Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold102
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1727112
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 166202 characters in sequence are not A, C, G, or T
File 5 of 5
Found at i:1098336 original size:230 final size:229
Alignment explanation
Indices: 1097932--1098392 Score: 913
Period size: 230 Copynumber: 2.0 Consensus size: 229
1097922 CTTCTTCTCT
1097932 AAAACCGCTTATCCAATTTCAACCAAATTTGGCACAAAGCATCCTTATGGGAGGGCGAATATAAA
1 AAAACCGCTTATCCAATTTCAACCAAATTTGGCACAAAGCATCCTTATGGGAGGGCGAATATAAA
1097997 TTGCAGAAATAAAAGTCCGATCTGTATTCAAAGCGGAGAAAACCTTGAAACTGTAGAAAAAGGGG
66 TTGCAGAAATAAAAGTCCGATCTGTATTCAAAGCGGAGAAAACCTTGAAACTGTAGAAAAAGGGG
1098062 GGTGCATTTTTAAAAATCTTCTTCTCAAGAACTACTGATTCCAATTCAGCGTAGTTTAGCATAAA
131 GGTGCATTTTTAAAAATCTTCTTCTCAAGAACTACTGATTCCAATTCAGCGTAGTTTAGCATAAA
1098127 TTATCCTTATGGGAAGGAAAATATAAATTGCAAA
196 TTATCCTTATGGGAAGGAAAATATAAATTGCAAA
1098161 ANAAACCGCTTATCCAATTTCAACCAAATTTGGCACAAAGCATCCTTATGGGAGGGCGAATATAA
1 A-AAACCGCTTATCCAATTTCAACCAAATTTGGCACAAAGCATCCTTATGGGAGGGCGAATATAA
1098226 ATTGCAGAAATAAAAGTCCGATCTGTATTCAAAGCGGAGAAAACCTTGAAACTGTAGAAAAAGGG
65 ATTGCAGAAATAAAAGTCCGATCTGTATTCAAAGCGGAGAAAACCTTGAAACTGTAGAAAAAGGG
1098291 GGGTGCATTTTTAAAAATCTTCTTCTCAAGAACTACTGATTCCAATTCAGCGTAGTTTAGCATAA
130 GGGTGCATTTTTAAAAATCTTCTTCTCAAGAACTACTGATTCCAATTCAGCGTAGTTTAGCATAA
1098356 ATTATCCTTATGGGAAGGAAAATATAAATTGCAAA
195 ATTATCCTTATGGGAAGGAAAATATAAATTGCAAA
1098391 AA
1 AA
1098393 TTAAGGTCTA
Statistics
Matches: 231, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
229 2 0.01
230 229 0.99
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.26
Consensus pattern (229 bp):
AAAACCGCTTATCCAATTTCAACCAAATTTGGCACAAAGCATCCTTATGGGAGGGCGAATATAAA
TTGCAGAAATAAAAGTCCGATCTGTATTCAAAGCGGAGAAAACCTTGAAACTGTAGAAAAAGGGG
GGTGCATTTTTAAAAATCTTCTTCTCAAGAACTACTGATTCCAATTCAGCGTAGTTTAGCATAAA
TTATCCTTATGGGAAGGAAAATATAAATTGCAAA
Found at i:1099634 original size:23 final size:23
Alignment explanation
Indices: 1099601--1099651 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
1099591 GTATGTAAGC
*
1099601 CCCGTACATTA-ATTTCACAATAA
1 CCCGTAAATTAGA-TTCACAATAA
*
1099624 CCCGTAAATTAGATTCACAATAG
1 CCCGTAAATTAGATTCACAATAA
1099647 CCCGT
1 CCCGT
1099652 GCAGTTATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.27
Consensus pattern (23 bp):
CCCGTAAATTAGATTCACAATAA
Found at i:1100198 original size:166 final size:165
Alignment explanation
Indices: 1099900--1100980 Score: 1304
Period size: 166 Copynumber: 6.5 Consensus size: 165
1099890 CACCTGAGAA
* * * *
1099900 TGGGGCCACAATGGGGGGTCGAAGTTTAACAAATGAATATATAGAGTAAATCTTTAGAAATCCTC
1 TGGGGCCACAAT-GGGGGTCGAAGTTTAACATATGAATATATACAGTAAATCTTTAAAAATCTTC
* * *
1099965 TTCTCAGAAACTAATC-GACCAAGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGA
65 TTCTCAGAAACTAATCAG-CCAGGAAAGCTGACACTTGTGTGGAAGCATCCTCAGGTAGTGAAGA
* *
1100029 TTCAAAGATGTGAAAATCATGACCCCTGGGGATAGGG
129 TTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGG
* * *
1100066 TGGGGCCACAATGGAGGGTCGAAGTTTAACATATGAGTATAAAAAGTAAATCTTTAAAAATCTTC
1 TGGGGCCACAATGG-GGGTCGAAGTTTAACATATGAATATATACAGTAAATCTTTAAAAATCTTC
** ** * *
1100131 TTCTCAGAAACTAATTGGCCAGGAAAGCTGACACTTGTGTGGATTCATCCTTATGTAGTGAAGAT
65 TTCTCAGAAACTAATCAGCCAGGAAAGCTGACACTTGTGTGGAAGCATCCTCAGGTAGTGAAGAT
* * *
1100196 TCAAATTTGTGAAAATCATGACCCCCGGGGGTAGGT
130 TCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGG
* * * * * * * *
1100232 TTGGGCTACAATGGGAGATCGACGTTTTACATAGGAATATACACAGTTAATCTTTAAAAATCTTC
1 TGGGGCCACAATGGG-GGTCGAAGTTTAACATATGAATATATACAGTAAATCTTTAAAAATCTTC
*
1100297 TTCTCAGAAACTAATCAGCCAGGAAAGCTGACACTTGTGTGGATGCATCCTCAGGTAGTGTAA-A
65 TTCTCAGAAACTAATCAGCCAGGAAAGCTGACACTTGTGTGGAAGCATCCTCAGGTAGTG-AAGA
* *
1100361 TTCAAAGTTGTAAAAATCATGACCCCCGGGGGTAGGG
129 TTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGG
* *
1100398 TTGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATACAGTAAATCTTTAAAAATCTTC
1 TGGGGCCACAATGGGGG-TCGAAGTTTAACATATGAATATATACAGTAAATCTTTAAAAATCTTC
* *
1100463 TTCTCAGTAACTAATTC-G-AAGGCAAAGCTGACACTTGTGTGGAAGCATCCTCAGGTAGTGAAG
65 TTCTCAGAAACTAA-TCAGCCAGG-AAAGCTGACACTTGTGTGGAAGCATCCTCAGGTAGTGAAG
* *
1100526 ATTCAAAGTTGTGAAAATCATGACCCCTGGGTGTAGGT
128 ATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGG
* * *
1100564 TGGGGCCACAATGGGGGATTGAAGTTAAACATATGATTATATACAGTAAATCTTTAAAAATCTTC
1 TGGGGCCACAATGGGGG-TCGAAGTTTAACATATGAATATATACAGTAAATCTTTAAAAATCTTC
* * * * * *
1100629 TTCTCAGAAACTAATTAGCCAGAAAAGCTAAAACTTGTGTGGAAGCATCCTCAGTTAGTGTAGAT
65 TTCTCAGAAACTAATCAGCCAGGAAAGCTGACACTTGTGTGGAAGCATCCTCAGGTAGTGAAGAT
** * *
1100694 TTGAATTTGTGAAAAGCATGACCCCTGGGGGTA-GG
130 TCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGG
* * * * * * *
1100729 TTGGGCCACAATGGGAGGTCGATGTTTTACAT-TGGAATAAACAGAGT-CATCTTTAAAAATCTT
1 TGGGGCCACAATGGG-GGTCGAAGTTTAACATAT-GAATATATACAGTAAATCTTTAAAAATCTT
* *
1100792 CTTCTCAGAAACTAATCAGCCAGGAAAGCTGGA-ACTTGTGTGAAAGCATCCTCAGGTAGTGTAG
64 CTTCTCAGAAACTAATCAGCCAGGAAAGCT-GACACTTGTGTGGAAGCATCCTCAGGTAGTGAAG
* * *
1100856 ATTTAAAGTTGTGAAAATAATGATCCCC-AGGGGTAGGG
128 ATTCAAAGTTGTGAAAATCATGA-CCCCTGGGGGTAGGG
* * * * **
1100894 TGGGGCCACAATGGGGGGAGGTCAAAGTTTAACAAAGGAATTTATAGGGTAAATCTTTAAAAA--
1 TGGGGCCACAAT---GGG-GGTCGAAGTTTAACATATGAATATATACAGTAAATCTTTAAAAATC
1100957 -TCTTCTCAGAAACTAATCAGCCAG
62 TTCTTCTCAGAAACTAATCAGCCAG
1100981 ATGATTCTTT
Statistics
Matches: 795, Mismatches: 100, Indels: 40
0.85 0.11 0.04
Matches are distributed among these distances:
164 98 0.12
165 62 0.08
166 592 0.74
167 7 0.01
168 25 0.03
169 11 0.01
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (165 bp):
TGGGGCCACAATGGGGGTCGAAGTTTAACATATGAATATATACAGTAAATCTTTAAAAATCTTCT
TCTCAGAAACTAATCAGCCAGGAAAGCTGACACTTGTGTGGAAGCATCCTCAGGTAGTGAAGATT
CAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGG
Found at i:1108531 original size:27 final size:27
Alignment explanation
Indices: 1108493--1108546 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1108483 TGTATCTCTC
1108493 CAAGTAAATATGTATTAAGTTTCAATA
1 CAAGTAAATATGTATTAAGTTTCAATA
1108520 CAAGTAAATATGTATTAAGTTTCAATA
1 CAAGTAAATATGTATTAAGTTTCAATA
1108547 TAGAAATCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.37
Consensus pattern (27 bp):
CAAGTAAATATGTATTAAGTTTCAATA
Found at i:1109634 original size:22 final size:22
Alignment explanation
Indices: 1109603--1109660 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
1109593 ATTTTTTGTT
* **
1109603 AATTTCGATCCCGATTACGATG
1 AATTTCGATCCCGATCACGACA
* *
1109625 AATTTTGATCCCTATCACGACA
1 AATTTCGATCCCGATCACGACA
1109647 AATTTCGATCCCGA
1 AATTTCGATCCCGA
1109661 GACGATCGCA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (22 bp):
AATTTCGATCCCGATCACGACA
Found at i:1109734 original size:20 final size:20
Alignment explanation
Indices: 1109709--1109746 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1109699 CGAATAACTA
*
1109709 TGAAATTTTGGTCGCAAAAT
1 TGAAATTTTAGTCGCAAAAT
1109729 TGAAATTTTAGTCGCAAA
1 TGAAATTTTAGTCGCAAA
1109747 TGCGACCGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (20 bp):
TGAAATTTTAGTCGCAAAAT
Found at i:1115771 original size:2 final size:2
Alignment explanation
Indices: 1115766--1115800 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1115756 TATGCAAAGA
*
1115766 AT AT AT A- AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1115801 NNNNNNNNNN
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1122412 original size:167 final size:165
Alignment explanation
Indices: 1121935--1122575 Score: 1021
Period size: 167 Copynumber: 3.9 Consensus size: 165
1121925 AACCGAAGGT
1121935 CCAAAACTGGGGCCCCAGGCGGGGTTCAAAGTTTAACATAGAAATACATAGGAAAATGTTTAAAA
1 CCAAAACTGGGGCCCCAGGCGGGGTTCAAAGTTTAACATAGAAATACATAGGAAAATGTTT-AAA
* *
1122000 AATGTTCTCCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTATACATAG
65 AATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTATACATAG
*
1122065 TGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGA
130 TGAAGATTCTAAATTGTAGAAATCGTGACCCTCGGA
1122101 CCAAAACTGGGGCCCCAGGCGGGGTTCAAAGTTTAACATAGAAATACATAGGAAAATGTTTAAAA
1 CCAAAACTGGGGCCCCAGGCGGGGTTCAAAGTTTAACATAGAAATACATAGGAAAATGTTTAAAA
* *
1122166 ATCTTCTTCTCAAGAACCACGGCACCAGAAATGCCAATATTTACACAAAAGCTTGTATATATAGT
66 ATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTATACATAGT
* *
1122231 GAAGATTTTAAATTGTAGAAATCGTGCCCCTCGGA
131 GAAGATTCTAAATTGTAGAAATCGTGACCCTCGGA
* * *
1122266 CCAAGACTGGGGCCCCAGGTGGGGTTCAAAGTTTAACATAGAAATACCTTAGGAAAATGTTTAGA
1 CCAAAACTGGGGCCCCAGGCGGGGTTCAAAGTTTAACATAGAAATA-CATAGGAAAATGTTTA-A
**
1122331 AAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTATGTATA
64 AAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTATACATA
*
1122396 ATGAAGATTCTAAATTGTAGAAATCGTGACCCTCGGA
129 GTGAAGATTCTAAATTGTAGAAATCGTGACCCTCGGA
* * * *
1122433 CCAAGACTGGGGCCCCAGGCGGGGTTCAAAGTTGAACATAGAACTACATATGAAAAATGTTTAAA
1 CCAAAACTGGGGCCCCAGGCGGGGTTCAAAGTTTAACATAGAAATACATA-GGAAAATGTTTAAA
* * * * ** *
1122498 AATTTTCTTCTGAAGAACCACTTCACCAAAAATGCCAATACATACACAAAAGGTTGTATACATAG
65 AATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTATACATAG
*
1122563 TGAAGATTGTAAA
130 TGAAGATTCTAAA
1122576 AATCGTGACC
Statistics
Matches: 441, Mismatches: 31, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
165 141 0.32
166 148 0.34
167 152 0.34
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (165 bp):
CCAAAACTGGGGCCCCAGGCGGGGTTCAAAGTTTAACATAGAAATACATAGGAAAATGTTTAAAA
ATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTATACATAGT
GAAGATTCTAAATTGTAGAAATCGTGACCCTCGGA
Found at i:1123394 original size:165 final size:165
Alignment explanation
Indices: 1123144--1124696 Score: 449
Period size: 165 Copynumber: 9.5 Consensus size: 165
1123134 CGGTATATAT
* * * * *
1123144 GGAAAATGTTTAAAAATCTTCTTT-TCGAGAACTACAATGCATCAATTTGTCAGATAACTACGTC
1 GGAAAATGTTTAAAAATCTT-TTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTA-GGC
* * * *
1123208 -AGCACCCTCAAATAGTGTAGATTCGAAATTA-TAAAAGCCGT-G-ATCTCAATCTAATACTGGG
64 AAGCATCCTCAAATAATGTAGATTCCAAATAATTAAAA-CCGTAGCA-CTCAA-CTAATACTGGG
* * *
1123269 GCCCCAAGAGGTGTTCAAAGTTTAGCATAGAAATATAGAG
126 GCCCCAAGAGGGGTTCAAAGTTTAACATAGAAAGATAGAG
* * * *
1123309 GGAAAATGTTGAAAAATCTTTTTCTAGGGAACTATAATGCTTCAGCTTGTGAGATAACTAGGCAA
1 GGAAAATGTTTAAAAATCTTTTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTAGGCAA
* ** ** *
1123374 GCATCCTTAAATAATGTAGATTCCAAATAATTAAAACTTTAGCACTGGACTAATACTGTGGCCCC
66 GCATCCTCAAATAATGTAGATTCCAAATAATTAAAACCGTAGCACTCAACTAATACTGGGGCCCC
* *
1123439 AAGAGGGGTTCAAAGTTTAACATAGAAAGATATAT
131 AAGAGGGGTTCAAAGTTTAACATAGAAAGATAGAG
* * * * *
1123474 TGAAAATGTTTTTAAAAA-GTTTTTCTCGAGAACTATAATGCTACAGTTTGTGAGATTACTATGC
1 GGAAAATG--TTTAAAAATCTTTTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTAGGC
* * * * * * *
1123538 AAGGATCCTCAAAT--TGT--NTGT--AGA-AA-T-----CGT-GACCCTCGGACCAAGACTGGG
64 AAGCATCCTCAAATAATGTAGAT-TCCAAATAATTAAAACCGTAG-CACTC-AACTAATACTGGG
* * * ** * * *
1123589 GCCCCAGGCGGGGTTCAAAGTTGAACATAGAACTACATAT
126 GCCCCAAGAGGGGTTCAAAGTTTAACATAGAAAGATAGAG
* * ** * *
1123629 GAAAAATGTTTAAAAAT-TTTCTTCT-GAAGAAC---CA--CTTCA-----CCA-A-AAAT-GCC
1 GGAAAATGTTTAAAAATCTTT-TTCTCG-AGAACTATAATGCTTCAGTTTGTGAGATAACTAGGC
* * * * * * * * * * * *
1123679 AATACATACAC-AA-AAGGTTG-TATACATAGTGAAGATTGTAAAAATCGTGACCCCTGAACAAA
64 AA-GCATCCTCAAATAATGTAGAT-TCCA-AAT--A-A-T-T-AAAACCGT-AGCACTCAACTAA
* * * * * *
1123741 AAGTGGGGCCCC-AGTAGGGGTTTAGATTTTAACAT---ATG-T--A-
119 TACTGGGGCCCCAAG-AGGGGTTCAAAGTTTAACATAGAAAGATAGAG
* * * * ** * * * * *
1123781 GGAAAATGTTTTAAAATCTTCTTCTCAAGAACTATAGTGCAACTGTTTGGGATATTACTATGCAT
1 GGAAAATGTTTAAAAATCTTTTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTAGGC--
