTAGGGTAG
41476303 AATTACCA
1 AATTACCA
41476311 TTTTGCCCCT
Statistics
Matches: 178, Mismatches: 25, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
46 36 0.20
48 3 0.02
49 5 0.03
50 1 0.01
51 4 0.02
52 4 0.02
53 5 0.03
54 115 0.65
55 5 0.03
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (54 bp):
AATTACCAAAATACCCTCGATAGGTAGAATTACTGAAATACCCCTGTAGGGTAG
Found at i:41476207 original size:19 final size:19
Alignment explanation
Indices: 41476183--41476255 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
41476173 TAGAATTACT
41476183 GAAATACCCCTGTAGGGTA
1 GAAATACCCCTGTAGGGTA
*
41476202 GAAATACCGAAATACCCCTGTAGGATA
1 GAAATA-C------CCC-TGTAGGGTA
*
41476229 GAATTACCCCTGTAGGGTA
1 GAAATACCCCTGTAGGGTA
41476248 GAAATACC
1 GAAATACC
41476256 GAAATACCCC
Statistics
Matches: 42, Mismatches: 4, Indels: 16
0.68 0.06 0.26
Matches are distributed among these distances:
19 21 0.50
20 4 0.10
26 4 0.10
27 13 0.31
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.21
Consensus pattern (19 bp):
GAAATACCCCTGTAGGGTA
Found at i:41476238 original size:46 final size:46
Alignment explanation
Indices: 41476187--41476280 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
41476177 ATTACTGAAA
41476187 TACCCCTGTAGGGTAGAAATACCGAAATACCCCTGTAGGATAGAAT
1 TACCCCTGTAGGGTAGAAATACCGAAATACCCCTGTAGGATAGAAT
41476233 TACCCCTGTAGGGTAGAAATACCGAAATACCCCTGTAGGATAGAAT
1 TACCCCTGTAGGGTAGAAATACCGAAATACCCCTGTAGGATAGAAT
41476279 TA
1 TA
41476281 TCGAGATACC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.22
Consensus pattern (46 bp):
TACCCCTGTAGGGTAGAAATACCGAAATACCCCTGTAGGATAGAAT
Found at i:41476260 original size:73 final size:73
Alignment explanation
Indices: 41476155--41476309 Score: 204
Period size: 73 Copynumber: 2.1 Consensus size: 73
41476145 GTAGAATTAC
* * *
41476155 TAAAA-TACCCCTATAGGGTAGAATTACTGAAATACCCCTGTAGGGTAGAAATACCGAAATACCC
1 TAAAATTACCCCTATAGGGTAGAAATACCGAAATACCCCTGTAGGATAGAAATACCGAAATACCC
41476219 CTGTAGGA
66 CTGTAGGA
* * * * *
41476227 TAGAATTACCCCTGTAGGGTAGAAATACCGAAATACCCCTGTAGGATAGAATTATCGAGATACCC
1 TAAAATTACCCCTATAGGGTAGAAATACCGAAATACCCCTGTAGGATAGAAATACCGAAATACCC
* * *
41476292 TTGTGGGG
66 CTGTAGGA
41476300 TAAAATTACC
1 TAAAATTACC
41476310 ATTTTGCCCC
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
72 4 0.06
73 66 0.94
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (73 bp):
TAAAATTACCCCTATAGGGTAGAAATACCGAAATACCCCTGTAGGATAGAAATACCGAAATACCC
CTGTAGGA
Found at i:41476613 original size:24 final size:25
Alignment explanation
Indices: 41476512--41476606 Score: 100
Period size: 25 Copynumber: 3.8 Consensus size: 25
41476502 AGGAAGTGCT
* * * *
41476512 AAAAGGGCTATGCCCTAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
* * * * * *
41476537 AAAATGACTTTGCTCTAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
41476562 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
41476587 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
41476607 ATTAAAAGAG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 60 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:41476619 original size:24 final size:24
Alignment explanation
Indices: 41476562--41476633 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 24
41476552 TAGTTTACCG
41476562 AAAAG-GGCTTTGCCCCAGTTTATC
1 AAAAGAGGCTTTGCCCCAG-TTATC
*
41476586 AAAA-AGGGCTTTGCCCCAGTTATT
1 AAAAGA-GGCTTTGCCCCAGTTATC
**
41476610 AAAAGAGGCTAGGCCTCCAGTTAT
1 AAAAGAGGCTTTGCC-CCAGTTAT
41476634 ATGATAAAGC
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 19 0.46
25 22 0.54
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (24 bp):
AAAAGAGGCTTTGCCCCAGTTATC
Found at i:41476910 original size:29 final size:29
Alignment explanation
Indices: 41476827--41476910 Score: 75
Period size: 29 Copynumber: 2.9 Consensus size: 29
41476817 CATTTACAGT
* *
41476827 AAAA-GCTTCGGCCCAGTGATATGATTTATG
1 AAAAGGCTTCGGCCCAGT-ATATG-TTAACG
* *
41476857 AAAAGGCTCCGGCCTAGTA-ACTGTTAAACG
1 AAAAGGCTTCGGCCCAGTATA-TGTT-AACG
41476887 -AAAGGCTTCGGCCCAGTATATGTT
1 AAAAGGCTTCGGCCCAGTATATGTT
41476911 GAGAATGAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
29 23 0.52
30 10 0.23
31 11 0.25
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (29 bp):
AAAAGGCTTCGGCCCAGTATATGTTAACG
Found at i:41494402 original size:55 final size:54
Alignment explanation
Indices: 41494261--41494457 Score: 236
Period size: 54 Copynumber: 3.6 Consensus size: 54
41494251 TTGGTAAGAT
* * *
41494261 AAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
* * * * *
41494315 AAGGAAATCATGTAAGTCCATGTCAAGACATGGCATTGATGAGTTACTATAAGGTA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTT-CTATAAGG-C
* * * *
41494371 AAGG-TCCCATGTAAGACCAGGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
* *
41494423 AAGGATACCATATAAGACCATGTCAAGACATGGCA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCA
41494458 ATGGTAAGTT
Statistics
Matches: 120, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
52 4 0.03
53 31 0.26
54 41 0.34
55 40 0.33
56 4 0.03
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
Found at i:41496620 original size:16 final size:15
Alignment explanation
Indices: 41496599--41496628 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
41496589 TTTCAATAGC
41496599 ATCACATAACATTTTT
1 ATCACATAAC-TTTTT
41496615 ATCACATAACTTTT
1 ATCACATAACTTTT
41496629 AGTCAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.43
Consensus pattern (15 bp):
ATCACATAACTTTTT
Found at i:41496853 original size:42 final size:42
Alignment explanation
Indices: 41496772--41496886 Score: 169
Period size: 42 Copynumber: 2.8 Consensus size: 42
41496762 GGGCACAGAA
* * *
41496772 CCTGCTAGGCAAT-AGGCCTGACATAATACACTGGAATAAAG
1 CCTGCTAGGCAATAAAGCCCGATATAATACACTGGAATAAAG
*
41496813 CCTGCTAGGCAATAAAGCCCGATATAATACACTGGCATAAAG
1 CCTGCTAGGCAATAAAGCCCGATATAATACACTGGAATAAAG
* *
41496855 CCTCCTAGGCAATAAAGCCCGATTTAATACAC
1 CCTGCTAGGCAATAAAGCCCGATATAATACAC
41496887 CAACACAAGT
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
41 13 0.19
42 54 0.81
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (42 bp):
CCTGCTAGGCAATAAAGCCCGATATAATACACTGGAATAAAG
Found at i:41501050 original size:50 final size:50
Alignment explanation
Indices: 41500938--41501070 Score: 160
Period size: 50 Copynumber: 2.7 Consensus size: 50
41500928 CTGGTATGCA
* * ** *
41500938 TAGTAGCCTGCACTTAGTACTACACATGCGACC-AATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCCGATACACG
* * *
41500987 TAGTAGCTTGCACTTAGTAGTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCCGATACACG
* * *
41501037 TAGTAGCCCGCACTTAGTACTGCACACGTAACCT
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCT
41501071 CACAATAGAT
Statistics
Matches: 70, Mismatches: 13, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
49 29 0.41
50 41 0.59
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCCGATACACG
Found at i:41506390 original size:10 final size:11
Alignment explanation
Indices: 41506375--41506420 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
41506365 ATTTTGATAT
*
41506375 ACATGATTTG-
1 ACATGATATGC
41506385 ACATGATATGC
1 ACATGATATGC
41506396 ACATGATATG-
1 ACATGATATGC
*
41506406 -TATGATATGC
1 ACATGATATGC
41506416 ACATG
1 ACATG
41506421 TTATATTCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
9 8 0.27
10 9 0.30
11 13 0.43
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.33
Consensus pattern (11 bp):
ACATGATATGC
Found at i:41506401 original size:11 final size:10
Alignment explanation
Indices: 41506369--41506420 Score: 54
Period size: 9 Copynumber: 5.2 Consensus size: 10
41506359 CATGAGATTT
41506369 TGATAT-ACA
1 TGATATGACA
*
41506378 TGATTTGACA
1 TGATATGACA
41506388 TGATATGCACA
1 TGATATG-ACA
*
41506399 TGATATG-TA
1 TGATATGACA
41506408 TGATATGCACA
1 TGATATG-ACA
41506419 TG
1 TG
41506421 TTATATTCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 13 0.37
10 9 0.26
11 13 0.37
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (10 bp):
TGATATGACA
Found at i:41506527 original size:24 final size:24
Alignment explanation
Indices: 41506496--41506541 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
41506486 AATTTATCGA
**
41506496 AAAGGGCTTTGCC-CCAGTTATTT
1 AAAGGGCTAGGCCTCCAGTTATTT
41506519 AAAGAGGCTAGGCCTCCAGTTAT
1 AAAG-GGCTAGGCCTCCAGTTAT
41506542 ATGATAAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 7 0.37
25 8 0.42
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (24 bp):
AAAGGGCTAGGCCTCCAGTTATTT
Found at i:41510666 original size:11 final size:10
Alignment explanation
Indices: 41510635--41510667 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
41510625 GTGGTTAAGT
41510635 GTGTTGAGAA
1 GTGTTGAGAA
41510645 GTGTTGAGAA
1 GTGTTGAGAA
41510655 GTGTTGGAGAA
1 GTGTT-GAGAA
41510666 GT
1 GT
41510668 CCTGGGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 15 0.68
11 7 0.32
ACGTcount: A:0.27, C:0.00, G:0.42, T:0.30
Consensus pattern (10 bp):
GTGTTGAGAA
Found at i:41511439 original size:27 final size:27
Alignment explanation
Indices: 41511409--41511521 Score: 127
Period size: 27 Copynumber: 4.2 Consensus size: 27
41511399 AAAGTACTCC
41511409 CGATTTACAAAATTACCGTTTTACCCT
1 CGATTTACAAAATTACCGTTTTACCCT
**
41511436 CGATTTACAAAATTGTCGTTTTACCCT
1 CGATTTACAAAATTACCGTTTTACCCT
*** * * *
41511463 CGATTTTTGAAATTATCATTTTACTCT
1 CGATTTACAAAATTACCGTTTTACCCT
* *
41511490 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAAAATTACCGTTTTACCCT
*
41511517 TGATT
1 CGATT
41511522 GTGAAATTAC
Statistics
Matches: 71, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 71 1.00
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43
Consensus pattern (27 bp):
CGATTTACAAAATTACCGTTTTACCCT
Found at i:41511556 original size:27 final size:27
Alignment explanation
Indices: 41511526--41511721 Score: 248
Period size: 27 Copynumber: 7.3 Consensus size: 27
41511516 TTGATTGTGA
*
41511526 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
41511553 AATTTCCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * * *
41511580 AATTACTAAAATACCCTTATAGGATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
