Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6
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: 4312818
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 226954 characters in sequence are not A, C, G, or T
File 7 of 14
Found at i:2238198 original size:25 final size:24
Alignment explanation
Indices: 2238157--2238227 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 24
2238147 AAATAATTAT
*
2238157 AATTATAAT-TTAATTATATTTAAAA
1 AATT-TAATATTATTTAT-TTTAAAA
*
2238182 AATTTAATATTATTTATTTTCAAA
1 AATTTAATATTATTTATTTTAAAA
**
2238206 TTTTTCAATATTATTTATTTTA
1 AATTT-AATATTATTTATTTTA
2238228 TGCATCATCT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
24 13 0.33
25 26 0.67
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (24 bp):
AATTTAATATTATTTATTTTAAAA
Found at i:2243818 original size:12 final size:11
Alignment explanation
Indices: 2243800--2243851 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
2243790 AAAACAACTA
2243800 AAAATAAAAAT
1 AAAATAAAAAT
*
2243811 AAACATAAACAT
1 AAA-ATAAAAAT
2243823 AAAATAAAAA-
1 AAAATAAAAAT
* *
2243833 AAACTAAAAAG
1 AAAATAAAAAT
2243844 AAAATAAA
1 AAAATAAA
2243852 TAAACTTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
10 9 0.26
11 16 0.46
12 10 0.29
ACGTcount: A:0.79, C:0.06, G:0.02, T:0.13
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:2244185 original size:20 final size:20
Alignment explanation
Indices: 2244160--2244202 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
2244150 GAGGATCCAC
2244160 TCCATGAAGTCGCTCAATAA
1 TCCATGAAGTCGCTCAATAA
*
2244180 TCCATGAAGTCGCTCAATCA
1 TCCATGAAGTCGCTCAATAA
2244200 TCC
1 TCC
2244203 TCATATGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (20 bp):
TCCATGAAGTCGCTCAATAA
Found at i:2245406 original size:19 final size:18
Alignment explanation
Indices: 2245371--2245428 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 18
2245361 ACTGAGGAAG
2245371 AAAAAGAAAAGTAATAAGAA
1 AAAAAG-AAA-TAATAAGAA
2245391 AATAAAGAAATAATAA-AA
1 AA-AAAGAAATAATAAGAA
*
2245409 ACAAAAGCAATAA-AAGAA
1 A-AAAAGAAATAATAAGAA
2245427 AA
1 AA
2245429 CAATTAAGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
17 3 0.09
18 15 0.44
19 7 0.21
20 5 0.15
21 4 0.12
ACGTcount: A:0.76, C:0.03, G:0.10, T:0.10
Consensus pattern (18 bp):
AAAAAGAAATAATAAGAA
Found at i:2250618 original size:18 final size:18
Alignment explanation
Indices: 2250595--2250632 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2250585 GACCAAAGGG
* *
2250595 TAAATATTCTGGATTATT
1 TAAATATTCTCGATAATT
2250613 TAAATATTCTCGATAATT
1 TAAATATTCTCGATAATT
2250631 TA
1 TA
2250633 TTCCACCTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (18 bp):
TAAATATTCTCGATAATT
Found at i:2251694 original size:18 final size:18
Alignment explanation
Indices: 2251673--2251714 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2251663 ATTAGAATGT
*
2251673 AAAAATTACACTAAAAAC
1 AAAAATTACAATAAAAAC
* *
2251691 AAAAATTATAATAAAAAT
1 AAAAATTACAATAAAAAC
2251709 AAAAAT
1 AAAAAT
2251715 GGCTAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAAATTACAATAAAAAC
Found at i:2252356 original size:43 final size:43
Alignment explanation
Indices: 2252298--2252536 Score: 388
Period size: 43 Copynumber: 5.6 Consensus size: 43
2252288 TTACAAAAAT
* * *
2252298 GCCGCTAAAGGTCATGACCTTTAGCGGTGCTTCTCCCACAAAC
1 GCCGCTATAGATCATGACTTTTAGCGGTGCTTCTCCCACAAAC
* * *
2252341 ACCGCTACAGATCATGACCTTTAGCGGTGCTTCTCCCACAAAC
1 GCCGCTATAGATCATGACTTTTAGCGGTGCTTCTCCCACAAAC
**
2252384 GCCGCTATAGATCATGACTTTTAGCGGCACTTCTCCCACAAAC
1 GCCGCTATAGATCATGACTTTTAGCGGTGCTTCTCCCACAAAC
**
2252427 GCCGCTATAGATCATGACTTTTAGCGGCACTTCTCCCACAAAC
1 GCCGCTATAGATCATGACTTTTAGCGGTGCTTCTCCCACAAAC
2252470 GCCGCTATAGATCATGACTTTTAGCGGTGCTTCTCCCACAAAC
1 GCCGCTATAGATCATGACTTTTAGCGGTGCTTCTCCCACAAAC
2252513 GCCGCTATAGATCATGACTTTTAG
1 GCCGCTATAGATCATGACTTTTAG
2252537 TGGCACTTTT
Statistics
Matches: 186, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 186 1.00
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (43 bp):
GCCGCTATAGATCATGACTTTTAGCGGTGCTTCTCCCACAAAC
Found at i:2252528 original size:129 final size:129
Alignment explanation
Indices: 2252298--2252581 Score: 419
Period size: 129 Copynumber: 2.2 Consensus size: 129
2252288 TTACAAAAAT
* **
2252298 GCCGCTAAAGGTCATGACCTTTAGCGGTGCTTCTCCCACAAACACCGCTACAGATCATGACCTTT
1 GCCGCTAAAGATCATGACCTTTAGCGGCACTTCTCCCACAAACACCGCTACAGATCATGACCTTT
2252363 AGCGGTGCTTCTCCCACAAACGCCGCTATAGATCATGACTTTTAGCGGCACTTCTCCCACAAAC
66 AGCGGTGCTTCTCCCACAAACGCCGCTATAGATCATGACTTTTAGCGGCACTTCTCCCACAAAC
* * * * *
2252427 GCCGCTATAGATCATGACTTTTAGCGGCACTTCTCCCACAAACGCCGCTATAGATCATGACTTTT
1 GCCGCTAAAGATCATGACCTTTAGCGGCACTTCTCCCACAAACACCGCTACAGATCATGACCTTT
* *** *
2252492 AGCGGTGCTTCTCCCACAAACGCCGCTATAGATCATGACTTTTAGTGGCACTT-TTTTATAAAC
66 AGCGGTGCTTCTCCCACAAACGCCGCTATAGATCATGACTTTTAGCGGCACTTCTCCCACAAAC
* *
2252555 GCCGCTAAAGAACACGA-CTTTAGCGGC
1 GCCGCTAAAGATCATGACCTTTAGCGGC
2252582 GTTTTTTAAA
Statistics
Matches: 138, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
127 9 0.07
128 20 0.14
129 109 0.79
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.26
Consensus pattern (129 bp):
GCCGCTAAAGATCATGACCTTTAGCGGCACTTCTCCCACAAACACCGCTACAGATCATGACCTTT
AGCGGTGCTTCTCCCACAAACGCCGCTATAGATCATGACTTTTAGCGGCACTTCTCCCACAAAC
Found at i:2252973 original size:21 final size:21
Alignment explanation
Indices: 2252949--2252991 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2252939 TTTCTTTGAA
*
2252949 CCTCAGCTTCTCTCGATGCTG
1 CCTCAGCTTCCCTCGATGCTG
* *
2252970 CCTCTGCTTCCCTCGCTGCTG
1 CCTCAGCTTCCCTCGATGCTG
2252991 C
1 C
2252992 ATTTGCTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.05, C:0.44, G:0.19, T:0.33
Consensus pattern (21 bp):
CCTCAGCTTCCCTCGATGCTG
Found at i:2252998 original size:21 final size:21
Alignment explanation
Indices: 2252954--2252999 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2252944 TTGAACCTCA
* *
2252954 GCTTCTCTCGATGCTGCCTCT
1 GCTTCCCTCGATGCTGCATCT
* *
2252975 GCTTCCCTCGCTGCTGCATTT
1 GCTTCCCTCGATGCTGCATCT
2252996 GCTT
1 GCTT
2253000 TAAGTTGTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.04, C:0.37, G:0.20, T:0.39
Consensus pattern (21 bp):
GCTTCCCTCGATGCTGCATCT
Found at i:2253000 original size:87 final size:87
Alignment explanation
Indices: 2252887--2253065 Score: 259
Period size: 87 Copynumber: 2.1 Consensus size: 87
2252877 CTTTCTCCTT
* * *
2252887 TGCTTCTCTCGCTGCTGCGTCAGCTTTAAGTTGTAGCTAGAGTTCTTCATGTTTTCTTTGAACCT
1 TGCTTCCCTCGCTGCTGCATCAGCTTTAAGTTGTAGCTAGAGTTCTTCATATTTTCTTTGAACCT
2252952 CAGCTTCTCTCGATGCTGCCTC
66 CAGCTTCTCTCGATGCTGCCTC
** * * * *
2252974 TGCTTCCCTCGCTGCTGCATTTGCTTTAAGTTGTGGTTGGAGTTCTTCATATTTTCTTTGGACCT
1 TGCTTCCCTCGCTGCTGCATCAGCTTTAAGTTGTAGCTAGAGTTCTTCATATTTTCTTTGAACCT
*
2253039 CAGCTTCTCTCGGTGCTGCCTC
66 CAGCTTCTCTCGATGCTGCCTC
*
2253061 CGCTT
1 TGCTT
2253066 TAAGTTGAGT
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.11, C:0.27, G:0.21, T:0.41
Consensus pattern (87 bp):
TGCTTCCCTCGCTGCTGCATCAGCTTTAAGTTGTAGCTAGAGTTCTTCATATTTTCTTTGAACCT
CAGCTTCTCTCGATGCTGCCTC
Found at i:2258666 original size:9 final size:9
Alignment explanation
Indices: 2258652--2258790 Score: 92
Period size: 9 Copynumber: 15.6 Consensus size: 9
2258642 TGATACATTT
*
2258652 TAAGTTAGG
1 TAAGTTATG
2258661 TAAGTTATG
1 TAAGTTATG
*
2258670 CAAGTTATG
1 TAAGTTATG
2258679 TAAGTTATG
1 TAAGTTATG
*
2258688 --A-TATATA
1 TAAGT-TATG
*
2258695 TAAGTTGT-
1 TAAGTTATG
*
2258703 TAACTTATG
1 TAAGTTATG
2258712 TAAGTTATG
1 TAAGTTATG
*
2258721 TGAGTTATG
1 TAAGTTATG
2258730 T-AGATTATG
1 TAAG-TTATG
* *
2258739 ATATGATATATA
1 -TAAG-T-TATG
2258751 TAAGTTAT-
1 TAAGTTATG
*
2258759 TAAGTTAGG
1 TAAGTTATG
2258768 TAAGTTATG
1 TAAGTTATG
* *
2258777 TGAGTTATT
1 TAAGTTATG
2258786 TAAGT
1 TAAGT
2258791 AATGGTATNN
Statistics
Matches: 103, Mismatches: 17, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
6 1 0.01
7 4 0.04
8 15 0.15
9 71 0.69
10 3 0.03
11 6 0.06
12 3 0.03
ACGTcount: A:0.35, C:0.01, G:0.21, T:0.43
Consensus pattern (9 bp):
TAAGTTATG
Found at i:2258711 original size:100 final size:98
Alignment explanation
Indices: 2258588--2258784 Score: 304
Period size: 100 Copynumber: 2.0 Consensus size: 98
2258578 TTATATATAT
* *
2258588 ATATATATAAGTTGTTAAGTTATGTAACTTATGTGAGTTATGTAGATTATGATATGATACATTTT
1 ATATATATAAGTTGTTAACTTATGTAACTTATGTGAGTTATGTAGATTATGATATGATACA-TAT
*
2258653 AAGTTAGGTAAGTTATGCAAGTTATGTAAGTTATG
65 AAGTTA-GTAAGTTAGGCAAGTTATGTAAGTTATG
* *
2258688 ATATATATAAGTTGTTAACTTATGTAAGTTATGTGAGTTATGTAGATTATGATATGATATATATA
1 ATATATATAAGTTGTTAACTTATGTAACTTATGTGAGTTATGTAGATTATGATATGATACATATA
* * *
2258753 AGTTATTAAGTTAGGTAAGTTATGTGAGTTAT
66 AGTTAGTAAGTTAGGCAAGTTATGTAAGTTAT
2258785 TTAAGTAATG
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
98 23 0.26
99 8 0.09
100 58 0.65
ACGTcount: A:0.35, C:0.02, G:0.20, T:0.44
Consensus pattern (98 bp):
ATATATATAAGTTGTTAACTTATGTAACTTATGTGAGTTATGTAGATTATGATATGATACATATA
AGTTAGTAAGTTAGGCAAGTTATGTAAGTTATG
Found at i:2258930 original size:18 final size:18
Alignment explanation
Indices: 2258907--2259303 Score: 147
Period size: 18 Copynumber: 22.1 Consensus size: 18
2258897 NNNNNNNNNN
*
2258907 TTATGTAAGTTATGTGAG
1 TTATGTAAGTTATGTAAG
*
2258925 TTATGT-AGATTATGATATG
1 TTATGTAAG-TTATG-TAAG
* *
2258944 ATACATATAAGTTAT-TAAG
1 -T-TATGTAAGTTATGTAAG
* *
2258963 TTAGGTAAGTTATGCAAG
1 TTATGTAAGTTATGTAAG
2258981 TTATGTAAGTTATGATAA-
1 TTATGTAAGTTATG-TAAG
* *
2258999 --ATATAAG-T-TGCTAAC
1 TTATGTAAGTTATG-TAAG
*
2259014 TTATGTAAGTTATGTGAG
1 TTATGTAAGTTATGTAAG
*
2259032 TTATGT-AGATTATGATAGG
1 TTATGTAAG-TTATG-TAAG
* * *
2259051 ATACATATAAGTGAT-TAAG
1 -T-TATGTAAGTTATGTAAG
* *
2259070 TTAGGTAAGTTATGCAAG
1 TTATGTAAGTTATGTAAG
*
2259088 TCATGTAAGTTATGATAA-
1 TTATGTAAGTTATG-TAAG
* *
2259106 --ATATAAG-T-TGCTAAC
1 TTATGTAAGTTATG-TAAG
*
2259121 TTATGTAAGTTATGTGAG
1 TTATGTAAGTTATGTAAG
*
2259139 TTATGT-AGATTATGATAGG
1 TTATGTAAG-TTATG-TAAG
* * *
2259158 ATACATATAAGTGAT-TAAG
1 -T-TATGTAAGTTATGTAAG
* *
2259177 TTAGGTAAGTTATGCAAG
1 TTATGTAAGTTATGTAAG
*
2259195 TCATGTAAGTTATGATAA-
1 TTATGTAAGTTATG-TAAG
* *
2259213 --ATATAAG-T-TGCTAAC
1 TTATGTAAGTTATG-TAAG
*
2259228 TTATGTAAGTTATGTGAG
1 TTATGTAAGTTATGTAAG
*
2259246 TTATGT-AGATTATGATATG
1 TTATGTAAG-TTATG-TAAG
*
2259265 ATATATATAAGTTAT-TAAG
1 -T-TATGTAAGTTATGTAAG
*
2259284 TTATGTAAGTTATGTGAG
1 TTATGTAAGTTATGTAAG
2259302 TT
1 TT
2259304 TCTGGGATTA
Statistics
Matches: 277, Mismatches: 60, Indels: 84
0.66 0.14 0.20
Matches are distributed among these distances:
14 15 0.05
15 3 0.01
16 18 0.06
17 62 0.22
18 108 0.39
19 32 0.12
20 4 0.01
21 27 0.10
22 8 0.03
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (18 bp):
TTATGTAAGTTATGTAAG
Found at i:2258997 original size:56 final size:55
Alignment explanation
Indices: 2258907--2259303 Score: 410
Period size: 56 Copynumber: 7.4 Consensus size: 55
2258897 NNNNNNNNNN
2258907 TTATGTAAGTTATGTGAGTTATGTAGATTATGATATGATACATATAAGTTATTAAG
1 TTATGTAAGTTATGTGAGTTATGTAGATTATGATATGATA-ATATAAGTTATTAAG
* ** ** *
2258963 TTAGGTAAGTTATGCAAGTTATGTA-AGTTATG--AT-A-AATATAAGTTGCTAAC
1 TTATGTAAGTTATGTGAGTTATGTAGA-TTATGATATGATAATATAAGTTATTAAG
* *
2259014 TTATGTAAGTTATGTGAGTTATGTAGATTATGATAGGATACATATAAGTGATTAAG
1 TTATGTAAGTTATGTGAGTTATGTAGATTATGATATGATA-ATATAAGTTATTAAG
* ** * ** *
2259070 TTAGGTAAGTTATGCAAGTCATGTA-AGTTATG--AT-A-AATATAAGTTGCTAAC
1 TTATGTAAGTTATGTGAGTTATGTAGA-TTATGATATGATAATATAAGTTATTAAG
* *
2259121 TTATGTAAGTTATGTGAGTTATGTAGATTATGATAGGATACATATAAGTGATTAAG
