Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 95 of 126
Found at i:28889844 original size:44 final size:44
Alignment explanation
Indices: 28889747--28889867 Score: 145
Period size: 44 Copynumber: 2.8 Consensus size: 44
28889737 GAAGATGGCA
* * *
28889747 AATCTTATCTCCCTGAATTTGCAATGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCAAT
* * **
28889791 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAGTTACA-
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCA-AT
* *
28889835 AGTCTTATCTCCCTGAAGTTACAGTGAAGCAGA
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGA
28889868 CTGAAGAAAG
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 64 0.98
45 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCAAT
Found at i:28889961 original size:73 final size:73
Alignment explanation
Indices: 28889838--28889975 Score: 181
Period size: 73 Copynumber: 1.9 Consensus size: 73
28889828 AGTTACAAGT
* *
28889838 CTTATCTCCCTGAAGTTACAGTGAAGCAGACTGAAGAAAGCAAGTTTTATC-CCCATGAAGTTGC
1 CTTATCCCCCTGAAGTTACAGTGAAGCAGACTGAAGAAAGCAAGTCTTATCTCCC-TGAAGTTGC
28889902 AACGGGGCA
65 AACGGGGCA
* ** **
28889911 CTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCGAA-TCTTATCTCCCTGAAGTTGC
1 CTTATCCCCCTGAAGTTACAGTGAAGCAGACTGAAGAAAGC-AAGTCTTATCTCCCTGAAGTTGC
28889975 A
65 A
28889976 GTGGAGCAGA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
73 51 0.91
74 5 0.09
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (73 bp):
CTTATCCCCCTGAAGTTACAGTGAAGCAGACTGAAGAAAGCAAGTCTTATCTCCCTGAAGTTGCA
ACGGGGCA
Found at i:28890080 original size:44 final size:44
Alignment explanation
Indices: 28889953--28890085 Score: 160
Period size: 44 Copynumber: 3.0 Consensus size: 44
28889943 GAAGATGGCG
* * * **
28889953 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGCCA-A
1 AATCCTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGTTACA
* *
28889996 TAATCCTATCTCCCTAAAGTTGTAGTAGAGCAGATTAAAGTTACA
1 -AATCCTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGTTACA
* * *
28890041 AATCCTATCTCCTTGAAGTTATAGTGGGGCAGATTAAAGTTACA
1 AATCCTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGTTACA
28890085 A
1 A
28890086 GTCTTATTGA
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
44 75 0.99
45 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (44 bp):
AATCCTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGTTACA
Found at i:28890521 original size:225 final size:223
Alignment explanation
Indices: 28890119--28890548 Score: 524
Period size: 225 Copynumber: 1.9 Consensus size: 223
28890109 TATCCACCTG
* * * * * *
28890119 AAGTTGTAGTGGGGCAGACTAAAGATAGCGAATCTCATTTTCCTGAAATTGTAGTGGAACAGATT
1 AAGTTATAGTGGAGCAGACTAAAGATAGCAAATCTCATTTTCCTGAAATTGCAATGGAACAGATC
* * ** *
28890184 AAAGCTATAAATCACAGATCTTATCTCTCTAAAGTTGCAGTAGAGTAGATCATGGAAAATCTTAT
66 AAAGCTATAAATCAAAGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATCACAGAAAACCTTAT
* * * *
28890249 CTCCCTGAAGTTGAAGTGAAGCAGATTAAAGCCAATAATCCTATCTCCCT-AAAGTTGTAGTGGA
131 CTCCCTAAAGTTGAAGTGAAGCAGATTAAAGACAACAATCCTATCTCCCTGAAA-TTGCAGTGGA
28890313 GCGGATTGAAGTGAGGTCTTATCTCCCCA
195 GCGGATTGAAGTGAGGTCTTATCTCCCCA
* * * *
28890342 AAGTTATAGTGGAGCAGACTGAAGATAGCAAATGTC-GTTTCTCTGAAGATTGCAATGGAATAGA
1 AAGTTATAGTGGAGCAGACTAAAGATAGCAAATCTCATTTTC-CTGAA-ATTGCAATGGAACAGA
* **
28890406 TCAAAGCTATAAATCATAAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCAAACCT
64 TCAAAGCTATAAATCA-AAGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATCACAGAAAACCT
* * * * * * * *
28890471 TATCTCCTTAAAGTTGTAGTGGAGCAGGTTGAAA-ATACCAATCTTATCTCCCTGACATTGCAGT
128 TATCTCCCTAAAGTTGAAGTGAAGCAGATT-AAAGACAACAATCCTATCTCCCTGAAATTGCAGT
28890535 GGAGCGGATTGAAG
192 GGAGCGGATTGAAG
28890549 CAACTAATCC
Statistics
Matches: 172, Mismatches: 30, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
222 4 0.02
223 36 0.21
224 28 0.16
225 99 0.58
226 5 0.03
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (223 bp):
AAGTTATAGTGGAGCAGACTAAAGATAGCAAATCTCATTTTCCTGAAATTGCAATGGAACAGATC
AAAGCTATAAATCAAAGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATCACAGAAAACCTTAT
CTCCCTAAAGTTGAAGTGAAGCAGATTAAAGACAACAATCCTATCTCCCTGAAATTGCAGTGGAG
CGGATTGAAGTGAGGTCTTATCTCCCCA
Found at i:28890536 original size:44 final size:45
Alignment explanation
Indices: 28890471--28890584 Score: 128
Period size: 44 Copynumber: 2.6 Consensus size: 45
28890461 CATCAAACCT
* * *
28890471 TATCTCCTTAAAGTTGTAGTGGAGCAGG-TTGAA-AATACCAATCT
1 TATCTCCCTAAAGTTGCAGTGGAGCAGGATTGAAGAA-ACCAATCC
* * *
28890515 TATCTCCCTGACA-TTGCAGTGGAGC-GGATTGAAGCAACTAATCC
1 TATCTCCCT-AAAGTTGCAGTGGAGCAGGATTGAAGAAACCAATCC
28890559 TATCTCCCTAAAGTTGCAGTGGAGCA
1 TATCTCCCTAAAGTTGCAGTGGAGCA
28890585 AATTAAAATA
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
43 4 0.07
44 51 0.88
45 3 0.05
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (45 bp):
TATCTCCCTAAAGTTGCAGTGGAGCAGGATTGAAGAAACCAATCC
Found at i:28890795 original size:89 final size:88
Alignment explanation
Indices: 28890688--28890923 Score: 271
Period size: 88 Copynumber: 2.7 Consensus size: 88
28890678 GACTGACGAT
* *
28890688 AGCATATCTTGTCTTCTTGTATTGGCAGTGAAGCAGATCGAAGACACTAGTCTTGCCTCCCTGAG
1 AGCAGATCTTGTCTTCTTGTATTGGCAGTGAAGCAGATCGAAGACAC-AGCCTTGCCTCCCTGAG
*
28890753 TTTGCAGAGGAACAGACT-AAAGAT
65 TTTGCAGAGGAACAGACTGAAA-AC
* *
28890777 AGCAGATAC-TGTCTTCTTGTATTGGCAGCGAAGCAAATCGAAGGAC-CAGCCTTGCCTCCCTGA
1 AGCAGAT-CTTGTCTTCTTGTATTGGCAGTGAAGCAGATCGAA-GACACAGCCTTGCCTCCCTGA
* **
28890840 GTTTGCAGCGGAGTAGACTGAAAAC
64 GTTTGCAGAGGAACAGACTGAAAAC
* * * ** * *
28890865 AGCAGATCTTCTCTTCCTGTACTGAAAGTGAAGTAGATCGAAAACACCAGCCTTGCCTC
1 AGCAGATCTTGTCTTCTTGTATTGGCAGTGAAGCAGATCGAAGACA-CAGCCTTGCCTC
28890924 TCTTAGTTGG
Statistics
Matches: 124, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
87 3 0.02
88 64 0.52
89 53 0.43
90 4 0.03
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.25
Consensus pattern (88 bp):
AGCAGATCTTGTCTTCTTGTATTGGCAGTGAAGCAGATCGAAGACACAGCCTTGCCTCCCTGAGT
TTGCAGAGGAACAGACTGAAAAC
Found at i:28890880 original size:88 final size:89
Alignment explanation
Indices: 28890665--28890923 Score: 274
Period size: 89 Copynumber: 2.9 Consensus size: 89
28890655 CTCCCTAAAG
* ** * * *
28890665 TTGCAACGGAGCAGACTGACGATAGCATATCTTGTCTTCTTGTATTGGCAGTGAAGCAGATCGAA
1 TTGCAGCGGAGCAGACTGAAAATAGCAGATCTTGTCTTCTTGTATTGGCAGCGAAGCAAATCGAA
*
28890730 GACACTAGTCTTGCCTCCCTGAGT
66 GACACTAGCCTTGCCTCCCTGAGT
* *
28890754 TTGCAGAGGAACAGACT-AAAGATAGCAGATAC-TGTCTTCTTGTATTGGCAGCGAAGCAAATCG
1 TTGCAGCGGAGCAGACTGAAA-ATAGCAGAT-CTTGTCTTCTTGTATTGGCAGCGAAGCAAATCG
28890817 AAGGAC-C-AGCCTTGCCTCCCTGAGT
64 AA-GACACTAGCCTTGCCTCCCTGAGT
* * * * * ** * * *
28890842 TTGCAGCGGAGTAGACTGAAAACAGCAGATCTTCTCTTCCTGTACTGAAAGTGAAGTAGATCGAA
1 TTGCAGCGGAGCAGACTGAAAATAGCAGATCTTGTCTTCTTGTATTGGCAGCGAAGCAAATCGAA
* *
28890907 AACACCAGCCTTGCCTC
66 GACACTAGCCTTGCCTC
28890924 TCTTAGTTGG
Statistics
Matches: 141, Mismatches: 22, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
87 3 0.02
88 66 0.47
89 68 0.48
90 4 0.03
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (89 bp):
TTGCAGCGGAGCAGACTGAAAATAGCAGATCTTGTCTTCTTGTATTGGCAGCGAAGCAAATCGAA
GACACTAGCCTTGCCTCCCTGAGT
Found at i:28891226 original size:131 final size:130
Alignment explanation
Indices: 28890933--28891346 Score: 549
Period size: 131 Copynumber: 3.1 Consensus size: 130
28890923 CTCTTAGTTG
* *
28890933 GCAGTGGTGTAGGTTGAAGATTGTAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
1 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
** *
28890998 GGCAAATCTTATCTTCCCAAGGTAGCAGAGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAG
66 GGTGAATCTTATCTTCCCAAGGTAGTAGA-AAGCAGATTTAAGCCACCA-TCCTATCTCCCTGAG
*
28891063 TA
129 CA
* * ** * *
28891065 GCAATAGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTATAGCAAATCGAAGAC
1 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
* *
28891130 GGTGAATCTTATCTTCCCAAGATAGTAGAAAGCAGATTTTAGCCACCATTCCTATCTCCCTGAGC
66 GGTGAATCTTATCTTCCCAAGGTAGTAGAAAGCAGATTTAAGCCACCA-TCCTATCTCCCTGAGC
28891195 A
130 A
* *
28891196 GTAGTGGAGTAGGTTGAAGATTGTATATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
1 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
* * * * * *
28891261 GGTGACTCTTATCTTACCGAGGTAGTAGGGAAGCATATTTAAGCCACCAACCTTATCTCCCTGAA
66 GGTGAATCTTATCTTCCCAAGGTAGTA-GAAAGCAGATTTAAGCCACCATCC-TATCTCCCTG-A
**
28891326 GTT
128 GCA
*
28891329 GCAGTGGAGCAGGTTGAA
1 GCAGTGGAGTAGGTTGAA
28891347 ATTACCAATT
Statistics
Matches: 244, Mismatches: 35, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
131 116 0.48
132 110 0.45
133 18 0.07
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.26
Consensus pattern (130 bp):
GCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
GGTGAATCTTATCTTCCCAAGGTAGTAGAAAGCAGATTTAAGCCACCATCCTATCTCCCTGAGCA
Found at i:28891649 original size:14 final size:14
Alignment explanation
Indices: 28891630--28891660 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28891620 AGCTCAAATA
*
28891630 AAAATAATAAACCC
1 AAAATAATAAACAC
28891644 AAAATAATAAACAC
1 AAAATAATAAACAC
28891658 AAA
1 AAA
28891661 GTCTAAGTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.71, C:0.16, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAATAATAAACAC
Found at i:28891833 original size:22 final size:22
Alignment explanation
Indices: 28891773--28891830 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
28891763 AATCTTCAAG
28891773 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
28891792 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
28891814 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
28891831 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:28897092 original size:47 final size:47
Alignment explanation
Indices: 28897020--28897114 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
28897010 CACTTCTATG
*
28897020 GTGAGTTGTAAGTTGTGTTACAAGGTTTTGCACTGCTGGGAAAGAGA
1 GTGAGTTGTAAGTTGTGTTAAAAGGTTTTGCACTGCTGGGAAAGAGA
28897067 GTGAGTTGTAAGTTGTGTTAAAAGGTTTTGCACTGCTGGGAAAGAGA
1 GTGAGTTGTAAGTTGTGTTAAAAGGTTTTGCACTGCTGGGAAAGAGA
28897114 G
1 G
28897115 CATAACAATA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.26, C:0.07, G:0.35, T:0.32
Consensus pattern (47 bp):
GTGAGTTGTAAGTTGTGTTAAAAGGTTTTGCACTGCTGGGAAAGAGA
Found at i:28900971 original size:3 final size:3
Alignment explanation
Indices: 28900963--28901019 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
28900953 ATTTGACATT
* ** *
28900963 TTA TTA TTA TTA TTA TTA CTA CCA TTA TTAA TCA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
28901008 TTA CTTA TTA TT
1 TTA -TTA TTA TT
28901020 CTTGTTATAC
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
2 2 0.04
3 38 0.84
4 5 0.11
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:28903275 original size:52 final size:48
Alignment explanation
Indices: 28903197--28903295 Score: 117
Period size: 52 Copynumber: 2.0 Consensus size: 48
28903187 ATTGTCACCT
* *
28903197 TTGATTGATGTAGATAGGATTTTCCTTCCTTCTTAAGATGACTTTGAAATCC
1 TTGATTGATGAAGATAGGATATTCCTT-C-TC--AAGATGACTTTGAAATCC
* * *
28903249 TTGATTGATGAATATGGGATATTCCTTCTCAAGATGACTTTTAAATC
1 TTGATTGATGAAGATAGGATATTCCTTCTCAAGATGACTTTGAAATC
28903296 GTGTTCTGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
48 16 0.38
50 2 0.05
51 1 0.02
52 23 0.55
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.41
Consensus pattern (48 bp):
TTGATTGATGAAGATAGGATATTCCTTCTCAAGATGACTTTGAAATCC