* * ** *
1123846 ACATGTACATCCTTAAATAATGTAGATT-CAAAAAATTGTAA-C-T--C-C-CGGAC-AAT--TG
64 A-A-G--CATCCTCAAATAATGTAGATTCCAAATAATTAAAACCGTAGCACTC-AACTAATACTG
* * * * *
1123901 ATGGGCACCAAGAGGGGTTCAAAATTTAAACATTTTAAAAAACATA-AA
124 --GGGCCCCAAGAGGGGTTCAAAGTTT-AACA---T-AGAAAGATAGAG
* * * * ** *
1123949 GGAAAA-GTTTAAAAAT-TTTATTCTCAAGAACTACAATGTTTTAGTTTGTG-GAATTTCTATGC
1 GGAAAATGTTTAAAAATCTTT-TTCTCGAGAACTATAATGCTTCAGTTTGTGAG-ATAACTAGGC
* ** * * *** * * * * *
1124011 ATGCATCCTTC-GCTTATGTAGATTCCTAATTGGTAAAATCGT-GACCCCCGGACCAATACTGGG
64 AAGCATCC-TCAAATAATGTAGATTCCAAATAATTAAAACCGTAG-CACTC-AACTAATACTGGG
* ** * * *
1124074 GCCCCAAGATGGGG-TCAAAATTTATTAAAGAAATATAAAG
126 GCCCCAAGA-GGGGTTCAAAGTTTAACATAGAAAGATAGAG
* * * * * * * *
1124114 GTAACATGTTAAAAAATCTTCTTCTCGAGAACTACAATGCTTCAATTTGTGAGATTACTATCATG
1 GGAAAATGTTTAAAAATCTTTTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAAC--T-AGG
* *** * * * * * ** * * ** *
1124179 CATA-CAACCTTGGATAATGAAGGTTCGACAGT-TTTAAAATAGTGACCCCTGGACTAATACTAG
63 CA-AGCATCCTCAAATAATGTAGATTCCA-AATAATTAAAACCGT-AGCACTCAACTAATACTGG
* * * * * ** * *
1124242 AGACCCAAGATGGGTTTAAAGTTAAATGTAGAAGTACCGGTATATAT
125 GGCCCCAAGAGGGGTTCAAAGTTTAACATAGAA--A---G-ATAGAG
* * * * *
1124289 GGAAAATGTTTAAAAATCTTCTTT-TCGAGAACTACAATGCATCAATTTGTCAGATAACTACGTC
1 GGAAAATGTTTAAAAATCTT-TTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTA-GGC
* * * *
1124353 -AGCACCCTCAAATAGTGTAGATTCGAAATTA-TAAAAGCCGT-G-ATCTCAATCTAATACTGGG
64 AAGCATCCTCAAATAATGTAGATTCCAAATAATTAAAA-CCGTAGCA-CTCAA-CTAATACTGGG
* * *
1124414 GCCCCAAGAGGTGTTCAAAGTTTAGCATAGAAATATAGAG
126 GCCCCAAGAGGGGTTCAAAGTTTAACATAGAAAGATAGAG
* * * *
1124454 GGAAAATGTTGAAAAATCTTTTTCTAGGGAACTATAATGCTTCAGCTTGTGAGATAACTAGGCAA
1 GGAAAATGTTTAAAAATCTTTTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTAGGCAA
* ** ** *
1124519 GCATCCTTAAATAATGTAGATTCCAAATAATTAAAACTTTAGCACTGGACTAATACTGTGGCCCC
66 GCATCCTCAAATAATGTAGATTCCAAATAATTAAAACCGTAGCACTCAACTAATACTGGGGCCCC
* *
1124584 AAGAGGGGTTCAAAGTTTAACATAGAAAGATATAT
131 AAGAGGGGTTCAAAGTTTAACATAGAAAGATAGAG
* * * * *
1124619 TGAAAATGTTTTTAAAAA-GTTTTTCTCGAGAACTATAATGCTACAGTTTGTGAGATTACTATGC
1 GGAAAATG--TTTAAAAATCTTTTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTAGGC
*
1124683 AAGGATCCTCAAAT
64 AAGCATCCTCAAAT
1124697 TGTGTAAACT
Statistics
Matches: 1007, Mismatches: 259, Indels: 243
0.67 0.17 0.16
Matches are distributed among these distances:
141 5 0.00
142 8 0.01
143 3 0.00
144 1 0.00
145 1 0.00
149 5 0.00
150 1 0.00
151 1 0.00
152 24 0.02
153 17 0.02
154 13 0.01
155 52 0.05
156 1 0.00
157 22 0.02
158 10 0.01
159 34 0.03
160 6 0.01
161 18 0.02
162 10 0.01
163 5 0.00
164 25 0.02
165 269 0.27
166 164 0.16
167 63 0.06
168 21 0.02
169 80 0.08
170 17 0.02
171 48 0.05
172 26 0.03
173 3 0.00
175 52 0.05
176 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.29
Consensus pattern (165 bp):
GGAAAATGTTTAAAAATCTTTTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTAGGCAA
GCATCCTCAAATAATGTAGATTCCAAATAATTAAAACCGTAGCACTCAACTAATACTGGGGCCCC
AAGAGGGGTTCAAAGTTTAACATAGAAAGATAGAG
Found at i:1128876 original size:14 final size:14
Alignment explanation
Indices: 1128857--1128886 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1128847 AAACATCTAA
1128857 TCGTATACTAGTAC
1 TCGTATACTAGTAC
1128871 TCGTATACTAGTAC
1 TCGTATACTAGTAC
1128885 TC
1 TC
1128887 CTATGAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (14 bp):
TCGTATACTAGTAC
Found at i:1144069 original size:21 final size:21
Alignment explanation
Indices: 1144054--1144094 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1144044 ATAGTTTTCC
1144054 ACCAATAAACTGTAGTTTACA
1 ACCAATAAACTGTAGTTTACA
*
1144075 ACCAGTAAACTGTAGTTTAC
1 ACCAATAAACTGTAGTTTAC
1144095 GCATCGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (21 bp):
ACCAATAAACTGTAGTTTACA
Found at i:1144989 original size:37 final size:37
Alignment explanation
Indices: 1144940--1145052 Score: 181
Period size: 37 Copynumber: 3.1 Consensus size: 37
1144930 TCGATCGACC
1144940 ATGTATGTATTCATTTGAATGTAAAATGTCTTCTTTT
1 ATGTATGTATTCATTTGAATGTAAAATGTCTTCTTTT
*
1144977 ATGTATATATTCATTTGAATGTAAAATGTCTTCTTTT
1 ATGTATGTATTCATTTGAATGTAAAATGTCTTCTTTT
* * * *
1145014 ATGCATGTATTTATTTAAATGTAAAATGACTTCTTTT
1 ATGTATGTATTCATTTGAATGTAAAATGTCTTCTTTT
1145051 AT
1 AT
1145053 TTATTGAGTG
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.50
Consensus pattern (37 bp):
ATGTATGTATTCATTTGAATGTAAAATGTCTTCTTTT
Found at i:1164746 original size:1 final size:1
Alignment explanation
Indices: 1164742--1164775 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
1164732 GATATAATAC
1164742 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1164776 AGGAAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:1166679 original size:30 final size:30
Alignment explanation
Indices: 1166645--1166705 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
1166635 AATACGTTGC
1166645 CGGTCCAATAGATCGCAGTCTATTGACCGG
1 CGGTCCAATAGATCGCAGTCTATTGACCGG
1166675 CGGTCCAATAGATCGCAGTCTATTGACCGG
1 CGGTCCAATAGATCGCAGTCTATTGACCGG
1166705 C
1 C
1166706 AGTTCAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.28, G:0.26, T:0.23
Consensus pattern (30 bp):
CGGTCCAATAGATCGCAGTCTATTGACCGG
Found at i:1168155 original size:43 final size:43
Alignment explanation
Indices: 1168108--1168266 Score: 300
Period size: 43 Copynumber: 3.7 Consensus size: 43
1168098 AACACCAGCA
1168108 GTAATCATAAGATTGGAGTACCAGATATTCCATGACACAACTG
1 GTAATCATAAGATTGGAGTACCAGATATTCCATGACACAACTG
* *
1168151 GTAATCATAAGATTGAAGTAACAGATATTCCATGACACAACTG
1 GTAATCATAAGATTGGAGTACCAGATATTCCATGACACAACTG
1168194 GTAATCATAAGATTGGAGTACCAGATATTCCATGACACAACTG
1 GTAATCATAAGATTGGAGTACCAGATATTCCATGACACAACTG
1168237 GTAATCATAAGATTGGAGTACCAGATATTC
1 GTAATCATAAGATTGGAGTACCAGATATTC
1168267 TTCAGCATCA
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 112 1.00
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.26
Consensus pattern (43 bp):
GTAATCATAAGATTGGAGTACCAGATATTCCATGACACAACTG
Found at i:1183819 original size:2 final size:2
Alignment explanation
Indices: 1183812--1183864 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1183802 CTCCTAGTGC
1183812 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1183854 AG AG AG AG AG A
1 AG AG AG AG AG A
1183865 TGTTAATTTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1185193 original size:165 final size:166
Alignment explanation
Indices: 1184833--1185195 Score: 543
Period size: 166 Copynumber: 2.2 Consensus size: 166
1184823 AGAAATTTTC
* * * * *
1184833 AAAAATCTTCTTCTCA-AGAACCAGA-AAGCCATGAAAGCTGAAACTTGTGTGAAAGCATCCTCA
1 AAAAATCTTCTTCTCAGA-AACTA-ATCAGCCAGGAAAGCTGAAACTTATGTGAAAGCAACCTCA
* * *
1184896 GGTAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGG
64 GGTAGTGCAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGAGG
*
1184961 GTCGAAGTTTTACATAGGAATATATAGTGTAAATCTTT
129 GTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* * * *
1184999 AAAAATTTTCTTTTCAGAAACTGATCAGCCAGGAAAGCTGAAACTTATGTGGAAGCAACCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTATGTGAAAGCAACCTCAGG
* *
1185064 TAGTGCAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGG-CACAATGGAGGGT
66 TAGTGCAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGAGGGT
1185128 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
131 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
*
1185164 GAAAATCTTCTTCTCAGAAACTAATCAGCCAG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAG
1185196 ACGATTCTTT
Statistics
Matches: 176, Mismatches: 19, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
165 76 0.43
166 99 0.56
167 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (166 bp):
AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTATGTGAAAGCAACCTCAGG
TAGTGCAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGAGGGT
CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
Found at i:1187554 original size:18 final size:18
Alignment explanation
Indices: 1187528--1187604 Score: 109
Period size: 18 Copynumber: 4.3 Consensus size: 18
1187518 GGTCACAATC
*
1187528 CAGGGGTGACTCTACAGC
1 CAGGGGTGACTCTACAGT
*
1187546 CATGGGTGACTCTACAGT
1 CAGGGGTGACTCTACAGT
* *
1187564 CAGGGGGGACTTTACAGT
1 CAGGGGTGACTCTACAGT
*
1187582 CAGGGGTGACTATACAGT
1 CAGGGGTGACTCTACAGT
1187600 CAGGG
1 CAGGG
1187605 AAATGTCAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 52 1.00
ACGTcount: A:0.23, C:0.21, G:0.35, T:0.21
Consensus pattern (18 bp):
CAGGGGTGACTCTACAGT
Found at i:1188718 original size:18 final size:18
Alignment explanation
Indices: 1188695--1188729 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1188685 CACAATCCAG
1188695 GGGTGACTCTACAGTCAT
1 GGGTGACTCTACAGTCAT
1188713 GGGTGACTCTACAGTCA
1 GGGTGACTCTACAGTCA
1188730 AGAGGGATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.26
Consensus pattern (18 bp):
GGGTGACTCTACAGTCAT
Found at i:1197626 original size:366 final size:369
Alignment explanation
Indices: 1196895--1197633 Score: 1340
Period size: 366 Copynumber: 2.0 Consensus size: 369
1196885 GAGTTGTCAT
*
1196895 TATATAAATAGTGCCTGTTTGGGAGGGTAACAGTTGAAATTGACACCCCGAGAAAACCATTGTCA
1 TATATAAATAGTGCCTGTTTGGGAGGGTAACAGTTGAAATTAACACCCCGAGAAAACCATTGTCA
1196960 ACCGACGCGAAGCGGAGGTTGACAATGGTTTTCGAGGGGTGTCAATTTCAACTGTTATCCTCCCA
66 ACCGACGCGAAGCGGAGGTTGACAATGGTTTTCGAGGGGTGTCAATTTCAACTGTTATCCTCCCA
1197025 AACAGGCACTATTTATTTTGTTATACTGAATGTCTTTTTTAAAATTTTTAAGAAAATTTTACTGC
131 AACAGGCACTATTTATTTTGTTATACTGAATGTC---TTT-AAATTTTTAAGAAAATTTTACTGC
*
1197090 TTTTATATAGGAATAACGTGAATTCTACAGCGAACCGTACGCGCATAATTTTCGCGCATGTAACA
192 TTTTATATAGGAATAACGTGAATTCTACAGCGAACCGTACGCGCATAATTTTCGCGCATATAACA
* * * *
1197155 TTTTTTAATGTTACCCGTTGCCAAGTGCGTTGCTAACGCTGAGGGTAATAGTAAATATTATTAAC
257 ATTTTTAATGTTACCCGTTGCCAAGTGCGTTGCTAACGCTGAGGGTAATAGAAAAAATTATGAAC
1197220 TGCGTCTTAACCAATCAGATTTCAGTATTTAACATGAAAGTATAACAA
322 TGCGTCTTAACCAATCAGATTTCAGTATTTAACATGAAAGTATAACAA
* *
1197268 TATATAAATAGTGCCTGTTTGGGAGGGTAACAGTTGAAATTAACATCCCGA-TAAACCATTGTCA
1 TATATAAATAGTGCCTGTTTGGGAGGGTAACAGTTGAAATTAACACCCCGAGAAAACCATTGTCA
1197332 ACCGACGCGAAGCGGAGGTTGACAATGGTTTTCGAGGGGTGTCAATTTCAACTGTTATCCTCCCA
66 ACCGACGCGAAGCGGAGGTTGACAATGGTTTTCGAGGGGTGTCAATTTCAACTGTTATCCTCCCA
1197397 AACAGGCACTATTTATTTTGTTATACTGAATGTC-TT-AATTTTTAAGAAAATTTTACTGCTTTT
131 AACAGGCACTATTTATTTTGTTATACTGAATGTCTTTAAATTTTTAAGAAAATTTTACTGCTTTT
1197460 ATATAGGAATAACGTGAATTCTACAGCGAACCGTACGCGCATAATTTTCGCGCATATAACAATTT
196 ATATAGGAATAACGTGAATTCTACAGCGAACCGTACGCGCATAATTTTCGCGCATATAACAATTT
*
1197525 TTAATGTTACCCGTTGCTAAGTGCGTTGCTAACGCTGAGGGTAATAGAAAAAATTATGAACTGCG
261 TTAATGTTACCCGTTGCCAAGTGCGTTGCTAACGCTGAGGGTAATAGAAAAAATTATGAACTGCG
1197590 TCTTAACCAATCAGATTTCAGTATTTAACATGAAAGTATAACAA
326 TCTTAACCAATCAGATTTCAGTATTTAACATGAAAGTATAACAA
1197634 AAGTATTTAT
Statistics
Matches: 357, Mismatches: 9, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
366 195 0.55
368 2 0.01
372 111 0.31
373 49 0.14
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (369 bp):
TATATAAATAGTGCCTGTTTGGGAGGGTAACAGTTGAAATTAACACCCCGAGAAAACCATTGTCA
ACCGACGCGAAGCGGAGGTTGACAATGGTTTTCGAGGGGTGTCAATTTCAACTGTTATCCTCCCA
AACAGGCACTATTTATTTTGTTATACTGAATGTCTTTAAATTTTTAAGAAAATTTTACTGCTTTT
ATATAGGAATAACGTGAATTCTACAGCGAACCGTACGCGCATAATTTTCGCGCATATAACAATTT
TTAATGTTACCCGTTGCCAAGTGCGTTGCTAACGCTGAGGGTAATAGAAAAAATTATGAACTGCG
TCTTAACCAATCAGATTTCAGTATTTAACATGAAAGTATAACAA
Found at i:1198246 original size:30 final size:30
Alignment explanation
Indices: 1198210--1198271 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
1198200 CAGCTTAATG
*
1198210 AATTATTTATACACAATTTAGTCAAAGGAA
1 AATTATTTATACACAATTTAATCAAAGGAA