1 TTATGTAAGTTATGTGAGTTATGTAGATTATGATATGATA-ATATAAGTTATTAAG
* ** * ** *
2259177 TTAGGTAAGTTATGCAAGTCATGTA-AGTTATG--AT-A-AATATAAGTTGCTAAC
1 TTATGTAAGTTATGTGAGTTATGTAGA-TTATGATATGATAATATAAGTTATTAAG
2259228 TTATGTAAGTTATGTGAGTTATGTAGATTATGATATGATATATATAAGTTATTAAG
1 TTATGTAAGTTATGTGAGTTATGTAGATTATGATATGATA-ATATAAGTTATTAAG
2259284 TTATGTAAGTTATGTGAGTT
1 TTATGTAAGTTATGTGAGTT
2259304 TCTGGGATTA
Statistics
Matches: 272, Mismatches: 48, Indels: 42
0.75 0.13 0.12
Matches are distributed among these distances:
51 113 0.42
52 6 0.02
53 7 0.03
54 7 0.03
55 6 0.02
56 133 0.49
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (55 bp):
TTATGTAAGTTATGTGAGTTATGTAGATTATGATATGATAATATAAGTTATTAAG
Found at i:2259022 original size:51 final size:51
Alignment explanation
Indices: 2258911--2259262 Score: 309
Period size: 51 Copynumber: 6.6 Consensus size: 51
2258901 NNNNNNTTAT
** ** *
2258911 GTAAGTTATGTGAGTTATGTAGATTATGATATGATACATATAAGTTATTAAGTTAG
1 GTAAGTTATGCAAGTTATGTAGATTATG--AT-A-A-ATATAAGTTGCTAACTTAG
*
2258967 GTAAGTTATGCAAGTTATGTA-AGTTATGATAAATATAAGTTGCTAACTTAT
1 GTAAGTTATGCAAGTTATGTAGA-TTATGATAAATATAAGTTGCTAACTTAG
** * *
2259018 GTAAGTTATGTGAGTTATGTAGATTATGATAGGATACATATAAG-TGATTAAGTTAG
1 GTAAGTTATGCAAGTTATGTAGATTATGAT---A-A-ATATAAGTTG-CTAACTTAG
* *
2259074 GTAAGTTATGCAAGTCATGTA-AGTTATGATAAATATAAGTTGCTAACTTAT
1 GTAAGTTATGCAAGTTATGTAGA-TTATGATAAATATAAGTTGCTAACTTAG
** * *
2259125 GTAAGTTATGTGAGTTATGTAGATTATGATAGGATACATATAAG-TGATTAAGTTAG
1 GTAAGTTATGCAAGTTATGTAGATTATGAT---A-A-ATATAAGTTG-CTAACTTAG
* *
2259181 GTAAGTTATGCAAGTCATGTA-AGTTATGATAAATATAAGTTGCTAACTTAT
1 GTAAGTTATGCAAGTTATGTAGA-TTATGATAAATATAAGTTGCTAACTTAG
**
2259232 GTAAGTTATGTGAGTTATGTAGATTATGATA
1 GTAAGTTATGCAAGTTATGTAGATTATGATA
2259263 TGATATATAT
Statistics
Matches: 244, Mismatches: 32, Indels: 45
0.76 0.10 0.14
Matches are distributed among these distances:
51 118 0.48
52 10 0.04
53 3 0.01
54 4 0.02
55 9 0.04
56 100 0.41
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.39
Consensus pattern (51 bp):
GTAAGTTATGCAAGTTATGTAGATTATGATAAATATAAGTTGCTAACTTAG
Found at i:2259315 original size:107 final size:107
Alignment explanation
Indices: 2258907--2259297 Score: 719
Period size: 107 Copynumber: 3.7 Consensus size: 107
2258897 NNNNNNNNNN
* *
2258907 TTATGTAAGTTATGTGAGTTATGTAGATTATGATATGATACATATAAGTTATTAAGTTAGGTAAG
1 TTATGTAAGTTATGTGAGTTATGTAGATTATGATAGGATACATATAAGTGATTAAGTTAGGTAAG
*
2258972 TTATGCAAGTTATGTAAGTTATGATAAATATAAGTTGCTAAC
66 TTATGCAAGTCATGTAAGTTATGATAAATATAAGTTGCTAAC
2259014 TTATGTAAGTTATGTGAGTTATGTAGATTATGATAGGATACATATAAGTGATTAAGTTAGGTAAG
1 TTATGTAAGTTATGTGAGTTATGTAGATTATGATAGGATACATATAAGTGATTAAGTTAGGTAAG
2259079 TTATGCAAGTCATGTAAGTTATGATAAATATAAGTTGCTAAC
66 TTATGCAAGTCATGTAAGTTATGATAAATATAAGTTGCTAAC
2259121 TTATGTAAGTTATGTGAGTTATGTAGATTATGATAGGATACATATAAGTGATTAAGTTAGGTAAG
1 TTATGTAAGTTATGTGAGTTATGTAGATTATGATAGGATACATATAAGTGATTAAGTTAGGTAAG
2259186 TTATGCAAGTCATGTAAGTTATGATAAATATAAGTTGCTAAC
66 TTATGCAAGTCATGTAAGTTATGATAAATATAAGTTGCTAAC
* * * *
2259228 TTATGTAAGTTATGTGAGTTATGTAGATTATGATATGATATATATAAGTTATTAAGTTATGTAAG
1 TTATGTAAGTTATGTGAGTTATGTAGATTATGATAGGATACATATAAGTGATTAAGTTAGGTAAG
2259293 TTATG
66 TTATG
2259298 TGAGTTTCTG
Statistics
Matches: 277, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 277 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (107 bp):
TTATGTAAGTTATGTGAGTTATGTAGATTATGATAGGATACATATAAGTGATTAAGTTAGGTAAG
TTATGCAAGTCATGTAAGTTATGATAAATATAAGTTGCTAAC
Found at i:2259333 original size:74 final size:76
Alignment explanation
Indices: 2259237--2259383 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 76
2259227 CTTATGTAAG
* *
2259237 TTATGTGAGTTATGTAGATTA-TGATAT-GATATATATAAGTTATTAAGTTATGTAAGTTATGTG
1 TTATGTGAGTTATGTAGATTATTGATATAGATATATATAAGTTATTAAGTTAGGTAACTTATGTG
2259300 AGTTTCTGGGA
66 AGTTTCTGGGA
* * *
2259311 TTATGTGATTTATTTA-AGTTATGGTTTGATATATATATATATAAGTTATTAAGTTAGGTAACTT
1 TTATGTGAGTTATGTAGA-TTA----TTGATATAGATATATATAAGTTATTAAGTTAGGTAACTT
2259375 ATGTGAGTT
61 ATGTGAGTT
2259384 ATTTAAGTAA
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
73 1 0.02
74 17 0.28
79 6 0.10
80 37 0.61
ACGTcount: A:0.31, C:0.01, G:0.20, T:0.47
Consensus pattern (76 bp):
TTATGTGAGTTATGTAGATTATTGATATAGATATATATAAGTTATTAAGTTAGGTAACTTATGTG
AGTTTCTGGGA
Found at i:2259377 original size:136 final size:127
Alignment explanation
Indices: 2259213--2259518 Score: 370
Period size: 136 Copynumber: 2.3 Consensus size: 127
2259203 GTTATGATAA
**
2259213 ATATAAGTTGCTAACTTATGTAAGTTATGTGAGTTATGTAGATTATGATATGATATATATAAGTT
1 ATATAAGTTATTAA-TTA-GTAAGTTATGTGAGTTATGTAGATTATGATATGATATATATAAG--
* *
2259278 ATTAAGTTATGTAAGTTATGTGAGTT-TCTGGGATTATGTGATTTATTTAAGTTATGGTTTGATA
62 -TT-A-TTATGTAAGTTATGTGAGTTATGT-AGATTATGTGATTTATTTAAGTTATGGTTTG--A
2259342 TATATAT
121 TATATAT
* * * *
2259349 ATATAAGTTATTAAGTTAGGTAACTTATGTGAGTTATTTA-AGTAATGGTATGATATATATAAGT
1 ATATAAGTTATTAA-TTA-GTAAGTTATGTGAGTTATGTAGA-TTATGATATGATATATATAAGT
* *
2259413 TATTATGTAAGTTATGTGAGTTATGTATATTATGTGATTTATTTAATTTATGGTTTGATATATAT
63 TATTATGTAAGTTATGTGAGTTATGTAGATTATGTGATTTATTTAAGTTATGGTTTGATATATAT
2259478 ATATAAGTTATT-A-T-GTAAGTTATGTGAGTTATGTAGATTAT
1 ATATAAGTTATTAATTAGTAAGTTATGTGAGTTATGTAGATTAT
2259519 CAATTTAATG
Statistics
Matches: 152, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
124 22 0.14
125 1 0.01
126 1 0.01
128 1 0.01
129 20 0.13
131 48 0.32
132 3 0.02
133 2 0.01
135 1 0.01
136 53 0.35
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (127 bp):
ATATAAGTTATTAATTAGTAAGTTATGTGAGTTATGTAGATTATGATATGATATATATAAGTTAT
TATGTAAGTTATGTGAGTTATGTAGATTATGTGATTTATTTAAGTTATGGTTTGATATATAT
Found at i:2259438 original size:18 final size:17
Alignment explanation
Indices: 2259415--2259518 Score: 57
Period size: 18 Copynumber: 5.7 Consensus size: 17
2259405 ATATAAGTTA
2259415 TTATGTAAGTTATGTGAG
1 TTATGTAA-TTATGTGAG
*
2259433 TTATGTATATTATGTGAT
1 TTATGTA-ATTATGTGAG
* **
2259451 TTATTTAATTTATGGTTTG
1 TTATGTAA-TTAT-GTGAG
* * * *
2259470 ATATATATATATAAGTTA-
1 TTATGTA-AT-TATGTGAG
2259488 TTATGTAAGTTATGTGAG
1 TTATGTAA-TTATGTGAG
2259506 TTATGTAGATTAT
1 TTATGTA-ATTAT
2259519 CAATTTAATG
Statistics
Matches: 65, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
17 7 0.11
18 42 0.65
19 13 0.20
20 3 0.05
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (17 bp):
TTATGTAATTATGTGAG
Found at i:2260261 original size:13 final size:13
Alignment explanation
Indices: 2260243--2260267 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2260233 TTAACCACAG
2260243 CATTAACCAGAAA
1 CATTAACCAGAAA
2260256 CATTAACCAGAA
1 CATTAACCAGAA
2260268 CTTGCAGCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.24, G:0.08, T:0.16
Consensus pattern (13 bp):
CATTAACCAGAAA
Found at i:2262753 original size:20 final size:20
Alignment explanation
Indices: 2262712--2262750 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2262702 AATCTGAAAC
2262712 CCCAAACCTCTAACCCCTAA
1 CCCAAACCTCTAACCCCTAA
* *
2262732 CCCAAATCT-TAAGCCCTAA
1 CCCAAACCTCTAACCCCTAA
2262751 ACCATTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.36, C:0.44, G:0.03, T:0.18
Consensus pattern (20 bp):
CCCAAACCTCTAACCCCTAA
Found at i:2263029 original size:7 final size:7
Alignment explanation
Indices: 2263013--2263050 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
2263003 TCCAAACTCT
2263013 TAACCCC
1 TAACCCC
*
2263020 TAACCTC
1 TAACCCC
2263027 TAACCCC
1 TAACCCC
2263034 TAACCCC
1 TAACCCC
2263041 TAACCCC
1 TAACCCC
2263048 TAA
1 TAA
2263051 ACCTTCAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (7 bp):
TAACCCC
Found at i:2263080 original size:20 final size:21
Alignment explanation
Indices: 2263042--2263080 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2263032 CCTAACCCCT
*
2263042 AACCCCTAAACCTTCAATCTC
1 AACCCCTAAACCATCAATCTC
*
2263063 AACCCTTAAACCAT-AATC
1 AACCCCTAAACCATCAATC
2263081 CCTAATCCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.23
Consensus pattern (21 bp):
AACCCCTAAACCATCAATCTC
Found at i:2263092 original size:14 final size:14
Alignment explanation
Indices: 2263073--2263114 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
2263063 AACCCTTAAA
2263073 CCATAATCCCTAAT
1 CCATAATCCCTAAT
2263087 CCATAATCCCTAAAT
1 CCATAATCCCT-AAT
*
2263102 CCATACTCCCTAA
1 CCATAATCCCTAA
2263115 ACCTTACACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.36, C:0.38, G:0.00, T:0.26
Consensus pattern (14 bp):
CCATAATCCCTAAT
Found at i:2263102 original size:15 final size:15
Alignment explanation
Indices: 2263069--2263115 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
2263059 TCTCAACCCT
2263069 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
2263083 T-AATCCATAATCCC
1 TAAATCCATAATCCC
*
2263097 TAAATCCATACTCCC
1 TAAATCCATAATCCC
2263112 TAAA
1 TAAA
2263116 CCTTACACTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 2 0.07
14 12 0.40
15 16 0.53
ACGTcount: A:0.40, C:0.34, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:2263552 original size:41 final size:40
Alignment explanation
Indices: 2263501--2263896 Score: 445
Period size: 41 Copynumber: 9.7 Consensus size: 40
2263491 TTGCGGCACA
* *
2263501 TTTTCAAAAACACCGCTAAAGCCCCGAGCATTAGCGGCGC
1 TTTTCAAAAACGCCGCTAAAGACCCGAGCATTAGCGGCGC
** * *
2263541 TTCTTGGAAAACGCCGCTATAG-CTCCGAGCATTAGCGACGC
1 TT-TTCAAAAACGCCGCTAAAGAC-CCGAGCATTAGCGGCGC
* * **
2263582 TTTTTTAAAAACGCTGCTAAATCCCCGAGCATTAGCGGCGC
1 -TTTTCAAAAACGCCGCTAAAGACCCGAGCATTAGCGGCGC
** *
2263623 TTCTTGGAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCC
1 TT-TTCAAAAACGCCGCTAAAGACCCGAGCATTAGCGGCG-C
* * *
2263665 TTTTCAAAAATGCCGCTAAAGACCCGAGCATTAGCGACACC
1 TTTTCAAAAACGCCGCTAAAGACCCGAGCATTAGCGGC-GC
*
2263706 TTTTCAAAAACGTCGCTAAAG-CCCTGAGCATTAGCGGCGTC
1 TTTTCAAAAACGCCGCTAAAGACCC-GAGCATTAGCGGCG-C
*
2263747 TTTTCAAAAACGCCGCTAAAGACCCGAGCATTAGTGGCGC
1 TTTTCAAAAACGCCGCTAAAGACCCGAGCATTAGCGGCGC
* *
2263787 ATTTTCAAAAACGCCGCTAAAGAGCCGAGCATTAGCGGCAC
1 -TTTTCAAAAACGCCGCTAAAGACCCGAGCATTAGCGGCGC
* * * *
2263828 ATTTTCAAAACCACCGTTAAAGACCCGAGCATTAGCGGCAC
1 -TTTTCAAAAACGCCGCTAAAGACCCGAGCATTAGCGGCGC
* *
2263869 TTTGTCAAAAACGCCACTAAAGCCCCGA
1 TTT-TCAAAAACGCCGCTAAAGACCCGA
2263897 AAGGTCAGAA
Statistics
Matches: 304, Mismatches: 40, Indels: 23
0.83 0.11 0.06
Matches are distributed among these distances:
40 12 0.04
41 283 0.93
42 9 0.03
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (40 bp):
TTTTCAAAAACGCCGCTAAAGACCCGAGCATTAGCGGCGC
Found at i:2263913 original size:29 final size:29
Alignment explanation
Indices: 2263872--2263939 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 29
2263862 GCGGCACTTT
2263872 GTCA-AAAACGCCACTAAAGCCCCGAAAG
1 GTCAGAAAACGCCACTAAAGCCCCGAAAG
2263900 GTCAGAAAACGCCACTAAAGCCCCGAAAG
1 GTCAGAAAACGCCACTAAAGCCCCGAAAG
*
2263929 GTTAGAAAACG
1 GTCAGAAAACG
2263940 ATGCTCTTGG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
28 4 0.11
29 34 0.89
ACGTcount: A:0.43, C:0.28, G:0.21, T:0.09
Consensus pattern (29 bp):
GTCAGAAAACGCCACTAAAGCCCCGAAAG
Found at i:2274192 original size:55 final size:55
Alignment explanation
Indices: 2274050--2274192 Score: 196
Period size: 55 Copynumber: 2.6 Consensus size: 55
2274040 GCCCACACCA
* *
2274050 CGTTAAAAATGTTGTTATATAAATATTTATTGTTATATATCATAGATTTTGGCATC
1 CGTTAAAAATGTTGTTATATAAATAATTA-TGTCATATATCATAGATTTTGGCATC
* * * * *
2274106 CATTAGAAATGTTGTTATATAAATAAATATGTCATATATTATAGATTTTGGTATC
1 CGTTAAAAATGTTGTTATATAAATAATTATGTCATATATCATAGATTTTGGCATC
* *
2274161 CGTTAAAAATGTTGTTATGTAAATAGTTATGT