Found at i:28914666 original size:20 final size:20
Alignment explanation
Indices: 28914637--28914676 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
28914627 TTCACCTCAT
*
28914637 GCATCGCATCATATGCATTA
1 GCATCACATCATATGCATTA
28914657 GCATCACATCATATGCATTA
1 GCATCACATCATATGCATTA
28914677 AAGACCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (20 bp):
GCATCACATCATATGCATTA
Found at i:28923221 original size:231 final size:231
Alignment explanation
Indices: 28922818--28923264 Score: 885
Period size: 231 Copynumber: 1.9 Consensus size: 231
28922808 TAGCAGTGCA
28922818 GTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCCAACATGGCAGTTGAACAAATTGAA
1 GTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCCAACATGGCAGTTGAACAAATTGAA
28922883 GATTACAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCT
66 GATTACAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCT
28922948 GAAGTTGCAGTAGAGTATATTGAAGCCAGTAATTCTATCTCCCAATACTGGTGGTGGAGTAGATC
131 GAAGTTGCAGTAGAGTATATTGAAGCCAGTAATTCTATCTCCCAATACTGGTGGTGGAGTAGATC
28923013 AAAGAAAGCAGATCTTGTCTTTTCCCTAACGATGCG
196 AAAGAAAGCAGATCTTGTCTTTTCCCTAACGATGCG
*
28923049 GTGGAACAGATTTAAGCTACGACGGCGGATCTGGTTTCCCCAACATGGCAGTTGAACAAATTGAA
1 GTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCCAACATGGCAGTTGAACAAATTGAA
28923114 GATTACAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCT
66 GATTACAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCT
28923179 GAAGTTGCAGTAGAGTATATTGAAGCCAGTAATTCTATCTCCCAATACTGGTGGTGGAGTAGATC
131 GAAGTTGCAGTAGAGTATATTGAAGCCAGTAATTCTATCTCCCAATACTGGTGGTGGAGTAGATC
28923244 AAAGAAAGCAGATCTTGTCTT
196 AAAGAAAGCAGATCTTGTCTT
28923265 CCCATACCGG
Statistics
Matches: 215, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
231 215 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (231 bp):
GTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCCAACATGGCAGTTGAACAAATTGAA
GATTACAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCT
GAAGTTGCAGTAGAGTATATTGAAGCCAGTAATTCTATCTCCCAATACTGGTGGTGGAGTAGATC
AAAGAAAGCAGATCTTGTCTTTTCCCTAACGATGCG
Found at i:28926570 original size:52 final size:48
Alignment explanation
Indices: 28926492--28926590 Score: 117
Period size: 52 Copynumber: 2.0 Consensus size: 48
28926482 ATTGTCACCT
* *
28926492 TTGATTGATGTAGATAGGATTTTCCTTCCTTCTTAAGATGACTTTGAAATCC
1 TTGATTGATGAAGATAGGATATTCCTT-C-TC--AAGATGACTTTGAAATCC
* * *
28926544 TTGATTGATGAATATGGGATATTCCTTCTCAAGATGACTTTTAAATC
1 TTGATTGATGAAGATAGGATATTCCTTCTCAAGATGACTTTGAAATC
28926591 GTGTTCTGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
48 16 0.38
50 2 0.05
51 1 0.02
52 23 0.55
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.41
Consensus pattern (48 bp):
TTGATTGATGAAGATAGGATATTCCTTCTCAAGATGACTTTGAAATCC
Found at i:28935168 original size:5 final size:5
Alignment explanation
Indices: 28935158--28935185 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
28935148 ATTCAAAAAG
28935158 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
28935186 CAATCACAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:28937777 original size:113 final size:113
Alignment explanation
Indices: 28937569--28937881 Score: 425
Period size: 113 Copynumber: 2.8 Consensus size: 113
28937559 TAAGCGCCGT
* *
28937569 AAAAAATGTTAACCAAAACGCATCGTTTGGTCTTGAGG-ATGTTAGAATTGGTGGCGCTTAA-GA
1 AAAAAATGTTAACCAAAACGCATCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGC-TAACGA
* * * * * **
28937632 AAAACGCCGCTATAGCATATTATCAGCGGCGTTTTGCACGAAACGCTGC
65 AAAAAGCCGCTATAGGATAATATTAGCGGCGTTTTGCACAAAACGCCAC
* *
28937681 AAAAAATGTTAACCAAAATGCATCGTTTGGTCTTGAGGTATATTAGAATTAGTGGTGCTAACGAA
1 AAAAAATGTTAACCAAAACGCATCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTAACGAA
* *
28937746 AAAAGCCGCTATAGGATAGTATTAGCGGCGTTTTGTACAAAACGCCAC
66 AAAAGCCGCTATAGGATAATATTAGCGGCGTTTTGCACAAAACGCCAC
* * * * *
28937794 AAAATATGTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCACT-TCCAA
1 AAAAAATGTTAACCAAAACGCATCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTAACGAA
28937858 AAAATGCCGCTATAGGATAATATT
66 AAAA-GCCGCTATAGGATAATATT
28937882 TACTTGAAAT
Statistics
Matches: 178, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
112 47 0.26
113 131 0.74
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.27
Consensus pattern (113 bp):
AAAAAATGTTAACCAAAACGCATCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTAACGAA
AAAAGCCGCTATAGGATAATATTAGCGGCGTTTTGCACAAAACGCCAC
Found at i:28939087 original size:21 final size:21
Alignment explanation
Indices: 28939061--28939153 Score: 132
Period size: 21 Copynumber: 4.4 Consensus size: 21
28939051 CTACAACTTA
* *
28939061 AAGCAGAGGCCGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
**
28939082 AAGCAGAGGCTACAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
*
28939103 AAGCAGAGGCGGCAGTGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
*
28939124 AAGCAGAGGCGGCAGCAAGAG
1 AAGCAGAGGCGGCAGCGAGAG
28939145 AAGCAGAGG
1 AAGCAGAGG
28939154 TTCAAAAGAA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 64 1.00
ACGTcount: A:0.35, C:0.18, G:0.44, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:28939712 original size:85 final size:84
Alignment explanation
Indices: 28939583--28939745 Score: 245
Period size: 85 Copynumber: 1.9 Consensus size: 84
28939573 TTTGTGAATC
* * *
28939583 AAGCGCCGCTAAAGAACGTGATTTTTAGCAGCGTTTTTCATTAAGCGCCGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCAGCGTTTTTCATTAAGCGCCGCTAAAGAACATGACC
28939648 TTTAGCGGCGTTTCTCTTT
66 TTTAGCGGCGTTTCTCTTT
* ** * *
28939667 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTTTTAAGCGTCGTTAAAGAACATGAC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCAGCGT-TTTTCATTAAGCGCCGCTAAAGAACATGAC
28939732 CTTTAGCGGCGTTT
65 CTTTAGCGGCGTTT
28939746 TTTTCGGTAA
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
84 31 0.44
85 39 0.56
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (84 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCAGCGTTTTTCATTAAGCGCCGCTAAAGAACATGACC
TTTAGCGGCGTTTCTCTTT
Found at i:28939749 original size:43 final size:42
Alignment explanation
Indices: 28939583--28939747 Score: 240
Period size: 42 Copynumber: 3.9 Consensus size: 42
28939573 TTTGTGAATC
* * * *
28939583 AAGCGCCGCTAAAGAACGTGATTTTTAGCAGCGTTTTTCATT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCTTT
*
28939625 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTCTCTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCTTT
*
28939667 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGT-TTTTCTTT
* * *
28939710 AAGCGTCGTTAAAGAACATGACCTTTAGCGGCGTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT
28939748 TTCGGTAAAC
Statistics
Matches: 112, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
42 75 0.67
43 37 0.33
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.33
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCTTT
Found at i:28941807 original size:27 final size:27
Alignment explanation
Indices: 28941769--28941825 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
28941759 AAATTTTTTT
*
28941769 AAATTGAGTTAAGT-GAAATAAAATTTA
1 AAATTGAGTTAAATCG-AATAAAATTTA
* *
28941796 AAATTGATTTAAATCGAGTAAAATTTA
1 AAATTGAGTTAAATCGAATAAAATTTA
28941823 AAA
1 AAA
28941826 ATTAAACATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.12, T:0.33
Consensus pattern (27 bp):
AAATTGAGTTAAATCGAATAAAATTTA
Found at i:28941992 original size:19 final size:19
Alignment explanation
Indices: 28941968--28942017 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
28941958 TTTTTAAAAA
28941968 TATAAATTTTGGAATTTTT
1 TATAAATTTTGGAATTTTT
* *
28941987 TATAAATATTTTGATTTTTT
1 TATAAAT-TTTGGAATTTTT
* *
28942007 TGTAATTTTTG
1 TATAAATTTTG
28942018 TTGAGGGAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (19 bp):
TATAAATTTTGGAATTTTT
Found at i:28944125 original size:12 final size:12
Alignment explanation
Indices: 28944108--28944132 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28944098 AGACCTGATA
28944108 AAATAAGAAAAC
1 AAATAAGAAAAC
28944120 AAATAAGAAAAC
1 AAATAAGAAAAC
28944132 A
1 A
28944133 TCTCCTGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.08, T:0.08
Consensus pattern (12 bp):
AAATAAGAAAAC
Found at i:28946782 original size:15 final size:15
Alignment explanation
Indices: 28946758--28946787 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28946748 ATCTAGATTT
28946758 GTAATCAAATTTTAA
1 GTAATCAAATTTTAA
*
28946773 GTAATTAAATTTTAA
1 GTAATCAAATTTTAA
28946788 AATCAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (15 bp):
GTAATCAAATTTTAA
Found at i:28949987 original size:23 final size:24
Alignment explanation
Indices: 28949956--28950010 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
28949946 ATTATTTGTG
* * *
28949956 AAAATAATATTT-ATCATTATTAT
1 AAAAAAATATTTAATCATAACTAT
*
28949979 AAAAAAATATTTAATTATAACTAT
1 AAAAAAATATTTAATCATAACTAT
28950003 AAAAAAAT
1 AAAAAAAT
28950011 TAAAAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 11 0.41
24 16 0.59
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (24 bp):
AAAAAAATATTTAATCATAACTAT
Found at i:28950285 original size:21 final size:21
Alignment explanation
Indices: 28950261--28950313 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
28950251 CATTGTTTCT
28950261 AATCTCACCGCTACAGTACCC
1 AATCTCACCGCTACAGTACCC
28950282 AATCTCACCGCTACAGTACCC
1 AATCTCACCGCTACAGTACCC
28950303 AATCTCACCGC
1 AATCTCACCGC
28950314 CACCTCTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.43, G:0.09, T:0.19
Consensus pattern (21 bp):
AATCTCACCGCTACAGTACCC
Found at i:28950665 original size:57 final size:58
Alignment explanation
Indices: 28950595--28950713 Score: 159
Period size: 57 Copynumber: 2.1 Consensus size: 58
28950585 TAGGCCTTGG
* *** *
28950595 TGTAGGAACAATTATCAAGTTCAGGGGGTAACTCG-TAAAAAAAGGTTCAAGCTCCAA
1 TGTAGGAAAAATTATCAAGTTCAGGACCTAACTCGAAAAAAAAAGGTTCAAGCTCCAA
* *
28950652 TGTAGGAAAAATTATCAAGTTCAGGACCTAACTTGAAAAAAAAAAGGTTCAGGCTCCAA
1 TGTAGGAAAAATTATCAAGTTCAGGACCTAACTCG-AAAAAAAAAGGTTCAAGCTCCAA
28950711 TGT
1 TGT
28950714 GAAAAAGGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
57 30 0.57
59 23 0.43
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (58 bp):
TGTAGGAAAAATTATCAAGTTCAGGACCTAACTCGAAAAAAAAAGGTTCAAGCTCCAA
Found at i:28966516 original size:26 final size:26
Alignment explanation
Indices: 28966467--28966519 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
28966457 TCAATTAATA
*
28966467 TTTATAATATAATTAATTTAATATAC
1 TTTATAATATAATTAATATAATATAC
*
28966493 TTTATAAT-TAATTTATAT-ATATA-
1 TTTATAATATAATTAATATAATATAC
28966516 TTTA
1 TTTA
28966520 AATTAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.16
24 5 0.20
25 8 0.32
26 8 0.32
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTATAATATAATTAATATAATATAC
Found at i:28966523 original size:22 final size:21
Alignment explanation
Indices: 28966474--28966525 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
28966464 ATATTTATAA
*
28966474 TATAATTAATTTAATATACTT
1 TATAATTAATTTAATATAATT
28966495 TATAATTAATTTATATATATATT
1 TATAATTAATTTA-ATATA-ATT
28966518 TA-AATTAA
1 TATAATTAA
28966526 ATCATTATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 13 0.46
22 11 0.39
23 4 0.14
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TATAATTAATTTAATATAATT
Found at i:28967443 original size:25 final size:25
Alignment explanation
Indices: 28967406--28967547 Score: 103