1198240 AATTATTTATACACAATTTAATCAAAGGAA
1 AATTATTTATACACAATTTAATCAAAGGAA
1198270 AA
1 AA
1198272 AAAATAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.32
Consensus pattern (30 bp):
AATTATTTATACACAATTTAATCAAAGGAA
Found at i:1211634 original size:15 final size:14
Alignment explanation
Indices: 1211614--1211649 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1211604 ATTTTTTTCT
1211614 GAAAAAAAAATTGTG
1 GAAAAAAAAATT-TG
1211629 G-AAAAAAAATTTG
1 GAAAAAAAAATTTG
1211642 GAAAAAAA
1 GAAAAAAA
1211650 TCAGGCTCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 3 0.15
14 16 0.80
15 1 0.05
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (14 bp):
GAAAAAAAAATTTG
Found at i:1211635 original size:14 final size:13
Alignment explanation
Indices: 1211616--1211649 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
1211606 TTTTTTCTGA
1211616 AAAAAAAATTGTGG
1 AAAAAAAATT-TGG
1211630 AAAAAAAATTTGG
1 AAAAAAAATTTGG
1211643 AAAAAAA
1 AAAAAAA
1211650 TCAGGCTCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.18
Consensus pattern (13 bp):
AAAAAAAATTTGG
Found at i:1218363 original size:162 final size:161
Alignment explanation
Indices: 1217938--1218430 Score: 697
Period size: 161 Copynumber: 3.1 Consensus size: 161
1217928 CAGTGTTCGT
* * * *
1217938 TCATTTTCTTCGCAAAGGATGAACATATTGAAATGAAATTCGGTATACAGGTTAATCATGATAAT
1 TCATTTTCTTCGCAGAGGATGAACATATTGGAATGAAATTTGGTATACAGGTTTATCATGATAAT
*
1218003 ATGTAGGTCAAGTTCGATATTGGATACGATCA-AGCAATTTTCGACAGAGTTATGGCCCTTGGAC
66 ATCTAGGTCAAGTTCGATATTGGATACGAT-AGAGCAATTTTCGACAGAGTTATGGCCCTTGGAC
* *
1218067 GTAGAAGAATTCCAGTTATTTACAGTTTCCGA
130 GTAGAAAAATTCCAGTTATTTGCAGTTTCCGA
* ** *
1218099 TCATTTTCTTCGCAGAGGATGAACATATTAGAATGAAATTTGGTATACAAATCTATCATGATAAT
1 TCATTTTCTTCGCAGAGGATGAACATATTGGAATGAAATTTGGTATACAGGTTTATCATGATAAT
* *
1218164 ATCTAGGTCAAGTTCGATATTGGATACGATCGAGCAATTTTCGATAGAGTTATGGCCCTTGGACG
66 ATCTAGGTCAAGTTCGATATTGGATACGATAGAGCAATTTTCGACAGAGTTATGGCCCTTGGACG
*
1218229 TAGAAAAATTCCAGTTATTTGCAGTTTCCGC
131 TAGAAAAATTCCAGTTATTTGCAGTTTCCGA
* * *
1218260 TTATTTTTTTTCGCAGAGGATGAACATATTGGAATGAAATTTGGTATACAGGTTTATC-TAAATA
1 TCA-TTTTCTTCGCAGAGGATGAACATATTGGAATGAAATTTGGTATACAGGTTTATCAT-GATA
* * * * * **
1218324 ATATCTAGGTCAAGTTTGATGTTGGGTATGATAGAGCAATTTTTGACAGAGTTATACCCCTTGGA
64 ATATCTAGGTCAAGTTCGATATTGGATACGATAGAGCAATTTTCGACAGAGTTATGGCCCTTGGA
*
1218389 CTTAGAAAAATTCCAGTTATTTGCAGTTT-C-A
129 CGTAGAAAAATTCCAGTTATTTGCAGTTTCCGA
1218420 TTCATTTTCTT
1 -TCATTTTCTT
1218431 TGTGGATGTT
Statistics
Matches: 294, Mismatches: 34, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
160 6 0.02
161 152 0.52
162 136 0.46
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (161 bp):
TCATTTTCTTCGCAGAGGATGAACATATTGGAATGAAATTTGGTATACAGGTTTATCATGATAAT
ATCTAGGTCAAGTTCGATATTGGATACGATAGAGCAATTTTCGACAGAGTTATGGCCCTTGGACG
TAGAAAAATTCCAGTTATTTGCAGTTTCCGA
Found at i:1220541 original size:152 final size:152
Alignment explanation
Indices: 1220265--1220569 Score: 592
Period size: 152 Copynumber: 2.0 Consensus size: 152
1220255 AGATTTTTAT
1220265 CCAATCAAATACTTAAATTAATGAATTCTATAATGCTGTCAAATAAAATGTGGGTTTATACACAG
1 CCAATCAAATACTTAAATTAATGAATTCTATAATGCTGTCAAATAAAATGTGGGTTTATACACAG
*
1220330 GGATTCTAAGGAATTCAAAAATGATAAACAACATAACAAAGTTTATATTTACAGCCTGGAAGACT
66 GGATTATAAGGAATTCAAAAATGATAAACAACATAACAAAGTTTATATTTACAGCCTGGAAGACT
*
1220395 CCTATTATTCTAATGGCAACCA
131 CCTATTATTCTAATGACAACCA
1220417 CCAATCAAATACTTAAATTAATGAATTCTATAATGCTGTCAAATAAAATGTGGGTTTATACACAG
1 CCAATCAAATACTTAAATTAATGAATTCTATAATGCTGTCAAATAAAATGTGGGTTTATACACAG
1220482 GGATTATAAGGAATTCAAAAATGATAAACAACATAACAAAGTTTATATTTACAGCCTGGAAGACT
66 GGATTATAAGGAATTCAAAAATGATAAACAACATAACAAAGTTTATATTTACAGCCTGGAAGACT
1220547 CCTATTATTCTAATGACAACCA
131 CCTATTATTCTAATGACAACCA
1220569 C
1 C
1220570 TGGAATTGGA
Statistics
Matches: 151, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
152 151 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.30
Consensus pattern (152 bp):
CCAATCAAATACTTAAATTAATGAATTCTATAATGCTGTCAAATAAAATGTGGGTTTATACACAG
GGATTATAAGGAATTCAAAAATGATAAACAACATAACAAAGTTTATATTTACAGCCTGGAAGACT
CCTATTATTCTAATGACAACCA
Found at i:1238369 original size:2 final size:2
Alignment explanation
Indices: 1238362--1238387 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1238352 TGAAACACTC
1238362 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
1238388 GGGGGGCGAG
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:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1239355 original size:168 final size:167
Alignment explanation
Indices: 1239155--1240060 Score: 1127
Period size: 168 Copynumber: 5.4 Consensus size: 167
1239145 GGTTGCGTGG
* * * * * *
1239155 TTATCATGTCCATGAGGCCCTCTACCAAAATTGTGAAATTTATGGCACCTTGGTCAGGGGTTCTG
1 TTATGATGTCCATGAAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTTGGTCAGGGGTTCAG
*
1239220 GCTCTATGGTGGGGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAGAAAACATTCTTCT
66 GCTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAGAAAAC-TTCTTCT
* * * * *
1239285 CTACTACCATATGTATTTTTTGAAAACTAAATGCATGA
130 CTACTCCCAAATATATTTGTTAAAAACTAAATGCATGA
* ** * * *
1239323 TTATGATATCCATGAAGCCCTCTATGAAAATTGTAAAATTCATGACCCCTGGGTTAGGGGTTCAG
1 TTATGATGTCCATGAAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTTGGTCAGGGGTTCAG
*
1239388 GCTCTA-GGTAGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATCTTAGAAAATCTTCTTC
66 GCTCTAGGGT-GGGGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAGAAAA-CTTCTTC
* *
1239452 TCCACTCCCAAATATATTTGTTAAAAACTCAATGCATGA
129 TCTACTCCCAAATATATTTGTTAAAAACTAAATGCATGA
* * * * * *
1239491 TTATGATGTCCATAAAGCCCTCAACCTAGATTGTGAAATTCATGACCTCTCGGTCAGGGGTTCAG
1 TTATGATGTCCATGAAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTTGGTCAGGGGTTCAG
* *
1239556 GCTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAAGGTATTAAATCTTAGAAAATATTCTTCT
66 GCTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAGAAAA-CTTCTTCT
* *
1239621 CTACTCTCATATATATTTGTTAAAAACTAAATGCATGA
130 CTACTCCCAAATATATTTGTTAAAAACTAAATGCATGA
* * * * *
1239659 TTATGATGTCCATGAGGCCCTCTATCGAAATTGTAAAATTCATGACCCCTGGGTCAGGGGTTCAG
1 TTATGATGTCCATGAAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTTGGTCAGGGGTTCAG
* * *
1239724 GCTCTAGGGTGGGGCCAATATGGCCAAATAATAAAAATGTAGTAAATCTTAGAAAATCTTCTTCT
66 GCTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAGAAAA-CTTCTTCT
* *
1239789 CTACTCCCAAATATATTTGTTAAAAACTAAATGCCTGG
130 CTACTCCCAAATATATTTGTTAAAAACTAAATGCATGA
* * *
1239827 TTATGATGTCCATG-AGACCCTCTACCAAAATTGTGAAATTCATGACCCCTTTGTTAGGTGTTCA
1 TTATGATGTCCATGAAG-CCCTCTACCAAAATTGTGAAATTCATGACCCCTTGGTCAGGGGTTCA
* * *
1239891 GGCTCTTGGGTGGGGCCAATATGGCCATATAGTAAAACTGTTTTAAATCTTA-AAAACTCTTCTT
65 GGCTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAGAAAA--CTTCTT
* * * ** ** * * *
1239955 CTCTACTCCCACACATGTGGGCAAAAAACTGAATACATGG
128 CTCTACTCCCAAATATATTTGTTAAAAACTAAATGCATGA
* * * * * * *
1239995 TTATGATATCCA-CAATCTCCTTTACCTAAATTGTAAAATTCATGGCCCCTTGGTCAGGGGTTCA
1 TTATGATGTCCATGAAGC-CCTCTACCAAAATTGTGAAATTCATGACCCCTTGGTCAGGGGTTCA
1240059 GG
65 GG
1240061 ACATGAAAGG
Statistics
Matches: 641, Mismatches: 90, Indels: 14
0.86 0.12 0.02
Matches are distributed among these distances:
167 9 0.01
168 628 0.98
169 4 0.01
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Consensus pattern (167 bp):
TTATGATGTCCATGAAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTTGGTCAGGGGTTCAG
GCTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAGAAAACTTCTTCTC
TACTCCCAAATATATTTGTTAAAAACTAAATGCATGA
Found at i:1261505 original size:21 final size:21
Alignment explanation
Indices: 1261490--1261548 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
1261480 AGTGGTTGCT
*
1261490 GGTGGCATGGTTGTGGTGGCG
1 GGTGGCATGGTGGTGGTGGCG
*
1261511 GGTGGCATGGTGGTAGTGGCG
1 GGTGGCATGGTGGTGGTGGCG
*
1261532 GGTGGCATAGTGGTGGT
1 GGTGGCATGGTGGTGGT
1261549 AACTGGTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.08, C:0.08, G:0.56, T:0.27
Consensus pattern (21 bp):
GGTGGCATGGTGGTGGTGGCG
Found at i:1262320 original size:11 final size:10
Alignment explanation
Indices: 1262293--1262347 Score: 83
Period size: 10 Copynumber: 5.3 Consensus size: 10
1262283 CGCGTCTTTT
1262293 AACCACAATG
1 AACCACAATG
1262303 AACCACAATG
1 AACCACAATG
1262313 ATACCACAATG
1 A-ACCACAATG
*
1262324 AATCACAATG
1 AACCACAATG
1262334 ATACCACAATG
1 A-ACCACAATG
1262345 AAC
1 AAC
1262348 TGATGATATT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
10 22 0.54
11 19 0.46
ACGTcount: A:0.49, C:0.27, G:0.09, T:0.15
Consensus pattern (10 bp):
AACCACAATG
Found at i:1262320 original size:21 final size:21
Alignment explanation
Indices: 1262294--1262347 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
1262284 GCGTCTTTTA
1262294 ACCACAATGAACCACAATGAT
1 ACCACAATGAACCACAATGAT
*
1262315 ACCACAATGAATCACAATGAT
1 ACCACAATGAACCACAATGAT
1262336 ACCACAATGAAC
1 ACCACAATGAAC
1262348 TGATGATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.48, C:0.28, G:0.09, T:0.15
Consensus pattern (21 bp):
ACCACAATGAACCACAATGAT
Found at i:1263683 original size:7 final size:7
Alignment explanation
Indices: 1263671--1263737 Score: 89
Period size: 7 Copynumber: 9.6 Consensus size: 7
1263661 GAGAAGGATC
1263671 ATTCGAG
1 ATTCGAG
1263678 ATTCGAG
1 ATTCGAG
*
1263685 ATTCGAA
1 ATTCGAG
*
1263692 ATACGAG
1 ATTCGAG
*
1263699 ATTCGAA
1 ATTCGAG
*
1263706 ATACGAG
1 ATTCGAG
1263713 ATTCGAG
1 ATTCGAG
*
1263720 ATTCGAA
1 ATTCGAG
1263727 ATTCGAG
1 ATTCGAG
1263734 ATTC
1 ATTC
1263738 AATATCTAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (7 bp):
ATTCGAG
Found at i:1264239 original size:2 final size:2
Alignment explanation
Indices: 1264232--1264275 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1264222 TTGTCGATAT
1264232 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1264274 GA
1 GA
1264276 CAGACAGACA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1264280 original size:4 final size:4
Alignment explanation
Indices: 1264273--1264302 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1264263 AGAGAGAGAG
1264273 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AG
1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AG
1264303 TTTTGTAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.27, T:0.00
Consensus pattern (4 bp):
AGAC
Found at i:1264488 original size:2 final size:2
Alignment explanation
Indices: 1264481--1264526 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1264471 TTTACATCGA
*
1264481 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1264523 CT CT
1 CT CT
1264527 TTCATCTCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:1266593 original size:7 final size:7
Alignment explanation
Indices: 1266578--1266644 Score: 89
Period size: 7 Copynumber: 9.6 Consensus size: 7
1266568 TTTAGATATT
1266578 GAATCTC
1 GAATCTC
*
1266585 GAATTTC
1 GAATCTC
1266592 GAATCTC
1 GAATCTC
1266599 GAATCTC
1 GAATCTC
* *
1266606 GTATTTC
1 GAATCTC
1266613 GAATCTC
1 GAATCTC
* *
1266620 GTATTTC
1 GAATCTC
1266627 GAATCTC
1 GAATCTC
1266634 GAATCTC
1 GAATCTC
1266641 GAAT
1 GAAT
1266645 GATCCTTCTC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (7 bp):
GAATCTC
Found at i:1266603 original size:21 final size:21
Alignment explanation
Indices: 1266578--1266644 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
1266568 TTTAGATATT
1266578 GAATCTCGAATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
*
1266599 GAATCTCGTATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
* * *
1266620 GTATTTCGAATCTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
1266641 GAAT
1 GAAT
1266645 GATCCTTCTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (21 bp):