1 CGTTAAAAATGTTGTTATATAAATAATTATGT
2274193 TGTTATTTAT
Statistics
Matches: 75, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
55 50 0.67
56 25 0.33
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.45
Consensus pattern (55 bp):
CGTTAAAAATGTTGTTATATAAATAATTATGTCATATATCATAGATTTTGGCATC
Found at i:2275829 original size:42 final size:42
Alignment explanation
Indices: 2275771--2275851 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
2275761 GATTTATGTG
* *
2275771 TAAGACCATTCTGGGACATTGGCGTCG-TATATGATTACGTA
1 TAAGACCATTCTGGGACAGTGGCATCGTTATATGATTACGTA
* *
2275812 TAAGACCCTGTCTGGGACAGTGGCATCGTTATTTGATTAC
1 TAAGACCAT-TCTGGGACAGTGGCATCGTTATATGATTAC
2275852 ATGTAAAACC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 8 0.24
42 16 0.47
43 10 0.29
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (42 bp):
TAAGACCATTCTGGGACAGTGGCATCGTTATATGATTACGTA
Found at i:2275868 original size:43 final size:42
Alignment explanation
Indices: 2275780--2275861 Score: 101
Period size: 43 Copynumber: 1.9 Consensus size: 42
2275770 GTAAGACCAT
* * * *
2275780 TCTGGGACATTGGCGTCGTATATGATTACGTATAAGACCCTG
1 TCTGGGACAGTGGCATCGTATATGATTACATATAAAACCCTG
* *
2275822 TCTGGGACAGTGGCATCGTTATTTGATTACATGTAAAACC
1 TCTGGGACAGTGGCATCG-TATATGATTACATATAAAACC
2275862 ACGTCTGAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
42 16 0.48
43 17 0.52
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (42 bp):
TCTGGGACAGTGGCATCGTATATGATTACATATAAAACCCTG
Found at i:2287039 original size:136 final size:135
Alignment explanation
Indices: 2286791--2287060 Score: 380
Period size: 136 Copynumber: 2.0 Consensus size: 135
2286781 ATATAAATAT
* * * **
2286791 GTAAAAAGACAAAATACTTTCATGTAATATTTGTTACTTTGTAAAAAAGTTAAGTTTTTAGTCAT
1 GTAAAAAGACAAAATACCTTCATATAATATTTGTTACTTCGTAAAAAAGAAAAGTTTTTAGTCAT
**
2286856 TTCTCAACTGAGCTGATGTTTGGTTGAATCGTGACACCAACTCAGTGAGAGACGTAAATATTTAG
66 TTCTCAACTGAGCTGATGTTCCGTTGAATCGTGACACCAACTCAGTGAGAGACGTAAATA--TAG
2286921 TATAGAC
129 TATAGAC
* *
2286928 GTAAAAAGATAAAATACCTTCATATAATATTTGTTACTTCGTAAAAAA-AAAAGTTTTTAGTTAT
1 GTAAAAAGACAAAATACCTTCATATAATATTTGTTACTTCGTAAAAAAGAAAAGTTTTTAGTCAT
* * * * * *
2286992 TTCTCAATTGAGTTGATGTTCCGTTGACTTGTGACACCAACTTAGTGAGAGACTTAAATATAGTA
66 TTCTCAACTGAGCTGATGTTCCGTTGAATCGTGACACCAACTCAGTGAGAGACGTAAATATAGTA
2287057 TAGA
131 TAGA
2287061 TAAGCACAAA
Statistics
Matches: 118, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
134 9 0.08
136 65 0.55
137 44 0.37
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (135 bp):
GTAAAAAGACAAAATACCTTCATATAATATTTGTTACTTCGTAAAAAAGAAAAGTTTTTAGTCAT
TTCTCAACTGAGCTGATGTTCCGTTGAATCGTGACACCAACTCAGTGAGAGACGTAAATATAGTA
TAGAC
Found at i:2288649 original size:16 final size:16
Alignment explanation
Indices: 2288628--2288682 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
2288618 TGAATTACTG
* *
2288628 ATTACAGTTTTATTCC
1 ATTACAGCTCTATTCC
* *
2288644 ATTACAACTCTATTCT
1 ATTACAGCTCTATTCC
2288660 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
2288676 ATTACAG
1 ATTACAG
2288683 TGAATCAAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.42
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:2289691 original size:13 final size:13
Alignment explanation
Indices: 2289673--2289697 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2289663 TTGTCGAGGG
2289673 AGCCTTACATTAC
1 AGCCTTACATTAC
2289686 AGCCTTACATTA
1 AGCCTTACATTA
2289698 TTGCACTGTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (13 bp):
AGCCTTACATTAC
Found at i:2292285 original size:136 final size:135
Alignment explanation
Indices: 2292037--2292306 Score: 380
Period size: 136 Copynumber: 2.0 Consensus size: 135
2292027 ATATAAATAT
* * * **
2292037 GTAAAAAGACAAAATACTTTCATGTAATATTTGTTACTTTGTAAAAAAGTTAAGTTTTTAGTCAT
1 GTAAAAAGACAAAATACCTTCATATAATATTTGTTACTTCGTAAAAAAGAAAAGTTTTTAGTCAT
**
2292102 TTCTCAACTGAGCTGATGTTTGGTTGAATCGTGACACCAACTCAGTGAGAGACGTAAATATTTAG
66 TTCTCAACTGAGCTGATGTTCCGTTGAATCGTGACACCAACTCAGTGAGAGACGTAAATA--TAG
2292167 TATAGAC
129 TATAGAC
* *
2292174 GTAAAAAGATAAAATACCTTCATATAATATTTGTTACTTCGTAAAAAA-AAAAGTTTTTAGTTAT
1 GTAAAAAGACAAAATACCTTCATATAATATTTGTTACTTCGTAAAAAAGAAAAGTTTTTAGTCAT
* * * * * *
2292238 TTCTCAATTGAGTTGATGTTCCGTTGACTTGTGACACCAACTTAGTGAGAGACTTAAATATAGTA
66 TTCTCAACTGAGCTGATGTTCCGTTGAATCGTGACACCAACTCAGTGAGAGACGTAAATATAGTA
2292303 TAGA
131 TAGA
2292307 TAAGCACAAA
Statistics
Matches: 118, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
134 9 0.08
136 65 0.55
137 44 0.37
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (135 bp):
GTAAAAAGACAAAATACCTTCATATAATATTTGTTACTTCGTAAAAAAGAAAAGTTTTTAGTCAT
TTCTCAACTGAGCTGATGTTCCGTTGAATCGTGACACCAACTCAGTGAGAGACGTAAATATAGTA
TAGAC
Found at i:2300700 original size:2 final size:2
Alignment explanation
Indices: 2300693--2300727 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2300683 ATTCATAAAC
* *
2300693 AT AT AT AT AT AT AT AT AT AT AC GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2300728 AAGTCGAACC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2301163 original size:2 final size:2
Alignment explanation
Indices: 2301158--2301195 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2301148 ATTCGAATCT
2301158 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2301196 ATAAACATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2303469 original size:13 final size:13
Alignment explanation
Indices: 2303451--2303478 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2303441 TAAAGAGGAG
2303451 TAAGCATATAGCT
1 TAAGCATATAGCT
2303464 TAAGCATATAGCT
1 TAAGCATATAGCT
2303477 TA
1 TA
2303479 GTAAGTATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (13 bp):
TAAGCATATAGCT
Found at i:2304460 original size:51 final size:50
Alignment explanation
Indices: 2304328--2304515 Score: 223
Period size: 51 Copynumber: 3.7 Consensus size: 50
2304318 TGATCATTCA
* ** * *
2304328 TACATGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGAAAAAATTTTTCGG
*
2304378 TTCACGTAGTAGCCTTCACATAGTACTACACACGTGAAAAAATCTTTTCGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGAAAAAAT-TTTTCGG
* * * * ** * *
2304429 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATTATTTATCGA
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGA-AAAAATTTTTCGG
*
2304480 TACACGTAATAGCCTTCACATAGTACTACACACGTG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTG
2304516 TTCATCGATA
Statistics
Matches: 117, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
50 38 0.32
51 76 0.65
52 3 0.03
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (50 bp):
TACACGTAGTAGCCTTCACATAGTACTACACACGTGAAAAAATTTTTCGG
Found at i:2310366 original size:9 final size:9
Alignment explanation
Indices: 2310352--2310382 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2310342 GTTAAATGAA
2310352 TCGAGTTAT
1 TCGAGTTAT
*
2310361 TCGAGTTAA
1 TCGAGTTAT
2310370 TCGAGTTAT
1 TCGAGTTAT
2310379 TCGA
1 TCGA
2310383 ATCAACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:2310452 original size:9 final size:9
Alignment explanation
Indices: 2310435--2310471 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
2310425 TGAGTTTTCG
2310435 AATTCGAAT
1 AATTCGAAT
*
2310444 AACTCGAAT
1 AATTCGAAT
*
2310453 AATTCAAAT
1 AATTCGAAT
2310462 AATTCGAAT
1 AATTCGAAT
2310471 A
1 A
2310472 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:2311965 original size:13 final size:13
Alignment explanation
Indices: 2311947--2311971 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2311937 TAACTAAAAC
2311947 AACACATAAATAA
1 AACACATAAATAA
2311960 AACACATAAATA
1 AACACATAAATA
2311972 TCATATAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (13 bp):
AACACATAAATAA
Found at i:2312691 original size:41 final size:41
Alignment explanation
Indices: 2312646--2312791 Score: 238
Period size: 41 Copynumber: 3.6 Consensus size: 41
2312636 ACCGGCACTT
* * * *
2312646 AGCCTGCTAGACATAAAGTCTGATATGTTTCACTGGTATCA
1 AGCCTGCTAGACGTAATGTCTGGTATGTTTCACTGGCATCA
2312687 AGCCTGCTAGACGTAATGTCTGGTATGTTTCACTGGCATCA
1 AGCCTGCTAGACGTAATGTCTGGTATGTTTCACTGGCATCA
*
2312728 AGCCTGCTAGACGTAATGTCTGGTATGTTTCACCGGCATCA
1 AGCCTGCTAGACGTAATGTCTGGTATGTTTCACTGGCATCA
*
2312769 AGCCTGCTAGAAGTAATGTCTGG
1 AGCCTGCTAGACGTAATGTCTGG
2312792 ATTGCTTCAC
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 99 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (41 bp):
AGCCTGCTAGACGTAATGTCTGGTATGTTTCACTGGCATCA
Found at i:2313516 original size:200 final size:200
Alignment explanation
Indices: 2313296--2313711 Score: 814
Period size: 200 Copynumber: 2.1 Consensus size: 200
2313286 ATATAAAAAC
2313296 ATATACATATATATACTCATATTTGTTCAAACCTTGTGCACTTATATAACTCCCATACATTCAAT
1 ATATACATATATATACTCATATTTGTTCAAACCTTGTGCACTTATATAACTCCCATACATTCAAT
*
2313361 TACATTCATCACAAATATATATATAAATTCATATATAAATATTCGAACATTGTATATATATACCT
66 TAAATTCATCACAAATATATATATAAATTCATATATAAATATTCGAACATTGTATATATATACCT
2313426 ATATACCCTTTCTTACTTTAACTAAATTAAAAGATCTATATAAGTATATGCCTATATATTCGAAT
131 ATATACCCTTTCTTACTTTAACTAAATTAAAAGATCTATATAAGTATATGCCTATATATTCGAAT
2313491 ATTGT
196 ATTGT
2313496 ATATACATATATATACTCATATTTGTTCAAACCTTGTGCACTTATATAACTCCCATACATTCAAT
1 ATATACATATATATACTCATATTTGTTCAAACCTTGTGCACTTATATAACTCCCATACATTCAAT
2313561 TAAATTCATCACAAATATATATATAAATTCATATATAAATATTCGAACATTGTATATATATACCT
66 TAAATTCATCACAAATATATATATAAATTCATATATAAATATTCGAACATTGTATATATATACCT
2313626 ATATACCCTTTCTTACTTTAACTAAATTAAAAGATCTATATAAGTATATGCCTATATATTCGAAT
131 ATATACCCTTTCTTACTTTAACTAAATTAAAAGATCTATATAAGTATATGCCTATATATTCGAAT
2313691 ATTGT
196 ATTGT
*
2313696 ATATACACATATATAC
1 ATATACATATATATAC
2313712 CATTTATACT
Statistics
Matches: 214, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
200 214 1.00
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.39
Consensus pattern (200 bp):
ATATACATATATATACTCATATTTGTTCAAACCTTGTGCACTTATATAACTCCCATACATTCAAT
TAAATTCATCACAAATATATATATAAATTCATATATAAATATTCGAACATTGTATATATATACCT
ATATACCCTTTCTTACTTTAACTAAATTAAAAGATCTATATAAGTATATGCCTATATATTCGAAT
ATTGT
Found at i:2315645 original size:14 final size:14
Alignment explanation
Indices: 2315626--2315672 Score: 76
Period size: 14 Copynumber: 3.3 Consensus size: 14
2315616 TTATAGACCG
2315626 TAAACCCTAAATCC
1 TAAACCCTAAATCC
*
2315640 TAAACCCTAAAATTC
1 TAAACCCT-AAATCC
2315655 TAAACCCTAAATCC
1 TAAACCCTAAATCC
2315669 TAAA
1 TAAA
2315673 TATTATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 17 0.57
15 13 0.43
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCCTAAATCC
Found at i:2315657 original size:22 final size:25
Alignment explanation
Indices: 2315632--2315690 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 25
2315622 ACCGTAAACC
2315632 CTAAATCCTAAACCCTAAA-A-T-T
1 CTAAATCCTAAACCCTAAATATTAT
* *
2315654 CTAAACCCTAAATCCTAAATATTAT
1 CTAAATCCTAAACCCTAAATATTAT
*
2315679 TTAAATCCTAAA
1 CTAAATCCTAAA
2315691 AAATTCTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 17 0.57
23 1 0.03
24 1 0.03
25 11 0.37
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.31
Consensus pattern (25 bp):
CTAAATCCTAAACCCTAAATATTAT
Found at i:2315690 original size:7 final size:7
Alignment explanation
Indices: 2315626--2315673 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
2315616 TTATAGACCG
*
2315626 TAAACCC
1 TAAATCC
2315633 TAAATCC
1 TAAATCC
*
2315640 TAAACCC
1 TAAATCC
*
2315647 TAAAATTC
1 T-AAATCC
*
2315655 TAAACCC
1 TAAATCC
2315662 TAAATCC
1 TAAATCC
2315669 TAAAT
1 TAAAT
2315674 ATTATTTAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
