Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007950.1 Hibiscus syriacus cultivar Beakdansim tig00110372_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: 1941792
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 10
Found at i:1592183 original size:20 final size:18
Alignment explanation
Indices: 1592139--1592193 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 18
1592129 ATTTATACAG
1592139 TATATACTACATATATAGTT
1 TATATA-TAC-TATATAGTT
1592159 TATATATACTATATAGTT
1 TATATATACTATATAGTT
*
1592177 TACATATGAACTATATA
1 TATATAT--ACTATATA
1592194 TAAAGTATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 15 0.47
19 3 0.09
20 14 0.44
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (18 bp):
TATATATACTATATAGTT
Found at i:1592227 original size:18 final size:18
Alignment explanation
Indices: 1592188--1592262 Score: 63
Period size: 18 Copynumber: 4.3 Consensus size: 18
1592178 ACATATGAAC
*
1592188 TATATATAAAGTATATGG
1 TATATATAAAGTATATAG
1592206 TATATAT-AAGCTATATA-
1 TATATATAAAG-TATATAG
1592223 T-TATAT--AGT-TCATTAG
1 TATATATAAAGTAT-A-TAG
*
1592239 TATATATAAATTATATAG
1 TATATATAAAGTATATAG
1592257 TATATA
1 TATATA
1592263 AATCATTAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
13 1 0.02
14 2 0.04
15 4 0.09
16 6 0.13
17 9 0.19
18 21 0.45
19 3 0.06
20 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (18 bp):
TATATATAAAGTATATAG
Found at i:1592247 original size:33 final size:33
Alignment explanation
Indices: 1592205--1592291 Score: 120
Period size: 33 Copynumber: 2.6 Consensus size: 33
1592195 AAAGTATATG
* **
1592205 GTATATATAAGCTATATATTATATAGTTCATTA
1 GTATATATAAACTATATATTATATAAATCATTA
* *
1592238 GTATATATAAATTATATAGTATATAAATCATTA
1 GTATATATAAACTATATATTATATAAATCATTA
*
1592271 GTATATATAACCTATATATTA
1 GTATATATAAACTATATATTA
1592292 ATTTATTAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.44
Consensus pattern (33 bp):
GTATATATAAACTATATATTATATAAATCATTA
Found at i:1592262 original size:16 final size:15
Alignment explanation
Indices: 1592241--1592277 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
1592231 TTCATTAGTA
*
1592241 TATATAAATTATATAG
1 TATATAAATCAT-TAG
1592257 TATATAAATCATTAG
1 TATATAAATCATTAG
1592272 TATATA
1 TATATA
1592278 TAACCTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (15 bp):
TATATAAATCATTAG
Found at i:1592452 original size:59 final size:61
Alignment explanation
Indices: 1592350--1592484 Score: 220
Period size: 59 Copynumber: 2.2 Consensus size: 61
1592340 TATAAGGATC
1592350 AAATTGAACAAATTTTAAATATGAAGCTAAAATTAATAAATTGCAACATTAAATTTGGACT
1 AAATTGAACAAATTTTAAATATGAAGCTAAAATTAATAAATTGCAACATTAAATTTGGACT
* * * *
1592411 AAATTGAACAAATTTT-AA-ATGAAGCTTAAATTAATACATTGCATCATTAAATTTGGGCT
1 AAATTGAACAAATTTTAAATATGAAGCTAAAATTAATAAATTGCAACATTAAATTTGGACT
1592470 AAATTGAACAAATTT
1 AAATTGAACAAATTT
1592485 AAAACTAGGA
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 52 0.74
60 2 0.03
61 16 0.23
ACGTcount: A:0.47, C:0.09, G:0.10, T:0.34
Consensus pattern (61 bp):
AAATTGAACAAATTTTAAATATGAAGCTAAAATTAATAAATTGCAACATTAAATTTGGACT
Found at i:1593176 original size:11 final size:12
Alignment explanation
Indices: 1593137--1593179 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
1593127 CCCTAATCCT
1593137 AACCCAAACTAG
1 AACCCAAACTAG
*
1593149 AACCCAAACCAG
1 AACCCAAACTAG
*
1593161 AACCC-AACTTG
1 AACCCAAACTAG
1593172 AACCCAAA
1 AACCCAAA
1593180 TGATCGCTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.49, C:0.37, G:0.07, T:0.07
Consensus pattern (12 bp):
AACCCAAACTAG
Found at i:1594966 original size:6 final size:6
Alignment explanation
Indices: 1594952--1595070 Score: 85
Period size: 6 Copynumber: 19.8 Consensus size: 6
1594942 GGAGTTATCA
* * * * ** * * *
1594952 CCAAAC CCAAGC CCAAAC ACGAAC CTAAAC CTGAAC CTAAAC CTAAAA
1 CCAAAC CCAAAC CCAAAC CCAAAC CCAAAC CCAAAC CCAAAC CCAAAC
* * * * * * *
1595000 CCAAAC CCGAAC CCGAAC CCAAAC CCAAAT CCGAAC CTAAAC TCAAAT
1 CCAAAC CCAAAC CCAAAC CCAAAC CCAAAC CCAAAC CCAAAC CCAAAC
*
1595048 CCAAAA CCAAAC CCAAAC CCAAA
1 CCAAAC CCAAAC CCAAAC CCAAA
1595071 TCTGAACCTG
Statistics
Matches: 88, Mismatches: 25, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 88 1.00
ACGTcount: A:0.48, C:0.40, G:0.05, T:0.07
Consensus pattern (6 bp):
CCAAAC
Found at i:1597810 original size:20 final size:20
Alignment explanation
Indices: 1597763--1597820 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
1597753 TTGATTATGC
*
1597763 TTGATTCTGTTTTATATTGT
1 TTGATTCTGTTTGATATTGT
*
1597783 TT-ACTTCTATTTGATATTGT
1 TTGA-TTCTGTTTGATATTGT
*
1597803 TTGATTCTGCTTGATATT
1 TTGATTCTGTTTGATATT
1597821 TGTAAGGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.17, C:0.09, G:0.14, T:0.60
Consensus pattern (20 bp):
TTGATTCTGTTTGATATTGT
Found at i:1598142 original size:43 final size:42
Alignment explanation
Indices: 1598036--1598199 Score: 141
Period size: 43 Copynumber: 3.8 Consensus size: 42
1598026 CGAAAAATGC
** * * *
1598036 CGCAATAGGTAATGATATATAGGGGCGTTTGTTTAACAAACGT
