Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 129 of 322
Found at i:42158852 original size:27 final size:27
Alignment explanation
Indices: 42158822--42158961 Score: 174
Period size: 27 Copynumber: 5.2 Consensus size: 27
42158812 ATTACTGTTT
** *
42158822 TACCCTCAATTTACAAAATTACTAAAA
1 TACCCTCAATTTGTAAAATTACCAAAA
* *
42158849 TACCCTTAGTTTGTAAAATTACCAAAA
1 TACCCTCAATTTGTAAAATTACCAAAA
* *
42158876 TACCC-CTAGTTTGTAAAATTATCAAAA
1 TACCCTC-AATTTGTAAAATTACCAAAA
** *
42158903 TACCCTTGATTTGTGAAATTACCAAAA
1 TACCCTCAATTTGTAAAATTACCAAAA
42158930 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCAATTTGTAAAATTACCAAAA
42158957 TACCC
1 TACCC
42158962 CTGATTTACA
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
27 96 1.00
ACGTcount: A:0.41, C:0.21, G:0.06, T:0.31
Consensus pattern (27 bp):
TACCCTCAATTTGTAAAATTACCAAAA
Found at i:42158880 original size:54 final size:54
Alignment explanation
Indices: 42158822--42159074 Score: 192
Period size: 54 Copynumber: 4.6 Consensus size: 54
42158812 ATTACTGTTT
**
42158822 TACCCTCAATTTACAAAATTACTAAAATACCCTT-AGTTTGTAAAATTACCAAAA
1 TACCCTCAATTTGTAAAATTACTAAAATACCCTTGA-TTTGTAAAATTACCAAAA
* *
42158876 TACCC-CTAGTTTGTAAAATTA-TCAAAATACCCTTGATTTGTGAAATTACCAAAA
1 TACCCTC-AATTTGTAAAATTACT-AAAATACCCTTGATTTGTAAAATTACCAAAA
* * ** *
42158930 TACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAGTTA-CAGAAA
1 TACCCTCAATTTGTAAAATTACTAAAATACCCTTGATTTGTAAAATTACCA-AAA
* * * * * ** **
42158984 TACCCATGACTTTCTAAAAATTA-TAGAAATACCATTGGTTTACAAAATTACGGAAA
1 TACCC-TCAATTTGT-AAAATTACTA-AAATACCCTTGATTTGTAAAATTACCAAAA
* * * * * *
42159040 TACCCTTAGTTTGTAGATTTACCAAAACACCCTTG
1 TACCCTCAATTTGTAAAATTACTAAAATACCCTTG
42159075 TAGGATGAAA
Statistics
Matches: 159, Mismatches: 29, Indels: 22
0.76 0.14 0.10
Matches are distributed among these distances:
53 4 0.03
54 104 0.65
55 16 0.10
56 35 0.22
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.31
Consensus pattern (54 bp):
TACCCTCAATTTGTAAAATTACTAAAATACCCTTGATTTGTAAAATTACCAAAA
Found at i:42158985 original size:81 final size:81
Alignment explanation
Indices: 42158837--42158988 Score: 220
Period size: 81 Copynumber: 1.9 Consensus size: 81
42158827 TCAATTTACA
* * * *
42158837 AAATTACTAAAATACCCTTAGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTATCAAA
1 AAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTAGATTGTAAAATTATCAAA
42158902 ATACCCTTGATTTGTG
66 ATACCCTTGATTTGTG
42158918 AAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCT-GATT-TACAAAGTTA-CA
1 AAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTAGATTGTA-AAA-TTATCA
42158980 GAAATACCC
64 -AAATACCC
42158989 ATGACTTTCT
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
79 2 0.03
80 8 0.12
81 54 0.84
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.30
Consensus pattern (81 bp):
AAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTAGATTGTAAAATTATCAAA
ATACCCTTGATTTGTG
Found at i:42159051 original size:27 final size:27
Alignment explanation
Indices: 42158835--42159073 Score: 155
Period size: 27 Copynumber: 8.8 Consensus size: 27
42158825 CCTCAATTTA
*
42158835 CAAAATTACTAAAATACCCTTAGTTTG
1 CAAAATTACCAAAATACCCTTAGTTTG
* *
42158862 TAAAATTACCAAAATACCCCTAGTTTG
1 CAAAATTACCAAAATACCCTTAGTTTG
* *
42158889 TAAAATTATCAAAATACCCTT-GATTTG
1 CAAAATTACCAAAATACCCTTAG-TTTG
** * *
42158916 TGAAATTACCAAAATACCCTCAATTTG
1 CAAAATTACCAAAATACCCTTAGTTTG
* * *
42158943 TAAAATTACCAAAATACCCCT-GATTTA
1 CAAAATTACCAAAATACCCTTAG-TTTG
* * *
42158970 CAAAGTTA-CAGAAATACCCATGACTTT-
1 CAAAATTACCA-AAATACCC-TTAGTTTG
* * * *
42158997 CTAAAAATTA-TAGAAATACCATTGGTTTA
1 C--AAAATTACCA-AAATACCCTTAGTTTG
**
42159026 CAAAATTACGGAAATACCCTTAGTTTG
1 CAAAATTACCAAAATACCCTTAGTTTG
* * * *
42159053 TAGATTTACCAAAACACCCTT
1 CAAAATTACCAAAATACCCTT
42159074 GTAGGATGAA
Statistics
Matches: 166, Mismatches: 36, Indels: 20
0.75 0.16 0.09
Matches are distributed among these distances:
26 3 0.02
27 140 0.84
28 7 0.04
29 16 0.10
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
CAAAATTACCAAAATACCCTTAGTTTG
Found at i:42159169 original size:27 final size:27
Alignment explanation
Indices: 42159092--42159169 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
42159082 AAATGACTAA
* **
42159092 AATACCCCTAT-TAGGTAAAAAAACCGT
1 AATACCCCTGTAT-GGTAAAATGACCGT
* *
42159119 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTATGGTAAAATGACCGT
42159146 AATACCCCTGTATGGTAAAATGAC
1 AATACCCCTGTATGGTAAAATGAC
42159170 GAATATGCCC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
26 1 0.02
27 39 0.95
28 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTATGGTAAAATGACCGT
Found at i:42160359 original size:25 final size:25
Alignment explanation
Indices: 42160330--42160377 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
42160320 TTATAATATG
* * *
42160330 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
42160355 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
42160378 GTTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:42160439 original size:20 final size:20
Alignment explanation
Indices: 42160414--42160464 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
42160404 ATTTTGATAA
*
42160414 ACATGATATGTATGATATGC
1 ACATGACATGTATGATATGC
42160434 ACATGACATGTATGATATGC
1 ACATGACATGTATGATATGC
*
42160454 ACATGAGATGT
1 ACATGACATGT
42160465 TCATAAATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (20 bp):
ACATGACATGTATGATATGC
Found at i:42160592 original size:25 final size:24
Alignment explanation
Indices: 42160511--42160679 Score: 202
Period size: 25 Copynumber: 7.0 Consensus size: 24
42160501 AGGAAGTGCA
*
42160511 AAAGGGCTTATGCCCCAGTTAT-C
1 AAAGGGCTTATGCCCCAGTTATAT
42160534 AAAGGGCTTATGCCCCAGTTAT-T
1 AAAGGGCTTATGCCCCAGTTATAT
42160557 AAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTAT-AT
*
42160582 GAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTAT-AT
* *
42160607 AAATGGCTTATGCCCCAGTTATAA
1 AAAGGGCTTATGCCCCAGTTATAT
* *
42160631 AAAGGGCTTTTGCCCTAGTTACTA-
1 AAAGGGCTTATGCCCCAGTTA-TAT
*
42160655 AAAGAGGC-TAGGCCTCCAGTTATAT
1 AAAG-GGCTTATGCC-CCAGTTATAT
42160680 GATAAAGCAG
Statistics
Matches: 129, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
23 44 0.34
24 29 0.22
25 56 0.43
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (24 bp):
AAAGGGCTTATGCCCCAGTTATAT
Found at i:42160674 original size:74 final size:73
Alignment explanation
Indices: 42160511--42160677 Score: 191
Period size: 74 Copynumber: 2.3 Consensus size: 73
42160501 AGGAAGTGCA
* * * *
42160511 AAAGGGCTTATGCCCCAGTTAT--CAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCA
1 AAAGGGCTTAGGCCCCAGTTATGATAAATGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCA
42160574 GTTATGAT
66 GTTATGAT
* * * *
42160582 GAAGGGCTTATGCCCCAGTTATGATAAATGGCTTATGCCCCAGTTATAAAAAGGGCTTTTGCCCT
1 AAAGGGCTTAGGCCCCAGTTATGATAAATGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCC
42160647 AGTTACT-A-
65 AGTTA-TGAT
42160655 AAAGAGGC-TAGGCCTCCAGTTAT
1 AAAG-GGCTTAGGCC-CCAGTTAT
42160678 ATGATAAAGC
Statistics
Matches: 82, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
71 21 0.26
73 29 0.35
74 31 0.38
75 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (73 bp):
AAAGGGCTTAGGCCCCAGTTATGATAAATGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCA
GTTATGAT
Found at i:42161153 original size:56 final size:56
Alignment explanation
Indices: 42161078--42161189 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
42161068 TGCAGGTGAG
42161078 CCTTGATATAGGGACTTGGAGCCGGAGGGGATTCAGAGTAGCCACGGTGATCGTCT
1 CCTTGATATAGGGACTTGGAGCCGGAGGGGATTCAGAGTAGCCACGGTGATCGTCT
42161134 CCTTGATATAGGGACTTGGAGCCGGAGGGGATTCAGAGTAGCCACGGTGATCGTCT
1 CCTTGATATAGGGACTTGGAGCCGGAGGGGATTCAGAGTAGCCACGGTGATCGTCT
42161190 TTGGGCTTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.21, C:0.20, G:0.36, T:0.23
Consensus pattern (56 bp):
CCTTGATATAGGGACTTGGAGCCGGAGGGGATTCAGAGTAGCCACGGTGATCGTCT
Found at i:42163583 original size:18 final size:19
Alignment explanation
Indices: 42163560--42163595 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
42163550 AAGCCCCCCC
42163560 AAAAAAAAA-CCTAACCCA
1 AAAAAAAAACCCTAACCCA
42163578 AAAAAAAAACCCTAACCC
1 AAAAAAAAACCCTAACCC
42163596 CCCCCCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.64, C:0.31, G:0.00, T:0.06
Consensus pattern (19 bp):
AAAAAAAAACCCTAACCCA
Found at i:42174389 original size:86 final size:86
Alignment explanation
Indices: 42174161--42174399 Score: 199
Period size: 86 Copynumber: 2.7 Consensus size: 86
42174151 GTTCATCAAA
* * * *
42174161 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAG-GT-CTCATGACGAGGTATT-TACG
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGAGTACAC-T-A--AGGTATTGT-CA
42174223 ATTTCCATT-T-TTC-AATTTATGTTTTTC
61 ATTT---TTGTGTTCTAATTTATG-TTTTC
* * * * *
42174250 AAAAATCAATTTATATTGCGAGAGGTGAGTTGAGCCTCAGGGTACACTGAGGTATTGTCAATTTT
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGAGTACACTAAGGTATTGTCAATTTT
42174315 TGTGTTCTAATTTATG-TTTC
66 TGTGTTCTAATTTATGTTTTC
* * *
42174335 AAAAAATCAACTCATATTATGGGAGGTGAGTTGAGCCTCA-AG-ACACGTTAAGGTATTTTCAAT
1 -AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGAGTACAC--TAAGGTATTGTCAAT
42174398 TT
63 TT
42174400 CTGTCTTTCA
Statistics
Matches: 127, Mismatches: 14, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
84 6 0.05
85 6 0.05
86 52 0.41
87 20 0.16
88 1 0.01
89 37 0.29
90 3 0.02
91 2 0.02
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (86 bp):
AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGAGTACACTAAGGTATTGTCAATTTT
TGTGTTCTAATTTATGTTTTC
Found at i:42174611 original size:71 final size:73
Alignment explanation
Indices: 42174323--42174623 Score: 394
Period size: 71 Copynumber: 4.1 Consensus size: 73
42174313 TTTGTGTTCT
** * * *
42174323 AATTTATG-TTTCAAAAAATCAACTCATATTATGGGAGGTGAGTTGAGCCTCAAGACACGTTAAG
1 AATTTATGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAG
42174387 GTATTTTC
66 GTATTTTC
* *
42174395 AATTTCTGTCTTTCAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACA
1 AATTTATGT-TTTC----AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG--ACA
*
42174460 CGCTGAGGTAATTTC
59 CGCTGAGGTATTTTC
* *
42174475 AATTTATGTTTGTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGA
1 AATTTATGTTT-TCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGA
42174539 GGTATTTTC
65 GGTATTTTC
* *
42174548 AATTTAT-TTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAAGACACGTTGAG
1 AATTTATGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAG
42174611 GTATTTTC
66 GTATTTTC
42174619 AATTT
1 AATTT
42174624 CTGCTCACAT
Statistics
Matches: 205, Mismatches: 15, Indels: 19
0.86 0.06 0.08
Matches are distributed among these distances:
71 62 0.30
72 10 0.05
73 23 0.11
74 4 0.02
75 41 0.20
78 38 0.19
79 2 0.01
80 25 0.12
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (73 bp):
AATTTATGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAG
GTATTTTC
Found at i:42174644 original size:58 final size:59
Alignment explanation
Indices: 42174569--42174685 Score: 191
Period size: 58 Copynumber: 2.0 Consensus size: 59
42174559 CAAAAATCAA
* *
42174569 CTCATATTGCGAGAGGTGAGTTAAGCCTCAAGACACGTTGAGGT-ATTTTCAATTTCTG
1 CTCACATTGCGAGAGGTGAGTTAAGCCTCAAGACACGCTGAGGTAATTTTCAATTTCTG
* *
42174627 CTCACATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTTCAATTTCTG
1 CTCACATTGCGAGAGGTGAGTTAAGCCTCAAGACACGCTGAGGTAATTTTCAATTTCTG
42174686 TTGTTAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
58 40 0.74
59 14 0.26
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.31
Consensus pattern (59 bp):
CTCACATTGCGAGAGGTGAGTTAAGCCTCAAGACACGCTGAGGTAATTTTCAATTTCTG
Found at i:42174752 original size:129 final size:125
Alignment explanation
Indices: 42174498--42174891 Score: 338
Period size: 135 Copynumber: 2.9 Consensus size: 125
42174488 CAAAAATCAA
* * *
42174498 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTATTTTTCAAA
1 CTCACATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTATTTTTAAAA
** * *
42174563 AATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTG
66 AATCAACTCATATTGCGAGAAATAAGTTAAGCCTCAAGACACGCTGAGG----TTCAATTTCTG
*
42174627 CTCACATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTTCAATTTCTGTTGTTA
1 CTCACATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT-ATTTTCAATTTAT-TT-TT-
* *
42174692 AAAAAAAATCAACTCATATTGCGAGAAATAAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAAT
62 --AAAAAATCAACTCATATTGCGAGAAATAAGTTAAGCCTCAAGACACGCTGAGG----TTCAAT
42174757 TTCTG
121 TTCTG
** * * *
42174762 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
1 ----C-----TC-A--C--ATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCA
* * * * * *
42174827 ATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGT
52 ATTTAT-TTTTAAAAAATCAACTCATATTGCGAGAAATAAGTTAAGCCTCAAGACACGCTGAGGT
