Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 12876159
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 54
Found at i:1036753 original size:34 final size:34
Alignment explanation
Indices: 1036677--1036848 Score: 167
Period size: 34 Copynumber: 4.9 Consensus size: 34
1036667 TTAGTTTGTG
*
1036677 CAATAAAAT-AAAATGTTAGTAAGTTAGTAAGAA
1 CAATAAAATAAAAAAGTTAGTAAGTTAGTAAGAA
* * *
1036710 CAATAAAAATAAAAAAGTCAGTATGTTAGTATGAA
1 CAAT-AAAATAAAAAAGTTAGTAAGTTAGTAAGAA
1036745 CAATAAAATAAAAATTAGAATGTTAGTAAGTTAGTAAGAA
1 CAATAAAAT--AAA--A-AA-GTTAGTAAGTTAGTAAGAA
*
1036785 CAATAAAA-ATAAAAAGTTAG-AATGTTAGTATGAA
1 CAATAAAATA-AAAAAGTTAGTAA-GTTAGTAAGAA
1036819 CAATAAAAT--AAAAGTTAG-AATGTTAGTAAG
1 CAATAAAATAAAAAAGTTAGTAA-GTTAGTAAG
1036849 TTAGAAAAAT
Statistics
Matches: 119, Mismatches: 9, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
32 20 0.17
33 6 0.05
34 33 0.28
35 26 0.22
36 4 0.03
37 1 0.01
38 3 0.03
39 2 0.02
40 24 0.20
ACGTcount: A:0.55, C:0.03, G:0.15, T:0.27
Consensus pattern (34 bp):
CAATAAAATAAAAAAGTTAGTAAGTTAGTAAGAA
Found at i:1036759 original size:40 final size:39
Alignment explanation
Indices: 1036681--1036831 Score: 140
Period size: 35 Copynumber: 4.1 Consensus size: 39
1036671 TTTGTGCAAT
* * *
1036681 AAAATAAAATGTTAGTAAGTTAGTAAGAACAAT--AA-A
1 AAAATAAAAAGTTAGTATGTTAGTATGAACAATAAAATA
* *
1036717 AATA-AAAAAGTCAGTATGTTAGTATGAACAATAAAATA
1 AAAATAAAAAGTTAGTATGTTAGTATGAACAATAAAATA
* * * *
1036755 AAAATTAGAATGTTAGTAAGTTAGTAAGAAC-----AATA
1 AAAA-TAAAAAGTTAGTATGTTAGTATGAACAATAAAATA
*
1036790 AAAATAAAAAGTTAGAATGTTAGTATGAACAATAAAATA
1 AAAATAAAAAGTTAGTATGTTAGTATGAACAATAAAATA
1036829 AAA
1 AAA
1036832 GTTAGAATGT
Statistics
Matches: 89, Mismatches: 16, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
34 21 0.24
35 32 0.36
36 3 0.03
37 2 0.02
38 4 0.04
39 7 0.08
40 20 0.22
ACGTcount: A:0.57, C:0.03, G:0.14, T:0.26
Consensus pattern (39 bp):
AAAATAAAAAGTTAGTATGTTAGTATGAACAATAAAATA
Found at i:1036819 original size:74 final size:75
Alignment explanation
Indices: 1036688--1036852 Score: 296
Period size: 74 Copynumber: 2.2 Consensus size: 75
1036678 AATAAAATAA
*
1036688 AATGTTAGTAAGTTAGTAAGAACAATAAAAATAAAAAAGTCAGTATGTTAGTATGAACAATAAAA
1 AATGTTAGTAAGTTAGTAAGAACAATAAAAATAAAAAAGTCAGAATGTTAGTATGAACAATAAAA
1036753 TAAAAATTAG
66 TAAAAATTAG
*
1036763 AATGTTAGTAAGTTAGTAAGAACAATAAAAAT-AAAAAGTTAGAATGTTAGTATGAACAATAAAA
1 AATGTTAGTAAGTTAGTAAGAACAATAAAAATAAAAAAGTCAGAATGTTAGTATGAACAATAAAA
*
1036827 TAAAAGTTAG
66 TAAAAATTAG
1036837 AATGTTAGTAAGTTAG
1 AATGTTAGTAAGTTAG
1036853 AAAAATTAGC
Statistics
Matches: 87, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
74 55 0.63
75 32 0.37
ACGTcount: A:0.53, C:0.03, G:0.16, T:0.28
Consensus pattern (75 bp):
AATGTTAGTAAGTTAGTAAGAACAATAAAAATAAAAAAGTCAGAATGTTAGTATGAACAATAAAA
TAAAAATTAG
Found at i:1036969 original size:5 final size:5
Alignment explanation
Indices: 1036959--1036987 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1036949 TAAATATATA
1036959 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1036988 GATTAGTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:1037076 original size:125 final size:125
Alignment explanation
Indices: 1036865--1037090 Score: 323
Period size: 125 Copynumber: 1.8 Consensus size: 125
1036855 AAATTAGCGG
* * * *
1036865 TTAGTGGTTAGCAGGGTTCAAACCATAATAATGTGGATCATACCCCAGAACGATTCACCACAAGG
1 TTAGTGGTTAGCAGAGTCCAAACCATAATAATGTAGATCATACCCCAGAACGAGTCACCACAAGG
* *
1036930 TCGAATCGAATAATTCAAATAAATATATAAA-AATAAAATAAAATAAAATAAAATAAAAGA
66 TCGAATCAAATAATTCAAAT-AATAAATAAATAATAAAATAAAATAAAATAAAATAAAAGA
* * *
1036990 TTAGTGGTTAGTAGAGTCCAAACCATAATAATGTAGATCATACCCCGGATCGAGTCACCACAAGG
1 TTAGTGGTTAGCAGAGTCCAAACCATAATAATGTAGATCATACCCCAGAACGAGTCACCACAAGG
1037055 TCGAATCAAAT-ATT-ATGAATAATAAATAAATAATAA
66 TCGAATCAAATAATTCA--AATAATAAATAAATAATAA
1037091 TGGTTAAAGT
Statistics
Matches: 89, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
123 1 0.01
124 12 0.13
125 76 0.85
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (125 bp):
TTAGTGGTTAGCAGAGTCCAAACCATAATAATGTAGATCATACCCCAGAACGAGTCACCACAAGG
TCGAATCAAATAATTCAAATAATAAATAAATAATAAAATAAAATAAAATAAAATAAAAGA
Found at i:1038044 original size:54 final size:54
Alignment explanation
Indices: 1038023--1038408 Score: 580
Period size: 54 Copynumber: 7.1 Consensus size: 54
1038013 GTTTCATACA
* *
1038023 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACTTTGCAAACT
1 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACTTTGCACACT
* * * *
1038077 TAGTGCTGAAAAGGTTATTCATCAACATATGATGAATTCCATACTTTGCACACT
1 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACTTTGCACACT
*
1038131 TAGTGCCGAAAAGGTTATTCATCAACATATGATGAATTTCGTACTTTGCACACT
1 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACTTTGCACACT
*
1038185 TAGTGCCGAAACGGTTATTCGTCAACATATGATGAATTTCGTACTTTGCACACT
1 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACTTTGCACACT
*
1038239 TAGTGCCGAAACGATTATTCATCAACATATGATGAA-TTCTGTACTTTGCACACT
1 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTC-GTACTTTGCACACT
* * * *
1038293 TAGTGTCGAAACGGTTATTCATCAACATATGATGAA-TTCTGTGA-ATTGAACAAT
1 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTC-GT-ACTTTGCACACT
* *
1038347 TAGTGCCGAAACGATTATTCATCAAACATATGATGAATTCCGTACTTTGCACACT
1 TAGTGCCGAAACGGTTATTCATC-AACATATGATGAATTTCGTACTTTGCACACT
1038402 TAGTGCC
1 TAGTGCC
1038409 TATTTGGTAA
Statistics
Matches: 305, Mismatches: 22, Indels: 9
0.91 0.07 0.03
Matches are distributed among these distances:
53 3 0.01
54 270 0.89
55 30 0.10
56 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Consensus pattern (54 bp):
TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACTTTGCACACT
Found at i:1043237 original size:54 final size:54
Alignment explanation
Indices: 1042633--1043944 Score: 1180
Period size: 54 Copynumber: 24.1 Consensus size: 54
1042623 AGAGAGTATA
* * * * * * *
1042633 GAACACGAGCAATCTTCTGCCAACGGGTTCACTCCCTATTACTTCAGGGAGCATG
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTA-G
* *** * * * *
1042688 GAACTCAAACAATCTTCTGTAAACGGGTTCACTCCCTATT-CTTTTTAGGGAGTATA
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGC--TTCAGGGAGTA-G
* * * * * *
1042744 GAACTTGAACAATCTTCT-ACTAACGGGTTCGCTCCCTATTACTTCAAGGAGTATA
1 GAACTCGAACAATCTTCTGCCT-ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTA-G
* ** * ** *
1042799 GAACTCGAACAATCTTCGGCAAACGGGTTCGCTCCCTATTTTATTCAGGGAGTATA
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCT-CTTGCTTCAGGGAGTA-G
* * * * *** * * * *
1042855 TAATTTGAAAAATCTTCTGAAAACAGGTTTGCT-CCTCTTACTTCAGGGAGTATT
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTA-G
* * ** * * * *
1042909 GAACTCGAATAATCTTCTACAAACGGGTTCGCTCCCTATTCCTTTCAAGGAGTATA
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGC-TTCAGGGAGTA-G
*** * * * *
1042965 GAACTCGAACAATCTTCTGAAAATGGGTTTGCTCCCTCTTTCTTCAGGGAGTATA
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTA-G
* * ** * * * *
1043020 GAACTCAAATAATCTTCTGCAAATGAGTTCGCTCCCTATTCCTTTCAGGGAGTATG
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGC-TTCAGGGAGTA-G
* * ** ** * * *
1043076 GAACTTGAACAATCTTTTGCAAACGGGTTTACTCCCTCTTACTTCAAGGTGTAG
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAG
* * *
1043130 GAACTCGAACAATTCATCTGCCTACGGGTTTGCTCCCTCTTACTTCAGGGAGTAG
1 GAACTCGAACAA-TCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAG
* * * * * *
1043185 GAACTTGAACAATCTTCTTCCTATGGGTTCGCTCCCTTTTGATTTAGGGAGTAG
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAG
* * * * ** * *
1043239 GAGCTCGAACAATCTTTTGCTTATGGGTTCATTCCCTATTCCTTCAGGGAGTA-
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAG
* * * *
1043292 GAACTCGAACAATTTTCTGTCTACGGGTTTGCTCCCTCTTACTTCAGGGAGTAG
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAG
* * * * *
1043346 GAACTCGAACAATATTCTACCTACGGGTTCACTCCCTCTTTCTTCAGGGAGTAC
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAG
* * * ** * *
1043400 GAACTCAAACAATCTTCTACCTAGGGGTTCATTCCCTCTTTCTTTAGGGAGTA-
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAG
* *
1043453 GAACTCGAACAATCTTCTACCTACGGGTTCGCTCCCTCTTGCTTCAAGGAGTAG
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAG
* * * *
1043507 GAACTCGAACAATCTTCTGCTTACGGGTTTGTTCCCTCTTGTTTCAGGGAGTAG
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAG
* *
1043561 GAACTTGAACAATCTTCTGCCTACGGGTTCGCTCCGTCTTGCTTCAGGGAGTAG
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAG
* * * * *
1043615 GAATTCGAACAATTTTCAGCCTACGGGTTCGCTCCCTTTTGCTTCAGGAAGTAG
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAG
* ** * **
1043669 GAACTCAAACAATCTTCTGCCTACGGGTTTTCTCCCTCTTGTTTCAGATAGTAG
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAG
* *
1043723 CAACTCGAACAATCTTCTGCCTACGGGTTCGTTCCCTCTTGCTTCAGGGAGTA-
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAG
* * *
1043776 GAACTCGAACAATCTTCTGCCTACGAGTTCGCTCCTTATTGCTTCAGGGAGTAG
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAG
* * * * * *
1043830 GAACGCAAACAATCTTCTACCGATGGGTTCGCTCCCTCTTGCTTCAGTGAGTAG
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAG
* *** * *
1043884 GAACTCGAACAATCTTCTGCCTACGAGTTTATTCCCTCTTGCTTTAGAGAGTA-
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAG
1043937 GAACTCGA
1 GAACTCGA
1043945 GAGAGTAGAA
Statistics
Matches: 1047, Mismatches: 197, Indels: 28
0.82 0.15 0.02
Matches are distributed among these distances:
53 144 0.14
54 542 0.52
55 188 0.18
56 172 0.16
57 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.32
Consensus pattern (54 bp):
GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAG
Found at i:1043336 original size:161 final size:162
Alignment explanation
Indices: 1042631--1043944 Score: 1199
Period size: 161 Copynumber: 8.1 Consensus size: 162
1042621 TCAGAGAGTA
* * * * * * *
1042631 TAGAACACGAGCAATCTTCTGCCAACGGGTTCACTCCCTATTACTTCAGGGAGCATGGAACTCAA
1 TAGAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTA-GGAACTCAA
*** * * * * *
1042696 ACAATCTTCTGTAAACGGGTTCACTCCCTATT-CTTTTTAGGGAGTATAGAACTTGAACAATCTT
65 ACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGC-TTTCAGGGAGTA-GGAACTCGAACAATCTT
* ** * * *
1042760 CT-ACTAACGGGTTCGCTCCCTATTACTTCAAGGAG
128 CTGCCT-ACGGGTTCATTCCCTCTTGCTTCAGGGAG
* ** * ** ** *
1042795 TATAGAACTCGAACAATCTTCGGCAAACGGGTTCGCTCCCTATTTTATTCAGGGAGTATATAATT
1 --TAGAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCT-CTTGCTTCAGGGAGTA-GGAA-C
* *** * * * * *
1042860 TGAAA-AATCTTCTGAAAACAGGTTTGCT-CCTCTTAC-TTCAGGGAGTATTGAACTCGAATAAT
61 TCAAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTTCAGGGAGTA-GGAACTCGAACAAT
* ** ** * * *
1042922 CTTCTACAAACGGGTTCGCTCCCTATTCCTTTCAAGGAG
125 CTTCTGCCTACGGGTTCATTCCCTCTTGC-TTCAGGGAG
*** * * * *
1042961 TATAGAACTCGAACAATCTTCTGAAAATGGGTTTGCTCCCTCTTTCTTCAGGGAGTATAGAACTC
1 --TAGAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTA-GGAACTC
* ** * * * * *
1043026 AAATAATCTTCTGCAAATGAGTTCGCTCCCTATTCCTTTCAGGGAGTATGGAACTTGAACAATCT
63 AAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTTCAGGGAGTA-GGAACTCGAACAATCT
* ** * * * * *
1043091 TTTGCAAACGGGTTTACTCCCTCTTACTTCAAGGTG
127 TCTGCCTACGGGTTCATTCCCTCTTGCTTCAGGGAG
* * * **
1043127 TAGGAACTCGAACAATTCATCTGCCTACGGGTTTGCTCCCTCTTACTTCAGGGAGTAGGAACTTG
1 TA-GAACTCGAACAA-TCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGGAACTCA
* * * * * *
1043192 AACAATCTTCTTCCTATGGGTTCGCTCCCTTTTGATTT-AGGGAGTAGGAGCTCGAACAATCTTT