41511607 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
41511634 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
41511661 AAATACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
41511688 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
41511715 AATTACC
1 AATTACC
41511722 ATTTTGCCCC
Statistics
Matches: 146, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 146 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:41511981 original size:27 final size:28
Alignment explanation
Indices: 41511921--41512001 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 28
41511911 GGAGGAAGCG
*
41511921 TTCTGGTGGCTATGCCACAAATATC--TA
1 TTCTGGTGGCTCTGCCAC-AATATCTGTA
41511948 TTCTGGTGGCTCTGCCACAATATCTGTA
1 TTCTGGTGGCTCTGCCACAATATCTGTA
* * *
41511976 TT-TGGTGACTCTGTCACAGTATCTGT
1 TTCTGGTGGCTCTGCCACAATATCTGT
41512002 TGACCGATCG
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.12
27 38 0.79
28 4 0.08
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (28 bp):
TTCTGGTGGCTCTGCCACAATATCTGTA
Found at i:41512333 original size:27 final size:27
Alignment explanation
Indices: 41512319--41512377 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
41512309 TTTGCCTCAT
41512319 TATCTGAT-TCTGGTGGCTCTGCCACAA
1 TATCT-ATATCTGGTGGCTCTGCCACAA
* * *
41512346 TATCTATATCTGGTGACTCTGTCACGA
1 TATCTATATCTGGTGGCTCTGCCACAA
41512373 TATCT
1 TATCT
41512378 CTTTTGGCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (27 bp):
TATCTATATCTGGTGGCTCTGCCACAA
Found at i:41512511 original size:6 final size:6
Alignment explanation
Indices: 41512502--41512629 Score: 138
Period size: 6 Copynumber: 20.8 Consensus size: 6
41512492 TTGCATTCAC
* *
41512502 ATTCTG ATTCTG ATTCTG TCATTCTG ATTCTG ATTCTG ATTCTG -TCACCTA
1 ATTCTG ATTCTG ATTCTG --ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG
*
41512553 ATTCTG ATTCTG ATTCTG ATTCTG -TTACTA ATAT-TG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG AT-TCTG ATTCTG ATTCTG
41512601 ATTCTG -TTACTG ATTCTG ATTCTG ATTCT
1 ATTCTG ATT-CTG ATTCTG ATTCTG ATTCT
41512630 CATTTTGGTT
Statistics
Matches: 105, Mismatches: 6, Indels: 22
0.79 0.05 0.17
Matches are distributed among these distances:
5 6 0.06
6 86 0.82
7 5 0.05
8 8 0.08
ACGTcount: A:0.19, C:0.18, G:0.14, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:41512524 original size:26 final size:25
Alignment explanation
Indices: 41512495--41512570 Score: 100
Period size: 26 Copynumber: 3.0 Consensus size: 25
41512485 GTTGGGATTG
41512495 CATTCACATTCTGATTCTGATTCTGT
1 CATTCA-ATTCTGATTCTGATTCTGT
*
41512521 CATTCTGATTCTGATTCTGATTCTGT
1 CATTC-AATTCTGATTCTGATTCTGT
*
41512547 CA-CCTAATTCTGATTCTGATTCTG
1 CATTC-AATTCTGATTCTGATTCTG
41512571 ATTCTGTTAC
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
25 20 0.43
26 26 0.57
ACGTcount: A:0.18, C:0.22, G:0.13, T:0.46
Consensus pattern (25 bp):
CATTCAATTCTGATTCTGATTCTGT
Found at i:41512591 original size:30 final size:30
Alignment explanation
Indices: 41512502--41512629 Score: 185
Period size: 30 Copynumber: 4.4 Consensus size: 30
41512492 TTGCATTCAC
41512502 ATTCTGATTCTGATTCTG-T-C--ATTCTG
1 ATTCTGATTCTGATTCTGTTACTAATTCTG
*
41512528 ATTCTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTCTGATTCTGTTA-CTAATTCTG
41512559 ATTCTGATTCTGATTCTGTTACTAATAT-TG
1 ATTCTGATTCTGATTCTGTTACTAAT-TCTG
*
41512589 ATTCTGATTCTGATTCTGTTACTGATTCTG
1 ATTCTGATTCTGATTCTGTTACTAATTCTG
41512619 ATTCTGATTCT
1 ATTCTGATTCT
41512630 CATTTTGGTT
Statistics
Matches: 92, Mismatches: 3, Indels: 10
0.88 0.03 0.10
Matches are distributed among these distances:
26 18 0.20
29 2 0.02
30 45 0.49
31 27 0.29
ACGTcount: A:0.19, C:0.18, G:0.14, T:0.49
Consensus pattern (30 bp):
ATTCTGATTCTGATTCTGTTACTAATTCTG
Found at i:41512647 original size:30 final size:30
Alignment explanation
Indices: 41512538--41512650 Score: 131
Period size: 30 Copynumber: 3.7 Consensus size: 30
41512528 ATTCTGATTC
*
41512538 TGATTCTGTCACCTAATTCTGATTCTGATTC
1 TGATTCTGTTACC-AATTCTGATTCTGATTC
*
41512569 TGATTCTGTTACTAATAT-TGATTCTGATTC
1 TGATTCTGTTACCAAT-TCTGATTCTGATTC
**
41512599 TGATTCTGTTACTGATTCTGATTCTGATTC
1 TGATTCTGTTACCAATTCTGATTCTGATTC
* *
41512629 TCATTTTGGTT-CCAATTCTGAT
1 TGATTCT-GTTACCAATTCTGAT
41512651 AATGTTTCTT
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
29 1 0.01
30 56 0.78
31 15 0.21
ACGTcount: A:0.19, C:0.18, G:0.14, T:0.49
Consensus pattern (30 bp):
TGATTCTGTTACCAATTCTGATTCTGATTC
Found at i:41518080 original size:46 final size:45
Alignment explanation
Indices: 41518030--41518202 Score: 190
Period size: 46 Copynumber: 3.8 Consensus size: 45
41518020 TGGTTGAGCA
41518030 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * * * *
41518076 TCCGAACTCGTTGAGTTGAGTCCAAGTTC-GTGA--AATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAA-T--G
*
41518121 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* *
41518169 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
41518203 GGGGCGGGTT
Statistics
Matches: 105, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 60 0.57
47 28 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAATG
Found at i:41518179 original size:93 final size:93
Alignment explanation
Indices: 41518027--41518197 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
41518017 GGATGGTTGA
* *
41518027 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
41518092 TGAGTCCAAGTTCGTGAAATGTAACTAG
66 TGAGTCCAAGTTCGTGAAATGTAACTAG
* *
41518120 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
41518185 TGAGTCCGAGTTC
66 TGAGTCCAAGTTC
41518198 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCAAGTTCGTGAAATGTAACTAG
Found at i:41522544 original size:49 final size:49
Alignment explanation
Indices: 41522472--41522645 Score: 269
Period size: 49 Copynumber: 3.5 Consensus size: 49
41522462 TGAGGTCACG
41522472 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* * * *
41522521 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGA-AGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA-ATT-GGTCGCA
* *
41522571 TGTGTAGTACTAAGTGCAGGCTACTACGTGCACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
41522620 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
41522646 TGCGTATTAG
Statistics
Matches: 112, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
48 1 0.01
49 69 0.62
50 41 0.37
51 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
Found at i:41522635 original size:99 final size:99
Alignment explanation
Indices: 41522464--41522645 Score: 346
Period size: 99 Copynumber: 1.8 Consensus size: 99
41522454 AGCTATTCTG
*
41522464 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGCACCAGATAATTGGTCGCATGTGTAGT
41522529 ACTAAGTGCAGGCTACTACGTGTATCAGAAGGTT
66 ACTAAGTGCAGGCTACTACGTGTATCAGAAGGTT
*
41522563 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGCACCGGATAATTGGTCGCATGTGTAGT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGCACCAGATAATTGGTCGCATGTGTAGT
41522628 ACTAAGTGCAGGCTACTA
66 ACTAAGTGCAGGCTACTA
41522646 TGCGTATTAG
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 81 1.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (99 bp):
AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGCACCAGATAATTGGTCGCATGTGTAGT
ACTAAGTGCAGGCTACTACGTGTATCAGAAGGTT
Found at i:41525385 original size:16 final size:15
Alignment explanation
Indices: 41525347--41525385 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
41525337 TGGATTCTCG
*
41525347 TATCATGGATTTCTT
1 TATCTTGGATTTCTT
41525362 TATCTTGGATTTCTT
1 TATCTTGGATTTCTT
41525377 TATTCTTGG
1 TA-TCTTGG
41525386 CTTCTCTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.15, C:0.13, G:0.15, T:0.56
Consensus pattern (15 bp):
TATCTTGGATTTCTT
Found at i:41527721 original size:49 final size:50
Alignment explanation
Indices: 41527643--41527888 Score: 280
Period size: 49 Copynumber: 4.9 Consensus size: 50
41527633 AGCTATTGTG
* *
41527643 AGGTCACATGTGAAGTACTAAGTACAGGCTACTACGTGTACCAGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * * *
41527693 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTAGCTGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * * * * **
41527743 CGATCACGTGAGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * *
41527793 AGGTCACGTGTGTAGTACTAAGTACAGGCTACTACGTGTGCCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
41527843 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
41527889 GCTTCGCCTA
Statistics
Matches: 161, Mismatches: 33, Indels: 5
0.81 0.17 0.03
Matches are distributed among these distances:
49 79 0.49
50 45 0.28
51 37 0.23
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:41529758 original size:18 final size:18
Alignment explanation
Indices: 41529735--41529769 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41529725 CGTTATTTAT
*
41529735 TCAAAAAATTTATGATGC
1 TCAAAAAATTGATGATGC
*
41529753 TCAAAAAGTTGATGATG
1 TCAAAAAATTGATGATG
41529770 ATTTGATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.31
Consensus pattern (18 bp):
TCAAAAAATTGATGATGC
Found at i:41532421 original size:131 final size:133
Alignment explanation
Indices: 41532259--41532711 Score: 413
Period size: 131 Copynumber: 3.5 Consensus size: 133
41532249 AAAAAACTGA
* * * *** *
41532259 AACCCAGCACAGTAGGGCATGGTTCCTCGAATTTTGAAACATCGAGCGTTGCCTT-ATTTTTAGA
1 AACCCAGCACGGTAGGGCACGATTCCTCGAATTGCCAAACATCGAGCATTGCCTTCATTTTTAGA
*
41532323 -ATTTTTTAAAAAACATGAGTGAAATTCTAAAGGAATATTCGATTGTTTTGAACAAAC-AGGAAA
66 GAGTTTTTAAAAAACATGAGTGAAATTCTAAAGGAATATTCGATTGTTTTGAACAAACGA-GAAA
41532386 TTGC
130 TTGC
* * * * * *
41532390 AACCCAGCACGGTAGGGCACAATTCCCCGAATTGCCAAACATCGAGTATTACCTT--TGTTTGGA
1 AACCCAGCACGGTAGGGCACGATTCCTCGAATTGCCAAACATCGAGCATTGCCTTCATTTTTAG-
* * * * ** **
41532453 AGAGTTTTT-AAAGATATGAGTGAAATTCCAAAGGAATCTTCGATTGTTCCGAACAAACGCTAAA
65 AGAGTTTTTAAAAAACATGAGTGAAATTCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAA
* *
41532517 TCGT
130 TTGC
* * * * * *
41532521 AACCAAGCACGATAGGGCACGATT--TCGAATTGCCAAACACCGAGTAATGCCTTCA-TTTTAAA
1 AACCCAGCACGGTAGGGCACGATTCCTCGAATTGCCAAACATCGAGCATTGCCTTCATTTTTAGA
* * * * * * * *
41532583 GAGTTTTTAGAAAACGTGAATGAAATTCTAAAGGGACATTCAATTATTTTGAGCAAACGAGAAAT