7 28 0.85
8 5 0.15
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.25
Consensus pattern (7 bp):
TAAATCC
Found at i:2321624 original size:20 final size:20
Alignment explanation
Indices: 2321599--2321717 Score: 80
Period size: 20 Copynumber: 6.0 Consensus size: 20
2321589 TTGTACGAGA
2321599 TTTGCACTTCGGTGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
*
2321619 TTTGCACTTTGGTGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
* * *** *
2321639 TATACACTTCGGCATCCTTG
1 TTTGCACTTCGGTGCCCCTG
* ** *
2321659 TTCGCA-TTATAGTGCCCCTA
1 TTTGCACTT-CGGTGCCCCTG
*
2321679 TTTGCACATT-TGTGCCCCTG
1 TTTGCAC-TTCGGTGCCCCTG
* *
2321699 TCTACACTTCGGTGCCCCT
1 TTTGCACTTCGGTGCCCCT
2321718 ATTATGCATC
Statistics
Matches: 71, Mismatches: 24, Indels: 8
0.69 0.23 0.08
Matches are distributed among these distances:
19 4 0.06
20 65 0.92
22 2 0.03
ACGTcount: A:0.12, C:0.33, G:0.19, T:0.36
Consensus pattern (20 bp):
TTTGCACTTCGGTGCCCCTG
Found at i:2345185 original size:7 final size:8
Alignment explanation
Indices: 2345153--2345194 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
2345143 GTAATTAGGG
*
2345153 TTAGGGTT
1 TTAGAGTT
*
2345161 TTGGAGTT
1 TTAGAGTT
*
2345169 TTTGAGTT
1 TTAGAGTT
2345177 TTAGA-TT
1 TTAGAGTT
2345184 TTAGAGTT
1 TTAGAGTT
2345192 TTA
1 TTA
2345195 AGGATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 7 0.24
8 22 0.76
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (8 bp):
TTAGAGTT
Found at i:2345190 original size:15 final size:16
Alignment explanation
Indices: 2345153--2345194 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
2345143 GTAATTAGGG
* *
2345153 TTAGGGTTTTGGAGTT
1 TTAGAGTTTTAGAGTT
*
2345169 TTTGAGTTTTAGA-TT
1 TTAGAGTTTTAGAGTT
2345184 TTAGAGTTTTA
1 TTAGAGTTTTA
2345195 AGGATAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (16 bp):
TTAGAGTTTTAGAGTT
Found at i:2345358 original size:96 final size:97
Alignment explanation
Indices: 2345220--2345436 Score: 337
Period size: 97 Copynumber: 2.2 Consensus size: 97
2345210 AAATAAGGGT
* * *
2345220 TTAGGGTTTAGGGTTTCTTAATTAAATTAAGTATAAATTTT-AAAAAATTAGATTAGGGTTTAGT
1 TTAGGGTTTAGGGTTACTTGAGTAAATTAAGTATAAATTTTAAAAAAATTAGATTAGGGTTTAGT
* * *
2345284 GTTTATGGTTTTTAAGGAAAAAATCAAATAAA
66 GTTGAGGGTTTTTAAGAAAAAAATCAAATAAA
* * *
2345316 TTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAAATTATATTAGGGTTTAGT
1 TTAGGGTTTAGGGTTACTTGAGTAAATTAAGTATAAATTTTAAAAAAATTAGATTAGGGTTTAGT
*
2345381 GTTGAGGGTTTTTTAGAAAAAAATCAAATAAA
66 GTTGAGGGTTTTTAAGAAAAAAATCAAATAAA
2345413 TTAGGGTTTAGGGTTACTTGAGTA
1 TTAGGGTTTAGGGTTACTTGAGTA
2345437 CNNNNNNNNN
Statistics
Matches: 109, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
96 36 0.33
97 73 0.67
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.40
Consensus pattern (97 bp):
TTAGGGTTTAGGGTTACTTGAGTAAATTAAGTATAAATTTTAAAAAAATTAGATTAGGGTTTAGT
GTTGAGGGTTTTTAAGAAAAAAATCAAATAAA
Found at i:2348252 original size:204 final size:205
Alignment explanation
Indices: 2347893--2348301 Score: 811
Period size: 204 Copynumber: 2.0 Consensus size: 205
2347883 TATATATTTT
2347893 TTAATTTTAAATATTTTAAATTATTCATTTATATGACATATAAAGTAAATAGTGTTATATTAATA
1 TTAATTTTAAATATTTTAAATTATTCATTTATATGACATATAAAGTAAATAGTGTTATATTAATA
2347958 TAAAAGTACATGTAGACAATCATACGGGTTGTCACATCAACCTTGTTAAAAAAAATAATGTTTCA
66 TAAAAGTACATGTAGACAATCATACGGGTTGTCACATCAACCTTGTTAAAAAAAATAATGTTTCA
2348023 ATTAACATTTCTGCTAAAAATCAATTTAACTCTTTTTTGAAAGGTTAAAGGCAAATTTAACTAAA
131 ATTAACATTTCTGCTAAAAATCAATTTAACTCTTTTTTGAAAGGTTAAAGGCAAATTTAACTAAA
2348088 AAAAGTCAAA
196 AAAAGTCAAA
2348098 TTAATTTT-AATATTTTAAATTATTCATTTATATGACATATAAAGTAAATAGTGTTATATTAATA
1 TTAATTTTAAATATTTTAAATTATTCATTTATATGACATATAAAGTAAATAGTGTTATATTAATA
2348162 TAAAAGTACATGTAGACAATCATACGGGTTGTCACATCAACCTTGTTAAAAAAAATAATGTTTCA
66 TAAAAGTACATGTAGACAATCATACGGGTTGTCACATCAACCTTGTTAAAAAAAATAATGTTTCA
2348227 ATTAACATTTCTGCTAAAAATCAATTTAACTCTTTTTTGAAAGGTTAAAGGCAAATTTAACTAAA
131 ATTAACATTTCTGCTAAAAATCAATTTAACTCTTTTTTGAAAGGTTAAAGGCAAATTTAACTAAA
2348292 AAAAGTCAAA
196 AAAAGTCAAA
2348302 CTGAAAAAAG
Statistics
Matches: 204, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
204 196 0.96
205 8 0.04
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (205 bp):
TTAATTTTAAATATTTTAAATTATTCATTTATATGACATATAAAGTAAATAGTGTTATATTAATA
TAAAAGTACATGTAGACAATCATACGGGTTGTCACATCAACCTTGTTAAAAAAAATAATGTTTCA
ATTAACATTTCTGCTAAAAATCAATTTAACTCTTTTTTGAAAGGTTAAAGGCAAATTTAACTAAA
AAAAGTCAAA
Found at i:2348852 original size:24 final size:24
Alignment explanation
Indices: 2348825--2348872 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2348815 CTGTTCTGTA
2348825 TAAATTATATGCGAAATTTGAGTT
1 TAAATTATATGCGAAATTTGAGTT
* ***
2348849 TAAATTTTATTTTAAATTTGAGTT
1 TAAATTATATGCGAAATTTGAGTT
2348873 CGTATTTGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.50
Consensus pattern (24 bp):
TAAATTATATGCGAAATTTGAGTT
Found at i:2348853 original size:12 final size:12
Alignment explanation
Indices: 2348838--2348872 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2348828 ATTATATGCG
2348838 AAATTTGAGTTT
1 AAATTTGAGTTT
* *
2348850 AAATTTTATTTT
1 AAATTTGAGTTT
2348862 AAATTTGAGTT
1 AAATTTGAGTT
2348873 CGTATTTGAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.54
Consensus pattern (12 bp):
AAATTTGAGTTT
Found at i:2352730 original size:19 final size:19
Alignment explanation
Indices: 2352693--2352731 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2352683 ATCATCCATT
*
2352693 TTCATTTTGTATATGCATA
1 TTCATTTTCTATATGCATA
2352712 TTCATCTTTCTATAT-CATA
1 TTCAT-TTTCTATATGCATA
2352731 T
1 T
2352732 GAACATTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.26, C:0.15, G:0.05, T:0.54
Consensus pattern (19 bp):
TTCATTTTCTATATGCATA
Found at i:2354091 original size:171 final size:172
Alignment explanation
Indices: 2353794--2354137 Score: 681
Period size: 171 Copynumber: 2.0 Consensus size: 172
2353784 ATCAAAAATT
2353794 ACTTAATAAAATATGTCTATCTAACAACCAAACTTAACAATCTACCATAAAACTTCATAAACATA
1 ACTTAATAAAATATGTCTATCTAACAACCAAACTTAACAATCTACCATAAAACTTCATAAACATA
2353859 TCAAATTCATTCATGACATAATTTATAACATTTAACAGTTTTATAATTTGACCCCCAGGTTAGCT
66 TCAAATTCATTCATGACATAATTTATAACATTTAACAGTTTTATAATTTGACCCCCAGGTTAGCT
2353924 AGATTAAGCTAAAACGAACTTAAAAACATAAAAATCATGAAA
131 AGATTAAGCTAAAACGAACTTAAAAACATAAAAATCATGAAA
2353966 ACTTAATAAAA-ATGTCTATCTAACAACCAAACTTAACAATCTACCATAAAACTTCATAAACATA
1 ACTTAATAAAATATGTCTATCTAACAACCAAACTTAACAATCTACCATAAAACTTCATAAACATA
2354030 TCAAATTCATTCATGACATAATTTATAACATTTAACAGTTTTATAATTTGACCCCCAGGTTAGCT
66 TCAAATTCATTCATGACATAATTTATAACATTTAACAGTTTTATAATTTGACCCCCAGGTTAGCT
2354095 AGATTAAGCTAAAACGAACTTAAAAACATAAAAATCATGAAA
131 AGATTAAGCTAAAACGAACTTAAAAACATAAAAATCATGAAA
2354137 A
1 A
2354138 AGGGGTAAAA
Statistics
Matches: 172, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
171 161 0.94
172 11 0.06
ACGTcount: A:0.46, C:0.18, G:0.06, T:0.29
Consensus pattern (172 bp):
ACTTAATAAAATATGTCTATCTAACAACCAAACTTAACAATCTACCATAAAACTTCATAAACATA
TCAAATTCATTCATGACATAATTTATAACATTTAACAGTTTTATAATTTGACCCCCAGGTTAGCT
AGATTAAGCTAAAACGAACTTAAAAACATAAAAATCATGAAA
Found at i:2356858 original size:51 final size:52
Alignment explanation
Indices: 2356775--2356875 Score: 143
Period size: 51 Copynumber: 2.0 Consensus size: 52
2356765 GTGAAAATGG
*
2356775 AGAAATGAGAAACTTTTGAAAATTATTATGGTTTTCTCCAAAATAAAAATAA
1 AGAAATGAGAAACATTTGAAAATTATTATGGTTTTCTCCAAAATAAAAATAA
* * *
2356827 AGAAATG-GAATCATTTGAAAATGTA-TGTGGTTTTCTCCAAAATGAAAAT
1 AGAAATGAGAAACATTTGAAAAT-TATTATGGTTTTCTCCAAAATAAAAAT
2356876 GGTCTGGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
51 35 0.80
52 9 0.20
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.33
Consensus pattern (52 bp):
AGAAATGAGAAACATTTGAAAATTATTATGGTTTTCTCCAAAATAAAAATAA
Found at i:2357017 original size:28 final size:26
Alignment explanation
Indices: 2356985--2357037 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 26
2356975 TTAGAATTGG
2356985 ATTGAGAAGATTATTTAATTGGAAATAT
1 ATTGAGAAGATTATTT--TTGGAAATAT
* *
2357013 ATTGAGATGTTTATTTTTGGAAATA
1 ATTGAGAAGATTATTTTTGGAAATA
2357038 CAAAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 9 0.39
28 14 0.61
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (26 bp):
ATTGAGAAGATTATTTTTGGAAATAT
Found at i:2357604 original size:125 final size:125
Alignment explanation
Indices: 2357380--2357610 Score: 408
Period size: 125 Copynumber: 1.8 Consensus size: 125
2357370 TTATTGAAGT
*
2357380 ATGGTGTTTAGAGCAAGTGCTGAGTGGGTAACGTATTAAGTGTGACTAAGAATGTAAGTCAGCAA
1 ATGGTGTTTAGAGCAAGTGCTGAGTGGGTAACGTATTAACTGTGACTAAGAATGTAAGTCAGCAA
*
2357445 GTGCGCCTTTCGGCGAAGTCTACATTCGGCGAGCTTGGTGGTTTGGTGGACTCCCTTGTA
66 GTGCGCCTTTCGGCGAAGTCTACATTAGGCGAGCTTGGTGGTTTGGTGGACTCCCTTGTA
* * *
2357505 ATGGTGTTTAGAGCAAGTTCTGAGTGGGTAAGGTATTAACTGTGACTAAGAATGTAAGTCTGCAA
1 ATGGTGTTTAGAGCAAGTGCTGAGTGGGTAACGTATTAACTGTGACTAAGAATGTAAGTCAGCAA
*
2357570 GTGCGCCTTTCGGCGAAGTCTACATTAGGTGAGCTTGGTGG
66 GTGCGCCTTTCGGCGAAGTCTACATTAGGCGAGCTTGGTGG
2357611 ACTCCCTTGT
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
125 100 1.00
ACGTcount: A:0.23, C:0.15, G:0.32, T:0.30
Consensus pattern (125 bp):
ATGGTGTTTAGAGCAAGTGCTGAGTGGGTAACGTATTAACTGTGACTAAGAATGTAAGTCAGCAA
GTGCGCCTTTCGGCGAAGTCTACATTAGGCGAGCTTGGTGGTTTGGTGGACTCCCTTGTA
Found at i:2364451 original size:16 final size:18
Alignment explanation
Indices: 2364425--2364458 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2364415 TTTATTTAGC
2364425 TAAATTAA-TTTCTCAAA
1 TAAATTAATTTTCTCAAA
2364442 TAAA-TAATTTTCTCAAA
1 TAAATTAATTTTCTCAAA
2364459 CACAATTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAA
Found at i:2386791 original size:51 final size:50
Alignment explanation
Indices: 2386695--2386791 Score: 115
Period size: 51 Copynumber: 1.9 Consensus size: 50
2386685 AGTTACCTAT
* * *
2386695 AAAGCCTTTGTGGAAAATTATCTGAAAGGCATATGTGGTGTATTATTTAG
1 AAAGCCTTAGTGGAAAATTATCTGAAAGGCATATGTGGCGAATTATTTAG
* * *
2386745 AAAGCCTTAGTGGCAAAGTTATCTGTAAA-GCCTTTGTGGCGAATTAT
1 AAAGCCTTAGTGG-AAAATTATCTG-AAAGGCATATGTGGCGAATTAT
2386792 CTGAAAGGCC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
50 12 0.31
51 24 0.62
52 3 0.08
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.34
Consensus pattern (50 bp):
AAAGCCTTAGTGGAAAATTATCTGAAAGGCATATGTGGCGAATTATTTAG
Found at i:2386809 original size:25 final size:24
Alignment explanation
Indices: 2386695--2386816 Score: 93
Period size: 25 Copynumber: 4.9 Consensus size: 24
2386685 AGTTACCTAT
* **
2386695 AAAGCCTTTGTGGAAAATTATCTG
1 AAAGCCTATGTGGCGAATTATCTG
* * * *
2386719 AAAGGCATATGTGGTGTATTATTTAG
1 AAA-GCCTATGTGGCGAATTATCT-G
*
2386745 AAAGCCT-TAGTGGCAAAGTTATCTG
1 AAAGCCTAT-GTGGCGAA-TTATCTG
*
2386770 TAAAGCCTTTGTGGCGAATTATCTG
1 -AAAGCCTATGTGGCGAATTATCTG
*
2386795 AAAGGCCTATGTGGCGTATTAT
1 AAA-GCCTATGTGGCGAATTAT
2386817 TCGTACAGCC
Statistics
Matches: 77, Mismatches: 14, Indels: 13
0.74 0.13 0.12
Matches are distributed among these distances:
24 7 0.09
25 46 0.60
26 23 0.30
27 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.34
Consensus pattern (24 bp):
AAAGCCTATGTGGCGAATTATCTG
Found at i:2386827 original size:76 final size:76
Alignment explanation
Indices: 2386469--2386842 Score: 333
Period size: 76 Copynumber: 5.0 Consensus size: 76
2386459 GAGTAGTCTT
* * * *
2386469 TAAAG-CTTTTTGGCGAATTATCTTAAAGGCCTTTATGGCGTATTATTCGGAAAGCCTTTGTGG-
1 TAAAGCCTTTGTGGCGAATTATCTGAAAGGCCTTTGTGGCGTATTATTCGGAAAGCCTTAGTGGC
** * *
2386532 TGAGTAATTTG
66 AAAGTTATCTG