64 AACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTTCAGGGAGTAGGAACTCGAACAATCTTC
* * * *
1043256 TGCTTATGGGTTCATTCCCTATTCCTTCAGGGAG
129 TGCCTACGGGTTCATTCCCTCTTGCTTCAGGGAG
* * * * *
1043290 TAGAACTCGAACAATTTTCTGTCTACGGGTTTGCTCCCTCTTACTTCAGGGAGTAGGAACTCGAA
1 TAGAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGGAACTCAAA
* * * * * * *
1043355 CAATATTCTACCTACGGGTTCACTCCCTCTTTC-TTCAGGGAGTACGAACTCAAACAATCTTCTA
66 CAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTTCAGGGAGTAGGAACTCGAACAATCTTCTG
* * *
1043419 CCTAGGGGTTCATTCCCTCTTTCTTTAGGGAG
131 CCTACGGGTTCATTCCCTCTTGCTTCAGGGAG
* * *
1043451 TAGAACTCGAACAATCTTCTACCTACGGGTTCGCTCCCTCTTGCTTCAAGGAGTAGGAACTCGAA
1 TAGAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGGAACTCAAA
* * * *
1043516 CAATCTTCTGCTTACGGGTTTGTTCCCTCTTG-TTTCAGGGAGTAGGAACTTGAACAATCTTCTG
66 CAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTTCAGGGAGTAGGAACTCGAACAATCTTCTG
** *
1043580 CCTACGGGTTCGCTCCGTCTTGCTTCAGGGAG
131 CCTACGGGTTCATTCCCTCTTGCTTCAGGGAG
* * * * *
1043612 TAGGAATTCGAACAATTTTCAGCCTACGGGTTCGCTCCCTTTTGCTTCAGGAAGTAGGAACTCAA
1 TA-GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGGAACTCAA
** ** *
1043677 ACAATCTTCTGCCTACGGGTTTTCTCCCTCTTG-TTTCAGATAGTAGCAACTCGAACAATCTTCT
65 ACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTTCAGGGAGTAGGAACTCGAACAATCTTCT
*
1043741 GCCTACGGGTTCGTTCCCTCTTGCTTCAGGGAG
130 GCCTACGGGTTCATTCCCTCTTGCTTCAGGGAG
* * * *
1043774 TAGAACTCGAACAATCTTCTGCCTACGAGTTCGCTCCTTATTGCTTCAGGGAGTAGGAACGCAAA
1 TAGAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGGAACTCAAA
* * * *
1043839 CAATCTTCTACCGATGGGTTCGCTCCCTCTTGC-TTCAGTGAGTAGGAACTCGAACAATCTTCTG
66 CAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTTCAGGGAGTAGGAACTCGAACAATCTTCTG
* * * *
1043903 CCTACGAGTTTATTCCCTCTTGCTTTAGAGAG
131 CCTACGGGTTCATTCCCTCTTGCTTCAGGGAG
1043935 TAGAACTCGA
1 TAGAACTCGA
1043945 GAGAGTAGAA
Statistics
Matches: 972, Mismatches: 162, Indels: 33
0.83 0.14 0.03
Matches are distributed among these distances:
160 2 0.00
161 409 0.42
162 156 0.16
163 43 0.04
164 14 0.01
165 129 0.13
166 134 0.14
167 81 0.08
168 4 0.00
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.32
Consensus pattern (162 bp):
TAGAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGGAACTCAAA
CAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTTCAGGGAGTAGGAACTCGAACAATCTTCTG
CCTACGGGTTCATTCCCTCTTGCTTCAGGGAG
Found at i:1043513 original size:215 final size:215
Alignment explanation
Indices: 1042633--1043944 Score: 1183
Period size: 215 Copynumber: 6.0 Consensus size: 215
1042623 AGAGAGTATA
* * * ** * * *
1042633 GAACACGAGCAATCTTCTGCCAACGGGTTCACTCCCTATTACTTCAGGGAGCATGGAACTCAAAC
1 GAACTCGAACAATCTTCTG-CTACGGGTTTGCTCCCTCTTACTTCAGGGAGTA-GGAACTCGAAC
*** * * * *
1042698 AATCTTCTGTAAACGGGTTCACTCCCTATT-CTTTTTAGGGAGTATAGAACTTGAACAATCTTCT
64 AATCTTCTGCCTACGGGTTCGCTCCCTATTGC--TTCAGGGAGTA-GGAACTCGAACAATCTTCT
* * * * * * **
1042762 A-CTAACGGGTTCGCTCCCTATTACTTCAAGGAGTATAGAACTCGAACAATCTTCGGCAAACGGG
126 ACCT-ATGGGTTCGCTCCCTCTTTCTTCAGGGAGTA-GGAACTCGAACAATCTTCTGCCTACGGG
* ** * *
1042826 TTCGCTCCCTATTTTATTCAGGGAGTATA
189 TTCGCTCCCT-CTTGCTTCAAGGAGTA-G
* * * * ** * * *
1042855 TAATTTGAAAAATCTTCTGAAAACAGGTTTGCT-CCTCTTACTTCAGGGAGTATTGAACTCGAAT
1 GAACTCGAACAATCTTCTG-CTACGGGTTTGCTCCCTCTTACTTCAGGGAGTA-GGAACTCGAAC
* ** * * *
1042919 AATCTTCTACAAACGGGTTCGCTCCCTATTCCTTTCAAGGAGTATAGAACTCGAACAATCTTCTG
64 AATCTTCTGCCTACGGGTTCGCTCCCTATTGC-TTCAGGGAGTA-GGAACTCGAACAATCTTCT-
** * * * * ** * *
1042984 A-AAATGGGTTTGCTCCCTCTTTCTTCAGGGAGTATAGAACTCAAATAATCTTCTGCAAATGAGT
126 ACCTATGGGTTCGCTCCCTCTTTCTTCAGGGAGTA-GGAACTCGAACAATCTTCTGCCTACGGGT
* * *
1043048 TCGCTCCCTATTCCTTTCAGGGAGTATG
190 TCGCTCCCTCTTGC-TTCAAGGAGTA-G
* * * * * *
1043076 GAACTTGAACAATCTTTTGCAAACGGGTTTACTCCCTCTTACTTCAAGGTGTAGGAACTCGAACA
1 GAACTCGAACAATCTTCTGC-TACGGGTTTGCTCCCTCTTACTTCAGGGAGTAGGAACTCGAACA
* * * * * *
1043141 ATTCATCTGCCTACGGGTTTGCTCCCTCTTACTTCAGGGAGTAGGAACTTGAACAATCTTCTTCC
65 A-TCTTCTGCCTACGGGTTCGCTCCCTATTGCTTCAGGGAGTAGGAACTCGAACAATCTTCTACC
* * * * * * *
1043206 TATGGGTTCGCTCCCT-TTTGATTTAGGGAGTAGGAGCTCGAACAATCTTTTGCTTATGGGTTCA
129 TATGGGTTCGCTCCCTCTTT-CTTCAGGGAGTAGGAACTCGAACAATCTTCTGCCTACGGGTTCG
* * * *
1043270 TTCCCTATTCCTTCAGGGAGTA-
193 CTCCCTCTTGCTTCAAGGAGTAG
*
1043292 GAACTCGAACAATTTTCTGTCTACGGGTTTGCTCCCTCTTACTTCAGGGAGTAGGAACTCGAACA
1 GAACTCGAACAATCTTCTG-CTACGGGTTTGCTCCCTCTTACTTCAGGGAGTAGGAACTCGAACA
* * * * * * *
1043357 ATATTCTACCTACGGGTTCACTCCCTCTTTCTTCAGGGAGTACGAACTCAAACAATCTTCTACCT
65 ATCTTCTGCCTACGGGTTCGCTCCCTATTGCTTCAGGGAGTAGGAACTCGAACAATCTTCTACCT
* ** * *
1043422 AGGGGTTCATTCCCTCTTTCTTTAGGGAGTA-GAACTCGAACAATCTTCTACCTACGGGTTCGCT
130 ATGGGTTCGCTCCCTCTTTCTTCAGGGAGTAGGAACTCGAACAATCTTCTGCCTACGGGTTCGCT
1043486 CCCTCTTGCTTCAAGGAGTAG
195 CCCTCTTGCTTCAAGGAGTAG
* ** *
1043507 GAACTCGAACAATCTTCTGCTTACGGGTTTGTTCCCTCTTGTTTCAGGGAGTAGGAACTTGAACA
1 GAACTCGAACAATCTTCTGC-TACGGGTTTGCTCCCTCTTACTTCAGGGAGTAGGAACTCGAACA
* * * *
1043572 ATCTTCTGCCTACGGGTTCGCTCCGTCTTGCTTCAGGGAGTAGGAATTCGAACAATTTTC-AGCC
65 ATCTTCTGCCTACGGGTTCGCTCCCTATTGCTTCAGGGAGTAGGAACTCGAACAATCTTCTA-CC
* * * **
1043636 TACGGGTTCGCTCCCT-TTTGCTTCAGGAAGTAGGAACTCAAACAATCTTCTGCCTACGGGTTTT
129 TATGGGTTCGCTCCCTCTTT-CTTCAGGGAGTAGGAACTCGAACAATCTTCTGCCTACGGGTTCG
* *
1043700 CTCCCTCTTGTTTC-AGATAGTAG
193 CTCCCTCTTGCTTCAAG-GAGTAG
* * * *
1043723 CAACTCGAACAATCTTCTGCCTACGGGTTCGTTCCCTCTTGCTTCAGGGAGTA-GAACTCGAACA
1 GAACTCGAACAATCTTCTG-CTACGGGTTTGCTCCCTCTTACTTCAGGGAGTAGGAACTCGAACA
* * * * *
1043787 ATCTTCTGCCTACGAGTTCGCTCCTTATTGCTTCAGGGAGTAGGAACGCAAACAATCTTCTACCG
65 ATCTTCTGCCTACGGGTTCGCTCCCTATTGCTTCAGGGAGTAGGAACTCGAACAATCTTCTACCT
* * * ***
1043852 ATGGGTTCGCTCCCTCTTGCTTCAGTGAGTAGGAACTCGAACAATCTTCTGCCTACGAGTTTATT
130 ATGGGTTCGCTCCCTCTTTCTTCAGGGAGTAGGAACTCGAACAATCTTCTGCCTACGGGTTCGCT
*
1043917 CCCTCTTGCTT-TAGAGAGTA-
195 CCCTCTTGCTTCAAG-GAGTAG
1043937 GAACTCGA
1 GAACTCGA
1043945 GAGAGTAGAA
Statistics
Matches: 916, Mismatches: 154, Indels: 48
0.82 0.14 0.04
Matches are distributed among these distances:
214 55 0.06
215 349 0.38
216 156 0.17
217 2 0.00
218 11 0.01
219 36 0.04
220 43 0.05
221 200 0.22
222 64 0.07
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.32
Consensus pattern (215 bp):
GAACTCGAACAATCTTCTGCTACGGGTTTGCTCCCTCTTACTTCAGGGAGTAGGAACTCGAACAA
TCTTCTGCCTACGGGTTCGCTCCCTATTGCTTCAGGGAGTAGGAACTCGAACAATCTTCTACCTA
TGGGTTCGCTCCCTCTTTCTTCAGGGAGTAGGAACTCGAACAATCTTCTGCCTACGGGTTCGCTC
CCTCTTGCTTCAAGGAGTAG
Found at i:1043947 original size:15 final size:15
Alignment explanation
Indices: 1043929--1043959 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1043919 CTCTTGCTTT
1043929 AGAGAGTAGAACTCG
1 AGAGAGTAGAACTCG
1043944 AGAGAGTAGAACTCG
1 AGAGAGTAGAACTCG
1043959 A
1 A
1043960 ACAATCTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.13, G:0.32, T:0.13
Consensus pattern (15 bp):
AGAGAGTAGAACTCG
Found at i:1045265 original size:8 final size:8
Alignment explanation
Indices: 1045254--1045374 Score: 57
Period size: 8 Copynumber: 14.2 Consensus size: 8
1045244 CTTTTGACAT
1045254 TTTTTTTA
1 TTTTTTTA
*
1045262 TTTTCTCTTT
1 TTTT-T-TTA
*
1045272 TTATTTTCTC
1 TT-TTTT-TA
1045282 TTTTTTTCA
1 TTTTTTT-A
1045291 TTTTTTTCA
1 TTTTTTT-A
*
1045300 -TTTTTCA
1 TTTTTTTA
*
1045307 TTTTTTCA
1 TTTTTTTA
*
1045315 TTTTTTCA
1 TTTTTTTA
1045323 TTTTTTCTA
1 TTTTTT-TA
*
1045332 TTTTTTTCC
1 TTTTTTT-A
**
1045341 TTTTTTCC
1 TTTTTTTA
*
1045349 TTTTCCTT-
1 TTTT-TTTA
*
1045357 TTTTTTTC
1 TTTTTTTA
1045365 TTTTTTTA
1 TTTTTTTA
1045373 TT
1 TT
1045375 CTTCAAGCAA
Statistics
Matches: 92, Mismatches: 11, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
7 3 0.03
8 50 0.54
9 29 0.32
10 8 0.09
11 2 0.02
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTTA
Found at i:1045272 original size:16 final size:16
Alignment explanation
Indices: 1045253--1045337 Score: 72
Period size: 16 Copynumber: 5.4 Consensus size: 16
1045243 ACTTTTGACA
*
1045253 TTTTTTTTATTTTCTC
1 TTTTTTTCATTTTCTC
1045269 --TTTTT-ATTTTCTC
1 TTTTTTTCATTTTCTC
1045282 TTTTTTTCATTTT-T-
1 TTTTTTTCATTTTCTC
*
1045296 TTCATTTTTCATTTTTTC
1 TT--TTTTTCATTTTCTC
* *
1045314 ATTTTTTCATTTTTTC
1 TTTTTTTCATTTTCTC
1045330 TATTTTTT
1 T-TTTTTT
1045338 TCCTTTTTTC
Statistics
Matches: 59, Mismatches: 2, Indels: 15
0.78 0.03 0.20
Matches are distributed among these distances:
13 8 0.14
14 7 0.12
15 6 0.10
16 30 0.51
17 7 0.12
18 1 0.02
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTTCATTTTCTC
Found at i:1045274 original size:13 final size:13
Alignment explanation
Indices: 1045256--1045286 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1045246 TTTGACATTT
1045256 TTTTTATTTTCTC
1 TTTTTATTTTCTC
1045269 TTTTTATTTTCTC
1 TTTTTATTTTCTC
1045282 TTTTT
1 TTTTT
1045287 TTCATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTATTTTCTC
Found at i:1045294 original size:7 final size:8
Alignment explanation
Indices: 1045269--1045352 Score: 91
Period size: 8 Copynumber: 10.4 Consensus size: 8
1045259 TTATTTTCTC
1045269 TTTTT-AT
1 TTTTTCAT
* *
1045276 TTTCTCTT
1 TTTTTCAT
1045284 TTTTTCATT
1 TTTTTCA-T
1045293 TTTTTCA-
1 TTTTTCAT
1045300 TTTTTCAT
1 TTTTTCAT
1045308 TTTTTCAT
1 TTTTTCAT
1045316 TTTTTCAT
1 TTTTTCAT
1045324 TTTTTCTATT
1 TTTTTC-A-T
*
1045334 TTTTTCCT
1 TTTTTCAT
*
1045342 TTTTTCCT
1 TTTTTCAT
1045350 TTT
1 TTT
1045353 CCTTTTTTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
7 11 0.16
8 40 0.60
9 9 0.13
10 7 0.10
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTCAT
Found at i:1045352 original size:24 final size:24
Alignment explanation
Indices: 1045262--1045371 Score: 100
Period size: 25 Copynumber: 4.5 Consensus size: 24
1045252 ATTTTTTTTA
* *
1045262 TTTTCTCTTTTT-ATTTTCTCTTT
1 TTTTCTTTTTTTCATTTTCTATTT
1045285 TTTTCATTTTTTTCATTTT-TCA-TT
1 TTTTC-TTTTTTTCATTTTCT-ATTT
*
1045309 TTTTCATTTTTTCATTTTTTCTATTT
1 TTTTCTTTTTTTCA--TTTTCTATTT
* * *
1045335 TTTTCCTTTTTTCCTTTTCCTTTTT
1 TTTTCTTTTTTTCATTTT-CTATTT
1045360 TTTTCTTTTTTT
1 TTTTCTTTTTTT
1045372 ATTCTTCAAG
Statistics
Matches: 72, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
23 13 0.18
24 18 0.25
25 26 0.36
26 15 0.21
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTTCTTTTTTTCATTTTCTATTT
Found at i:1045370 original size:18 final size:17
Alignment explanation
Indices: 1045253--1045370 Score: 64
Period size: 17 Copynumber: 6.9 Consensus size: 17
1045243 ACTTTTGACA
* *
1045253 TTTTTTTTATTTTCTCT
1 TTTTTTTTCTTTTTTCT
1045270 TTTTATTTTCTCTTTTT-T
1 TTTT-TTTTCT-TTTTTCT
*
1045288 TCATTTTTTTCATTTTTC-
1 T--TTTTTTTCTTTTTTCT
* *
1045306 -ATTTTTTCATTTTTTCA
1 TTTTTTTTC-TTTTTTCT
* *
1045323 TTTTTTCTATTTTTT-T
1 TTTTTTTTCTTTTTTCT
** * *
1045339 CCTTTTTTCCTTTTCCT
1 TTTTTTTTCTTTTTTCT
1045356 TTTTTTTTCTTTTTT
1 TTTTTTTTCTTTTTT
1045371 TATTCTTCAA
Statistics
Matches: 73, Mismatches: 19, Indels: 18
0.66 0.17 0.16
Matches are distributed among these distances:
15 7 0.10
16 15 0.21
17 22 0.30
18 17 0.23
19 9 0.12
20 3 0.04
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTTTCTTTTTTCT
Found at i:1045376 original size:11 final size:10
Alignment explanation
Indices: 1045253--1045377 Score: 53
Period size: 11 Copynumber: 11.9 Consensus size: 10
1045243 ACTTTTGACA
*
1045253 TTTTTT-TTA
1 TTTTTTCTTT
*
1045262 TTTTCTCTTT
1 TTTTTTCTTT
*
1045272 TTATTTTCTCT
1 TT-TTTTCTTT
*
1045283 TTTTTTC-AT
1 TTTTTTCTTT