66 GAGTTTTTAAAAAACATGAGTGAAATTCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAAT
*
41532648 TAC
131 TGC
* * * * *
41532651 AACCCAACACGTTAGGGCACGATT-CTGCGAATTGTCAAATATCGAACATTGCCTTCATTTT
1 AACCCAGCACGGTAGGGCACGATTCCT-CGAATTGCCAAACATCGAGCATTGCCTTCATTTT
41532712 AATAAATTTT
Statistics
Matches: 251, Mismatches: 62, Indels: 16
0.76 0.19 0.05
Matches are distributed among these distances:
129 34 0.14
130 69 0.27
131 115 0.46
132 30 0.12
133 3 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (133 bp):
AACCCAGCACGGTAGGGCACGATTCCTCGAATTGCCAAACATCGAGCATTGCCTTCATTTTTAGA
GAGTTTTTAAAAAACATGAGTGAAATTCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAAT
TGC
Found at i:41539470 original size:29 final size:29
Alignment explanation
Indices: 41539428--41539486 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
41539418 AGTGGTGAAA
41539428 TCACAAGCTTCAATTTGTATGATGGATTT
1 TCACAAGCTTCAATTTGTATGATGGATTT
41539457 TCACAAGCTTCAATTTGTATGATGGATTT
1 TCACAAGCTTCAATTTGTATGATGGATTT
41539486 T
1 T
41539487 TTTTTCTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (29 bp):
TCACAAGCTTCAATTTGTATGATGGATTT
Found at i:41541868 original size:40 final size:38
Alignment explanation
Indices: 41541766--41541868 Score: 109
Period size: 39 Copynumber: 2.6 Consensus size: 38
41541756 ATGTGGTATT
* * *
41541766 ATATCCGAGTTAAATCCCGCAGGCTTAATGCTGGAATT
1 ATATCCGGGTTAAATCCCGCAGGCCTAATGCTGGAATG
* * *
41541804 ATATCCGGACTTATAGT-CCGCAGGCCTAGTGCTGGTAATAG
1 ATATCCGG-GTTA-AATCCCGCAGGCCTAATGCTGG-AAT-G
41541845 ATATCCGGGTTAAATCCCGCAGGC
1 ATATCCGGGTTAAATCCCGCAGGC
41541869 TTTGTGCTAG
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
38 7 0.13
39 21 0.40
40 16 0.31
41 8 0.15
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.26
Consensus pattern (38 bp):
ATATCCGGGTTAAATCCCGCAGGCCTAATGCTGGAATG
Found at i:41541876 original size:40 final size:38
Alignment explanation
Indices: 41541766--41541876 Score: 116
Period size: 40 Copynumber: 2.8 Consensus size: 38
41541756 ATGTGGTATT
* * *
41541766 ATATCCGAGTTAAATCCCGCAGGCTTAATGCTGGAATT
1 ATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGAATG
* * *
41541804 ATATCCGGACTTATAGT-CCGCAGGCCTAGTGCTGGTAATAG
1 ATATCCGG-GTTA-AATCCCGCAGGCTTAGTGCTGG-AAT-G
*
41541845 ATATCCGGGTTAAATCCCGCAGGCTTTGTGCT
1 ATATCCGGGTTAAATCCCGCAGGCTTAGTGCT
41541877 AGAAATTGGA
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
38 7 0.12
39 21 0.36
40 22 0.38
41 8 0.14
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (38 bp):
ATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGAATG
Found at i:41546751 original size:40 final size:40
Alignment explanation
Indices: 41546657--41546801 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
41546647 TACTCGAATG
*
41546657 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
41546698 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
41546738 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
41546778 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
41546802 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:41554762 original size:40 final size:40
Alignment explanation
Indices: 41554668--41554812 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
41554658 TACTCGAATG
*
41554668 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
41554709 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
41554749 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
41554789 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
41554813 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:41572714 original size:49 final size:49
Alignment explanation
Indices: 41572650--41572823 Score: 222
Period size: 49 Copynumber: 3.5 Consensus size: 49
41572640 ATGGTACGCA
* * * *
41572650 TAGTAGCCTACACTTAGTACTACACATACGACCAATTATCTGGTACATG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGATACATG
* * * **
41572699 TAGTAGCCTGTACTTAGTACTACACACGTGACCTAACCATCTGATACATG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACC-AATAATCTGATACATG
* * **
41572749 TAGCAGCCTGCACTTAGTACTACACATGCGACCAATAATCCGATACACA
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGATACATG
41572798 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
41572824 CGTGACCTCA
Statistics
Matches: 106, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
49 64 0.60
50 42 0.40
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGATACATG
Found at i:41575790 original size:13 final size:13
Alignment explanation
Indices: 41575772--41575805 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
41575762 CAAAGACATG
41575772 GCCGTGTGTCTCA
1 GCCGTGTGTCTCA
41575785 GCCGTGTGTCTCA
1 GCCGTGTGTCTCA
*
41575798 ACCGTGTG
1 GCCGTGTG
41575806 AACGACACGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.09, C:0.29, G:0.32, T:0.29
Consensus pattern (13 bp):
GCCGTGTGTCTCA
Found at i:41578653 original size:28 final size:27
Alignment explanation
Indices: 41578554--41578652 Score: 121
Period size: 27 Copynumber: 3.6 Consensus size: 27
41578544 AGCTGAGTAG
* *
41578554 ATTATCGAAATACCCCCAATTTGTAAA
1 ATTATCAAAATACCCCTAATTTGTAAA
41578581 ATTATCAAAATACCCCTAATTTGTAAA
1 ATTATCAAAATACCCCTAATTTGTAAA
*
41578608 ATTA-CTAAAATACCCCTGATTTG-AAA
1 ATTATC-AAAATACCCCTAATTTGTAAA
*
41578634 ATTTTATCGAAATACCCCT
1 A--TTATCAAAATACCCCT
41578653 GTAAGGTAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
26 5 0.08
27 45 0.70
28 13 0.20
29 1 0.02
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.32
Consensus pattern (27 bp):
ATTATCAAAATACCCCTAATTTGTAAA
Found at i:41579156 original size:27 final size:26
Alignment explanation
Indices: 41579065--41579157 Score: 71
Period size: 27 Copynumber: 3.5 Consensus size: 26
41579055 TATGTTGATT
* * *
41579065 ATGGCTTTGTGCAAATCGTATTTACC
1 ATGGCTATGTGCAGATCATATTTACC
* **
41579091 AGTGGCTATGTGCATATCATATTTATTG
1 A-TGGCTATGTGCAGATCATATTTA-CC
* *
41579119 ATGACTCTGTGTC-GATCATATTTACCC
1 ATGGCTATGTG-CAGATCATATTTA-CC
41579146 ATGGCTATGTGC
1 ATGGCTATGTGC
41579158 CAAATATATT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
26 2 0.04
27 47 0.92
28 2 0.04
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (26 bp):
ATGGCTATGTGCAGATCATATTTACC
Found at i:41579188 original size:32 final size:32
Alignment explanation
Indices: 41579146--41579235 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 32
41579136 ATATTTACCC
41579146 ATGGCTATGTGCCAAATATATTACCGTCACTG
1 ATGGCTATGTGCCAAATATATTACCGTCACTG
* * * *
41579178 ATGGCAATGTGCCGAACT-TATTACAGTTACTG
1 ATGGCTATGTGCC-AAATATATTACCGTCACTG
* * *
41579210 ATGGCTTTGTGCCAATTATAATACCG
1 ATGGCTATGTGCCAAATATATTACCG
41579236 CTACTGAAGG
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
31 3 0.06
32 41 0.87
33 3 0.06
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (32 bp):
ATGGCTATGTGCCAAATATATTACCGTCACTG
Found at i:41579241 original size:32 final size:30
Alignment explanation
Indices: 41579146--41579247 Score: 89
Period size: 32 Copynumber: 3.2 Consensus size: 30
41579136 ATATTTACCC
*
41579146 ATGGCTATGTGCCAAATATATTACCGTCACTG
1 ATGGCTATGTGCCAATTATA-TACCGT-ACTG
* *
41579178 ATGGCAATGTGCCGAACTTAT-TACAGTTACTG
1 ATGGCTATGTGCC-AA-TTATATACCG-TACTG
*
41579210 ATGGCTTTGTGCCAATTATAATACCGCTACTG
1 ATGGCTATGTGCCAATTAT-ATACCG-TACTG
*
41579242 AAGGCT
1 ATGGCT
41579248 TAAAGCCGTA
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
30 4 0.07
31 2 0.04
32 45 0.79
33 3 0.05
34 3 0.05
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (30 bp):
ATGGCTATGTGCCAATTATATACCGTACTG
Found at i:41581871 original size:28 final size:28
Alignment explanation
Indices: 41581806--41581956 Score: 205
Period size: 28 Copynumber: 5.4 Consensus size: 28
41581796 GAGATTGGCG
* * * *
41581806 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
41581835 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
41581863 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
41581891 CTAAGTGTGCGAGTTTGATTATATATCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
41581919 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
* *
41581946 CTGAGAGTGCG
1 CTAAGTGTGCG
41581957 GACTTAATAT
Statistics
Matches: 112, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
27 22 0.20
28 75 0.67
29 15 0.13
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:41592552 original size:45 final size:45
Alignment explanation
Indices: 41592457--41592728 Score: 385
Period size: 45 Copynumber: 6.1 Consensus size: 45
41592447 TTTTCTCAAA
* *
41592457 TCACCGGCATT-TCA-CCTGCTAGGCTC-GAGGCCC-AA-AATCATT
1 TCACCGGCATTAT-AGCCTGCTAGGCTCAAAGGCCCGAATAAT-ATC
* *
41592499 TCACCGGCATTATAGCCTGTTAGGCTCGAAA-GCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTC-AAAGGCCCGAATAATATC
41592544 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
* *
41592589 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
* *
41592634 TCACCGGCATTATAGCCTGCTAGGCTCAAAAGCCCGAATAATATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
* *
41592679 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
41592724 TCACC
1 TCACC
41592729 AGTTCTTTCC
Statistics
Matches: 211, Mismatches: 12, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
42 12 0.06
43 12 0.06
44 7 0.03
45 178 0.84
46 2 0.01
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.23
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
Found at i:41594997 original size:40 final size:40
Alignment explanation
Indices: 41594942--41595169 Score: 345
Period size: 40 Copynumber: 5.7 Consensus size: 40
41594932 CGAATGATAA
*
41594942 CCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGATTTTAT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGTGATTATAT
41594982 CCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGATTATAT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGTGATTATAT
*
41595022 CCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGAGATTATAT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGTGATTATAT
*
41595062 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTATAT
* *
41595102 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTATAT
* *