1 CGCAATAGGTGTTGAGATTTAGCGGCGTTTGTTT-ACAAACGT
* * ** * *
1598079 TGTAATAGGTACTGATATTTAGCGGTGTTTGTCTTACAAACGT
1 CGCAATAGGTGTTGAGATTTAGCGGCGTTTGT-TTACAAACGT
* * *
1598122 CGCAATAGGTGTTGAGATTTAGCGGCATTT-TTATCATAAACGC
1 CGCAATAGGTGTTGAGATTTAGCGGCGTTTGTT-T-ACAAACGT
* *
1598165 CGCAATAGGTGTTGAGATTTAGTGGCGTTTTTTTA
1 CGCAATAGGTGTTGAGATTTAGCGGCGTTTGTTTA
1598200 TGTAAACGCC
Statistics
Matches: 100, Mismatches: 17, Indels: 9
0.79 0.13 0.07
Matches are distributed among these distances:
41 1 0.01
42 3 0.03
43 92 0.92
44 4 0.04
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36
Consensus pattern (42 bp):
CGCAATAGGTGTTGAGATTTAGCGGCGTTTGTTTACAAACGT
Found at i:1598315 original size:88 final size:89
Alignment explanation
Indices: 1598163--1598331 Score: 207
Period size: 88 Copynumber: 1.9 Consensus size: 89
1598153 TATCATAAAC
* * ** * *
1598163 GCCGCAATAGGTGTTGAGATTTAGTGGCGTTTTTTTATGTAAACGCCGCTAAAATTCTGGTATAT
1 GCCGCAATAGGTGTTAAGATTTAGTAGCGTTTTTTTATACAAACGCCACTAAAATTCTGATATAT
*
1598228 TGCGACGTTTTTATTAAAAAAAAT
66 TGCGACATTTTTATTAAAAAAAAT
* * *
1598252 GCCGCAATAGGTGTTAATATTTCGTAGCG-TTTTTTATACAAACGCCACT-AAATGTGTGATATA
1 GCCGCAATAGGTGTTAAGATTTAGTAGCGTTTTTTTATACAAACGCCACTAAAAT-TCTGATATA
* *
1598315 TTGTGGCATTTTTATTA
65 TTGCGACATTTTTATTA
1598332 CAAACGCCGC
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
87 4 0.06
88 38 0.57
89 25 0.37
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.38
Consensus pattern (89 bp):
GCCGCAATAGGTGTTAAGATTTAGTAGCGTTTTTTTATACAAACGCCACTAAAATTCTGATATAT
TGCGACATTTTTATTAAAAAAAAT
Found at i:1603043 original size:5 final size:5
Alignment explanation
Indices: 1603029--1603092 Score: 83
Period size: 5 Copynumber: 12.8 Consensus size: 5
1603019 GTCCGTCCGT
* * * * *
1603029 CTCGT CTCGG CTCGG CACGG CACGG CACGG CACGG CTCGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
1603079 CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCG
1603093 TGGTCGAGGT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 56 1.00
ACGTcount: A:0.06, C:0.41, G:0.38, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:1603105 original size:6 final size:6
Alignment explanation
Indices: 1603090--1603180 Score: 146
Period size: 6 Copynumber: 15.2 Consensus size: 6
1603080 TCGGCTCGGC
* * * *
1603090 TCGTGG TCGAGG TCGAGG TCGAGG TCGAGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1603138 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1603181 AATACGTGTC
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 83 1.00
ACGTcount: A:0.04, C:0.16, G:0.49, T:0.30
Consensus pattern (6 bp):
TCGTGG
Found at i:1604739 original size:81 final size:81
Alignment explanation
Indices: 1604597--1604754 Score: 262
Period size: 81 Copynumber: 2.0 Consensus size: 81
1604587 GTAACGATGG
* *
1604597 AGGTGATGACGAGTAGCAGCAAGAATGACGGCTTCAAGCGGCGACGAGCAGCAGCAATTGAGTAC
1 AGGTGATGACGAGCAGCAGCAAGAACGACGGCTTCAAGCGGCGACGAGCAGCAGCAATTGAGTAC
1604662 CGGGCAGCGACGGTGT
66 CGGGCAGCGACGGTGT
* * * *
1604678 AGGTGATGATGAGCAGCAGCAGGAACGACGGCTTCAAGCGGCGACGAGCAGCAGTAGTTGAGTAC
1 AGGTGATGACGAGCAGCAGCAAGAACGACGGCTTCAAGCGGCGACGAGCAGCAGCAATTGAGTAC
1604743 CGGGCAGCGACG
66 CGGGCAGCGACG
1604755 TTGTTAAAGC
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 71 1.00
ACGTcount: A:0.28, C:0.22, G:0.38, T:0.13
Consensus pattern (81 bp):
AGGTGATGACGAGCAGCAGCAAGAACGACGGCTTCAAGCGGCGACGAGCAGCAGCAATTGAGTAC
CGGGCAGCGACGGTGT
Found at i:1606645 original size:42 final size:42
Alignment explanation
Indices: 1606598--1606725 Score: 165
Period size: 42 Copynumber: 3.1 Consensus size: 42
1606588 TAAACGCTAT
1606598 TAATTTACCACTCTATTGTGACATTTGTGGTATAAACGCCGC
1 TAATTTACCACTCTATTGTGACATTTGTGGTATAAACGCCGC
* *
1606640 TAATTTACCACTCTATTATGACATTTGTGGTATAAACGTCGC
1 TAATTTACCACTCTATTGTGACATTTGTGGTATAAACGCCGC
* *
1606682 TACA-TTAACACTCTATTG-CAGCATTTG-GGCTA-AAACGCCGC
1 TA-ATTTACCACTCTATTGTGA-CATTTGTGG-TATAAACGCCGC
1606723 TAA
1 TAA
1606726 ATGTCTACTT
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
40 1 0.01
41 13 0.17
42 62 0.81
43 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.34
Consensus pattern (42 bp):
TAATTTACCACTCTATTGTGACATTTGTGGTATAAACGCCGC
Found at i:1607706 original size:38 final size:38
Alignment explanation
Indices: 1607653--1607736 Score: 97
Period size: 38 Copynumber: 2.3 Consensus size: 38
1607643 ATAAGACAAT
1607653 AACTAAA-TT-TAATATA-AGAATT-TGAATTAATATAAA
1 AACTAAATTTATAATATATA-AATTAT-AATTAATATAAA
*
1607689 AA-TCAAATTTATAATATATAAATTATAATTAATATTAA
1 AACT-AAATTTATAATATATAAATTATAATTAATATAAA
1607727 AACTAAATTT
1 AACTAAATTT
1607737 CAAAAATTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
35 1 0.02
36 5 0.12
37 2 0.05
38 30 0.73
39 3 0.07
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (38 bp):
AACTAAATTTATAATATATAAATTATAATTAATATAAA
Found at i:1607933 original size:16 final size:16
Alignment explanation
Indices: 1607899--1607938 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1607889 CGAGTCAATT
*
1607899 ACAGGTCAGGTTCATA