** * * * * * *
2386543 TAAAATCTTTATGGCAAATTATCTGAATGGCCTTTGTGGCGTATTATTTGGGAAGCCTTTA-TAG
1 TAAAGCCTTTGTGGCGAATTATCTGAAAGGCCTTTGTGGCGTATTATTCGGAAAGCC-TTAGTGG
* *
2386607 C-GAGTAATCTG
65 CAAAGTTATCTG
* * * * * ** * * *
2386618 TAAAGCCTTTGTGGTGAATTATTTGAATGGCCTTTGTAGTGTATTATTCAAAAAGCTTTAGTAGT
1 TAAAGCCTTTGTGGCGAATTATCTGAAAGGCCTTTGTGGCGTATTATTCGGAAAGCCTTAGTGGC
* *
2386683 AAAGTTACCTA
66 AAAGTTATCTG
** * * * **
2386694 TAAAGCCTTTGTGGAAAATTATCTGAAAGGCATATGTGGTGTATTATTTAGAAAGCCTTAGTGGC
1 TAAAGCCTTTGTGGCGAATTATCTGAAAGGCCTTTGTGGCGTATTATTCGGAAAGCCTTAGTGGC
2386759 AAAGTTATCTG
66 AAAGTTATCTG
* * * *
2386770 TAAAGCCTTTGTGGCGAATTATCTGAAAGGCCTATGTGGCGTATTATTCGTACAGCCTTAGTGGT
1 TAAAGCCTTTGTGGCGAATTATCTGAAAGGCCTTTGTGGCGTATTATTCGGAAAGCCTTAGTGGC
*
2386835 GAAGTTAT
66 AAAGTTAT
2386843 GTGGGAATCC
Statistics
Matches: 242, Mismatches: 53, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
74 7 0.03
75 102 0.42
76 133 0.55
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (76 bp):
TAAAGCCTTTGTGGCGAATTATCTGAAAGGCCTTTGTGGCGTATTATTCGGAAAGCCTTAGTGGC
AAAGTTATCTG
Found at i:2396383 original size:23 final size:24
Alignment explanation
Indices: 2396357--2396409 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
2396347 ATTAGCTTGG
*
2396357 ATAATTTTTTTA-AAAT-TATAAAA
1 ATAATTTTGTTACAAATGTA-AAAA
*
2396380 ATAATATTGTTACAAATGTAAAAA
1 ATAATTTTGTTACAAATGTAAAAA
2396404 ATAATT
1 ATAATT
2396410 ATCAATAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 10 0.40
24 13 0.52
25 2 0.08
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (24 bp):
ATAATTTTGTTACAAATGTAAAAA
Found at i:2398154 original size:18 final size:20
Alignment explanation
Indices: 2398133--2398171 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
2398123 AAATTTATAT
2398133 GTTTTTAAA-AA-ATATAAA
1 GTTTTTAAAGAATATATAAA
2398151 GTTTTTAAAGAATATATAAA
1 GTTTTTAAAGAATATATAAA
2398171 G
1 G
2398172 AAATTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
19 2 0.11
20 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.38
Consensus pattern (20 bp):
GTTTTTAAAGAATATATAAA
Found at i:2402904 original size:16 final size:16
Alignment explanation
Indices: 2402883--2402922 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
2402873 GATTTTGAGA
*
2402883 GGAGAAATGCGGATTT
1 GGAGAAAAGCGGATTT
2402899 GGAGAAAAGCGGATTT
1 GGAGAAAAGCGGATTT
2402915 GGAGAAAA
1 GGAGAAAA
2402923 AGATAGAGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.40, C:0.05, G:0.38, T:0.17
Consensus pattern (16 bp):
GGAGAAAAGCGGATTT
Found at i:2412035 original size:44 final size:45
Alignment explanation
Indices: 2411984--2412655 Score: 220
Period size: 45 Copynumber: 15.5 Consensus size: 45
2411974 GTGAAGATCG
2411984 AGTCTTATCTCCCTGAAGTTGCAAT-AGAGCAGACT-AAG-TAGGCA
1 AGTCTTATCTCCCTGAAGTTGCAATGAG-GCAGACTAAAGAT-GGCA
*
2412028 AGTCTTATC-CTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAATGAGGCAGACTAAAGATGGCA
* * * * *** *
2412073 AATCTTATCTCCCTGAAGTTACAGTG-GAGCAGATTAAAGCCAGTA
1 AGTCTTATCTCCCTGAAGTTGCAATGAG-GCAGACTAAAGATGGCA
* ** * * * ****
2412118 A-TCCTATCTTGCTGAAGTGGCAGTGAGTG-A-ATTAAA-ACCTTA
1 AGTCTTATCTCCCTGAAGTTGCAATGAG-GCAGACTAAAGATGGCA
* * * *
2412160 AATCTTATCTCTCTGAAGTTGC-A-GAGAGCAGA-T--CGCAT--CT
1 AGTCTTATCTCCCTGAAGTTGCAATGAG-GCAGACTAAAG-ATGGCA
*
2412200 AGTCTTATC-CTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAATGAGGCAGACTAAAGATGGCA
* * * ** *
2412245 AATCTTATCTCCCTGAAGTTGCAGTG-GAGCAGATTAAAGCCGGTA
1 AGTCTTATCTCCCTGAAGTTGCAATGAG-GCAGACTAAAGATGGCA
* * * * * *
2412290 A-TCCTATCTCGCTGAAGTTGCAGTGA-GCAGATTAAA-A--CCTT
1 AGTCTTATCTCCCTGAAGTTGCAATGAGGCAGACTAAAGATGGC-A
* * *
2412331 AGATCTTATCTCTCTGAAGTTAC-A-GA-G-AG--T--AGATCGCA
1 AG-TCTTATCTCCCTGAAGTTGCAATGAGGCAGACTAAAGATGGCA
* *
2412369 TCTAGTCTTATC-CTTCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCA
1 ---AGTCTTATCTC-CCTGAAGTTGCAATGAGGCAGACTAAAGATGGCA
* * * **
2412417 AATCTTATCTCCCTGAAGTTGCAGTG-GAGCAGATTAAAGCCGAG-A
1 AGTCTTATCTCCCTGAAGTTGCAATGAG-GCAGACTAAAGATG-GCA
* * * * *
2412462 A-TCCTATCTCGCTGAAGTTGCAATGA-GCAGATTAAA-A--CCTT
1 AGTCTTATCTCCCTGAAGTTGCAATGAGGCAGACTAAAGATGGC-A
** * * *
2412503 AGATCTTATCTCTTTGAAGTTAC-A-GAGAGCAGA-T--CGCAT--CT
1 AG-TCTTATCTCCCTGAAGTTGCAATGAG-GCAGACTAAAG-ATGGCA
* **
2412544 AGTCTTATCTCCTTGAAGTTGCGGTG-GAGCAGACT-AAG-TAGGCA
1 AGTCTTATCTCCCTGAAGTTGCAATGAG-GCAGACTAAAGAT-GGCA
*
2412588 AGTCTTATC-CTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAATGAGGCAGACTAAAGATGGCA
* *
2412633 AATCTTATCTCCCTGAAATTGCA
1 AGTCTTATCTCCCTGAAGTTGCA
2412656 GTGGAGCAGA
Statistics
Matches: 485, Mismatches: 77, Indels: 131
0.70 0.11 0.19
Matches are distributed among these distances:
36 1 0.00
37 1 0.00
38 1 0.00
39 3 0.01
40 55 0.11
41 29 0.06
42 19 0.04
43 87 0.18
44 128 0.26
45 146 0.30
46 8 0.02
48 7 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (45 bp):
AGTCTTATCTCCCTGAAGTTGCAATGAGGCAGACTAAAGATGGCA
Found at i:2412216 original size:40 final size:41
Alignment explanation
Indices: 2412162--2412785 Score: 259
Period size: 43 Copynumber: 14.6 Consensus size: 41
2412152 AAACCTTAAA
* *
2412162 TCTTATCTCTCTGAAGTTGCAGAGAGCAGA-TCGCATCTAG
1 TCTTATCTCTCTGAAGTTGCAGTGAGCAGATTAGCATCTAG
* * *
2412202 TCTTATC-CTCCTGAAGTTGCAGTGAGGCAGACTAAAG-ATGGCAAA
1 TCTTATCTCT-CTGAAGTTGCAGTGA-GCAGA-T-TAGCAT--CTAG
* *** *
2412247 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAA
1 TCTTATCTCTCTGAAGTTGCAGT-GAGCAGATT--AGCATCTAG
* * ** *
2412291 TCCTATCTCGCTGAAGTTGCAGTGAGCAGATTAAAACCTTAG
1 TCTTATCTCTCTGAAGTTGCAGTGAGCAGATTAGCATC-TAG
* * * *
2412333 ATCTTATCTCTCTGAAGTTACAGAGAGTAGA-TCGCATCTAG
1 -TCTTATCTCTCTGAAGTTGCAGTGAGCAGATTAGCATCTAG
* * *
2412374 TCTTATC-CTTCTGAAGTTGCAGTGAGGCAGACTAAAG-ATGGCAAA
1 TCTTATCTC-TCTGAAGTTGCAGTGA-GCAGA-T-TAGCAT--CTAG
* *
2412419 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC--CGAG
1 TCTTATCTCTCTGAAGTTGCAGT-GAGCAGATT--AGCATCTAG
* * * ** *
2412461 AATCCTATCTCGCTGAAGTTGCAATGAGCAGATTAAAACCTTAG
1 --TCTTATCTCTCTGAAGTTGCAGTGAGCAGATTAGCATC-TAG
* * * *
2412505 ATCTTATCTCTTTGAAGTTACAGAGAGCAGA-TCGCATCTAG
1 -TCTTATCTCTCTGAAGTTGCAGTGAGCAGATTAGCATCTAG
* * * * *
2412546 TCTTATCTC-CTTGAAGTTGCGGTGGAGCAGACTAAGTAGGCAAG
1 TCTTATCTCTC-TGAAGTTGCAGT-GAGCAGA-TTAGCA-TCTAG
* * *
2412590 TCTTATC-CTCCTGAAGTTGCAGTGAGGCAGACTAAAG-ATGGCAAA
1 TCTTATCTCT-CTGAAGTTGCAGTGA-GCAGA-T-TAGCAT--CTAG
* * *** *
2412635 TCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGCCGATAA
1 TCTTATCTCTCTGAAGTTGCAGT-GAGCAGATT--AGCATCTAG
** * * * ** *
2412679 TCCAATCTCGCTGAAGTGGCAGTGAGCGGATTAAAACCTTAG
1 TCTTATCTCTCTGAAGTTGCAGTGAGCAGATTAGCATC-TAG
** *
2412721 ATCTTATCTCTCTGAAGTTGCAGAAAGCAGA-TCGCATCTAG
1 -TCTTATCTCTCTGAAGTTGCAGTGAGCAGATTAGCATCTAG
2412762 TCTTATC-CTCCTGAAGTTGCAGTG
1 TCTTATCTCT-CTGAAGTTGCAGTG
2412786 TAGGCAGACT
Statistics
Matches: 435, Mismatches: 99, Indels: 100
0.69 0.16 0.16
Matches are distributed among these distances:
39 5 0.01
40 79 0.18
41 28 0.06
42 15 0.03
43 109 0.25
44 99 0.23
45 91 0.21
46 9 0.02
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (41 bp):
TCTTATCTCTCTGAAGTTGCAGTGAGCAGATTAGCATCTAG
Found at i:2412276 original size:172 final size:172
Alignment explanation
Indices: 2412028--2412670 Score: 960
Period size: 172 Copynumber: 3.7 Consensus size: 172
2412018 TAAGTAGGCA
2412028 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTT
1 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTT
* * * *
2412093 ACAGTGGAGCAGATTAAAGCCAGTAATCCTATCTTGCTGAAGTGGCAGTGAG-TGAATTAAAACC
66 GCAGTGGAGCAGATTAAAGCCAGTAATCCTATCTCGCTGAAGTTGCAGTGAGCAG-ATTAAAACC
* *
2412157 TTAAATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCT
130 TTAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCT
2412200 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTT
1 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTT
*
2412265 GCAGTGGAGCAGATTAAAGCCGGTAATCCTATCTCGCTGAAGTTGCAGTGAGCAGATTAAAACCT
66 GCAGTGGAGCAGATTAAAGCCAGTAATCCTATCTCGCTGAAGTTGCAGTGAGCAGATTAAAACCT
*
2412330 TAGATCTTATCTCTCTGAAGTTACAGAGAGTAGATCGCATCT
131 TAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCT
*
2412372 AGTCTTATCCTTCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTT
1 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTT
*
2412437 GCAGTGGAGCAGATTAAAGCCGAG-AATCCTATCTCGCTGAAGTTGCAATGAGCAGATTAAAACC
66 GCAGTGGAGCAGATTAAAGCC-AGTAATCCTATCTCGCTGAAGTTGCAGTGAGCAGATTAAAACC
*
2412501 TTAGATCTTATCTCTTTGAAGTTACAGAGAGCAGATCGCATCT
130 TTAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCT
* *
2412544 AGTCTTAT-CTCCTTGAAGTTGCGGTG-GAGCAGACT-AAG-TAGGCAAGTCTTATC-CTCCTGA
1 AGTCTTATCCTCC-TGAAGTTGCAGTGAG-GCAGACTAAAGAT-GGCAAATCTTATCTC-CCTGA
* *** * * * *
2412604 AGTTGCAGT-GAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAATTGCAGTGGAGCAGATT
62 AGTTGCAGTGGA-GCAGATTAAAGCCAG-TAATCCTATCTCGCTGAAGTTGCAGT-GAGCAGATT
2412668 AAA
124 AAA
2412671 GCCGATAATC
Statistics
Matches: 437, Mismatches: 24, Indels: 19
0.91 0.05 0.04
Matches are distributed among these distances:
170 5 0.01
171 43 0.10
172 375 0.86
173 14 0.03
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (172 bp):
AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTT
GCAGTGGAGCAGATTAAAGCCAGTAATCCTATCTCGCTGAAGTTGCAGTGAGCAGATTAAAACCT
TAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCT
Found at i:2412606 original size:216 final size:218
Alignment explanation
Indices: 2412372--2412814 Score: 723
Period size: 216 Copynumber: 2.0 Consensus size: 218
2412362 GATCGCATCT
* *
2412372 AGTCTTATCCTTCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTT
1 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAATT
* *
2412437 GCAGTGGAGCAGATTAAAGCCGAGAATCCTATCTCGCTGAAGTTGCAATGAGCAGATTAAAACCT
66 GCAGTGGAGCAGATTAAAGCCGAGAATCCAATCTCGCTGAAGTGGCAATGAGCAGATTAAAACCT
* *
2412502 TAGATCTTATCTCTTTGAAGTTACAGAGAGCAGATCGCATCTAGTCTTAT-CTCCTTGAAGTTGC
131 TAGATCTTATCTCTCTGAAGTTACAGAAAGCAGATCGCATCTAGTCTTATCCTCC-TGAAGTTGC
*
2412566 GGTGGA-GCAGACT-AAG-TAGGCA
195 AGTGGAGGCAGACTGAAGAT-GGCA
2412588 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAATT
1 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAATT
* * *
2412653 GCAGTGGAGCAGATTAAAGCCGATAATCCAATCTCGCTGAAGTGGCAGTGAGCGGATTAAAACCT
66 GCAGTGGAGCAGATTAAAGCCGAGAATCCAATCTCGCTGAAGTGGCAATGAGCAGATTAAAACCT
*
2412718 TAGATCTTATCTCTCTGAAGTTGCAGAAAGCAGATCGCATCTAGTCTTATCCTCCTGAAGTTGCA
131 TAGATCTTATCTCTCTGAAGTTACAGAAAGCAGATCGCATCTAGTCTTATCCTCCTGAAGTTGCA
*
2412783 GTGTAGGCAGACTGAAGATGGCA
196 GTGGAGGCAGACTGAAGATGGCA
*
2412806 AATCTTATC
1 AGTCTTATC
2412815 TTTCCAAGAT
Statistics
Matches: 210, Mismatches: 13, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
216 183 0.87
217 11 0.05
218 15 0.07
219 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (218 bp):
AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAATT
GCAGTGGAGCAGATTAAAGCCGAGAATCCAATCTCGCTGAAGTGGCAATGAGCAGATTAAAACCT
TAGATCTTATCTCTCTGAAGTTACAGAAAGCAGATCGCATCTAGTCTTATCCTCCTGAAGTTGCA
GTGGAGGCAGACTGAAGATGGCA
Found at i:2412664 original size:89 final size:87
Alignment explanation
Indices: 2412546--2412815 Score: 221
Period size: 89 Copynumber: 3.1 Consensus size: 87
2412536 TCGCATCTAG
* * *
2412546 TCTTATCTCCTTGAAGTTGCGGTGGAGCAGACTAAGTAGGCAAGTCTTATCCTCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TAAG-AGCCAAGTCTTATCCTCCTGAAGTTGCA
2412611 GTGAGGCAGACTAAAGATGGCAAA
64 GTGAGGCAGACTAAAGATGGCAAA
* * ** *
2412635 TCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAA-AGCCGATAATCCAAT-CTCGCTGAAGTGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TAAGAGCC-A-AGTCTTATCCTC-CTGAAGTTG