42174892 AATTTCAATT
Statistics
Matches: 226, Mismatches: 19, Indels: 29
0.82 0.07 0.11
Matches are distributed among these distances:
129 42 0.19
130 12 0.05
131 2 0.01
132 2 0.01
135 60 0.27
139 1 0.00
140 1 0.00
144 52 0.23
145 1 0.00
147 3 0.01
148 15 0.07
149 35 0.15
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (125 bp):
CTCACATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTATTTTTAAAA
AATCAACTCATATTGCGAGAAATAAGTTAAGCCTCAAGACACGCTGAGGTTCAATTTCTG
Found at i:42175041 original size:221 final size:217
Alignment explanation
Indices: 42174627--42176012 Score: 1329
Period size: 221 Copynumber: 6.1 Consensus size: 217
42174617 TCAATTTCTG
*
42174627 CTCACATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTTCAATTTCTGTTGTTA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAA-TTTCAATTTCTGTT-TT-
* * * *
42174692 AAAAAAAATCAACTCATATTGCGAGAAATAAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAAT
63 --CAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAAT
* ** * *
42174757 TTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG-ACACGTTGAGGTA
126 TTCTGTTTTAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTACACGCTGAGGTA
*
42174821 ATTTCAATTTCTGTTTTCAAAATTCAA
191 ATTTCAATTTCTGTTTTCAAAAATCAA
**
42174848 CTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT-TGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTCAA
* * * * *
42174912 AATTCAACACATATTGCGAGAAATGAGTTGTGCCTCAAGACATGCTGAGGTATTTTCAATTTTTG
66 AAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTG
* *
42174977 TTTTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACACTGAGGTA
131 --TTTT--AAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT-ACACGCTGAGGTA
*
42175042 ATTTCAATTTATGTTTGTCAAAAATCAA
191 ATTTCAATTTCTGTTT-TCAAAAATCAA
* *
42175070 CTCATATTGCGAGAGGTGAGTTAAGCCTCAGTACACGCTGAGGTAATTTTCAATTTCTGTTGTTA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAA-TTTCAATTTCTGTT-TT-
* ** * *
42175135 AAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTATTTTTAGTT
63 -CAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATT
* * *
42175200 TATGTTTT--AAATT-GACTCATATTGCGAGAGGTGAGTTAAGCCTCA-GTACACGCTGAGGTAA
127 TCTGTTTTAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTACACGCTGAGGTAA
*
42175261 TTTTCAATTTCTGTTGTTAAAAAAAATCAA
192 -TTTCAATTTCTGTT-TT--CAAAAATCAA
** *
42175291 CTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTGTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTC-A
** * *
42175356 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTTC
65 AAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTC
* * ** * * * *
42175421 TGTTTTCAAAATTCAACTCATATTACGAGAAATGAGTTGAGCCTCAAG-AAACGTTGAGGTATTT
129 TGTTTTAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTACACGCTGAGGTAATT
*
42175485 TCAATTTCTGTTTTCAAAAAAAAAGTGAA
194 TCAATTTCTGTTTTC----AAAAA-TCAA
* * *
42175514 CTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAATTTCTGTCTT
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTAATTTCAATTTCTGT-TT
* * ** * * * *
42175578 TCAAAAAAATCAACTCATTTTGCAAGAGGTGAGTTGAGCTTTAGATCACACACT-ATGGTATTTT
62 TC--AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCA-A-GACACGCTGA-GGTA--TT
* * ** * * * * *
42175642 TTCAATTTATATTGCGAAAGGTGAGTTGAGCTTTTTAATTTCTGCGAGAGGTGAGTTGAGCCTC-
120 TTCAATTTCTGTT-TTAAA----AATTCAAC----TCATAT-TGCGAGAGGTGAGTTGAGCCTCA
* * *
42175706 GAGTCACATG-TCGAGGTATTTTCAAAATCTGCTTTTCAAGATAAGTTTCAAAAATCAA
175 G-GT-ACACGCT-GAGGTAATTTC--AA------TTTC-TG-T---TTTCAAAAATCAA
*
42175764 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTTTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTCAA
* *
42175829 AATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTG
66 AAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTG
* * * * *
42175894 TTTTCAAAAAAGTGAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTAT
131 TTTT--AAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-T-ACACGCTGAGGTAA
42175958 TTTCAATTTCTGTCTTTCAAAAAAATCAA
192 TTTCAATTTCTGT-TTTC--AAAAATCAA
* *
42175987 CTCATTTTGCAAGAGGTGAGTTGAGC
1 CTCATATTGCGAGAGGTGAGTTGAGC
42176013 TTTAGATCAC
Statistics
Matches: 966, Mismatches: 127, Indels: 142
0.78 0.10 0.11
Matches are distributed among these distances:
215 59 0.06
217 4 0.00
218 20 0.02
219 117 0.12
220 56 0.06
221 147 0.15
222 97 0.10
223 73 0.08
224 5 0.01
225 35 0.04
226 30 0.03
227 65 0.07
228 9 0.01
230 12 0.01
231 4 0.00
232 1 0.00
233 41 0.04
234 5 0.01
235 5 0.01
238 5 0.01
239 4 0.00
240 20 0.02
241 14 0.01
242 17 0.02
243 9 0.01
244 4 0.00
245 32 0.03
247 4 0.00
248 24 0.02
250 35 0.04
251 8 0.01
252 1 0.00
255 4 0.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (217 bp):
CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTCAA
AAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTG
TTTTAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTACACGCTGAGGTAATTTC
AATTTCTGTTTTCAAAAATCAA
Found at i:42175258 original size:145 final size:146
Alignment explanation
Indices: 42174627--42176012 Score: 1289
Period size: 149 Copynumber: 9.2 Consensus size: 146
42174617 TCAATTTCTG
* *
42174627 CTCACATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTTCAATTTCTGTTGTTA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGTACACGCTGAGGTAATTTTCAATTTCTGTT-TT-
*
42174692 AAAAAAAATCAACTCATATTGCGAGAAATAAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAAT
64 AAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAAT
42174757 TTCTGTTTTCAAAATTCAA
129 TTCTGTTTT-AAAATTCAA
** *
42174776 CTCATATTGCGAGAAATGAGTTGAGCCTCAAG-ACACGTTGAGGTAA-TTTCAATTTCTGTTTT-
1 CTCATATTGCGAGAGGTGAGTTGAGCCTC-AGTACACGCTGAGGTAATTTTCAATTTCTGTTTTA
* *
42174838 -CAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
65 AAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
42174902 T-TGTTTTCAAAATTCAA
130 TCTGTTTT-AAAATTCAA
* ** * * *
42174919 CACATATTGCGAGAAATGAGTTGTGCCTCAAG-ACATGCTGAGGT-ATTTTCAATTTTTGTTTTT
1 CTCATATTGCGAGAGGTGAGTTGAGCCTC-AGTACACGCTGAGGTAATTTTCAATTTCTG--TTT
** *
42174982 TAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACACTGAGGTAATTTC
63 TAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGG--ACACGCTGAGGTAATTTC
* *
42175047 AATTTATGTTTGTCAAAAATCAA
126 AATTTCTGTTT-T-AAAATTCAA
*
42175070 CTCATATTGCGAGAGGTGAGTTAAGCCTCAGTACACGCTGAGGTAATTTTCAATTTCTGTTGTTA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGTACACGCTGAGGTAATTTTCAATTTCTGTT-TTA
* ** * * *
42175135 AAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTATTTTTAGTT
65 AAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
* *
42175200 TATGTTTT-AAATT-GA
130 TCTGTTTTAAAATTCAA
*
42175215 CTCATATTGCGAGAGGTGAGTTAAGCCTCAGTACACGCTGAGGTAATTTTCAATTTCTGTTGTTA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGTACACGCTGAGGTAATTTTCAATTTCTGTT-TTA
42175280 AAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
65 AAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
*
42175345 TCTGTTGTCAAAAAATTCAA
130 TCTGTT-T--TAAAATTCAA
** * * *
42175365 CTCATATTGCGAGAAATGAGTTGAGCCTCGGGACACGTTGAGGTAA-TTTCAATTTCTGTTTT--
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGTACACGCTGAGGTAATTTTCAATTTCTGTTTTAA
* * * * * * *
42175427 CAAAATTCAACTCATATTACGAGAAATGAGTTGAGCCTCAAGAAACGTTGAGGTATTTTCAATTT
66 AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
* *
42175492 CTGTTTTCAAAAAAAAAGTGAA
131 CTGTTTT------AAAATTCAA
* * *
42175514 CTTATATTGCGAGAGGTGAGTTGAGCCTCGGTTCACATGCTGAGGT-ATTTTCAATTTCTGTCTT
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAG-T-ACACGCTGAGGTAATTTTCAATTTCTGT-TT
* * * ** * * * * *
42175578 TCAAAAAAATCAACTCATTTTGCAAGAGGTGAGTTGAGCTTTAGATCACACACT-ATGGTATTTT
63 TAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAG--GACACGCTGA-GGTA--AT
* * ** * *
42175642 TTCAATTTATATTGCGAAAGGTGAGTTGAG
123 TTCAATTTCTGTT-TTAAA----A-TTCAA
* * * **
42175672 CTTTTTAATTTCTGCGAGAGGTGAGTTGAGCCTCGAGTCACATG-TCGAGGT-ATTTTCAAAATC
1 C----TCATAT-TGCGAGAGGTGAGTTGAGCCTC-AGT-ACACGCT-GAGGTAATTTTCAATTTC
**
42175735 TGCTTTTCAAGATAAGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
58 TG-TTTT----A-AA-----AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACAC
*
42175800 GCTGAGGTAATTTCAATTTTTGTTTTCAAAATTCAA
112 GCTGAGGTAATTTCAATTTCTGTTTT-AAAATTCAA
** * *
42175836 CTCATATTGCGAGAAATGAGTTGAGCCTCAAG-ACACGTTGAGGT-ATTTTCAATTTCTGTTTTC
1 CTCATATTGCGAGAGGTGAGTTGAGCCTC-AGTACACGCTGAGGTAATTTTCAATTTCTGTTTTA
* * * ** * *
42175899 AAAAAAGTGAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCA
65 AAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGG---ACACGCTGAGGTAATTTCA
*
42175963 ATTTCTGTCTTTCAAAAAAATCAA
127 ATTTCTGT-TTT---AAAATTCAA
* *
42175987 CTCATTTTGCAAGAGGTGAGTTGAGC
1 CTCATATTGCGAGAGGTGAGTTGAGC
42176013 TTTAGATCAC
Statistics
Matches: 1044, Mismatches: 125, Indels: 134
0.80 0.10 0.10
Matches are distributed among these distances:
142 1 0.00
143 67 0.06
144 62 0.06
145 137 0.13
146 103 0.10
147 40 0.04
148 41 0.04
149 143 0.14
150 53 0.05
151 143 0.14
152 16 0.02
153 3 0.00
154 31 0.03
155 1 0.00
156 12 0.01
157 22 0.02
158 18 0.02
159 22 0.02
160 4 0.00
162 5 0.00
163 49 0.05
164 6 0.01
165 1 0.00
168 2 0.00
169 15 0.01
171 10 0.01
172 1 0.00
173 36 0.03
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (146 bp):
CTCATATTGCGAGAGGTGAGTTGAGCCTCAGTACACGCTGAGGTAATTTTCAATTTCTGTTTTAA
AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
CTGTTTTAAAATTCAA
Found at i:42175584 original size:77 final size:74
Alignment explanation
Indices: 42174627--42176012 Score: 1279
Period size: 72 Copynumber: 18.4 Consensus size: 74
42174617 TCAATTTCTG
*
42174627 CTCACATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTTCAATTTCTGTTGTTA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT-ATTTTCAATTTCTGTT-TT-
*
42174692 AAAAAAAATCAA
63 CAAAAAAATCAA
** * *
42174704 CTCATATTGCGAGAAATAAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTC--
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTCAA
*
42174767 AAAATTCAA
66 AAAAATCAA
** * * *
42174776 CTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTTTC--
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTCAA
*
42174839 AAAATTCAA
66 AAAAATCAA
** *
42174848 CTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT-TGTTTTC--
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTCAA
*
42174910 AAAATTCAA
66 AAAAATCAA
* ** * * * * *
42174919 CACATATTGCGAGAAATGAGTTGTGCCTCAAGACATGCTGAGGTATTTTCAATTTTTGTTTTTTA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTG--TTTTC
42174984 AAAAAAATCAA
64 AAAAAAATCAA
* * *
42174995 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACACTGAGGTAATTTCAATTTATGTTTGT
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCTGAGGTATTTTCAATTTCTGTTT-T
42175060 C--AAAAATCAA
63 CAAAAAAATCAA
* * *
42175070 CTCATATTGCGAGAGGTGAGTTAAGCCTCAGTACACGCTGAGGTAATTTTCAATTTCTGTTGTTA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT-ATTTTCAATTTCTGTT-TTC
42175135 AAAAAAATCAA
64 AAAAAAATCAA
** * ** * * *
42175146 CTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTATTTTTAGTTTATGTTTT---
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTCAA
**
42175208 --AAATTGA
66 AAAAATCAA
* * *
42175215 CTCATATTGCGAGAGGTGAGTTAAGCCTCAGTACACGCTGAGGTAATTTTCAATTTCTGTTGTTA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT-ATTTTCAATTTCTGTT-TTC
42175280 AAAAAAATCAA
64 AAAAAAATCAA
** * *
42175291 CTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTGTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTCAA
*
42175356 AAAATTCAA
66 AAAAATCAA
** * * *
42175365 CTCATATTGCGAGAAATGAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTTCTGTTTTC--
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTCAA
*
42175428 AAAATTCAA
66 AAAAATCAA
* ** * * *
42175437 CTCATATTACGAGAAATGAGTTGAGCCTCAAGAAACGTTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTC--
*
42175502 AAAAAAAGTGAA
64 AAAAAAA-TCAA
* *
42175514 CTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAATTTCTGTCTT
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTATTTTCAATTTCTGT-TT
42175578 TCAAAAAAATCAA
62 TCAAAAAAATCAA
* * * * * * * *
42175591 CTCATTTTGCAAGAGGTGAGTTGAGCTTTAGATCACACACT-ATGGTATTTTTTCAATTTAT-AT
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAG--GACACGCTGA-GGTA--TTTTCAATTTCTGTT
* * ** * *
42175654 TGCGAAAGGTGAGTTGAG
61 TTC-AAA---AAAATCAA
* * * * **
42175672 CTTTTTAATTTCTGCGAGAGGTGAGTTGAGCCTCGAGTCACATG-TCGAGGTATTTTCAAAATCT
1 C----TCATAT-TGCGAGAGGTGAGTTGAGCCTC-AG-GACACGCT-GAGGTATTTTCAATTTCT
42175736 GCTTTTCAAGATAAGTTTCAAAAATCAA
58 G-TTTTC-----AA-----AAAAATCAA
* *
42175764 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTTTGTTTTC--
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTCAA
*
42175827 AAAATTCAA
66 AAAAATCAA
** * *
42175836 CTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTCAA
* *
42175901 AAAAGTGAA
66 AAAAATCAA