1 ACAGGTCAGGTTCAAA
*
1607915 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTCAAA
*
1607931 ACATGTCA
1 ACAGGTCA
1607939 TGTAATATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (16 bp):
ACAGGTCAGGTTCAAA
Found at i:1611916 original size:172 final size:171
Alignment explanation
Indices: 1611631--1611973 Score: 677
Period size: 172 Copynumber: 2.0 Consensus size: 171
1611621 GGGGACAACA
1611631 TTTTTTCTCATAAAGATGGCATTTGGTGAAAGAAATGGGTGATGACTGTGAGTCTGTGATCCCAA
1 TTTTTTCTCATAAAGATGGCATTTGGTGAAAGAAATGGGTGATGACTGTGAGTCTGTGATCCCAA
1611696 ACTTTGGGCTACATCCTTGGTAATATATAACTGTTCTTTGGGTTTTCAATCTTTTAATTTATTTT
66 ACTTTGGGCTACATCCTTGGTAATATATAACTGTTCTTTGGGTTTTCAATCTTTTAATTTATTTT
1611761 GTTTGGGGTCGATCCTTAGTTATTGCTTTGATAGGTTCGTT
131 GTTTGGGGTCGATCCTTAGTTATTGCTTTGATAGGTTCGTT
1611802 TTTTTTCTCATAAAGATTGGCATTTGGTGAAAGAAATGGGTGATGACTGTGAGTCTGTGATCCCA
1 TTTTTTCTCATAAAGA-TGGCATTTGGTGAAAGAAATGGGTGATGACTGTGAGTCTGTGATCCCA
1611867 AACTTTGGGCTACATCCTTGGTAATATATAACTGTTCTTTGGGTTTTCAATCTTTTAATTTATTT
65 AACTTTGGGCTACATCCTTGGTAATATATAACTGTTCTTTGGGTTTTCAATCTTTTAATTTATTT
1611932 TGTTTGGGGTCGATCCTTAGTTATTGCTTTGATAGGTTCGTT
130 TGTTTGGGGTCGATCCTTAGTTATTGCTTTGATAGGTTCGTT
1611974 GAAGGAAGGA
Statistics
Matches: 171, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
171 16 0.09
172 155 0.91
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.43
Consensus pattern (171 bp):
TTTTTTCTCATAAAGATGGCATTTGGTGAAAGAAATGGGTGATGACTGTGAGTCTGTGATCCCAA
ACTTTGGGCTACATCCTTGGTAATATATAACTGTTCTTTGGGTTTTCAATCTTTTAATTTATTTT
GTTTGGGGTCGATCCTTAGTTATTGCTTTGATAGGTTCGTT
Found at i:1618149 original size:2 final size:2
Alignment explanation
Indices: 1618142--1618190 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1618132 TGATTCAGTC
1618142 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
1618184 AT AT AT A
1 AT AT AT A
1618191 CCATTTCTAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1619878 original size:21 final size:21
Alignment explanation
Indices: 1619852--1619896 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1619842 GATTTCTGGG
* *
1619852 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1619873 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1619894 CAA
1 CAA
1619897 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1619966 original size:23 final size:22
Alignment explanation
Indices: 1619922--1619966 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1619912 AATGCCAGAG
*
1619922 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
1619944 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
1619967 AAATGTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:1620824 original size:2 final size:2
Alignment explanation
Indices: 1620817--1620891 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
1620807 TAATCTGAGA
1620817 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
1620859 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1620892 GATGGATATG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1621216 original size:30 final size:30
Alignment explanation
Indices: 1621172--1621325 Score: 274
Period size: 30 Copynumber: 5.1 Consensus size: 30
1621162 TCGAGACATA
1621172 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
1621203 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1621233 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1621263 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* *
1621293 TGGACAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1621322 TGGA
1 TGGA
1621326 TAGGTCCTTC
Statistics
Matches: 121, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
29 18 0.15
30 96 0.79
31 7 0.06
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:1624361 original size:21 final size:20
Alignment explanation
Indices: 1624335--1624378 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1624325 GATTTCTGGG
* *
1624335 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCC-TT
1624356 CAAGGGGAACCGATACCCTT
1 CAAGGGGAACCGATACCCTT
1624376 CAA
1 CAA
1624379 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (20 bp):
CAAGGGGAACCGATACCCTT
Found at i:1625280 original size:2 final size:2
Alignment explanation
Indices: 1625273--1625315 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1625263 AATCTTGAGA
1625273 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
1625315 A
1 A
1625316 GATGGATATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1625619 original size:30 final size:30
Alignment explanation
Indices: 1625578--1625743 Score: 307
Period size: 30 Copynumber: 5.5 Consensus size: 30
1625568 TTTACCTATG
1625578 TCTTTA-GACCTCTGGACAGTTACCGAGGA
1 TCTTTATGACCTCTGGACAGTTACCGAGGA
1625607 TCTTTATGACCTCTGGACAGTTACCGAGGA
1 TCTTTATGACCTCTGGACAGTTACCGAGGA
1625637 TCTTTATGACCTCTGGACAGTTACCGAGGA
1 TCTTTATGACCTCTGGACAGTTACCGAGGA
1625667 TCTTTATGACCTCTGGACAGTTACCGAGGA
1 TCTTTATGACCTCTGGACAGTTACCGAGGA
1625697 TCTTTATGACCTCTGGACAGTTACCGAGGA
1 TCTTTATGACCTCTGGACAGTTACCGAGGA