41595142 CTGGGCTAAGTCCCGAAGGCATTCGTGC
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC
41595170 GAGTTTCTAT
Statistics
Matches: 180, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
39 1 0.01
40 179 0.99
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.28
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTATAT
Found at i:41597466 original size:46 final size:46
Alignment explanation
Indices: 41597416--41597588 Score: 176
Period size: 46 Copynumber: 3.7 Consensus size: 46
41597406 TGGTTGAGCA
41597416 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
41597462 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* * *
41597507 CATCCAAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
41597555 -CCCAAGCTTGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTA
41597589 GGGGCGGGTT
Statistics
Matches: 103, Mismatches: 14, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 7 0.07
46 55 0.53
47 28 0.27
48 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:41597572 original size:93 final size:93
Alignment explanation
Indices: 41597413--41597583 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
41597403 GGATGGTTGA
* * * *
41597413 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCCCAACTCGTTGAGT
41597478 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
41597506 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACG-CCCAAGCTTGTTGAG
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCCCAA-CTCGTTGAG
41597570 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
41597584 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 4 0.06
93 68 0.94
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCCCAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:41600547 original size:15 final size:15
Alignment explanation
Indices: 41600509--41600552 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
41600499 TATAGTATCG
* *
41600509 TATCTTGGGTTTCTT
1 TATCTTGGATTTCTC
41600524 TAT-TCTGGATTTCTC
1 TATCT-TGGATTTCTC
41600539 TATCTTGGATTTCT
1 TATCTTGGATTTCT
41600553 TTATTCGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 1 0.04
15 23 0.92
16 1 0.04
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.57
Consensus pattern (15 bp):
TATCTTGGATTTCTC
Found at i:41602897 original size:39 final size:40
Alignment explanation
Indices: 41602759--41602975 Score: 291
Period size: 40 Copynumber: 5.5 Consensus size: 40
41602749 TGGATGATAA
* *
41602759 CCGGGCTAAGTCCCGAAGGCATTTTGTGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCA-TTTGTGCGAGTTACTA-TAT
* *
41602800 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
41602840 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
41602880 CC-GGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
41602919 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
41602958 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
41602976 TACTTGGCTT
Statistics
Matches: 160, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
38 15 0.09
39 53 0.33
40 71 0.44
41 21 0.13
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:41602907 original size:79 final size:79
Alignment explanation
Indices: 41602759--41602975 Score: 296
Period size: 79 Copynumber: 2.7 Consensus size: 79
41602749 TGGATGATAA
* *
41602759 CCGGGCTAAGTCCCGAAGGCATTTTGTGCTAGTGACTAGT-TCCGGGCTAAGTCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCA-TTTGTGCGAGTTACTA-TATCC-GGCTAAGTCCCGAAGGCATT
* *
41602823 TGTGCGAGTTATTACAT
63 GGTGCGAGTTACTACAT
41602840 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGCTAAGTCCCGAAGGCATTGGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGCTAAGTCCCGAAGGCATTGGT
*
41602905 GCGAGTTACTATAT
66 GCGAGTTACTACAT
* * * *
41602919 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATATCCGGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGCTAAGTCCCGAAGG
41602976 TACTTGGCTT
Statistics
Matches: 125, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
77 2 0.02
78 30 0.24
79 55 0.44
80 17 0.14
81 21 0.17
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGCTAAGTCCCGAAGGCATTGGT
GCGAGTTACTACAT
Found at i:41606136 original size:46 final size:46
Alignment explanation
Indices: 41606084--41606256 Score: 183
Period size: 46 Copynumber: 3.7 Consensus size: 46
41606074 TGGTTGAGCA
41606084 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
41606130 TTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
41606175 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
41606223 CCCGAGCTCGTTGAGTTGAGTTCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
41606257 GGGGCGGGTT
Statistics
Matches: 102, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 58 0.57
47 27 0.26
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:41606218 original size:93 final size:93
Alignment explanation
Indices: 41606081--41606251 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
41606071 GGATGGTTGA
* **
41606081 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
41606146 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
41606174 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
41606239 TGAGTTCGAGTTC
66 TGAGTCCGAGTTC
41606252 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:41609964 original size:28 final size:28
Alignment explanation
Indices: 41609878--41610001 Score: 182
Period size: 28 Copynumber: 4.5 Consensus size: 28
41609868 ATATTAAGTC
* *
41609878 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
* *
41609905 CACACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
41609933 --CACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
41609959 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
41609987 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41610002 GTACAATTTA
Statistics
Matches: 89, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
26 24 0.27
27 21 0.24
28 44 0.49
ACGTcount: A:0.34, C:0.28, G:0.11, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:41609970 original size:54 final size:54
Alignment explanation
Indices: 41609880--41610001 Score: 183
Period size: 54 Copynumber: 2.2 Consensus size: 54
41609870 ATTAAGTCCG
* * *
41609880 CACACTCAGTGCTATATAATCAACTCACACACTTAGTGCTATATAATCAAACT-
1 CACACTTAGTGCTACATAATCAACTCACACACTTAGTGCTACATAATCAAACTC
*
41609933 CACACTTAGTGCTACATAATCAAGCTCGCACACTTAGTGCTACATAATCAAACTC
1 CACACTTAGTGCTACATAATCAA-CTCACACACTTAGTGCTACATAATCAAACTC
41609988 GCACACTTAGTGCT
1 -CACACTTAGTGCT
41610002 GTACAATTTA
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
53 21 0.34
54 28 0.45
56 13 0.21
ACGTcount: A:0.34, C:0.28, G:0.11, T:0.27
Consensus pattern (54 bp):
CACACTTAGTGCTACATAATCAACTCACACACTTAGTGCTACATAATCAAACTC
Found at i:41610024 original size:29 final size:28
Alignment explanation
Indices: 41609877--41610026 Score: 155
Period size: 28 Copynumber: 5.4 Consensus size: 28
41609867 TATATTAAGT
* *
41609877 CCGCACACTCAGTGCTATATAATC-AAC
1 CCGCACACTTAGTGCTACATAATCAAAC
* * *
41609904 TCACACACTTAGTGCTATATAATCAAA-
1 CCGCACACTTAGTGCTACATAATCAAAC
* *
41609931 -CTCACACTTAGTGCTACATAATCAAGC
1 CCGCACACTTAGTGCTACATAATCAAAC
*
41609958 TCGCACACTTAGTGCTACATAATCAAAC
1 CCGCACACTTAGTGCTACATAATCAAAC
* * *
41609986 TCGCACACTTAGTGCTGTACA-ATTTAAAC
1 CCGCACACTTAGTGC--TACATAATCAAAC
41610015 CCGCACACTTAG
1 CCGCACACTTAG
41610027 CGCCAATCTC
Statistics
Matches: 107, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
26 23 0.21
27 21 0.20
28 42 0.39
29 17 0.16
30 4 0.04
ACGTcount: A:0.34, C:0.29, G:0.11, T:0.26
Consensus pattern (28 bp):
CCGCACACTTAGTGCTACATAATCAAAC
Found at i:41613266 original size:25 final size:25
Alignment explanation
Indices: 41613238--41613307 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
41613228 CTCTTTTAAT
41613238 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTTGATA
*
41613263 AACTGGGGCAAAGCCCTTTTTGGTA
1 AACTGGGGCAAAGCCCTTTTTGATA
*
41613288 AACTAGGGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
41613308 AGCACTTCCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTTGATA
Found at i:41613756 original size:27 final size:27
Alignment explanation
Indices: 41613510--41613748 Score: 327
Period size: 27 Copynumber: 8.9 Consensus size: 27
41613500 GGCAAAATGA
* * * * *
41613510 TAATTTTACCCCACATGGGTATCTCGG
1 TAATTCTACCCTACAGGGGTATTTCAG
*
41613537 TAATTCTACCCTATAGGGGTATTTCAG
1 TAATTCTACCCTACAGGGGTATTTCAG
* * *
41613564 TATTTCTACCCTACAAGGGTATTTCGG
1 TAATTCTACCCTACAGGGGTATTTCAG
*
41613591 TAATTCTACCTTACAGGGGTATTTCAG
1 TAATTCTACCCTACAGGGGTATTTCAG
*
41613618 TAATTCTACCCTACAGGGGTATTTCGG
1 TAATTCTACCCTACAGGGGTATTTCAG
*
41613645 TAATTCTACCTTACAGGGGTATTTCAG
1 TAATTCTACCCTACAGGGGTATTTCAG
41613672 TAATTCTACCCTACAGGGGTATTTCAG
1 TAATTCTACCCTACAGGGGTATTTCAG
* *
41613699 TATTTCTA-CCTACAAGGGTATTTCAG
1 TAATTCTACCCTACAGGGGTATTTCAG
* *
41613725 TAATTCTACCCCATAGGGGTATTT
1 TAATTCTACCCTACAGGGGTATTT
41613749 TGGTAATTTT
Statistics
Matches: 186, Mismatches: 25, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 24 0.13
27 162 0.87
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (27 bp):
TAATTCTACCCTACAGGGGTATTTCAG
Found at i:41613771 original size:27 final size:28
Alignment explanation
Indices: 41613739--41613893 Score: 149
Period size: 27 Copynumber: 5.7 Consensus size: 28
41613729 TCTACCCCAT
* *
41613739 AGGGGTATTTTGGTAATTTTACTGATCG
1 AGGGGTATTTTGGTAATTTTACTAAACG
* * * *
41613767 A-GGGTATTCTGTTAATTTT-GTAAACT
1 AGGGGTATTTTGGTAATTTTACTAAACG
* *
41613793 AGGGGTATTTTAGTAATTTTAC-AAACC
1 AGGGGTATTTTGGTAATTTTACTAAACG
* *
41613820 AGGGGTATTTTGGTAATTTTACTGATCG
1 AGGGGTATTTTGGTAATTTTACTAAACG
* *
41613848 A-GGGTATTTTGGTAATTTT-GTAAACC
1 AGGGGTATTTTGGTAATTTTACTAAACG
* *
41613874 AAGGGTATTTTAGTAATTTT
1 AGGGGTATTTTGGTAATTTT
41613894 GTAAATTGAG
Statistics
Matches: 103, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
26 8 0.08
27 91 0.88
28 4 0.04
ACGTcount: A:0.26, C:0.07, G:0.23, T:0.43
Consensus pattern (28 bp):
AGGGGTATTTTGGTAATTTTACTAAACG
Found at i:41613905 original size:54 final size:54
Alignment explanation
Indices: 41613779--41613961 Score: 154
Period size: 54 Copynumber: 3.4 Consensus size: 54