* *
42175910 CTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAATTTCTGTCTT
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTATTTTCAATTTCTGT-TT
42175974 TCAAAAAAATCAA
62 TCAAAAAAATCAA
* *
42175987 CTCATTTTGCAAGAGGTGAGTTGAGC
1 CTCATATTGCGAGAGGTGAGTTGAGC
42176013 TTTAGATCAC
Statistics
Matches: 1098, Mismatches: 147, Indels: 128
0.80 0.11 0.09
Matches are distributed among these distances:
69 42 0.04
70 13 0.01
71 68 0.06
72 264 0.24
73 12 0.01
74 125 0.11
75 70 0.06
76 175 0.16
77 144 0.13
78 33 0.03
79 35 0.03
80 4 0.00
81 4 0.00
84 14 0.01
85 25 0.02
86 34 0.03
87 25 0.02
88 4 0.00
90 2 0.00
92 4 0.00
95 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (74 bp):
CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTCAA
AAAAATCAA
Found at i:42176096 original size:396 final size:397
Alignment explanation
Indices: 42175355--42176223 Score: 1571
Period size: 396 Copynumber: 2.2 Consensus size: 397
42175345 TCTGTTGTCA
** * *
42175355 AAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGACACGTTGAGGTAATTTCAATTT
1 AAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
42175420 CTGTTTTCAAAATTCAACTCATATTACGAGAAATGAGTTGAGCCTCAAGAAACGTTGAGGTATTT
65 CTGTTTTCAAAATTCAACTCATATTACGAGAAATGAGTTGAGCCTCAAGAAACGTTGAGGTATTT
42175485 TCAATTTCTGTTTTCAAAAAAAAAGTGAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGTTCAC
130 TCAATTTCTGTTTTC--AAAAAAAGTGAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGTTCAC
42175550 ATGCTGAGGTATTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATTTTGCAAGAGGTGAGTTGA
193 ATGCTGAGGTATTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATTTTGCAAGAGGTGAGTTGA
42175615 GCTTTAGATCACACACTATGGTATTTTTTCAATTTATATTGCGAAAGGTGAGTTGAGCTTTTTAA
258 GCTTTAGATCACACACTATGGTATTTTTTCAATTTATATTGCGAAAGGTGAGTTGAGCTTTTTAA
42175680 TTTCTGCGAGAGGTGAGTTGAGCCTCGAGTCACATGTCGAGGTATTTTCAAAATCTGCTTTTCAA
323 TTTCTGCGAGAGGTGAGTTGAGCCTCGAGTCACATGTCGAGGTATTTTCAAAATCTGCTTTTCAA
42175745 GATAAGTTTC
388 GATAAGTTTC
*
42175755 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
* *
42175820 TGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTT
66 TGTTTTCAAAATTCAACTCATATTACGAGAAATGAGTTGAGCCTCAAGAAACGTTGAGGTATTTT
42175885 CAATTTCTGTTTTC-AAAAAAGTGAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGTTCACATG
131 CAATTTCTGTTTTCAAAAAAAGTGAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGTTCACATG
42175949 CTGAGGTATTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATTTTGCAAGAGGTGAGTTGAGCT
196 CTGAGGTATTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATTTTGCAAGAGGTGAGTTGAGCT
42176014 TTAGATCACACACTATGGTATTTTTTCAATTTATATTGCGAAAGGTGAGTTGAGCTTTTTAATTT
261 TTAGATCACACACTATGGTATTTTTTCAATTTATATTGCGAAAGGTGAGTTGAGCTTTTTAATTT
42176079 CTGCGAGAGGTGAGTTGAGCCTCGAGTCACATGTCGAGGTATTTTCAAAATCTGCTTTTCAAGAT
326 CTGCGAGAGGTGAGTTGAGCCTCGAGTCACATGTCGAGGTATTTTCAAAATCTGCTTTTCAAGAT
42176144 AAGTTTC
391 AAGTTTC
* * * *
42176151 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCT-TGGCTCACACGCTGAGCTATTTTCAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTAATTTCAAT
42176215 TTCTGTTTT
63 TTCTGTTTT
42176224 TAATGTCTGT
Statistics
Matches: 454, Mismatches: 12, Indels: 8
0.96 0.03 0.02
Matches are distributed among these distances:
395 2 0.00
396 288 0.63
398 27 0.06
399 132 0.29
400 5 0.01
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35
Consensus pattern (397 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
TGTTTTCAAAATTCAACTCATATTACGAGAAATGAGTTGAGCCTCAAGAAACGTTGAGGTATTTT
CAATTTCTGTTTTCAAAAAAAGTGAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGTTCACATG
CTGAGGTATTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATTTTGCAAGAGGTGAGTTGAGCT
TTAGATCACACACTATGGTATTTTTTCAATTTATATTGCGAAAGGTGAGTTGAGCTTTTTAATTT
CTGCGAGAGGTGAGTTGAGCCTCGAGTCACATGTCGAGGTATTTTCAAAATCTGCTTTTCAAGAT
AAGTTTC
Found at i:42188182 original size:88 final size:88
Alignment explanation
Indices: 42188033--42188200 Score: 336
Period size: 88 Copynumber: 1.9 Consensus size: 88
42188023 TCTAGGTGGA
42188033 TTTTTCCTTAGCTATTGTCTTAATCAATCGAATTTTCTAAAAAGTATTTTCCCAAATTTTCTTTC
1 TTTTTCCTTAGCTATTGTCTTAATCAATCGAATTTTCTAAAAAGTATTTTCCCAAATTTTCTTTC
42188098 TGTGCATTCTTAGTTAGTAATTT
66 TGTGCATTCTTAGTTAGTAATTT
42188121 TTTTTCCTTAGCTATTGTCTTAATCAATCGAATTTTCTAAAAAGTATTTTCCCAAATTTTCTTTC
1 TTTTTCCTTAGCTATTGTCTTAATCAATCGAATTTTCTAAAAAGTATTTTCCCAAATTTTCTTTC
42188186 TGTGCATTCTTAGTT
66 TGTGCATTCTTAGTT
42188201 TAGATAACTA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 80 1.00
ACGTcount: A:0.24, C:0.17, G:0.09, T:0.50
Consensus pattern (88 bp):
TTTTTCCTTAGCTATTGTCTTAATCAATCGAATTTTCTAAAAAGTATTTTCCCAAATTTTCTTTC
TGTGCATTCTTAGTTAGTAATTT
Found at i:42189733 original size:56 final size:56
Alignment explanation
Indices: 42189642--42189762 Score: 179
Period size: 56 Copynumber: 2.2 Consensus size: 56
42189632 TATCTGTGCA
* *
42189642 AGTAAGACCACGTTTAATACGTTGGCATCAATATGTGAGTTCGATATATGTGTGTG
1 AGTAAGACCACGTTTAATACGTTGGCATCAATATGTGACTCCGATATATGTGTGTG
* * ** *
42189698 AGTAAGACTACGTTTAATACGTTGGTATCGCTATGTGCCTCCGATATATGTGTGTG
1 AGTAAGACCACGTTTAATACGTTGGCATCAATATGTGACTCCGATATATGTGTGTG
42189754 AGTAAGACC
1 AGTAAGACC
42189763 CTGTCTAGGA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (56 bp):
AGTAAGACCACGTTTAATACGTTGGCATCAATATGTGACTCCGATATATGTGTGTG
Found at i:42189789 original size:56 final size:56
Alignment explanation
Indices: 42189642--42189791 Score: 151
Period size: 56 Copynumber: 2.7 Consensus size: 56
42189632 TATCTGTGCA
* * * * * *
42189642 AGTAAGACCACGTTTAATACGTTGGCATCAATATGTGAGTTCGATATATGTGTGTG
1 AGTAAGACTACGTCTAAGACGTTGGCATCGATATGTGACTCCGATATATGTGTGTG
* * * * *
42189698 AGTAAGACTACGTTTAATACGTTGGTATCGCTATGTGCCTCCGATATATGTGTGTG
1 AGTAAGACTACGTCTAAGACGTTGGCATCGATATGTGACTCCGATATATGTGTGTG
* *
42189754 AGTAAGAC-CCTGTCTAGGACAG-TGGCATCGATATGTGA
1 AGTAAGACTAC-GTCTAAGAC-GTTGGCATCGATATGTGA
42189792 TTATATGTAA
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
55 1 0.01
56 76 0.97
57 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (56 bp):
AGTAAGACTACGTCTAAGACGTTGGCATCGATATGTGACTCCGATATATGTGTGTG
Found at i:42192477 original size:50 final size:48
Alignment explanation
Indices: 42192362--42192488 Score: 139
Period size: 48 Copynumber: 2.6 Consensus size: 48
42192352 TACGAGATGT
* * * *
42192362 GTCAGTGTAAGACCATGTCTGCGACATGGCATCAGCACATATAGAAGT
1 GTCAGTGTAAGACCATGTCTGGGACATGGCAGCAGCACAGATAGAAGA
* * * *
42192410 GTCAGTGTAAGATCATGTTTGGGACATGGCAGCAGCAGAGATATGTGAGA
1 GTCAGTGTAAGACCATGTCTGGGACATGGCAGCAGCACAGATA-G-AAGA
*
42192460 G-CTAGTGTAAGACCATGTCTAGGACATGG
1 GTC-AGTGTAAGACCATGTCTGGGACATGG
42192489 TGTCGGCTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
48 37 0.57
49 2 0.03
50 26 0.40
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.24
Consensus pattern (48 bp):
GTCAGTGTAAGACCATGTCTGGGACATGGCAGCAGCACAGATAGAAGA
Found at i:42198376 original size:16 final size:16
Alignment explanation
Indices: 42198342--42198384 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
42198332 GTAGATCGGC
42198342 AAAAGCTGAAATGCTG
1 AAAAGCTGAAATGCTG
*
42198358 AAAATCTGAAATG-TCG
1 AAAAGCTGAAATGCT-G
*
42198374 AAAAGCAGAAA
1 AAAAGCTGAAA
42198385 GTCTGGCTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 1 0.04
16 22 0.96
ACGTcount: A:0.51, C:0.12, G:0.21, T:0.16
Consensus pattern (16 bp):
AAAAGCTGAAATGCTG
Found at i:42198706 original size:29 final size:28
Alignment explanation
Indices: 42198606--42198730 Score: 112
Period size: 29 Copynumber: 4.4 Consensus size: 28
42198596 TTTGGGCCAC
**
42198606 ATGGGCCATAT-AA-ATGAGATTGGGCCT
1 ATGGGCCATATGAATATGA-ATTGGGCGG
**
42198633 ATGGGCCATATGAACGTGAATTGGGCTGG
1 ATGGGCCATATGAATATGAATTGGGC-GG
*
42198662 ATGGGCTATATGAATATGAATTGGGTCGG
1 ATGGGCCATATGAATATGAATTGGG-CGG
* * **
42198691 ATGGGCCATATAAATAAG-ATTGGGCCTA
1 ATGGGCCATATGAATATGAATTGGG-CGG
42198719 ATGGGCCATATG
1 ATGGGCCATATG
42198731 CATGTATGTA
Statistics
Matches: 81, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
27 11 0.14
28 27 0.33
29 42 0.52
30 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.32, T:0.26
Consensus pattern (28 bp):
ATGGGCCATATGAATATGAATTGGGCGG
Found at i:42205865 original size:50 final size:49
Alignment explanation
Indices: 42205752--42205927 Score: 176
Period size: 50 Copynumber: 3.5 Consensus size: 49
42205742 CTGGTACGCA
* * ** *
42205752 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTGGTACACT
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAGTCTAATACACG
* *
42205801 TAGTAGCCTGCACTTAATACTACACACGTGACCTCACCA-TCTAATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAACAGTCTAATACACG
* *** * *
42205851 TAGTAGCCTGCACTTAGTACTACACACGTGATC-ACAGTTTTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAG---TCTAATACACG
42205902 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
42205928 TGCGACCTCA
Statistics
Matches: 106, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
49 28 0.26
50 39 0.37
51 36 0.34
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAGTCTAATACACG
Found at i:42205925 original size:101 final size:99
Alignment explanation
Indices: 42205752--42205938 Score: 259
Period size: 101 Copynumber: 1.9 Consensus size: 99
42205742 CTGGTACGCA
* * *
42205752 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTGGTACACTTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCGGGTACACATAGTAGCCTGCACTTA
*
42205817 ATACTACACACGTGACCTCACCATCTAATACACG
66 ATACTACACACGCGACCTCACCATCTAATACACG
* * *
42205851 TAGTAGCCTGCACTTAGTACTACACACGTGATC-ACAGTTTTCGGGTACGCATAGTAGCCTGCAC
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAG---TCGGGTACACATAGTAGCCTGCAC
* *
42205915 TTAGTACTACACATGCGACCTCAC
63 TTAATACTACACACGCGACCTCAC
42205939 AATAGATCAT
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
98 4 0.05
99 30 0.39
101 42 0.55
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.25
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCGGGTACACATAGTAGCCTGCACTTA
ATACTACACACGCGACCTCACCATCTAATACACG
Found at i:42217053 original size:16 final size:15
Alignment explanation
Indices: 42217028--42217057 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
42217018 ATCCTCCTAT
42217028 TTCTTTTTTTATTTA
1 TTCTTTTTTTATTTA
42217043 TTCTTTATTTTATTT
1 TTCTTT-TTTTATTT
42217058 TATTTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (15 bp):
TTCTTTTTTTATTTA
Found at i:42217060 original size:21 final size:22
Alignment explanation
Indices: 42217033--42217084 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
42217023 CCTATTTCTT
42217033 TTTTTATTTATTCTTTATTTT-A
1 TTTTTATTTATT-TTTATTTTGA
*
42217055 -TTTTATTTATTTTTCTTTTGA
1 TTTTTATTTATTTTTATTTTGA
42217076 TTTTTATTT
1 TTTTTATTT
42217085 TCATTTCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 7 0.26
21 12 0.44
22 8 0.30
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTTTATTTATTTTTATTTTGA
Found at i:42217068 original size:32 final size:35
Alignment explanation
Indices: 42217034--42217109 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 35
42217024 CTATTTCTTT
*
42217034 TTTTATTT-ATTCTTTATTTT-ATTT-TA-TTTATT
1 TTTTATTTGATT-TTTATTTTCATTTCAATTTTATT
42217066 TTTCT-TTTGATTTTTATTTTCATTTCAATTTTATT
1 TTT-TATTTGATTTTTATTTTCATTTCAATTTTATT
42217101 ATTTTATTT
1 -TTTTATTT
42217110 TGAATGGCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
32 14 0.39
33 8 0.22
34 1 0.03
35 7 0.19
36 6 0.17
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.75
Consensus pattern (35 bp):
TTTTATTTGATTTTTATTTTCATTTCAATTTTATT
Found at i:42217090 original size:12 final size:11
Alignment explanation
Indices: 42217033--42217110 Score: 63
Period size: 12 Copynumber: 6.9 Consensus size: 11
42217023 CCTATTTCTT
42217033 TTTTTA-TTTA
1 TTTTTATTTTA
42217043 TTCTTTATTTTA
1 TT-TTTATTTTA
42217055 -TTTTA-TTTA
1 TTTTTATTTTA
*
42217064 TTTTTCTTTTGA
1 TTTTTATTTT-A
42217076 TTTTTATTTTCA
1 TTTTTATTTT-A
**
42217088 TTTCAATTTTA
1 TTTTTATTTTA
42217099 TTATTTTATTTT
1 -T-TTTTATTTT
42217111 GAATGGCATA
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
9 4 0.07
10 10 0.19
11 9 0.17
12 24 0.44
13 7 0.13
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.76
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:42220313 original size:163 final size:163
Alignment explanation
Indices: 42220043--42220358 Score: 542
Period size: 163 Copynumber: 1.9 Consensus size: 163
42220033 AGTTATTACT
* *
42220043 AGTACTTTTGGTTCCCTTGGGTACAATATCCCGGTCTTGCCATTACTATACTATTGTTCGATAGG
1 AGTACTTTTGGTTCCCTTGGGTACAATATCCCGATCTTGCCATTACTATACAATTGTTCGATAGG
* *
42220108 TGCGCTTGCCTTTTCATCGTGATAATAGTTAGTCTAGGTTTGATCTTCATTATAAATATTTATTA
66 TGCGCTTGCCTTTTCATCATGATAATAATTAGTCTAGGTTTGATCTTCATTATAAATATTTATTA
42220173 CTTGTTACGAATCACGCGATCACGTCTTTATCA
131 CTTGTTACGAATCACGCGATCACGTCTTTATCA
* * *
42220206 AGTACTTTTGGTTCCCTTGGGTACGATATCCCGATGTTGCCATTACTATACAATTGTTTGATAGG