1625727 TCTTTATCTGACCTCTG
1 TCTTTA--TGACCTCTG
1625744 ACCTCTGGAC
Statistics
Matches: 134, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
29 6 0.04
30 119 0.89
32 9 0.07
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.31
Consensus pattern (30 bp):
TCTTTATGACCTCTGGACAGTTACCGAGGA
Found at i:1633583 original size:22 final size:20
Alignment explanation
Indices: 1633542--1633594 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1633532 GATTTTCCAG
1633542 AATCGCAACGCGAATATAAA
1 AATCGCAACGCGAATATAAA
* *
1633562 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATATAAA
*
1633582 AATCGCAAAGCGA
1 AATCGCAACGCGA
1633595 TTCTGACTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.47, C:0.23, G:0.17, T:0.13
Consensus pattern (20 bp):
AATCGCAACGCGAATATAAA
Found at i:1633648 original size:20 final size:20
Alignment explanation
Indices: 1633603--1633894 Score: 261
Period size: 20 Copynumber: 14.4 Consensus size: 20
1633593 GATTCTGACT
1633603 ATCGCAACGAGTATCCGTAAAA
1 ATCGCAACGAGTATCCGT--AA
1633625 ATCGCAACGCA-TATCCGTAA
1 ATCGCAACG-AGTATCCGTAA
** *
1633645 ATCGCAACGACAATACGTAAA
1 ATCGCAACGAGTATCCGT-AA
*
1633666 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
* *
1633686 ATCGCAACGAGAATACGTAA
1 ATCGCAACGAGTATCCGTAA
* * *
1633706 ATCGCAACGCG-ATTC-TGATT
1 ATCGCAACGAGTATCCGT-A-A
* * *
1633726 ATCGCAACGAGAATACGTTA
1 ATCGCAACGAGTATCCGTAA
* *
1633746 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
* *
1633766 ATCGCAACGAGAATACGTAAA
1 ATCGCAACGAGTATCCGT-AA
* *
1633787 ATCGCAACGAGAATCTGTAA
1 ATCGCAACGAGTATCCGTAA
* **
1633807 ATCGCAACGAGAATCTATAA
1 ATCGCAACGAGTATCCGTAA
1633827 ATCGCAACGA-TAATCCGTAA
1 ATCGCAACGAGT-ATCCGTAA
1633847 ATCGCAACGA-TAATCCGTAA
1 ATCGCAACGAGT-ATCCGTAA
* *
1633867 ATCGCAACGAGAATCTGTAA
1 ATCGCAACGAGTATCCGTAA
1633887 ATCGCAAC
1 ATCGCAAC
1633895 ACTGAAATTT
Statistics
Matches: 227, Mismatches: 33, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
18 1 0.00
19 5 0.02
20 166 0.73
21 37 0.16
22 17 0.07
23 1 0.00
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGAGTATCCGTAA
Found at i:1633730 original size:40 final size:40
Alignment explanation
Indices: 1633561--1633894 Score: 302
Period size: 40 Copynumber: 8.2 Consensus size: 40
1633551 GCGAATATAA
* * ** * *
1633561 AAATCGCAACGCGAACATATAAATCGCAAAGCGATTCTG-
1 AAATCGCAACGAGAATACGTAAATCGCAACGCGATTCCGT
* * *
1633600 ACTATCGCAACGAGTATCCGTAAAAATCGCAACGC-ATATCCGT
1 A-AATCGCAACGAGAATACGT--AAATCGCAACGCGAT-TCCGT
*
1633643 AAATCGCAACGACAATACGTAAAATCGCAACGCG-TATCCGT
1 AAATCGCAACGAGAATACGT-AAATCGCAACGCGAT-TCCGT
*
1633684 AAATCGCAACGAGAATACGTAAATCGCAACGCGATTCTG-
1 AAATCGCAACGAGAATACGTAAATCGCAACGCGATTCCGT
* * *
1633723 ATTATCGCAACGAGAATACGTTAATCGCAATGCG-TATCCGT
1 A-AATCGCAACGAGAATACGTAAATCGCAACGCGAT-TCCGT
* * *
1633764 AAATCGCAACGAGAATACGTAAAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATACGT-AAATCGCAACGCGATTCCGT
* ** *
1633805 AAATCGCAACGAGAAT-CTATAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATAC-GTAAATCGCAACGCGATTCCGT
* * * * *
1633845 AAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATACGTAAATCGCAACGCGATTCCGT
1633885 AAATCGCAAC
1 AAATCGCAAC
1633895 ACTGAAATTT
Statistics
Matches: 249, Mismatches: 32, Indels: 27
0.81 0.10 0.09
Matches are distributed among these distances:
39 3 0.01
40 141 0.57
41 75 0.30
42 29 0.12
43 1 0.00
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (40 bp):
AAATCGCAACGAGAATACGTAAATCGCAACGCGATTCCGT
Found at i:1633789 original size:101 final size:99
Alignment explanation
Indices: 1633603--1633894 Score: 315
Period size: 101 Copynumber: 2.9 Consensus size: 99
1633593 GATTCTGACT
* * * * * *
1633603 ATCGCAACGAGTATCCGTAAAAATCGCAACGCA-TATCCGTAAATCGCAACGACAATACGTAAAA
1 ATCGCAACGAGAAT-C-TATAAATCGCAACG-AGAATACGTAAATCGCAACGATAATCCGT-AAA
* *
1633667 TCGCAACGCGTATCCGTAAATCGCAACGAGAATAC-GTAA
62 TCGCAACGAGAAT-CGTAAATCGCAACGAGAAT-CTGTAA
* * * *
1633706 ATCGCAACGCGATTCTGAT-TATCGCAACGAGAATACGTTAATCGCAATGCG-T-ATCCGTAAAT
1 ATCGCAACGAGAATCT-ATAAATCGCAACGAGAATACGTAAATCGCAA--CGATAATCCGTAAAT
1633768 CGCAACGAGAATACGTAAAATCGCAACGAGAATCTGTAA
63 CGCAACGAGAAT-CGT-AAATCGCAACGAGAATCTGTAA
* *
1633807 ATCGCAACGAGAATCTATAAATCGCAACGATAATCCGTAAATCGCAACGATAATCCGTAAATCGC
1 ATCGCAACGAGAATCTATAAATCGCAACGAGAATACGTAAATCGCAACGATAATCCGTAAATCGC
1633872 AACGAGAATCTGTAAATCGCAAC
66 AACGAGAATC-GTAAATCGCAAC
1633895 ACTGAAATTT
Statistics
Matches: 160, Mismatches: 19, Indels: 23
0.79 0.09 0.11
Matches are distributed among these distances:
99 2 0.01
100 33 0.21
101 110 0.69
102 2 0.01
103 13 0.08
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.20
Consensus pattern (99 bp):
ATCGCAACGAGAATCTATAAATCGCAACGAGAATACGTAAATCGCAACGATAATCCGTAAATCGC
AACGAGAATCGTAAATCGCAACGAGAATCTGTAA
Found at i:1633807 original size:121 final size:122
Alignment explanation
Indices: 1633542--1633835 Score: 394
Period size: 121 Copynumber: 2.4 Consensus size: 122
1633532 GATTTTCCAG
* ** * * * *