Period size: 25 Copynumber: 5.7 Consensus size: 25
28967396 TAAATAATAC
*
28967406 GCCATAAAGGCTTTTCACAAGATTA
1 GCCACAAAGGCTTTTCACAAGATTA
* * * *
28967431 ACCACAAAAGC-TTTC-CAGGTAATA
1 GCCACAAAGGCTTTTCACAAG-ATTA
**
28967455 CGCCACAAAGGCTTTTCACGGGATTA
1 -GCCACAAAGGCTTTTCACAAGATTA
* * * *
28967481 ACCACAAAAGATTTTCAGATA-A-TA
1 GCCACAAAGGCTTTTCACA-AGATTA
* *
28967505 CGCCACAAAGGCTTTTTATAAGATTA
1 -GCCACAAAGGCTTTTCACAAGATTA
28967531 GCCACAAAGGCTTTTCA
1 GCCACAAAGGCTTTTCA
28967548 GAGAATTCTC
Statistics
Matches: 88, Mismatches: 21, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
23 3 0.03
24 10 0.11
25 63 0.72
26 9 0.10
27 3 0.03
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (25 bp):
GCCACAAAGGCTTTTCACAAGATTA
Found at i:28967466 original size:50 final size:50
Alignment explanation
Indices: 28967399--28967549 Score: 203
Period size: 50 Copynumber: 3.0 Consensus size: 50
28967389 GTCTTTCTAA
*
28967399 ATAATACGCCATAAAGGCTTTTCACAAGATTAACCACAAAAGCTTTCCAG
1 ATAATACGCCACAAAGGCTTTTCACAAGATTAACCACAAAAGCTTTCCAG
* ** * *
28967449 GTAATACGCCACAAAGGCTTTTCACGGGATTAACCACAAAAGATTTTCAG
1 ATAATACGCCACAAAGGCTTTTCACAAGATTAACCACAAAAGCTTTCCAG
* * * * *
28967499 ATAATACGCCACAAAGGCTTTTTATAAGATTAGCCACAAAGGCTTTTCAG
1 ATAATACGCCACAAAGGCTTTTCACAAGATTAACCACAAAAGCTTTCCAG
28967549 A
1 A
28967550 GAATTCTCGA
Statistics
Matches: 87, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 87 1.00
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (50 bp):
ATAATACGCCACAAAGGCTTTTCACAAGATTAACCACAAAAGCTTTCCAG
Found at i:28970142 original size:16 final size:16
Alignment explanation
Indices: 28970105--28970146 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
28970095 TTAATCATAT
*
28970105 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
28970121 TT-AAATATATTATAA
1 TTAAAATATATTATAA
28970136 TTAAAATATAT
1 TTAAAATATAT
28970147 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:28970153 original size:14 final size:15
Alignment explanation
Indices: 28970114--28970155 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28970104 TTTAAACATA
*
28970114 ATTATTATTAAATAT
1 ATTATAATTAAATAT
28970129 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
28970143 A-TATAATTTAATA
1 ATTATAATTAAATA
28970156 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:28970652 original size:22 final size:21
Alignment explanation
Indices: 28970617--28971548 Score: 329
Period size: 19 Copynumber: 48.7 Consensus size: 21
28970607 AAAGGGTATC
* *
28970617 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
28970638 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
28970661 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28970680 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28970699 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28970718 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28970737 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28970756 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28970775 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28970794 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28970813 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28970832 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28970851 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28970870 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28970889 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28970908 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28970927 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28970946 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28970965 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28970984 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971003 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971022 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971041 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971060 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971079 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971098 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971117 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971136 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971155 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971174 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971193 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971212 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971231 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971250 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971269 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971288 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971307 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971326 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971345 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971364 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971383 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971402 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971421 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971440 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971459 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971478 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971497 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* * *
28971516 TATATAT--TATATCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28971535 TGCATATCATATCT
1 TACAAATCATATCT
28971549 AAGATTGCAT
Statistics
Matches: 808, Mismatches: 97, Indels: 12
0.88 0.11 0.01
Matches are distributed among these distances:
17 2 0.00
19 774 0.96
21 7 0.01
22 15 0.02
23 10 0.01
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:28970660 original size:23 final size:22
Alignment explanation
Indices: 28970617--28970674 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
28970607 AAAGGGTATC
* *
28970617 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
28970638 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
28970661 TGCATATCATATCT
1 TACAAATCATATCT
28970675 AAGATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:28970700 original size:38 final size:38
Alignment explanation
Indices: 28970653--28971554 Score: 1795
Period size: 38 Copynumber: 23.7 Consensus size: 38
28970643 AATCATATCT
28970653 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
28970691 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
28970729 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
28970767 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
28970805 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
28970843 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
28970881 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
28970919 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
28970957 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
28970995 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
28971033 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
28971071 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
28971109 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
28971147 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
28971185 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
28971223 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
28971261 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
28971299 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
28971337 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
28971375 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
28971413 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
28971451 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
*
28971489 TCTAAGATTGCATATCATATCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
28971527 TCTAAGATTGCATATCATATCTAAGATT
1 TCTAAGATTGCATATCATATCTAAGATT
28971555 GCATATCCCT
Statistics
Matches: 863, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 863 1.00
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (38 bp):
TCTAAGATTGCATATCATATCTAAGATTATATATCATA
Found at i:28972112 original size:132 final size:132
Alignment explanation
Indices: 28971890--28974300 Score: 4342
Period size: 132 Copynumber: 18.3 Consensus size: 132
28971880 TAGGACTTAC
* * * * *
28971890 AATCTTCAACCTATTCCACTGCTGACCAGGG-AGATATG-ATTACTGGCTTCAATGTACTCTACT
1 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAG-TA-GAATTACTGGCTTCAATGTACTCCACT
* * *
28971953 GTAACCACAGGGAGGTAAAATCTGTCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGAC
64 GTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGAC
28972018 CTGA
129 CTGA
* * *
28972022 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGAACTCCACTAT
1 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
* * *
28972087 AACCACAGGGAGGTAAAATCTGTCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGACCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
28972152 GA
131 GA
28972154 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
* *
28972219 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTACTTCACTACTGCTTAGGGAGATAAGACCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
28972284 GA
131 GA
28972286 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
28972351 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
28972416 GA
131 GA
28972418 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
28972483 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
28972548 GA
131 GA
28972550 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
28972615 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
28972680 GA
131 GA
28972682 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
28972747 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
28972812 GA
131 GA
28972814 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
28972879 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
28972944 GA
131 GA
28972946 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
* *
28973011 AACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGTTTAGGGAGATAAGACCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
*
28973076 GG
131 GA
* * * *
28973078 AATCTTCAATCTATTCCACTGTTGTCCAGGAAAGTAGAATTACTAGCTTCAATGTACTCCACTAT
1 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
* * *
28973143 AACCACAGGGAGGTAAAATCTGTCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGACCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
28973208 GA
131 GA
28973210 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
28973275 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
28973340 GA
131 GA
28973342 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
* *
28973407 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTACTTCACTACTGCTTAGGGAGATAAGACCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
28973472 GA
131 GA
28973474 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
*
28973539 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
28973604 GA
131 GA
*
28973606 AATCTTCAATCTATTCCACTGTTGT-TCAGGGAAGTAGAATTATTGGCTTCAATGTACTCCACTG
1 AATCTTCAATCTATTCCACTGTTGTCT-AGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTG
*
28973670 TAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATC
65 TAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACC
28973735 TGA
130 TGA
* * * * *
28973738 AATCTTTAATCTATTCCACTATTGCCCAGGGAAATAGAATTACTGGCTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
* *
28973803 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTACTTCACTACTGCTTAGGGAGATAAGACCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
28973868 GA
131 GA
28973870 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
* *
28973935 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTACTTCACTACTGCTTAGGGAGATAAGACCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
28974000 GA
131 GA
28974002 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
* *
28974067 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTACTTCACTACTGCTTAGGGAGATAAGACCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
28974132 GA
131 GA
* * *
28974134 AATCTTCAATCTATTCCACTGTTGTCCAAGGAAGTAGAATTACTGGCTTTAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
** *
28974199 AACCACATTGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
28974264 GA
131 GA
28974266 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGT
1 AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGT
28974301 GCTCCACTAC
Statistics
Matches: 2213, Mismatches: 62, Indels: 8
0.97 0.03 0.00
Matches are distributed among these distances:
131 2 0.00
132 2209 1.00
133 2 0.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (132 bp):
AATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
GA
Found at i:28973039 original size:88 final size:88
Alignment explanation
Indices: 28972947--28973318 Score: 215
Period size: 88 Copynumber: 4.2 Consensus size: 88
28972937 AAGACCTGAA
* * *
28972947 ATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTA
1 ATCTTCAATCTACTCCACTATTGTCTAGGGAAGTAGAATTACTGGCTTCAATCTACTCCACTGTA
28973012 ACCACAGGGAGGTAAAATCTGCC
66 ACCACAGGGAGGTAAAATCTGCC
* * * * * * *
28973035 ATCTTCGATCTGCTCCACTACTGTTTAGGG-AG-ATAA-GACCTGGAATCTTCAATCTATTCCAC
1 ATCTTCAATCTACTCCACTATTGTCTAGGGAAGTAGAATTA-CTGG---CTTCAATCTACTCCAC
*** * * * * *
28973097 TGTTGTC-CAGGAAAGTAGAAT-TACT
62 TGTAACCACAGGGAGGTAAAATCTGCC
* * *** * * * * *
28973122 AGCTTCAATGTACTCCACTATAACCACAGGGAGGTA-AAAT-CTGTCATCTTCGATCTACTCCAC
1 ATCTTCAATCTACTCCACTATTGTC-TAGGGAAGTAGAATTACTG---GCTTCAATCTACTCCAC
** * * * **
28973185 --T-ACTGCTTAGGGAGATAAGACCTGAA
62 TGTAAC--CACAGGGAGGTAAAATCTGCC
* * *
28973211 ATCTTCAATCTATTCCACTGTTGTCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTA
1 ATCTTCAATCTACTCCACTATTGTCTAGGGAAGTAGAATTACTGGCTTCAATCTACTCCACTGTA
*
28973276 ACCACAGGGAGGTAAAATCCGCC
66 ACCACAGGGAGGTAAAATCTGCC
* *
28973299 ATCTTCGATCTGCTCCACTA
1 ATCTTCAATCTACTCCACTA
28973319 CTGCTTAGGG
Statistics
Matches: 194, Mismatches: 70, Indels: 40
0.64 0.23 0.13
Matches are distributed among these distances:
85 1 0.01
86 8 0.04
87 35 0.18
88 100 0.52
89 44 0.23
90 6 0.03
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (88 bp):
ATCTTCAATCTACTCCACTATTGTCTAGGGAAGTAGAATTACTGGCTTCAATCTACTCCACTGTA
ACCACAGGGAGGTAAAATCTGCC
Found at i:28973900 original size:44 final size:45
Alignment explanation
Indices: 28973852--28974159 Score: 108
Period size: 44 Copynumber: 7.0 Consensus size: 45
28973842 CACTACTGCT
28973852 TAGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTC-
1 TAGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCA
* * * * * ***
28973896 TAGGGAAGTAGAATTA-CTG---GCTTCAATGTACTCCACTGTAACCA
1 TAGGG-AG-ATAA-GACCTGAAATCTTCAATCTATTCCACTGTTGTCA
* * * ** * ** *
28973940 CAGGGAGGTAAAATCC-GCCATCTTCGATCTACTT-CACTACTG-CT
1 TAGGGAGATAAGA-CCTGAAATCTTCAATCTA-TTCCACTGTTGTCA
28973984 TAGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTC-
1 TAGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCA
* * * * * ***
28974028 TAGGGAAGTAGAATTA-CTG---GCTTCAATGTACTCCACTGTAACCA
1 TAGGG-AG-ATAA-GACCTGAAATCTTCAATCTATTCCACTGTTGTCA
* * * ** * ** *
28974072 CAGGGAGGTAAAATCC-GCCATCTTCGATCTACTT-CACTACTG-CT
1 TAGGGAGATAAGA-CCTGAAATCTTCAATCTA-TTCCACTGTTGTCA
28974116 TAGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTC
1 TAGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTC
28974160 CAAGGAAGTA
Statistics
Matches: 180, Mismatches: 58, Indels: 51
0.62 0.20 0.18
Matches are distributed among these distances:
41 2 0.01
42 6 0.03
43 50 0.28
44 76 0.42
45 30 0.17
46 14 0.08
47 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (45 bp):
TAGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCA
Found at i:28979781 original size:4 final size:4
Alignment explanation
Indices: 28979774--28979807 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
28979764 ATTTATTTAT
*
28979774 ATAA ATAA ATGA ATAA ATAAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA AT-AA ATAA ATAA ATAA A
28979808 ATTCAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:28979817 original size:13 final size:13
Alignment explanation
Indices: 28979774--28979809 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
28979764 ATTTATTTAT
*
28979774 ATAAAT-AAATGA
1 ATAAATAAAATAA
28979786 ATAAATAAAATAA
1 ATAAATAAAATAA
28979799 ATAAATAAAAT
1 ATAAATAAAAT
28979810 TCAAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 6 0.27
13 16 0.73
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (13 bp):
ATAAATAAAATAA
Found at i:28989651 original size:64 final size:64
Alignment explanation
Indices: 28989547--28989675 Score: 215
Period size: 64 Copynumber: 2.0 Consensus size: 64
28989537 GCAAGAAGCG
28989547 TAAGACTATTGCAGGGGTTGTGCACGTCAGTTCTGTGAGTGAGAAAGAAGGAATAATGAACAAT
1 TAAGACTATTGCAGGGGTTGTGCACGTCAGTTCTGTGAGTGAGAAAGAAGGAATAATGAACAAT
* * *
28989611 TAAGACTATTGCAGGGGTTGTGCGCGTCAGTTCT-TCGAGTGAGAAGGAAGGAATAATTAACAAT
1 TAAGACTATTGCAGGGGTTGTGCACGTCAGTTCTGT-GAGTGAGAAAGAAGGAATAATGAACAAT
28989675 T
1 T
28989676 GTAGCTATAT
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 1 0.02
64 60 0.98
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (64 bp):
TAAGACTATTGCAGGGGTTGTGCACGTCAGTTCTGTGAGTGAGAAAGAAGGAATAATGAACAAT
Found at i:28990724 original size:140 final size:140
Alignment explanation
Indices: 28990472--28990736 Score: 521
Period size: 140 Copynumber: 1.9 Consensus size: 140
28990462 GGGTAGATAT
28990472 GGACAAGCTGGGTTTTGAAGTGATTTTTCCTTCTAGCAATGCGTGTGACTCATTTATGTCCACTT
1 GGACAAGCTGGGTTTTGAAGTGATTTTTCCTTCTAGCAATGCGTGTGACTCATTTATGTCCACTT
*
28990537 GGAAGAACTCTTCAGATTTTTACTTAGAAGAGGACCTAGTTGGGAATGAGGATGTGGCCCTTTTG
66 GGAAGAACTCTTCAAATTTTTACTTAGAAGAGGACCTAGTTGGGAATGAGGATGTGGCCCTTTTG
28990602 CTGCGAATGA
131 CTGCGAATGA
28990612 GGACAAGCTGGGTTTTGAAGTGATTTTTCCTTCTAGCAATGCGTGTGACTCATTTATGTCCACTT
1 GGACAAGCTGGGTTTTGAAGTGATTTTTCCTTCTAGCAATGCGTGTGACTCATTTATGTCCACTT
28990677 GGAAGAACTCTTCAAATTTTTACTTAGAAGAGGACCTAGTTGGGAATGAGGATGTGGCCC
66 GGAAGAACTCTTCAAATTTTTACTTAGAAGAGGACCTAGTTGGGAATGAGGATGTGGCCC
28990737 CTTCTAATAA
Statistics
Matches: 124, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 124 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (140 bp):
GGACAAGCTGGGTTTTGAAGTGATTTTTCCTTCTAGCAATGCGTGTGACTCATTTATGTCCACTT
GGAAGAACTCTTCAAATTTTTACTTAGAAGAGGACCTAGTTGGGAATGAGGATGTGGCCCTTTTG
CTGCGAATGA
Found at i:28991098 original size:58 final size:58
Alignment explanation
Indices: 28991003--28991226 Score: 256
Period size: 58 Copynumber: 3.9 Consensus size: 58
28990993 TGTTAGCTGA
* *
28991003 GGATATGAATCTGTGAGCTATTTTATACTTGTAAAAATTTTGAAAGATAATCAACTGG
1 GGATGTGAATCTGTGAGCTATTTTATACTTGTGAAAATTTTGAAAGATAATCAACTGG
*
28991061 GGATGTGAATCTGTGAGCTATTTTATACTTGTGAAAATTTTGAAAGATAATCAATTGG
1 GGATGTGAATCTGTGAGCTATTTTATACTTGTGAAAATTTTGAAAGATAATCAACTGG
* * ** * * * *
28991119 GGATGTGAATTTGAGAAATGTTTTATACTTGTGAAAACTTTGAAACATAA-CATATCT-A
1 GGATGTGAATCTGTGAGCTATTTTATACTTGTGAAAATTTTGAAAGATAATCA-A-CTGG
* * * * *
28991177 AGAGTTTGAATCTGCGAGCTGTTTTATACTTGTGAAAATTTT-AAAAATAA
1 GGA-TGTGAATCTGTGAGCTATTTTATACTTGTGAAAATTTTGAAAGATAA
28991227 CATAGCTGAG
Statistics
Matches: 143, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
57 2 0.01
58 108 0.76
59 33 0.23
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37
Consensus pattern (58 bp):
GGATGTGAATCTGTGAGCTATTTTATACTTGTGAAAATTTTGAAAGATAATCAACTGG
Found at i:28991565 original size:69 final size:69
Alignment explanation
Indices: 28991289--28991574 Score: 245
Period size: 69 Copynumber: 4.1 Consensus size: 69
28991279 ATCCTGCCAA
* ** * * *
28991289 CCTTAGTATGACAGTTGGGAGTTTTACTCTCTTTAATTGTGTTAGAGGTTGCGACTCTTTGCCTA
1 CCTTAGTATGACAGTTGGGAGCTTTACTCTCACTAACTGTGTTAGAGGCTGCGACTCTTCGCCTA
28991354 CGAG
66 CGAG
* * * * * * * *
28991358 CCTAAATATGATAGTTGGGAGTTTTACTCTCATTAACTGTGTTAGAGTCTGCTG-CCCTTCGCAT
1 CCTTAGTATGACAGTTGGGAGCTTTACTCTCACTAACTGTGTTAGAGGCTGC-GACTCTTCGCCT
*
28991422 GCGAG
65 ACGAG
* * * * * ** * * * * *
28991427 CCTCAATATTACAGCTGGGAGCTCTGTTCTCGCTAACTGTGTTGGAGGTTGCGACTTTTCACCTA
1 CCTTAGTATGACAGTTGGGAGCTTTACTCTCACTAACTGTGTTAGAGGCTGCGACTCTTCGCCTA
28991492 CGAG
66 CGAG
* * *
28991496 CCTTAGTATGACAGTTGGGAGCTTTGCTCTCACTAACTGT-TTTGAAGGCTGCGGCTCTTCG-CT
1 CCTTAGTATGACAGTTGGGAGCTTTACTCTCACTAACTGTGTTAG-AGGCTGCGACTCTTCGCCT
*
28991559 CGCGAG
65 -ACGAG
28991565 CCTTAGTATG
1 CCTTAGTATG
28991575 GCATAAATGT
Statistics
Matches: 171, Mismatches: 42, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
68 6 0.04
69 164 0.96
70 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.35
Consensus pattern (69 bp):
CCTTAGTATGACAGTTGGGAGCTTTACTCTCACTAACTGTGTTAGAGGCTGCGACTCTTCGCCTA
CGAG
Found at i:29003368 original size:2 final size:2
Alignment explanation
Indices: 29003361--29003386 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29003351 GAGTTTCTAT
29003361 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
29003387 AAAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:29004465 original size:2 final size:2
Alignment explanation
Indices: 29004458--29004495 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
29004448 AAGCTACCCC
* *
29004458 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29004496 GAAATAAGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:29007281 original size:17 final size:17
Alignment explanation
Indices: 29007245--29007286 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
29007235 GTAAAGTATG
*
29007245 ATAAAAGAAAAGGGAAA
1 ATAAAAGAAAAGAGAAA
29007262 ATAAAAGAAAA-AGAATA
1 ATAAAAGAAAAGAGAA-A
29007279 ATATAAAG
1 ATA-AAAG
29007287 GGAAGAGAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 15 0.68
18 4 0.18
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (17 bp):
ATAAAAGAAAAGAGAAA
Found at i:29009579 original size:19 final size:22
Alignment explanation
Indices: 29009533--29009581 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
29009523 AAAAAGAACT
29009533 TATTTTCTGTTGACTTGTAAGTC
1 TATTTTCTGTTGAC-TGTAAGTC
29009556 T-TTTTCTGTTGA-T-TAAG-C
1 TATTTTCTGTTGACTGTAAGTC
29009574 TATTTTCT
1 TATTTTCT
29009582 ATGAAGCTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.08
19 10 0.40
20 1 0.04
22 11 0.44
23 1 0.04
ACGTcount: A:0.16, C:0.12, G:0.14, T:0.57
Consensus pattern (22 bp):
TATTTTCTGTTGACTGTAAGTC
Found at i:29010156 original size:23 final size:23
Alignment explanation
Indices: 29010130--29010177 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
29010120 GCCAATATAT
*
29010130 AAATCAAATC-TCTTAAGATTACA
1 AAATCAAATCTTC-TAAAATTACA
29010153 AAATCAAATCTTCTAAAATTACA
1 AAATCAAATCTTCTAAAATTACA
29010176 AA
1 AA
29010178 TCTTCCAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.29
Consensus pattern (23 bp):
AAATCAAATCTTCTAAAATTACA