1 AGTACTTTTGGTTCCCTTGGGTACAATATCCCGATCTTGCCATTACTATACAATTGTTCGATAGG
* *
42220271 TGCGCTTGCCTTTTCGTCATGATAATAATTAGTCTAGGTTTGATCTTTATTATAAATATTTATTA
66 TGCGCTTGCCTTTTCATCATGATAATAATTAGTCTAGGTTTGATCTTCATTATAAATATTTATTA
*
42220336 CTTGTTACGAATCACGTGATCAC
131 CTTGTTACGAATCACGCGATCAC
42220359 TCGATGACAT
Statistics
Matches: 143, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
163 143 1.00
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.41
Consensus pattern (163 bp):
AGTACTTTTGGTTCCCTTGGGTACAATATCCCGATCTTGCCATTACTATACAATTGTTCGATAGG
TGCGCTTGCCTTTTCATCATGATAATAATTAGTCTAGGTTTGATCTTCATTATAAATATTTATTA
CTTGTTACGAATCACGCGATCACGTCTTTATCA
Found at i:42229001 original size:58 final size:59
Alignment explanation
Indices: 42228902--42229022 Score: 154
Period size: 58 Copynumber: 2.1 Consensus size: 59
42228892 CCCTCCCTAA
* * * *
42228902 TCCCGAAAGGTAGAATTCGGATACTATTACATGTTCAGTACCCAATAATGAATGAATCG
1 TCCCGAAAGGTAGAAATCAGATACCATTACATGTTCAGTACCCAACAATGAATGAATCG
* * * * *
42228961 TCCC-AAAGGTAGAAATCAGATACCGTTGCATGTTCGGTACCCACCAATGAATGAATTG
1 TCCCGAAAGGTAGAAATCAGATACCATTACATGTTCAGTACCCAACAATGAATGAATCG
42229019 TCCC
1 TCCC
42229023 TGTCCCTCCC
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
58 49 0.92
59 4 0.08
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (59 bp):
TCCCGAAAGGTAGAAATCAGATACCATTACATGTTCAGTACCCAACAATGAATGAATCG
Found at i:42235719 original size:43 final size:43
Alignment explanation
Indices: 42235577--42235754 Score: 209
Period size: 42 Copynumber: 4.2 Consensus size: 43
42235567 AATGGTTCGA
*
42235577 GAGCCTCGAGCAGCA-CTGGCACCTTGGTG-CTCGGATGTGCGG
1 GAGCCTCGAGCAGCATC-GGCACCTTGGTGCCTCAGATGTGCGG
* * *
42235619 GAGCCTCGAGCAGCATCGGCACCTTGGT-ACTTAGATGTGGGG
1 GAGCCTCGAGCAGCATCGGCACCTTGGTGCCTCAGATGTGCGG
* *
42235661 GAGCCTTGAGCAGCATCGGCACCTTGGTGCCTCAGATGTGTGG
1 GAGCCTCGAGCAGCATCGGCACCTTGGTGCCTCAGATGTGCGG
* * * * ** *
42235704 GACCCTCGAGTAGCATCGGTACCTTGGTGCTTTGGATATGCGG
1 GAGCCTCGAGCAGCATCGGCACCTTGGTGCCTCAGATGTGCGG
42235747 GAGCCTCG
1 GAGCCTCG
42235755 GACACCATCG
Statistics
Matches: 116, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
42 63 0.54
43 53 0.46
ACGTcount: A:0.16, C:0.26, G:0.35, T:0.22
Consensus pattern (43 bp):
GAGCCTCGAGCAGCATCGGCACCTTGGTGCCTCAGATGTGCGG
Found at i:42235720 original size:85 final size:84
Alignment explanation
Indices: 42235577--42235754 Score: 232
Period size: 85 Copynumber: 2.1 Consensus size: 84
42235567 AATGGTTCGA
* *
42235577 GAGCCTCGAGCAGCACTGGCACCTTGGTGCTCGGATGTGCGGGAGCCTCGAGCAGCATCGGCACC
1 GAGCCTCGAGCAGCACTGGCACCTTGGTGCTCAGATGTGCGGGACCCTCGAGCAGCATCGGCACC
42235642 TTGGTACTTAGATGTGGGG
66 TTGGTACTTAGATGTGGGG
* * * *
42235661 GAGCCTTGAGCAGCA-TCGGCACCTTGGTGCCTCAGATGTGTGGGACCCTCGAGTAGCATCGGTA
1 GAGCCTCGAGCAGCACT-GGCACCTTGGTG-CTCAGATGTGCGGGACCCTCGAGCAGCATCGGCA
* * * *
42235725 CCTTGGTGCTTTGGATATGCGG
64 CCTTGGTAC-TTAGATGTGGGG
42235747 GAGCCTCG
1 GAGCCTCG
42235755 GACACCATCG
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
83 1 0.01
84 26 0.32
85 37 0.46
86 16 0.20
ACGTcount: A:0.16, C:0.26, G:0.35, T:0.22
Consensus pattern (84 bp):
GAGCCTCGAGCAGCACTGGCACCTTGGTGCTCAGATGTGCGGGACCCTCGAGCAGCATCGGCACC
TTGGTACTTAGATGTGGGG
Found at i:42235764 original size:43 final size:43
Alignment explanation
Indices: 42235577--42236229 Score: 318
Period size: 43 Copynumber: 15.4 Consensus size: 43
42235567 AATGGTTCGA
* *
42235577 GAGCCTC-GAGCAGCA-CTGGCACCTTGGTGCTCGGATGTGCGG
1 GAGCCTCGGAGCACCATC-GGCACCTTGGTGCTTGGATGTGCGG
* * * *
42235619 GAGCCTC-GAGCAGCATCGGCACCTTGGTACTTAGATGTGGGG
1 GAGCCTCGGAGCACCATCGGCACCTTGGTGCTTGGATGTGCGG
* * ** *
42235661 GAGCCT-TGAGCAGCATCGGCACCTTGGTGCCTCAGATGTGTGG
1 GAGCCTCGGAGCACCATCGGCACCTTGGTG-CTTGGATGTGCGG
* * * * *
42235704 GACCCTC-GAGTAGCATCGGTACCTTGGTGCTTTGGATATGCGG
1 GAGCCTCGGAGCACCATCGGCACCTTGGTGC-TTGGATGTGCGG
* * * ** *
42235747 GAGCCTCGGA-CACCATCGACAAACTAGGCCCTTGGTTGTGCGG
1 GAGCCTCGGAGCACCATCGGC-ACCTTGGTGCTTGGATGTGCGG
* *
42235790 GAGCCTCGG-GCACCA-CTGGCACCTTGGTGCTTGGATATGCTG
1 GAGCCTCGGAGCACCATC-GGCACCTTGGTGCTTGGATGTGCGG
** * * *
42235832 GAGCCTCGG-GCACCATCAACACCTTGGTGCTTAGATGTGTGA
1 GAGCCTCGGAGCACCATCGGCACCTTGGTGCTTGGATGTGCGG
* * *
42235874 GAGCCAC-G-GCACCATTGGCAACCTAGGCT-CTTGG-TCGTGCGG
1 GAGCCTCGGAGCACCATCGGC-ACCTTGG-TGCTTGGAT-GTGCGG
* **
42235916 GAGCCTCGGA-CACCATCGGCAACCTAGGCCCTTGG-TCGTGCGG
1 GAGCCTCGGAGCACCATCGGC-ACCTTGGTGCTTGGAT-GTGCGG
* ** * ** * *
42235959 GAGCCTCGG-GCACCATTGATAACTTAGGCCCTT-GATCATGTGG
1 GAGCCTCGGAGCACCATCGGCACCTT-GGTGCTTGGAT-GTGCGG
* * * * *
42236002 GAGCCTCGG-GCACCATCAGCAACCTAGGTCCTTGGTTGTGCGA
1 GAGCCTCGGAGCACCATCGGC-ACCTTGGTGCTTGGATGTGCGG
* * * * *
42236045 GAGCTTC-G-GTACCATCGGCACATTGGTTCTTGGATGTGCGA
1 GAGCCTCGGAGCACCATCGGCACCTTGGTGCTTGGATGTGCGG
* * * * ** * *
42236086 GAGCCTCAG-GCACGATCGGTAACCTAGGCCCTTGG-TCTTGCGA
1 GAGCCTCGGAGCACCATCGG-CACCTTGGTGCTTGGAT-GTGCGG
* * ** * *
42236129 GAGCCTCGG-GCACCACCGGCAACCTAGGCCCTTGG-TCGTGTGA
1 GAGCCTCGGAGCACCATCGGC-ACCTTGGTGCTTGGAT-GTGCGG
* *
42236172 GAGCCTC--AGCACCATCGGCACCTTAGG-GCTTAGATGTGCCG
1 GAGCCTCGGAGCACCATCGGCACCTT-GGTGCTTGGATGTGCGG
*
42236213 GAGCCTTGGA-CACCATC
1 GAGCCTCGGAGCACCATC
42236230 AGCAACCGAG
Statistics
Matches: 482, Mismatches: 99, Indels: 60
0.75 0.15 0.09
Matches are distributed among these distances:
41 51 0.11
42 183 0.38
43 235 0.49
44 13 0.03
ACGTcount: A:0.18, C:0.29, G:0.32, T:0.22
Consensus pattern (43 bp):
GAGCCTCGGAGCACCATCGGCACCTTGGTGCTTGGATGTGCGG
Found at i:42236090 original size:127 final size:126
Alignment explanation
Indices: 42235747--42236307 Score: 481
Period size: 127 Copynumber: 4.4 Consensus size: 126
42235737 GGATATGCGG
* * * * *
42235747 GAGCCTCGGACACCATCGACAAACTAGGCCCTTGGTTGTGCGGGAGCCTCGGGCACCA-CTGGCA
1 GAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGAGAGCCTC-GGCACCATC-GGCA
* * * * * ** *
42235811 CCTTGGTGCTTGGATATGCTGGAGCCTCGGGCACCATCAACACCTT-GGTGCTTAGAT-GTGTGA
64 CCTTGGTCCTTGGATGTGC-GGAGCCTCGGGCACCATCGATAACTTAGGCCCTT-GATCATGTGA
* * * *
42235874 GAGCCAC-GGCACCATTGGCAACCTAGGCTCTTGGTCGTGCGGGAGCCTCGGACACCATCGGCAA
1 GAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGAGAGCCTCGG-CACCATCGGC-A
* * * *
42235938 CCTAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCACCATTGATAACTTAGGCCCTTGATCATGTGG
64 CCTTGGTCCTTGGAT-GTGC-GGAGCCTCGGGCACCATCGATAACTTAGGCCCTTGATCATGTGA
* * * * * *
42236002 GAGCCTCGGGCACCATCAGCAACCTAGGTCCTTGGTTGTGCGAGAGCTTCGGTACCATCGGCACA
1 GAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGAGAGCCTCGGCACCATCGGCACC
* * * * * * * *
42236067 TTGGTTCTTGGATGTGCGAGAGCCTCAGGCACGATCGGTAACCTAGGCCCTTGGTCTTGCGA
66 TTGGTCCTTGGATGTGCG-GAGCCTCGGGCACCATCGATAACTTAGGCCCTTGATCATGTGA
* * *
42236129 GAGCCTCGGGCACCACCGGCAACCTAGGCCCTTGGTCGTGTGAGAGCCTCAGCACCATCGGCACC
1 GAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGAGAGCCTCGGCACCATCGGCACC
* * * * * ** * * * *
42236194 TTAGG-GCTTAGATGTGCCGGAGCCTTGGACACCATC-AGCAACCGAGGCCCTTGGTCGTGCGG
66 TT-GGTCCTTGGATGTG-CGGAGCCTCGGGCACCATCGA-TAACTTAGGCCCTTGATCATGTGA
* **
42236256 GA-CCTACAGGCACCATCGGCAACCTAGGCCCTTGGTCAAGCGAGAGCCTCGG
1 GAGCCT-CGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGAGAGCCTCGG
42236308 GCACTCTCGG
Statistics
Matches: 353, Mismatches: 68, Indels: 26
0.79 0.15 0.06
Matches are distributed among these distances:
125 2 0.01
126 49 0.14
127 236 0.67
128 29 0.08
129 37 0.10
ACGTcount: A:0.19, C:0.30, G:0.31, T:0.20
Consensus pattern (126 bp):
GAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGAGAGCCTCGGCACCATCGGCACC
TTGGTCCTTGGATGTGCGGAGCCTCGGGCACCATCGATAACTTAGGCCCTTGATCATGTGA
Found at i:42236113 original size:170 final size:169
Alignment explanation
Indices: 42235717--42236311 Score: 546
Period size: 170 Copynumber: 3.5 Consensus size: 169
42235707 CCTCGAGTAG
* * * * *
42235717 CATCGGTACCTTGGTGCTTTGGATATGCGGGAGCCTCGGACACCATCGACAAACTAGGCCCTTGG
1 CATCGGCACCTTGGTTC-TTGGATGTGCGGGAGCCTCGGACACCATCGGCAACCTAGGCCCTTGG
* * **
42235782 TTGTGCGGGAGCCTCGGGCACCACTGGCACCTT-GGTGCTTGGAT-ATGCT-GGAGCCTCGGGCA
65 TCGTGCGGGAGCCTCGGGCACCACTGGCAACTTAGGCCCTT-GATCATG-TGGGAGCCTCGGGCA
* * *
42235844 CCATCAACACCTTGGTGCTTAGATGTGTGAGAGCCACGGCAC
128 CCATCAACACCTAGGTCCTTAGATGTGCGAGAGCCACGGCAC
* * *
42235886 CATTGGCAACCTAGGCTCTTGG-TCGTGCGGGAGCCTCGGACACCATCGGCAACCTAGGCCCTTG
1 CATCGGC-ACCTTGGTTCTTGGAT-GTGCGGGAGCCTCGGACACCATCGGCAACCTAGGCCCTTG
* **
42235950 GTCGTGCGGGAGCCTCGGGCACCATTGATAACTTAGGCCCTTGATCATGTGGGAGCCTCGGGCAC
64 GTCGTGCGGGAGCCTCGGGCACCACTGGCAACTTAGGCCCTTGATCATGTGGGAGCCTCGGGCAC
* * * ** *
42236015 CATCAGCAACCTAGGTCCTTGGTTGTGCGAGAGCTTCGGTAC
129 CATCAAC-ACCTAGGTCCTTAGATGTGCGAGAGCCACGGCAC
* * * *
42236057 CATCGGCACATTGGTTCTTGGATGTGCGAGAGCCTCAGG-CACGATCGGTAACCTAGGCCCTTGG
1 CATCGGCACCTTGGTTCTTGGATGTGCGGGAGCCTC-GGACACCATCGGCAACCTAGGCCCTTGG
* * * * * * * *
42236121 TCTTGCGAGAGCCTCGGGCACCACCGGCAACCTAGGCCCTTGGTCGTGTGAGAGCCTC-AGCACC
65 TCGTGCGGGAGCCTCGGGCACCACTGGCAACTTAGGCCCTTGATCATGTGGGAGCCTCGGGCACC
** * **
42236185 ATCGGCACCTTAGG-GCTTAGATGTGCCG-GAGCCTTGGACAC
130 ATCAACACC-TAGGTCCTTAGATGTG-CGAGAGCCACGG-CAC
* ** **
42236226 CATCAGCAACCGAGGCCCTTGG-TCGTGCGGGA-CCTACAGG-CACCATCGGCAACCTAGGCCCT
1 CATCGGC-ACCTTGGTTCTTGGAT-GTGCGGGAGCCT-C-GGACACCATCGGCAACCTAGGCCCT
** *
42236288 TGGTCAAGCGAGAGCCTCGGGCAC
62 TGGTCGTGCGGGAGCCTCGGGCAC
42236312 TCTCGGGCAC
Statistics
Matches: 352, Mismatches: 60, Indels: 27
0.80 0.14 0.06
Matches are distributed among these distances:
168 19 0.05
169 107 0.30
170 191 0.54
171 35 0.10
ACGTcount: A:0.18, C:0.30, G:0.31, T:0.21
Consensus pattern (169 bp):
CATCGGCACCTTGGTTCTTGGATGTGCGGGAGCCTCGGACACCATCGGCAACCTAGGCCCTTGGT
CGTGCGGGAGCCTCGGGCACCACTGGCAACTTAGGCCCTTGATCATGTGGGAGCCTCGGGCACCA
TCAACACCTAGGTCCTTAGATGTGCGAGAGCCACGGCAC
Found at i:42236285 original size:43 final size:43
Alignment explanation
Indices: 42235742--42236453 Score: 420
Period size: 43 Copynumber: 16.5 Consensus size: 43
42235732 GCTTTGGATA
* * *
42235742 TGCGGGAGCCTC-GGACACCATCGACAAACTAGGCCCTTGGTTG
1 TGCGGGAGCCTCAGG-CACCATCGGCAACCTAGGCCCTTGGTCG
* * ** *
42235785 TGCGGGAGCCTCGGGCACCA-CTGGC-ACCTTGGTGCTTGGAT-A
1 TGCGGGAGCCTCAGGCACCATC-GGCAACCTAGGCCCTTGG-TCG
* * ** * ** *
42235827 TGCTGGAGCCTCGGGCACCATCAAC-ACCTTGGTGCTTAGAT-G
1 TGCGGGAGCCTCAGGCACCATCGGCAACCTAGGCCCTT-GGTCG
* * * * *
42235869 TGTGAGAGCCAC-GGCACCATTGGCAACCTAGGCTCTTGGTCG
1 TGCGGGAGCCTCAGGCACCATCGGCAACCTAGGCCCTTGGTCG
42235911 TGCGGGAGCCTC-GGACACCATCGGCAACCTAGGCCCTTGGTCG
1 TGCGGGAGCCTCAGG-CACCATCGGCAACCTAGGCCCTTGGTCG
* * ** * * *
42235954 TGCGGGAGCCTCGGGCACCATTGATAACTTAGGCCCTTGATCA
1 TGCGGGAGCCTCAGGCACCATCGGCAACCTAGGCCCTTGGTCG
* * * * *
42235997 TGTGGGAGCCTCGGGCACCATCAGCAACCTAGGTCCTTGGTTG
1 TGCGGGAGCCTCAGGCACCATCGGCAACCTAGGCCCTTGGTCG
* * * * * **
42236040 TGCGAGAGCTTC-GGTACCATCGGC-ACATTGGTTCTTGGAT-G
1 TGCGGGAGCCTCAGGCACCATCGGCAACCTAGGCCCTTGG-TCG
* * * *
42236081 TGCGAGAGCCTCAGGCACGATCGGTAACCTAGGCCCTTGGTCT
1 TGCGGGAGCCTCAGGCACCATCGGCAACCTAGGCCCTTGGTCG
* * *
42236124 TGCGAGAGCCTCGGGCACCACCGGCAACCTAGGCCCTTGGTCG
1 TGCGGGAGCCTCAGGCACCATCGGCAACCTAGGCCCTTGGTCG
* * * *
42236167 TGTGAGAGCCTCA-GCACCATCGGC-ACCTTAGG-GCTTAGAT-G
1 TGCGGGAGCCTCAGGCACCATCGGCAACC-TAGGCCCTT-GGTCG
* * * *
42236208 TGCCGGAGCCT-TGGACACCATCAGCAACCGAGGCCCTTGGTCG
1 TGCGGGAGCCTCAGG-CACCATCGGCAACCTAGGCCCTTGGTCG
*
42236251 TGCGGGA-CCTACAGGCACCATCGGCAACCTAGGCCCTTGGTCA
1 TGCGGGAGCCT-CAGGCACCATCGGCAACCTAGGCCCTTGGTCG
* * * * * *
42236294 AGCGAGAGCCTCGGGCACTCTCGGGCACTATCGGTAACCTAGGCCCTTGATCA
1 TGCGGGAGCCT----CA------GGCACCATCGGCAACCTAGGCCCTTGGTCG
* * * * *
42236347 TGCGGGAGCCTCAAGAACCATCGG-TACCTTGGTACC-TGGAT-G
1 TGCGGGAGCCTCAGGCACCATCGGCAACCTAGG-CCCTTGG-TCG
* ** * * *
42236389 TGCGGGATCCTTGGGCACCATCGGCAACCTAAGCTCTTGGTTG
1 TGCGGGAGCCTCAGGCACCATCGGCAACCTAGGCCCTTGGTCG
*
42236432 TGCGGGAGCCTCGGGCACCATC
1 TGCGGGAGCCTCAGGCACCATC
42236454 AGTACCTTGG
Statistics
Matches: 521, Mismatches: 111, Indels: 74
0.74 0.16 0.10
Matches are distributed among these distances:
41 50 0.10
42 156 0.30
43 266 0.51
44 9 0.02
47 2 0.00
49 2 0.00
53 36 0.07
ACGTcount: A:0.19, C:0.30, G:0.31, T:0.21
Consensus pattern (43 bp):
TGCGGGAGCCTCAGGCACCATCGGCAACCTAGGCCCTTGGTCG
Found at i:42236477 original size:43 final size:42
Alignment explanation
Indices: 42236347--42236479 Score: 124
Period size: 43 Copynumber: 3.1 Consensus size: 42
42236337 CCCTTGATCA
** * *
42236347 TGCGGGAGCCTCAAGAACCATCGGTACCTTGGTACCTGGATG
1 TGCGGGAGCCTCGGGCACCATCGGTACCTTGGTGCCTGGATG
* * * * * * *
42236389 TGCGGGATCCTTGGGCACCATCGGCAACCTAAGCT-CTTGGTTG
1 TGCGGGAGCCTCGGGCACCATCGG-TACCT-TGGTGCCTGGATG
*
42236432 TGCGGGAGCCTCGGGCACCATCAGTACCTTGGTGCCTCGGATG
1 TGCGGGAGCCTCGGGCACCATCGGTACCTTGGTGCCT-GGATG
42236475 TGCGG
1 TGCGG
42236480 ACTAAAGAAA
Statistics
Matches: 69, Mismatches: 18, Indels: 7
0.73 0.19 0.07
Matches are distributed among these distances:
41 2 0.03
42 25 0.36
43 40 0.58
44 2 0.03
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.23
Consensus pattern (42 bp):