1633542 AATCGCAACGCGAATATAAAAATCGCAACGCGAACATATAAATCGCAAAGCGATTCTGACTATCG
1 AATCGCAACGCGAATCTGTAAATCGCAACGAGAATACATAAATCGCAACGCGATTCTGACTATCG
* *
1633607 CAACGAGTATCCGTAAAAATCGCAACGCATATCCGTAAATCGCAACGACAATACGTAA
66 CAACGAGAATACGT-AAAATCGCAACGCATATCCGTAAATCGCAACGACAATACGTAA
* * * *
1633665 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAAATCGCAACGCGATTCTGATTATCG
1 AATCGCAACGCGAATCTGTAAATCGCAACGAGAATACATAAATCGCAACGCGATTCTGACTATCG
* * * *
1633730 CAACGAGAATACGT-TAATCGCAATGCGTATCCGTAAATCGCAACGAGAATACGTAA
66 CAACGAGAATACGTAAAATCGCAACGCATATCCGTAAATCGCAACGACAATACGTAA
*
1633786 AATCGCAACGAGAATCTGTAAATCGCAACGAGAAT-CTATAAATCGCAACG
1 AATCGCAACGCGAATCTGTAAATCGCAACGAGAATAC-ATAAATCGCAACG
1633836 ATAATCCGTA
Statistics
Matches: 149, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
120 1 0.01
121 82 0.55
123 66 0.44
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.19
Consensus pattern (122 bp):
AATCGCAACGCGAATCTGTAAATCGCAACGAGAATACATAAATCGCAACGCGATTCTGACTATCG
CAACGAGAATACGTAAAATCGCAACGCATATCCGTAAATCGCAACGACAATACGTAA
Found at i:1633851 original size:121 final size:121
Alignment explanation
Indices: 1633561--1633894 Score: 359
Period size: 121 Copynumber: 2.7 Consensus size: 121
1633551 GCGAATATAA
* * * * * * * * *
1633561 AAATCGCAACGCGAACATATAAATCGCAAAGCGATTCTGACT-ATCGCAACGAGTATCCGTAAAA
1 AAATCGCAACGAGAATACATAAATCGCAACGAGAATCCGA-TAATCGCAACGAGAATACGT--AA
* * *
1633625 ATCGCAACGCATATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGT
63 ATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGAGAATCCGT
* * * * * *
1633684 AAATCGCAACGAGAATACGTAAATCGCAACGCGATTCTGATTATCGCAACGAGAATACGTTAATC
1 AAATCGCAACGAGAATACATAAATCGCAACGAGAATCCGATAATCGCAACGAGAATACGTAAATC
* * *
1633749 GCAATGCGTATCCGTAAATCGCAACGAGAATACGTAAAATCGCAACGAGAATCTGT
66 GCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGAGAATCCGT
* * *
1633805 AAATCGCAACGAGAAT-CTATAAATCGCAACGATAATCCG-TAAATCGCAACGATAATCCGTAAA
1 AAATCGCAACGAGAATAC-ATAAATCGCAACGAGAATCCGAT-AATCGCAACGAGAATACGTAAA
* * *
1633868 TCGCAACGAGAATCTGTAAATCGCAAC
64 TCGCAACGCGTATCCGTAAATCGCAAC
1633895 ACTGAAATTT
Statistics
Matches: 181, Mismatches: 27, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
120 2 0.01
121 127 0.70
122 1 0.01
123 51 0.28
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (121 bp):
AAATCGCAACGAGAATACATAAATCGCAACGAGAATCCGATAATCGCAACGAGAATACGTAAATC
GCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGAGAATCCGT
Found at i:1634577 original size:12 final size:12
Alignment explanation
Indices: 1634556--1634589 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1634546 ACCACATTTC
*
1634556 CAATACCAAACA
1 CAATATCAAACA
1634568 CAATATCAAACA
1 CAATATCAAACA
*
1634580 CAATCTCAAA
1 CAATATCAAA
1634590 ACCTACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1637319 original size:14 final size:14
Alignment explanation
Indices: 1637300--1637387 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
1637290 CGGAAATTAC
1637300 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1637314 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1637333 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1637347 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1637366 AATCGCAACGAGGG
1 AATCGCAACGAGAG
1637380 AATCGCAA
1 AATCGCAA
1637388 TGCGAAATTA
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 27 0.46
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 20 0.34
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1637337 original size:33 final size:33
Alignment explanation
Indices: 1637281--1637408 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
1637271 CTTAATGACT
* * *
1637281 ATCGCAACGCGGAAATTACAATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1637315 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1637348 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1637381 ATCGCAATGCGAAATTAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1637409 CGAATTTAGT
Statistics
Matches: 89, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
33 80 0.90
34 9 0.10
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1637338 original size:19 final size:19
Alignment explanation
Indices: 1637314--1637412 Score: 83
Period size: 19 Copynumber: 5.7 Consensus size: 19
1637304 GCAACGAGAG
1637314 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1637333 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1637347 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
**
1637366 AATCGCAA--CG--A-GGG
1 AATCGCAATGCGAAATGAA
*
1637380 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
1637399 AATCGCAACGCGAA
1 AATCGCAATGCGAA
1637413 TTTAGTTTCG
Statistics
Matches: 62, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.50
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1637450 original size:19 final size:19
Alignment explanation
Indices: 1637418--1637483 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
1637408 GCGAATTTAG
* *
1637418 TTTCGCGTTTCGATTTTCA
1 TTTCGCATTGCGATTTTCA