Found at i:29012638 original size:24 final size:24
Alignment explanation
Indices: 29012606--29012666 Score: 108
Period size: 24 Copynumber: 2.6 Consensus size: 24
29012596 CACATTGTAG
29012606 AATTGAGAAATTAAGTATAAATGA
1 AATTGAGAAATTAAGTATAAATGA
29012630 AATTGAGAAATTAAGTATAAATGA
1 AATTGAGAAATTAAGTATAAATGA
29012654 AATT--GAAATTAAG
1 AATTGAGAAATTAAG
29012667 GTGGATAGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
22 9 0.24
24 28 0.76
ACGTcount: A:0.54, C:0.00, G:0.16, T:0.30
Consensus pattern (24 bp):
AATTGAGAAATTAAGTATAAATGA
Found at i:29014966 original size:68 final size:68
Alignment explanation
Indices: 29014852--29014993 Score: 203
Period size: 68 Copynumber: 2.1 Consensus size: 68
29014842 CTTAGAATTG
* * * *
29014852 GAAGTCCGTCAAGACAGTAAACATGAGATCATATTGTGTGAGACCATAGTTAGGCTATGACAGCA
1 GAAGTCCGCCAAGACAGTAAACATGAGATCATATTGTATAAGACCATAGATAGGCTATGACAGCA
29014917 TAT
66 TAT
* * * * *
29014920 GAAGTCCGCCAGGACAGTAAACATGGGATCATATTGTATAATACCATAGATGGGCTATGGCAGCA
1 GAAGTCCGCCAAGACAGTAAACATGAGATCATATTGTATAAGACCATAGATAGGCTATGACAGCA
29014985 TAT
66 TAT
29014988 GAAGTC
1 GAAGTC
29014994 TGCTAAGATA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.24
Consensus pattern (68 bp):
GAAGTCCGCCAAGACAGTAAACATGAGATCATATTGTATAAGACCATAGATAGGCTATGACAGCA
TAT
Found at i:29021237 original size:25 final size:24
Alignment explanation
Indices: 29021187--29021239 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
29021177 AAGTTTAAGC
* *
29021187 GAGCCATATCAGGAAGCTTATTAA
1 GAGCCATATCAGGAAGCTCATAAA
* *
29021211 GAGCCTATATCGGGACGCTCATAAA
1 GAGCC-ATATCAGGAAGCTCATAAA
29021236 GAGC
1 GAGC
29021240 TATGGTATGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.21
Consensus pattern (24 bp):
GAGCCATATCAGGAAGCTCATAAA
Found at i:29021325 original size:64 final size:64
Alignment explanation
Indices: 29021224--29021376 Score: 243
Period size: 64 Copynumber: 2.4 Consensus size: 64
29021214 CCTATATCGG
* * *
29021224 GACGCTCATAAAGAGCTATGGTATGTCCACATTATATGCAAGATCCATACCAATCATATAACAA
1 GACGCTCACAAAGAGCTGTAGTATGTCCACATTATATGCAAGATCCATACCAATCATATAACAA
* * *
29021288 GACGCTCACAAAGAGCTGCAGTATGTCCACATTATATGCAAGATTCATACCAATCATATAACAG
1 GACGCTCACAAAGAGCTGTAGTATGTCCACATTATATGCAAGATCCATACCAATCATATAACAA
*
29021352 GATGCTCACAAAGAGCTGTAGTATG
1 GACGCTCACAAAGAGCTGTAGTATG
29021377 ATCGCAACAC
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 81 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (64 bp):
GACGCTCACAAAGAGCTGTAGTATGTCCACATTATATGCAAGATCCATACCAATCATATAACAA
Found at i:29025823 original size:13 final size:13
Alignment explanation
Indices: 29025799--29025833 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
29025789 AAATAAATAA
*
29025799 AAATAAACAAAAC
1 AAATAAAAAAAAC
*
29025812 AATTAAAAAAAAC
1 AAATAAAAAAAAC
29025825 AAATAAAAA
1 AAATAAAAA
29025834 GGGGTAAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.80, C:0.09, G:0.00, T:0.11
Consensus pattern (13 bp):
AAATAAAAAAAAC
Found at i:29031006 original size:19 final size:19
Alignment explanation
Indices: 29030982--29031021 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
29030972 CCGTTAGTTA
29030982 ATGTTAGTTAAGTCTGTTG
1 ATGTTAGTTAAGTCTGTTG
29031001 ATGTTAGTTAAGTCTGTTG
1 ATGTTAGTTAAGTCTGTTG
29031020 AT
1 AT
29031022 TTGGATTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.47
Consensus pattern (19 bp):
ATGTTAGTTAAGTCTGTTG
Found at i:29035462 original size:10 final size:10
Alignment explanation
Indices: 29035434--29035491 Score: 57
Period size: 10 Copynumber: 5.8 Consensus size: 10
29035424 TAGTTAGCTA
*
29035434 TTAGTTAGTCG
1 TTAGTTAAT-G
29035445 TTAGTTAATG
1 TTAGTTAATG
*
29035455 TTAATTAATG
1 TTAGTTAATG
29035465 TTAGTTAA-G
1 TTAGTTAATG
*
29035474 TCT-GTTGATG
1 T-TAGTTAATG
29035484 TTAGTTAA
1 TTAGTTAA
29035492 GTCTGTTGAC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
9 7 0.18
10 24 0.62
11 8 0.21
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.48
Consensus pattern (10 bp):
TTAGTTAATG
Found at i:29035486 original size:19 final size:19
Alignment explanation
Indices: 29035462--29035500 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
29035452 ATGTTAATTA
29035462 ATGTTAGTTAAGTCTGTTG
1 ATGTTAGTTAAGTCTGTTG
29035481 ATGTTAGTTAAGTCTGTTG
1 ATGTTAGTTAAGTCTGTTG
29035500 A
1 A
29035501 CTTGGATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.05, G:0.26, T:0.46
Consensus pattern (19 bp):
ATGTTAGTTAAGTCTGTTG
Found at i:29037159 original size:24 final size:24
Alignment explanation
Indices: 29037123--29037185 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
29037113 TGGTATAGGA
* * *
29037123 GTCAAAAATTGTATTTGCAGAAAT
1 GTCACAAACTGTATTTACAGAAAT
29037147 GT-AGCAAACTGTATTTACAGAAAT
1 GTCA-CAAACTGTATTTACAGAAAT
*
29037171 GTCACAAATTGTATT
1 GTCACAAACTGTATT
29037186 CTAGAATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 1 0.03
24 31 0.94
25 1 0.03
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (24 bp):
GTCACAAACTGTATTTACAGAAAT
Found at i:29037372 original size:54 final size:54
Alignment explanation
Indices: 29037306--29037675 Score: 390
Period size: 54 Copynumber: 6.9 Consensus size: 54
29037296 GTAGTCCTTA
* * ** *
29037306 AGATTC-TAAAAATCTTGTATGTAGAAGGTCGTGATCGTAAATCAGTGGACCATG
1 AGATTCGT-AAAATCTTGAAAGTAGAAGGTCGTGATCGTAAATCAGCAGACCGTG
* * *
29037360 AGATTCGTAAAATCTTGAAAGTAGAAGGTCGTGATCGTAACTTAACAGACCGTG
1 AGATTCGTAAAATCTTGAAAGTAGAAGGTCGTGATCGTAAATCAGCAGACCGTG
** ** * * * *
29037414 AGATTCACAAAATCTCAAAAATAAAAGGTCGTGATTGTAAATCAGTAGACCGTG
1 AGATTCGTAAAATCTTGAAAGTAGAAGGTCGTGATCGTAAATCAGCAGACCGTG
* * * *
29037468 AGATTTGTAAAATCTCGAAAGTAAAAGGTCGTGATCATAAATC-G-ACGAACCGTG
1 AGATTCGTAAAATCTTGAAAGTAGAAGGTCGTGATCGTAAATCAGCA-G-ACCGTG
* * * * *
29037522 AGATTTGTAAAATCTCGAAAATAGAAGGTC-TGATCATAAATCAGCAGACTGTG
1 AGATTCGTAAAATCTTGAAAGTAGAAGGTCGTGATCGTAAATCAGCAGACCGTG
* * * **
29037575 AGATTCGTAAAATCTTAAAAATAGAAGGTCGTGATTGTAAATCAGCAGACCAAG
1 AGATTCGTAAAATCTTGAAAGTAGAAGGTCGTGATCGTAAATCAGCAGACCGTG
*
29037629 AAATTCGTAAAAT-TTCGAAAGTAGAAGGTCGTGATCGTAAATCAGCA
1 AGATTCGTAAAATCTT-GAAAGTAGAAGGTCGTGATCGTAAATCAGCA
29037676 TAACAACCCA
Statistics
Matches: 268, Mismatches: 41, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
52 1 0.00
53 48 0.18
54 217 0.81
55 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.26
Consensus pattern (54 bp):
AGATTCGTAAAATCTTGAAAGTAGAAGGTCGTGATCGTAAATCAGCAGACCGTG
Found at i:29037619 original size:161 final size:162
Alignment explanation
Indices: 29037330--29037674 Score: 460
Period size: 161 Copynumber: 2.1 Consensus size: 162
29037320 TTGTATGTAG
* * * *
29037330 AAGGTCGTGATCGTAAATCAGTGGACCATGAGATTCGTAAAATCTTGAAAGTAGAAGGTCGTGAT
1 AAGGTCGTGATCGTAAATCAGCGAACCATGAGATTCGTAAAATCTCGAAAATAGAAGGTCGTGAT
* * * *
29037395 CGTAACTTAACAGACCGTGAGATTCACAAAATCTCAAAAATAAAAGGTCGTGATTGTAAATCAGT
66 CATAAATCAACAGACCGTGAGATTCACAAAATCTCAAAAATAAAAGGTCGTGATTGTAAATCAGC
** * *
29037460 AGACCGTGAGATTTGTAAAATCTCGAAAGTAA
131 AGACCAAGAAATTCGTAAAATCTCGAAAGTAA
* * *
29037492 AAGGTCGTGATCATAAATC-GACGAACCGTGAGATTTGTAAAATCTCGAAAATAGAAGGTC-TGA
1 AAGGTCGTGATCGTAAATCAG-CGAACCATGAGATTCGTAAAATCTCGAAAATAGAAGGTCGTGA
* * ** * *
29037555 TCATAAATCAGCAGACTGTGAGATTCGTAAAATCTTAAAAATAGAAGGTCGTGATTGTAAATCAG
65 TCATAAATCAACAGACCGTGAGATTCACAAAATCTCAAAAATAAAAGGTCGTGATTGTAAATCAG
* *
29037620 CAGACCAAGAAATTCGTAAAATTTCGAAAGTAG
130 CAGACCAAGAAATTCGTAAAATCTCGAAAGTAA
29037653 AAGGTCGTGATCGTAAATCAGC
1 AAGGTCGTGATCGTAAATCAGC
29037675 ATAACAACCC
Statistics
Matches: 157, Mismatches: 24, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
161 105 0.67
162 52 0.33
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (162 bp):
AAGGTCGTGATCGTAAATCAGCGAACCATGAGATTCGTAAAATCTCGAAAATAGAAGGTCGTGAT
CATAAATCAACAGACCGTGAGATTCACAAAATCTCAAAAATAAAAGGTCGTGATTGTAAATCAGC
AGACCAAGAAATTCGTAAAATCTCGAAAGTAA
Found at i:29046617 original size:23 final size:24
Alignment explanation
Indices: 29046569--29046617 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
29046559 CATGAGTAAA
* * *
29046569 AAATGTTGCGAACTGTATTTATAG
1 AAATGTCGCAAACTATATTTATAG
29046593 AAATGTCGCAAACTATA-TTATAG
1 AAATGTCGCAAACTATATTTATAG
29046616 AA
1 AA
29046618 TATTGTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (24 bp):
AAATGTCGCAAACTATATTTATAG
Found at i:29046679 original size:23 final size:22
Alignment explanation
Indices: 29046649--29046748 Score: 85
Period size: 22 Copynumber: 4.4 Consensus size: 22
29046639 AAATGTCACA
*
29046649 AATTGTATTGTAGAATTATTGCG
1 AATTGTATTGTAGAA-TATCGCG
* **
29046672 AATTGTATTGTAGAATACCATG
1 AATTGTATTGTAGAATATCGCG
*
29046694 AACTGTATT-TACAGAATTATCGCG
1 AATTGTATTGT--AGAA-TATCGCG
* *
29046718 AATTGTATTATAGAATATTGCG
1 AATTGTATTGTAGAATATCGCG
*
29046740 AACTGTATT
1 AATTGTATT
29046749 TACATAAATG
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
21 1 0.02
22 25 0.40
23 23 0.37
24 12 0.19
25 1 0.02
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (22 bp):
AATTGTATTGTAGAATATCGCG
Found at i:29046719 original size:46 final size:46
Alignment explanation
Indices: 29046660--29046752 Score: 132
Period size: 46 Copynumber: 2.0 Consensus size: 46
29046650 ATTGTATTGT
* * *
29046660 AGAATTATTGCGAATTGTATTGTAGAATACCATGAACTGTATTTAC
1 AGAATTATCGCGAATTGTATTATAGAATACCACGAACTGTATTTAC
***
29046706 AGAATTATCGCGAATTGTATTATAGAATATTGCGAACTGTATTTAC
1 AGAATTATCGCGAATTGTATTATAGAATACCACGAACTGTATTTAC
29046752 A
1 A
29046753 TAAATGCTGC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (46 bp):
AGAATTATCGCGAATTGTATTATAGAATACCACGAACTGTATTTAC
Found at i:29046746 original size:22 final size:23
Alignment explanation
Indices: 29046652--29046748 Score: 81
Period size: 23 Copynumber: 4.3 Consensus size: 23
29046642 TGTCACAAAT
* * *
29046652 TGTATTGTAGAATTATTGCGAAT
1 TGTATTATAGAATTATCGCGAAC
* * **
29046675 TGTATTGTAGAA-TACCATGAAC
1 TGTATTATAGAATTATCGCGAAC
* *
29046697 TGTATTTACAGAATTATCGCGAAT
1 TGTA-TTATAGAATTATCGCGAAC
*
29046721 TGTATTATAGAA-TATTGCGAAC
1 TGTATTATAGAATTATCGCGAAC
29046743 TGTATT
1 TGTATT
29046749 TACATAAATG
Statistics
Matches: 58, Mismatches: 14, Indels: 5
0.75 0.18 0.06
Matches are distributed among these distances:
22 23 0.40
23 25 0.43
24 10 0.17
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (23 bp):
TGTATTATAGAATTATCGCGAAC
Found at i:29046765 original size:46 final size:46
Alignment explanation
Indices: 29046660--29046770 Score: 120
Period size: 46 Copynumber: 2.4 Consensus size: 46
29046650 ATTGTATTGT
* *
29046660 AGAATTAT-TGCGAATTGTATTGTAGAATACCATGAACTGTATTTAC
1 AGAA-TATCTGCGAATTGTATTATAGAATACCACGAACTGTATTTAC
***
29046706 AGAATTATC-GCGAATTGTATTATAGAATATTGCGAACTGTATTTAC
1 AGAA-TATCTGCGAATTGTATTATAGAATACCACGAACTGTATTTAC
*
29046752 ATAA-ATGCTGCGAATTGTA
1 AGAATAT-CTGCGAATTGTA
29046771 GTCCATAAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
44 2 0.04
45 1 0.02
46 53 0.95
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (46 bp):
AGAATATCTGCGAATTGTATTATAGAATACCACGAACTGTATTTAC
Found at i:29046844 original size:54 final size:54
Alignment explanation
Indices: 29046798--29047147 Score: 380
Period size: 54 Copynumber: 6.5 Consensus size: 54
29046788 AATCTTGTAT
* * * *
29046798 GTAAAAGGTCTTGATCGTAAATCAGCGGACCATGAGATTCGTAAAATCTTGAAA
1 GTAAAAGGTCGTGATCGTAAATCAGCAGACCGTGAGATTCGTAAAATCTCGAAA
* * *
29046852 GTAAAAGGTCGTGATCGTAAATCAGCAAACCGTGAGATTCGCAAAATCTCAAAA
1 GTAAAAGGTCGTGATCGTAAATCAGCAGACCGTGAGATTCGTAAAATCTCGAAA
* * *
29046906 GTAGAAGGTCGTGATTGTAAATCAGTAGACCGTGAGATTCGTAAAATCTCGAAA