1045292 TTTTTTCATTT
1 TTTTTTC-TTT
*
1045303 TTCATTTT-TTCA
1 TT--TTTTCTT-T
*
1045315 TTTTTTC--A
1 TTTTTTCTTT
1045323 TTTTTTCTATT
1 TTTTTTCT-TT
*
1045334 TTTTTCCTTTT
1 TTTTTTC-TTT
1045345 TTCCTTTTCCTTT
1 TT--TTTT-CTTT
1045358 TTTTTTCTTT
1 TTTTTTCTTT
1045368 TTTTATTCTT
1 TTTT-TTCTT
1045378 CAAGCAAAAT
Statistics
Matches: 90, Mismatches: 10, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
8 8 0.09
9 13 0.14
10 21 0.23
11 32 0.36
12 3 0.03
13 12 0.13
14 1 0.01
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:1050212 original size:55 final size:55
Alignment explanation
Indices: 1050113--1050265 Score: 182
Period size: 55 Copynumber: 2.8 Consensus size: 55
1050103 GAAATATTCG
* * *
1050113 ATCAACTTCAAACTT-CTTCATTCATCGGATGTCTTTCTTAATGGATCGGTCTAAA
1 ATCAATTTCAAA-TTCCTTCATTCATCGGATGTCTTTCTTCATGGATCAGTCTAAA
* * * **
1050168 ATCAGTTTCATATTCCTTCATTCATTGGATGTCTTTCTTCATGGATCAGTCTTTA
1 ATCAATTTCAAATTCCTTCATTCATCGGATGTCTTTCTTCATGGATCAGTCTAAA
* * * *
1050223 ATCAATTTTAAATTTCTTCATTCATCAGATGTATTTCTTCATG
1 ATCAATTTCAAATTCCTTCATTCATCGGATGTCTTTCTTCATG
1050266 AATCCTTGTA
Statistics
Matches: 82, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
54 2 0.02
55 80 0.98
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.44
Consensus pattern (55 bp):
ATCAATTTCAAATTCCTTCATTCATCGGATGTCTTTCTTCATGGATCAGTCTAAA
Found at i:1050836 original size:46 final size:46
Alignment explanation
Indices: 1050768--1050901 Score: 197
Period size: 41 Copynumber: 3.0 Consensus size: 46
1050758 CACACCTACT
1050768 TATGTCTGTGTGGAGGTGAATACCATCACGAGGACCATAAGGCATGA
1 TATGTCTGTGTGGA-GTGAATACCATCACGAGGACCATAAGGCATGA
1050815 TATGTCTGTGTGGAGTGAATACCATCACGAGGACCATAAGGCATG-
1 TATGTCTGTGTGGAGTGAATACCATCACGAGGACCATAAGGCATGA
***
1050860 -A-G-CT-CCAGGAGTGAATACCATCACGAGGACCATAAGGCATGA
1 TATGTCTGTGTGGAGTGAATACCATCACGAGGACCATAAGGCATGA
1050902 GCTCCAGGAG
Statistics
Matches: 83, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
41 34 0.41
42 2 0.02
43 1 0.01
44 1 0.01
46 31 0.37
47 14 0.17
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.21
Consensus pattern (46 bp):
TATGTCTGTGTGGAGTGAATACCATCACGAGGACCATAAGGCATGA
Found at i:1054941 original size:163 final size:162
Alignment explanation
Indices: 1054671--1054996 Score: 643
Period size: 163 Copynumber: 2.0 Consensus size: 162
1054661 CCTTAAATCC
1054671 TCATCATCGGGAATACAAAATCTTCCACGGTAATATAAACATCCATTATCCCTCGTTTCGAAATC
1 TCATCATCGGGAATACAAAATCTTCCACGGTAATATAAACATCCATTATCCCTCGTTTCGAAATC
1054736 TTTGGTTTTTTCTTTTTCAACTTGCGCCATTCTCATCAAGCATTTCTTATCTCAACCTTGCAACT
66 TTTGGTTTTTTCTTTTTCAACTTGCGCCATTCTCATCAAGCATTTCTTATCTCAACCTTGCAACT
1054801 CTTTTAACCGATCCAAAAACATCGGCTTTAACT
131 CTTTT-ACCGATCCAAAAACATCGGCTTTAACT
1054834 TCATCATCGGGAATACAAAATCTTCCACGGTAATATAAACATCCATTATCCCTCGTTTCGAAATC
1 TCATCATCGGGAATACAAAATCTTCCACGGTAATATAAACATCCATTATCCCTCGTTTCGAAATC
1054899 TTTGGTTTTTTCTTTTTCAACTTGCGCCATTCTCATCAAGCATTTCTTATCTCAACCTTGCAACT
66 TTTGGTTTTTTCTTTTTCAACTTGCGCCATTCTCATCAAGCATTTCTTATCTCAACCTTGCAACT
1054964 CTTTTACCGATCCAAAAACATCGGCTTTAACT
131 CTTTTACCGATCCAAAAACATCGGCTTTAACT
1054996 T
1 T
1054997 TAATTCAGAA
Statistics
Matches: 163, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
162 28 0.17
163 135 0.83
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.37
Consensus pattern (162 bp):
TCATCATCGGGAATACAAAATCTTCCACGGTAATATAAACATCCATTATCCCTCGTTTCGAAATC
TTTGGTTTTTTCTTTTTCAACTTGCGCCATTCTCATCAAGCATTTCTTATCTCAACCTTGCAACT
CTTTTACCGATCCAAAAACATCGGCTTTAACT
Found at i:1058842 original size:54 final size:55
Alignment explanation
Indices: 1058784--1059029 Score: 324
Period size: 54 Copynumber: 4.6 Consensus size: 55
1058774 TAAACTCAAT
* *
1058784 ATGAATTCTGTTA-GTTGCACA-TATAGTACCGAAACGGTTATTCATCAACATATG
1 ATGAATTCTGTTACTTTGCACACT-TAGTGCCGAAACGGTTATTCATCAACATATG
* * *
1058838 ATGAATTC-CTTACTTTGCACACTTAATGCCGAAATGGTTATTCATCAACATATG
1 ATGAATTCTGTTACTTTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATG
*
1058892 ATGAATTCTG-TACTTTGCACACTTAGTGCCGAAATGGTTATTCATCAACATATG
1 ATGAATTCTGTTACTTTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATG
** * * * *
1058946 ATGAATTCCATGA-ATTGCACACTTAGTGCAGAAACGGTTATTCATCAATATATG
1 ATGAATTCTGTTACTTTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATG
*
1059000 ATGAATTCCG-TACTTTGCACACTTAGTGCC
1 ATGAATTCTGTTACTTTGCACACTTAGTGCC
1059030 TATTTGGTAA
Statistics
Matches: 169, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
53 4 0.02
54 163 0.96
55 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (55 bp):
ATGAATTCTGTTACTTTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATG
Found at i:1059413 original size:22 final size:21
Alignment explanation
Indices: 1059375--1059418 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1059365 TCTATACCCC
*
1059375 TACCATGGTATCAATACTACTA
1 TACCATGGTACCAATACT-CTA
*
1059397 TACCATGGTACCGATACTCTA
1 TACCATGGTACCAATACTCTA
1059418 T
1 T
1059419 TATGGTATCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (21 bp):
TACCATGGTACCAATACTCTA
Found at i:1059500 original size:19 final size:19
Alignment explanation
Indices: 1059476--1059525 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
1059466 CCTTCCTCAC
1059476 AGTATCGATACTGTAATAG
1 AGTATCGATACTGTAATAG
*
1059495 AGTATCGATACCGTAATAG
1 AGTATCGATACTGTAATAG
1059514 AGTATCGATACT
1 AGTATCGATACT
1059526 TCTTGCATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (19 bp):
AGTATCGATACTGTAATAG
Found at i:1059914 original size:13 final size:13
Alignment explanation
Indices: 1059896--1059928 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
1059886 AATCACCTTT
1059896 GAGCTATGGAGGA
1 GAGCTATGGAGGA
1059909 GAGCTATGGAGGA
1 GAGCTATGGAGGA
1059922 GAGCTAT
1 GAGCTAT
1059929 TCTTGATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.42, T:0.18
Consensus pattern (13 bp):
GAGCTATGGAGGA
Found at i:1061069 original size:61 final size:61
Alignment explanation
Indices: 1061000--1061192 Score: 184
Period size: 61 Copynumber: 3.2 Consensus size: 61
1060990 GATATTTGGT
*
1061000 GTTGAAGATGACATTGCTCATCCATGTTGAAGAGATCTGGCCGCTTTCAGATAAATTTTTG
1 GTTGAAGATGACATTGCTCATCCATGTTGAAGAGATCTGGTCGCTTTCAGATAAATTTTTG
* * * * * ** * * *
1061061 GTTGAAGATGACGTTGTTCTTTCATGTTG-AG-GACTTTGGGTCAATAT-GGAT-AA-TTTGG
1 GTTGAAGATGACATTGCTCATCCATGTTGAAGAGA-TCT-GGTCGCTTTCAGATAAATTTTTG
*
1061119 TGTTGAAGACGACACTT-CTCATCCATGTTGAAGAGATCTGGTCGCTTTCAGATAAATTGTTT-
1 -GTTGAAGATGACA-TTGCTCATCCATGTTGAAGAGATCTGGTCGCTTTCAGATAAATT-TTTG
1061181 GTTGAAGATGAC
1 GTTGAAGATGAC
1061193 GTTGTTTCTT
Statistics
Matches: 99, Mismatches: 23, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
58 4 0.04
59 31 0.31
60 16 0.16
61 45 0.45
62 1 0.01
63 2 0.02
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (61 bp):
GTTGAAGATGACATTGCTCATCCATGTTGAAGAGATCTGGTCGCTTTCAGATAAATTTTTG
Found at i:1061158 original size:120 final size:119
Alignment explanation
Indices: 1060946--1061198 Score: 395
Period size: 120 Copynumber: 2.1 Consensus size: 119
1060936 AAAGGATTCA
** *
1060946 AAGATGACACTGTTCATTTATATTGAGGACTTTGGGTCAATATAGATATTTGGTGTTGAAGATGA
1 AAGATGACGTTGTTCATTTATATTGAGGACTTTGGGTCAATATAGATATTTGGTGTTGAAGACGA
1061011 CATTGCTCATCCATGTTGAAGAGATCTGGCCGCTTTCAGATAAATT-TTTGGTTG
66 CATTGCTCATCCATGTTGAAGAGATCTGGCCGCTTTCAGATAAATTGTTT-GTTG
* *
1061065 AAGATGACGTTGTTC-TTTCATGTTGAGGACTTTGGGTCAATATGGATAATTTGGTGTTGAAGAC
1 AAGATGACGTTGTTCATTT-ATATTGAGGACTTTGGGTCAATATAGAT-ATTTGGTGTTGAAGAC
*
1061129 GACACTT-CTCATCCATGTTGAAGAGATCTGGTCGCTTTCAGATAAATTGTTTGTTG
64 GACA-TTGCTCATCCATGTTGAAGAGATCTGGCCGCTTTCAGATAAATTGTTTGTTG
1061185 AAGATGACGTTGTT
1 AAGATGACGTTGTT
1061199 TCTTCTTATT
Statistics
Matches: 124, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
118 3 0.02
119 39 0.31
120 77 0.62
121 5 0.04
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.37
Consensus pattern (119 bp):
AAGATGACGTTGTTCATTTATATTGAGGACTTTGGGTCAATATAGATATTTGGTGTTGAAGACGA
CATTGCTCATCCATGTTGAAGAGATCTGGCCGCTTTCAGATAAATTGTTTGTTG
Found at i:1061223 original size:120 final size:120
Alignment explanation
Indices: 1060980--1061248 Score: 350
Period size: 120 Copynumber: 2.2 Consensus size: 120
1060970 GAGGACTTTG
* *
1060980 GGTCAATATAGAT-ATTTGGTGTTGAAGATGACATTGCTCATCCATGTTGAAGAGATCTGGCCGC
1 GGTCAATATGGATAATTTGGTGTTGAAGACGACATTGCTCATCCATGTTGAAGAGATCTGGCCGC
* * ** **
1061044 TTTCAGATAAATTTTTGGTTGAAGATGACGTTGTTCTTTCATGTTGAGGACTTTG
66 TTTCAGATAAATTTTTGGTTGAAGATGACGTTGTTCTTTCATATTAAGGAAGTCA
*
1061099 GGTCAATATGGATAATTTGGTGTTGAAGACGACACTT-CTCATCCATGTTGAAGAGATCTGGTCG
1 GGTCAATATGGATAATTTGGTGTTGAAGACGACA-TTGCTCATCCATGTTGAAGAGATCTGGCCG
*
1061163 CTTTCAGATAAATTGTTT-GTTGAAGATGACGTTGTT-TCTTCTTATTAAGGAAGTCA
65 CTTTCAGATAAATT-TTTGGTTGAAGATGACGTTGTTCT-TTCATATTAAGGAAGTCA
* *
1061219 GGTCAATCTGGAGATACTTTGGTG-TGAAGA
1 GGTCAATAT-G-GATAATTTGGTGTTGAAGA
1061249 TGTTCTAGAA
Statistics
Matches: 132, Mismatches: 12, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
119 13 0.10
120 96 0.73
121 12 0.09
122 11 0.08
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (120 bp):
GGTCAATATGGATAATTTGGTGTTGAAGACGACATTGCTCATCCATGTTGAAGAGATCTGGCCGC
TTTCAGATAAATTTTTGGTTGAAGATGACGTTGTTCTTTCATATTAAGGAAGTCA
Found at i:1061496 original size:139 final size:139
Alignment explanation
Indices: 1061329--1061749 Score: 556
Period size: 139 Copynumber: 3.0 Consensus size: 139
1061319 GATGTCACTA
* * * * * *
1061329 CTCCTACGCATTGA-AGAGATCTAATTGGTGGACGATATTATTCATACGTGATGAAGATGTCTAG
1 CTCCTACGCATGGAGA-AGATCTAGTTGGTGGATGACATTATTCCTACGTGATGAGGATGTCTAG
* * *
1061393 CCATCTTTAGGGATAACTTGGACACAACACGGTTCCTACGTGATGAGGAAGTCTGGTTGCCTGAG
65 CCGTCTTTAGGGATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGGTTGCCTGAG
1061458 GATGACGCTG
130 GATGACGCTG
* * * * * *
1061468 CTCCTATGTATTGAGAAGATCTGGTTGGTGGATGACATTATTCCTATGTGATGAGGATGTCTATC
1 CTCCTACGCATGGAGAAGATCTAGTTGGTGGATGACATTATTCCTACGTGATGAGGATGTCTAGC
* *
1061533 CGTATTTAGGGATAATTTGGAGACAACACGGTTCTTACGTGATGAGGAAGTCTGGTTGCCTGAGG
66 CGTCTTTAGGGATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGGTTGCCTGAGG
1061598 ATGACGCTG
131 ATGACGCTG
* * * *
1061607 CTCCTACGCGTGGAGGAGATCTAGTCGGTGGATGACATTATTCCTACATGATGAGGATGTCTAGC
1 CTCCTACGCATGGAGAAGATCTAGTTGGTGGATGACATTATTCCTACGTGATGAGGATGTCTAGC
* * ** * *
1061672 CGTCTTTTGGGGATAATTTGGAGACAACACGGTTCCTACATGATGAGGAAACCTGATTGCCTTAG
66 CGTC-TTTAGGGATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGGTTGCCTGAG
* *
1061737 AATGACACTG
130 GATGACGCTG
1061747 CTC
1 CTC
1061750 TTACACGTTG
Statistics
Matches: 245, Mismatches: 35, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
139 180 0.73
140 65 0.27
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (139 bp):
CTCCTACGCATGGAGAAGATCTAGTTGGTGGATGACATTATTCCTACGTGATGAGGATGTCTAGC
CGTCTTTAGGGATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGGTTGCCTGAGG
ATGACGCTG
Found at i:1065012 original size:2 final size:2
Alignment explanation
Indices: 1065005--1065034 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1064995 TTAACTTTAT
1065005 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1065035 ATTATATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1066095 original size:45 final size:46
Alignment explanation
Indices: 1066030--1066117 Score: 151
Period size: 45 Copynumber: 1.9 Consensus size: 46
1066020 TTATTAGTTC
*
1066030 TTTTAATTTATGGCATCATTTCATGCCGATAATGCACCGTTATACA
1 TTTTAATTTATGACATCATTTCATGCCGATAATGCACCGTTATACA