1637437 TTTCGCATTGCGA--TTC-
1 TTTCGCATTGCGATTTTCA
*
1637453 TCTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
1637470 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1637484 AGTCATTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
14 6 0.16
16 7 0.18
17 7 0.18
19 18 0.47
ACGTcount: A:0.12, C:0.23, G:0.18, T:0.47
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:1637491 original size:19 final size:17
Alignment explanation
Indices: 1637433--1637483 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
1637423 CGTTTCGATT
1637433 TTCATTTCGCATTGCGA
1 TTCATTTCGCATTGCGA
*
1637450 TTC-TCTCG--TTGCGA
1 TTCATTTCGCATTGCGA
1637464 TTTTCATTTCGCATTGCGA
1 --TTCATTTCGCATTGCGA
1637483 T
1 T
1637484 AGTCATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
14 6 0.22
16 7 0.26
17 8 0.30
19 6 0.22
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (17 bp):
TTCATTTCGCATTGCGA
Found at i:1637609 original size:14 final size:14
Alignment explanation
Indices: 1637590--1637626 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1637580 CATCAATTAA
1637590 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1637604 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1637618 ACAAATCAA
1 ACAAATCAA
1637627 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1639061 original size:42 final size:42
Alignment explanation
Indices: 1638976--1639061 Score: 95
Period size: 42 Copynumber: 2.0 Consensus size: 42
1638966 GTGAATCGGG
* * *
1638976 CTCTTGAATGGTGGGAGGGACCTCTTCAATGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTCAAGGATGACAGGGGC
* *
1639018 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACCTCTTCAAGG-ATGACAGGGGC
1639060 CT
1 CT
1639062 TTTCAACGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
41 4 0.11
42 29 0.78
43 4 0.11
ACGTcount: A:0.21, C:0.19, G:0.37, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTCAAGGATGACAGGGGC
Found at i:1639547 original size:19 final size:19
Alignment explanation
Indices: 1639491--1639646 Score: 125
Period size: 19 Copynumber: 8.6 Consensus size: 19
1639481 TAGTTTACTT
* *
1639491 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* **
1639511 TCGCAACGTGAAAAATGACTA
1 TCGCAACGCG--AAATGAAAA
1639532 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1639551 TCGCAACG-G----GAGAA
1 TCGCAACGCGAAATGAAAA
*
1639565 TCGCAACGAGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1639584 TCGCAA--CG--AT-AGAA
1 TCGCAACGCGAAATGAAAA
1639598 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
**
1639617 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1639636 TCGCAACGCGA
1 TCGCAACGCGA
1639647 TTATAGTTTC
Statistics
Matches: 109, Mismatches: 15, Indels: 25
0.73 0.10 0.17
Matches are distributed among these distances:
14 21 0.19
15 3 0.03
16 2 0.02
17 1 0.01
18 3 0.03
19 56 0.51
20 8 0.07
21 12 0.11
22 3 0.03
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1639578 original size:33 final size:33
Alignment explanation
Indices: 1639531--1639624 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
1639521 AAAAATGACT
*
1639531 ATCGCAACGCGAAATGAAAATCGCAACGGGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
1639564 ATCGCAACGAGAAATGAAAATCGCAACGATAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1639597 ATCGCAACGCGAAATGAAAATCGCAACG
1 ATCGCAACGCGAAATGAAAATCGCAACG
1639625 CGAAACCAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:1639699 original size:19 final size:19
Alignment explanation
Indices: 1639672--1639777 Score: 115
Period size: 19 Copynumber: 5.4 Consensus size: 19
1639662 GCGATTTTGT
1639672 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* *
1639691 CGTTACGATTTTCATTTCT
1 CGTTGCGATTTTCATTTCG
1639710 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
**
1639729 CGTTGCGATAGTCATTTTTCAG
1 CGTTGCGATTTTCA--TTTC-G
*
1639751 -GTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
1639770 TGTTGCGA
1 CGTTGCGA
1639778 AAGTAAACTA
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
19 47 0.64
20 11 0.15
21 14 0.19
22 1 0.01
ACGTcount: A:0.14, C:0.18, G:0.22, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1639722 original size:38 final size:38
Alignment explanation
Indices: 1639671--1639761 Score: 128
Period size: 38 Copynumber: 2.3 Consensus size: 38
1639661 TGCGATTTTG
**
1639671 TCGTTGCGATTTTCATTTCGCGTTACGATTTTCATTTC
1 TCGTTGCGATTTTCATTTCGCGTTACGATAGTCATTTC
* *
1639709 TCGTTGCGATTTTCATTTCGCGTTGCGATAGTCATTTT
1 TCGTTGCGATTTTCATTTCGCGTTACGATAGTCATTTC
1639747 TCAGGTTGCGATTTT
1 TC--GTTGCGATTTT
1639762 AAGTTTCGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
38 36 0.77
40 11 0.23
ACGTcount: A:0.13, C:0.19, G:0.20, T:0.48
Consensus pattern (38 bp):
TCGTTGCGATTTTCATTTCGCGTTACGATAGTCATTTC
Found at i:1639974 original size:93 final size:95
Alignment explanation
Indices: 1639842--1640104 Score: 406
Period size: 94 Copynumber: 2.8 Consensus size: 95
1639832 AACCAATAGA
* * *
1639842 AAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTTTGGCAGAATTGGCAGCAACCGA