GAATCTCGAATTTCGAATCTC
Found at i:1272249 original size:20 final size:19
Alignment explanation
Indices: 1272226--1272277 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
1272216 ATTCAAACTC
1272226 TTGATAT-AAAAAAAAATTCT
1 TTGATATCAAAAAAAAA-T-T
* *
1272246 TTGAT-TGAAAACAAAATT
1 TTGATATCAAAAAAAAATT
1272264 TTGATATCAAAAAA
1 TTGATATCAAAAAA
1272278 TCTATTTCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 6 0.22
19 8 0.30
20 13 0.48
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.33
Consensus pattern (19 bp):
TTGATATCAAAAAAAAATT
Found at i:1272348 original size:21 final size:22
Alignment explanation
Indices: 1272308--1272368 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 22
1272298 TTTTTCTTTG
* *
1272308 ATATCATAAAATAGA-ATTCTTA
1 ATATCACAAAATAGATTTTC-TA
*
1272330 ATATCA-AAAAT-GATTTTCTG
1 ATATCACAAAATAGATTTTCTA
1272350 ATATCACAAAATAGATTTT
1 ATATCACAAAATAGATTTT
1272369 TTTATATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 9 0.26
21 13 0.38
22 12 0.35
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.38
Consensus pattern (22 bp):
ATATCACAAAATAGATTTTCTA
Found at i:1272366 original size:22 final size:22
Alignment explanation
Indices: 1272299--1272368 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
1272289 ATATCAGATT
1272299 TTTTCTTTGATATCATAAAATAGA
1 TTTTC-TTGATATCA-AAAATAGA
* *
1272323 -ATTCTTAATATCAAAAAT-GA
1 TTTTCTTGATATCAAAAATAGA
1272343 TTTTC-TGATATCACAAAATAGA
1 TTTTCTTGATATCA-AAAATAGA
1272365 TTTT
1 TTTT
1272369 TTTATATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 9 0.23
21 13 0.33
22 14 0.36
23 3 0.08
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (22 bp):
TTTTCTTGATATCAAAAATAGA
Found at i:1272375 original size:22 final size:21
Alignment explanation
Indices: 1272308--1272384 Score: 66
Period size: 22 Copynumber: 3.6 Consensus size: 21
1272298 TTTTTCTTTG
* *
1272308 ATATCATAAAATAGAATTCTTA
1 ATATCA-AAAATAGATTTTTTA
* *
1272330 ATATCAAAAAT-GATTTTCTG
1 ATATCAAAAATAGATTTTTTA
*
1272350 ATATCACAAAATAGATTTTTTT
1 ATATCA-AAAATAGATTTTTTA
*
1272372 ATATAAATAAATA
1 ATATCAA-AAATA
1272385 AAGTTGATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
20 11 0.24
21 11 0.24
22 23 0.51
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (21 bp):
ATATCAAAAATAGATTTTTTA
Found at i:1272968 original size:20 final size:21
Alignment explanation
Indices: 1272922--1272981 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
1272912 TGGTTCGTAT
* *
1272922 TTTCTGATATCAAGAATTCGAA
1 TTTCTGATATCAAAAAATC-AA
1272944 TTTCTGATATCAAAAAATC-A
1 TTTCTGATATCAAAAAATCAA
*
1272964 TTTCTGATATCAGAAAAT
1 TTTCTGATATCAAAAAAT
1272982 ACCTCAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
20 18 0.51
22 17 0.49
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (21 bp):
TTTCTGATATCAAAAAATCAA
Found at i:1273766 original size:34 final size:34
Alignment explanation
Indices: 1273723--1274173 Score: 717
Period size: 34 Copynumber: 13.3 Consensus size: 34
1273713 TGTCTTTCTA
*
1273723 ACATGACTTATTATACAACACGCCGTGTTTACTG
1 ACATGACTTATTATACAACACGCCATGTTTACTG
** *
1273757 ACATGACTTATTATACAACACGTTATGTTTACTA
1 ACATGACTTATTATACAACACGCCATGTTTACTG
*
1273791 ACATGACTT-TTCATACAACACGCCATGTTTACTA
1 ACATGACTTATT-ATACAACACGCCATGTTTACTG
1273825 ACATGACTTATTATACAACACGCCATGTTTACTG
1 ACATGACTTATTATACAACACGCCATGTTTACTG
*
1273859 ACATGCCTTATTATACAACACGCCATGTTTACTG
1 ACATGACTTATTATACAACACGCCATGTTTACTG
*
1273893 ACATGCCTTATTATACAACACGCCATGTTTACTG
1 ACATGACTTATTATACAACACGCCATGTTTACTG
*
1273927 ACATGCCTTATTATACAACACGCCATGTTTACTG
1 ACATGACTTATTATACAACACGCCATGTTTACTG
*
1273961 ACATGCCTTATTATACAACACGCCATGTTTACTG
1 ACATGACTTATTATACAACACGCCATGTTTACTG
*
1273995 ACATGACTTATTATACAACACGCCATGTTTACTA
1 ACATGACTTATTATACAACACGCCATGTTTACTG
* *
1274029 ACATGACTTATTATACAACACGCCATGTTTTCTA
1 ACATGACTTATTATACAACACGCCATGTTTACTG
* *
1274063 ACTTGACTT-TTCATACAACACGCCATGTTTACTA
1 ACATGACTTATT-ATACAACACGCCATGTTTACTG
1274097 ACATGACTTATTATACAACACGCCATGTTTACTG
1 ACATGACTTATTATACAACACGCCATGTTTACTG
* *
1274131 ACATGACTTATTATACAACACGTCATGTTTACTA
1 ACATGACTTATTATACAACACGCCATGTTTACTG
*
1274165 ACATCACTT
1 ACATGACTT
1274174 CGCACAACAC
Statistics
Matches: 395, Mismatches: 18, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
33 4 0.01
34 387 0.98
35 4 0.01
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.33
Consensus pattern (34 bp):
ACATGACTTATTATACAACACGCCATGTTTACTG
Found at i:1274889 original size:20 final size:20
Alignment explanation
Indices: 1274864--1274904 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1274854 CAGCAAATAA
1274864 AACAATACTGAACATTTAGC
1 AACAATACTGAACATTTAGC
1274884 AACAATACTGAACATTTAGC
1 AACAATACTGAACATTTAGC
1274904 A
1 A
1274905 CTCCGTCGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (20 bp):
AACAATACTGAACATTTAGC
Found at i:1275070 original size:2 final size:2
Alignment explanation
Indices: 1275063--1275088 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1275053 AACAGGTGTT
1275063 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1275089 NNNNNNNNNN
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1286618 original size:42 final size:41
Alignment explanation
Indices: 1286553--1286829 Score: 315
Period size: 42 Copynumber: 6.6 Consensus size: 41
1286543 TATCTACATC
1286553 ATCAAATTCTA-GAACAAAACCAGCCAATCCTATGCCTGCATT
1 ATCAAATTC-AGGAAC-AAACCAGCCAATCCTATGCCTGCATT
* * *
1286595 ATTAAATTCAGGAACAAAGCCAGCCAATCTTATGCCTGCATC
1 ATCAAATTCAGGAACAAA-CCAGCCAATCCTATGCCTGCATT
1286637 ATCAAATTCAGGAACAAAACCAGCCAAT-CTAATGCCTGCATT
1 ATCAAATTCAGGAAC-AAACCAGCCAATCCT-ATGCCTGCATT
* *
1286679 ATCAAATTCTGGAACAAAACCAGCCAATCCTATGCCTGCATC
1 ATCAAATTCAGGAAC-AAACCAGCCAATCCTATGCCTGCATT
* * * *
1286721 ATCAAATTCTGGAACAAACTCAGCCGATCCTATGTCTGCATC
1 ATCAAATTCAGGAACAAAC-CAGCCAATCCTATGCCTGCATT
* * *
1286763 ATCAAATTCTGGAACAAACTCAGCCAATCCTTTGCCTGCTTT
1 ATCAAATTCAGGAACAAAC-CAGCCAATCCTATGCCTGCATT
** **
1286805 ATTGAATTCAATAACAATACCAGCC
1 ATCAAATTCAGGAACAA-ACCAGCC
1286830 TGCAATCACA
Statistics
Matches: 208, Mismatches: 20, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
41 9 0.04
42 192 0.92
43 7 0.03
ACGTcount: A:0.36, C:0.28, G:0.12, T:0.25
Consensus pattern (41 bp):
ATCAAATTCAGGAACAAACCAGCCAATCCTATGCCTGCATT
Found at i:1286813 original size:84 final size:83
Alignment explanation
Indices: 1286549--1286801 Score: 359
Period size: 84 Copynumber: 3.0 Consensus size: 83
1286539 GCCATATCTA
* * *
1286549 CATCATCAAATTCTAGAACAAAACCAGCCAATCCTATGCCTGCATTATTAAATTCAGGAACAAAG
1 CATCATCAAATTCTGGAACAAAACCAGCCAATCCTATGCCTGCATTATCAAATTCTGGAACAAA-
1286614 CCAGCCAAT-CTTATGCCTG
65 CCAGCCAATCCTT-TGCCTG
*
1286633 CATCATCAAATTCAGGAACAAAACCAGCCAAT-CTAATGCCTGCATTATCAAATTCTGGAACAAA
1 CATCATCAAATTCTGGAACAAAACCAGCCAATCCT-ATGCCTGCATTATCAAATTCTGGAAC-AA
*
1286697 ACCAGCCAATCCTATGCCTG
64 ACCAGCCAATCCTTTGCCTG
* * *
1286717 CATCATCAAATTCTGGAAC-AAACTCAGCCGATCCTATGTCTGCATCATCAAATTCTGGAACAAA
1 CATCATCAAATTCTGGAACAAAAC-CAGCCAATCCTATGCCTGCATTATCAAATTCTGGAACAAA
1286781 CTCAGCCAATCCTTTGCCTG
65 C-CAGCCAATCCTTTGCCTG
1286801 C
1 C
1286802 TTTATTGAAT
Statistics
Matches: 153, Mismatches: 10, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
83 10 0.07
84 136 0.89
85 7 0.05
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.24
Consensus pattern (83 bp):
CATCATCAAATTCTGGAACAAAACCAGCCAATCCTATGCCTGCATTATCAAATTCTGGAACAAAC
CAGCCAATCCTTTGCCTG
Found at i:1286813 original size:126 final size:126
Alignment explanation
Indices: 1286553--1286791 Score: 374
Period size: 126 Copynumber: 1.9 Consensus size: 126
1286543 TATCTACATC
* *
1286553 ATCAAATTCTAGAACAAAACCAGCCAATCCTATGCCTGCATTATTAAATTCAGGAACAAAGCCAG
1 ATCAAATTCTAGAACAAAACCAGCCAATCCTATGCCTGCATCATCAAATTCAGGAACAAAGCCAG
*
1286618 CCAATCTTATGCCTGCATCATCAAATTCAGGAACAAAACCAGCCAATCTAATGCCTGCATT
66 CCAATCCTATGCCTGCATCATCAAATTCAGGAACAAAACCAGCCAATCTAATGCCTGCATT
* *
1286679 ATCAAATTCTGGAACAAAACCAGCCAATCCTATGCCTGCATCATCAAATTCTGGAACAAA-CTCA
1 ATCAAATTCTAGAACAAAACCAGCCAATCCTATGCCTGCATCATCAAATTCAGGAACAAAGC-CA
* * *
1286743 GCCGATCCTATGTCTGCATCATCAAATTCTGGAAC-AAACTCAGCCAATC
65 GCCAATCCTATGCCTGCATCATCAAATTCAGGAACAAAAC-CAGCCAATC
1286792 CTTTGCCTGC
Statistics
Matches: 103, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
125 5 0.05
126 98 0.95
ACGTcount: A:0.37, C:0.28, G:0.12, T:0.23
Consensus pattern (126 bp):
ATCAAATTCTAGAACAAAACCAGCCAATCCTATGCCTGCATCATCAAATTCAGGAACAAAGCCAG
CCAATCCTATGCCTGCATCATCAAATTCAGGAACAAAACCAGCCAATCTAATGCCTGCATT
Found at i:1286821 original size:126 final size:126
Alignment explanation
Indices: 1286553--1286829 Score: 362
Period size: 126 Copynumber: 2.2 Consensus size: 126
1286543 TATCTACATC
* * *
1286553 ATCAAATTCTAGAACAAAACCAGCCAATCCTATGCCTGCATTATTAAATTCAGGAACAAAGCCAG
1 ATCAAATTCAAGAACAAAACCAGCCAATCCTATGCCTGCATCATCAAATTCAGGAACAAAGCCAG
*
1286618 CCAATCTTATGCCTGCATCATCAAATTCAGGAACAAAACCAGCCAATCTAATGCCTGCATT
66 CCAATCCTATGCCTGCATCATCAAATTCAGGAACAAAACCAGCCAATCTAATGCCTGCATT
** *
1286679 ATCAAATTCTGGAACAAAACCAGCCAATCCTATGCCTGCATCATCAAATTCTGGAACAAA-CTCA
1 ATCAAATTCAAGAACAAAACCAGCCAATCCTATGCCTGCATCATCAAATTCAGGAACAAAGC-CA
* * * * *
1286743 GCCGATCCTATGTCTGCATCATCAAATTCTGGAAC-AAACTCAGCCAATCCT-TTGCCTGCTTT
65 GCCAATCCTATGCCTGCATCATCAAATTCAGGAACAAAAC-CAGCCAAT-CTAATGCCTGCATT
** * *
1286805 ATTGAATTCAATAACAATACCAGCC
1 ATCAAATTCAAGAACAAAACCAGCC
1286830 TGCAATCACA
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
125 5 0.04
126 125 0.95
127 2 0.02
ACGTcount: A:0.36, C:0.28, G:0.12, T:0.25
Consensus pattern (126 bp):
ATCAAATTCAAGAACAAAACCAGCCAATCCTATGCCTGCATCATCAAATTCAGGAACAAAGCCAG
CCAATCCTATGCCTGCATCATCAAATTCAGGAACAAAACCAGCCAATCTAATGCCTGCATT
Found at i:1288295 original size:2 final size:2
Alignment explanation
Indices: 1288290--1288336 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1288280 ACACACACAT
1288290 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1288332 TC TC T
1 TC TC T
1288337 TTTCTGTGGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1290507 original size:17 final size:18
Alignment explanation
Indices: 1290485--1290524 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1290475 GGTAGGTAGG
1290485 AAAAAA-AATTTATTTTT
1 AAAAAATAATTTATTTTT
*
1290502 AAAAAATATTTTATTTTT
1 AAAAAATAATTTATTTTT
1290520 AAAAA
1 AAAAA
1290525 CTTCAAGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAAAATAATTTATTTTT
Found at i:1298235 original size:27 final size:27
Alignment explanation
Indices: 1298207--1298505 Score: 285
Period size: 27 Copynumber: 10.7 Consensus size: 27
1298197 GTGAAGAAAT
*
1298207 TGTTGTTGGTTTGGTAGTTGTTGGCAT
1 TGTTGTTGGTTTGGTAGTTGTTGGCAA
* *
1298234 TGTTGTT-GTTTCGGTTGTAGTTGGCAA
1 TGTTGTTGGTTT-GGTAGTTGTTGGCAA
* *
1298261 TGTAGTTGGTTTGGCAGTTGTTGGCAA
1 TGTTGTTGGTTTGGTAGTTGTTGGCAA
1298288 TGTTGTTGGTTTGGTAGTTGTTGGCAA
1 TGTTGTTGGTTTGGTAGTTGTTGGCAA
* * * * *
1298315 TGTAGATGGTTTCGTAGTTGATGGCGA
1 TGTTGTTGGTTTGGTAGTTGTTGGCAA
* *
1298342 TGTTGTTGGTATCGTAGTTGTTGGCAA
1 TGTTGTTGGTTTGGTAGTTGTTGGCAA
* * * * *
1298369 TGTAGATGGTTTTGTAGTTGGCTTGGTAGT
1 TGTTGTTGGTTTGGTAGTT-G-TTGGCA-A
* *
1298399 TGTTGGCAATATTGGTTTGGTCGTAGTTGGCAA
1 TGTT-G-----TTGGTTTGGTAGTTGTTGGCAA
* *
1298432 TGTTGATGGTTTCGTAGTTGTTGGCAA
1 TGTTGTTGGTTTGGTAGTTGTTGGCAA
* * *
1298459 CGTTGTTGGTTTAGTAGTTGTTGGCAT
1 TGTTGTTGGTTTGGTAGTTGTTGGCAA
1298486 TGTTGTTGGTTTGGTAGTTG
1 TGTTGTTGGTTTGGTAGTTG
1298506 GCTTGGTACT
Statistics
Matches: 219, Mismatches: 42, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
26 4 0.02
27 180 0.82
28 5 0.02
29 5 0.02
30 3 0.01
31 1 0.00
32 1 0.00
33 4 0.02
34 5 0.02
35 1 0.00
36 10 0.05
ACGTcount: A:0.13, C:0.06, G:0.35, T:0.45
Consensus pattern (27 bp):