*
1066076 TTTT-ATTTATGACATCATTTCATGCCGGTAATGCACCGTTAT
1 TTTTAATTTATGACATCATTTCATGCCGATAATGCACCGTTAT
1066118 TCATCAAACT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 36 0.90
46 4 0.10
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (46 bp):
TTTTAATTTATGACATCATTTCATGCCGATAATGCACCGTTATACA
Found at i:1066604 original size:112 final size:109
Alignment explanation
Indices: 1066410--1066616 Score: 326
Period size: 112 Copynumber: 1.9 Consensus size: 109
1066400 CCTAATACTG
*
1066410 AAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACATAAATTCATAAA
1 AAATTCATAAACTCATTATGAATTTCTCAGGTTGCACACACAGTGCCAATACATAAATTCATAAA
*
1066475 CTTATTATGAATTTCTTAGTTTTGCACACACAGTGCTCATACAA
66 CTTATTATGAATTTCTTACTTTTGCACACACAGTGCTCATACAA
* * *
1066519 AAATTCATAAACTTATTATGAATTTCTCAGTTTTGCACACACACAGTGCCCATACGA-AAATTCA
1 AAATTCATAAACTCATTATGAATTTCTCAG-GTTG--CACACACAGTGCCAATAC-ATAAATTCA
1066583 TAAACTTATTATGAATTTCTTACTTTTGCACACA
62 TAAACTTATTATGAATTTCTTACTTTTGCACACA
1066617 TATAGTGCCA
Statistics
Matches: 89, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
109 28 0.31
110 3 0.03
112 57 0.64
113 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (109 bp):
AAATTCATAAACTCATTATGAATTTCTCAGGTTGCACACACAGTGCCAATACATAAATTCATAAA
CTTATTATGAATTTCTTACTTTTGCACACACAGTGCTCATACAA
Found at i:1066625 original size:57 final size:54
Alignment explanation
Indices: 1066410--1066616 Score: 308
Period size: 55 Copynumber: 3.8 Consensus size: 54
1066400 CCTAATACTG
* * *
1066410 AAATTCATAAACTCATTATGAATTTCTTAG-GTTGCACACACAGTGCCAATACA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACA
*
1066463 TAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCTCATACAA
1 -AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATAC-A
*
1066519 AAATTCATAAACTTATTATGAATTTCTCAGTTTTGCACACACACAGTGCCCATACGA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTG--CACACACAGTGCCCATAC-A
*
1066576 AAATTCATAAACTTATTATGAATTTCTTACTTTTGCACACA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACA
1066617 TATAGTGCCA
Statistics
Matches: 140, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
54 29 0.21
55 59 0.42
56 1 0.01
57 51 0.36
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (54 bp):
AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACA
Found at i:1070747 original size:22 final size:22
Alignment explanation
Indices: 1070719--1070762 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1070709 ATGCACCGTT
**
1070719 AGGCATTTATTCTTTCATCCAA
1 AGGCATTTAACCTTTCATCCAA
1070741 AGGCATTTAACCTTTCATCCAA
1 AGGCATTTAACCTTTCATCCAA
1070763 CTTGCATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (22 bp):
AGGCATTTAACCTTTCATCCAA
Found at i:1071139 original size:108 final size:109
Alignment explanation
Indices: 1070959--1071282 Score: 472
Period size: 108 Copynumber: 3.0 Consensus size: 109
1070949 GCAAACCTAA
* * * * ** * **
1070959 TGCCAATATGGAAATTCATAAACTAAGTATGAATTTCTTAGGTTACACACACAGTGCTAATACGA
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTATTTTGCACACACAGTGCCCATACGA
1071024 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
66 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
* *
1071068 TGCCCATAGGGAAATTCATAAACTTATTATGAA-TTCTTATTTTGCACGCACAGTGCCCATACGA
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTATTTTGCACACACAGTGCCCATACGA
*
1071132 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACATAG
66 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
* * *
1071176 TGCCCATACGGAAATTCATGAACTTATTATGAATTTCTTAGTTTTGCACACATAGTTCCCATACG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTA-TTTTGCACACACAGTGCCCATACG
*
1071241 AAAATTCATGAAA-TTATTATGAATTTCTTAGTTTCGCACACA
65 AAAATTCAT-AAACTTATTATGAATTTCTTAGTTTTGCACACA
1071283 TATAGTGCCA
Statistics
Matches: 195, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
108 99 0.51
109 35 0.18
110 58 0.30
111 3 0.02
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (109 bp):
TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTATTTTGCACACACAGTGCCCATACGA
AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
Found at i:1071207 original size:163 final size:164
Alignment explanation
Indices: 1070970--1071279 Score: 455
Period size: 163 Copynumber: 1.9 Consensus size: 164
1070960 GCCAATATGG
*
1070970 AAATTCATAAACTAAGTATGAATTTCTTAGGTTACACACACAGTGCTAATACGAAAATTCATAAA
1 AAATTCATAAACTAAGTATGAATTTCTTAGGTTACACACACAGTGCCAATACGAAAATTCATAAA
* *
1071035 CTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATAGGGAAATTCAT-AAACTTATTATG
66 CTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGAAAATTCATGAAA-TTATTATG
*
1071099 AA-TTCTTA-TTTTGCACGCACAGTGCCCATACGA
130 AATTTCTTAGTTTCGCACGCACAGTGCCCATACGA
* * * * * * * *
1071132 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACATAGTGCCCATACGGAAATTCATGA
1 AAATTCATAAACTAAGTATGAATTTCTTAG-GTTACACACACAGTGCCAATACGAAAATTCATAA
* *
1071197 ACTTATTATGAATTTCTTAGTTTTGCACACATAGTTCCCATACGAAAATTCATGAAATTATTATG
65 ACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGAAAATTCATGAAATTATTATG
1071262 AATTTCTTAGTTTCGCAC
130 AATTTCTTAGTTTCGCAC
1071280 ACATATAGTG
Statistics
Matches: 130, Mismatches: 14, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
162 28 0.22
163 86 0.66
164 9 0.07
165 7 0.05
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (164 bp):
AAATTCATAAACTAAGTATGAATTTCTTAGGTTACACACACAGTGCCAATACGAAAATTCATAAA
CTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGAAAATTCATGAAATTATTATGA
ATTTCTTAGTTTCGCACGCACAGTGCCCATACGA
Found at i:1071284 original size:55 final size:55
Alignment explanation
Indices: 1070970--1071282 Score: 454
Period size: 55 Copynumber: 5.7 Consensus size: 55
1070960 GCCAATATGG
* * * * **
1070970 AAATTCATAAACTAAGTATGAATTTCTTAG-GTTACACACACAGTGCTAATACGA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGA
* *
1071024 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATAGGG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGA
*
1071079 AAATTCATAAACTTATTATGAA-TTCTTA-TTTTGCACGCACAGTGCCCATACGA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGA
* *
1071132 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACATAGTGCCCATACGG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGA
* * *
1071187 AAATTCATGAACTTATTATGAATTTCTTAGTTTTGCACACATAGTTCCCATACGA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGA
*
1071242 AAATTCATGAAA-TTATTATGAATTTCTTAGTTTCGCACACA
1 AAATTCAT-AAACTTATTATGAATTTCTTAGTTTTGCACACA
1071283 TATAGTGCCA
Statistics
Matches: 236, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
53 44 0.19
54 40 0.17
55 150 0.64
56 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (55 bp):
AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACGA
Found at i:1073986 original size:22 final size:22
Alignment explanation
Indices: 1073959--1074019 Score: 122
Period size: 22 Copynumber: 2.8 Consensus size: 22
1073949 TTTTGTAAAG
1073959 GGGAAAGGTTCTAGTTTAGCTA
1 GGGAAAGGTTCTAGTTTAGCTA
1073981 GGGAAAGGTTCTAGTTTAGCTA
1 GGGAAAGGTTCTAGTTTAGCTA
1074003 GGGAAAGGTTCTAGTTT
1 GGGAAAGGTTCTAGTTT
1074020 TGCCCAGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.26, C:0.08, G:0.33, T:0.33
Consensus pattern (22 bp):
GGGAAAGGTTCTAGTTTAGCTA
Found at i:1074931 original size:25 final size:24
Alignment explanation
Indices: 1074890--1074968 Score: 140
Period size: 24 Copynumber: 3.2 Consensus size: 24
1074880 AATCGAAAAC
1074890 GATTTTCTTTTGAAAACAAAAATA
1 GATTTTCTTTTGAAAACAAAAATA
*
1074914 GATTTTCTTTTTTAAAACAAAAATA
1 GATTTTC-TTTTGAAAACAAAAATA
1074939 GATTTTCTTTTGAAAACAAAAATA
1 GATTTTCTTTTGAAAACAAAAATA
1074963 GATTTT
1 GATTTT
1074969 GAAAGCCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
24 29 0.56
25 23 0.44
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.42
Consensus pattern (24 bp):
GATTTTCTTTTGAAAACAAAAATA
Found at i:1074969 original size:19 final size:20
Alignment explanation
Indices: 1074946--1074993 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1074936 ATAGATTTTC
*
1074946 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATAAAA
* *
1074965 TTTTGAAAGCCAAAATAAAA
1 TTTTGAAAACAAAAATAAAA
1074985 TTTTGAAAA
1 TTTTGAAAA
1074994 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.54, C:0.06, G:0.10, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATAAAA
Found at i:1077595 original size:141 final size:141
Alignment explanation
Indices: 1077341--1077622 Score: 564
Period size: 141 Copynumber: 2.0 Consensus size: 141
1077331 AGTTTTCTTT
1077341 TGAAGGATTGGACTTTCAGAGGTATGGAATAAATCCTATCCACTTGGAGGCTCTCGAAGTTGAAT
1 TGAAGGATTGGACTTTCAGAGGTATGGAATAAATCCTATCCACTTGGAGGCTCTCGAAGTTGAAT
1077406 AAAGTTGTATACTCTTCTATTATTGGCTTCAAATCTTGTCTATTGAATGTGAAGTAGCTGTAAGC
66 AAAGTTGTATACTCTTCTATTATTGGCTTCAAATCTTGTCTATTGAATGTGAAGTAGCTGTAAGC
1077471 AGGATTCCATA
131 AGGATTCCATA
1077482 TGAAGGATTGGACTTTCAGAGGTATGGAATAAATCCTATCCACTTGGAGGCTCTCGAAGTTGAAT
1 TGAAGGATTGGACTTTCAGAGGTATGGAATAAATCCTATCCACTTGGAGGCTCTCGAAGTTGAAT
1077547 AAAGTTGTATACTCTTCTATTATTGGCTTCAAATCTTGTCTATTGAATGTGAAGTAGCTGTAAGC
66 AAAGTTGTATACTCTTCTATTATTGGCTTCAAATCTTGTCTATTGAATGTGAAGTAGCTGTAAGC
1077612 AGGATTCCATA
131 AGGATTCCATA
1077623 ATCGGACCAA
Statistics
Matches: 141, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
141 141 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (141 bp):
TGAAGGATTGGACTTTCAGAGGTATGGAATAAATCCTATCCACTTGGAGGCTCTCGAAGTTGAAT
AAAGTTGTATACTCTTCTATTATTGGCTTCAAATCTTGTCTATTGAATGTGAAGTAGCTGTAAGC
AGGATTCCATA
Found at i:1090996 original size:15 final size:15
Alignment explanation
Indices: 1090947--1090997 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
1090937 CCAGTCACCG
1090947 AGTCAACTCGGTCTA
1 AGTCAACTCGGTCTA
* * *
1090962 ATTCAACCCGTTC-A
1 AGTCAACTCGGTCTA
*
1090976 AGTCAACTCGGTCTG
1 AGTCAACTCGGTCTA
1090991 AGTCAAC
1 AGTCAAC
1090998 CCATCCGAGT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.25
Consensus pattern (15 bp):
AGTCAACTCGGTCTA
Found at i:1096890 original size:28 final size:28
Alignment explanation
Indices: 1096858--1096914 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1096848 CTCTTCATTT
* * *
1096858 ACATTATGTTGTTGAGTCAATGCTTGAA
1 ACATTATGTCGTCGAGCCAATGCTTGAA
*
1096886 ACATTATGTCGTCGAGCCAGTGCTTGAA
1 ACATTATGTCGTCGAGCCAATGCTTGAA
1096914 A
1 A
1096915 GCAACAACGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (28 bp):
ACATTATGTCGTCGAGCCAATGCTTGAA
Found at i:1098123 original size:43 final size:43
Alignment explanation
Indices: 1098055--1098153 Score: 146
Period size: 43 Copynumber: 2.3 Consensus size: 43
1098045 AGCTTCTGAA
* *
1098055 TTCAATTAGAAACCTAGACATGGATCATTAATTTACCTTAT-CC
1 TTCAATTAGAAACCTAAACAGGGATCATTAATTTACCTT-TGCC
1098098 TTCAATTAGAAACCTAAACAGGGATCATTAATTTACCTTTGCC
1 TTCAATTAGAAACCTAAACAGGGATCATTAATTTACCTTTGCC
*
1098141 TTCCAATGAGAAA
1 TT-CAATTAGAAA
1098154 GTGAGAAACG
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
42 1 0.02
43 41 0.80
44 9 0.18
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.32
Consensus pattern (43 bp):
TTCAATTAGAAACCTAAACAGGGATCATTAATTTACCTTTGCC
Found at i:1100113 original size:31 final size:31
Alignment explanation
Indices: 1100074--1100223 Score: 124
Period size: 31 Copynumber: 4.9 Consensus size: 31
1100064 TGGGCTTATG
*
1100074 GGCTTACCCAAGAAAGTTCTCAGGGCCAC-A
1 GGCTTACCCAAGAAAGATCTCAGGGCCACAA
* *
1100104 GTGCTTACCCAAGAAAGATGTCAGGGCCGCAA
1 G-GCTTACCCAAGAAAGATCTCAGGGCCACAA