41613769 GGTATTCTGT
* * ** * *
41613779 TAATTTTGTAAA-CTAGGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGG
1 TAATTTTGTAAATCGA-GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTAG
* *
41613833 TAATTTTACT-GATCGAGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTAG
1 TAATTTT-GTAAATCGAGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTAG
* **** * * ***
41613887 TAATTTTGTAAATTGAGGGTAAAACGATAATTTTGTAAATCAAGGGTAAAATAG
1 TAATTTTGTAAATCGAGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTAG
* *
41613941 TAATTCTATAAATCGAGGGTA
1 TAATTTTGTAAATCGAGGGTA
41613962 AAACAATAAT
Statistics
Matches: 103, Mismatches: 23, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
53 1 0.01
54 99 0.96
55 3 0.03
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (54 bp):
TAATTTTGTAAATCGAGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTAG
Found at i:41613907 original size:81 final size:81
Alignment explanation
Indices: 41613739--41613893 Score: 274
Period size: 81 Copynumber: 1.9 Consensus size: 81
41613729 TCTACCCCAT
* * *
41613739 AGGGGTATTTTGGTAATTTTACTGATCGAGGGTATTCTGTTAATTTTGTAAACTAGGGGTATTTT
1 AGGGGTATTTTGGTAATTTTACTGATCGAGGGTATTCTGGTAATTTTGTAAACCAAGGGTATTTT
41613804 AGTAATTTTACAAACC
66 AGTAATTTTACAAACC
*
41613820 AGGGGTATTTTGGTAATTTTACTGATCGAGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTT
1 AGGGGTATTTTGGTAATTTTACTGATCGAGGGTATTCTGGTAATTTTGTAAACCAAGGGTATTTT
41613885 AGTAATTTT
66 AGTAATTTT
41613894 GTAAATTGAG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 70 1.00
ACGTcount: A:0.26, C:0.07, G:0.23, T:0.43
Consensus pattern (81 bp):
AGGGGTATTTTGGTAATTTTACTGATCGAGGGTATTCTGGTAATTTTGTAAACCAAGGGTATTTT
AGTAATTTTACAAACC
Found at i:41613917 original size:27 final size:27
Alignment explanation
Indices: 41613895--41614066 Score: 220
Period size: 27 Copynumber: 6.4 Consensus size: 27
41613885 AGTAATTTTG
* * * *
41613895 TAAATTGAGGGTAAAACGATAATTTTG
1 TAAATCGAGGGTAAAATGATAATTCTA
*
41613922 TAAATCAAGGGTAAAAT-AGTAATTCTA
1 TAAATCGAGGGTAAAATGA-TAATTCTA
**
41613949 TAAATCGAGGGTAAAACAATAATTCTA
1 TAAATCGAGGGTAAAATGATAATTCTA
* *
41613976 TAAGTCGAGGGTAAAATGGTAATTCTA
1 TAAATCGAGGGTAAAATGATAATTCTA
*
41614003 TAAATCGAGGGTAAAATGATAATTCTG
1 TAAATCGAGGGTAAAATGATAATTCTA
*
41614030 TAAATCGAGGGTAAAATGGTAATTCTA
1 TAAATCGAGGGTAAAATGATAATTCTA
*
41614057 TAAATTGAGG
1 TAAATCGAGG
41614067 ATATTTGGGT
Statistics
Matches: 126, Mismatches: 17, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
26 1 0.01
27 124 0.98
28 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (27 bp):
TAAATCGAGGGTAAAATGATAATTCTA
Found at i:41613918 original size:81 final size:81
Alignment explanation
Indices: 41613752--41613920 Score: 205
Period size: 81 Copynumber: 2.1 Consensus size: 81
41613742 GGTATTTTGG
* * *
41613752 TAATTTTACTGATCGAGGGTATTCTGTTAATTTTGTAAACTAGGGGTATTTTAGTAATTTTACAA
1 TAATTTTACTGATCGAGGGTATTCTGGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTACAA
**** *
41613817 ACCAGGGGTATTTTGG
66 ACCAGGGGTAAAACGA
* **
41613833 TAATTTTACTGATCGAGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTGTAA
1 TAATTTTACTGATCGAGGGTATTCTGGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTACAA
**
41613898 A-TTGAGGGTAAAACGA
66 ACCAG-GGGTAAAACGA
41613914 TAATTTT
1 TAATTTT
41613921 GTAAATCAAG
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
80 1 0.01
81 73 0.99
ACGTcount: A:0.30, C:0.07, G:0.21, T:0.42
Consensus pattern (81 bp):
TAATTTTACTGATCGAGGGTATTCTGGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTACAA
ACCAGGGGTAAAACGA
Found at i:41613962 original size:54 final size:54
Alignment explanation
Indices: 41613860--41614066 Score: 252
Period size: 54 Copynumber: 3.8 Consensus size: 54
41613850 GGTATTTTGG
* * *** * * *
41613860 TAATTTTGTAAACCAAGGGTATTTTAGTAATTTTGTAAATTGAGGGTAAAACGA
1 TAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACGA
* *
41613914 TAATTTTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACAA
1 TAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACGA
* * * * *
41613968 TAATTCTATAAGTCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGA
1 TAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACGA
* * *
41614022 TAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATTGAGG
1 TAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGG
41614067 ATATTTGGGT
Statistics
Matches: 135, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 135 1.00
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (54 bp):
TAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACGA
Found at i:41614086 original size:81 final size:81
Alignment explanation
Indices: 41613895--41614096 Score: 210
Period size: 81 Copynumber: 2.5 Consensus size: 81
41613885 AGTAATTTTG
* * * * * *
41613895 TAAATTGAGGGTAAAACGATAATTTTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGG
1 TAAATCGAGGATAAAATGGTAATTTTATAAATCGAGGGTAAAATAGTAATTCTATAAATCGAGGG
41613960 TAAAACAATAATTCTA
66 TAAAACAATAATTCTA
* * * *
41613976 TAAGTCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAAT-GATAATTCTGTAAATCGAGG
1 TAAATCGAGGATAAAATGGTAATTTTATAAATCGAGGGTAAAATAG-TAATTCTATAAATCGAGG
***
41614040 GTAAAATGGTAATTCTA
65 GTAAAACAATAATTCTA
* ** * *
41614057 TAAATTGAGGAT-ATTTGGGTAGTTTTATAAATCGGGGGTA
1 TAAATCGAGGATAAAAT-GGTAATTTTATAAATCGAGGGTA
41614097 CTTTGGTAAT
Statistics
Matches: 100, Mismatches: 19, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
80 3 0.03
81 97 0.97
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.31
Consensus pattern (81 bp):
TAAATCGAGGATAAAATGGTAATTTTATAAATCGAGGGTAAAATAGTAATTCTATAAATCGAGGG
TAAAACAATAATTCTA
Found at i:41618226 original size:16 final size:16
Alignment explanation
Indices: 41618205--41618253 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
41618195 GAGTGAATTG
41618205 AATTGAATCGAACTAT
1 AATTGAATCGAACTAT
41618221 AATTGAATCG---TAT
1 AATTGAATCGAACTAT
41618234 AATTAGAATCGAACTAT
1 AATT-GAATCGAACTAT
41618251 AAT
1 AAT
41618254 ACTTGCAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 7 0.24
14 6 0.21
16 10 0.34
17 6 0.21
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (16 bp):
AATTGAATCGAACTAT
Found at i:41618450 original size:22 final size:22
Alignment explanation
Indices: 41618425--41618477 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
41618415 TAGCTCGTAT
* *
41618425 GAGCTTCCCGTTCCGCTCAAAA
1 GAGCTTCCCGTTCAGATCAAAA
* *
41618447 GAGCTTCCTGTTCAGATCAATA
1 GAGCTTCCCGTTCAGATCAAAA
41618469 GAGCTTCCC
1 GAGCTTCCC
41618478 ATTTCCAGCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (22 bp):
GAGCTTCCCGTTCAGATCAAAA
Found at i:41618797 original size:26 final size:26
Alignment explanation
Indices: 41618761--41618813 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
41618751 TTAAATGGTA
*
41618761 AGTTTAATTCTGAAGTATACGAGCTT
1 AGTTTAATTCTGAAGTATACAAGCTT
*
41618787 AGTTTAATTCTGAATTATACAAGCTT
1 AGTTTAATTCTGAAGTATACAAGCTT
41618813 A
1 A
41618814 CTAAGCTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (26 bp):
AGTTTAATTCTGAAGTATACAAGCTT
Found at i:41626625 original size:36 final size:36
Alignment explanation
Indices: 41626578--41626650 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
41626568 CATAGTGGCC
41626578 TTCACTTAGCACCACTCATGTGACCTAGCTCAATTG
1 TTCACTTAGCACCACTCATGTGACCTAGCTCAATTG
*
41626614 TTCACTTAGCACCACTCATGTGACCTAGCTCGATTG
1 TTCACTTAGCACCACTCATGTGACCTAGCTCAATTG
41626650 T
1 T
41626651 ACACACAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (36 bp):
TTCACTTAGCACCACTCATGTGACCTAGCTCAATTG
Found at i:41629182 original size:25 final size:25
Alignment explanation
Indices: 41629154--41629202 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
41629144 TAGGGTTACT
41629154 AGGTATTACCAATCAATACACATCG
1 AGGTATTACCAATCAATACACATCG
41629179 AGGTATTACCAATCAATACACATC
1 AGGTATTACCAATCAATACACATC
41629203 ATTTAACCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.24
Consensus pattern (25 bp):
AGGTATTACCAATCAATACACATCG
Found at i:41638514 original size:26 final size:25
Alignment explanation
Indices: 41638443--41638515 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
41638433 CTGACGAGTT
**
41638443 GAATCAGTAAGCTCCCACGAGCTAA
1 GAATCAGTAAGCTCATACGAGCTAA
**
41638468 GAA-CAGTAAGCTTTTACGAGCTAA
1 GAATCAGTAAGCTCATACGAGCTAA
* *
41638492 TATATCAGTAAGCTCATATGAGCT
1 GA-ATCAGTAAGCTCATACGAGCT
41638516 GTGGTGAGTC
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
24 19 0.49
25 4 0.10
26 16 0.41
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.25
Consensus pattern (25 bp):
GAATCAGTAAGCTCATACGAGCTAA
Found at i:41640192 original size:42 final size:42
Alignment explanation
Indices: 41640081--41640192 Score: 143
Period size: 43 Copynumber: 2.6 Consensus size: 42
41640071 TACCGTACCA
* * * **
41640081 ATGCCATATCCTAGATATGGTATTACATGTGATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* *
41640123 ATGCCAATAGCCCAGCTATGGTCTTACACGAAATCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAATCTCATATCG
*
41640166 ATGCCATATCCCAGATTTGGTCTTACA
1 ATGCCATATCCCAGATATGGTCTTACA
41640193 TTTAAATCTC
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 24 0.41
43 35 0.59
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
Found at i:41642612 original size:39 final size:40
Alignment explanation
Indices: 41642495--41642679 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
41642485 GCTACTCGTT
* *
41642495 CAAACGCCTTCGGGACATAGCCC-GATTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
41642535 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
41642575 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
41642614 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
*
41642655 CAAA-GCCTTCGAGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41642680 CATCATTCAA
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.02
39 33 0.27
40 74 0.60
41 14 0.11
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:41642639 original size:79 final size:80
Alignment explanation
Indices: 41642495--41642679 Score: 198
Period size: 79 Copynumber: 2.3 Consensus size: 80
41642485 GCTACTCGTT
* * *