TGTTGTTGGTTTGGTAGTTGTTGGCAA
Found at i:1298377 original size:39 final size:39
Alignment explanation
Indices: 1298334--1298408 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 39
1298324 TTTCGTAGTT
*
1298334 GATGGCGATGTTGTTGG-TATCGTAGTTGTTGGCAATGTA
1 GATGGCGATGTAGTTGGCT-TCGTAGTTGTTGGCAATGTA
*** *
1298373 GATGGTTTTGTAGTTGGCTTGGTAGTTGTTGGCAAT
1 GATGGCGATGTAGTTGGCTTCGTAGTTGTTGGCAAT
1298409 ATTGGTTTGG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
39 29 0.97
40 1 0.03
ACGTcount: A:0.16, C:0.07, G:0.36, T:0.41
Consensus pattern (39 bp):
GATGGCGATGTAGTTGGCTTCGTAGTTGTTGGCAATGTA
Found at i:1298413 original size:24 final size:24
Alignment explanation
Indices: 1298386--1298432 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1298376 GGTTTTGTAG
*
1298386 TTGGCTTGGTAGTTGTTGGCAATA
1 TTGGCTTGGTAGTAGTTGGCAATA
* *
1298410 TTGGTTTGGTCGTAGTTGGCAAT
1 TTGGCTTGGTAGTAGTTGGCAAT
1298433 GTTGATGGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.09, G:0.34, T:0.43
Consensus pattern (24 bp):
TTGGCTTGGTAGTAGTTGGCAATA
Found at i:1298476 original size:117 final size:118
Alignment explanation
Indices: 1298261--1298520 Score: 351
Period size: 117 Copynumber: 2.2 Consensus size: 118
1298251 TAGTTGGCAA
* * * *
1298261 TGTAGTTGGTTTGGCAGTTGTTGGCAATGTTGTTGGTTTGGTAGTTGTTGGCAATGTAGATGGTT
1 TGTAGTTGGCTTGGTAGTTGTTGGCAA--TTATTGGTTTGGTAGTAGTTGGCAATGTAGATGGTT
* * *
1298326 TCGTAGTTGATGGCGATGTTGTTGGTATCGTAGTTGTTGGCAATGTAGATGGTTT
64 TCGTAGTTGATGGCAACGTTGTTGGTATAGTAGTTGTTGGCAATGTAGATGGTTT
* *
1298381 TGTAGTTGGCTTGGTAGTTGTTGGCAA-TATTGGTTTGGTCGTAGTTGGCAATGTTGATGGTTTC
1 TGTAGTTGGCTTGGTAGTTGTTGGCAATTATTGGTTTGGTAGTAGTTGGCAATGTAGATGGTTTC
* * * * *
1298445 GTAGTTGTTGGCAACGTTGTTGGTTTAGTAGTTGTTGGCATTGTTGTTGGTTT
66 GTAGTTGATGGCAACGTTGTTGGTATAGTAGTTGTTGGCAATGTAGATGGTTT
* *
1298498 GGTAGTTGGCTTGGTACTTGTTG
1 TGTAGTTGGCTTGGTAGTTGTTG
1298521 CTCGCTCAAT
Statistics
Matches: 124, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
117 99 0.80
120 25 0.20
ACGTcount: A:0.13, C:0.07, G:0.35, T:0.45
Consensus pattern (118 bp):
TGTAGTTGGCTTGGTAGTTGTTGGCAATTATTGGTTTGGTAGTAGTTGGCAATGTAGATGGTTTC
GTAGTTGATGGCAACGTTGTTGGTATAGTAGTTGTTGGCAATGTAGATGGTTT
Found at i:1298695 original size:66 final size:66
Alignment explanation
Indices: 1298619--1298905 Score: 324
Period size: 66 Copynumber: 4.3 Consensus size: 66
1298609 TAATAAAGAA
* * * * ** * * *
1298619 GTTGTTGTTGTCGGTATTGTTGTTGATGACTGTGTTGTTGATGGTTGCGGTGTTGTTGATTGCTG
1 GTTGTTGTTGTCGGTAATGTTGTAGATGACTGCGTTGTTGAGGGGGGTGGTGTCGTGGATTGCTG
1298684 G
66 G
* * ** * * * *
1298685 GTTGTAGTTGTCGGTAACGTTGTAGATGACTGCGTTGTTGAGGGTTGTGGCGTGGTAGA-TGTTT
1 GTTGTTGTTGTCGGTAATGTTGTAGATGACTGCGTTGTTGAGGGGGGTGGTGTCGTGGATTG-CT
*
1298749 GA
65 GG
* * *
1298751 GTTGTAGTTGTCGGTAATGTTGTGGATGACTGCGTTGTAGAGGGGGGTGGTGTCGTGGATTGCTG
1 GTTGTTGTTGTCGGTAATGTTGTAGATGACTGCGTTGTTGAGGGGGGTGGTGTCGTGGATTGCTG
1298816 G
66 G
* * *
1298817 GTTGTTGTTGTCGGTAACGTTGTAGATGACTGCGTTGTAGAGGGGGATGGTGTCGTGGATTGCTG
1 GTTGTTGTTGTCGGTAATGTTGTAGATGACTGCGTTGTTGAGGGGGGTGGTGTCGTGGATTGCTG
1298882 G
66 G
* *
1298883 GTTGTTGTTGTCGGCAGTGTTGT
1 GTTGTTGTTGTCGGTAATGTTGT
1298906 CGAAGCTTGT
Statistics
Matches: 190, Mismatches: 29, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
65 2 0.01
66 186 0.98
67 2 0.01
ACGTcount: A:0.11, C:0.08, G:0.41, T:0.40
Consensus pattern (66 bp):
GTTGTTGTTGTCGGTAATGTTGTAGATGACTGCGTTGTTGAGGGGGGTGGTGTCGTGGATTGCTG
G
Found at i:1298722 original size:33 final size:33
Alignment explanation
Indices: 1298685--1298856 Score: 111
Period size: 33 Copynumber: 5.2 Consensus size: 33
1298675 TGATTGCTGG
1298685 GTTGTAGTTGTCGGTAACGTTGTAGATGACTGC
1 GTTGTAGTTGTCGGTAACGTTGTAGATGACTGC
* ** *
1298718 GTTGTTGAGGGTTGT-GG---CGTGGTAGATGTTTGA
1 GTTG-T-A--GTTGTCGGTAACGTTGTAGATGACTGC
* *
1298751 GTTGTAGTTGTCGGTAATGTTGTGGATGACTGC
1 GTTGTAGTTGTCGGTAACGTTGTAGATGACTGC
** ** *** * * *
1298784 GTTGTAGAGGGGGGTGGTGTCGTGGATTG-CTGG
1 GTTGTAGTTGTCGGTAACGTTGTAGA-TGACTGC
*
1298817 GTTGTTGTTGTCGGTAACGTTGTAGATGACTGC
1 GTTGTAGTTGTCGGTAACGTTGTAGATGACTGC
1298850 GTTGTAG
1 GTTGTAG
1298857 AGGGGGATGG
Statistics
Matches: 99, Mismatches: 30, Indels: 20
0.66 0.20 0.13
Matches are distributed among these distances:
29 5 0.05
30 2 0.02
31 1 0.01
32 3 0.03
33 77 0.78
34 3 0.03
35 1 0.01
36 2 0.02
37 5 0.05
ACGTcount: A:0.14, C:0.08, G:0.41, T:0.37
Consensus pattern (33 bp):
GTTGTAGTTGTCGGTAACGTTGTAGATGACTGC
Found at i:1298779 original size:132 final size:132
Alignment explanation
Indices: 1298618--1298860 Score: 369
Period size: 132 Copynumber: 1.8 Consensus size: 132
1298608 GTAATAAAGA
* * * * * * ** * *
1298618 AGTTGTTGTTGTCGGTATTGTTGTTGATGACTGTGTTGTTGATGGTTGCGGTGTTGTTGATTGCT
1 AGTTGTAGTTGTCGGTAATGTTGTGGATGACTGCGTTGTAGAGGGGGGCGGTGTCGTGGATTGCT
*
1298683 GGGTTGTAGTTGTCGGTAACGTTGTAGATGACTGCGTTGTTGAGGGTTGTGGCGTGGTAGATGTT
66 GGGTTGTAGTTGTCGGTAACGTTGTAGATGACTGCGTTGTAGAGGGTTGTGGCGTGGTAGATGTT
1298748 TG
131 TG
*
1298750 AGTTGTAGTTGTCGGTAATGTTGTGGATGACTGCGTTGTAGAGGGGGGTGGTGTCGTGGATTGCT
1 AGTTGTAGTTGTCGGTAATGTTGTGGATGACTGCGTTGTAGAGGGGGGCGGTGTCGTGGATTGCT
*
1298815 GGGTTGTTGTTGTCGGTAACGTTGTAGATGACTGCGTTGTAGAGGG
66 GGGTTGTAGTTGTCGGTAACGTTGTAGATGACTGCGTTGTAGAGGG
1298861 GGATGGTGTC
Statistics
Matches: 98, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
132 98 1.00
ACGTcount: A:0.13, C:0.07, G:0.40, T:0.40
Consensus pattern (132 bp):
AGTTGTAGTTGTCGGTAATGTTGTGGATGACTGCGTTGTAGAGGGGGGCGGTGTCGTGGATTGCT
GGGTTGTAGTTGTCGGTAACGTTGTAGATGACTGCGTTGTAGAGGGTTGTGGCGTGGTAGATGTT
TG
Found at i:1298926 original size:132 final size:132
Alignment explanation
Indices: 1298618--1298926 Score: 363
Period size: 132 Copynumber: 2.3 Consensus size: 132
1298608 GTAATAAAGA
* * * ** * *
1298618 AGTTGTTGTTGTCGGTATTGTTGTTGATGACTGTGTTGTTGATGGTTGCGGTGTTGTTGATTGCT
1 AGTTGTTGTTGTCGGTAATGTTGTCGATGACTGTGTTGTTGAGGGGGGCGGTGTCGTGGATTGCT
* * * *
1298683 GGGTTGTAGTTGTCGGTAACGTTGTAGATGACTGCGTTGTTGAGGGTTGTGGCGTGGTAGATGTT
66 GGGTTGTAGTTGTCGGTAACGTTGTAGATGACTGCGTTGTAGAGGGTGGTGGCGTCGTAGATGTC
1298748 TG
131 TG
* * * * *
1298750 AGTTGTAGTTGTCGGTAATGTTGTGGATGACTGCGTTGTAGAGGGGGGTGGTGTCGTGGATTGCT
1 AGTTGTTGTTGTCGGTAATGTTGTCGATGACTGTGTTGTTGAGGGGGGCGGTGTCGTGGATTGCT
* * *
1298815 GGGTTGTTGTTGTCGGTAACGTTGTAGATGACTGCGTTGTAGAGGG-GGATGGTGTCGTGGAT-T
66 GGGTTGTAGTTGTCGGTAACGTTGTAGATGACTGCGTTGTAGAGGGTGG-TGGCGTCGTAGATGT
1298878 GCTG
130 -CTG
* * * *
1298882 GGTTGTTGTTGTCGGCAGTGTTGTCGAAG-CTTGTGTTGTTGAGGG
1 AGTTGTTGTTGTCGGTAATGTTGTCGATGAC-TGTGTTGTTGAGGG
1298927 CAGTGGAGTT
Statistics
Matches: 148, Mismatches: 26, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
131 3 0.02
132 145 0.98
ACGTcount: A:0.12, C:0.08, G:0.41, T:0.39
Consensus pattern (132 bp):
AGTTGTTGTTGTCGGTAATGTTGTCGATGACTGTGTTGTTGAGGGGGGCGGTGTCGTGGATTGCT
GGGTTGTAGTTGTCGGTAACGTTGTAGATGACTGCGTTGTAGAGGGTGGTGGCGTCGTAGATGTC
TG
Found at i:1299112 original size:2 final size:2
Alignment explanation
Indices: 1299107--1299170 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
1299097 CACACACACA
*
1299107 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1299149 CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT
1299171 TACCTCCATG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:1301035 original size:33 final size:33
Alignment explanation
Indices: 1300999--1301137 Score: 226
Period size: 33 Copynumber: 4.2 Consensus size: 33
1300989 ATTGATTTTT
* *
1300999 GTAATAATGTATTGCTGTCATCAACAAATACGT
1 GTAATAACGTATTGCTGTCATCAACAAATACGC
1301032 GTAATAACGTATTGCTGTCATCAACAAATACGC
1 GTAATAACGTATTGCTGTCATCAACAAATACGC
*
1301065 GTAATAACGTATTTCTGTCATCAACAAATACGC
1 GTAATAACGTATTGCTGTCATCAACAAATACGC
*
1301098 GTAATAACATATTGCTGTCATCAACAAATACAG-
1 GTAATAACGTATTGCTGTCATCAACAAATAC-GC
1301131 GTAATAA
1 GTAATAA
1301138 AAAGCTCCTT
Statistics
Matches: 100, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
33 99 0.99
34 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (33 bp):
GTAATAACGTATTGCTGTCATCAACAAATACGC
Found at i:1303475 original size:32 final size:32
Alignment explanation
Indices: 1303439--1303537 Score: 153
Period size: 32 Copynumber: 3.1 Consensus size: 32
1303429 TGATAACTTC
1303439 TCATTCATAATAGGGTTAATGAATCAAAGGTT
1 TCATTCATAATAGGGTTAATGAATCAAAGGTT
*
1303471 TCATTCAAAATAGGGTTAATGAATCAAAGGTT
1 TCATTCATAATAGGGTTAATGAATCAAAGGTT
* * * *
1303503 TCATCCATATTAGGATTAATGTATCAAAGGTT
1 TCATTCATAATAGGGTTAATGAATCAAAGGTT
1303535 TCA
1 TCA
1303538 CAAAAGTCAT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.34
Consensus pattern (32 bp):
TCATTCATAATAGGGTTAATGAATCAAAGGTT
Found at i:1305091 original size:2 final size:2
Alignment explanation
Indices: 1305084--1305112 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1305074 ATTGATAAAT
1305084 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1305113 TCTAAACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1313824 original size:20 final size:19
Alignment explanation
Indices: 1313801--1313843 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1313791 AATTTGTGAA
1313801 TCAACCAAAAATTTGCATAT
1 TCAACCAAAAA-TTGCATAT
** *
1313821 TCAATGAAAAATTGCATTT
1 TCAACCAAAAATTGCATAT
1313840 TCAA
1 TCAA
1313844 AATATTCTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (19 bp):
TCAACCAAAAATTGCATAT
Found at i:1314271 original size:23 final size:23
Alignment explanation
Indices: 1314245--1314291 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1314235 TAACAAACAG
1314245 TGTACTTCCAAAAACAGAGATTA
1 TGTACTTCCAAAAACAGAGATTA
1314268 TGTACTTCCAAAAACAGAGATTA
1 TGTACTTCCAAAAACAGAGATTA
1314291 T
1 T
1314292 CTCTGCCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.28
Consensus pattern (23 bp):
TGTACTTCCAAAAACAGAGATTA
Found at i:1315876 original size:18 final size:17
Alignment explanation
Indices: 1315852--1315898 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 17
1315842 TTTTGATGAG
1315852 AAAGAGAGAGACAGAGA
1 AAAGAGAGAGACAGAGA
1315869 ACAAGAGAGAGACAGAGA
1 A-AAGAGAGAGACAGAGA
1315887 AAGAGAGAGAGA
1 AA-AGAGAGAGA
1315899 TTTTTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 2 0.07
18 26 0.93
ACGTcount: A:0.57, C:0.06, G:0.36, T:0.00
Consensus pattern (17 bp):
AAAGAGAGAGACAGAGA
Found at i:1319818 original size:2 final size:2
Alignment explanation
Indices: 1319811--1319857 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1319801 TAAGTTTGTG
1319811 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1319853 CT CT C
1 CT CT C
1319858 ACACACACAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1325795 original size:167 final size:166
Alignment explanation
Indices: 1325519--1325851 Score: 657
Period size: 167 Copynumber: 2.0 Consensus size: 166
1325509 CGTCCAGACG
1325519 CTAATGGTCACGTGGTGGTGGAATCCAGTAAAAGCAGACTTTGTGTTATATGCTGATCAGATTGT
1 CTAATGGTCACGTGGTGGTGGAATCCAGTAAAAGCAGACTTTGTGTTATATGCTGATCAGATTGT
1325584 TGTAAATGGCTTGGATTAACGATGAACAAAATTAATTATTACATATTTATAGATATACTCAAAAC
66 TGTAAATGGCTTGGATTAACGATGAACAAAATTAATTATTACATATTTATAGATATACTCAAAAC
1325649 ATTCGAATACTGTTACGTACATATATATATATATAT
131 ATTCGAATACTGTTACGTACATATATATATATATAT
1325685 NCTAATGGTCACGTGGTGGTGGAATCCAGTAAAAGCAGACTTTGTGTTATATGCTGATCAGATTG
1 -CTAATGGTCACGTGGTGGTGGAATCCAGTAAAAGCAGACTTTGTGTTATATGCTGATCAGATTG
1325750 TTGTAAATGGCTTGGATTAACGATGAACAAAATTAATTATTACATATTTATAGATATACTCAAAA
65 TTGTAAATGGCTTGGATTAACGATGAACAAAATTAATTATTACATATTTATAGATATACTCAAAA
1325815 CATTCGAATACTGTTACGTACATATATATATATATAT
130 CATTCGAATACTGTTACGTACATATATATATATATAT
1325852 ATANNNNNNN
Statistics
Matches: 166, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
167 166 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (166 bp):
CTAATGGTCACGTGGTGGTGGAATCCAGTAAAAGCAGACTTTGTGTTATATGCTGATCAGATTGT