* * **
1100136 GGCCTACCCAAGAATGATCTCAGGGCCACGG
1 GGCTTACCCAAGAAAGATCTCAGGGCCACAA
* * * * * * *
1100167 GGCCTACCCAAAAAAAATCCCAAGG-CGCAG
1 GGCTTACCCAAGAAAGATCTCAGGGCCACAA
* * *
1100197 GGCCTACCCAAGAATGATCTCGGGGCC
1 GGCTTACCCAAGAAAGATCTCAGGGCC
1100224 GAAGAGCCTA
Statistics
Matches: 95, Mismatches: 22, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
30 23 0.24
31 70 0.74
32 2 0.02
ACGTcount: A:0.30, C:0.31, G:0.26, T:0.13
Consensus pattern (31 bp):
GGCTTACCCAAGAAAGATCTCAGGGCCACAA
Found at i:1100215 original size:61 final size:62
Alignment explanation
Indices: 1100073--1100223 Score: 178
Period size: 62 Copynumber: 2.5 Consensus size: 62
1100063 TTGGGCTTAT
* * * * * * * ** *
1100073 GGGCTTACCCAAGAAAGTTCTCAGGGCCACAGTGCTTACCCAAGAAAGATGTCAGGGCCGCA
1 GGGCCTACCCAAGAATGATCTCAGGGCCACAGGGCCTACCCAAAAAAAATCCCAAGGCCGCA
* *
1100135 AGGCCTACCCAAGAATGATCTCAGGGCCACGGGGCCTACCCAAAAAAAATCCCAAGG-CGCA
1 GGGCCTACCCAAGAATGATCTCAGGGCCACAGGGCCTACCCAAAAAAAATCCCAAGGCCGCA
*
1100196 GGGCCTACCCAAGAATGATCTCGGGGCC
1 GGGCCTACCCAAGAATGATCTCAGGGCC
1100224 GAAGAGCCTA
Statistics
Matches: 75, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
61 30 0.40
62 45 0.60
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.13
Consensus pattern (62 bp):
GGGCCTACCCAAGAATGATCTCAGGGCCACAGGGCCTACCCAAAAAAAATCCCAAGGCCGCA
Found at i:1102494 original size:30 final size:29
Alignment explanation
Indices: 1102459--1102529 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 29
1102449 TGACTTTTTG
*
1102459 GTCAAAGTCAATAGTTAACGAGTTGACTC
1 GTCAAAGTCAATAGTCAACGAGTTGACTC
*
1102488 AGTCAAAGTCAATAGTCAACGGGTTGACTC
1 -GTCAAAGTCAATAGTCAACGAGTTGACTC
1102518 GATCAAAGTCAA
1 G-TCAAAGTCAA
1102530 AGAGTTGACC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 1 0.03
30 37 0.97
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (29 bp):
GTCAAAGTCAATAGTCAACGAGTTGACTC
Found at i:1104684 original size:31 final size:31
Alignment explanation
Indices: 1104639--1104804 Score: 154
Period size: 31 Copynumber: 5.4 Consensus size: 31
1104629 TGGTCCTATA
* * **
1104639 GGCCTACCCCAGAAAGTTCTCAGGGCCATGG
1 GGCCTACCCAAGAAAGATCTCAGGGCCACAG
* * * *
1104670 GGGCTACCCAAGAAAGATGTCAGGGCCGCAA
1 GGCCTACCCAAGAAAGATCTCAGGGCCACAG
* *
1104701 GGCCTACCCAAGAATGATCTCAGGGCCACCG
1 GGCCTACCCAAGAAAGATCTCAGGGCCACAG
* * *
1104732 GGCCTATCCAAGAAA-ATTTATAGGGCCACAG
1 GGCCTACCCAAGAAAGATCT-CAGGGCCACAG
* * * *
1104763 GGCTTACCCAAGAATGATCTCGGGGCCGCAG
1 GGCCTACCCAAGAAAGATCTCAGGGCCACAG
*
1104794 AGCCTACCCAA
1 GGCCTACCCAA
1104805 TAGTCATATT
Statistics
Matches: 105, Mismatches: 28, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
30 3 0.03
31 99 0.94
32 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.14
Consensus pattern (31 bp):
GGCCTACCCAAGAAAGATCTCAGGGCCACAG
Found at i:1104743 original size:62 final size:62
Alignment explanation
Indices: 1104638--1104804 Score: 174
Period size: 62 Copynumber: 2.7 Consensus size: 62
1104628 TTGGTCCTAT
* * * ** * *
1104638 AGGCCTACCCCAGAAAGTTCTCAGGGCCATGGGGGCTACCCAAGAAAGATGT-CAGGGCCGCA
1 AGGCCTACCCAAGAATGATCTCAGGGCCACCGGGCCTACCCAAGAAA-ATGTACAGGGCCACA
* * *
1104700 AGGCCTACCCAAGAATGATCTCAGGGCCACCGGGCCTATCCAAGAAAATTTATAGGGCCACA
1 AGGCCTACCCAAGAATGATCTCAGGGCCACCGGGCCTACCCAAGAAAATGTACAGGGCCACA
* * * * * *
1104762 GGGCTTACCCAAGAATGATCTCGGGGCCGCAGAGCCTACCCAA
1 AGGCCTACCCAAGAATGATCTCAGGGCCACCGGGCCTACCCAA
1104805 TAGTCATATT
Statistics
Matches: 87, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
61 3 0.03
62 84 0.97
ACGTcount: A:0.29, C:0.30, G:0.27, T:0.14
Consensus pattern (62 bp):
AGGCCTACCCAAGAATGATCTCAGGGCCACCGGGCCTACCCAAGAAAATGTACAGGGCCACA
Found at i:1106103 original size:65 final size:64
Alignment explanation
Indices: 1105973--1106156 Score: 185
Period size: 65 Copynumber: 2.9 Consensus size: 64
1105963 AATTAAATTG
* * * *
1105973 AACATTGAATTCATTTCATGCATCGATGCACTTACCATGCACCGATGCACTAAGGATTTTATGAA
1 AACATCGAATACATTTGATGCATCGATGCACTCACCATGCACCGATGCACTAAGGATTTTATG-A
* * ** *
1106038 AACATCGAATGCATTTGATGCATCGATGCAC-CAGCCATGCATCGATGCACTCTGGCTATTT-TG
1 AACATCGAATACATTTGATGCATCGATGCACTCA-CCATGCACCGATGCACTAAGGAT-TTTATG
1106101 A
64 A
* * ** *
1106102 AACATCGAATACACTTGATGCATCGATGTACTC-TTAGTGCACCGATGTACTAAGG
1 AACATCGAATACATTTGATGCATCGATGCACTCACCA-TGCACCGATGCACTAAGG
1106157 GTCCAACGGT
Statistics
Matches: 98, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
63 1 0.01
64 44 0.45
65 50 0.51
66 3 0.03
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (64 bp):
AACATCGAATACATTTGATGCATCGATGCACTCACCATGCACCGATGCACTAAGGATTTTATGA
Found at i:1106148 original size:64 final size:63
Alignment explanation
Indices: 1105990--1106156 Score: 151
Period size: 64 Copynumber: 2.6 Consensus size: 63
1105980 AATTCATTTC
* * * *
1105990 ATGCATCGATGCACTTACCATGCACCGATGCACTAAGGATTTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCAC-CAGC-TGCACCGATGCACTAAGGATTTTATGAAAACATCGAATACACTTG
* ** *
1106055 ATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTT-TG-AAACATCGAATACACTT
1 ATGCATCGATGCACCAG-C-TGCACCGATGCACTAAGGAT-TTTATGAAAACATCGAATACACTT
1106118 G
63 G
* *
1106119 ATGCATCGATGTACTCTTAG-TGCACCGATGTACTAAGG
1 ATGCATCGATGCAC-C--AGCTGCACCGATGCACTAAGG
1106157 GTCCAACGGT
Statistics
Matches: 84, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
64 44 0.52
65 35 0.42
66 3 0.04
67 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (63 bp):
ATGCATCGATGCACCAGCTGCACCGATGCACTAAGGATTTTATGAAAACATCGAATACACTTG
Found at i:1114007 original size:2 final size:2
Alignment explanation
Indices: 1114000--1114060 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1113990 CAGCTTAAGC
1114000 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1114042 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1114061 CAATTGGCTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1114613 original size:65 final size:64
Alignment explanation
Indices: 1114544--1114728 Score: 189
Period size: 65 Copynumber: 2.9 Consensus size: 64
1114534 AATTAAATTG
* * *
1114544 AACATTGAATACATTTCATGCATCGATGCACTTACCATGCACCGATGCACTAAGGAT-TTTATGA
1 AACATCGAATGCATTTAATGCATCGATGCACTTACCATGCACCGATGCACTAAGGATATTT-T-A
1114608 A
64 A
* * ** *
1114609 AACATCGAATGCATTTAATGCATCGATGCAC-CAGCCATGCATCGATGCACTCTGGGCTATTTTA
1 AACATCGAATGCATTTAATGCATCGATGCACTTA-CCATGCACCGATGCACT-AAGGATATTTTA
1114673 A
64 A
* * *
1114674 AACATCGAATGCACTTGATGCATCGATGCACTCTTA--GTGCACCGATGCACTAAGG
1 AACATCGAATGCATTTAATGCATCGATGCA--CTTACCATGCACCGATGCACTAAGG
1114729 GTCCAACGGT
Statistics
Matches: 99, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
64 3 0.03
65 87 0.88
66 4 0.04
67 4 0.04
68 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTAATGCATCGATGCACTTACCATGCACCGATGCACTAAGGATATTTTAA
Found at i:1114704 original size:17 final size:19
Alignment explanation
Indices: 1114676--1114724 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1114666 TATTTTAAAA
1114676 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1114694 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1114713 CACCGATGCACT
1 CATCGATGCACT
1114725 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1125495 original size:67 final size:67
Alignment explanation
Indices: 1125387--1125519 Score: 257
Period size: 67 Copynumber: 2.0 Consensus size: 67
1125377 AAATGTTTAC
*
1125387 TCTTAGTCCCTCTTCCATTGCTACCTATCTAAATATCAACAATGATGGTTCTTTCAAGGACAATT
1 TCTTAGTCCCTCTTCCATTACTACCTATCTAAATATCAACAATGATGGTTCTTTCAAGGACAATT
1125452 CT
66 CT
1125454 TCTTAGTCCCTCTTCCATTACTACCTATCTAAATATCAACAATGATGGTTCTTTCAAGGACAATT
1 TCTTAGTCCCTCTTCCATTACTACCTATCTAAATATCAACAATGATGGTTCTTTCAAGGACAATT
1125519 C
66 C
1125520 ATATGTTCAA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.37
Consensus pattern (67 bp):
TCTTAGTCCCTCTTCCATTACTACCTATCTAAATATCAACAATGATGGTTCTTTCAAGGACAATT
CT
Found at i:1126808 original size:20 final size:21
Alignment explanation
Indices: 1126764--1126812 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
1126754 GGCTTTTCTG
*
1126764 GTATCGATACCATGGTGTTGA
1 GTATCGATACCATGGTGGTGA
1126785 -TATCGATA-C-TGGTTGGTGA
1 GTATCGATACCATGG-TGGTGA
1126804 GTATCGATA
1 GTATCGATA
1126813 TTCACATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 3 0.12
19 6 0.24
20 16 0.64
ACGTcount: A:0.24, C:0.12, G:0.29, T:0.35
Consensus pattern (21 bp):
GTATCGATACCATGGTGGTGA
Found at i:1135414 original size:11 final size:9
Alignment explanation
Indices: 1135397--1135435 Score: 53
Period size: 8 Copynumber: 4.2 Consensus size: 9
1135387 ATTATTATTA
1135397 TTTATTTATT
1 TTTATTT-TT
1135407 TTTCATTTTT
1 TTT-ATTTTT
1135417 TTTA-TTTT
1 TTTATTTTT
1135425 TTTATTTTT
1 TTTATTTTT
1135434 TT
1 TT
1135436 GCAGGTCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.30
9 7 0.26
10 8 0.30
11 4 0.15
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTATTTTT
Found at i:1135420 original size:16 final size:17
Alignment explanation
Indices: 1135401--1135435 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1135391 TTATTATTTA
1135401 TTTA-TTTTTCATTTTT
1 TTTATTTTTTCATTTTT
*
1135417 TTTATTTTTTTATTTTT
1 TTTATTTTTTCATTTTT
1135434 TT
1 TT
1135436 GCAGGTCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTATTTTTTCATTTTT
Found at i:1135473 original size:13 final size:13
Alignment explanation
Indices: 1135455--1135500 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
1135445 GTACAATTTA
1135455 AGCCCAAACAGTG
1 AGCCCAAACAGTG
*
1135468 AGCCC-AACAGCCG
1 AGCCCAAACAG-TG
*
1135481 -GCACAAACAGTG
1 AGCCCAAACAGTG
1135493 AGCCCAAA
1 AGCCCAAA
1135501 AGTTGGCCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
12 9 0.35
13 17 0.65
ACGTcount: A:0.39, C:0.35, G:0.22, T:0.04
Consensus pattern (13 bp):
AGCCCAAACAGTG
Found at i:1137015 original size:2 final size:2
Alignment explanation
Indices: 1137008--1137089 Score: 164
Period size: 2 Copynumber: 41.0 Consensus size: 2
1136998 AATATTTTTA
1137008 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1137050 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1137090 TTAAATGCAT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1143528 original size:89 final size:89
Alignment explanation
Indices: 1143355--1143528 Score: 287
Period size: 89 Copynumber: 2.0 Consensus size: 89
1143345 CCCCGAATAT
* * *
1143355 TTAATTTCAATTAATTAAATATAGATTTACTTAATTTGAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAACTTGAAATAATAAAATCCCTAATATGATTAG
1143420 GGTAACTTGGATATAAAAGGATTA
66 GGTAACTTGGATATAAAAGGATTA
*
1143444 TTAAATTCTAATTAATTAAATATATATTTAATTAACTTGAAATAATAAAA-CCCTAATATGATTA
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAACTTGAAATAATAAAATCCCTAATATGATTA
*
1143508 GGGTAACTTGGCTATAAAAGG
65 GGGTAACTTGGATATAAAAGG
1143529 GTCTGTTAGG
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
89 41 0.52
90 38 0.48
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.37
Consensus pattern (89 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAACTTGAAATAATAAAATCCCTAATATGATTAG
GGTAACTTGGATATAAAAGGATTA
Found at i:1150104 original size:20 final size:21
Alignment explanation
Indices: 1150080--1150149 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
1150070 ATATATAGAC
1150080 TTAATTAAATATATGTTTTAA
1 TTAATTAAATATATGTTTTAA
* * *
1150101 -TAATCCTAAATATTTAATTTCAA
1 TTAAT--TAAATATAT-GTTTTAA
*
1150124 TTAATTAAATATA-GATTTAA
1 TTAATTAAATATATGTTTTAA
1150144 TTAATT
1 TTAATT