41642495 CAAACGCCTTCGGGACATAGCCC-GATTATAGTAACTCGCACAATTGCCTTCGGGACTTAACCCG
1 CAAA-GCCTTCGGG-CTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
* *
41642559 GATTTAGTAAC-TCGCA
64 GATATAGTAACTTAGCA
* **
41642575 CAAATGCCTTCGGGCTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAA-GCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
* *
41642638 GATATGGTCACTTAGCA
64 GATATAGTAACTTAGCA
*
41642655 CAAAGCCTTCGAGACTTAGCCCGGA
1 CAAAGCCTTCG-GGCTTAGCCCGGA
41642680 CATCATTCAA
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
78 3 0.03
79 50 0.56
80 36 0.40
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
CAAAGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
TATAGTAACTTAGCA
Found at i:41646797 original size:29 final size:27
Alignment explanation
Indices: 41646779--41646848 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
41646769 ATATTAAGTC
41646779 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
41646806 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
41646834 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
41646849 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:41646842 original size:28 final size:28
Alignment explanation
Indices: 41646779--41646876 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
41646769 ATATTAAGTC
*
41646779 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
41646806 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
41646834 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
41646863 CGCACACTTAGTGC
1 CGCACACTTAGTGC
41646877 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:41654878 original size:29 final size:27
Alignment explanation
Indices: 41654860--41654929 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
41654850 ATATTAAGTC
41654860 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
41654887 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
41654915 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
41654930 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:41654923 original size:28 final size:28
Alignment explanation
Indices: 41654860--41654957 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
41654850 ATATTAAGTC
*
41654860 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
41654887 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
41654915 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
41654944 CGCACACTTAGTGC
1 CGCACACTTAGTGC
41654958 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:41661872 original size:15 final size:16
Alignment explanation
Indices: 41661852--41661881 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41661842 AAGATCATGA
41661852 AATCATAA-CTTACTC
1 AATCATAACCTTACTC
41661867 AATCATAACCTTACT
1 AATCATAACCTTACT
41661882 GAGGGTACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.27, G:0.00, T:0.33
Consensus pattern (16 bp):
AATCATAACCTTACTC
Found at i:41667312 original size:26 final size:26
Alignment explanation
Indices: 41667279--41667427 Score: 221
Period size: 26 Copynumber: 5.8 Consensus size: 26
41667269 GAGGAAGTGC
*
41667279 AAAA-GGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
41667304 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
41667330 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
41667356 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* **
41667382 AAAAGGGCTT-TGCCCCAATTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
41667407 AAAAGGGCTTTTGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
41667428 ATTAAAGAGG
Statistics
Matches: 113, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
25 26 0.23
26 87 0.77
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:41675309 original size:20 final size:20
Alignment explanation
Indices: 41675276--41675350 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
41675266 ATACGTGGGA
41675276 TATGATAT--ACATGAT-TG
1 TATGATATGCACATGATATG
*
41675293 ATATTATATGCACATGATATG
1 -TATGATATGCACATGATATG
41675314 TATGATATGCACATGATATG
1 TATGATATGCACATGATATG
*
41675334 TATGAAATGCACATGAT
1 TATGATATGCACATGAT
41675351 GAATTCATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
18 7 0.14
20 42 0.82
21 2 0.04
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.36
Consensus pattern (20 bp):
TATGATATGCACATGATATG
Found at i:41675329 original size:11 final size:11
Alignment explanation
Indices: 41675298--41675350 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
41675288 GATTGATATT
41675298 ATATGCACATG
1 ATATGCACATG
*
41675309 ATATG--TATG
1 ATATGCACATG
41675318 ATATGCACATG
1 ATATGCACATG
*
41675329 ATATG--TATG
1 ATATGCACATG
*
41675338 AAATGCACATG
1 ATATGCACATG
41675349 AT
1 AT
41675351 GAATTCATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
9 15 0.47
11 17 0.53
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (11 bp):
ATATGCACATG
Found at i:41675456 original size:25 final size:26
Alignment explanation
Indices: 41675400--41675544 Score: 195
Period size: 26 Copynumber: 5.7 Consensus size: 26
41675390 GAGGAAGTGC
41675400 AAAGGGCTTATGCCCCAGTTTATTGA
1 AAAGGGCTTATGCCCCAGTTTATTGA
41675426 AAAGGGCTTATGCCCCAGTTT-TTGA
1 AAAGGGCTTATGCCCCAGTTTATTGA
* **
41675451 AAAGGGCTTATGCCCTAGTTTACCGA
1 AAAGGGCTTATGCCCCAGTTTATTGA
41675477 AAAGGGCTTATGCCCCAGTTTATTGA
1 AAAGGGCTTATGCCCCAGTTTATTGA
* * **
41675503 AAAAGGCTT-TGCCTCAGTTTACCGA
1 AAAGGGCTTATGCCCCAGTTTATTGA
* *
41675528 AAAGGGTTTTTGCCCCA
1 AAAGGGCTTATGCCCCA
41675545 ATTATTAAAG
Statistics
Matches: 104, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
25 44 0.42
26 60 0.58
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (26 bp):
AAAGGGCTTATGCCCCAGTTTATTGA
Found at i:41675479 original size:51 final size:52
Alignment explanation
Indices: 41675400--41675544 Score: 206
Period size: 51 Copynumber: 2.8 Consensus size: 52
41675390 GAGGAAGTGC
* **
41675400 AAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTT-TTGA
1 AAAGGGCTTATGCCCTAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTGA
41675451 AAAGGGCTTATGCCCTAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTGA
1 AAAGGGCTTATGCCCTAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTGA
* * *
41675503 AAAAGGCTT-TG-CCTCAGTTTACCGAAAAGGGTTTTTGCCCCA
1 AAAGGGCTTATGCCCT-AGTTTACCGAAAAGGGCTTATGCCCCA
41675545 ATTATTAAAG
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
50 3 0.03
51 71 0.83
52 12 0.14
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (52 bp):
AAAGGGCTTATGCCCTAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTGA
Found at i:41679940 original size:90 final size:89
Alignment explanation
Indices: 41679787--41679951 Score: 294
Period size: 90 Copynumber: 1.8 Consensus size: 89
41679777 CAAGAAAATC
* *
41679787 ACCCAAGAATTCCACCATCTTTATCATCATTTCCAAAATATGACTTTTTCTGTAATGCCCCAAAA
1 ACCCAAAAATTCCACCATCTTTATCATCAATTCCAAAATATGACTTTTTCTGTAATGCCCCAAAA
41679852 ATATTAGTTCTACCCTAAACCCTAA
66 A-ATTAGTTCTACCCTAAACCCTAA
*
41679877 ACCCAAAAATTTCACCATCTTTATCATCAATTCCAAAATATGACTTTTTCTGTAATGCCCCAAAA
1 ACCCAAAAATTCCACCATCTTTATCATCAATTCCAAAATATGACTTTTTCTGTAATGCCCCAAAA
41679942 AATTAGTTCT
66 AATTAGTTCT
41679952 TTATTTCCAC
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 9 0.12
90 63 0.88
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.33
Consensus pattern (89 bp):
ACCCAAAAATTCCACCATCTTTATCATCAATTCCAAAATATGACTTTTTCTGTAATGCCCCAAAA
AATTAGTTCTACCCTAAACCCTAA
Found at i:41682443 original size:45 final size:44
Alignment explanation
Indices: 41682369--41682495 Score: 136
Period size: 45 Copynumber: 2.9 Consensus size: 44
41682359 GTGTTACATT
* * **
41682369 TATTCGGGCCTTTGAGCTTAGCAAACTATAATGCCGGTGAGATAC
1 TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGA-AC
*
41682414 TATTCGGGCCTTCGAGCCTAGTAGGCTATAATGCCGGT--GAAC
1 TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGAAC
* *
41682456 TGATATCGGGCC-TCGAGCCTAACAGGCGA-AATGCCGGTGA
1 T-AT-TCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGA
41682496 TTTGAGAAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
42 12 0.17
43 18 0.26
44 7 0.10
45 33 0.47
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (44 bp):
TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGAAC
Found at i:41692122 original size:30 final size:31
Alignment explanation
Indices: 41692074--41692131 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
41692064 TTTTTGAGCC
41692074 TAGGGGCAAAATCATAATTCTG-CAAAGGTT
1 TAGGGGCAAAATCATAATTCTGCCAAAGGTT
*
41692104 TAGGGGCAAAATTC-TAATTTTGCCAAAG
1 TAGGGGCAAAA-TCATAATTCTGCCAAAG
41692132 TTTGAGTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (31 bp):
TAGGGGCAAAATCATAATTCTGCCAAAGGTT
Found at i:41692878 original size:47 final size:46
Alignment explanation
Indices: 41692758--41693263 Score: 242
Period size: 47 Copynumber: 10.8 Consensus size: 46
41692748 GAATTGACGG
* * *
41692758 TTAAGGATGCCATGTAAGACCATGTCAAGACATGGCATTGGTAAGA
1 TTAAGGATCCCATGTAAGACCATGTCAAGACATGGCATCGGCAAGA
* * * *
41692804 -CAAGGATCCCGTGTAAGACAATGTCAAGACATGGCATCGGCATTGA
1 TTAAGGATCCCATGTAAGACCATGTCAAGACATGGCATCGGCA-AGA
** *** *
41692850 TTAAGGA-CTCCATGTAAGACCACATCAAGATGGGGCATTGGCACTAAGA
1 TTAAGGATC-CCATGTAAGACCATGTCAAGACATGGCATCGG--C-AAGA
* * * *** * *
41692899 -CAAGGATACCATGGAAGACCATGTTTGGAACATGGCATTTGGTAAGA
1 TTAAGGATCCCATGTAAGACCATGTCAAG-ACATGGCA-TCGGCAAGA
* *** * *
41692946 -TAATGG-TACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGA
1 TTAA-GGATCCCATGTAAGACCATGTCAAG-ACATGGCA-TCGGCAAGA
** * *
41692993 -TAAGGATATCATGTAAGACCATGTCAAGACATGGCATTGGAAAG-
1 TTAAGGATCCCATGTAAGACCATGTCAAGACATGGCATCGGCAAGA
** *
41693037 GCAAGGATCCCATGTAAGACCATGTCAAGACATGGCATCGGCATTGA
1 TTAAGGATCCCATGTAAGACCATGTCAAGACATGGCATCGGCA-AGA
* ** *
41693084 TTAAGGA-CTCCATGTAAGACCATATCAAGATGTGGCATTGGCACTAAGA
1 TTAAGGATC-CCATGTAAGACCATGTCAAGACATGGCATCGG--C-AAGA
* ** *** * * *
41693133 -CAAGGATAACATGTAAGACCATGTTTGGAACATGACATTTGGTAAGA
1 TTAAGGATCCCATGTAAGACCATGTCAAG-ACATGGCA-TCGGCAAGA
* * *** * *
41693180 -CAAGGATACCATGTAAGACCATGTTTGGAACATGGTATTCGGTAAGA
1 TTAAGGATCCCATGTAAGACCATGTCAAG-ACATGGCA-TCGGCAAGA
** * *
41693227 -TAAGGATATCATGTAAGACCATGCCAAGGCATGGCAT