TGTAAATGGCTTGGATTAACGATGAACAAAATTAATTATTACATATTTATAGATATACTCAAAAC
ATTCGAATACTGTTACGTACATATATATATATATAT
Found at i:1333321 original size:67 final size:67
Alignment explanation
Indices: 1333221--1333723 Score: 691
Period size: 67 Copynumber: 7.5 Consensus size: 67
1333211 ATAGGCTTGT
*
1333221 CTCACTTCCTATTCACTGGAGGTTGATATCATTGCTGTTATATTAGATGTAACTGATACAGGCTA
1 CTCACTTCCTATTCACTGGAGGTTGATATCATTGCTGTTATATTAGATGTCACTGATACAGGCTA
1333286 GC
66 GC
* * *
1333288 CTCACTTCCTATTCACTGGAGGTTGAAATCATTGCTGTTATATTAGATGTCACTGACACAGACTA
1 CTCACTTCCTATTCACTGGAGGTTGATATCATTGCTGTTATATTAGATGTCACTGATACAGGCTA
1333353 GC
66 GC
* * *
1333355 CTCACTTCCTATTAACTGGATGTTGATATCATTGCTGTTATATTAGATGTCACCGATACAGGCTA
1 CTCACTTCCTATTCACTGGAGGTTGATATCATTGCTGTTATATTAGATGTCACTGATACAGGCTA
1333420 GC
66 GC
* * * * * *
1333422 CTCAATTACTATTCCCTGGAGGTTGATATCACTGCTGTTATATTATATGTCACTGATACAGGCTT
1 CTCACTTCCTATTCACTGGAGGTTGATATCATTGCTGTTATATTAGATGTCACTGATACAGGCTA
1333487 GC
66 GC
* * * * * *
1333489 CTCATTTCCTATTCACTGGAGGTTCATATCATTGCTGTTTTATTAAATGTCACTTATACAGGCTT
1 CTCACTTCCTATTCACTGGAGGTTGATATCATTGCTGTTATATTAGATGTCACTGATACAGGCTA
1333554 GC
66 GC
* * * * *
1333556 CTCACTTCCCATTCACTAGAGGTTCATATCATTGCTGTTATTTTAGATGTCAATGATACAGGCTA
1 CTCACTTCCTATTCACTGGAGGTTGATATCATTGCTGTTATATTAGATGTCACTGATACAGGCTA
*
1333621 GT
66 GC
* * * ** * * *
1333623 CTCACTTCCTATTCACTGGAAGTTCATTTCATTGCTGTTATAGGAGATGTCACTAATACAGACAA
1 CTCACTTCCTATTCACTGGAGGTTGATATCATTGCTGTTATATTAGATGTCACTGATACAGGCTA
*
1333688 GA
66 GC
*
1333690 CTCACTTCCTATTCACTGGAGGTTGATATAATTG
1 CTCACTTCCTATTCACTGGAGGTTGATATCATTG
1333724 GTATTAGACG
Statistics
Matches: 383, Mismatches: 53, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
67 383 1.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.36
Consensus pattern (67 bp):
CTCACTTCCTATTCACTGGAGGTTGATATCATTGCTGTTATATTAGATGTCACTGATACAGGCTA
GC
Found at i:1336622 original size:99 final size:99
Alignment explanation
Indices: 1336475--1336692 Score: 253
Period size: 99 Copynumber: 2.2 Consensus size: 99
1336465 AGGAAATGAT
* * * *
1336475 TACGACCAATTTGTCTGGGAGAGTCGATGAAAACATCAATGATCTAATT-ACTATTGCTCAGACC
1 TACGACCAATTTGTCTGGGAGAGTCAATGAAAACATCAAGGATCTAATTAAC-ATAGCTCAGA-A
* * * *
1336539 A-AGCAGCGATTTCTAACACAGGAAATGGTGTCTCA
64 AGAGCAGCGACTCCTAACAAAAGAAATGGTGTCTCA
* * * * *
1336574 TGCGACCAATTTGTCTGGTAGAGTCAATTACAAA-ATCAGGGATTTAATTAACATAGCTCAGAAA
1 TACGACCAATTTGTCTGGGAGAGTCAATGA-AAACATCAAGGATCTAATTAACATAGCTCAGAAA
* *
1336638 GAGCAGCTACTCCTAACAAAAGAAATGGTGTCTCT
65 GAGCAGCGACTCCTAACAAAAGAAATGGTGTCTCA
1336673 TACGACCAATTTGTCTGGGA
1 TACGACCAATTTGTCTGGGA
1336693 AAATTGAGAA
Statistics
Matches: 99, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
98 1 0.01
99 93 0.94
100 5 0.05
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (99 bp):
TACGACCAATTTGTCTGGGAGAGTCAATGAAAACATCAAGGATCTAATTAACATAGCTCAGAAAG
AGCAGCGACTCCTAACAAAAGAAATGGTGTCTCA
Found at i:1336931 original size:93 final size:92
Alignment explanation
Indices: 1336772--1337048 Score: 315
Period size: 93 Copynumber: 3.0 Consensus size: 92
1336762 CTTCAATTAT
* * *
1336772 AACCAAATATGATACTCTTGATCAGATGAACAA-AGACGAAATAAAGATTTTGAATAAAAGTGAG
1 AACCAAAAATGATACTCTTGATCAGATGAACAATA-ATGAAATAAAGAGTTTGAATAAAAGTGAG
*
1336836 AATATCATTGACGATATGGAAAATTTACA
65 AATATCATTGACGATATGG-AAATATACA
* * * *
1336865 AACCAAAAATGATACTCTTGATCAGATGGACAATAATGAAATTATGAGTTTGAATAAAAGTAAGA
1 AACCAAAAATGATACTCTTGATCAGATGAACAATAATGAAATAAAGAGTTTGAATAAAAGTGAGA
* *
1336930 ATATCCTTGACGATATAGGGAATATACA
66 ATATCATTGACGATAT-GGAAATATACA
* * * ** * * * * *
1336958 AACCAAAAACGATACGCTTGATCAAAAAAATATTGATGAAATAAAGGGTCTGAA-AAAAGTGAGA
1 AACCAAAAATGATACTCTTGATCAGATGAACAATAATGAAATAAAGAGTTTGAATAAAAGTGAGA
*
1337022 ATATCATTGACGATATGGGGAATATAC
66 ATATCATTGACGATAT-GGAAATATAC
1337049 TATATAAATA
Statistics
Matches: 156, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
92 34 0.22
93 119 0.76
94 3 0.02
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.25
Consensus pattern (92 bp):
AACCAAAAATGATACTCTTGATCAGATGAACAATAATGAAATAAAGAGTTTGAATAAAAGTGAGA
ATATCATTGACGATATGGAAATATACA
Found at i:1339567 original size:21 final size:20
Alignment explanation
Indices: 1339543--1339636 Score: 55
Period size: 21 Copynumber: 4.5 Consensus size: 20
1339533 TTACCCCTGA
*
1339543 ATATAATGATGTAATCACAGT
1 ATATAATGATGTAA-CACAGC
* * *
1339564 ATATGATGATGTTAGCA-ATGT
1 ATATAATGATG-TAACACA-GC
* *
1339585 AAATAATGATGCTAACACTGC
1 ATATAATGATG-TAACACAGC
* * *
1339606 ATATACTGATGTTACCACTGC
1 ATATAATGATG-TAACACAGC
1339627 ATATAATGAT
1 ATATAATGAT
1339637 ATTACTATCG
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
20 1 0.02
21 54 0.95
22 2 0.04
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (20 bp):
ATATAATGATGTAACACAGC
Found at i:1339633 original size:42 final size:42
Alignment explanation
Indices: 1339533--1339636 Score: 106
Period size: 42 Copynumber: 2.5 Consensus size: 42
1339523 AATAAAGATT
* *
1339533 TTACCCCTGAATATAATGATGTAATCACAGTATATGATGATG
1 TTACCACTGAATATAATGATGTAATCACAGCATATGATGATG
* * *
1339575 TTAGCAATGTAA-ATAATGATGCTAA-CACTGCATAT-ACTGATG
1 TTACCACTG-AATATAATGATG-TAATCACAGCATATGA-TGATG
*
1339617 TTACCACTGCATATAATGAT
1 TTACCACTGAATATAATGAT
1339637 ATTACTATCG
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
41 2 0.04
42 43 0.86
43 5 0.10
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (42 bp):
TTACCACTGAATATAATGATGTAATCACAGCATATGATGATG
Found at i:1339641 original size:21 final size:21
Alignment explanation
Indices: 1339600--1339675 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
1339590 ATGATGCTAA
* *
1339600 CACTGCATATACTGATGTTAC
1 CACTGCATATAATGATATTAC
1339621 CACTGCATATAATGATATTAC
1 CACTGCATATAATGATATTAC
* *
1339642 TA-TCGCATATAAATGA-AATAC
1 CACT-GCATAT-AATGATATTAC
* *
1339663 CAATTCATATAAT
1 CACTGCATATAAT
1339676 ATGAAATTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 4 0.09
21 36 0.78
22 6 0.13
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.33
Consensus pattern (21 bp):
CACTGCATATAATGATATTAC
Found at i:1349734 original size:3 final size:3
Alignment explanation
Indices: 1349720--1349775 Score: 76
Period size: 3 Copynumber: 18.7 Consensus size: 3
1349710 AGAAACATGG
* * * *
1349720 TGA TGA TAA TGA TGA TGA TAA TGA TGA TGA AGA TGA TGA TGA TGA CGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1349768 TGA TGA TG
1 TGA TGA TG
1349776 CAAAAAAAGG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.38, C:0.02, G:0.30, T:0.30
Consensus pattern (3 bp):
TGA
Found at i:1352600 original size:2 final size:2
Alignment explanation
Indices: 1352593--1352651 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1352583 ACTGTACAAC
1352593 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1352635 AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG A
1352652 AAGCGAGAGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1354911 original size:4 final size:4
Alignment explanation
Indices: 1354904--1354950 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
1354894 TTTTGTCTGT
* * * *
1354904 CGTC CGTC TGTC CGTC TGTC CGTC CGTC TGTC CGTC CGTC TGTC CGT
1 CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGT
1354951 AAACTTTTTA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.00, C:0.40, G:0.26, T:0.34
Consensus pattern (4 bp):
CGTC
Found at i:1354918 original size:8 final size:8
Alignment explanation
Indices: 1354905--1354950 Score: 65
Period size: 8 Copynumber: 5.8 Consensus size: 8
1354895 TTTGTCTGTC
1354905 GTCCGTCT
1 GTCCGTCT
1354913 GTCCGTCT
1 GTCCGTCT
*
1354921 GTCCGTCC
1 GTCCGTCT
* *
1354929 GTCTGTCC
1 GTCCGTCT
1354937 GTCCGTCT
1 GTCCGTCT
1354945 GTCCGT
1 GTCCGT
1354951 AAACTTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.00, C:0.39, G:0.26, T:0.35
Consensus pattern (8 bp):
GTCCGTCT
Found at i:1354928 original size:12 final size:12
Alignment explanation
Indices: 1354913--1354950 Score: 76
Period size: 12 Copynumber: 3.2 Consensus size: 12
1354903 TCGTCCGTCT
1354913 GTCCGTCTGTCC
1 GTCCGTCTGTCC
1354925 GTCCGTCTGTCC
1 GTCCGTCTGTCC
1354937 GTCCGTCTGTCC
1 GTCCGTCTGTCC
1354949 GT
1 GT
1354951 AAACTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.00, C:0.39, G:0.26, T:0.34
Consensus pattern (12 bp):
GTCCGTCTGTCC
Found at i:1355454 original size:17 final size:18
Alignment explanation
Indices: 1355418--1355455 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
1355408 TCAAAAAATG
1355418 TGTTGCTATGGTTAAAATTA
1 TGTTGCTATGG-T-AAATTA
1355438 TGTTGCTATGG-AAATTA
1 TGTTGCTATGGTAAATTA
1355455 T
1 T
1355456 TTAATTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
20 11 0.61
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (18 bp):
TGTTGCTATGGTAAATTA
Found at i:1362021 original size:12 final size:12
Alignment explanation
Indices: 1362004--1362038 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
1361994 TATCACCTTT
1362004 TGTCCGTCTGTC
1 TGTCCGTCTGTC
1362016 TGTCCGTCTGTC
1 TGTCCGTCTGTC
*
1362028 CGTCCGTCTGT
1 TGTCCGTCTGT
1362039 AAACTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.34, G:0.26, T:0.40
Consensus pattern (12 bp):
TGTCCGTCTGTC
Found at i:1384501 original size:3 final size:3
Alignment explanation
Indices: 1384495--1384522 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1384485 GTTTTTTTTA
1384495 GTT GTT GTT GTT GTT GTT GTT GTT GTT G
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT G
1384523 AACTATCTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.36, T:0.64
Consensus pattern (3 bp):
GTT
Found at i:1387065 original size:32 final size:32
Alignment explanation
Indices: 1387024--1387089 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
1387014 AATCCCCGAC
* *
1387024 GTCGGAGATTTACGTAA-ACAGCCGAGCGTCTG
1 GTCGGAGATTTACG-AAGACAACCGAGCATCTG
*
1387056 GTCGGAGATTTCCGAAGACAACCGAGCATCTG
1 GTCGGAGATTTACGAAGACAACCGAGCATCTG
1387088 GT
1 GT
1387090 TGAACGAGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 2 0.07
32 28 0.93
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (32 bp):
GTCGGAGATTTACGAAGACAACCGAGCATCTG
Found at i:1389381 original size:19 final size:20
Alignment explanation
Indices: 1389357--1389395 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
1389347 CGGCATAGCA
1389357 TTACCTTATTTC-ATAATTT
1 TTACCTTATTTCAATAATTT
1389376 TTACCTTATTTCAATAATTT
1 TTACCTTATTTCAATAATTT
1389396 ATATTGCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.56
Consensus pattern (20 bp):
TTACCTTATTTCAATAATTT
Found at i:1392199 original size:2 final size:2
Alignment explanation
Indices: 1392188--1392242 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
1392178 TAATTAACAA
1392188 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1392229 CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT
1392243 GTTTATTTGC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:1393655 original size:2 final size:2
Alignment explanation
Indices: 1393599--1393642 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1393589 ATCATGATTT
1393599 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1393641 TC
1 TC
1393643 AGTCAGACTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1396213 original size:28 final size:28
Alignment explanation
Indices: 1396181--1396237 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
1396171 GTAGAATCGT
* * *
1396181 GACCCCCGGACTAATACTGGGGCCCCAA
1 GACCCCCAGACCAATACTGAGGCCCCAA
1396209 GACCCCCAGACCAATACTGAGGCCCCAA
1 GACCCCCAGACCAATACTGAGGCCCCAA
1396237 G
1 G
1396238 TGGGGTTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.28, C:0.40, G:0.23, T:0.09
Consensus pattern (28 bp):
GACCCCCAGACCAATACTGAGGCCCCAA
Found at i:1397075 original size:2 final size:2