1 AAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGA
* *
1639907 ACAAATTTACTTTCAACCAAAAGATAAAAC
66 ATAAATTTACTTTCAACCAAAAGACAAAAC
* * *
1639937 -AAAGACAACTACT-ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAATCGA
1 AAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGA
1640000 ATAAATTTAC-TTCAACCAAAAGACAAAAC
66 ATAAATTTACTTTCAACCAAAAGACAAAAC
* * *
1640029 AAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAACAGTATTGGCAGCAACCGA
1 AAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGA
1640094 ATAAATTTACT
66 ATAAATTTACT
1640105 AAGCAATCTA
Statistics
Matches: 151, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
92 18 0.12
93 66 0.44
94 67 0.44
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.23
Consensus pattern (95 bp):
AAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGA
ATAAATTTACTTTCAACCAAAAGACAAAAC
Found at i:1641824 original size:19 final size:19
Alignment explanation
Indices: 1641800--1641872 Score: 84
Period size: 19 Copynumber: 4.1 Consensus size: 19
1641790 TCTTTTGGTT
1641800 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1641819 GAAATGAAAATTGCAA--C
1 GAAATGAAAATCGCAACGC
*
1641836 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1641852 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1641871 GA
1 GA
1641873 TTTTGGTTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
14 9 0.20
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 29 0.66
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1641983 original size:21 final size:21
Alignment explanation
Indices: 1641892--1641983 Score: 76
Period size: 21 Copynumber: 4.8 Consensus size: 21
1641882 CCCGTTGCGA
*
1641892 TTCTCTCATTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
1641913 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
1641934 TT-T-TGCGTT--GA----GA-
1 TTCTCT-CGTTGCGATTTTCAT
1641947 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
1641968 TTCTCTCGTTGCGATT
1 TTCTCTCGTTGCGATT
1641984 CTTCTGCAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 20
0.69 0.06 0.25
Matches are distributed among these distances:
13 2 0.04
14 6 0.11
15 1 0.02
16 2 0.04
18 2 0.04
19 1 0.02
20 6 0.11
21 36 0.64
ACGTcount: A:0.12, C:0.22, G:0.17, T:0.49
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1642547 original size:20 final size:20
Alignment explanation
Indices: 1642522--1642760 Score: 209
Period size: 20 Copynumber: 11.7 Consensus size: 20
1642512 CTTTAAAAAT
1642522 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1642542 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
1642562 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
1642583 CGCGTTGCGATTTTACGGATT
1 CGCGTTGCGA-TTTACGGATA
* * *
1642604 CTCGTTGCGATATT-C-AAAA
1 CGCGTTGCGAT-TTACGGATA
* *
1642623 TCGCGTTGCGATTTACGTATT
1 -CGCGTTGCGATTTACGGATA
*
1642644 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1642664 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
1642684 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
1642705 CGCATTGCGATTTTTACGGATA
1 CGCGTTGCGA--TTTACGGATA
* * * *
1642727 CTCGTTGCGATAGTAAGAAT-
1 CGCGTTGCGAT-TTACGGATA
1642747 CGCGTTGCGATTTA
1 CGCGTTGCGATTTA
1642761 TATGTTCGCG
Statistics
Matches: 176, Mismatches: 29, Indels: 29
0.75 0.12 0.12
Matches are distributed among these distances:
19 5 0.03
20 93 0.53
21 60 0.34
22 18 0.10
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1642581 original size:41 final size:41
Alignment explanation
Indices: 1642524--1642759 Score: 309
Period size: 41 Copynumber: 5.8 Consensus size: 41
1642514 TTAAAAATCG
*
1642524 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
1642565 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
1642606 CGTTGCGATATT-C-AAAATCGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGAT-TTACGGATA-CGCGTTGCGATTTTACGTATTCT
*
1642646 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
1642687 CGTTGCGATTTACGGATACGCATTGCGATTTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTTACGTATTCT
* * *
1642729 CGTTGCGATAGTAAGAAT-CGCGTTGCGATTT
1 CGTTGCGAT-TTACGGATACGCGTTGCGATTT
1642760 ATATGTTCGC
Statistics
Matches: 172, Mismatches: 16, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
39 2 0.01
40 33 0.19
41 102 0.59
42 30 0.17
43 5 0.03
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:1642660 original size:81 final size:82
Alignment explanation
Indices: 1642542--1642798 Score: 274
Period size: 81 Copynumber: 3.1 Consensus size: 82
1642532 TTTACGGATA
*
1642542 CGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATTCTC
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATTCTC
1642607 GTTGCGATATTCAAAAT
66 GTTGCGATATTCAAAAT
* *
1642624 CGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTC
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATTCTC
**
1642688 GTTGCGAT-TT-ACGGAT
66 GTTGCGATATTCA-AAAT
* * * * * * *
1642704 ACGCATTGCGATTTTTACGGATACTCGTTGCGATAGTAAGAAT-CGCGTTGCGATTTATA-TG-T