* * **** *
2412698 CAGTGA-GCGGATTAAA-ACCTTAGA
62 CAGTGAGGCAGACTAAAGATGGCAAA
* ** * * *
2412722 TCTTATCTCTCTGAAGTTGCAG-AAAGCAGAT-CGCA-TCTAGTCTTATCCTCCTGAAGTTGCAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAG-AGCCAAGTCTTATCCTCCTGAAGTTGCAG
*
2412784 TGTAGGCAGACTGAAGATGGCAAA
65 TG-AGGCAGACTAAAGATGGCAAA
2412808 TCTTATCT
1 TCTTATCT
2412816 TTCCAAGATA
Statistics
Matches: 137, Mismatches: 35, Indels: 21
0.71 0.18 0.11
Matches are distributed among these distances:
83 18 0.13
84 4 0.03
85 9 0.07
86 18 0.13
87 26 0.19
88 12 0.09
89 50 0.36
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (87 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAGAGCCAAGTCTTATCCTCCTGAAGTTGCAGT
GAGGCAGACTAAAGATGGCAAA
Found at i:2414482 original size:16 final size:17
Alignment explanation
Indices: 2414463--2414505 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
2414453 TTTTTATGAT
2414463 TTATATATTTAT-TACC
1 TTATATATTTATGTACC
* *
2414479 TTATATATATATGTACG
1 TTATATATTTATGTACC
2414496 TATATATATT
1 T-TATATATT
2414506 ATACTTTCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 11 0.50
17 4 0.18
18 7 0.32
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (17 bp):
TTATATATTTATGTACC
Found at i:2414593 original size:20 final size:20
Alignment explanation
Indices: 2414568--2414627 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 20
2414558 CTTTATGATC
*
2414568 TATATATTTATTAACTTATA
1 TATATATATATTAACTTATA
2414588 TATATATATATGT-ACGTGTATA
1 TATATATATAT-TAAC-T-TATA
2414610 TATATATATATTATACTT
1 TATATATATATTA-ACTT
2414628 TCTATCCATA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
20 12 0.35
21 4 0.12
22 16 0.47
23 2 0.06
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (20 bp):
TATATATATATTAACTTATA
Found at i:2414596 original size:22 final size:21
Alignment explanation
Indices: 2414568--2414662 Score: 63
Period size: 22 Copynumber: 4.4 Consensus size: 21
2414558 CTTTATGATC
2414568 TATATATTTATTAAC-TTATA
1 TATATATTTATTAACTTTATA
* *
2414588 TATATATATATGT-ACGTGTATA
1 TATATATTTAT-TAAC-TTTATA
* *
2414610 TATATATATATTATACTTTCTA
1 TATATATTTATTA-ACTTTATA
*
2414632 TCCATAT-TTTA-TAATTTCTATA
1 T--ATATATTTATTAACTT-TATA
2414654 TATATATTT
1 TATATATTT
2414663 TTCTTTATTC
Statistics
Matches: 59, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
20 16 0.27
21 8 0.14
22 26 0.44
23 5 0.08
24 4 0.07
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.54
Consensus pattern (21 bp):
TATATATTTATTAACTTTATA
Found at i:2414658 original size:20 final size:20
Alignment explanation
Indices: 2414496--2414661 Score: 80
Period size: 20 Copynumber: 8.5 Consensus size: 20
2414486 TATATGTACG
*
2414496 TATATATATTATACTTTCTA
1 TATATATATTATAATTTCTA
* *
2414516 TACATATTTTATAATTTCTA
1 TATATATATTATAATTTCTA
*
2414536 TATATATA-TATGAA-ATC-A
1 TATATATATTAT-AATTTCTA
* *
2414554 T-TATCT-TTATGA--TCTA
1 TATATATATTATAATTTCTA
* * *
2414570 TATATTTATTA-ACTTATATA
1 TATATATATTATAATT-TCTA
* * *
2414590 TATATATATGTACGT-GTATATA
1 TATATATAT-TA--TAATTTCTA
*
2414612 TATATATATTATACTTTCTA
1 TATATATATTATAATTTCTA
** *
2414632 TCCATATTTTATAATTTCTA
1 TATATATATTATAATTTCTA
2414652 TATATATATT
1 TATATATATT
2414662 TTTCTTTATT
Statistics
Matches: 108, Mismatches: 25, Indels: 26
0.68 0.16 0.16
Matches are distributed among these distances:
15 2 0.02
16 3 0.03
17 11 0.10
18 5 0.05
19 6 0.06
20 63 0.58
21 4 0.04
22 13 0.12
23 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.52
Consensus pattern (20 bp):
TATATATATTATAATTTCTA
Found at i:2420052 original size:19 final size:18
Alignment explanation
Indices: 2420022--2420057 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
2420012 TATATAATGC
2420022 TATATAATATATTAATAT
1 TATATAATATATTAATAT
2420040 TATATATATATATTAATA
1 TATATA-ATATATTAATA
2420058 GTTTTAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATATAATATATTAATAT
Found at i:2420468 original size:19 final size:21
Alignment explanation
Indices: 2420443--2420491 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
2420433 TAATAATATT
*
2420443 AATAAAAATT-AATATTAAT-
1 AATAAAAATTAAACATTAATC
2420462 AA-AAAAATTAAACATTAATC
1 AATAAAAATTAAACATTAATC
2420482 AAATAAAAAT
1 -AATAAAAAT
2420492 AATTAATAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 7 0.28
19 10 0.40
21 2 0.08
22 6 0.24
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (21 bp):
AATAAAAATTAAACATTAATC
Found at i:2420472 original size:18 final size:16
Alignment explanation
Indices: 2420436--2420466 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2420426 GTAAAGATAA
2420436 TAATATTAATAAAAAT
1 TAATATTAATAAAAAT
2420452 TAATATTAATAAAAA
1 TAATATTAATAAAAA
2420467 AATTAAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATATTAATAAAAAT
Found at i:2420473 original size:25 final size:25
Alignment explanation
Indices: 2420445--2420497 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
2420435 ATAATATTAA
2420445 TAAAAATTAAT-ATTAATAAAAA-AAT
1 TAAAAATTAATCA--AATAAAAATAAT
*
2420470 TAAACATTAATCAAATAAAAATAAT
1 TAAAAATTAATCAAATAAAAATAAT
2420495 TAA
1 TAA
2420498 TAGTAAAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 8 0.32
25 16 0.64
26 1 0.04
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (25 bp):
TAAAAATTAATCAAATAAAAATAAT
Found at i:2423143 original size:54 final size:54
Alignment explanation
Indices: 2422996--2423143 Score: 176
Period size: 56 Copynumber: 2.7 Consensus size: 54
2422986 CCACATGACG
* * *
2422996 CCATAGT-CCTAGACTAGGTCTTACACTATATGGT-TCTCTTATCCTCATATGATG
1 CCATAGTACC-AGACTAGGTCTTACACTATATGGTCT-TCCTATCCCCATATGATA
*
2423050 CCATAGCCACCATGACTAGGTCTTACACTATATGGTCTTCACT-TCCCCATATGATA
1 CCATAG-TACCA-GACTAGGTCTTACACTATATGGTCTTC-CTATCCCCATATGATA
* *
2423106 CTATAGTACCAGACTAGGTCTTACACTATATGATCTTC
1 CCATAGTACCAGACTAGGTCTTACACTATATGGTCTTC
2423144 TTGCCATGGC
Statistics
Matches: 82, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
54 32 0.39
55 5 0.06
56 43 0.52
57 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (54 bp):
CCATAGTACCAGACTAGGTCTTACACTATATGGTCTTCCTATCCCCATATGATA
Found at i:2425263 original size:8 final size:8
Alignment explanation
Indices: 2425250--2425278 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
2425240 TTTTAAATGA
2425250 TATTTTAT
1 TATTTTAT
2425258 TATTTTAT
1 TATTTTAT
2425266 TATTTTAT
1 TATTTTAT
2425274 TATTT
1 TATTT
2425279 AGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:2427635 original size:40 final size:40
Alignment explanation
Indices: 2427556--2427823 Score: 315
Period size: 40 Copynumber: 6.7 Consensus size: 40
2427546 AAAATTATCA
* *
2427556 AAGTATAAATAGGGGCACGTATGTGCAA-TATGGGGTACCG
1 AAGTACAAACAGGGGCACGTATGTGCAATTA-GGGGTACCG
* * * * * *
2427596 AAGTGCAAATAGAGGCACGTGTGTGTAATTAGGGATACCG
1 AAGTACAAACAGGGGCACGTATGTGCAATTAGGGGTACCG
*
2427636 AAGTACAAATAGGGGCACGTATGTGCAATTAGGGGTACCG
1 AAGTACAAACAGGGGCACGTATGTGCAATTAGGGGTACCG
* * * * *
2427676 ACGTACAAACAGGGGCACGTGTGTGTAATTAGGAGTACTG
1 AAGTACAAACAGGGGCACGTATGTGCAATTAGGGGTACCG
* *
2427716 AAGTACAAACATGGGCACGTATGTGCAATAAGGGGTACC-
1 AAGTACAAACAGGGGCACGTATGTGCAATTAGGGGTACCG
* * ** *
2427755 AAGTACAAACAGGGGCACGTATATGAAATCGGGGGTACCA
1 AAGTACAAACAGGGGCACGTATGTGCAATTAGGGGTACCG
*
2427795 AAGTACAAACAGGGGCACGTACGTGCAAT
1 AAGTACAAACAGGGGCACGTATGTGCAAT
2427824 CAATATAATT
Statistics
Matches: 194, Mismatches: 32, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
39 34 0.18
40 158 0.81
41 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.19
Consensus pattern (40 bp):
AAGTACAAACAGGGGCACGTATGTGCAATTAGGGGTACCG
Found at i:2427668 original size:20 final size:20
Alignment explanation
Indices: 2427562--2427670 Score: 71
Period size: 20 Copynumber: 5.5 Consensus size: 20
2427552 ATCAAAGTAT
2427562 AAATAGGGGCACGTATGTGC
1 AAATAGGGGCACGTATGTGC
* *
2427582 -AATATGGGGTACCG-AAGTGC
1 AAATA-GGGGCA-CGTATGTGC
* * *
2427602 AAATAGAGGCACGTGTGTGT
1 AAATAGGGGCACGTATGTGC
* ** * *
2427622 AATTAGGGATACCG-AAGTAC
1 AAATAGGGGCA-CGTATGTGC
2427642 AAATAGGGGCACGTATGTGC
1 AAATAGGGGCACGTATGTGC
*
2427662 AATTAGGGG
1 AAATAGGGG
2427671 TACCGACGTA
Statistics
Matches: 62, Mismatches: 21, Indels: 12
0.65 0.22 0.13
Matches are distributed among these distances:
19 8 0.13
20 46 0.74
21 8 0.13
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.21
Consensus pattern (20 bp):
AAATAGGGGCACGTATGTGC
Found at i:2430231 original size:16 final size:17
Alignment explanation
Indices: 2430184--2430227 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
2430174 CTGTTTAAAA
2430184 AATTTGAATTTATTTCCC
1 AATTT-AATTTATTTCCC
2430202 AATTTAATTTATTT-CC
1 AATTTAATTTATTTCCC
2430218 AATTT-ATTTA
1 AATTTAATTTA
2430228 ATTTTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.19
16 7 0.27
17 9 0.35
18 5 0.19
ACGTcount: A:0.32, C:0.11, G:0.02, T:0.55
Consensus pattern (17 bp):
AATTTAATTTATTTCCC
Found at i:2433627 original size:80 final size:80
Alignment explanation
Indices: 2433489--2433683 Score: 223
Period size: 80 Copynumber: 2.4 Consensus size: 80
2433479 GATTGAAATT
* * * * * * *
2433489 ACCAAGGTATAAATAGGGGCACGTATCT-ATAATCAGGGGTACTGAAGTACAAATAGGGGCACGT
1 ACCAAAGTACAAACAGGGGCACGTATGTGA-AATCAGGGGTACTCAAGTACAAACAGGGGCACAT
** *
2433553 GTGTGTTGGCAGGGGA
65 GTGTGTAAGCAAGGGA
2433569 ACCAAAGTACAAACAGGGGCACGTATGTGAAATCAGGGGTA-TCATAGTACAAACAGGGGCACAT
1 ACCAAAGTACAAACAGGGGCACGTATGTGAAATCAGGGGTACTCA-AGTACAAACAGGGGCACAT
* *
2433633 GTGTGTAATCAAGGGT
65 GTGTGTAAGCAAGGGA
* * *
2433649 ACCGAAGTGCAAACAGGGGCACGTATGTGCAATCA
1 ACCAAAGTACAAACAGGGGCACGTATGTGAAATCA
2433684 ATATAATTAA
Statistics
Matches: 98, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
79 2 0.02
80 95 0.97
81 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.19
Consensus pattern (80 bp):
ACCAAAGTACAAACAGGGGCACGTATGTGAAATCAGGGGTACTCAAGTACAAACAGGGGCACATG
TGTGTAAGCAAGGGA
Found at i:2433680 original size:20 final size:20
Alignment explanation
Indices: 2433578--2433680 Score: 68
Period size: 20 Copynumber: 5.2 Consensus size: 20
2433568 AACCAAAGTA
2433578 CAAACAGGGGCACGTATGTG
1 CAAACAGGGGCACGTATGTG
* * *
2433598 -AAATCAGGGGTATCATA-GTA
1 CAAA-CAGGGGCA-CGTATGTG
* *
2433618 CAAACAGGGGCACATGTGTG
1 CAAACAGGGGCACGTATGTG
* * * * *
2433638 TAATCAAGGGTACCG-AAGTG
1 CAAACAGGGGCA-CGTATGTG
2433658 CAAACAGGGGCACGTATGTG
1 CAAACAGGGGCACGTATGTG
2433678 CAA
1 CAA
2433681 TCAATATAAT
Statistics
Matches: 59, Mismatches: 18, Indels: 12
0.66 0.20 0.13
Matches are distributed among these distances:
19 8 0.14
20 44 0.75
21 7 0.12
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.17
Consensus pattern (20 bp):
CAAACAGGGGCACGTATGTG
Found at i:2433684 original size:40 final size:40
Alignment explanation
Indices: 2433503--2433683 Score: 193
Period size: 40 Copynumber: 4.5 Consensus size: 40
2433493 AGGTATAAAT
* * * *
2433503 AGGGGCACGTATCTATAATCAGGGGTACTGAAGTACAAAT
1 AGGGGCACGTATGTGTAATCAGGGGTACCGAAGTACAAAC
* *** * *
2433543 AGGGGCACGTGTGTGTTGGCAGGGGAACCAAAGTACAAAC
1 AGGGGCACGTATGTGTAATCAGGGGTACCGAAGTACAAAC
* *
2433583 AGGGGCACGTATGTGAAATCAGGGGTATC-ATAGTACAAAC
1 AGGGGCACGTATGTGTAATCAGGGGTACCGA-AGTACAAAC
* * * *
2433623 AGGGGCACATGTGTGTAATCAAGGGTACCGAAGTGCAAAC
1 AGGGGCACGTATGTGTAATCAGGGGTACCGAAGTACAAAC
*
2433663 AGGGGCACGTATGTGCAATCA
1 AGGGGCACGTATGTGTAATCA
2433684 ATATAATTAA
Statistics
Matches: 113, Mismatches: 26, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
39 1 0.01
40 111 0.98
41 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.32, T:0.19
Consensus pattern (40 bp):
AGGGGCACGTATGTGTAATCAGGGGTACCGAAGTACAAAC