TGCGGGAGCCTCGGGCACCATCGGTACCTTGGTGCCTGGATG
Found at i:42256301 original size:43 final size:42
Alignment explanation
Indices: 42256249--42256380 Score: 147
Period size: 43 Copynumber: 3.1 Consensus size: 42
42256239 CCTTGGGGCT
*
42256249 TTGGATGTGCGGGAGCCTCGGACACCATCGGTAAACTAGGCCC
1 TTGGATGTGCGGGAGCCTCGGACACCATCGG-AACCTAGGCCC
* * * * * * **
42256292 TTGGTTGTGCAGGAGCCTCGGGCACTATCGGCACCTTGGTAC
1 TTGGATGTGCGGGAGCCTCGGACACCATCGGAACCTAGGCCC
* *
42256334 TTGGATGTGCGGGAGCCTCCGACACCATCGGCAACCCAGGCCC
1 TTGGATGTGCGGGAGCCTCGGACACCATCGG-AACCTAGGCCC
42256377 TTGG
1 TTGG
42256381 NNNNNNNNNN
Statistics
Matches: 69, Mismatches: 19, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
42 32 0.46
43 37 0.54
ACGTcount: A:0.17, C:0.30, G:0.33, T:0.20
Consensus pattern (42 bp):
TTGGATGTGCGGGAGCCTCGGACACCATCGGAACCTAGGCCC
Found at i:42256349 original size:42 final size:42
Alignment explanation
Indices: 42256091--42256366 Score: 200
Period size: 42 Copynumber: 6.5 Consensus size: 42
42256081 AGTGGTACGA
* * * **
42256091 GAGCCTCGAGTAGCACCGGCACCTTGGTACTCAGATGTGTAG
1 GAGCCTCGAGCAGCATCGGCACCTTGGTACTCGGATGTGCGG
* * * *
42256133 GAGCCTCGAGCAGCATCAGCACCTTGCTGCTCAGATGTG-GAG
1 GAGCCTCGAGCAGCATCGGCACCTTGGTACTCGGATGTGCG-G
* * *
42256175 GAGCCTCGAGCAGCATCGGCACCTTGGTGCCTCGAATGTACGG
1 GAGCCTCGAGCAGCATCGGCACCTTGGT-ACTCGGATGTGCGG
* * ** *
42256218 GAGCCTCAAGCAGCATCAGCACCTTGGGGCTTTGGATGTGCGG
1 GAGCCTCGAGCAGCATCGGCACCTTGGTAC-TCGGATGTGCGG
* * * * ** * * *
42256261 GAGCCTCG-GACACCATCGGTAAACTAGGCCCTTGGTTGTGCAG
1 GAGCCTCGAG-CAGCATCGG-CACCTTGGTACTCGGATGTGCGG
* *
42256304 GAGCCTCGGGCA-CTATCGGCACCTTGGTACTTGGATGTGCGG
1 GAGCCTCGAGCAGC-ATCGGCACCTTGGTACTCGGATGTGCGG
*
42256346 GAGCCTCCGA-CACCATCGGCA
1 GAGCCT-CGAGCAGCATCGGCA
42256367 ACCCAGGCCC
Statistics
Matches: 187, Mismatches: 37, Indels: 20
0.77 0.15 0.08
Matches are distributed among these distances:
42 95 0.51
43 84 0.45
44 8 0.04
ACGTcount: A:0.20, C:0.29, G:0.32, T:0.20
Consensus pattern (42 bp):
GAGCCTCGAGCAGCATCGGCACCTTGGTACTCGGATGTGCGG
Found at i:42256726 original size:43 final size:41
Alignment explanation
Indices: 42256527--42256803 Score: 150
Period size: 43 Copynumber: 6.5 Consensus size: 41
42256517 GATGTGCGGA
* * * *
42256527 AGCCTCGAACACCATCGACAAACTATGCCCTTGGT-TGTGCAGG
1 AGCCTCG-GCACCATCGGCAACCTAGGCCCTTGGTGTGTG--GG
* * * ***
42256570 AACCTCAGGAATCATCGGCAACCTAGGCCCCTTGGTCGTGCAAG
1 AGCCTC-GGCACCATCGGCAACCTAGG-CCCTTGGT-GTGTGGG
* * * * *
42256614 AGCCTCGGACACCATCGGC-AGCTGGGCGCTCGGATGTGCGGG
1 AGCCTCGG-CACCATCGGCAACCTAGGCCCTTGG-TGTGTGGG
* * * * *
42256656 A-CTGTTGAACACCATCGACAAACTAGGCCCTTGGTCGTGTGGG
1 AGC-CTCG-GCACCATCGGCAACCTAGGCCCTTGGT-GTGTGGG
*
42256699 AGCCTCAGGCACCATTGGCAACCTAGGCCCTTGGTAGTGTGGG
1 AGCCTC-GGCACCATCGGCAACCTAGGCCCTTGGT-GTGTGGG
* * *
42256742 AGCCTCGGACACCATCGAC-ACCTTGGTGCC-TGGATGTGTGGG
1 AGCCTCGG-CACCATCGGCAACCTAGG-CCCTTGG-TGTGTGGG
42256784 AGCCTCGGGCACCATCGGCA
1 AGCCTC-GGCACCATCGGCA
42256804 CCTTGGTGCC
Statistics
Matches: 177, Mismatches: 40, Indels: 34
0.71 0.16 0.14
Matches are distributed among these distances:
41 1 0.01
42 56 0.32
43 93 0.53
44 25 0.14
46 2 0.01
ACGTcount: A:0.21, C:0.30, G:0.30, T:0.19
Consensus pattern (41 bp):
AGCCTCGGCACCATCGGCAACCTAGGCCCTTGGTGTGTGGG
Found at i:42256790 original size:42 final size:42
Alignment explanation
Indices: 42256735--42256814 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
42256725 GCCCTTGGTA
42256735 GTGTGGGAGCCTCGGACACCATCGACACCTTGGTGCCTGGAT
1 GTGTGGGAGCCTCGGACACCATCGACACCTTGGTGCCTGGAT
* *
42256777 GTGTGGGAGCCTCGGGCACCATCGGCACCTTGGTGCCT
1 GTGTGGGAGCCTCGGACACCATCGACACCTTGGTGCCT
42256815 CGAATGTGCG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.14, C:0.30, G:0.35, T:0.21
Consensus pattern (42 bp):
GTGTGGGAGCCTCGGACACCATCGACACCTTGGTGCCTGGAT
Found at i:42258041 original size:43 final size:42
Alignment explanation
Indices: 42257993--42258255 Score: 226
Period size: 43 Copynumber: 6.2 Consensus size: 42
42257983 TAACCTTGGA
* * *
42257993 CACCATTGGTAACCTAGGCCCTTGATCGTGCAGGAGCCTAGGG
1 CACCATCGGTAACCTAGGCCCTTGGTCGTGC-GGAGCCTCGGG
* * * *
42258036 CACCATCGGTAACCTAGGCCCCTGGTCGTGCGAAAGCCT-TGA
1 CACCATCGGTAACCTAGGCCCTTGGTCGTGCG-GAGCCTCGGG
* * * ** *
42258078 CACCATTGGCAA-CTTGGTGCTTGGAT-GTGCGGGAGCCTCGGA
1 CACCATCGGTAACCTAGGCCCTTGG-TCGTGC-GGAGCCTCGGG
* * * * *
42258120 CACCATCAGCAATCTCGGCCCTTGGTCGTGTGAGAGCCTCGGG
1 CACCATCGGTAACCTAGGCCCTTGGTCGTGCG-GAGCCTCGGG
* * *
42258163 CACCATCGGTACCCTAAGCCCTTGGTCGTGCGGTAGCTTCGGG
1 CACCATCGGTAACCTAGGCCCTTGGTCGTGCGG-AGCCTCGGG
* * *
42258206 CACCATCGATAACCTAGGCCCTTGGTCATGCGCCAGCCTCGGG
1 CACCATCGGTAACCTAGGCCCTTGGTCGTGCG-GAGCCTCGGG
42258249 CACCATC
1 CACCATC
42258256 AGTACCTTGG
Statistics
Matches: 176, Mismatches: 35, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
41 17 0.10
42 29 0.16
43 130 0.74
ACGTcount: A:0.18, C:0.32, G:0.29, T:0.21
Consensus pattern (42 bp):
CACCATCGGTAACCTAGGCCCTTGGTCGTGCGGAGCCTCGGG
Found at i:42261280 original size:38 final size:38
Alignment explanation
Indices: 42261219--42261331 Score: 154
Period size: 38 Copynumber: 2.9 Consensus size: 38
42261209 ATTTGATGTG
*
42261219 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAAAA
1 TATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTAAAA
**
42261259 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAAA
* * *
42261297 TATCCGGGATAAATCCCGCAGGCCTAGTGCTGGTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTA
42261332 TTATATTCGA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
38 54 0.81
39 5 0.07
40 8 0.12
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.26
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAAA
Found at i:42261332 original size:38 final size:38
Alignment explanation
Indices: 42261235--42261337 Score: 161
Period size: 38 Copynumber: 2.7 Consensus size: 38
42261225 GGCTTAAAGA
** *
42261235 CCCGCAGGCTTCGTGCTGGTAAAATATCCGGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTATTATATCCGGGATAAAT
42261273 CCCGCAGGCTTCGTGCTGGTATTATATCCGGGATAAAT
1 CCCGCAGGCTTCGTGCTGGTATTATATCCGGGATAAAT
* *
42261311 CCCGCAGGCCTAGTGCTGGTATTATAT
1 CCCGCAGGCTTCGTGCTGGTATTATAT
42261338 TCGACCCTTC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 60 1.00
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.28
Consensus pattern (38 bp):
CCCGCAGGCTTCGTGCTGGTATTATATCCGGGATAAAT
Found at i:42261371 original size:41 final size:43
Alignment explanation
Indices: 42261314--42261395 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 43
42261304 GATAAATCCC
42261314 GCAGGCCTAGTGCTGGT-AT-TATATTCGACCCTTCGTGCCTA
1 GCAGGCCTAGTGCTGGTGATGTATATTCGACCCTTCGTGCCTA
* * * **
42261355 GCAGGCTTTGTGCTGGTGATGTGTATTCGGGCCTTCGTGCC
1 GCAGGCCTAGTGCTGGTGATGTATATTCGACCCTTCGTGCC
42261396 GGTGATGTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 15 0.44
42 2 0.06
43 17 0.50
ACGTcount: A:0.12, C:0.24, G:0.30, T:0.33
Consensus pattern (43 bp):
GCAGGCCTAGTGCTGGTGATGTATATTCGACCCTTCGTGCCTA
Found at i:42261402 original size:27 final size:27
Alignment explanation
Indices: 42261364--42261422 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
42261354 AGCAGGCTTT
*
42261364 GTGCTGGTGATGTGTATTCGGGCCTTC
1 GTGCCGGTGATGTGTATTCGGGCCTTC
42261391 GTGCCGGTGATGTGTATTCGGGCCTTC
1 GTGCCGGTGATGTGTATTCGGGCCTTC
42261418 GTGCC
1 GTGCC
42261423 TAGCAGGCGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.07, C:0.22, G:0.37, T:0.34
Consensus pattern (27 bp):
GTGCCGGTGATGTGTATTCGGGCCTTC
Found at i:42268828 original size:43 final size:43
Alignment explanation
Indices: 42268663--42268826 Score: 220
Period size: 43 Copynumber: 3.8 Consensus size: 43
42268653 TCCGACACCT
* *
42268663 TAGGCCCTTGGTCGTGCCAGAGCATCGGGCACCATCGGCAACC
1 TAGGCCCTTGGTCGTGCGAGAGCCTCGGGCACCATCGGCAACC
* * *
42268706 TAGGCCCTTGGTCATGCGAGAGCCTCGTGTACCATCGGCAACC
1 TAGGCCCTTGGTCGTGCGAGAGCCTCGGGCACCATCGGCAACC
* * * * *
42268749 TAGGCCTTTGGTCGTACGAGAGCCTCGGGAACCATTGGTAACC
1 TAGGCCCTTGGTCGTGCGAGAGCCTCGGGCACCATCGGCAACC
**
42268792 TAGGCCCTTGGTCGTGCGAGAGCCTCAAGCACCAT
1 TAGGCCCTTGGTCGTGCGAGAGCCTCGGGCACCAT
42268827 TGACACCTTG
Statistics
Matches: 104, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 104 1.00
ACGTcount: A:0.20, C:0.31, G:0.29, T:0.20
Consensus pattern (43 bp):
TAGGCCCTTGGTCGTGCGAGAGCCTCGGGCACCATCGGCAACC
Found at i:42269321 original size:11 final size:11
Alignment explanation
Indices: 42269305--42269347 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
42269295 ATGTGCCTGT
42269305 ATATTAATGTA
1 ATATTAATGTA
42269316 ATATTAATGTA
1 ATATTAATGTA
* *
42269327 ATAATAATAT-
1 ATATTAATGTA
42269337 ATATTAATGTA
1 ATATTAATGTA
42269348 TTAATGTAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 8 0.30
11 19 0.70
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (11 bp):
ATATTAATGTA
Found at i:42271357 original size:16 final size:16
Alignment explanation
Indices: 42271336--42271390 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
42271326 GTTTGGTTCA
42271336 CTGTAATGGAATA-AGG
1 CTGTAATGGAATAGA-G
*
42271352 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
* *
42271368 TTGTAATGAAATAGAG
1 CTGTAATGGAATAGAG
42271384 CTGTAAT
1 CTGTAAT
42271391 CAGTAATTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
16 32 0.97
17 1 0.03
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.31
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:42271570 original size:25 final size:26
Alignment explanation
Indices: 42271537--42271586 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
42271527 GTAGATAGAT
*
42271537 GATTATTGTT-ATTAAATTTTAATAA
1 GATTATTGTTCAATAAATTTTAATAA
*
42271562 GATTATTGTTCAATATATTTTAATA
1 GATTATTGTTCAATAAATTTTAATA
42271587 TAAATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (26 bp):
GATTATTGTTCAATAAATTTTAATAA
Found at i:42271705 original size:13 final size:12
Alignment explanation
Indices: 42271651--42271727 Score: 56
Period size: 12 Copynumber: 6.4 Consensus size: 12
42271641 TTTAATAAAA
42271651 TAATATATAA-TT
1 TAATA-ATAATTT
*
42271663 TAATAA-CATTCT
1 TAATAATAATT-T
42271675 TAAT-ATAATTAT
1 TAATAATAATT-T
42271687 TAATAAT-A-TT
1 TAATAATAATTT
42271697 TAATAATAATTT
1 TAATAATAATTT
*
42271709 TAATATAAAATTAT
1 TAATA-ATAATT-T
42271723 TAATA
1 TAATA
42271728 TAAAATTATT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
10 9 0.17
11 5 0.09
12 26 0.49
13 7 0.13
14 6 0.11
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (12 bp):
TAATAATAATTT
Found at i:42271712 original size:34 final size:37
Alignment explanation
Indices: 42271651--42271734 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 37
42271641 TTTAATAAAA
*
42271651 TAATATATAATTTAATAACATTCTTAATAT-AATTAT
1 TAATATATAATTTAATAAAATTCTTAATATAAATTAT
42271687 TAATA-AT-ATTTAATAATAATT-TTAATATAAAATTAT
1 TAATATATAATTTAATAA-AATTCTTAATAT-AAATTAT
*
42271723 TAATATAAAATT
1 TAATATATAATT
42271735 ATTATTAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
34 16 0.39
35 5 0.12
36 16 0.39
37 1 0.02
38 3 0.07
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (37 bp):
TAATATATAATTTAATAAAATTCTTAATATAAATTAT
Found at i:42271725 original size:14 final size:14
Alignment explanation
Indices: 42271699--42271738 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
42271689 ATAATATTTA
42271699 ATAATAATT-TTAAT
1 ATAA-AATTATTAAT
42271713 ATAAAATTATTAAT
1 ATAAAATTATTAAT
42271727 ATAAAATTATTA
1 ATAAAATTATTA
42271739 TTAAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 4 0.16
14 21 0.84
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATAAAATTATTAAT
Found at i:42272126 original size:31 final size:31
Alignment explanation
Indices: 42272091--42272166 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
42272081 CATAGTCCGT
42272091 TGTTATTCAAAAAC-CATAGTCCTTAA-T-TTTA
1 TGTTATTCAAAAACTCATAG---TTAATTCTTTA
42272122 TGTTATTCAAAAACTCATAGTTAATTCTTTA
1 TGTTATTCAAAAACTCATAGTTAATTCTTTA
42272153 TGTTATTCAAAAAC
1 TGTTATTCAAAAAC
42272167 ATGCAGAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
29 4 0.10
30 1 0.02
31 32 0.76
32 5 0.12
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (31 bp):
TGTTATTCAAAAACTCATAGTTAATTCTTTA
Found at i:42279145 original size:14 final size:14
Alignment explanation
Indices: 42279126--42279152 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42279116 CTTGCAGGTG
42279126 CTCTACTGCTAGCC
1 CTCTACTGCTAGCC
42279140 CTCTACTGCTAGC
1 CTCTACTGCTAGC
42279153 ACCACTACCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.41, G:0.15, T:0.30
Consensus pattern (14 bp):
CTCTACTGCTAGCC
Found at i:42282066 original size:46 final size:46
Alignment explanation
Indices: 42282006--42282123 Score: 139
Period size: 46 Copynumber: 2.6 Consensus size: 46
42281996 AGGCCGAAGT
* * * *
42282006 ATGTCCCAGGCATGTCTTCCACTAGCTCTCGTCTCAATG-CCGACAC
1 ATGTCCCAGACATGTCTTACACTAGCTCTCATAT-AATGTCCGACAC
* * **