1150150 TGAAATAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 14 0.37
22 15 0.39
23 5 0.13
24 4 0.11
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (21 bp):
TTAATTAAATATATGTTTTAA
Found at i:1154296 original size:134 final size:133
Alignment explanation
Indices: 1154135--1154433 Score: 438
Period size: 134 Copynumber: 2.2 Consensus size: 133
1154125 AATCGAATTT
* * *
1154135 GATTCAATCTTCCCTGAAGAACAGTGGAATGAATTAATGTTTCCATATATGATTTT-CTCTGAAG
1 GATTCAATCTTCCCTGAAAAACAGTGGAATGAATGAATGTTTCCATATATGATTTTCCT-TAAAG
** * *
1154199 AAGCAACAGAACAGATCCCCTTTTTCCAGATTTGGTCTTCCCCTGATGAACAATGGAACAAGTCT
65 AAGCAACAGAACAGATCCCCTTTTTCCAGATTTAATATT-CCCTGAGGAACAATGGAACAAGTCT
1154264 GCCTC
129 GCCTC
*
1154269 GATTCAATCTTCCCTGAAAAATAGTGGAATGAATGAATGTTTCCATATATGATTTTCCTTAAAGA
1 GATTCAATCTTCCCTGAAAAACAGTGGAATGAATGAATGTTTCCATATATGATTTTCCTTAAAGA
** * * *
1154334 AGCAGTAGAACAGATCCCCTTTTTCCAGATTTAATATTCCCTGAGGAATAGTGGAACAAGTCTGT
66 AGCAACAGAACAGATCCCCTTTTTCCAGATTTAATATTCCCTGAGGAACAATGGAACAAGTCTGC
*
1154399 CTT
131 CTC
*
1154402 GATTCAATATTCCCTGAAAAACAGTGGAATGA
1 GATTCAATCTTCCCTGAAAAACAGTGGAATGA
1154434 GTCAACATTT
Statistics
Matches: 148, Mismatches: 16, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
133 55 0.37
134 91 0.61
135 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Consensus pattern (133 bp):
GATTCAATCTTCCCTGAAAAACAGTGGAATGAATGAATGTTTCCATATATGATTTTCCTTAAAGA
AGCAACAGAACAGATCCCCTTTTTCCAGATTTAATATTCCCTGAGGAACAATGGAACAAGTCTGC
CTC
Found at i:1154689 original size:3 final size:3
Alignment explanation
Indices: 1154681--1154732 Score: 50
Period size: 3 Copynumber: 16.3 Consensus size: 3
1154671 ATCGAAACCA
* * *
1154681 TAT TAT TAT TAT TCT TAT TATT TATT TAT TATT TAT TTT TTT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TA-T TAT TA-T TAT TAT TAT TAT TAT
1154729 TAT T
1 TAT T
1154733 TTGCAGGCCC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 33 0.77
4 10 0.23
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (3 bp):
TAT
Found at i:1154711 original size:11 final size:11
Alignment explanation
Indices: 1154695--1154733 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
1154685 ATTATTATTC
1154695 TTATTATTTAT
1 TTATTATTTAT
1154706 TTATTATTTAT
1 TTATTATTTAT
1154717 TT-TT-TTTA-
1 TTATTATTTAT
1154725 TTATTATTT
1 TTATTATTT
1154734 TGCAGGCCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 2 0.08
9 6 0.23
10 5 0.19
11 13 0.50
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTATTATTTAT
Found at i:1154711 original size:20 final size:17
Alignment explanation
Indices: 1154686--1154729 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 17
1154676 AACCATATTA
1154686 TTATTATTCTTATTATTTAT
1 TTATTATT-TTATT-TTT-T
1154706 TTATTA-TTTATTTTTT
1 TTATTATTTTATTTTTT
1154722 TTATTATT
1 TTATTATT
1154730 ATTTTGCAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 7 0.30
17 4 0.17
18 5 0.22
19 1 0.04
20 6 0.26
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (17 bp):
TTATTATTTTATTTTTT
Found at i:1154733 original size:15 final size:15
Alignment explanation
Indices: 1154681--1154734 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
1154671 ATCGAAACCA
* * *
1154681 TATTATTATTATTCT
1 TATTATTTTTTTTAT
*
1154696 TATTA-TTTATTTAT
1 TATTATTTTTTTTAT
1154710 TATTTATTTTTTTTAT
1 TA-TTATTTTTTTTAT
1154726 TATTATTTT
1 TATTATTTT
1154735 GCAGGCCCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 7 0.22
15 15 0.47
16 10 0.31
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTATTTTTTTTAT
Found at i:1155279 original size:23 final size:23
Alignment explanation
Indices: 1155253--1155307 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
1155243 TCTAAAAGTG
1155253 AAAGAGGAAGAAACCTGAAAGGA
1 AAAGAGGAAGAAACCTGAAAGGA
1155276 AAAGAGGAAGAAACCTGAAAGGA
1 AAAGAGGAAGAAACCTGAAAGGA
1155299 AAAGAGGAA
1 AAAGAGGAA
1155308 AAAAATCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.58, C:0.07, G:0.31, T:0.04
Consensus pattern (23 bp):
AAAGAGGAAGAAACCTGAAAGGA
Found at i:1158789 original size:23 final size:23
Alignment explanation
Indices: 1158735--1158789 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1158725 AAGATTACTG
*
1158735 AAAGACAGAGATAAACATGTCAC
1 AAAGACATAGATAAACATGTCAC
* *
1158758 AAATG-CATATATAAACATGTCAT
1 AAA-GACATAGATAAACATGTCAC
1158781 AAAGACATA
1 AAAGACATA
1158790 ATTATTCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 1 0.04
23 25 0.93
24 1 0.04
ACGTcount: A:0.53, C:0.15, G:0.13, T:0.20
Consensus pattern (23 bp):
AAAGACATAGATAAACATGTCAC
Found at i:1159665 original size:12 final size:12
Alignment explanation
Indices: 1159637--1159682 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 12
1159627 TTTTAAATGC
*
1159637 TAGAAACAAGGT
1 TAGAAACAAGAT
*
1159649 AAGAAACAAGAT
1 TAGAAACAAGAT
1159661 TAG-AACAAGAT
1 TAGAAACAAGAT
*
1159672 TA-AAAAAAGAT
1 TAGAAACAAGAT
1159683 AAAGAAATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 17 0.59
12 12 0.41
ACGTcount: A:0.61, C:0.07, G:0.17, T:0.15
Consensus pattern (12 bp):
TAGAAACAAGAT
Found at i:1162472 original size:21 final size:21
Alignment explanation
Indices: 1162443--1162508 Score: 123
Period size: 21 Copynumber: 3.1 Consensus size: 21
1162433 TCAAGAATAT
1162443 CAATGATGTTTGAGTTCAAGC
1 CAATGATGTTTGAGTTCAAGC
*
1162464 CAATAATGTTTGAGTTCAAGC
1 CAATGATGTTTGAGTTCAAGC
1162485 CAATGATGTTTGAGTTCAAGC
1 CAATGATGTTTGAGTTCAAGC
1162506 CAA
1 CAA
1162509 CGACGTATCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (21 bp):
CAATGATGTTTGAGTTCAAGC
Found at i:1163134 original size:19 final size:18
Alignment explanation
Indices: 1163115--1163163 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
1163105 ATTATTTTTA
1163115 AAATAAAAAATAAGAATT
1 AAATAAAAAATAAGAATT
* *
1163133 AAATAAAAGAAAAATAATT
1 AAATAAAA-AATAAGAATT
1163152 AAATAAACAAAT
1 AAATAAA-AAAT
1163164 TAAAGAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.20
Consensus pattern (18 bp):
AAATAAAAAATAAGAATT
Found at i:1165677 original size:11 final size:11
Alignment explanation
Indices: 1165652--1165690 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
1165642 AAGTTTGCTG
1165652 AAAATAAAAC-
1 AAAATAAAACA
*
1165662 GAAATAAAACA
1 AAAATAAAACA
1165673 AAAATAAAAACA
1 AAAAT-AAAACA
1165685 AAAATA
1 AAAATA
1165691 TAACCAATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 9 0.36
11 5 0.20
12 11 0.44
ACGTcount: A:0.79, C:0.08, G:0.03, T:0.10
Consensus pattern (11 bp):
AAAATAAAACA
Found at i:1171832 original size:25 final size:24
Alignment explanation
Indices: 1171785--1171832 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
1171775 AAATCCTAAT
** *
1171785 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACAGATATAAAC
1171809 TAAAATACCTAAAACAGATATAAA
1 TAAAATA-CTAAAACAGATATAAA
1171833 ATATAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.58, C:0.15, G:0.02, T:0.25
Consensus pattern (24 bp):
TAAAATACTAAAACAGATATAAAC
Found at i:1174773 original size:37 final size:37
Alignment explanation
Indices: 1174726--1174803 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
1174716 TTACACTTCT
1174726 TCCTCTTTTTCTTCATCTTCACGTGGGTATTCTCTCC
1 TCCTCTTTTTCTTCATCTTCACGTGGGTATTCTCTCC
1174763 TCCTCTTTTTCTTCATCTTCACGTGGGTATTCTCTCC
1 TCCTCTTTTTCTTCATCTTCACGTGGGTATTCTCTCC
1174800 TCCT
1 TCCT
1174804 AGCACAAGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.08, C:0.33, G:0.10, T:0.49
Consensus pattern (37 bp):
TCCTCTTTTTCTTCATCTTCACGTGGGTATTCTCTCC
Found at i:1175508 original size:95 final size:96
Alignment explanation
Indices: 1175355--1175529 Score: 239
Period size: 95 Copynumber: 1.8 Consensus size: 96
1175345 AGGCAATATC
* * * *
1175355 GATACCATTGTAAGGGTATCGATATCAAGAAAACATCGAATCTAATTTCGATATCGATACC-GTA
1 GATACCATTGTAAGCGTATCGATACCAAGAAAACATCGAACCTAATTTCGATATCGATACCAGGA
1175419 AGGAAGTATCGGTACCATAGAAGGGTAGTATT
66 AGG-AGTATCGGTACCATAGAAGGGTAGTATT
* * *
1175451 GATACCA-TGTTAAGCGTATCGATACCATG-AAACATCGAACCTAATTTTGGTATCGATACCAGG
1 GATACCATTG-TAAGCGTATCGATACCAAGAAAACATCGAACCTAATTTCGATATCGATACCAGG
*
1175514 AAGGGGTATCGGTACC
65 AAGGAGTATCGGTACC
1175530 CTAGTGTAGA
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
95 41 0.59
96 28 0.41
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.26
Consensus pattern (96 bp):
GATACCATTGTAAGCGTATCGATACCAAGAAAACATCGAACCTAATTTCGATATCGATACCAGGA
AGGAGTATCGGTACCATAGAAGGGTAGTATT
Found at i:1175558 original size:20 final size:20
Alignment explanation
Indices: 1175519--1175571 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
1175509 CCAGGAAGGG
*
1175519 GTATCGGTACCCTAGTGTAGAA
1 GTATCGGTA--CTAGAGTAGAA
*
1175541 GTATCGGTACTAGAGTAGTA
1 GTATCGGTACTAGAGTAGAA
*
1175561 GTATCGATACT
1 GTATCGGTACT
1175572 TTGGAACCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 19 0.68
22 9 0.32
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (20 bp):
GTATCGGTACTAGAGTAGAA
Found at i:1176145 original size:90 final size:90
Alignment explanation
Indices: 1175970--1176179 Score: 237
Period size: 90 Copynumber: 2.3 Consensus size: 90
1175960 TGAAAATACT
* * *
1175970 AATGCATATGGGTGCATTATCG-GCATGAAAGGATGCCATAGTTGAAATGTATATGGGTACATTA
1 AATGCATATGGGTGCATTAT-GAACATGAAAGGATACCATAGTTGAAATGCATATGGGTACATTA
* *
1176034 TCAACATAAAAATATACTATAGTTGA
65 TCAACAGAAAAATAGACTATAGTTGA
* * *
1176060 AATGCATATGGGTGCATTATGAACA-GAAAAGTATACTATAGTTGAAATGCATATGGGTGCATTA
1 AATGCATATGGGTGCATTATGAACATG-AAAGGATACCATAGTTGAAATGCATATGGGTACATTA
* ** *
1176124 TCAACAGAAAAGTAGGTTATAGTTTA
65 TCAACAGAAAAATAGACTATAGTTGA
* *
1176150 AAGTGCATAAT-GGTGTATTATAAACATGAA
1 AA-TGCAT-ATGGGTGCATTATGAACATGAA
1176180 TGAAGGTTAC
Statistics
Matches: 101, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
89 2 0.02
90 76 0.75
91 20 0.20
92 3 0.03
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (90 bp):
AATGCATATGGGTGCATTATGAACATGAAAGGATACCATAGTTGAAATGCATATGGGTACATTAT
CAACAGAAAAATAGACTATAGTTGA
Found at i:1176147 original size:45 final size:45
Alignment explanation
Indices: 1175970--1176137 Score: 230
Period size: 45 Copynumber: 3.7 Consensus size: 45
1175960 TGAAAATACT
** * * *
1175970 AATGCATATGGGTGCATTATCGGCATG-AAAGGATGCCATAGTTGA
1 AATGCATATGGGTGCATTATCAACA-GAAAAGTATACTATAGTTGA
* * * *
1176015 AATGTATATGGGTACATTATCAACATAAAAATATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
*
1176060 AATGCATATGGGTGCATTATGAACAGAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
1176105 AATGCATATGGGTGCATTATCAACAGAAAAGTA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTA
1176138 GGTTATAGTT
Statistics
Matches: 107, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
45 107 1.00
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
Found at i:1177530 original size:18 final size:18
Alignment explanation
Indices: 1177509--1177544 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1177499 AAATAGAGTC
1177509 AAAGCTATTGAAAGAGCT
1 AAAGCTATTGAAAGAGCT
1177527 AAAGCTATTGAAAGAGCT
1 AAAGCTATTGAAAGAGCT
1177545 TAGGAGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (18 bp):
AAAGCTATTGAAAGAGCT
Found at i:1179710 original size:23 final size:23
Alignment explanation
Indices: 1179674--1179737 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
1179664 CAGCTCATAT
* *
1179674 AAATTCACCGAAGTGCCACGTAG
1 AAATGCACCAAAGTGCCACGTAG
* * * *
1179697 AATTGCATCAAAGTGTCGCGTAG
1 AAATGCACCAAAGTGCCACGTAG
*
1179720 AAATGCACCGAAGTGCCA
1 AAATGCACCAAAGTGCCA
1179738 TATAAGATGT