Found at i:2434844 original size:39 final size:39
Alignment explanation
Indices: 2434790--2434887 Score: 153
Period size: 39 Copynumber: 2.5 Consensus size: 39
2434780 TAATTTAGTT
* *
2434790 TGAGTGTTTAATTATGTCATAATTTGAACATCATTAATA
1 TGAGTTTTTAATTATGTCATAATTTGAACAACATTAATA
2434829 TGAGTTTTTAATTATGTCATAATTTGAACAACATTAATA
1 TGAGTTTTTAATTATGTCATAATTTGAACAACATTAATA
* *
2434868 AG-GGTTTTAATTATGTCATA
1 TGAGTTTTTAATTATGTCATA
2434888 GTTTAGGATA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
38 17 0.31
39 38 0.69
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (39 bp):
TGAGTTTTTAATTATGTCATAATTTGAACAACATTAATA
Found at i:2434935 original size:27 final size:26
Alignment explanation
Indices: 2434905--2434969 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
2434895 ATATCTTTAA
*
2434905 TACATGTTTTAAGTATGTTTAAATTCG
1 TACAT-TTTTAAGTATGTTTAAATTCC
* * *
2434932 TACATCTTTAATGTTTGTTTAATTTCC
1 TACATTTTTAA-GTATGTTTAAATTCC
*
2434959 TACATATTTAA
1 TACATTTTTAA
2434970 AGTGTGTCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 5 0.16
27 27 0.84
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (26 bp):
TACATTTTTAAGTATGTTTAAATTCC
Found at i:2437984 original size:17 final size:18
Alignment explanation
Indices: 2437951--2437984 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2437941 AAAGGTAATG
2437951 TAGTAAGTTCATAGAACT
1 TAGTAAGTTCATAGAACT
*
2437969 TAGTGAGTTC-TAGAAC
1 TAGTAAGTTCATAGAAC
2437985 AGACATTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (18 bp):
TAGTAAGTTCATAGAACT
Found at i:2444145 original size:37 final size:37
Alignment explanation
Indices: 2444098--2444207 Score: 168
Period size: 37 Copynumber: 3.0 Consensus size: 37
2444088 AGATGTATAG
*
2444098 CTCTTATGAGCATTTGGCGTGTTATCAGTTGGATTAA
1 CTCTTATGAGCATTTGGCGTGTTATCGGTTGGATTAA
* *
2444135 CTCTTATGAGCATTTGGCGTGTTATCGGTTGTATTAG
1 CTCTTATGAGCATTTGGCGTGTTATCGGTTGGATTAA
* *
2444172 CTCTTATGAGCATTTGGCATGTT-TGGGTTGGATTAA
1 CTCTTATGAGCATTTGGCGTGTTATCGGTTGGATTAA
2444208 TTGTGTACTC
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
36 10 0.15
37 56 0.85
ACGTcount: A:0.19, C:0.13, G:0.26, T:0.42
Consensus pattern (37 bp):
CTCTTATGAGCATTTGGCGTGTTATCGGTTGGATTAA
Found at i:2448160 original size:17 final size:18
Alignment explanation
Indices: 2448127--2448160 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2448117 AAAGGTAATG
2448127 TAGTAAGTTCATAGAACT
1 TAGTAAGTTCATAGAACT
*
2448145 TAGTGAGTTC-TAGAAC
1 TAGTAAGTTCATAGAAC
2448161 AGACATTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (18 bp):
TAGTAAGTTCATAGAACT
Found at i:2454321 original size:37 final size:37
Alignment explanation
Indices: 2454274--2454383 Score: 168
Period size: 37 Copynumber: 3.0 Consensus size: 37
2454264 AGATGTATAG
*
2454274 CTCTTATGAGCATTTGGCGTGTTATCAGTTGGATTAA
1 CTCTTATGAGCATTTGGCGTGTTATCGGTTGGATTAA
* *
2454311 CTCTTATGAGCATTTGGCGTGTTATCGGTTGTATTAG
1 CTCTTATGAGCATTTGGCGTGTTATCGGTTGGATTAA
* *
2454348 CTCTTATGAGCATTTGGCATGTT-TGGGTTGGATTAA
1 CTCTTATGAGCATTTGGCGTGTTATCGGTTGGATTAA
2454384 TTGTGTACTC
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
36 10 0.15
37 56 0.85
ACGTcount: A:0.19, C:0.13, G:0.26, T:0.42
Consensus pattern (37 bp):
CTCTTATGAGCATTTGGCGTGTTATCGGTTGGATTAA
Found at i:2462652 original size:18 final size:18
Alignment explanation
Indices: 2462631--2462667 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2462621 TGAGTTTTCG
2462631 AATTCGAATAACTCAAAT
1 AATTCGAATAACTCAAAT
*
2462649 AATTCGAATAATTCAAAT
1 AATTCGAATAACTCAAAT
2462667 A
1 A
2462668 TCAAACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (18 bp):
AATTCGAATAACTCAAAT
Found at i:2462750 original size:30 final size:30
Alignment explanation
Indices: 2462716--2462800 Score: 152
Period size: 30 Copynumber: 2.8 Consensus size: 30
2462706 AAACCTTTTT
* *
2462716 ACTTTTCCCTCAAAACTTTTACTCCTTCCC
1 ACTTTCCCCCCAAAACTTTTACTCCTTCCC
2462746 ACTTTCCCCCCAAAACTTTTACTCCTTCCC
1 ACTTTCCCCCCAAAACTTTTACTCCTTCCC
2462776 ACTTTCCCCCCAAAACTTTTACTCC
1 ACTTTCCCCCCAAAACTTTTACTCC
2462801 CCTCCCCTCC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.21, C:0.44, G:0.00, T:0.35
Consensus pattern (30 bp):
ACTTTCCCCCCAAAACTTTTACTCCTTCCC
Found at i:2468250 original size:27 final size:27
Alignment explanation
Indices: 2468212--2468266 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2468202 ATGGTTATTT
2468212 TTCCATACACAAGTTTGTAAAAGGACA
1 TTCCATACACAAGTTTGTAAAAGGACA
2468239 TTCCATACACAAGTTTGTAAAAGGACA
1 TTCCATACACAAGTTTGTAAAAGGACA
2468266 T
1 T
2468267 ACCTAAGGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (27 bp):
TTCCATACACAAGTTTGTAAAAGGACA
Found at i:2487584 original size:51 final size:51
Alignment explanation
Indices: 2487508--2487610 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
2487498 CTATAGGGAT
* *
2487508 CATGCTCGATGGATGAAATGTTATAGGAAAATTAGTACCCAAGTCTCGTTG
1 CATGCTCGATGGAGGAAACGTTATAGGAAAATTAGTACCCAAGTCTCGTTG
*
2487559 CATGCTCGATGGAGGAAACGTTATAGGCAAATTAGTACCCAAGTCTCGTTG
1 CATGCTCGATGGAGGAAACGTTATAGGAAAATTAGTACCCAAGTCTCGTTG
2487610 C
1 C
2487611 CATTCTCCTT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (51 bp):
CATGCTCGATGGAGGAAACGTTATAGGAAAATTAGTACCCAAGTCTCGTTG
Found at i:2490847 original size:27 final size:27
Alignment explanation
Indices: 2490793--2491149 Score: 396
Period size: 27 Copynumber: 13.3 Consensus size: 27
2490783 AGGTATACCA
*
2490793 GTCATTTTACCCTAT-GGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
** *
2490819 GTCATTTTACCCTATAAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
2490846 GTCATTTTACCTTATGAGAGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
*
2490873 GTCATTTTACCCTGTGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
2490900 ATCATTTTACCTTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
2490927 ATCATTTTACCCTATAGAGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
2490954 GTTATTTTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
2490981 TTCATTTTACACTAT--GGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
2491006 GTCATTTTACCCGATAGGGGTACTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
2491033 GTCATTTTACCCTATGAGGGTGTTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
2491060 ATCATTTTATCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
2491087 GTCATTTTACCCTATAGGGCTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
2491114 GTCATTTAACCCTGTGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
2491141 GTCATTTTA
1 GTCATTTTA
2491150 ACTATTCAGA
Statistics
Matches: 275, Mismatches: 53, Indels: 5
0.83 0.16 0.02
Matches are distributed among these distances:
25 21 0.08
26 15 0.05
27 239 0.87
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:2491428 original size:20 final size:19
Alignment explanation
Indices: 2491399--2491440 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
2491389 AGCCCATTAA
*
2491399 GCCCACGTGGCCAATTTCG
1 GCCCACGTGGCCAATTACG
*
2491418 GCCCAACGTGGCCCATTACG
1 GCCC-ACGTGGCCAATTACG
2491438 GCC
1 GCC
2491441 TAAGCCCATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.17, C:0.40, G:0.26, T:0.17
Consensus pattern (19 bp):
GCCCACGTGGCCAATTACG
Found at i:2503987 original size:20 final size:20
Alignment explanation
Indices: 2503951--2503989 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2503941 CTGCACCGAT
2503951 TCTGTAAGTGTTCTAAAAAC
1 TCTGTAAGTGTTCTAAAAAC
*
2503971 TCTGATAAGT-TTTTAAAAA
1 TCTG-TAAGTGTTCTAAAAA
2503990 TATGAGTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (20 bp):
TCTGTAAGTGTTCTAAAAAC
Found at i:2513817 original size:30 final size:30
Alignment explanation
Indices: 2513759--2513817 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
2513749 AGAATCAATC
* *
2513759 TGGGCCTGAGCCCTATACAGTAGCAGTGTA
1 TGGGCATGAGCCCTATACAGTAACAGTGTA
*
2513789 TGGGCATGAGCCCTATACAGTAATAGTGT
1 TGGGCATGAGCCCTATACAGTAACAGTGT
2513818 GGGCCTTAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.25
Consensus pattern (30 bp):
TGGGCATGAGCCCTATACAGTAACAGTGTA
Found at i:2514054 original size:26 final size:26
Alignment explanation
Indices: 2513953--2514053 Score: 130
Period size: 26 Copynumber: 3.9 Consensus size: 26
2513943 ACCAATATTG
* *
2513953 CAGCAAAGCTGCCAGTAATAGTAACG
1 CAGCAAAGCTGCCAGTAACAGTAACA
*
2513979 CAGCAAAGCTGCTAGTAACAGTAACA
1 CAGCAAAGCTGCCAGTAACAGTAACA
* * * *
2514005 CAGTAGAGCTGCCAGTATCAGTATCA
1 CAGCAAAGCTGCCAGTAACAGTAACA
*
2514031 CAGCAAAGCTGCCACTAACAGTA
1 CAGCAAAGCTGCCAGTAACAGTA
2514054 TTTGTGGCAA
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 63 1.00
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.17
Consensus pattern (26 bp):
CAGCAAAGCTGCCAGTAACAGTAACA
Found at i:2514263 original size:27 final size:27
Alignment explanation
Indices: 2514214--2514280 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
2514204 CACAATGCCT
* *
2514214 TAACAGTCATTTCATCTCCTAGGGGCA
1 TAACAGTCATTTTATCCCCTAGGGGCA
*
2514241 TAACAGTCATTTTA-CCCCATAGGGGTA
1 TAACAGTCATTTTATCCCC-TAGGGGCA
**
2514268 TTTCAGTCATTTT
1 TAACAGTCATTTT
2514281 CCCTTTTGGG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 3 0.09
27 31 0.91
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36
Consensus pattern (27 bp):
TAACAGTCATTTTATCCCCTAGGGGCA
Found at i:2514292 original size:27 final size:28
Alignment explanation
Indices: 2514244--2514362 Score: 86
Period size: 27 Copynumber: 4.4 Consensus size: 28
2514234 AGGGGCATAA
** *
2514244 CAGTCATTTTACCCCAT-AGGGGTATTT
1 CAGTCATTTTACCCTTTCGGGGGTATTT
*
2514271 CAGTCATTTT-CCCTTTTGGGGGTATTT
1 CAGTCATTTTACCCTTTCGGGGGTATTT
* * *
2514298 -TGATAATTTTACCC-TTCGAGGGTATTT
1 CAG-TCATTTTACCCTTTCGGGGGTATTT
* * *
2514325 CGGTCATTTTACCC-TTCGAGGTTATTT
1 CAGTCATTTTACCCTTTCGGGGGTATTT
* *
2514352 CGGTAATTTTA
1 CAGTCATTTTA
2514363 TGGCCCAAGC
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
26 5 0.06
27 68 0.88
28 4 0.05
ACGTcount: A:0.18, C:0.18, G:0.19, T:0.44
Consensus pattern (28 bp):
CAGTCATTTTACCCTTTCGGGGGTATTT
Found at i:2515783 original size:10 final size:10
Alignment explanation
Indices: 2515768--2515801 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
2515758 GAATTTGTGT
*
2515768 CAAACACTCC
1 CAAACACACC
2515778 CAAACACACC
1 CAAACACACC
2515788 CAAACACACC
1 CAAACACACC
2515798 CAAA
1 CAAA
2515802 TCACTTAGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (10 bp):
CAAACACACC
Found at i:2518785 original size:50 final size:50
Alignment explanation
Indices: 2518719--2518960 Score: 313
Period size: 50 Copynumber: 4.8 Consensus size: 50
2518709 TTTTCTGTAC
* * ** *
2518719 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * ** *
2518769 TGCCCATGCCATATCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
2518819 TGTCAATGCCATGTCCCAAACATAGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
2518869 TGCCAACGCCATGTCCCAGACATAGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
2518919 TGCCAACGCCATGTCCCAGACATGATCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
2518961 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 170 1.00
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:2520638 original size:25 final size:25
Alignment explanation
Indices: 2520604--2520658 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
2520594 TGTTTAGACA
2520604 AGAAATACATCAGTCAGTGATATTT
1 AGAAATACATCAGTCAGTGATATTT
2520629 AGAAATACATCAGTCAGTGATATTT
1 AGAAATACATCAGTCAGTGATATTT
2520654 AGAAA
1 AGAAA
2520659 GACAAGAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (25 bp):