1 TTAAGGATCCCATGTAAGACCATGTCAAGACATGGCAT
41693264 TGATAAGTTC
Statistics
Matches: 367, Mismatches: 72, Indels: 43
0.76 0.15 0.09
Matches are distributed among these distances:
45 81 0.22
46 21 0.06
47 198 0.54
48 41 0.11
49 16 0.04
50 10 0.03
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (46 bp):
TTAAGGATCCCATGTAAGACCATGTCAAGACATGGCATCGGCAAGA
Found at i:41693174 original size:234 final size:234
Alignment explanation
Indices: 41692759--41693265 Score: 854
Period size: 234 Copynumber: 2.2 Consensus size: 234
41692749 AATTGACGGT
** * *
41692759 TAAGGATGCCATGTAAGACCATGTCAAGACATGGCATTGGTAAGACAAGGATCCCGTGTAAGACA
1 TAAGGATATCATGTAAGACCATGTCAAGACATGGCATTGGAAAGACAAGGATCCCATGTAAGACA
41692824 ATGTCAAGACATGGCATCGGCATTGATTAAGGACTCCATGTAAGACCACATCAAGATGGGGCATT
66 ATGTCAAGACATGGCATCGGCATTGATTAAGGACTCCATGTAAGACCACATCAAGATGGGGCATT
* * *
41692889 GGCACTAAGACAAGGATACCATGGAAGACCATGTTTGGAACATGGCATTTGGTAAGATAATGG-T
131 GGCACTAAGACAAGGATAACATGGAAGACCATGTTTGGAACATGACATTTGGTAAGACAA-GGAT
*
41692953 ACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGA
195 ACCATGTAAGACCATGTTTGGAACATGGCATTCGGTAAGA
* *
41692993 TAAGGATATCATGTAAGACCATGTCAAGACATGGCATTGGAAAGGCAAGGATCCCATGTAAGACC
1 TAAGGATATCATGTAAGACCATGTCAAGACATGGCATTGGAAAGACAAGGATCCCATGTAAGACA
* *
41693058 ATGTCAAGACATGGCATCGGCATTGATTAAGGACTCCATGTAAGACCATATCAAGATGTGGCATT
66 ATGTCAAGACATGGCATCGGCATTGATTAAGGACTCCATGTAAGACCACATCAAGATGGGGCATT
*
41693123 GGCACTAAGACAAGGATAACATGTAAGACCATGTTTGGAACATGACATTTGGTAAGACAAGGATA
131 GGCACTAAGACAAGGATAACATGGAAGACCATGTTTGGAACATGACATTTGGTAAGACAAGGATA
*
41693188 CCATGTAAGACCATGTTTGGAACATGGTATTCGGTAAGA
196 CCATGTAAGACCATGTTTGGAACATGGCATTCGGTAAGA
* *
41693227 TAAGGATATCATGTAAGACCATGCCAAGGCATGGCATTG
1 TAAGGATATCATGTAAGACCATGTCAAGACATGGCATTG
41693266 ATAAGTTCTA
Statistics
Matches: 256, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
233 2 0.01
234 254 0.99
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (234 bp):
TAAGGATATCATGTAAGACCATGTCAAGACATGGCATTGGAAAGACAAGGATCCCATGTAAGACA
ATGTCAAGACATGGCATCGGCATTGATTAAGGACTCCATGTAAGACCACATCAAGATGGGGCATT
GGCACTAAGACAAGGATAACATGGAAGACCATGTTTGGAACATGACATTTGGTAAGACAAGGATA
CCATGTAAGACCATGTTTGGAACATGGCATTCGGTAAGA
Found at i:41693357 original size:55 final size:54
Alignment explanation
Indices: 41693228--41693424 Score: 245
Period size: 54 Copynumber: 3.6 Consensus size: 54
41693218 TCGGTAAGAT
* * *
41693228 AAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
* * * * *
41693282 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTAATGAGTTACTATAAGGAA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTT-CTATAAGG-C
* * *
41693338 AAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
* *
41693390 AAGGATACCACGTAAGACCATGTCAAGACATGGCA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCA
41693425 ATGGTAAGTT
Statistics
Matches: 122, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
52 4 0.03
53 32 0.26
54 41 0.34
55 41 0.34
56 4 0.03
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
Found at i:41695895 original size:30 final size:30
Alignment explanation
Indices: 41695861--41695921 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
41695851 TCCTTAGCTC
41695861 AAACTTTGGCAAAATTACAATTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
* * * * *
41695891 AAACTTTTGCATATTTACACTTTTTCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
41695921 A
1 A
41695922 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTGCCCCT
Found at i:41707723 original size:53 final size:53
Alignment explanation
Indices: 41707518--41707724 Score: 193
Period size: 53 Copynumber: 3.8 Consensus size: 53
41707508 ATTAGGATTT
* * * * *
41707518 AAGGATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCCACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGATAAGTT-CATAAGGC
* * * * *
41707572 AAGGAAATCATGTAAGACCATGTCAAGACATGGC-ATAGATAAACTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAAT-GAT-AAGTTC-ATAAGGC
* * * *
41707627 AAAGATCCCATGTAAGTCCATGCCAAGGCATGGCAAT-AGTAAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGA-TAAGTTCATAAGGC
* * * *
41707680 AAGGATACCATGTAAGTCCATGTCAAGATATGGAAATGATAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGATAAGTT
41707725 AAAAAGGAAA
Statistics
Matches: 122, Mismatches: 25, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
53 45 0.37
54 38 0.31
55 37 0.30
56 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGATAAGTTCATAAGGC
Found at i:41710693 original size:37 final size:37
Alignment explanation
Indices: 41710643--41710722 Score: 117
Period size: 37 Copynumber: 2.2 Consensus size: 37
41710633 CTTATTACGA
* *
41710643 AGTCTTACCCGGACATAA-TCTCCACACGAAGTTATCG
1 AGTCTTACCCGGACAAAATTC-CCACACGAAGTCATCG
*
41710680 AGTCTTACCCGGACAAAATTCCCACACGTAGTCATCG
1 AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
41710717 AGTCTT
1 AGTCTT
41710723 TAGAGCTCGG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
37 37 0.95
38 2 0.05
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (37 bp):
AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
Found at i:41710918 original size:47 final size:47
Alignment explanation
Indices: 41710840--41711360 Score: 862
Period size: 47 Copynumber: 11.0 Consensus size: 47
41710830 CCCTTCGGGA
* * * * * * *
41710840 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
41710887 CCTGTCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41710934 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41710981 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41711028 CTTATCACATATATACACTTTTACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41711075 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41711122 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41711169 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41711216 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41711265 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41711312 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41711359 CT
1 CT
41711361 CACTATCATT
Statistics
Matches: 449, Mismatches: 23, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
47 403 0.90
49 46 0.10
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41715210 original size:25 final size:24
Alignment explanation
Indices: 41715172--41715241 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 24
41715162 AGGAAGTGCT
* *
41715172 AAAACGGCTCTGCCCTC-GTTTACC
1 AAAAGGGCTTTGCCC-CAGTTTACC
*
41715196 GAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTACC
41715221 AGAAAGGGCTTTGCCCCAGTT
1 A-AAAGGGCTTTGCCCCAGTT
41715242 ATTAAAAGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
24 2 0.05
25 38 0.95
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTACC
Found at i:41715254 original size:24 final size:23
Alignment explanation
Indices: 41715197--41715268 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 23
41715187 TCGTTTACCG
41715197 AAAAGGGCTTTGCCCCAGTTTATC
1 AAAAGGGCTTTGCCCCAG-TTATC
*
41715221 AGAAAGGGCTTTGCCCCAGTTATT
1 A-AAAGGGCTTTGCCCCAGTTATC
**
41715245 AAAAGAGGCTAGGCCTCCAGTTAT
1 AAAAG-GGCTTTGCC-CCAGTTAT
41715269 ATGATAAAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
23 4 0.10
24 13 0.31
25 25 0.60
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (23 bp):
AAAAGGGCTTTGCCCCAGTTATC
Found at i:41715453 original size:41 final size:42
Alignment explanation
Indices: 41715389--41715480 Score: 141
Period size: 41 Copynumber: 2.2 Consensus size: 42
41715379 TAGTCTCCCC
* *
41715389 AAATAGGCTTGCATACATTCATTGACATGACATGTGATATT-
1 AAATGGGCTTGCATACATCCATTGACATGACATGTGATATTG
* *
41715430 AAATGGGCTTGCATACATCCATTGACATTATATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATGACATGTGATATTG
41715472 AAATGGGCT
1 AAATGGGCT
41715481 AAGGGCCATA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 37 0.80
42 9 0.20
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.34
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATGACATGTGATATTG
Found at i:41715541 original size:31 final size:31
Alignment explanation
Indices: 41715502--41715616 Score: 207
Period size: 31 Copynumber: 3.8 Consensus size: 31
41715492 CGTTTACAGT
41715502 AAAA-GCTTCGGCCCAGTGATATGATTTATG
1 AAAAGGCTTCGGCCCAGTGATATGATTTATG
41715532 AAAAGGCTTCGGCCCAGTGATATGATTTATG
1 AAAAGGCTTCGGCCCAGTGATATGATTTATG
41715563 AAAAGGCTTCGGCCCAGTGATATGATTTATG
1 AAAAGGCTTCGGCCCAGTGATATGATTTATG
*
41715594 GAAAGGCTTCGGCCCAGT-ATATG
1 AAAAGGCTTCGGCCCAGTGATATG
41715617 TCAAGACTAA
Statistics
Matches: 83, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
30 9 0.11
31 74 0.89
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (31 bp):
AAAAGGCTTCGGCCCAGTGATATGATTTATG
Found at i:41716376 original size:16 final size:16
Alignment explanation
Indices: 41716355--41716394 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
41716345 ACATATCATT
41716355 TATTTCATTATATCAA
1 TATTTCATTATATCAA
41716371 TATTTCATTATATCAA
1 TATTTCATTATATCAA
41716387 TATTTCAT
1 TATTTCAT
41716395 ATACCGTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTTCATTATATCAA
Found at i:41724162 original size:53 final size:53
Alignment explanation
Indices: 41723980--41724183 Score: 182
Period size: 53 Copynumber: 3.8 Consensus size: 53
41723970 ATTAGGGTTT
* * *
41723980 AAGGATACCAAGTAAGACCATGCCAAGGA-ATGGCATTGGTAACTTC-TACACGGC
1 AAGGATACCATGTAAGACCATGTCAA-GACATGGCAATGGTAACTTCATA-A-GGC
* * * ** *
41724034 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTAATAAACTACTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGT-AACTTC-ATAAGGC
* * * *
41724089 AAAGAT-CTCATGTAAGACCATG-CTAAGGCATGGCAATGGTGAGTTCATAAGGC
1 AAGGATAC-CATGTAAGACCATGTC-AAGACATGGCAATGGTAACTTCATAAGGC
* *
41724142 AAGGATACCACGTAAGACCATGTCAAGACATGGAAATGGTAA
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAA
41724184 GTTAAAAAGG
Statistics
Matches: 120, Mismatches: 22, Indels: 17
0.75 0.14 0.11
Matches are distributed among these distances:
53 42 0.35
54 37 0.31
55 38 0.32
56 1 0.01
57 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAACTTCATAAGGC
Found at i:41740116 original size:28 final size:28