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.19
Consensus pattern (23 bp):
AAATGCACCAAAGTGCCACGTAG
Found at i:1184168 original size:24 final size:24
Alignment explanation
Indices: 1184139--1184191 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
1184129 GAAGAAAGTC
*
1184139 TTGAGATTTGGGCAAAAAGGAAAG
1 TTGAGATTTGGGAAAAAAGGAAAG
1184163 TTGAGATTTGGGAAAAAAGGAAAG
1 TTGAGATTTGGGAAAAAAGGAAAG
1184187 TTGAG
1 TTGAG
1184192 TCCGAGATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.42, C:0.02, G:0.34, T:0.23
Consensus pattern (24 bp):
TTGAGATTTGGGAAAAAAGGAAAG
Found at i:1185462 original size:19 final size:21
Alignment explanation
Indices: 1185438--1185488 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
1185428 TCTAATTTCG
*
1185438 GTATCGATACCGT-AAGGG-A
1 GTATCGATACCATAAAGGGTA
1185457 GTATCGATACCATAGAAGGGTA
1 GTATCGATACCATA-AAGGGTA
1185479 GTATCGATAC
1 GTATCGATAC
1185489 GATGTTAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 12 0.43
21 5 0.18
22 11 0.39
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (21 bp):
GTATCGATACCATAAAGGGTA
Found at i:1185577 original size:95 final size:96
Alignment explanation
Indices: 1185398--1185579 Score: 226
Period size: 95 Copynumber: 1.9 Consensus size: 96
1185388 AATACCATTG
* * *
1185398 TAAGGGTATCGATACCAAGCAAACATCGAATCTAATTTCGGTATCGATACCGTAAGGGAGTATCG
1 TAAGGGTATCGATACCAAGCAAACATCGAACCTAATTTCGGTATCGATACCGGAAAGGAGTATCG
* *
1185463 ATACCATAGAAGGGTAGTATCGATACGATGT
66 ATACCATAGAAGAGAAGTATCGATACGATGT
* * *
1185494 TAAGGGTATCGATACCATG-AAACATCGAACCTAATTTTGGTATTGATACCAGGAAAGG-GTATC
1 TAAGGGTATCGATACCAAGCAAACATCGAACCTAATTTCGGTATCGATACC-GGAAAGGAGTATC
* * *
1185557 GGTACCCTAG-TGTAGAAGTATCG
65 GATACCATAGAAG-AGAAGTATCG
1185580 GTACTGGAGT
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
94 1 0.01
95 49 0.67
96 23 0.32
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (96 bp):
TAAGGGTATCGATACCAAGCAAACATCGAACCTAATTTCGGTATCGATACCGGAAAGGAGTATCG
ATACCATAGAAGAGAAGTATCGATACGATGT
Found at i:1186106 original size:45 final size:45
Alignment explanation
Indices: 1186016--1186359 Score: 527
Period size: 45 Copynumber: 7.7 Consensus size: 45
1186006 TGAAAATAAT
* * * * * *
1186016 AATGCATTTGGTTGCATTATCAGCATG-AAAGGATGCCATAGTTGA
1 AATGCATATGGGTGCATTATCAACA-GAAAAGTATACTATAGTTGA
* * * *
1186061 AATGTATATGGGTACATTATCAACAGAAAAATATACTATAATTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
1186106 AATGCAT-TGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
*
1186150 AATGCATATGGGTGCATTATCAATAGAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
*
1186195 AATGCATATGGGTGCATTATCAACTGAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
1186240 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
1186285 AATGCATATGGGTGCATTATCAACAG---AGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
*
1186327 AATGCATATGGGTGCATTATCAATAGAAAAGTA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTA
1186360 GGTTATAGTT
Statistics
Matches: 275, Mismatches: 19, Indels: 10
0.90 0.06 0.03
Matches are distributed among these distances:
42 41 0.15
44 42 0.15
45 192 0.70
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
Found at i:1188290 original size:31 final size:31
Alignment explanation
Indices: 1188218--1188299 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
1188208 ATGTGAACTT
* * *
1188218 TTAAATATTATAAAATGGTCATTAAAATTTA
1 TTAAATATTACAAAATGATCAATAAAATTTA
* *
1188249 TCAAATTATTACAAAATGATCAAT-ACATTTA
1 TTAAA-TATTACAAAATGATCAATAAAATTTA
*
1188280 TTAAACTATTACATAATGAT
1 TTAAA-TATTACAAAATGAT
1188300 TCTTAAACTT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 27 0.64
32 15 0.36
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.39
Consensus pattern (31 bp):
TTAAATATTACAAAATGATCAATAAAATTTA
Found at i:1192923 original size:135 final size:133
Alignment explanation
Indices: 1192632--1192909 Score: 382
Period size: 135 Copynumber: 2.1 Consensus size: 133
1192622 GGTCCAGTCG
* * * ***
1192632 TCTAAGAGTGACACGACTCCTACATGATGAGGAGATCTGGTCGAGGGATGACACTGTTCATACGT
1 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGAGGGATGACACAACTCATACGT
* * * *
1192697 GATGAAGAGTTCTTGGCCATCTTTAGGAAGGTTGATAACTCGATTCCTACGTGATGAGGACGGCT
66 GATGAAGAGTTCTTAGCCATCTTT--GAAGGATAATAACACGATTCCTACGTGATGAGGACGGCT
1192762 GGTTA
129 GGTTA
*
1192767 TCTAAGGGTGACATGGCTCCTACGTGATGAGGAGATCTGGTCG-GTGGATGACACAACTCATACG
1 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGAG-GGATGACACAACTCATACG
* *
1192831 TGATGAAGAGTTC-TAGCCATCTTT-AAGGATAATAACACGGTTCCTACGTGATGAGGATGGCTG
65 TGATGAAGAGTTCTTAGCCATCTTTGAAGGATAATAACACGATTCCTACGTGATGAGGACGGCTG
1192894 GTTA
130 GTTA
1192898 TCTAAAGGGTGA
1 TCT-AAGGGTGA
1192910 TAACACGGTT
Statistics
Matches: 128, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
131 41 0.32
132 8 0.06
134 11 0.09
135 68 0.53
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (133 bp):
TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGAGGGATGACACAACTCATACGT
GATGAAGAGTTCTTAGCCATCTTTGAAGGATAATAACACGATTCCTACGTGATGAGGACGGCTGG
TTA
Found at i:1195367 original size:201 final size:197
Alignment explanation
Indices: 1195074--1195492 Score: 522
Period size: 201 Copynumber: 2.1 Consensus size: 197
1195064 CAGACAGCCA
* * *
1195074 TCTCGCCTTGAGCTATGTTGTAAATTTGACTTAGAGATATAGTTCCTTGTTTCTAAATCGCAACC
1 TCTCGCCTTGAGATATGTTGTAAATTTGACTTAGAGAGATAGTTCCTTGTTGCTAAATCGCAACC
* * **
1195139 AACCCAAGTCTTCTTCTTGACTTAAAGACCTCAGTTTAAACTTCAACCTAAAAGTAGTTTGTCGC
66 AACACAAGTCTTCTTCTTGACTTAAAGACCTCAGTTTAAACTTCAACCGAAAAGTAGTTCCTCGC
* * * * *
1195204 TGCTACCATGAGGTTGATATGTCA-TCGAGTTGAATGGAATCAAACTCAAAAGTTTTCGTTCACA
131 TGCT--C----GGTTGATAAG-CACTCGAGCTGAATGAAATCAAACTCAAAAGTTCTCATTCACA
*
1195268 GATAGTCCT
189 GATAGCCCT
* *
1195277 TCTCGCCTTGAGATATGTTGTAAATTTGAC-T-GAGAGATAGTTCTTTGTTGCTAAATCGCAGCC
1 TCTCGCCTTGAGATATGTTGTAAATTTGACTTAGAGAGATAGTTCCTTGTTGCTAAATCGCAACC
*** * * *
1195340 AACATTGGTCTTCTTCTTGATTTAAAGACCTCAGTTTAAACTTTAACCGAAAAGTAGTTCCTTGC
66 AACACAAGTCTTCTTCTTGACTTAAAGACCTCAGTTTAAACTTCAACCGAAAAGTAGTTCCTCGC
* * *
1195405 TGCTCGGTTGATAAGCACTCGAGCTGAATGAAATCGAACTCAAAAGTTCTCATTGATAGATAGCC
131 TGCTCGGTTGATAAGCACTCGAGCTGAATGAAATCAAACTCAAAAGTTCTCATTCACAGATAGCC
1195470 CT
196 CT
1195472 TCTCGCCTTGAGCA-ATGTTGT
1 TCTCGCCTTGAG-ATATGTTGT
1195493 GAACAGTTCC
Statistics
Matches: 190, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
194 2 0.01
195 69 0.36
196 1 0.01
199 1 0.01
201 87 0.46
202 1 0.01
203 29 0.15
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (197 bp):
TCTCGCCTTGAGATATGTTGTAAATTTGACTTAGAGAGATAGTTCCTTGTTGCTAAATCGCAACC
AACACAAGTCTTCTTCTTGACTTAAAGACCTCAGTTTAAACTTCAACCGAAAAGTAGTTCCTCGC
TGCTCGGTTGATAAGCACTCGAGCTGAATGAAATCAAACTCAAAAGTTCTCATTCACAGATAGCC
CT
Found at i:1197105 original size:35 final size:33
Alignment explanation
Indices: 1197049--1197117 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 33
1197039 ATTTCCTTTG
1197049 TTTTTCTTTTTGATTTTTCTTTGCTCTTTGTTT
1 TTTTTCTTTTTGATTTTTCTTTGCTCTTTGTTT
* * *
1197082 TTTTTTTTTTTGCTTTTCATCTTTTCTCTTTGTTT
1 TTTTTCTTTTTGATTTT--TCTTTGCTCTTTGTTT
1197117 T
1 T
1197118 AATTTGATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 15 0.48
35 16 0.52
ACGTcount: A:0.03, C:0.13, G:0.07, T:0.77
Consensus pattern (33 bp):
TTTTTCTTTTTGATTTTTCTTTGCTCTTTGTTT
Found at i:1203108 original size:11 final size:11
Alignment explanation
Indices: 1203087--1203111 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1203077 TCTTTTGTTA
1203087 TTTTCTTTTTC
1 TTTTCTTTTTC
1203098 TTTTCTTTTTC
1 TTTTCTTTTTC
1203109 TTT
1 TTT
1203112 ATTACATTAT
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:1203242 original size:22 final size:23
Alignment explanation
Indices: 1203214--1203257 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
1203204 AGTAGATTAA
1203214 AGTGCAAGATAG-ATAAAAATAC
1 AGTGCAAGATAGAATAAAAATAC
*
1203236 AGTGCAAGATAGAATTAAAATA
1 AGTGCAAGATAGAATAAAAATA
1203258 TATAATTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.55, C:0.07, G:0.18, T:0.20
Consensus pattern (23 bp):
AGTGCAAGATAGAATAAAAATAC
Found at i:1208465 original size:3 final size:3
Alignment explanation
Indices: 1208457--1208484 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1208447 GAATATGATT
1208457 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1208485 ATTATAATTA
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:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:1208803 original size:40 final size:35
Alignment explanation
Indices: 1208723--1208798 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
1208713 AAAAAAGTCC
*
1208723 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
* *
1208758 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
1208793 TCAATT
1 TCAATT
1208799 CAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
Found at i:1209340 original size:130 final size:130
Alignment explanation
Indices: 1209194--1209441 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
1209184 TATTTATATA
* ** *
1209194 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAAGATCTGACATGTG
* *
1209259 TTAGCACATGATCATGACATGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACATATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
1209324 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAAGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAAGATCTGACATGTG
* *
1209389 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACATATGTCATTGGTGACACATGTCACCACCTAATTA
1209442 GAAGAAAATT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAAGATCTGACATGTG
TTAACACATGATCATGACATATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:1209472 original size:130 final size:129
Alignment explanation
Indices: 1209208--1209472 Score: 309
Period size: 130 Copynumber: 2.0 Consensus size: 129
1209198 ATTTGGTCCT
* ** * *
1209208 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAAGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
1209273 TGACATGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACATATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
1209338 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAAGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAAGATCTGACATGTGTTAACACATGATCA
* * *
1209403 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACATATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
1209467 -A
128 CA
1209468 AAATT
1 AAATT
1209473 TGGGTCTTGG
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
130 100 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAAGATCTGACATGTGTTAACACATGATCA
TGACATATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:1209799 original size:28 final size:27
Alignment explanation
Indices: 1209768--1209830 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
1209758 AGTTGATACA
*
1209768 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
1209796 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
1209824 ATATTTT
1 ATATTTT
1209831 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:1209931 original size:16 final size:18
Alignment explanation
Indices: 1209910--1209943 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1209900 ATTTCTTATT
1209910 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
1209926 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
1209944 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:1213911 original size:27 final size:27