1 GTAAAAGGTCGTGATCGTAAATCAGCAGACCGTGAGATTCGTAAAATCTCGAAA
* * *
29046960 GTAAAAGGTCGTGATCATAAATCAACGGACCGTGAGATTCGTAAAATCTCGAAA
1 GTAAAAGGTCGTGATCGTAAATCAGCAGACCGTGAGATTCGTAAAATCTCGAAA
* * * * * * *
29047014 GTAGAAGGT-TTGATCATAAATCAACAGACTGTGAGATTAGTAAAATCTCAAAA
1 GTAAAAGGTCGTGATCGTAAATCAGCAGACCGTGAGATTCGTAAAATCTCGAAA
* * * * * * * * ** *
29047067 ATAGAAGGTCGTGATTGTAAATCAACGGATCATGAAATTTATAAAAT-TTGAAAA
1 GTAAAAGGTCGTGATCGTAAATCAGCAGACCGTGAGATTCGTAAAATCTCG-AAA
* *
29047121 ATAGAAGGTCGTGATCGTAAATCAGCA
1 GTAAAAGGTCGTGATCGTAAATCAGCA
29047148 TGACAACCCA
Statistics
Matches: 253, Mismatches: 41, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
53 48 0.19
54 205 0.81
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.25
Consensus pattern (54 bp):
GTAAAAGGTCGTGATCGTAAATCAGCAGACCGTGAGATTCGTAAAATCTCGAAA
Found at i:29047088 original size:161 final size:162
Alignment explanation
Indices: 29046798--29047090 Score: 453
Period size: 161 Copynumber: 1.8 Consensus size: 162
29046788 AATCTTGTAT
* * * *
29046798 GTAAAAGGTCTTGATCGTAAATCAGCGGACCATGAGATTCGTAAAATCTTGAAAGTAAAAGGTCG
1 GTAAAAGGTCGTGATCATAAATCAACGGACCATGAGATTCGTAAAATCTCGAAAGTAAAAGGTCG
* * * *
29046863 TGATCGTAAATCAGCAAACCGTGAGATTCGCAAAATCTCAAAAGTAGAAGGTCGTGATTGTAAAT
66 TGATCATAAATCAACAAACCGTGAGATTAGCAAAATCTCAAAAATAGAAGGTCGTGATTGTAAAT
29046928 CAGTAGACCGTGAGATTCGTAAAATCTCGAAA
131 CAGTAGACCGTGAGATTCGTAAAATCTCGAAA
* * *
29046960 GTAAAAGGTCGTGATCATAAATCAACGGACCGTGAGATTCGTAAAATCTCGAAAGTAGAAGGT-T
1 GTAAAAGGTCGTGATCATAAATCAACGGACCATGAGATTCGTAAAATCTCGAAAGTAAAAGGTCG
* * *
29047024 TGATCATAAATCAACAGACTGTGAGATTAGTAAAATCTCAAAAATAGAAGGTCGTGATTGTAAAT
66 TGATCATAAATCAACAAACCGTGAGATTAGCAAAATCTCAAAAATAGAAGGTCGTGATTGTAAAT
29047089 CA
131 CA
29047091 ACGGATCATG
Statistics
Matches: 117, Mismatches: 14, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
161 60 0.51
162 57 0.49
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (162 bp):
GTAAAAGGTCGTGATCATAAATCAACGGACCATGAGATTCGTAAAATCTCGAAAGTAAAAGGTCG
TGATCATAAATCAACAAACCGTGAGATTAGCAAAATCTCAAAAATAGAAGGTCGTGATTGTAAAT
CAGTAGACCGTGAGATTCGTAAAATCTCGAAA
Found at i:29047131 original size:161 final size:162
Alignment explanation
Indices: 29046799--29047144 Score: 444
Period size: 161 Copynumber: 2.1 Consensus size: 162
29046789 ATCTTGTATG
* * *
29046799 TAAAAGGTCTTGATCGTAAATCAGCGGACCATGAGATTCGTAAAATCTTGAAAGTAAAAGGTCGT
1 TAAAAGGTCGTGATCGTAAATCAACGGACCATGAGATTCGTAAAATCTCGAAAGTAAAAGGTCGT
* * * *
29046864 GATCGTAAATCAGCAAACCGTGAGATTCGCAAAATCTCAAAAGTAGAAGGTCGTGATTGTAAATC
66 GATCATAAATCAACAAACCGTGAGATTAGCAAAATCTCAAAAATAGAAGGTCGTGATTGTAAATC
** * * * *
29046929 AGTAGACCGTGAGATTCGTAAAATCTCGAAAG
131 AACAGACCATGAAATTCATAAAATCTCGAAAA
* * * *
29046961 TAAAAGGTCGTGATCATAAATCAACGGACCGTGAGATTCGTAAAATCTCGAAAGTAGAAGGT-TT
1 TAAAAGGTCGTGATCGTAAATCAACGGACCATGAGATTCGTAAAATCTCGAAAGTAAAAGGTCGT
* * *
29047025 GATCATAAATCAACAGACTGTGAGATTAGTAAAATCTCAAAAATAGAAGGTCGTGATTGTAAATC
66 GATCATAAATCAACAAACCGTGAGATTAGCAAAATCTCAAAAATAGAAGGTCGTGATTGTAAATC
* * * *
29047090 AACGGATCATGAAATTTATAAAAT-TTGAAAAA
131 AACAGACCATGAAATTCATAAAATCTCG-AAAA
*
29047122 TAGAAGGTCGTGATCGTAAATCA
1 TAAAAGGTCGTGATCGTAAATCA
29047145 GCATGACAAC
Statistics
Matches: 157, Mismatches: 26, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
160 2 0.01
161 99 0.63
162 56 0.36
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (162 bp):
TAAAAGGTCGTGATCGTAAATCAACGGACCATGAGATTCGTAAAATCTCGAAAGTAAAAGGTCGT
GATCATAAATCAACAAACCGTGAGATTAGCAAAATCTCAAAAATAGAAGGTCGTGATTGTAAATC
AACAGACCATGAAATTCATAAAATCTCGAAAA
Found at i:29048150 original size:22 final size:23
Alignment explanation
Indices: 29048124--29048166 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
29048114 TAAAACAACC
29048124 AAGAAATGGAAA-ATAAAATTTA
1 AAGAAATGGAAAGATAAAATTTA
* *
29048146 AAGAATTGGAAAGATGAAATT
1 AAGAAATGGAAAGATAAAATT
29048167 ATGCTTCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (23 bp):
AAGAAATGGAAAGATAAAATTTA
Found at i:29057190 original size:42 final size:41
Alignment explanation
Indices: 29057130--29057212 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 41
29057120 TCGAAGACCC
29057130 AAGCTTGTCTTTCACTAGAACAAGCTTGACCACAGACTCTG
1 AAGCTTGTCTTTCACTAGAACAAGCTTGACCACAGACTCTG
* *
29057171 NAAGCTTGTCTTTCCCTAGACCAAGCTTGACCACAGACTCTG
1 -AAGCTTGTCTTTCACTAGAACAAGCTTGACCACAGACTCTG
29057213 CTACCACCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (41 bp):
AAGCTTGTCTTTCACTAGAACAAGCTTGACCACAGACTCTG
Found at i:29064526 original size:87 final size:87
Alignment explanation
Indices: 29064380--29064732 Score: 670
Period size: 87 Copynumber: 4.1 Consensus size: 87
29064370 GGTGTGAACG
29064380 GTGTGTTTCCGAGGGGTGATCCAAGCAAGTCTTTTATGTTAATTCGTAGGTGTTTATTACGCAAT
1 GTGTGTTTCCGAGGGGTGATCCAAGCAAGTCTTTTATGTTAATTCGTAGGTGTTTATTACGCAAT
29064445 TATGATTTGGGAAATAAAGGCA
66 TATGATTTGGGAAATAAAGGCA
29064467 GTGTGTTTCCGAGGGGTGATCCAAGCAAGTCTTTTATGTTAATTCGTAGGTGTTTATTACGCAAT
1 GTGTGTTTCCGAGGGGTGATCCAAGCAAGTCTTTTATGTTAATTCGTAGGTGTTTATTACGCAAT
29064532 TATGATTTGGGAAATAAAGGCA
66 TATGATTTGGGAAATAAAGGCA
29064554 GTGTGTTTCCGAGGGGTGATCCAAGCAAGTCTTTTATGTTAATTCGTAGGTGTTTATTACGCAAT
1 GTGTGTTTCCGAGGGGTGATCCAAGCAAGTCTTTTATGTTAATTCGTAGGTGTTTATTACGCAAT
29064619 TATGATTTGGGAAATAAAGGCA
66 TATGATTTGGGAAATAAAGGCA
* * *
29064641 GTGTGTTTCCGAGGGGTGATCCAAGCAAGTCTTTTATGTTAATTTGTAGGTGTTTATTACCCATT
1 GTGTGTTTCCGAGGGGTGATCCAAGCAAGTCTTTTATGTTAATTCGTAGGTGTTTATTACGCAAT
29064706 TATGATTTGGGAAATAAAGGCA
66 TATGATTTGGGAAATAAAGGCA
*
29064728 ATGTG
1 GTGTG
29064733 GTAGAACTAT
Statistics
Matches: 262, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 262 1.00
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.36
Consensus pattern (87 bp):
GTGTGTTTCCGAGGGGTGATCCAAGCAAGTCTTTTATGTTAATTCGTAGGTGTTTATTACGCAAT
TATGATTTGGGAAATAAAGGCA
Found at i:29066469 original size:114 final size:114
Alignment explanation
Indices: 29066290--29066635 Score: 649
Period size: 114 Copynumber: 3.0 Consensus size: 114
29066280 TTTCTCTCTT
*
29066290 TTTCCTTTCTTCTACACGTTGGAAGCATGGGACATATGAAGACATATCTTCATATTTCCTTAATA
1 TTTCATTTCTTCTACACGTTGGAAGCATGGGACATATGAAGACATATCTTCATATTTCCTTAATA
29066355 ATTATCTTAATAATAAATAATTTAGATAAAAAAATATTCAACATCATAA
66 ATTATCTTAATAATAAATAATTTAGATAAAAAAATATTCAACATCATAA
29066404 TTTCATTTCTTCTACACGTTGGAAGCATGGGACATATGAAGACATATCTTCATATTTCCTTAATA
1 TTTCATTTCTTCTACACGTTGGAAGCATGGGACATATGAAGACATATCTTCATATTTCCTTAATA
29066469 ATTATCTTAATAATAAATAATTTAGATAAAAAAATATTCAACATCATAA
66 ATTATCTTAATAATAAATAATTTAGATAAAAAAATATTCAACATCATAA
*
29066518 TTTCATTTCTTCTACACGTTGGAAGCATGGGACATATGAAGACATTTCTTCATATTTCCTTAATA
1 TTTCATTTCTTCTACACGTTGGAAGCATGGGACATATGAAGACATATCTTCATATTTCCTTAATA
* *
29066583 ATTATCTTAATAATAAATAATTTAAAT-AAAAAACATTCAACATCATAA
66 ATTATCTTAATAATAAATAATTTAGATAAAAAAATATTCAACATCATAA
29066631 TTTCA
1 TTTCA
29066636 ATGTAAGGGC
Statistics
Matches: 228, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
113 25 0.11
114 203 0.89
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (114 bp):
TTTCATTTCTTCTACACGTTGGAAGCATGGGACATATGAAGACATATCTTCATATTTCCTTAATA
ATTATCTTAATAATAAATAATTTAGATAAAAAAATATTCAACATCATAA
Found at i:29067754 original size:30 final size:31
Alignment explanation
Indices: 29067715--29067774 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
29067705 GGAGGTGAGA
*
29067715 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
29067746 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
29067775 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:29067950 original size:21 final size:21
Alignment explanation
Indices: 29067910--29067950 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
29067900 GGAGGTAAGT
*
29067910 GGGAATAAGTAAAAGTTTTGA
1 GGGAATAAGTAAAAATTTTGA
29067931 GGGAA-AAGTAAAAATGTTTG
1 GGGAATAAGTAAAAAT-TTTG
29067951 GGAGTTTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.29, T:0.27
Consensus pattern (21 bp):
GGGAATAAGTAAAAATTTTGA
Found at i:29068002 original size:9 final size:9
Alignment explanation
Indices: 29067988--29068015 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
29067978 TATAGTTTGA
29067988 TATTCGAAT
1 TATTCGAAT
29067997 TATTCGAAT
1 TATTCGAAT
29068006 TATTCGAAT
1 TATTCGAAT
29068015 T
1 T
29068016 CGAAAACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:29068271 original size:29 final size:30
Alignment explanation
Indices: 29068207--29068317 Score: 100
Period size: 31 Copynumber: 3.7 Consensus size: 30
29068197 ATATCAAAAT
* * *
29068207 TATACAT-AAACTTTGATTTAATGTGCAGTTG
1 TATACATGAAACTTTAATTT--GGTGCAATTG
*
29068238 TATACATG-AACTTTAATTTGGTGCAATTA
1 TATACATGAAACTTTAATTTGGTGCAATTG
* * * *
29068267 TATACGTGAAACTCTAATTGTGGTTCAAATG
1 TATACATGAAACTTTAATT-TGGTGCAATTG
*
29068298 TATACTTGAAACTTTAATTT
1 TATACATGAAACTTTAATTT
29068318 TGATTTAATC
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
29 14 0.21
30 10 0.15
31 42 0.64
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.41
Consensus pattern (30 bp):
TATACATGAAACTTTAATTTGGTGCAATTG
Found at i:29072785 original size:30 final size:29
Alignment explanation
Indices: 29072751--29072810 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 29
29072741 AATTTTAAAA
*
29072751 TTTTAAAAATTCAGAAA-CATATAAAATTAT
1 TTTTAAAAATT-AAAAATCAT-TAAAATTAT
29072781 TTTTAAAAATTAAAAATCATTAAAATTAT
1 TTTTAAAAATTAAAAATCATTAAAATTAT
29072810 T
1 T
29072811 AAAAAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (29 bp):
TTTTAAAAATTAAAAATCATTAAAATTAT
Found at i:29072788 original size:29 final size:29
Alignment explanation
Indices: 29072750--29072818 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
29072740 TAATTTTAAA
*
29072750 ATTTT-AAAAATTCAGAAA-CATATAAAATT
1 ATTTTAAAAAATT-AAAAATCAT-TAAAATT
*
29072779 ATTTTTAAAAATTAAAAATCATTAAAATT
1 ATTTTAAAAAATTAAAAATCATTAAAATT
*
29072808 A-TTAAAAAAAT
1 ATTTTAAAAAAT
29072819 AAACATTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 8 0.23
29 17 0.49
30 10 0.29
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (29 bp):
ATTTTAAAAAATTAAAAATCATTAAAATT
Found at i:29096815 original size:36 final size:36
Alignment explanation
Indices: 29096768--29096958 Score: 211
Period size: 36 Copynumber: 5.0 Consensus size: 36
29096758 GCTAAGCTAC
*
29096768 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
* *
29096804 CACTTATCACTTTTTCACTTGATCTGATAAGTATAA
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
* *
29096840 CACTTATCGCTTTTTCACTTGATCAAATAAGTGTAGCTAAAG
1 CACTTATCACTTTTTCACTTGATCAGATAA--GTA--T--AG
* * *
29096882 CTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 ----CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
29096922 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
29096958 C
1 C
29096959 TAAAGCTACC
Statistics
Matches: 131, Mismatches: 14, Indels: 20
0.79 0.08 0.12
Matches are distributed among these distances:
36 95 0.73
38 3 0.02
40 3 0.02
42 2 0.02
44 2 0.02
46 26 0.20
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (36 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
Found at i:29096892 original size:46 final size:46
Alignment explanation
Indices: 29096840--29096994 Score: 186
Period size: 46 Copynumber: 3.6 Consensus size: 46
29096830 ATAAGTATAA
* *
29096840 CACTTATCGCTTTTTCACTTGATCAAATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
29096886 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AG----
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