AGAAATACATCAGTCAGTGATATTT
Found at i:2527426 original size:45 final size:45
Alignment explanation
Indices: 2527298--2527433 Score: 197
Period size: 44 Copynumber: 3.1 Consensus size: 45
2527288 TTATACGCCA
* * *
2527298 AAAATGAGTAAGACCATAGCTAAAAGATGTTATGGAATCATGATG
1 AAAATGAGTAAGACCATAGCTGAAAGATATTATGGCATCATGATG
2527343 AAAATGAGTAAGACCATA-CTGAAAGATATTATGGCATCATGATG
1 AAAATGAGTAAGACCATAGCTGAAAGATATTATGGCATCATGATG
* *
2527387 AAAAT-ATGTAAGACCATAGTTGAAAGACATTATGGCATCAT-ATG
1 AAAATGA-GTAAGACCATAGCTGAAAGATATTATGGCATCATGATG
2527431 AAA
1 AAA
2527434 GCGCGCCAGA
Statistics
Matches: 84, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
43 1 0.01
44 45 0.54
45 38 0.45
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (45 bp):
AAAATGAGTAAGACCATAGCTGAAAGATATTATGGCATCATGATG
Found at i:2532753 original size:24 final size:24
Alignment explanation
Indices: 2532721--2532777 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
2532711 GTCCCAAAGG
**
2532721 TTACAGTGGATTGAACCTTGAGGA
1 TTACAGTGGATTGAACCTTGAAAA
2532745 TTACAGTGGATTGAACCTTGAAAA
1 TTACAGTGGATTGAACCTTGAAAA
2532769 TTACAGTGG
1 TTACAGTGG
2532778 GGGCAATCCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (24 bp):
TTACAGTGGATTGAACCTTGAAAA
Found at i:2533268 original size:44 final size:44
Alignment explanation
Indices: 2533128--2533460 Score: 199
Period size: 44 Copynumber: 7.7 Consensus size: 44
2533118 ATCGAAGACC
* ** *
2533128 CCAATCCTATCTCCCTAAAGTTGCAGTGGAATAGATTA-AA-AATA
1 CCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGA-CACAAGAA-A
* * * * *
2533172 -CAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TC--GCAA
1 CCA-ATCCTATCTCCCTGAAGTTGCAGTGGAGCAGACACAAGAAA
* * * * *
2533213 CCAGTCTTATCTCCCTAAATTTACAGTGGAGCAGACACAAGAAA
1 CCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGACACAAGAAA
** *
2533257 CCAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATCA-AA-ATGA
1 CCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGA-CACAAGA-AA
*** * * * *
2533301 TGGAT-CTCATCTCTCTGAAGTTGCAGTAGAGCAGA-TC--GCAA
1 CCAATCCT-ATCTCCCTGAAGTTGCAGTGGAGCAGACACAAGAAA
* * * * *
2533342 CCAGTCTTATCTCCCTAAATTTACAGTGGAGCAGACACAAGAAA
1 CCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGACACAAGAAA
* ** *
2533386 CCAATCCTATCTCCCTGAAGTTGCAGTGGAGC-G-GATTAGAAC
1 CCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGACACAAGAAA
2533428 CGCAAATCCTATCTCCCTGAAGTTGCAGTGGAG
1 C-C-AATCCTATCTCCCTGAAGTTGCAGTGGAG
2533461 TGGATCAAAA
Statistics
Matches: 216, Mismatches: 55, Indels: 36
0.70 0.18 0.12
Matches are distributed among these distances:
41 51 0.24
42 12 0.06
43 7 0.03
44 144 0.67
45 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (44 bp):
CCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGACACAAGAAA
Found at i:2533442 original size:129 final size:128
Alignment explanation
Indices: 2533128--2533456 Score: 500
Period size: 129 Copynumber: 2.5 Consensus size: 128
2533118 ATCGAAGACC
* * * * *
2533128 CCAATCCTATCTCCCTAAAGTTGCAGTGGAATAGATTAAAAATACAGATCTTATCTCTCTGAAGT
1 CCAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATT-AAAATGCAGATCCTATCTCTCTGAAGT
2533193 TGCAGTAGAGCAGATCGCAACCAGTCTTATCTCCCTAAATTTACAGTGGAGCAGACACAAGAAA
65 TGCAGTAGAGCAGATCGCAACCAGTCTTATCTCCCTAAATTTACAGTGGAGCAGACACAAGAAA
*
2533257 CCAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATCAAAATG-ATGGAT-CTCATCTCTCTGAA
1 CCAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATGCA--GATCCT-ATCTCTCTGAA
2533320 GTTGCAGTAGAGCAGATCGCAACCAGTCTTATCTCCCTAAATTTACAGTGGAGCAGACACAAGAA
63 GTTGCAGTAGAGCAGATCGCAACCAGTCTTATCTCCCTAAATTTACAGTGGAGCAGACACAAGAA
2533385 A
128 A
* ** * *
2533386 CCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAGAACCGCAAATCCTATCTCCCTGAAGT
1 CCAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTA-AAATGCAGATCCTATCTCTCTGAAGT
2533451 TGCAGT
65 TGCAGT
2533457 GGAGTGGATC
Statistics
Matches: 182, Mismatches: 12, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
127 1 0.01
128 6 0.03
129 169 0.93
130 5 0.03
131 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (128 bp):
CCAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATGCAGATCCTATCTCTCTGAAGTT
GCAGTAGAGCAGATCGCAACCAGTCTTATCTCCCTAAATTTACAGTGGAGCAGACACAAGAAA
Found at i:2533486 original size:44 final size:42
Alignment explanation
Indices: 2533136--2533511 Score: 174
Period size: 44 Copynumber: 8.7 Consensus size: 42
2533126 CCCCAATCCT
* ** * *
2533136 ATCTCCCTAAAGTTGCAGTGGAATAGATTAAAAATAC-AGATCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGA-T-CAAA-ACGAGATCTC
* * ** * *
2533180 ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCAACCAG-TCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAACGAGATCTC
* * * * *
2533221 ATCTCCCTAAATTTACAGTGGAGCAGACACAAGAAACCA-ATC-C
1 ATCTCCCTGAAGTTGCAGTGGAGCAGA-TC-A-AAACGAGATCTC
** *
2533264 TATCTCCCTGAAGTTGCAGTGGAGTGGATCAAAATGATGGATCTC
1 -ATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAACGA--GATCTC
* * ** * *
2533309 ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCAACCAG-TCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAACGAGATCTC
* * * * *
2533350 ATCTCCCTAAATTTACAGTGGAGCAGACACAAGAAACCA-ATC-C
1 ATCTCCCTGAAGTTGCAGTGGAGCAGA-TC-A-AAACGAGATCTC
* * * *
2533393 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAGAACCGCAAATC-C
1 -ATCTCCCTGAAGTTGCAGTGGAGCAGATCA-AAACG-AGATCTC
** *
2533437 TATCTCCCTGAAGTTGCAGTGGAGTGGATCAAAATGATGGATCTC
1 -ATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAACGA--GATCTC
* * *
2533482 ATCTCTCTGAAGTTGCAGTAGAGTAGATCA
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATCA
2533512 CATCAGACTT
Statistics
Matches: 253, Mismatches: 59, Indels: 40
0.72 0.17 0.11
Matches are distributed among these distances:
41 57 0.23
42 13 0.05
43 6 0.02
44 175 0.69
45 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (42 bp):
ATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAACGAGATCTC
Found at i:2562839 original size:116 final size:117
Alignment explanation
Indices: 2562695--2562928 Score: 461
Period size: 116 Copynumber: 2.0 Consensus size: 117
2562685 AGAATTAAAT
2562695 AAAAATAATTTTTGAAGTTTAAATTTTTTAGGTTATAGTAGGACCATGTGTTTAAATAAAACAAA
1 AAAAATAATTTTTGAAGTTTAAATTTTTTAGGTTATAGTAGGACCATGTGTTTAAATAAAACAAA
2562760 ATTATTAAGAAATTTGAAAAATCATCTCTTTAGGTGCAATTTGGAAAAAGGA
66 ATTATTAAGAAATTTGAAAAATCATCTCTTTAGGTGCAATTTGGAAAAAGGA
2562812 AAAAATAA-TTTTGAAGTTTAAATTTTTTAGGTTATAGTAGGACCATGTGTTTAAATAAAACAAA
1 AAAAATAATTTTTGAAGTTTAAATTTTTTAGGTTATAGTAGGACCATGTGTTTAAATAAAACAAA
2562876 ATTATTAAGAAATTTGAAAAATCATCTCTTTAGGTGCAATTTGGAAAAAGGA
66 ATTATTAAGAAATTTGAAAAATCATCTCTTTAGGTGCAATTTGGAAAAAGGA
2562928 A
1 A
2562929 TTAAGCTATT
Statistics
Matches: 117, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
116 109 0.93
117 8 0.07
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.35
Consensus pattern (117 bp):
AAAAATAATTTTTGAAGTTTAAATTTTTTAGGTTATAGTAGGACCATGTGTTTAAATAAAACAAA
ATTATTAAGAAATTTGAAAAATCATCTCTTTAGGTGCAATTTGGAAAAAGGA
Found at i:2568432 original size:24 final size:22
Alignment explanation
Indices: 2568388--2568433 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2568378 TGTGATACAT
*
2568388 TTATCTTATTTCATTGTTTCTA
1 TTATCTTATTTCATTGGTTCTA
*
2568410 TTATTTTATATTCATTTGGTTCTA
1 TTATCTTAT-TTCA-TTGGTTCTA
2568434 CATGTAATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
23 4 0.20
24 8 0.40
ACGTcount: A:0.20, C:0.11, G:0.07, T:0.63
Consensus pattern (22 bp):
TTATCTTATTTCATTGGTTCTA
Found at i:2570802 original size:28 final size:28
Alignment explanation
Indices: 2570771--2570835 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
2570761 CAGTGATAGT
*
2570771 ACAGTGTGGGCCTTAGCCCGATACAGTA
1 ACAGTGTGGGCCTTAGCCCAATACAGTA
2570799 ACAGTGTGGGCCTTAGCCCAATACAGTA
1 ACAGTGTGGGCCTTAGCCCAATACAGTA
2570827 ACAGTGTGG
1 ACAGTGTGG
2570836 TAATGCAACC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (28 bp):
ACAGTGTGGGCCTTAGCCCAATACAGTA
Found at i:2570925 original size:58 final size:58
Alignment explanation
Indices: 2570855--2571101 Score: 494
Period size: 58 Copynumber: 4.3 Consensus size: 58
2570845 CCATTCCAAT
2570855 CCAGCCAACACACCACTCCATACCACCATCACACCATGTGGGGATAAAATCGACCCAC
1 CCAGCCAACACACCACTCCATACCACCATCACACCATGTGGGGATAAAATCGACCCAC
2570913 CCAGCCAACACACCACTCCATACCACCATCACACCATGTGGGGATAAAATCGACCCAC
1 CCAGCCAACACACCACTCCATACCACCATCACACCATGTGGGGATAAAATCGACCCAC
2570971 CCAGCCAACACACCACTCCATACCACCATCACACCATGTGGGGATAAAATCGACCCAC
1 CCAGCCAACACACCACTCCATACCACCATCACACCATGTGGGGATAAAATCGACCCAC
2571029 CCAGCCAACACACCACTCCATACCACCATCACACCATGTGGGGATAAAATCGACCCAC
1 CCAGCCAACACACCACTCCATACCACCATCACACCATGTGGGGATAAAATCGACCCAC
2571087 CCAGCCAACACACCA
1 CCAGCCAACACACCA
2571102 ATATTGCAGC
Statistics
Matches: 189, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 189 1.00
ACGTcount: A:0.35, C:0.42, G:0.12, T:0.11
Consensus pattern (58 bp):
CCAGCCAACACACCACTCCATACCACCATCACACCATGTGGGGATAAAATCGACCCAC
Found at i:2571378 original size:27 final size:26
Alignment explanation
Indices: 2571348--2571486 Score: 118
Period size: 27 Copynumber: 5.2 Consensus size: 26
2571338 TATAACAGTC
*
2571348 ATTTTACCCTATGAGGGTATTTTGGTT
1 ATTTTACCCT-TGAGGGTATTTCGGTT
* * * *
2571375 ATTTTATCCTTTAGGGGATTTCGGTC
1 ATTTTACCCTTGAGGGTATTTCGGTT
** *
2571401 ATTTTATCTTTTGA-GGTATTTCGATT
1 ATTTTA-CCCTTGAGGGTATTTCGGTT
* * *
2571427 ATTTTGCCCTTTGGGGGTATTTCGATT
1 ATTTTACCC-TTGAGGGTATTTCGGTT
* *
2571454 ATTTTACCCTTCGAAGGTATTTCGGTC
1 ATTTTACCCTT-GAGGGTATTTCGGTT
2571481 ATTTTA
1 ATTTTA
2571487 TTGACCCCAC
Statistics
Matches: 87, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
25 1 0.01
26 37 0.43
27 49 0.56
ACGTcount: A:0.17, C:0.14, G:0.20, T:0.49
Consensus pattern (26 bp):
ATTTTACCCTTGAGGGTATTTCGGTT
Found at i:2571416 original size:53 final size:53
Alignment explanation
Indices: 2571345--2571487 Score: 153
Period size: 53 Copynumber: 2.7 Consensus size: 53
2571335 GGGTATAACA
* *
2571345 GTCATTTTACCCTATGAGGGTATTTTGGTTATTTTATCCTTTAGGGG-ATTTCG
1 GTCATTTTACCCTTTGA-GGTATTTCGGTTATTTTATCCTTTAGGGGTATTTCG
* * * ** *
2571398 GTCATTTTATCTTTTGAGGTATTTCGATTATTTTGCCCTTTGGGGGTATTTCG
1 GTCATTTTACCCTTTGAGGTATTTCGGTTATTTTATCCTTTAGGGGTATTTCG
* * * *
2571451 ATTATTTTACCCTTCGAAGGTATTTCGGTCATTTTAT
1 GTCATTTTACCCTTTG-AGGTATTTCGGTTATTTTAT
2571488 TGACCCCACG
Statistics
Matches: 71, Mismatches: 17, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
52 24 0.34
53 31 0.44
54 16 0.23
ACGTcount: A:0.17, C:0.14, G:0.20, T:0.49
Consensus pattern (53 bp):
GTCATTTTACCCTTTGAGGTATTTCGGTTATTTTATCCTTTAGGGGTATTTCG
Found at i:2572576 original size:13 final size:13
Alignment explanation
Indices: 2572539--2572576 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
2572529 CGGCAACCAG
*
2572539 AGAGAAAAGGGAA
1 AGAGAAAAGTGAA
2572552 AGAGAAAA-TGAA
1 AGAGAAAAGTGAA
*
2572564 ATAGAAAAGTGAA
1 AGAGAAAAGTGAA
2572577 CAAACCCGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.63, C:0.00, G:0.29, T:0.08
Consensus pattern (13 bp):
AGAGAAAAGTGAA
Found at i:2575090 original size:25 final size:23
Alignment explanation
Indices: 2575044--2575091 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
2575034 TTTTTAATTG
*
2575044 AGTTATTGTTATTAAATTGAATA
1 AGTTATAGTTATTAAATTGAATA
*
2575067 AGTTATAGTATATTAAGGTTGAATA
1 AGTTATAGT-TATTAA-ATTGAATA
2575092 TGTATGTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 6 0.29
25 7 0.33
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.44
Consensus pattern (23 bp):
AGTTATAGTTATTAAATTGAATA
Done.