Alignment explanation
Indices: 1213873--1213940 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
1213863 ATGTAGGAAT
*
1213873 TATAGAG-T-TGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCA
1213898 TATAGAGATATGATTTGTTACCATTCA
1 TATAGAGATATGATTTGTTACCATTCA
1213925 TATAGAGATATGATTT
1 TATAGAGATATGATTT
1213941 CTACAATTCC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 7 0.17
26 1 0.03
27 32 0.80
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCA
Found at i:1217662 original size:27 final size:27
Alignment explanation
Indices: 1217620--1217718 Score: 168
Period size: 27 Copynumber: 3.8 Consensus size: 27
1217610 GTGTAGCAAT
1217620 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
1217645 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
1217672 TATAGAGATATGATTTGTTACCATTCA
1 TATAGAGATATGATTTGTTACCATTCC
1217699 TATAGAGATATGATTT-TTAC
1 TATAGAGATATGATTTGTTAC
1217719 AATCCCTTAT
Statistics
Matches: 71, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
25 7 0.10
26 4 0.06
27 60 0.85
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:1219336 original size:25 final size:25
Alignment explanation
Indices: 1219307--1219371 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 25
1219297 AGTACTTATT
*
1219307 ATAATTAATAATATATA-TTAGTTTC
1 ATAA-TAATAATATATACTTAGTTTA
*
1219332 ATAAT-ATAATATATACTTATTTTA
1 ATAATAATAATATATACTTAGTTTA
1219356 ATAAATAATTAATATA
1 AT-AATAA-TAATATA
1219372 ATTTATAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 10 0.29
24 9 0.26
25 7 0.21
26 1 0.03
27 7 0.21
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (25 bp):
ATAATAATAATATATACTTAGTTTA
Found at i:1219340 original size:23 final size:23
Alignment explanation
Indices: 1219299--1219364 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
1219289 TTTTAATAAG
*
1219299 TACTTA-TTATAATTAATAATATA
1 TACTTAGTT-TAATAAATAATATA
*
1219322 TA-TTAGTTTCATAATATAATATA
1 TACTTAGTTTAATAA-ATAATATA
*
1219345 TACTTATTTTAATAAATAAT
1 TACTTAGTTTAATAAATAAT
1219365 TAATATAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 7 0.19
23 19 0.53
24 10 0.28
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (23 bp):
TACTTAGTTTAATAAATAATATA
Found at i:1219664 original size:21 final size:21
Alignment explanation
Indices: 1219624--1219665 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1219614 AAATAAATTA
*
1219624 TATAAATTATTTTCTAAAAAT
1 TATAAATTATTTTATAAAAAT
*
1219645 TATAATTTATTTTATGAAAAA
1 TATAAATTATTTTAT-AAAAA
1219666 CTTTTCCGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
TATAAATTATTTTATAAAAAT
Found at i:1222109 original size:3 final size:3
Alignment explanation
Indices: 1222101--1222138 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1222091 TCTACAAAAA
1222101 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1222139 ACTTCTTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1225075 original size:24 final size:24
Alignment explanation
Indices: 1225048--1225098 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1225038 TGGTGGTTGA
*
1225048 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
1225072 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
1225096 TTT
1 TTT
1225099 GTTCTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.61
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:1231923 original size:19 final size:21
Alignment explanation
Indices: 1231886--1231928 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1231876 TAACTTTTTC
*
1231886 TTTTCTCTTTCTTTATTAA-T
1 TTTTCTCTTTCATTATTAACT
1231906 TTTTCTCTTTCATT-TTAACT
1 TTTTCTCTTTCATTATTAACT
1231926 TTT
1 TTT
1231929 ACTTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCTCTTTCATTATTAACT
Found at i:1234231 original size:24 final size:24
Alignment explanation
Indices: 1234204--1234253 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1234194 TGGTGGTTGA
*
1234204 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
1234228 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
1234252 TT
1 TT
1234254 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:1239225 original size:23 final size:23
Alignment explanation
Indices: 1239189--1239244 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
1239179 TAGAGAGAAT
*
1239189 CGATACCCCC-TTGAAGGGGAAC
1 CGATTCCCCCTTTGAAGGGGAAC
1239211 CGATTCCCCCTTTGAAGGGGAAC
1 CGATTCCCCCTTTGAAGGGGAAC
1239234 CGATTCCCCCT
1 CGATTCCCCCT
1239245 AGGGGAATCG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 9 0.28
23 23 0.72
ACGTcount: A:0.21, C:0.36, G:0.23, T:0.20
Consensus pattern (23 bp):
CGATTCCCCCTTTGAAGGGGAAC
Found at i:1240865 original size:18 final size:18
Alignment explanation
Indices: 1240844--1240884 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1240834 AGAATAGCAC
1240844 GAGGAACAAGCACGAA-CA
1 GAGGAACAAGCAC-AACCA
1240862 GAGGAACAAGCACAACCA
1 GAGGAACAAGCACAACCA
1240880 GAGGA
1 GAGGA
1240885 TCAAAAGCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.49, C:0.22, G:0.29, T:0.00
Consensus pattern (18 bp):
GAGGAACAAGCACAACCA
Found at i:1241417 original size:2 final size:2
Alignment explanation
Indices: 1241410--1241447 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1241400 TAGCAGCTTA
1241410 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1241448 GTAATCAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1243936 original size:20 final size:22
Alignment explanation
Indices: 1243896--1243946 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
1243886 TTATGTTTTA
1243896 TTTTATTTTGATCATTTATATG
1 TTTTATTTTGATCATTTATATG
*
1243918 -TTTATTTTGGTCA-TTATATG
1 TTTTATTTTGATCATTTATATG
1243938 TTTTATTTT
1 TTTTATTTT
1243947 ATTTTATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.20, C:0.04, G:0.10, T:0.67
Consensus pattern (22 bp):
TTTTATTTTGATCATTTATATG
Found at i:1246123 original size:31 final size:31
Alignment explanation
Indices: 1246085--1246224 Score: 235
Period size: 31 Copynumber: 4.5 Consensus size: 31
1246075 AGGGTCGAGG
1246085 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1246116 GTTTACCTATGTTCTTCGAGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1246147 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1246178 ATTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
** *
1246209 GACTACCTAGGTTCTT
1 GTTTACCTATGTTCTT
1246225 TGGAATCTAT
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 102 1.00
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1246896 original size:21 final size:21
Alignment explanation
Indices: 1246870--1246912 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1246860 TTACAAAGTT
1246870 ACTGTAGCAGCGCATCGATGC
1 ACTGTAGCAGCGCATCGATGC
*
1246891 ACTGTAGCAGTGCATCGATGC
1 ACTGTAGCAGCGCATCGATGC
1246912 A
1 A
1246913 TAATTGATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.21
Consensus pattern (21 bp):
ACTGTAGCAGCGCATCGATGC
Found at i:1248403 original size:2 final size:2
Alignment explanation
Indices: 1248396--1248428 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1248386 ATTTGGATCC
1248396 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1248429 GATTAAGACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1249819 original size:20 final size:20
Alignment explanation
Indices: 1249794--1249831 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1249784 TTTTTGGGTA
1249794 GGTGCATCGATGCATTAAGG
1 GGTGCATCGATGCATTAAGG
1249814 GGTGCATCGATGCATTAA
1 GGTGCATCGATGCATTAA
1249832 TGCATCGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (20 bp):
GGTGCATCGATGCATTAAGG
Found at i:1249837 original size:16 final size:17
Alignment explanation
Indices: 1249795--1249844 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 17
1249785 TTTTGGGTAG
1249795 GTGCATCGATGCATTAA
1 GTGCATCGATGCATTAA
1249812 GGGGTGCATCGATGCATTAA
1 ---GTGCATCGATGCATTAA
1249832 -TGCATCGATGCAT
1 GTGCATCGATGCAT
1249845 GGATATTTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 13 0.43
20 17 0.57
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (17 bp):
GTGCATCGATGCATTAA
Found at i:1250815 original size:31 final size:31
Alignment explanation
Indices: 1250777--1250963 Score: 286
Period size: 31 Copynumber: 6.0 Consensus size: 31
1250767 AGGGTCGAGG
*
1250777 GTTTACCTATGTTATTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1250808 GTTTACCTATGTTCTTCGGGACATATTGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1250839 GCTTACCTATGTTCATCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1250870 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1250901 ATTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1250932 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1250963 G
1 G
1250964 GTCCTTCGGG
Statistics
Matches: 143, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
31 142 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1251613 original size:21 final size:21
Alignment explanation
Indices: 1251587--1251629 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1251577 TTACGAAGTT
*
1251587 ACTGTAGCAGTGTATCGATGC
1 ACTGTAGCAGTGCATCGATGC
1251608 ACTGTAGCAGTGCATCGATGC
1 ACTGTAGCAGTGCATCGATGC
1251629 A
1 A
1251630 TAATTGATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATGC
Found at i:1251671 original size:12 final size:12
Alignment explanation
Indices: 1251653--1251693 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1251643 AATTTTTTCC
1251653 CTGTTCACGGTA
1 CTGTTCACGGTA
* *
1251665 TTGTTCA--TTA
1 CTGTTCACGGTA
1251675 CTGTTCACGGTA
1 CTGTTCACGGTA
1251687 CTGTTCA
1 CTGTTCA
1251694 TACCGTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
10 8 0.35
12 15 0.65
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (12 bp):
CTGTTCACGGTA
Found at i:1251681 original size:22 final size:22
Alignment explanation
Indices: 1251653--1251694 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1251643 AATTTTTTCC
*
1251653 CTGTTCACGGTATTGTTCATTA
1 CTGTTCACGGTACTGTTCATTA
1251675 CTGTTCACGGTACTGTTCAT
1 CTGTTCACGGTACTGTTCAT
1251695 ACCGTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (22 bp):
CTGTTCACGGTACTGTTCATTA
Found at i:1255581 original size:15 final size:15
Alignment explanation
Indices: 1255554--1255607 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 15
1255544 AATCAAAGCC
1255554 AAAAGAA-AAAAATA
1 AAAAGAACAAAAATA
1255568 AAAAGAACAAAAATA
1 AAAAGAACAAAAATA
*
1255583 AAAA-AGCAAAGAA-A
1 AAAAGAACAAA-AATA
1255597 AAAAGAGACAA
1 AAAAGA-ACAA
1255608 GAAGCAAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
14 17 0.50
15 14 0.41
16 3 0.09
ACGTcount: A:0.80, C:0.06, G:0.11, T:0.04
Consensus pattern (15 bp):
AAAAGAACAAAAATA
Found at i:1256818 original size:36 final size:36
Alignment explanation
Indices: 1256711--1256820 Score: 114
Period size: 38 Copynumber: 3.0 Consensus size: 36
1256701 ATCTGTCGTC
* * *
1256711 TTTCTCTCAAAACAAAATGTCATCTCGCTAGAGACAG
1 TTTCTCTCAAAAC-AAATTTCATCTCGCTTGAGACAA
* **
1256748 TTT-TCTTGAAAAACAAATTTTTGTCTCGCTTGAGACAA
1 TTTCTC-T-CAAAACAAA-TTTCATCTCGCTTGAGACAA
*
1256786 TTTCTCTCAAAGCAAATTTCATCTCGCTTGAGACA
1 TTTCTCTCAAAACAAATTTCATCTCGCTTGAGACA
1256821 TTTTTTCTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
36 19 0.32
37 14 0.24
38 24 0.41
39 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.34
Consensus pattern (36 bp):
TTTCTCTCAAAACAAATTTCATCTCGCTTGAGACAA
Done.