Alignment explanation
Indices: 1397068--1397119 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1397058 TTTATCATGA
1397068 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1397110 TC TC TC TC TC
1 TC TC TC TC TC
1397120 AGAATCTTCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1406700 original size:1 final size:1
Alignment explanation
Indices: 1406694--1406718 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1406684 ACGTTGTGAC
1406694 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
1406719 AAATTCCAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1408321 original size:17 final size:17
Alignment explanation
Indices: 1408299--1408359 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
1408289 TATTTAATAC
1408299 TTTACTTATAATTATAA
1 TTTACTTATAATTATAA
*
1408316 TTTACTTATAATTAT-C
1 TTTACTTATAATTATAA
*
1408332 TGTACTGTATAATTACTAA
1 TTTACT-TATAATTA-TAA
1408351 TTATACTTA
1 TT-TACTTA
1408360 CTTTTGCAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 5 0.14
17 23 0.64
18 1 0.03
19 3 0.08
20 4 0.11
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.51
Consensus pattern (17 bp):
TTTACTTATAATTATAA
Found at i:1411642 original size:1 final size:1
Alignment explanation
Indices: 1411636--1411665 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
1411626 CTTATCTTGG
*
1411636 TTTTTTTTTTTTTTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1411666 ACAAGTCTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:1416817 original size:1 final size:1
Alignment explanation
Indices: 1416811--1416835 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1416801 TGGGACAGAC
1416811 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
1416836 AGCTTCGCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1417426 original size:34 final size:36
Alignment explanation
Indices: 1417359--1417429 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
1417349 CTTTCCCCCG
*
1417359 TTTCCCCATTGCTTTGTCTTCTTTTTTTAATCAATC
1 TTTCCCCATTGCTTTGTCATCTTTTTTTAATCAATC
*
1417395 TTTCCCCATTTCTTTGTCATC-TTTTTT-ATCAATC
1 TTTCCCCATTGCTTTGTCATCTTTTTTTAATCAATC
1417429 T
1 T
1417430 ATTTTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 8 0.24
35 6 0.18
36 19 0.58
ACGTcount: A:0.14, C:0.25, G:0.04, T:0.56
Consensus pattern (36 bp):
TTTCCCCATTGCTTTGTCATCTTTTTTTAATCAATC
Found at i:1417458 original size:17 final size:16
Alignment explanation
Indices: 1417416--1417455 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
1417406 CTTTGTCATC
*
1417416 TTTTTTATCAATCTAT
1 TTTTTTTTCAATCTAT
1417432 TTTTTTTTCAATCTAT
1 TTTTTTTTCAATCTAT
1417448 TTTTTTTT
1 TTTTTTTT
1417456 TCATTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTTTTCAATCTAT
Found at i:1420215 original size:2 final size:2
Alignment explanation
Indices: 1420208--1420269 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
1420198 GGATATCTTC
1420208 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1420250 AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG
1420270 NNNNNNNNNN
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1420495 original size:15 final size:15
Alignment explanation
Indices: 1420475--1420504 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1420465 AGTGGGGCCT
*
1420475 CAGATATCCGGACGC
1 CAGATAACCGGACGC
1420490 CAGATAACCGGACGC
1 CAGATAACCGGACGC
1420505 TTCAGTTTAC
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:0.30, C:0.33, G:0.27, T:0.10
Consensus pattern (15 bp):
CAGATAACCGGACGC
Found at i:1433932 original size:227 final size:228
Alignment explanation
Indices: 1433537--1433992 Score: 815
Period size: 227 Copynumber: 2.0 Consensus size: 228
1433527 GGTCGATGGC
1433537 CTATTTTTTGAGTTAATGGTCATTGAATATTTTTGGAAAATTTAAGAAAAATCCCAAAACATTTT
1 CTATTTTTTGAGTTAATGGTCATTGAATATTTTTGGAAAATTTAAGAAAAATCCCAAAACATTTT
*
1433602 ACACTATAACTGAGGTTTTCTTAAATGTGAAAATAATACCCATTGCTAAACCTTTTAAAAAAGAA
66 ACACTATAACTGAGATTTTCTTAAATGTGAAAATAATACCCATTGCTAAACCTTTTAAAAAAGAA
* *
1433667 ATACAATTTATGAATGGCAGTGACACTTAATAGATACAAAGCATTAAGTTTTCATTTACAATTCT
131 ATAAAATTTATGAATGGCAGTGACACTTAAAAGATACAAAGCATTAAGTTTTCATTTACAATTCT
1433732 TATAAAT-GTTTCAGTACTAATTTCCTCTGTAA
196 TATAAATAGTTTCAGTACTAATTTCCTCTGTAA
* *
1433764 CTATTTTTTTAGTTAATGGTCATTGAATATTTTTGGAAAATTTAAGAAAAATCCCTAAACATTTT
1 CTATTTTTTGAGTTAATGGTCATTGAATATTTTTGGAAAATTTAAGAAAAATCCCAAAACATTTT
*
1433829 ACACTATAACTGAGATTTTCTTAATTGTGAAAATAATACCCATTGCTAAACCTTTTAAAAAAGAA
66 ACACTATAACTGAGATTTTCTTAAATGTGAAAATAATACCCATTGCTAAACCTTTTAAAAAAGAA
*
1433894 ATAAAATTTATGAATGGCAGTGACACTTAAAAGATACAAAGCTTTAAGTTTTCATTTACAATTCT
131 ATAAAATTTATGAATGGCAGTGACACTTAAAAGATACAAAGCATTAAGTTTTCATTTACAATTCT
* * *
1433959 TATAAATATTTTCATTACTTATTTCCTCTGTAA
196 TATAAATAGTTTCAGTACTAATTTCCTCTGTAA
1433992 C
1 C
1433993 GGGATGGGAG
Statistics
Matches: 218, Mismatches: 10, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
227 195 0.89
228 23 0.11
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (228 bp):
CTATTTTTTGAGTTAATGGTCATTGAATATTTTTGGAAAATTTAAGAAAAATCCCAAAACATTTT
ACACTATAACTGAGATTTTCTTAAATGTGAAAATAATACCCATTGCTAAACCTTTTAAAAAAGAA
ATAAAATTTATGAATGGCAGTGACACTTAAAAGATACAAAGCATTAAGTTTTCATTTACAATTCT
TATAAATAGTTTCAGTACTAATTTCCTCTGTAA
Found at i:1434542 original size:205 final size:205
Alignment explanation
Indices: 1434204--1434629 Score: 816
Period size: 205 Copynumber: 2.1 Consensus size: 205
1434194 GGGGTTGGTC
1434204 ACGGCACCAAATGTAACGTGATGGGATGAATAATGACGGACCAGACCGGGATTCAAACCCGGCCC
1 ACGGCACCAAATGTAACGTGATGGGATGAATAATGACGGACCAGACCGGGATTCAAACCCGGCCC
1434269 CCCTTAATCTCTTGTCAGGTGTCCTACCAACTGAACTATCTGGCGCAGGTATTCAAACTGGTCTG
66 CCCTTAATCTCTTGTCAGGTGTCCTACCAACTGAACTATCTGGCGCAGGTATTCAAACTGGTCTG
*
1434334 ACCGTCACTTTCCTCCACTTTCGCCCTCGAGGATCACCTCAGGTTCTTCCCCTTGGCAGAATCCA
131 ACCGTCACTTTCCTCCACTTTCGCCCTCGAAGATCACCTCAGGTTCTTCCCCTTGGCAGAATCCA
1434399 GGGACAGGTT
196 GGGACAGGTT
1434409 ACGGCACCAAATGTAACGTGATGGGATGAATAATGACGGACCAGACCGGGATTCAAACCCGGCCC
1 ACGGCACCAAATGTAACGTGATGGGATGAATAATGACGGACCAGACCGGGATTCAAACCCGGCCC
* *
1434474 CCCTTAATCTCTTGTCAGGTGTTCTACCATCTGAACTATCTGGCGCAGGTATTCAAACTGGTCTG
66 CCCTTAATCTCTTGTCAGGTGTCCTACCAACTGAACTATCTGGCGCAGGTATTCAAACTGGTCTG
1434539 ACCGTCACTTTCCTCCACTTTCGCCCTCGAAGATCACCTCAGGTTCTTCCCCTTGGCAGAATCCA
131 ACCGTCACTTTCCTCCACTTTCGCCCTCGAAGATCACCTCAGGTTCTTCCCCTTGGCAGAATCCA
*
1434604 GGGGCAGGTT
196 GGGACAGGTT
1434614 ACGGCACCAAATGTAA
1 ACGGCACCAAATGTAA
1434630 AAGGAAAGGA
Statistics
Matches: 217, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
205 217 1.00
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.24
Consensus pattern (205 bp):
ACGGCACCAAATGTAACGTGATGGGATGAATAATGACGGACCAGACCGGGATTCAAACCCGGCCC
CCCTTAATCTCTTGTCAGGTGTCCTACCAACTGAACTATCTGGCGCAGGTATTCAAACTGGTCTG
ACCGTCACTTTCCTCCACTTTCGCCCTCGAAGATCACCTCAGGTTCTTCCCCTTGGCAGAATCCA
GGGACAGGTT
Found at i:1435038 original size:109 final size:109
Alignment explanation
Indices: 1434847--1435064 Score: 427
Period size: 109 Copynumber: 2.0 Consensus size: 109
1434837 TGAATTCGTC
1434847 ACACCAGATTGCACACCTGAAACTCGTGGCCGACATGTAGTATTCCTTTCGTGGTTTTTGTATTT
1 ACACCAGATTGCACACCTGAAACTCGTGGCCGACATGTAGTATTCCTTTCGTGGTTTTTGTATTT
1434912 TATGCATTTAAATCTTATTTTATGTGCAAATTCTGTTTGTAAAT
66 TATGCATTTAAATCTTATTTTATGTGCAAATTCTGTTTGTAAAT
*
1434956 ACACCAGATTGCACACCTGAACCTCGTGGCCGACATGTAGTATTCCTTTCGTGGTTTTTGTATTT
1 ACACCAGATTGCACACCTGAAACTCGTGGCCGACATGTAGTATTCCTTTCGTGGTTTTTGTATTT
1435021 TATGCATTTAAATCTTATTTTATGTGCAAATTCTGTTTGTAAAT
66 TATGCATTTAAATCTTATTTTATGTGCAAATTCTGTTTGTAAAT
1435065 TATATTTTGA
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 108 1.00
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (109 bp):
ACACCAGATTGCACACCTGAAACTCGTGGCCGACATGTAGTATTCCTTTCGTGGTTTTTGTATTT
TATGCATTTAAATCTTATTTTATGTGCAAATTCTGTTTGTAAAT
Found at i:1439024 original size:14 final size:14
Alignment explanation
Indices: 1439005--1439037 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
1438995 GGTAAAGTTA
1439005 GCTACTAGTAACTG
1 GCTACTAGTAACTG
1439019 GCTACTAGTAACTG
1 GCTACTAGTAACTG
1439033 GCTAC
1 GCTAC
1439038 GAGAAGTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (14 bp):
GCTACTAGTAACTG
Found at i:1439071 original size:37 final size:37
Alignment explanation
Indices: 1439019--1439148 Score: 199
Period size: 37 Copynumber: 3.5 Consensus size: 37
1439009 CTAGTAACTG
1439019 GCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTA
1 GCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTA
* * * * *
1439056 GCTACTAGTAGCTGGCTACGAG-ATTAAATAAAAGTTG
1 GCTACTAGTAACTGGCTACGAGAAGT-AAGAAAAGCTA
1439093 GCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTA
1 GCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTA
1439130 GCTACTAGTAACTGGCTAC
1 GCTACTAGTAACTGGCTAC
1439149 NNNNNNNNNN
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
36 2 0.02
37 77 0.95
38 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (37 bp):
GCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTA
Found at i:1442389 original size:183 final size:183
Alignment explanation
Indices: 1442081--1442412 Score: 549
Period size: 183 Copynumber: 1.8 Consensus size: 183
1442071 TCTTTAGATA
*
1442081 TATTGACAAAACCGCCAGAAAATAAAGATATTTGTAACAAAATGCACAAGTAAATGACTACATAA
1 TATTGACAAAACCACCAGAAAATAAAGATATTTGTAACAAAATGCACAAGTAAATGACTACATAA
*
1442146 AGAGAGATATATGAGTAATTGTGTCGTAATATTATGCAGATGACTTGACAGAATGTTGATATTAG
66 AGAGAGACATATGAGTAATTGTGTCGTAATATTATGCAGATGACTTGACAGAATGTTGATATTAG
*
1442211 CATGTATGGCATATATCTTTTATCTATATATTCAGCTACTGAAGATATACATG
131 CAAGTATGGCATATATCTTTTATCTATATATTCAGCTACTGAAGATATACATG
** *
1442264 TATTGACAAAACCACCA-AAAGATAAAGATATTTGTAACAAAATGCACAAGTACCTGACTACATT
1 TATTGACAAAACCACCAGAAA-ATAAAGATATTTGTAACAAAATGCACAAGTAAATGACTACATA
* * **
1442328 AAGAGGGACATCTGAGTAATTGTGTCGTAATATTATGTGGATGACTTGACAGAATGTTGATATTA
65 AAGAGAGACATATGAGTAATTGTGTCGTAATATTATGCAGATGACTTGACAGAATGTTGATATTA
*
1442393 GCAAGTCTGGCATATATCTT
130 GCAAGTATGGCATATATCTT
1442413 CAATTTATAT
Statistics
Matches: 137, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
182 3 0.02
183 134 0.98
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (183 bp):
TATTGACAAAACCACCAGAAAATAAAGATATTTGTAACAAAATGCACAAGTAAATGACTACATAA
AGAGAGACATATGAGTAATTGTGTCGTAATATTATGCAGATGACTTGACAGAATGTTGATATTAG
CAAGTATGGCATATATCTTTTATCTATATATTCAGCTACTGAAGATATACATG
Found at i:1442619 original size:14 final size:14
Alignment explanation
Indices: 1442600--1442632 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1442590 TTCTTCTCGA
*
1442600 AGCCAGTTACTAGT
1 AGCCAGTTACGAGT
1442614 AGCCAGTTACGAGT
1 AGCCAGTTACGAGT
1442628 AGCCA
1 AGCCA
1442633 AATTTGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.21
Consensus pattern (14 bp):
AGCCAGTTACGAGT
Found at i:1443629 original size:41 final size:40
Alignment explanation
Indices: 1443552--1443632 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 40
1443542 TCTTTTTGTT
* *
1443552 TACATTGTTAGAATGTAATTTTCTTTTTTTACTTAATAATA
1 TACATTGTTAAAATGTAATTTTCTTCTTTTA-TTAATAATA
1443593 TACATTGTTAAAATGTAATTTTCCTCTCTTTT-TTAATAAT
1 TACATTGTTAAAATGTAATTTT-CT-TCTTTTATTAATAAT
1443633 GAAAATTTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
41 29 0.81
42 2 0.06
43 5 0.14
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.53
Consensus pattern (40 bp):
TACATTGTTAAAATGTAATTTTCTTCTTTTATTAATAATA
Found at i:1450635 original size:16 final size:16
Alignment explanation
Indices: 1450611--1450650 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1450601 TTCAAGGGTA
* * *
1450611 TACGTTTTCTCCCGGT
1 TACGATTTCTCCAGGG
1450627 TACGATTTCTCCAGGG
1 TACGATTTCTCCAGGG
1450643 TACGATTT
1 TACGATTT