29096922 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
29096968 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTTTCACTTGATCAGA
29096995 AGTACTCAAA
Statistics
Matches: 91, Mismatches: 8, Indels: 20
0.76 0.07 0.17
Matches are distributed among these distances:
36 28 0.31
38 2 0.02
39 1 0.01
40 3 0.03
42 3 0.03
43 1 0.01
44 2 0.02
46 51 0.56
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (46 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:29096897 original size:82 final size:82
Alignment explanation
Indices: 29096804--29096994 Score: 310
Period size: 82 Copynumber: 2.3 Consensus size: 82
29096794 ATAAGTATAG
* * * *
29096804 CACTTATCACTTTTTCACTTGATCTGATAAGTATAACACTTATCGCTTTTTCACTTGATCAAATA
1 CACTTATCACTTTATCTCTTGATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAAATA
29096869 AGTGTAGCTAAAGCTAC
66 AGTGTAGCTAAAGCTAC
* * * *
29096886 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCACTTATCACTTTTTCACTTGATCAGATA
1 CACTTATCACTTTATCTCTTGATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAAATA
29096951 AGTGTAGCTAAAGCTAC
66 AGTGTAGCTAAAGCTAC
29096968 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTATCTCTTGATCAGA
29096995 AGTACTCAAA
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 101 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (82 bp):
CACTTATCACTTTATCTCTTGATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAAATA
AGTGTAGCTAAAGCTAC
Found at i:29096900 original size:118 final size:117
Alignment explanation
Indices: 29096742--29096953 Score: 379
Period size: 118 Copynumber: 1.8 Consensus size: 117
29096732 CATTTGTCCC
*
29096742 TGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCAC
1 TGATCAAATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCAC
*
29096807 TTATCACTTTTTCACTTGATCTGATAAGTATAACACTTATCGCTTTTTCACT
66 TTATCACTTTTTCACTTGATCAGATAAGTATAACACTTATCGCTTTTTCACT
* *
29096859 TGATCAAATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCA
1 TGATCAAATAAGTGTAGCT-AAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCA
29096924 CTTATCACTTTTTCACTTGATCAGATAAGT
65 CTTATCACTTTTTCACTTGATCAGATAAGT
29096954 GTAGCTAAAG
Statistics
Matches: 90, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
117 18 0.20
118 72 0.80
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.37
Consensus pattern (117 bp):
TGATCAAATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCAC
TTATCACTTTTTCACTTGATCAGATAAGTATAACACTTATCGCTTTTTCACT
Found at i:29099406 original size:73 final size:73
Alignment explanation
Indices: 29099279--29099426 Score: 233
Period size: 73 Copynumber: 2.0 Consensus size: 73
29099269 CAGAGAATAT
* * *
29099279 TTACTATTCATGCATCTTTTCTTGAAGGGACTATTTACTGTTTACGCCATAGAATATTTCCTGTT
1 TTACTATTCATGCATCTTTTCTTGAAGGGAATATTTACTGCTTACGCCAGAGAATATTTCCTGTT
29099344 CACTTGTC
66 CACTTGTC
* * **
29099352 TTACTATTCATGCGTCTTTTCTTGCAGGGAATATTTACTGCTTACGTTAGAGAATATTTCCTGTT
1 TTACTATTCATGCATCTTTTCTTGAAGGGAATATTTACTGCTTACGCCAGAGAATATTTCCTGTT
29099417 CACTTGTC
66 CACTTGTC
29099425 TT
1 TT
29099427 TTCTTGCATC
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.21, C:0.20, G:0.15, T:0.45
Consensus pattern (73 bp):
TTACTATTCATGCATCTTTTCTTGAAGGGAATATTTACTGCTTACGCCAGAGAATATTTCCTGTT
CACTTGTC
Found at i:29100522 original size:37 final size:37
Alignment explanation
Indices: 29100481--29100553 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
29100471 AATGTCTCTT
29100481 TTAAAACATTTTTGAGAGATTTTGGTTTGTGTAAAAC
1 TTAAAACATTTTTGAGAGATTTTGGTTTGTGTAAAAC
*
29100518 TTAAAACATTTTTGAGAGATTTTGGTTTTTGTAAAA
1 TTAAAACATTTTTGAGAGATTTTGGTTTGTGTAAAA
29100554 TAAACTCTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.45
Consensus pattern (37 bp):
TTAAAACATTTTTGAGAGATTTTGGTTTGTGTAAAAC
Found at i:29102267 original size:16 final size:15
Alignment explanation
Indices: 29102246--29102293 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
29102236 GATGTGAATA
29102246 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
29102262 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
29102277 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
29102293 A
1 A
29102294 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:29102276 original size:8 final size:8
Alignment explanation
Indices: 29102242--29102293 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
29102232 CAATGATGTG
*
29102242 AATAATAA
1 AATATTAA
29102250 AATATATAA
1 AATAT-TAA
29102259 AATA-TAA
1 AATATTAA
29102266 AATATTAA
1 AATATTAA
*
29102274 AATATCAA
1 AATATTAA
*
29102282 AATATTAG
1 AATATTAA
29102290 AATA
1 AATA
29102294 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:29102293 original size:24 final size:24
Alignment explanation
Indices: 29102241--29102297 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
29102231 ACAATGATGT
*
29102241 GAATAATAAAATATATAAAATATA
1 GAATAATAAAATATACAAAATATA
* *
29102265 AAATATTAAAATAT-CAAAATATTA
1 GAATAATAAAATATACAAAATA-TA
29102289 GAATAATAA
1 GAATAATAA
29102298 TAATTAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
GAATAATAAAATATACAAAATATA
Found at i:29115454 original size:30 final size:29
Alignment explanation
Indices: 29115359--29115505 Score: 170
Period size: 30 Copynumber: 4.9 Consensus size: 29
29115349 TGTAGGTACA
*
29115359 AGTT-GTGGTGGAGCAAGTGTGGTTAGTGG
1 AGTTGGTGGTGGAG-AAGTGTGGCTAGTGG
* **
29115388 AGTAGGTAATGGAGCAAGTGTGGCTAGTGG
1 AGTTGGTGGTGGAG-AAGTGTGGCTAGTGG
*
29115418 ATTTGGTGGTGGAGAAGGTGTGGCTAGTGG
1 AGTTGGTGGTGGAGAA-GTGTGGCTAGTGG
* *
29115448 AGTTGGTGGTGGAAAATGAGTGGCTAGTGG
1 AGTTGGTGGTGGAGAA-GTGTGGCTAGTGG
*
29115478 AGTTGGTGGTGGAAAAGGTGTGGCTAGT
1 AGTTGGTGGTGGAGAA-GTGTGGCTAGT
29115506 TGAGAAAAGT
Statistics
Matches: 102, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
29 5 0.05
30 97 0.95
ACGTcount: A:0.21, C:0.04, G:0.47, T:0.28
Consensus pattern (29 bp):
AGTTGGTGGTGGAGAAGTGTGGCTAGTGG
Found at i:29123609 original size:13 final size:13
Alignment explanation
Indices: 29123591--29123616 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29123581 GTAAGCATGT
29123591 GATTTCATAAAAA
1 GATTTCATAAAAA
29123604 GATTTCATAAAAA
1 GATTTCATAAAAA
29123617 AATTCAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
GATTTCATAAAAA
Found at i:29124171 original size:29 final size:28
Alignment explanation
Indices: 29124129--29124190 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 28
29124119 ATTGGATAGC
*
29124129 CCACTAAGGAAGGAA-GAAGCCCAAACTGT
1 CCACTAAGGAAGGAATG-AGCCC-AACCGT
29124158 CCACTAAGGAAGGAATGAGCCCAACCGT
1 CCACTAAGGAAGGAATGAGCCCAACCGT
29124186 CCACT
1 CCACT
29124191 TGAGGTGCCC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 10 0.32
29 20 0.65
30 1 0.03
ACGTcount: A:0.37, C:0.29, G:0.23, T:0.11
Consensus pattern (28 bp):
CCACTAAGGAAGGAATGAGCCCAACCGT
Found at i:29128720 original size:16 final size:16
Alignment explanation
Indices: 29128682--29128720 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
29128672 TGTATGCGGT
29128682 AATA-AGAAGAGAAAA
1 AATAGAGAAGAGAAAA
29128697 AA-AGGAGAAGAGAAAA
1 AATA-GAGAAGAGAAAA
29128713 AATAGAGA
1 AATAGAGA
29128721 TGCATGGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 1 0.05
15 2 0.10
16 17 0.81
17 1 0.05
ACGTcount: A:0.69, C:0.00, G:0.26, T:0.05
Consensus pattern (16 bp):
AATAGAGAAGAGAAAA
Found at i:29132912 original size:18 final size:18
Alignment explanation
Indices: 29132889--29132951 Score: 76
Period size: 18 Copynumber: 3.5 Consensus size: 18
29132879 AAAACTAAAG
29132889 AAAAATCATTAAAA-TTCA
1 AAAAATCATTAAAACTT-A
29132907 AAAAATCATTAAAACTTA
1 AAAAATCATTAAAACTTA
* *
29132925 AAAAATTATAAAAAC-TA
1 AAAAATCATTAAAACTTA
29132942 AAAGAATCAT
1 AAA-AATCAT
29132952 AATCTATATT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
17 5 0.12
18 33 0.82
19 2 0.05
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.25
Consensus pattern (18 bp):
AAAAATCATTAAAACTTA
Found at i:29133027 original size:18 final size:18
Alignment explanation
Indices: 29132976--29133019 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
29132966 ATTTGTGTGC
* *
29132976 AAAATTTTTTAAAAATTT
1 AAAAATTTTCAAAAATTT
*
29132994 AAAAATTTTCATAAATTT
1 AAAAATTTTCAAAAATTT
*
29133012 TAAAATTT
1 AAAAATTT
29133020 CGAAAAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
AAAAATTTTCAAAAATTT
Found at i:29133212 original size:12 final size:11
Alignment explanation
Indices: 29133194--29133223 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
29133184 AAGTTTTAGT
29133194 ATTTTTTTGGG
1 ATTTTTTTGGG
29133205 ATTTTTTTGGG
1 ATTTTTTTGGG
29133216 ATTTTTTT
1 ATTTTTTT
29133224 AATGTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.20, T:0.70
Consensus pattern (11 bp):
ATTTTTTTGGG
Found at i:29148896 original size:50 final size:52
Alignment explanation
Indices: 29148837--29148966 Score: 140
Period size: 50 Copynumber: 2.5 Consensus size: 52
29148827 GTGTGTTCTG
* * *
29148837 CATTTAATAAAGTTATGCATTATGTAACTTCTATGCTAG-TTAAGTGTGCAT
1 CATTAAATAAAGTTATGCATTATGTAACTCCCATGCTAGTTTAAGTGTGCAT
* ** * *
29148888 CA-TAAATAATGACATGCATTATGTAACTCCCATGTTAGTTTAAGTTTGCAT
1 CATTAAATAAAGTTATGCATTATGTAACTCCCATGCTAGTTTAAGTGTGCAT
* *
29148939 CATTAAATTAAGTCT-TGCATTAAGTAAC
1 CATTAAATAAAGT-TATGCATTATGTAAC
29148967 GCATTTAGTT
Statistics
Matches: 63, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
50 29 0.46
51 15 0.24
52 19 0.30
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (52 bp):
CATTAAATAAAGTTATGCATTATGTAACTCCCATGCTAGTTTAAGTGTGCAT
Found at i:29150178 original size:16 final size:17
Alignment explanation
Indices: 29150147--29150179 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
29150137 ACGAAATTAG
29150147 AATTAGATTAAAGAAAT
1 AATTAGATTAAAGAAAT
*
29150164 AATTTGATT-AAGAAAT
1 AATTAGATTAAAGAAAT
29150180 TAACTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (17 bp):
AATTAGATTAAAGAAAT
Found at i:29151438 original size:21 final size:21
Alignment explanation
Indices: 29151412--29151464 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
29151402 TATATGGCCA
29151412 GGCCATGTGGCTTAGGGACAT
1 GGCCATGTGGCTTAGGGACAT
29151433 GGCCATGTGGCTTAGGGACAT
1 GGCCATGTGGCTTAGGGACAT
* *
29151454 GGTCGTGTGGC
1 GGCCATGTGGC
29151465 CAAACTATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.15, C:0.19, G:0.42, T:0.25
Consensus pattern (21 bp):
GGCCATGTGGCTTAGGGACAT
Found at i:29153005 original size:70 final size:70
Alignment explanation
Indices: 29152908--29153139 Score: 322
Period size: 70 Copynumber: 3.3 Consensus size: 70
29152898 ATAAAAATGT
* * * *
29152908 ACAAGACTATGGTTAGACCATGACAATGTTTACATAAGACCATAGGCTAGGCTATGGCAGTTTTT
1 ACAAGACCATGGTTGGACCATGGCAATGTTTACATAAGACCATAGGCTGGGCTATGGCAGTTTTT
29152973 TAGAC
66 TAGAC
* *
29152978 ACAAGACCATGGTTGGACCATGGCAATGTTTACATAATACCATAGGCTGGGCTATGGCATTTTTT
1 ACAAGACCATGGTTGGACCATGGCAATGTTTACATAAGACCATAGGCTGGGCTATGGCA-GTTTT
29153043 TTAGAC
65 TTAGAC
* * * * *
29153049 GCAAGACCATGGTTGGACCATTGCAATGTTTACGTAAGACCATA-GTTGGGCTATGACAGTTTTT
1 ACAAGACCATGGTTGGACCATGGCAATGTTTACATAAGACCATAGGCTGGGCTATGGCAGTTTTT
*
29153113 CAGAC
66 TAGAC
**
29153118 GTAAGACCATGGTTGGACCATG
1 ACAAGACCATGGTTGGACCATG
29153140 ACAGTGTATA
Statistics
Matches: 145, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
69 29 0.20
70 66 0.46
71 50 0.34
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (70 bp):
ACAAGACCATGGTTGGACCATGGCAATGTTTACATAAGACCATAGGCTGGGCTATGGCAGTTTTT
TAGAC
Found at i:29153036 original size:34 final size:34