Alignment explanation
Indices: 41740065--41740119 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
41740055 ACAGGGGTTT
*
41740065 TCACACGGCCTGACACATGCCCGTGTCCC
1 TCACACAGCCTGACACA-GCCCGTGTCCC
41740094 TCACACAGCCATGACAC-GCCCGTGTC
1 TCACACAGCC-TGACACAGCCCGTGTC
41740120 TTAGCCCGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 9 0.38
29 9 0.38
30 6 0.25
ACGTcount: A:0.20, C:0.44, G:0.20, T:0.16
Consensus pattern (28 bp):
TCACACAGCCTGACACAGCCCGTGTCCC
Found at i:41742445 original size:16 final size:16
Alignment explanation
Indices: 41742426--41742456 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41742416 CTTCTTCACT
41742426 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
41742442 TACTTACTTACTTAA
1 TACTCACTTACTTAA
41742457 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:41742462 original size:20 final size:20
Alignment explanation
Indices: 41742423--41742462 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
41742413 AAACTTCTTC
* *
41742423 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
41742443 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
41742463 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:41742839 original size:108 final size:110
Alignment explanation
Indices: 41742695--41742891 Score: 290
Period size: 108 Copynumber: 1.8 Consensus size: 110
41742685 ATCCTTTTGA
* * * **
41742695 AACTTACCATTGCCATGTCTTCACATGGTCTTACATGGTATCCTTGCCTTATGAA-CTAACCAA-
1 AACTTACCAATGCCATGTCTTCACATGGTCTTACATGATATCCTTGCCATACAAACCTAACCAAT
41742758 TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTTCCTTATAGT
66 TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTTCCTTATAGT
* * * *
41742803 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCATACAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTCACATGGTCTTACATGATATCCTTGCCATACAAACCTAACCAAT
*
41742868 TTCCATGCCTTGGCATGGTCTTAC
66 TGCCATGCCTTGGCATGGTCTTAC
41742892 GTGGTTTCCT
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
108 47 0.61
109 7 0.09
110 23 0.30
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.35
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTCACATGGTCTTACATGATATCCTTGCCATACAAACCTAACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTTCCTTATAGT
Found at i:41742900 original size:55 final size:54
Alignment explanation
Indices: 41742648--41742902 Score: 206
Period size: 55 Copynumber: 4.8 Consensus size: 54
41742638 ACATGGGTAC
* * * *
41742648 CTTACC-ATTGCCATGACTTGTCATGGTCTTACGTGGTATCCTT----TTGAAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCATAGAAA
* * *
41742697 CTTACC-ATTGCCATGTCTTCACATGGTCTTACATGGTATCCTTGCCTTATG-AA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCATA-GAAA
* * * * *
41742750 CTAACCAA-TGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTTCCTTATAGTAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCC--ATAGAAA
* * * * *
41742805 CTTATCAA-TGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCATACAAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCATAGAAA
* * * *
41742858 CCTTACCAATTTCCATGCCTTGGCATGGTCTTACGTGGTTTCCTT
1 -CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTT
41742903 AAACCCTAAT
Statistics
Matches: 165, Mismatches: 28, Indels: 20
0.77 0.13 0.09
Matches are distributed among these distances:
49 39 0.24
52 2 0.01
53 43 0.26
54 10 0.06
55 69 0.42
56 2 0.01
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.37
Consensus pattern (54 bp):
CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCATAGAAA
Found at i:41761602 original size:44 final size:47
Alignment explanation
Indices: 41761440--41761606 Score: 141
Period size: 46 Copynumber: 3.6 Consensus size: 47
41761430 CAGATGAGGT
* * * * *
41761440 CTAGTGTAAGACATGTCTGGGACATGCTTCAGCCAT-ATTA-TGA-GTG
1 CTAGTGTAAAACATGTCTGGGACATGCATCGGCC-TCA-CAGAGATGTG
* * *
41761486 CTAGAGTAAGACATGTCTGGGACATGCATCGGCCTCGACAGAGAT-AG
1 CTAGTGTAAAACATGTCTGGGACATGCATCGGCCTC-ACAGAGATGTG
* * * * *
41761533 CCAGTGTAAAACGTGTTTGGCACATGCATCGG-CT-A-AGAGTTGTG
1 CTAGTGTAAAACATGTCTGGGACATGCATCGGCCTCACAGAGATGTG
41761577 CTAGTGTAAAACATGTCTGGGACATGCATC
1 CTAGTGTAAAACATGTCTGGGACATGCATC
41761607 AGCTCGCATA
Statistics
Matches: 98, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
43 5 0.05
44 28 0.29
45 1 0.01
46 34 0.35
47 30 0.31
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26
Consensus pattern (47 bp):
CTAGTGTAAAACATGTCTGGGACATGCATCGGCCTCACAGAGATGTG
Found at i:41763674 original size:42 final size:40
Alignment explanation
Indices: 41763605--41763734 Score: 163
Period size: 42 Copynumber: 3.2 Consensus size: 40
41763595 GATATCTTGT
* *
41763605 ACACTAAGTGTCGTACATAGCCGAAGCTATCTCAAATCGC
1 ACACTAAGTGTCATATATAGCCGAAGCTATCTCAAATCGC
* *
41763645 ACACTAAGTGTCATATATATAGCCGAAGCTATCTCAATCTCCC
1 ACACTAAGTGTC--ATATATAGCCGAAGCTATCTCAA-ATCGC
*
41763688 ACACTAAGTGCCATATATAGCCGAAGCTATGC-CAAATCGC
1 ACACTAAGTGTCATATATAGCCGAAGCTAT-CTCAAATCGC
*
41763728 ATACTAA
1 ACACTAA
41763735 ATGCCACATA
Statistics
Matches: 78, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
40 21 0.27
41 21 0.27
42 22 0.28
43 14 0.18
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.24
Consensus pattern (40 bp):
ACACTAAGTGTCATATATAGCCGAAGCTATCTCAAATCGC
Found at i:41763716 original size:41 final size:40
Alignment explanation
Indices: 41763605--41763747 Score: 153
Period size: 40 Copynumber: 3.5 Consensus size: 40
41763595 GATATCTTGT
* * * *
41763605 ACACTAAGTGTCGTACATAGCCGAAGCTATCTCAAATCGC
1 ACACTAAGTGCCATATATAGCCGAAGCTATCTCAAATCCC
* *
41763645 ACACTAAGTGTCATATATATAGCCGAAGCTATCTCAATCTCCC
1 ACACTAAGTG-C-CATATATAGCCGAAGCTATCTCAA-ATCCC
*
41763688 ACACTAAGTGCCATATATAGCCGAAGCTATGC-CAAATCGC
1 ACACTAAGTGCCATATATAGCCGAAGCTAT-CTCAAATCCC
* * *
41763728 ATACTAAATGCCACATATAG
1 ACACTAAGTGCCATATATAG
41763748 TTGATTTATC
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
40 30 0.34
41 21 0.24
42 23 0.26
43 13 0.15
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.24
Consensus pattern (40 bp):
ACACTAAGTGCCATATATAGCCGAAGCTATCTCAAATCCC
Found at i:41768778 original size:26 final size:26
Alignment explanation
Indices: 41768727--41768781 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
41768717 ATAAGTATGA
*
41768727 ATATATAACAAATTTTCTTTAAAAAT
1 ATATATAACAAATTTTCTATAAAAAT
*
41768753 ATATATAACAAA-TTTGTATAATAAAT
1 ATATATAACAAATTTTCTATAA-AAAT
41768779 ATA
1 ATA
41768782 CTTATTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (26 bp):
ATATATAACAAATTTTCTATAAAAAT
Found at i:41773762 original size:15 final size:14
Alignment explanation
Indices: 41773742--41773776 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
41773732 TTTACATTTC
*
41773742 AATTTTAAATTTTAA
1 AATTTTAAA-ATTAA
41773757 AATTTTAAAATTAA
1 AATTTTAAAATTAA
41773771 AATTTT
1 AATTTT
41773777 CATAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AATTTTAAAATTAA
Found at i:41776150 original size:28 final size:28
Alignment explanation
Indices: 41776110--41776192 Score: 150
Period size: 28 Copynumber: 3.0 Consensus size: 28
41776100 ACCATAGGCC
41776110 CATGTGTGACATATAGTCGTATGGCTAA
1 CATGTGTGACATATAGTCGTATGGCTAA
41776138 CATGTGTGACATATAGTCGTATGGCTAA
1 CATGTGTGACATATAGTCGTATGGCTAA
*
41776166 CATGTGTGACATATAGT-GTGTGGCTAA
1 CATGTGTGACATATAGTCGTATGGCTAA
41776193 GCCATGTGGC
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
27 9 0.17
28 45 0.83
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.33
Consensus pattern (28 bp):
CATGTGTGACATATAGTCGTATGGCTAA
Found at i:41793933 original size:225 final size:224
Alignment explanation
Indices: 41793513--41793961 Score: 772
Period size: 225 Copynumber: 2.0 Consensus size: 224
41793503 GTTTTTGCTG
* *
41793513 GGCATTATCAAGCTAGTTATAGAAGACTATCGAGCCATCGTAGCCTGACCTCTGAACATGTCTTC
1 GGCATTATCAAGCTAGTTATAGAAGACTATCGAGCCATCGTAGCCTAACCTCCGAACATGTCTTC
* *
41793578 TAGCTTATCCAGAATTACTTTGGCAATATTGCAGCTCTTCAGCTGCTTATATAAAGTGTTGGTTA
66 TAGCTTATCCAGAATCACTTTGGCAATATTACAGCTCTTCAGCTGCTTATATAAAGTGTTGGTTA
*
41793643 TGCTTGCCAGCATATAGTAATGAGCTATCTGATCAGACTCCTTGCAACATTGTCTAGCCTCAATT
131 TGCTTGCCAGCATATAGCAATGAGCTATCTGATCAGACTCCTTGCAACATTGTCTAGCCTCAATT
41793708 TGAGTAACCGGTGGGCGCTTATTATCAAA
196 TGAGTAACCGGTGGGCGCTTATTATCAAA
41793737 GGCATTCATCAAGCTAGTTATAGAAGACTATCGAGCCATCGTAGCCTAACCTCCGAACATGTCTT
1 GGCATT-ATCAAGCTAGTTATAGAAGACTATCGAGCCATCGTAGCCTAACCTCCGAACATGTCTT
* *
41793802 CTAGTTTATCCAGAATCATTTTGGCAATATTACAGCTCTTCAGCTGCTTATATAAAGTGTTGGTT
65 CTAGCTTATCCAGAATCACTTTGGCAATATTACAGCTCTTCAGCTGCTTATATAAAGTGTTGGTT
* * * * *
41793867 ATGCTTGCCAGCATATAGCAATGAGCTATCTGATCATACTTCTTGCAGCATTGTTTAGCTTCAAT
130 ATGCTTGCCAGCATATAGCAATGAGCTATCTGATCAGACTCCTTGCAACATTGTCTAGCCTCAAT
*
41793932 TTGAGTAGCCGGTGGGCGCTTATTATCAAA
195 TTGAGTAACCGGTGGGCGCTTATTATCAAA
41793962 AACTATTTTA
Statistics
Matches: 211, Mismatches: 13, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
224 6 0.03
225 205 0.97
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (224 bp):
GGCATTATCAAGCTAGTTATAGAAGACTATCGAGCCATCGTAGCCTAACCTCCGAACATGTCTTC
TAGCTTATCCAGAATCACTTTGGCAATATTACAGCTCTTCAGCTGCTTATATAAAGTGTTGGTTA
TGCTTGCCAGCATATAGCAATGAGCTATCTGATCAGACTCCTTGCAACATTGTCTAGCCTCAATT
TGAGTAACCGGTGGGCGCTTATTATCAAA
Found at i:41794433 original size:23 final size:23
Alignment explanation
Indices: 41794403--41794452 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
41794393 GTTACATAAC
*
41794403 CATGAACTTAACACCT-ATCGCAT
1 CATGAACTCAACA-CTGATCGCAT
*
41794426 CATGAACTCAACATTGATCGCAT
1 CATGAACTCAACACTGATCGCAT
41794449 CATG
1 CATG
41794453 CACAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (23 bp):
CATGAACTCAACACTGATCGCAT
Found at i:41796512 original size:16 final size:16
Alignment explanation
Indices: 41796502--41796544 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
41796492 CCATAATAGT
41796502 CACATATCAT-ATAAA
1 CACATATCATAATAAA
* *
41796517 CACATATCACAATACA
1 CACATATCATAATAAA
41796533 CACATATTCATA
1 CACATA-TCATA
41796545 TATTATGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 9 0.39
16 10 0.43
17 4 0.17
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (16 bp):
CACATATCATAATAAA
Done.