42282052 ATGTCCCAGACATGTCTTACACTGGCTCTCATATTATGTCCGATGC
1 ATGTCCCAGACATGTCTTACACTAGCTCTCATATAATGTCCGACAC
*
42282098 ATGTCCCAGACATGTCTTGCACTAGC
1 ATGTCCCAGACATGTCTTACACTAGC
42282124 ACACATATCA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
45 3 0.05
46 58 0.95
ACGTcount: A:0.21, C:0.32, G:0.18, T:0.29
Consensus pattern (46 bp):
ATGTCCCAGACATGTCTTACACTAGCTCTCATATAATGTCCGACAC
Found at i:42291208 original size:22 final size:22
Alignment explanation
Indices: 42291177--42291220 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
42291167 AATGAATAGG
42291177 AATAAATAGAA-TAAAATATTAA
1 AATAAATAGAATTAAAA-ATTAA
*
42291199 AATAATTAGAATTAAAAATTAA
1 AATAAATAGAATTAAAAATTAA
42291221 GGTTTAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (22 bp):
AATAAATAGAATTAAAAATTAA
Found at i:42292774 original size:9 final size:9
Alignment explanation
Indices: 42292755--42292813 Score: 64
Period size: 9 Copynumber: 5.9 Consensus size: 9
42292745 GCATGCTAAG
42292755 TAAGTTATAA
1 TAAG-TATAA
42292765 TAAGTATAA
1 TAAGTATAA
42292774 TAATGTGATATGA
1 TAA-GT-ATA--A
42292787 TAAGTTATAA
1 TAAG-TATAA
42292797 TAAGTATAA
1 TAAGTATAA
42292806 TAAGTATA
1 TAAGTATA
42292814 GTGGCTTGGC
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
9 21 0.48
10 11 0.25
11 3 0.07
12 4 0.09
13 5 0.11
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (9 bp):
TAAGTATAA
Found at i:42297651 original size:49 final size:49
Alignment explanation
Indices: 42297485--42297709 Score: 306
Period size: 49 Copynumber: 4.5 Consensus size: 49
42297475 TGAGGTCGCA
* * * * *
42297485 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-T-TGGTCACG
* * **
42297536 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT-GGTCACG
*
42297586 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
* *
42297635 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
*
42297684 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
42297710 TGCGTACCAG
Statistics
Matches: 156, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
49 79 0.51
50 44 0.28
51 33 0.21
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
Found at i:42297660 original size:99 final size:100
Alignment explanation
Indices: 42297478--42297717 Score: 322
Period size: 99 Copynumber: 2.4 Consensus size: 100
42297468 TCTATTGTGA
* *
42297478 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACGTGTGTAG
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCGAAAACTGTGATCACGTGTGTAG
* **
42297543 TACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
66 TACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * ** * *
42297578 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAA-T-TGGTCACGTGTGTA
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCGAAAACTGTGATCACGTGTGTA
*
42297641 GTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
65 GTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
42297677 GGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACC
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACC
42297718 AGATAGCTTT
Statistics
Matches: 121, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
98 35 0.29
99 45 0.37
100 1 0.01
101 40 0.33
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (100 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCGAAAACTGTGATCACGTGTGTAG
TACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:42302678 original size:69 final size:68
Alignment explanation
Indices: 42302602--42302864 Score: 284
Period size: 69 Copynumber: 3.8 Consensus size: 68
42302592 TTTGGAAAGT
* ** * *
42302602 ACATTAAGCATTTAAAAT-GAACATAAATGAACAAAGTTTTAAGACAACAAATCAGCCCTATACA
1 ACATTAAGAATTT-AAATCGAATGTAAATGAACACA-TTTTAAGACAACAAATCAGCCCTTTACA
42302666 ACAAC
64 ACAAC
*
42302671 ACATTAAGAACTTAAATCGAATGTAAATGAACACATTTTAAAGA-ATACAAATCAGCCCTTTACA
1 ACATTAAGAATTTAAATCGAATGTAAATGAACACATTTT-AAGACA-ACAAATCAGCCCTTTACA
*
42302735 GCAAC
64 ACAAC
* *
42302740 ACATTAA-ATATTTAAATCGAATGTAAATTAACACATTTTAAGGACTACAAATCAGCCCTTTACA
1 ACATTAAGA-ATTTAAATCGAATGTAAATGAACACATTTTAA-GACAACAAATCAGCCCTTTACA
** *
42302804 GTAGC
64 ACAAC
* * *
42302809 ACATTAA-AGATTTAAATCGAATGTAGATTAACACATTTTAAAGACTAC-AATCAGCC
1 ACATTAAGA-ATTTAAATCGAATGTAAATGAACACATTTT-AAGACAACAAATCAGCC
42302865 TTCCATCACA
Statistics
Matches: 173, Mismatches: 14, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
68 20 0.12
69 151 0.87
70 2 0.01
ACGTcount: A:0.46, C:0.18, G:0.10, T:0.26
Consensus pattern (68 bp):
ACATTAAGAATTTAAATCGAATGTAAATGAACACATTTTAAGACAACAAATCAGCCCTTTACAAC
AAC
Found at i:42306757 original size:94 final size:94
Alignment explanation
Indices: 42306659--42306832 Score: 253
Period size: 94 Copynumber: 1.9 Consensus size: 94
42306649 TGTATATCGT
* **
42306659 GAGGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT-AGTCTTAAT-GCCGATACATGTCC
1 GAGGCCGATGCATGTCCCAAACATGTCTTACACTAGCTCTCA-TAGT-ATGGCCGATACATGTCC
42306722 CAAACATGTCTTACACTGGCTTAAATATCTC
64 CAAACATGTCTTACACTGGCTTAAATATCTC
* * * *
42306753 GAGGCTGATGCATGTCCCAAACATGTCTTACACTGGCTCTCATAGTGTGGCCGATGCATGTCCCA
1 GAGGCCGATGCATGTCCCAAACATGTCTTACACTAGCTCTCATAGTATGGCCGATACATGTCCCA
42306818 AACATGTCTTACACT
66 AACATGTCTTACACT
42306833 AGCACATATA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
93 1 0.01
94 69 0.97
95 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (94 bp):
GAGGCCGATGCATGTCCCAAACATGTCTTACACTAGCTCTCATAGTATGGCCGATACATGTCCCA
AACATGTCTTACACTGGCTTAAATATCTC
Found at i:42306776 original size:48 final size:46
Alignment explanation
Indices: 42306651--42306832 Score: 208
Period size: 46 Copynumber: 3.9 Consensus size: 46
42306641 AACTAGCTTG
* *
42306651 TATATCGTGAGGCCGATGCATGTCCCAGACATGTCTTACACTAGCTC
1 TATATC-TGAGGCCGATGCATGTCCCAAACATGTCTTACACTGGCTC
* * * *
42306698 TA-GTCTTAATGCCGATACATGTCCCAAACATGTCTTACACTGGCT-
1 TATATC-TGAGGCCGATGCATGTCCCAAACATGTCTTACACTGGCTC
*
42306743 TAAATATCTCGAGGCTGATGCATGTCCCAAACATGTCTTACACTGGCTC
1 T--ATATCT-GAGGCCGATGCATGTCCCAAACATGTCTTACACTGGCTC
* *
42306792 TCATA-GTGTGGCCGATGCATGTCCCAAACATGTCTTACACT
1 T-ATATCTGAGGCCGATGCATGTCCCAAACATGTCTTACACT
42306833 AGCACATATA
Statistics
Matches: 114, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
45 1 0.01
46 68 0.60
47 5 0.04
48 39 0.34
49 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (46 bp):
TATATCTGAGGCCGATGCATGTCCCAAACATGTCTTACACTGGCTC
Found at i:42306844 original size:94 final size:94
Alignment explanation
Indices: 42306651--42306844 Score: 241
Period size: 94 Copynumber: 2.1 Consensus size: 94
42306641 AACTAGCTTG
* **
42306651 TATATCGTGAGGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTAGTCTTAATGCCGATAC
1 TATATCGTGAGGCCGATGCATGTCCCAAACATGTCTTACACTAGCTCTAGTAGTAATGCCGATAC
* **
42306716 ATGTCCCAAACATGTCTTACACTGGCTTA
66 ATGTCCCAAACATGTCTTACACTAGCACA
* * * *
42306745 AATATC-TCGAGGCTGATGCATGTCCCAAACATGTCTTACACTGGCTCTCA-TAGT-GTGGCCGA
1 TATATCGT-GAGGCCGATGCATGTCCCAAACATGTCTTACACTAGCTCT-AGTAGTAAT-GCCGA
*
42306807 TGCATGTCCCAAACATGTCTTACACTAGCACA
63 TACATGTCCCAAACATGTCTTACACTAGCACA
42306839 TATATC
1 TATATC
42306845 ACTCAATATC
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
93 2 0.02
94 82 0.96
95 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (94 bp):
TATATCGTGAGGCCGATGCATGTCCCAAACATGTCTTACACTAGCTCTAGTAGTAATGCCGATAC
ATGTCCCAAACATGTCTTACACTAGCACA
Found at i:42313056 original size:20 final size:21
Alignment explanation
Indices: 42313031--42313070 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
42313021 CATTTGAAAC
42313031 AGGGC-ACATGCCCATGTGGA
1 AGGGCAACATGCCCATGTGGA
*
42313051 AGGGCAACATGCCCGTGTGG
1 AGGGCAACATGCCCATGTGG
42313071 CTATTATGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.23, C:0.25, G:0.38, T:0.15
Consensus pattern (21 bp):
AGGGCAACATGCCCATGTGGA
Found at i:42325360 original size:14 final size:15
Alignment explanation
Indices: 42325332--42325374 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
42325322 CACTTTTTCC
*
42325332 ACTCTTTTTCTTTTT
1 ACTCTTTTTCATTTT
*
42325347 ATTCTTTTT-ATTTT
1 ACTCTTTTTCATTTT
*
42325361 GCTCTTTTTCATTT
1 ACTCTTTTTCATTT
42325375 GATCTCTCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.09, C:0.16, G:0.02, T:0.72
Consensus pattern (15 bp):
ACTCTTTTTCATTTT
Found at i:42327429 original size:6 final size:7
Alignment explanation
Indices: 42327403--42327442 Score: 53
Period size: 7 Copynumber: 5.3 Consensus size: 7
42327393 AATTCTTCTT
42327403 TTTTTTA
1 TTTTTTA
42327410 TTTTCTTTA
1 -TTT-TTTA
42327419 TTTTTTA
1 TTTTTTA
42327426 TTTTTTTA
1 -TTTTTTA
42327434 TTTTTTA
1 TTTTTTA
42327441 TT
1 TT
42327443 CATAATTCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 13 0.43
8 13 0.43
9 4 0.13
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTA
Found at i:42327430 original size:8 final size:8
Alignment explanation
Indices: 42327402--42327439 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 8
42327392 AAATTCTTCT
42327402 TTTTTTTA
1 TTTTTTTA
42327410 TTTTCTTTA
1 TTTT-TTTA
42327419 -TTTTTTA
1 TTTTTTTA
42327426 TTTTTTTA
1 TTTTTTTA
42327434 TTTTTT
1 TTTTTT
42327440 ATTCATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 4 0.14
8 20 0.71
9 4 0.14
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTA
Found at i:42327433 original size:15 final size:16
Alignment explanation
Indices: 42327403--42327442 Score: 73
Period size: 15 Copynumber: 2.6 Consensus size: 16
42327393 AATTCTTCTT
42327403 TTTTTTATTTTCTTTA
1 TTTTTTATTTTCTTTA
42327419 TTTTTTATTTT-TTTA
1 TTTTTTATTTTCTTTA
42327434 TTTTTTATT
1 TTTTTTATT
42327443 CATAATTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTTTATTTTCTTTA
Found at i:42328914 original size:27 final size:26
Alignment explanation
Indices: 42328884--42328936 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
42328874 GCAATTTAAT
*
42328884 TTGTCTTAAACAAGACATATTTGAAAG
1 TTGTCTCAAACAAGACATATTT-AAAG
* *
42328911 TTGTCTCAAGCTAGACATATTTAAAG
1 TTGTCTCAAACAAGACATATTTAAAG
42328937 GATGTCCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (26 bp):
TTGTCTCAAACAAGACATATTTAAAG
Found at i:42332094 original size:50 final size:48
Alignment explanation
Indices: 42331978--42332154 Score: 205
Period size: 50 Copynumber: 3.6 Consensus size: 48
42331968 CTGATATGCA
* * * *
42331978 TAGTAGCCTGCACTTAGTATTACACATGCGA-TCAATAATCCCGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGATTC-ATCAT-CTGTACACG
*
42332027 TAGTAGCCTGCACTTAGTACTACACACGTGATGTCATCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGAT-TCATCATCTG-TACACG
* * *
42332077 TAGTAGCCTGCACTTAGTACTACACATGCGACTT-AACAGTATGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGA-TTCATCA-TCT-GTACACG
42332127 TAGTAGCCTGCACTTAGTACTACACACG
1 TAGTAGCCTGCACTTAGTACTACACACG
42332155 TGTATTCACA
Statistics
Matches: 112, Mismatches: 10, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
49 33 0.29
50 75 0.67
51 4 0.04
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (48 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGATTCATCATCTGTACACG
Found at i:42333782 original size:14 final size:14
Alignment explanation
Indices: 42333763--42333790 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42333753 ACGCAGACTC
42333763 AACTTGCCTTTTCG
1 AACTTGCCTTTTCG
42333777 AACTTGCCTTTTCG
1 AACTTGCCTTTTCG
42333791 GCCAAACCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.29, G:0.14, T:0.43
Consensus pattern (14 bp):
AACTTGCCTTTTCG
Found at i:42337595 original size:53 final size:53
Alignment explanation
Indices: 42337537--42337642 Score: 185
Period size: 53 Copynumber: 2.0 Consensus size: 53
42337527 GCTGGCTTAT
*
42337537 ATACTTCTTTCTAAACTCCTCTTGGAAGAAATCCCATATAACCCTTTCTTTCA
1 ATACTTCTTTCTAAACTCCTATTGGAAGAAATCCCATATAACCCTTTCTTTCA
* *
42337590 ATACTTCTTTCTAAACTCCTATTGGAAGAAATCCCATGTAATCCTTTCTTTCA
1 ATACTTCTTTCTAAACTCCTATTGGAAGAAATCCCATATAACCCTTTCTTTCA
42337643 GAACCACAGA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.28, C:0.26, G:0.07, T:0.39
Consensus pattern (53 bp):
ATACTTCTTTCTAAACTCCTATTGGAAGAAATCCCATATAACCCTTTCTTTCA
Found at i:42339591 original size:50 final size:49
Alignment explanation
Indices: 42339537--42339713 Score: 189
Period size: 50 Copynumber: 3.5 Consensus size: 49
42339527 CTGATATGCA
42339537 TAGTAGCCTGCACTTAGTACTACACACATGACCTTATCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACATGACCTTATCAT-TGATACACG
* * ** * *
42339587 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTCATTGAGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACATGACCTTA-TCATTGA-TACACG
* * *
42339638 TAGTAGCCTGCAGTTAGTACT--ACACATG-CTACTTAACAGTATGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACATGAC--CTTATCA-T-TGATACACG
42339688 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
42339714 TGTGTATTCA
Statistics
Matches: 103, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
49 8 0.08
50 62 0.60
51 30 0.29
52 3 0.03
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACATGACCTTATCATTGATACACG
Found at i:42347611 original size:29 final size:29
Alignment explanation
Indices: 42347569--42347624 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
42347559 GAAGAAAGAT
*
42347569 GGTTTGATGAGGTTATGTATCGATTATCG
1 GGTTCGATGAGGTTATGTATCGATTATCG
42347598 GGTTCGATGAGGTTATGTATCGATTAT
1 GGTTCGATGAGGTTATGTATCGATTAT
42347625 TGGCAACTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.07, G:0.30, T:0.41
Consensus pattern (29 bp):
GGTTCGATGAGGTTATGTATCGATTATCG
Found at i:42351750 original size:25 final size:25
Alignment explanation
Indices: 42351716--42351765 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
42351706 AGTCAAAAAG
42351716 AAAAAAAAAGGAAAACAAATATGTA
1 AAAAAAAAAGGAAAACAAATATGTA
42351741 AAAAAAAAAGGAAAACAAATATGTA
1 AAAAAAAAAGGAAAACAAATATGTA
42351766 GATCAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.72, C:0.04, G:0.12, T:0.12
Consensus pattern (25 bp):
AAAAAAAAAGGAAAACAAATATGTA
Found at i:42351938 original size:24 final size:21
Alignment explanation
Indices: 42351889--42351938 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 21
42351879 TGCCAGAGTG
* *
42351889 TTATTATTGGAGTATTCAAAT
1 TTATTATTAGAGTATTAAAAT
42351910 TTATTATTAGAGTAATTGAAAAT
1 TTATTATTAGAGT-ATT-AAAAT
42351933 TATATT
1 T-TATT
42351939 TGTATCCATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 12 0.50
22 3 0.12
23 5 0.21
24 4 0.17
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (21 bp):
TTATTATTAGAGTATTAAAAT
Found at i:42356757 original size:26 final size:26
Alignment explanation
Indices: 42356728--42356777 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
42356718 TTAGTGTACT
*
42356728 AAATATTTTCTTATAAAATTATAACG
1 AAATATTTTCTCATAAAATTATAACG
*
42356754 AAATATTTTCTCATACAATTATAA
1 AAATATTTTCTCATAAAATTATAA
42356778 AATAATTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (26 bp):
AAATATTTTCTCATAAAATTATAACG
Found at i:42358023 original size:38 final size:38
Alignment explanation
Indices: 42357967--42358045 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
42357957 AAGATATAAC
*
42357967 TCAAACACAACATGAAAAGAAAATTCATTCTTAATCAA
1 TCAAACACAACATAAAAAGAAAATTCATTCTTAATCAA
42358005 TCAAACACAACATAAAAAGAAAATTCATTCTTAATCAA
1 TCAAACACAACATAAAAAGAAAATTCATTCTTAATCAA
42358043 TCA
1 TCA
42358046 TTATTGACAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.53, C:0.19, G:0.04, T:0.24
Consensus pattern (38 bp):
TCAAACACAACATAAAAAGAAAATTCATTCTTAATCAA
Found at i:42358452 original size:32 final size:32
Alignment explanation
Indices: 42358416--42358482 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
42358406 TTGAGTTGGG
42358416 ATAACCTTAATTACATTGTTCTATATATATAT
1 ATAACCTTAATTACATTGTTCTATATATATAT
42358448 ATAACCTTAATTACATTGTTCTATATATATAT
1 ATAACCTTAATTACATTGTTCTATATATATAT
42358480 ATA
1 ATA
42358483 TTACATAGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.39, C:0.12, G:0.03, T:0.46
Consensus pattern (32 bp):
ATAACCTTAATTACATTGTTCTATATATATAT
Found at i:42359715 original size:30 final size:30
Alignment explanation
Indices: 42359681--42359740 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
42359671 AATCAAAATG
42359681 AATGATTAATATAATTATTATAATTTTGTC
1 AATGATTAATATAATTATTATAATTTTGTC
42359711 AATGATTAATATAATTATTATAATTTTGTC
1 AATGATTAATATAATTATTATAATTTTGTC
42359741 TTTCCATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (30 bp):
AATGATTAATATAATTATTATAATTTTGTC
Found at i:42360793 original size:20 final size:20
Alignment explanation
Indices: 42360768--42360817 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
42360758 TGGCTTAAAA
42360768 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
42360788 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
42360805 GTGGTAGTGGATT
1 TTGGTAGTGGATT
42360818 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:42365432 original size:20 final size:20
Alignment explanation
Indices: 42365407--42365456 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
42365397 TGGCTTAAAA
42365407 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
42365427 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
42365444 GTGGTAGTGGATT
1 TTGGTAGTGGATT
42365457 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:42366129 original size:22 final size:22
Alignment explanation
Indices: 42366102--42366146 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
42366092 AATTTGATTC
42366102 TAATTCTAATAATTCAATAAAT
1 TAATTCTAATAATTCAATAAAT
42366124 TAATTCTAATAATTCAATAAAT
1 TAATTCTAATAATTCAATAAAT
42366146 T
1 T
42366147 TAACCCTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (22 bp):
TAATTCTAATAATTCAATAAAT
Found at i:42392294 original size:77 final size:77
Alignment explanation
Indices: 42392201--42392348 Score: 224
Period size: 77 Copynumber: 1.9 Consensus size: 77
42392191 CACATGGATG
*
42392201 TGTGACCACAAAAGAATTGAAAATTTTTGCTAAGTTCTAAAAATTCTAAATGTGTTTGGTTTGGT
1 TGTGACCACAAAAGAATTGAAAATTTTTGCTAAGTTCTAAAAATTCTAAATGTGTTCGGTTTGGT
*
42392266 TCCGACTGCCCA
66 CCCGACTGCCCA
* * * * * *
42392278 TGTGACCACAACAGAATTGAAAATTTTTGCTAAGTTTTGAAATTTTTGAATGTGTTCGGTTTGGT
1 TGTGACCACAAAAGAATTGAAAATTTTTGCTAAGTTCTAAAAATTCTAAATGTGTTCGGTTTGGT
42392343 CCCGAC
66 CCCGAC
42392349 CTTTTCTGAA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
77 63 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (77 bp):
TGTGACCACAAAAGAATTGAAAATTTTTGCTAAGTTCTAAAAATTCTAAATGTGTTCGGTTTGGT
CCCGACTGCCCA
Found at i:42397437 original size:18 final size:18
Alignment explanation
Indices: 42397414--42397456 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
42397404 CTGTTTTTGT
42397414 GCTTAATTATGAAAAAGG
1 GCTTAATTATGAAAAAGG
42397432 GCTTAATTATGAAAAAGG
1 GCTTAATTATGAAAAAGG
*
42397450 ACTTAAT
1 GCTTAAT
42397457 CGCATAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (18 bp):
GCTTAATTATGAAAAAGG
Found at i:42406372 original size:45 final size:45
Alignment explanation
Indices: 42406193--42406369 Score: 214
Period size: 45 Copynumber: 3.9 Consensus size: 45
42406183 CGATATCCTT
* * *
42406193 TCACTGGCATTATAGCCCGCTAGGCTCGAAA-GCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTC-AAAGGCCCAAATAGTATC
* * * *
42406238 TCACTGGCATTGTAGCCTGCTAGGCACAAAGGCCTAAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCAAATAGTATC
* * *
42406283 TCACCGGCATTATAGCCTACAAGGCTCAAAGG-CCAGAATAGTGTC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCA-AATAGTATC
* *
42406328 TCACCGGTATTATAGCCTGCTTGGCTCAAAGGCCCAAATAGT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCAAATAGT
42406370 GTCGTACGAT
Statistics
Matches: 113, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
44 5 0.04
45 105 0.93
46 3 0.03
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCAAATAGTATC
Found at i:42408641 original size:32 final size:32
Alignment explanation
Indices: 42408605--42408668 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
42408595 ACACCTTGAG
42408605 GTGGGAATTTTGACATGCAAATCCACCTATTT
1 GTGGGAATTTTGACATGCAAATCCACCTATTT
42408637 GTGGGAATTTTGACATGCAAATCCACCTATTT
1 GTGGGAATTTTGACATGCAAATCCACCTATTT
42408669 CATACTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (32 bp):
GTGGGAATTTTGACATGCAAATCCACCTATTT
Found at i:42413850 original size:45 final size:45
Alignment explanation
Indices: 42413679--42413847 Score: 277
Period size: 45 Copynumber: 3.8 Consensus size: 45
42413669 TTTCACTGGA
*
42413679 ATTATAGCCTGCTAGGATCGAAA-GCCCGAATAGTATCTCACCGGC
1 ATTATAGCCTGCTAGGCTC-AAAGGCCCGAATAGTATCTCACCGGC
* *
42413724 ATTGTAGCCTGCTAGGCTCAAAGGCCCGAATAGTATGTCACCGGC
1 ATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCGGC
*
42413769 ATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTGTCTCACCGGC
1 ATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCGGC
*
42413814 ATTATAGCCTGCTAGGCTCAAAGGCCCAAATAGT
1 ATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGT
42413848 GTCGTACGAT
Statistics
Matches: 116, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
44 3 0.03
45 113 0.97
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (45 bp):
ATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCGGC
Found at i:42415813 original size:32 final size:32
Alignment explanation
Indices: 42415777--42415840 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
42415767 ACACCTTGAG
42415777 GTGGGAATTTTGACATGCAAATCCACCTATTT
1 GTGGGAATTTTGACATGCAAATCCACCTATTT
42415809 GTGGGAATTTTGACATGCAAATCCACCTATTT
1 GTGGGAATTTTGACATGCAAATCCACCTATTT
42415841 CATACTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (32 bp):
GTGGGAATTTTGACATGCAAATCCACCTATTT
Found at i:42426076 original size:79 final size:78
Alignment explanation
Indices: 42425974--42426196 Score: 272
Period size: 79 Copynumber: 2.8 Consensus size: 78
42425964 GCTCCTCGTT
* *
42425974 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
42426039 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
* *
42426054 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
*
42426118 ATTAGTATCTCGCA
65 ATTAGTAACTCGCA
* * * * *
42426132 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
42426195 GA
63 GA
42426197 CATCATTCAA
Statistics
Matches: 125, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
78 45 0.36
79 60 0.48
80 20 0.16
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:42426091 original size:39 final size:40
Alignment explanation
Indices: 42425974--42426196 Score: 280
Period size: 39 Copynumber: 5.7 Consensus size: 40
42425964 GCTCCTCGTT
* *
42425974 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
42426014 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
42426054 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
42426093 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * *
42426132 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAAC-TCGCA
42426173 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42426197 CATCATTCAA
Statistics
Matches: 167, Mismatches: 10, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
38 2 0.01
39 88 0.53
40 67 0.40
41 10 0.06
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:42432997 original size:28 final size:28
Alignment explanation
Indices: 42432965--42433020 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
42432955 AATCCCAGAG
*
42432965 AACAACACCTCATATATATATAATTCTT
1 AACAACACCTCATATATATATAACTCTT
*
42432993 AACAACTCCTCATATATATATAACTCTT
1 AACAACACCTCATATATATATAACTCTT
42433021 TCATGAATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.41, C:0.23, G:0.00, T:0.36
Consensus pattern (28 bp):
AACAACACCTCATATATATATAACTCTT
Found at i:42440378 original size:79 final size:81
Alignment explanation
Indices: 42440242--42440426 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
42440232 TTGAATGATG
* *
42440242 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
42440306 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
42440321 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
42440383 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
42440401 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
42440427 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:42440440 original size:40 final size:40
Alignment explanation
Indices: 42440243--42440426 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
42440233 TGAATGATGT
* * * *
42440243 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
42440283 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
42440323 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
42440361 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
42440402 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
42440427 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:42440448 original size:79 final size:79
Alignment explanation
Indices: 42440295--42440449 Score: 199
Period size: 79 Copynumber: 2.0 Consensus size: 79
42440285 GGACTAAGAT
* * **
42440295 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
42440360 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* *
42440374 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
*
42440437 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
42440450 ATTTCGAAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
78 2 0.03
79 39 0.59
80 25 0.38
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:42442729 original size:36 final size:36
Alignment explanation
Indices: 42442682--42442753 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
42442672 CAAAAGTATA
42442682 GCATTCATATAGCTAAACGAATAATTTCATATGCAC
1 GCATTCATATAGCTAAACGAATAATTTCATATGCAC
*
42442718 GCATTCATATAGCTAAACGGATAATTTCATATGCAC
1 GCATTCATATAGCTAAACGAATAATTTCATATGCAC
42442754 AAATTCTCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (36 bp):
GCATTCATATAGCTAAACGAATAATTTCATATGCAC
Found at i:42443035 original size:39 final size:40
Alignment explanation