Alignment explanation
Indices: 29152931--29153036 Score: 106
Period size: 34 Copynumber: 3.1 Consensus size: 34
29152921 TAGACCATGA
*
29152931 CAATGTTTACATAAGACCATAGGCTAGGCTATGG
1 CAATGTTTACATAAGACCATAGGCTGGGCTATGG
* * * * * *
29152965 CAGTTTTTTAGACACAAGACCAT-GGTTGGACCATGG
1 CA-ATGTTT--ACATAAGACCATAGGCTGGGCTATGG
*
29153001 CAATGTTTACATAATACCATAGGCTGGGCTATGG
1 CAATGTTTACATAAGACCATAGGCTGGGCTATGG
29153035 CA
1 CA
29153037 TTTTTTTTAG
Statistics
Matches: 54, Mismatches: 14, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
33 10 0.19
34 14 0.26
35 8 0.15
36 11 0.20
37 11 0.20
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (34 bp):
CAATGTTTACATAAGACCATAGGCTGGGCTATGG
Found at i:29157369 original size:15 final size:16
Alignment explanation
Indices: 29157349--29157380 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
29157339 AATTGAATTG
29157349 GAATATATATAT-TAT
1 GAATATATATATATAT
29157364 GAATATATATATATAT
1 GAATATATATATATAT
29157380 G
1 G
29157381 TGTAAATGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (16 bp):
GAATATATATATATAT
Found at i:29157545 original size:27 final size:25
Alignment explanation
Indices: 29157512--29157648 Score: 137
Period size: 25 Copynumber: 5.7 Consensus size: 25
29157502 GAACTTTAGT
*
29157512 GTGCTCTCTGATTTTTAGCACGTTA
1 GTGCTCTCTGATTATTAGCACGTTA
29157537 GTGCTCTCTGATTATTAGCACGTTA
1 GTGCTCTCTGATTATTAGCACGTTA
*
29157562 GTGCTCTCTGATTACTAGCACGTTA
1 GTGCTCTCTGATTATTAGCACGTTA
* * * *
29157587 ATACTCTCCG--T-TTAGCACATCT-
1 GTGCTCTCTGATTATTAGCACGT-TA
*
29157609 GTGCTCTCTG--TA-TAGCACTTTA
1 GTGCTCTCTGATTATTAGCACGTTA
29157631 GTGCTCTCTG-TTCATTAG
1 GTGCTCTCTGATT-ATTAG
29157649 TGCATAATAA
Statistics
Matches: 95, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
21 1 0.01
22 32 0.34
23 3 0.03
24 1 0.01
25 58 0.61
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.40
Consensus pattern (25 bp):
GTGCTCTCTGATTATTAGCACGTTA
Found at i:29164167 original size:16 final size:16
Alignment explanation
Indices: 29164146--29164176 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29164136 TTCACTATTA
*
29164146 TGTCTTTTGTATTTTC
1 TGTCTTTTATATTTTC
29164162 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
29164177 ACATACATGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:29169198 original size:18 final size:18
Alignment explanation
Indices: 29169175--29169211 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29169165 GGCGGCCCTA
*
29169175 GTGGATCACGCTTCTTTG
1 GTGGATCAAGCTTCTTTG
*
29169193 GTGGATCAAGTTTCTTTG
1 GTGGATCAAGCTTCTTTG
29169211 G
1 G
29169212 CTTTGATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.16, G:0.30, T:0.41
Consensus pattern (18 bp):
GTGGATCAAGCTTCTTTG
Found at i:29170102 original size:21 final size:22
Alignment explanation
Indices: 29170076--29170122 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
29170066 CTCTGCTCAA
*
29170076 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
29170097 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
29170119 ACTC
1 ACTC
29170123 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:29176826 original size:22 final size:22
Alignment explanation
Indices: 29176801--29176891 Score: 76
Period size: 22 Copynumber: 4.0 Consensus size: 22
29176791 GAGATTTCAA
29176801 TAAATTATATTTAAAATTATTT
1 TAAATTATATTTAAAATTATTT
* * *
29176823 TAAATGAAAATTTAATAATTTTTT
1 TAAAT-TATATTTAA-AATTATTT
* * *
29176847 TTAATT-TATCTAAAAATATTTT
1 TAAATTATATTTAAAATTA-TTT
* *
29176869 TAAATTATATTTAACATTTTTT
1 TAAATTATATTTAAAATTATTT
29176891 T
1 T
29176892 TAAGTTCCCT
Statistics
Matches: 51, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
21 3 0.06
22 22 0.43
23 15 0.29
24 11 0.22
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (22 bp):
TAAATTATATTTAAAATTATTT
Found at i:29176867 original size:45 final size:45
Alignment explanation
Indices: 29176803--29176894 Score: 107
Period size: 45 Copynumber: 2.0 Consensus size: 45
29176793 GATTTCAATA
* *
29176803 AATTATATTTAAAATTA-TTTTAAATGAAAATTTAATAATTTTTTTT
1 AATTATATCTAAAAATATTTTTAAAT-AAAATTTAA-AATTTTTTTT
* * *
29176849 AATT-TATCTAAAAATATTTTTAAATTATATTTAACATTTTTTTT
1 AATTATATCTAAAAATATTTTTAAATAAAATTTAAAATTTTTTTT
29176893 AA
1 AA
29176895 GTTCCCTATG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
44 11 0.28
45 17 0.43
46 12 0.30
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (45 bp):
AATTATATCTAAAAATATTTTTAAATAAAATTTAAAATTTTTTTT
Found at i:29200413 original size:20 final size:20
Alignment explanation
Indices: 29200388--29200427 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
29200378 TATTTTAAAA
29200388 TTTGAAAATTATTTTGAATT
1 TTTGAAAATTATTTTGAATT
29200408 TTTGAAAATTATTTTGAATT
1 TTTGAAAATTATTTTGAATT
29200428 ATTTTGTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (20 bp):
TTTGAAAATTATTTTGAATT
Found at i:29201751 original size:12 final size:12
Alignment explanation
Indices: 29201736--29201765 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
29201726 AATAATTAAA
29201736 TAAATTAGAAAT
1 TAAATTAGAAAT
*
29201748 TAAATTGGAAAT
1 TAAATTAGAAAT
29201760 TAAATT
1 TAAATT
29201766 CAGATTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (12 bp):
TAAATTAGAAAT
Found at i:29203030 original size:23 final size:23
Alignment explanation
Indices: 29203004--29203148 Score: 220
Period size: 23 Copynumber: 6.3 Consensus size: 23
29202994 ATAAGTGCCA
29203004 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
29203027 CACTGATATGTAGCTGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
29203050 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
29203073 CACTGAAATGTAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
29203096 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
29203119 CACTGGA-ATGTAGCCGAAGCTAC
1 CACT-GATATGTAGCCGAAGCTAC
29203142 CACTGAT
1 CACTGAT
29203149 CAATAACACT
Statistics
Matches: 110, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
22 2 0.02
23 106 0.96
24 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:29203115 original size:69 final size:69
Alignment explanation
Indices: 29203004--29203147 Score: 252
Period size: 69 Copynumber: 2.1 Consensus size: 69
29202994 ATAAGTGCCA
* *
29203004 CACTGATATGTAGCCGAAGCTACCACTGATATGTAGCTGTAGCTACCACTGAAATGTAGCCGAAG
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTACCACTGAAATGTAGCCGAAG
29203069 CTAC
66 CTAC
* *
29203073 CACTGAAATGTAGTCGAAGCTACCACTGATATGTAGCCGTAGCTACCACTGGAATGTAGCCGAAG
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTACCACTGAAATGTAGCCGAAG
29203138 CTAC
66 CTAC
29203142 CACTGA
1 CACTGA
29203148 TCAATAACAC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (69 bp):
CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTACCACTGAAATGTAGCCGAAG
CTAC
Found at i:29207344 original size:3 final size:3
Alignment explanation
Indices: 29207336--29207394 Score: 75
Period size: 3 Copynumber: 20.0 Consensus size: 3
29207326 TATTTTAATG
* * *
29207336 TTA TTA TTA TTA TTG TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
29207384 CTA TTA -TA TTA
1 TTA TTA TTA TTA
29207395 ATATAATTAC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:29208292 original size:110 final size:109
Alignment explanation
Indices: 29208073--29208351 Score: 452
Period size: 110 Copynumber: 2.6 Consensus size: 109
29208063 AAGTTTTTCT
* * ** *
29208073 AAATGAGGCAATATTTACCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATT
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCAATT
*
29208138 TTTCTCGTTCAACCAAATAGCTAAATATCATTTTAAAAAATTCA
66 TTTCTCGTTCAACCAAATAGCTAAATATCATTTCAAAAAATTCA
*
29208182 AAATAAGGCAATGTTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTTTCAAT
1 AAATAAGGCAATG-TTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCAAT
* * *
29208247 TTTTCTCGTTCAACCAAATAGCTAAATATCCTTTCAGAAATTTCA
65 TTTTCTCGTTCAACCAAATAGCTAAATATCATTTCAAAAAATTCA
29208292 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG-AAACGTGCCCTAATGTGCTGGGTTTC
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTC
29208352 GGTTTCTCGT
Statistics
Matches: 158, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
108 25 0.16
109 32 0.20
110 101 0.64
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Consensus pattern (109 bp):
AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCAATT
TTTCTCGTTCAACCAAATAGCTAAATATCATTTCAAAAAATTCA
Found at i:29211168 original size:22 final size:21
Alignment explanation
Indices: 29211137--29211178 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
29211127 TTCTTGCAAA
*
29211137 AATAAAATAGTAAAAATAAAT
1 AATAAAATAGGAAAAATAAAT
*
29211158 AATAATAATAGGAAAATTAAA
1 AATAA-AATAGGAAAAATAAA
29211179 ATGTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (21 bp):
AATAAAATAGGAAAAATAAAT
Found at i:29219139 original size:8 final size:8
Alignment explanation
Indices: 29219128--29219156 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
29219118 AATAAATAAA
29219128 AAAATATT
1 AAAATATT
29219136 AAAATATT
1 AAAATATT
29219144 -AAATATT
1 AAAATATT
29219151 AAAATA
1 AAAATA
29219157 AAATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AAAATATT
Found at i:29220767 original size:52 final size:52
Alignment explanation
Indices: 29220689--29220793 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
29220679 GACTAGTTGT
29220689 TCTAAAGTGGGAAGAAGGACGCTTGCATATTGTAGATGAGCTCTAGCAGGAA
1 TCTAAAGTGGGAAGAAGGACGCTTGCATATTGTAGATGAGCTCTAGCAGGAA
*
29220741 TCTAAAGTGGGAAGAAGGACGCTTGCATATTGTAGATGAGCTCTATCAGGAA
1 TCTAAAGTGGGAAGAAGGACGCTTGCATATTGTAGATGAGCTCTAGCAGGAA
29220793 T
1 T
29220794 GGAGGCAGAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.25
Consensus pattern (52 bp):
TCTAAAGTGGGAAGAAGGACGCTTGCATATTGTAGATGAGCTCTAGCAGGAA
Found at i:29224292 original size:26 final size:27
Alignment explanation
Indices: 29224263--29224331 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 27
29224253 TAAGATGGGT
29224263 ATATAAAAAATTTT-AATAAATAAAA-A
1 ATATAAAAAATTTTAAAT-AATAAAATA
* *
29224289 ATATATAAAATTATTAAATATTAAAATA
1 ATATAAAAAATT-TTAAATAATAAAATA
*
29224317 AAATAAAATAATTTT
1 ATATAAAA-AATTTT
29224332 TTTAAAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
26 11 0.31
27 8 0.23
28 12 0.34
29 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
ATATAAAAAATTTTAAATAATAAAATA
Found at i:29233028 original size:34 final size:33
Alignment explanation
Indices: 29232984--29233051 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 33
29232974 AATTTGAATT
29232984 ATTTAAAGGATAAAAAGTAAAAGTAAGTAGGGA
1 ATTTAAAGGATAAAAAGTAAAAGTAAGTAGGGA
29233017 ANTTTAAAGGATAAAAAGTAAAAGTAAGTAGGGA
1 A-TTTAAAGGATAAAAAGTAAAAGTAAGTAGGGA
29233051 A
1 A
29233052 AGGAAAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 1 0.03
34 33 0.97
ACGTcount: A:0.54, C:0.00, G:0.24, T:0.21
Consensus pattern (33 bp):
ATTTAAAGGATAAAAAGTAAAAGTAAGTAGGGA
Found at i:29233053 original size:28 final size:29
Alignment explanation
Indices: 29232987--29233059 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 29
29232977 TTGAATTATT
29232987 TAAAGGATAAAAAGTAAAAGTAAGTAGGG
1 TAAAGGATAAAAAGTAAAAGTAAGTAGGG
29233016 AANTTTAAAGGATAAAAAGTAAAAGTAAGTAGGG
1 -----TAAAGGATAAAAAGTAAAAGTAAGTAGGG
29233050 -AAAGGA-AAAA
1 TAAAGGATAAAA
29233060 TTAACTCCCC
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
27 4 0.10
28 6 0.15
34 29 0.74
ACGTcount: A:0.58, C:0.00, G:0.25, T:0.16
Consensus pattern (29 bp):
TAAAGGATAAAAAGTAAAAGTAAGTAGGG
Done.