1450651 TTCCTAATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.15, C:0.25, G:0.20, T:0.40
Consensus pattern (16 bp):
TACGATTTCTCCAGGG
Found at i:1450726 original size:20 final size:21
Alignment explanation
Indices: 1450701--1450743 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1450691 TGCATGCCTA
*
1450701 TTTGTTTTGCATCGGTGT-TG
1 TTTGTTTTACATCGGTGTATG
*
1450721 TTTGTTTTACATCTGTGTATG
1 TTTGTTTTACATCGGTGTATG
1450742 TT
1 TT
1450744 GATTTTGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.09, C:0.09, G:0.23, T:0.58
Consensus pattern (21 bp):
TTTGTTTTACATCGGTGTATG
Found at i:1462354 original size:4 final size:4
Alignment explanation
Indices: 1462342--1462394 Score: 88
Period size: 4 Copynumber: 12.8 Consensus size: 4
1462332 GGGGGGGGGT
1462342 TTTG TTTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTTG
1 TTTG -TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG -TTTG
1462392 TTT
1 TTT
1462395 TGGGGTTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
4 39 0.83
5 8 0.17
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTTG
Found at i:1463920 original size:5 final size:5
Alignment explanation
Indices: 1463912--1463936 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1463902 TTCTTATTCT
1463912 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
1463937 AACTTGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:1464430 original size:17 final size:17
Alignment explanation
Indices: 1464408--1464447 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1464398 AATGTAATGC
**
1464408 TTATTTGGATCAGTGTG
1 TTATTTGGATCAACGTG
1464425 TTATTTGGATCAACGTG
1 TTATTTGGATCAACGTG
1464442 TTATTT
1 TTATTT
1464448 TAGACATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.20, C:0.07, G:0.23, T:0.50
Consensus pattern (17 bp):
TTATTTGGATCAACGTG
Found at i:1472508 original size:2 final size:2
Alignment explanation
Indices: 1472501--1472554 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1472491 TCTCAAACTT
1472501 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1472543 GA GA GA GA GA GA
1 GA GA GA GA GA GA
1472555 TCTGTAAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1474393 original size:18 final size:18
Alignment explanation
Indices: 1474370--1474406 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1474360 AAACAAAACT
1474370 TCTATGTAGAACCATACA
1 TCTATGTAGAACCATACA
1474388 TCTATGTAGAACCATACA
1 TCTATGTAGAACCATACA
1474406 T
1 T
1474407 TTTTAATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.30
Consensus pattern (18 bp):
TCTATGTAGAACCATACA
Found at i:1474903 original size:11 final size:11
Alignment explanation
Indices: 1474889--1474913 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1474879 AACTTTTGGT
1474889 TATAGAATAGA
1 TATAGAATAGA
1474900 TATAGAATAGA
1 TATAGAATAGA
1474911 TAT
1 TAT
1474914 CAATTCTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (11 bp):
TATAGAATAGA
Found at i:1478637 original size:173 final size:172
Alignment explanation
Indices: 1478348--1478803 Score: 797
Period size: 173 Copynumber: 2.6 Consensus size: 172
1478338 GCAGTATACT
* ** *
1478348 AGTATCGACCAAGGCTGATTTAGGAACTTGATCAAGGTATTAGTGGTATAAACATTTAGTATAAA
1 AGTATCGACCAATGCTGATTTTCGAACTTGATCAAGGTATTAGTGGTATAAACATTTGGTATAAA
1478413 TTTCAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAA
66 TTT-AATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAA
*
1478478 ATGGAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAA
130 ACGGAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAA
* *
1478521 AGTATCGACCAATGCTGATTTTCGAACTTGGATCAAAGTATTAGTGGTATAAACACTTGGTATAA
1 AGTATCGACCAATGCTGATTTTCGAACTT-GATCAAGGTATTAGTGGTATAAACATTTGGTATAA
1478586 ATTTAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAA
65 ATTTAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAA
1478651 ACGGAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAA
130 ACGGAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAA
* *
1478694 AGTATCGACCAATGCTGATTTTCGAACTTGACCAAGGTAATAGTGGTATAAACATTTGGTATAAA
1 AGTATCGACCAATGCTGATTTTCGAACTTGATCAAGGTATTAGTGGTATAAACATTTGGTATAAA
*
1478759 TTTAATGAAAA-ACGTCAAAATTTGTAGGCATGAGAGCGCTTACAA
66 TTTAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAA
1478804 AAAAAGTAAG
Statistics
Matches: 270, Mismatches: 12, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
171 33 0.12
172 43 0.16
173 158 0.59
174 36 0.13
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (172 bp):
AGTATCGACCAATGCTGATTTTCGAACTTGATCAAGGTATTAGTGGTATAAACATTTGGTATAAA
TTTAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAA
CGGAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAA
Found at i:1492982 original size:18 final size:18
Alignment explanation
Indices: 1492959--1492994 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1492949 GAAAAAGAAA
*
1492959 GGAAAGAAGGGCAAAAAG
1 GGAAAGAAAGGCAAAAAG
1492977 GGAAAGAAAGGCAAAAAG
1 GGAAAGAAAGGCAAAAAG
1492995 AAGAAGTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.06, G:0.36, T:0.00
Consensus pattern (18 bp):
GGAAAGAAAGGCAAAAAG
Found at i:1497864 original size:16 final size:15
Alignment explanation
Indices: 1497843--1497872 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1497833 AATATATTAC
1497843 TTATTACATTATTTAT
1 TTATTACATT-TTTAT
1497859 TTATTACATTTTTA
1 TTATTACATTTTTA
1497873 GAAATGTAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATTACATTTTTAT
Found at i:1507270 original size:9 final size:9
Alignment explanation
Indices: 1507255--1507287 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
1507245 GTCCGTTGTC
1507255 TGTCGTCGT
1 TGTCGTCGT
*
1507264 CGTCGTCGT
1 TGTCGTCGT
1507273 TGTCGTCGT
1 TGTCGTCGT
1507282 TGTCGT
1 TGTCGT
1507288 TGTTAACTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.00, C:0.24, G:0.33, T:0.42
Consensus pattern (9 bp):
TGTCGTCGT
Found at i:1508079 original size:165 final size:166
Alignment explanation
Indices: 1507460--1508658 Score: 1649
Period size: 165 Copynumber: 7.4 Consensus size: 166
1507450 GGTATTTTTC
* ** * * ** * *
1507460 AAAAATCTTCTTCTCAAAAACTATTTGGCTTGAAAAGCTAAAACTTGTGTGGAGGCATCCTCGGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGAATGGAAGCATCCTCAGG
* *
1507525 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGAGGGGCCACAATTGGGGGA
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATTGGGGGA
*
1507590 TCAAGTTTTACATAGGAATATAAAGAGAAAATCTTT
131 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* * ** * *
1507626 AAAAATCTTCTTCTCAAAAACTATTGGGCCAGAAAAGCTCAAAATAAAATGGTAGCATCCACAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGAATGGAAGCATCCTCAGG
* *
1507691 TAGTGTAGATTCAAATTCT-TTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGG
66 TAGTGTAGATTCAAGTT-TGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATTGGGGG
* * *
1507755 ATCATGTTTTACATAGTAATATTTAGAGAAAATCTTT
130 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* * ** * *
1507792 AAAAATCTTCATCTCAAAAACTATTGGGCCAGAAAAGCTCAAATTAAAATGGGAGCATCCACAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGAATGGAAGCATCCTCAGG
*
1507857 TAGTGTAGATTCAAATTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATTGGGGGA
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATTGGGGGA
*
1507922 TCAAGTTTTACATAGGAATATATAGAGAAAATTTTT
131 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* * * *
1507958 AAAAATCTTCTTCTCAAAAA-TATTAGGCTAGGAAAGCTCAAATTTGAGTGGAAGCATCCTCAGA
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGAATGGAAGCATCCTCAGG
* *
1508022 TAGTGTAGATTCAAGTTTGTTCAAATCATGATCCCTGGGGGTAGGGTGGGGCCACAATAGGGGGA
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATTGGGGGA
* *
1508087 TCAATTTTTACAT-CGAATATATAGAGAAAATCTTT
131 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* * *
1508122 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCCAATTAT-AATGGAATCATCTTCAG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATT-TGAATGGAAGCATCCTCAG
* * *
1508186 GTAGTGTAGATTCAAGTTCGTTCAAATCATGGTACCC-GGGGGTAGGGTGGGGCCAAAATGGGGG
65 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGT-CCCTGGGGGTAGGGTGGGGCCACAATTGGGG
*
1508250 GATCAAGTTTTACATAGGAATATATAGAG-AAATCTAT
129 GATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* * * ** *
1508287 AAAAATCTTCTTCTCAAAAACAATTTGGCCAGAAAAGATCAAATTAAAAGGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGAATGGAAGCATCCTCAGG
* *
1508352 TAGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCTGGGGGTAGGGTGGGGCCACAATGGGGGGA
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATTGGGGGA
*
1508417 TCATGTTTTACATAGGAATATAT-------A---TT
131 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* *
1508443 AAAAATCTTCTTCTCAAAAACTATTGGGCCAGAAAAGCTCAAATTTGAATGGAAGCATCCTCGGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGAATGGAAGCATCCTCAGG
1508508 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGTCCACAATTGGGGG
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGG-CCACAATTGGGGG
1508573 ATCAAGTTTTACATAGGAATATATAGAG---A----T
130 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* *
1508603 ---AATCTTCTTCTCAAAAACTATTAGGCCAGGAATGCTCAAATTTGAATGGAAGCATC
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGAATGGAAGCATC
1508659 NNNNNNNNNN
Statistics
Matches: 937, Mismatches: 83, Indels: 35
0.89 0.08 0.03
Matches are distributed among these distances:
156 109 0.12
157 88 0.09
159 1 0.00
160 1 0.00
161 1 0.00
164 43 0.05
165 357 0.38
166 336 0.36
167 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.28
Consensus pattern (166 bp):
AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGAATGGAAGCATCCTCAGG
TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTGGGGCCACAATTGGGGGA
TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
Found at i:1516264 original size:17 final size:17
Alignment explanation
Indices: 1516242--1516275 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1516232 AACTTTGGGG
1516242 GTGCGTATTATACACGA
1 GTGCGTATTATACACGA
1516259 GTGCGTATTATACACGA
1 GTGCGTATTATACACGA
1516276 TACATTACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (17 bp):
GTGCGTATTATACACGA
Found at i:1516951 original size:16 final size:16
Alignment explanation
Indices: 1516930--1516967 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
1516920 TAGTAATCAC
*
1516930 TCTGTCCGTCCGTCCT
1 TCTGTCCGTCCGTCCG
1516946 TCTGTCCGTCCGTCCG
1 TCTGTCCGTCCGTCCG
1516962 TCTGTC
1 TCTGTC
1516968 ACTCTTCCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.00, C:0.42, G:0.21, T:0.37
Consensus pattern (16 bp):
TCTGTCCGTCCGTCCG
Found at i:1517187 original size:31 final size:31
Alignment explanation
Indices: 1517147--1517213 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
1517137 ACTATGCATA
1517147 AGAA-GAATGGGCAAAGAGAGATAACTGCTG
1 AGAATGAATGGGCAAAGAGAGATAACTGCTG
1517177 AGAATGAATGGGCAAAGAGAGATAACTGCTG
1 AGAATGAATGGGCAAAGAGAGATAACTGCTG
1517208 AGAATG
1 AGAATG
1517214 TTACCATTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 4 0.11
31 32 0.89
ACGTcount: A:0.43, C:0.09, G:0.33, T:0.15
Consensus pattern (31 bp):
AGAATGAATGGGCAAAGAGAGATAACTGCTG
Found at i:1517562 original size:55 final size:54
Alignment explanation
Indices: 1517499--1517607 Score: 200
Period size: 55 Copynumber: 2.0 Consensus size: 54
1517489 ATAGAGGCAA
*
1517499 AGCCTAGGTATCATTGCATTGGTATCAATTCTTTGTTTTTTTAACAAATTTTAT
1 AGCCTAGGTATCATTGCATTGGTATCAACTCTTTGTTTTTTTAACAAATTTTAT
1517553 NAGCCTAGGTATCATTGCATTGGTATCAACTCTTTGTTTTTTTAACAAATTTTAT
1 -AGCCTAGGTATCATTGCATTGGTATCAACTCTTTGTTTTTTTAACAAATTTTAT
1517608 TTCATCCCAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.47
Consensus pattern (54 bp):
AGCCTAGGTATCATTGCATTGGTATCAACTCTTTGTTTTTTTAACAAATTTTAT
Done.