Indices: 42442990--42443157 Score: 106
Period size: 40 Copynumber: 4.2 Consensus size: 40
42442980 CGGGGTTTAG
* *
42442990 CCGGATATAACCACTCGCAT-AAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * * *
42443029 CCGGATATGGTCACTAGCATAAATGCCTTTGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
42443069 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
42443109 CTGGATATAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
42443150 CCGGATAT
1 CCGGATAT
42443158 CATTCGAGTA
Statistics
Matches: 108, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
39 19 0.18
40 59 0.55
41 27 0.25
42 3 0.03
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:42443148 original size:41 final size:40
Alignment explanation
Indices: 42443013--42443157 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
42443003 CTCGCATAAG
* * * * *
42443013 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
*
42443053 GCCTTTGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
42443093 GCCTTC-GGATCTTAGTCTGGATATAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
42443134 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
42443158 CATTCGAGTA
Statistics
Matches: 90, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
39 3 0.03
40 57 0.63
41 27 0.30
42 3 0.03
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:42444386 original size:38 final size:38
Alignment explanation
Indices: 42444344--42444419 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
42444334 CAAGAACTCC
*
42444344 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTGTCGGCCAAAAGAAATGAA
42444382 TTCCTCCTTCCTTAGAATTGTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTGTCGGCCAAAAGAAATGAA
42444420 AAAGGATGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (38 bp):
TTCCTCCTTCCTTAGAATTGTCGGCCAAAAGAAATGAA
Found at i:42447627 original size:47 final size:47
Alignment explanation
Indices: 42447546--42447796 Score: 328
Period size: 47 Copynumber: 5.4 Consensus size: 47
42447536 TAATTGAATA
* * *
42447546 AATGTGAA-AGTGTATATGTGTGAATAGGGCCGAATGGCCAATGTGATG
1 AATGTGAACA-TGTGTATGTGAG-ATAAGGCCGAATGGCCAATGTGATG
** *
42447594 AATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTGTATGTGAGATAAGGCCGAATGGCCAATGTGATG
*
42447641 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTGTATGTGAGATAAGGCCGAATGGCCAATGTGATG
* * * *
42447688 AAAGTGAACAGGTGTATGTGTGATAAGGCCGAGTGGCCAATGTGATG
1 AATGTGAACATGTGTATGTGAGATAAGGCCGAATGGCCAATGTGATG
* * * *
42447735 AATGTGAGCATGTGTATGTGAGATAGGGCCTAATGGCCGATGTGATG
1 AATGTGAACATGTGTATGTGAGATAAGGCCGAATGGCCAATGTGATG
42447782 AATGTGAA-A-GTGTAT
1 AATGTGAACATGTGTAT
42447797 AATTGTGATA
Statistics
Matches: 182, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
45 6 0.03
46 1 0.01
47 157 0.86
48 17 0.09
49 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.33, T:0.26
Consensus pattern (47 bp):
AATGTGAACATGTGTATGTGAGATAAGGCCGAATGGCCAATGTGATG
Found at i:42447983 original size:37 final size:37
Alignment explanation
Indices: 42447927--42448006 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
42447917 CCGGACTCTA
* * *
42447927 AAGACCCGATGACTGCGTGTGG-GAATTTTGTCCGGGT
1 AAGACTCGATAACTGCGTGTGGAG-ATTATGTCCGGGT
*
42447964 AAGACTCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACTCGATAACTGCGTGTGGAGATTATGTCCGGGT
42448001 AAGACT
1 AAGACT
42448007 TCGTAATAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (37 bp):
AAGACTCGATAACTGCGTGTGGAGATTATGTCCGGGT
Found at i:42453193 original size:40 final size:40
Alignment explanation
Indices: 42453146--42453290 Score: 157
Period size: 40 Copynumber: 3.6 Consensus size: 40
42453136 CTCACACAAG
* * * *
42453146 GCCTTCGGGTCTTAACCCGGATATGGTCATTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCATTAGCACAAAT
* **
42453186 GCCTTCGGGACTTAGCTCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCATTAGCACAAAT
* * * * *
42453226 GCCTTC-GGATCTTAGTCTGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTC-ATTAGCACAAAT
42453267 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
42453291 CATTCGAGTA
Statistics
Matches: 85, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
39 3 0.04
40 53 0.62
41 26 0.31
42 3 0.04
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.28
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCATTAGCACAAAT
Found at i:42455598 original size:32 final size:32
Alignment explanation
Indices: 42455561--42455624 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
42455551 ATTATAAAAT
42455561 TCAAATCATCATAGAAAAACATTCTATGTTCA
1 TCAAATCATCATAGAAAAACATTCTATGTTCA
*
42455593 TCAAATCATCATAGCAAAACATTCTATGTTCA
1 TCAAATCATCATAGAAAAACATTCTATGTTCA
42455625 AAATAAACCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.42, C:0.20, G:0.06, T:0.31
Consensus pattern (32 bp):
TCAAATCATCATAGAAAAACATTCTATGTTCA
Found at i:42457882 original size:23 final size:22
Alignment explanation
Indices: 42457856--42457903 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
42457846 CATAGTCACA
*
42457856 AGGCCTTGTGCCTCCTTTCATAC
1 AGGCCATGTGCCTCC-TTCATAC
*
42457879 AGG-CATGTGCCTCCTTCATAT
1 AGGCCATGTGCCTCCTTCATAC
42457900 AGGC
1 AGGC
42457904 AGTTGACCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 9 0.41
22 10 0.45
23 3 0.14
ACGTcount: A:0.17, C:0.31, G:0.21, T:0.31
Consensus pattern (22 bp):
AGGCCATGTGCCTCCTTCATAC
Found at i:42457898 original size:21 final size:22
Alignment explanation
Indices: 42457862--42457904 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
42457852 CACAAGGCCT
42457862 TGTGCCTCCTTTCATACAGGCA
1 TGTGCCTCCTTTCATACAGGCA
*
42457884 TGTGCCTCC-TTCATATAGGCA
1 TGTGCCTCCTTTCATACAGGCA
42457905 GTTGACCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.33
Consensus pattern (22 bp):
TGTGCCTCCTTTCATACAGGCA
Found at i:42467370 original size:18 final size:19
Alignment explanation
Indices: 42467332--42467375 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
42467322 GCCTTTTTCA
**
42467332 AAATAAAAATAATTGACAT
1 AAATAAAAATAAAAGACAT
42467351 AAATAAAAATAAAAGA-AT
1 AAATAAAAATAAAAGACAT
*
42467369 AACTAAA
1 AAATAAA
42467376 TATTTAGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (19 bp):
AAATAAAAATAAAAGACAT
Found at i:42470227 original size:25 final size:23
Alignment explanation
Indices: 42470199--42470244 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
42470189 TTGGCTTTTA
42470199 TACATCAATTAACTATTAATTATTC
1 TACATCAATTAA-T-TTAATTATTC
* *
42470224 TACATTAGTTAATTTAATTAT
1 TACATCAATTAATTTAATTAT
42470245 AGATTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 1 0.05
25 10 0.53
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (23 bp):
TACATCAATTAATTTAATTATTC
Found at i:42470747 original size:33 final size:33
Alignment explanation
Indices: 42470703--42470765 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
42470693 ATCATGGCCG
*
42470703 AATCTAGCGATGTCACATGCTAGTGTGTTTGAA
1 AATCTACCGATGTCACATGCTAGTGTGTTTGAA
42470736 AATCTACCGATGTCACATGCTAGTGTGTTT
1 AATCTACCGATGTCACATGCTAGTGTGTTT
42470766 AGAACCTACC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.35
Consensus pattern (33 bp):
AATCTACCGATGTCACATGCTAGTGTGTTTGAA
Found at i:42471325 original size:33 final size:34
Alignment explanation
Indices: 42471283--42471352 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 34
42471273 TGATAGTCAT
42471283 GCAGTAGGGCCTTAG-CTCATCACAGT-ACAGTAA
1 GCAGTAGGGCCTTAGCCT-ATCACAGTAACAGTAA
*
42471316 GCAGTAGGGCCTTAGCCTATTACAGTAACAGTAA
1 GCAGTAGGGCCTTAGCCTATCACAGTAACAGTAA
42471350 GCA
1 GCA
42471353 TCAATGCAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 22 0.65
34 12 0.35
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.21
Consensus pattern (34 bp):
GCAGTAGGGCCTTAGCCTATCACAGTAACAGTAA
Found at i:42471923 original size:33 final size:33
Alignment explanation
Indices: 42471881--42471950 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
42471871 TGGCCAACAC
* **
42471881 GGCCTAATTTGGCCTTGGTCGTGTGGCTCACAA
1 GGCCCAATTTGGCCTTGACCGTGTGGCTCACAA
* *
42471914 GGCCCAATTTGGCCTTGACCGTGTGGTTCACAC
1 GGCCCAATTTGGCCTTGACCGTGTGGCTCACAA
42471947 GGCC
1 GGCC
42471951 TGGCCCAGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.14, C:0.29, G:0.30, T:0.27
Consensus pattern (33 bp):
GGCCCAATTTGGCCTTGACCGTGTGGCTCACAA
Found at i:42474280 original size:24 final size:24
Alignment explanation
Indices: 42474248--42474297 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
42474238 AAGGCCTATT
42474248 GTGAGGAGTGGATCCTAACAACAA
1 GTGAGGAGTGGATCCTAACAACAA
42474272 GTGAGGAGTGGATCCTAACAACAA
1 GTGAGGAGTGGATCCTAACAACAA
42474296 GT
1 GT
42474298 CTTTGTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.16, G:0.30, T:0.18
Consensus pattern (24 bp):
GTGAGGAGTGGATCCTAACAACAA
Found at i:42481412 original size:35 final size:35
Alignment explanation
Indices: 42481363--42481431 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
42481353 TGGCTACGTA
*
42481363 TAAATAATTAATAATA-ACTACTATGT-AATTTAGTG
1 TAAACAATTAATAATATA-TACTAT-TAAATTTAGTG
*
42481398 TAAACAATTTATAATATATACTATTAAATTTAGT
1 TAAACAATTAATAATATATACTATTAAATTTAGT
42481432 TAATTATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 1 0.03
35 28 0.93
36 1 0.03
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (35 bp):
TAAACAATTAATAATATATACTATTAAATTTAGTG
Found at i:42485837 original size:86 final size:85
Alignment explanation
Indices: 42485747--42486149 Score: 327
Period size: 86 Copynumber: 4.8 Consensus size: 85
42485737 TTTATTTGAG
* *
42485747 AATAATAATAAAAATTGAATAAAATCTGTTCCGGGATTTATTCCCGCCGTTTAACAGATTTTATT
1 AATAATAATAAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTTAACAGATTTTATT
42485812 CCATTTTTTATTTTGTTTCCA
66 CCA-TTTTTATTTTGTTTCCA
* * * * * * * *
42485833 AATAAGAATTAAAATTAAATAAAATCTATTTTGGAATTTATTCCCGTCGTTCAATAGATTTTATT
1 AATAATAATAAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTTAACAGATTTTATT
*
42485898 CCATTTTTATTTTATTTCCAA
66 CCATTTTTATTTTGTTTCC-A
* * * *** * *
42485919 AATGAGT-ATTAAAATTCAATAAAATCTGTTTCAAAATTTATTCCCACCGTTTAACAGATTTTAC
1 AAT-AATAATAAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTTAACAGATTTTAT
*
42485983 TCCATTTTT-TTTTATTT--A
65 TCCATTTTTATTTTGTTTCCA
** ** * * * ** * *
42486001 GTTGCCAA-ACGAGAAATTAAATTAAATATGTTTCGGGATTTATTCCTACCATTTAACAAATTTT
1 AAT---AATAATAAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTTAACAGATTTT
* * *
42486065 ATTCGATTTTTATTTTGCTCCCA
63 ATTCCATTTTTATTTTGTTTCCA
* * * * * * *
42486088 AATTATAAT-TAAATTGAAT--AATCTGTTTCGGGATTTATTCCTGTCGTTCAACATATTTTATT
1 AATAATAATAAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTTAACAGATTTTATT
42486150 TTGATTTTTT
Statistics
Matches: 250, Mismatches: 58, Indels: 22
0.76 0.18 0.07
Matches are distributed among these distances:
82 39 0.16
84 61 0.24
85 29 0.12
86 118 0.47
87 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (85 bp):
AATAATAATAAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTTAACAGATTTTATT
CCATTTTTATTTTGTTTCCA
Found at i:42486226 original size:30 final size:30
Alignment explanation
Indices: 42486190--42486251 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
42486180 ATAATTTTGT
*
42486190 TTCGAGATTTAATCCTATCGTTTAACACAC
1 TTCGAGATTTAATCCTATCATTTAACACAC
*
42486220 TTCGAGATTTAATCCTATCATTTAACATAC
1 TTCGAGATTTAATCCTATCATTTAACACAC
42486250 TT
1 TT
42486252 GATTTTGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (30 bp):
TTCGAGATTTAATCCTATCATTTAACACAC
Found at i:42487083 original size:7 final size:7
Alignment explanation
Indices: 42487016--42487147 Score: 102
Period size: 7 Copynumber: 18.4 Consensus size: 7
42487006 TTAATTATCA
*
42487016 TTATAGT
1 TTATGGT
*
42487023 TTAAGGT
1 TTATGGT
*
42487030 TTATAGT
1 TTATGGT
*
42487037 TTAAGGT
1 TTATGGT
*
42487044 TTATAGT
1 TTATGGT
*
42487051 TTAAGGT
1 TTATGGT
*
42487058 ATATGGT
1 TTATGGT
42487065 TTATGGT
1 TTATGGT
42487072 TTATGGT
1 TTATGGT
42487079 TTATGGT
1 TTATGGT
*
42487086 TGATGAGT
1 TTATG-GT
* **
42487094 TAATATT
1 TTATGGT
*
42487101 TTAAGGT
1 TTATGGT
*
42487108 TTATGGA
1 TTATGGT
42487115 TTATGGGT
1 TTAT-GGT
* *
42487123 TTAAGGA
1 TTATGGT
42487130 TTATGGGT
1 TTAT-GGT
42487138 TTATGGT
1 TTATGGT
42487145 TTA
1 TTA
42487148 AGGGTTGGGT
Statistics
Matches: 94, Mismatches: 28, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
7 78 0.83
8 16 0.17
ACGTcount: A:0.25, C:0.00, G:0.26, T:0.49
Consensus pattern (7 bp):
TTATGGT
Found at i:42487125 original size:15 final size:15
Alignment explanation
Indices: 42487105--42487153 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
42487095 AATATTTTAA
42487105 GGTTTATGGATTATG
1 GGTTTATGGATTATG
*
42487120 GGTTTAAGGATTATG
1 GGTTTATGGATTATG
* *
42487135 GGTTTATGGTTTAAG
1 GGTTTATGGATTATG
42487150 GGTT
1 GGTT
42487154 GGGTTTGAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.20, C:0.00, G:0.35, T:0.45
Consensus pattern (15 bp):
GGTTTATGGATTATG
Done.