1 -CGCGTTGCGA-TTTTACGTATTCTCGTTGCGAT-TTACGGATACGCGTTGCGATTT-TACGGAT
* * * *
1642766 TCGCGTTGCGATTTTCATATT
62 TCTCGTTGCGATATTCAAAAT
*
1642787 AGCGTTGCGATT
1 CGCGTTGCGATT
1642799 CTGAAAAATC
Statistics
Matches: 147, Mismatches: 20, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
79 1 0.01
80 4 0.03
81 70 0.48
82 29 0.20
83 35 0.24
84 8 0.05
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (82 bp):
CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATTCTC
GTTGCGATATTCAAAAT
Found at i:1642769 original size:20 final size:20
Alignment explanation
Indices: 1642746--1642798 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1642736 ATAGTAAGAA
*
1642746 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
1642766 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
*
1642786 TAGCGTTGCGATT
1 TCGCGTTGCGATT
1642799 CTGAAAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:1642817 original size:123 final size:123
Alignment explanation
Indices: 1642521--1642843 Score: 316
Period size: 123 Copynumber: 2.6 Consensus size: 123
1642511 GCTTTAAAAA
* * *** * **
1642521 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGC
1 TCGCGTTGCGATTTACAGATACGCGTTGCGATTTGAAAAATCGTCAATGCGATTTACGGATACGC
* * * *
1642586 GTTGCGA-TTTTACGGATTCTCGTTGCGATATTCAAAATCGCGTTGCGATTTACGTAT
66 ATTGCGATTTTTACGGATACTCGTTGCGATAGTCAAAATCGCGTTGCGATTTACATAT
* * * *** * **
1642643 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGC
1 TCGCGTTGCGATTTACAGATACGCGTTGCGATTTGAAAAATCGTCAATGCGATTTACGGATACGC
* *
1642708 ATTGCGATTTTTACGGATACTCGTTGCGATAGT-AAGAATCGCGTTGCGATTTATATGT
66 ATTGCGATTTTTACGGATACTCGTTGCGATAGTCAA-AATCGCGTTGCGATTTACATAT
* * *
1642766 TCGCGTTGCGATTTTCATATTA-GCGTTGCGATTCTGAAAAATCG-CAATGCGAATTT--GTACT
1 TCGCGTTGCGATTTACAGA-TACGCGTTGCGATT-TGAAAAATCGTCAATGCG-ATTTACGGA-T
1642827 ATCGCATTGCGATTTTT
62 A-CGCATTGCGATTTTT
1642844 CAGAATCGCG
Statistics
Matches: 175, Mismatches: 19, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
122 74 0.42
123 75 0.43
124 26 0.15
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (123 bp):
TCGCGTTGCGATTTACAGATACGCGTTGCGATTTGAAAAATCGTCAATGCGATTTACGGATACGC
ATTGCGATTTTTACGGATACTCGTTGCGATAGTCAAAATCGCGTTGCGATTTACATAT
Found at i:1644425 original size:23 final size:23
Alignment explanation
Indices: 1644394--1644439 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1644384 TGTTCTTTGC
1644394 CTTTATGACACGTTTATCTCTGT
1 CTTTATGACACGTTTATCTCTGT
* *
1644417 CTTTGTGACACGTTTTTCTCTGT
1 CTTTATGACACGTTTATCTCTGT
1644440 TTTTTGGTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.13, C:0.22, G:0.15, T:0.50
Consensus pattern (23 bp):
CTTTATGACACGTTTATCTCTGT
Found at i:1644647 original size:16 final size:16
Alignment explanation
Indices: 1644626--1644658 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1644616 TAATAAATAG
1644626 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1644642 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1644658 A
1 A
1644659 AAAAAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1644739 original size:10 final size:10
Alignment explanation
Indices: 1644724--1644798 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
1644714 CATTTAATAA
1644724 ATAAACGAAC
1 ATAAACGAAC
1644734 ATAAACGAAC
1 ATAAACGAAC
1644744 ----ACGAAC
1 ATAAACGAAC
1644750 ATAAACGAAC
1 ATAAACGAAC
** *
1644760 ACGAAC-ATAA
1 ATAAACGA-AC
1644770 ATGAACACGAAC
1 AT-AA-ACGAAC
1644782 ATAAACGAAC
1 ATAAACGAAC
1644792 ATAAACG
1 ATAAACG
1644799 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1644749 original size:16 final size:16
Alignment explanation
Indices: 1644728--1644792 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
1644718 TAATAAATAA
1644728 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1644744 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1644760 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1644776 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1644792 A
1 A
1644793 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1645182 original size:63 final size:63
Alignment explanation
Indices: 1645104--1645230 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
1645094 TTTTTCTCTT
1645104 TACTGATGCTCGTATACTTCCGATTGTTACCTTTATATTCCCATCTATTTCTAGAAAGAAGTA
1 TACTGATGCTCGTATACTTCCGATTGTTACCTTTATATTCCCATCTATTTCTAGAAAGAAGTA
1645167 TACTGATGCTCGTATACTTCCGATTGTTACCTTTATATTCCCATCTATTTCTAGAAAGAAGTA
1 TACTGATGCTCGTATACTTCCGATTGTTACCTTTATATTCCCATCTATTTCTAGAAAGAAGTA
1645230 T
1 T
1645231 GATGTTTTCT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (63 bp):
TACTGATGCTCGTATACTTCCGATTGTTACCTTTATATTCCCATCTATTTCTAGAAAGAAGTA
Found at i:1645629 original size:24 final size:24
Alignment explanation
Indices: 1645589--1645663 Score: 73
Period size: 24 Copynumber: 3.1 Consensus size: 24
1645579 AGATTGGGTA
*
1645589 AACATAAATGAATGAACATAAACG
1 AACATAAATGAACGAACATAAACG
*
1645613 AACAT-AATCGAACGAACATAATCG
1 AACATAAAT-GAACGAACATAAACG
* * *
1645637 AACGA-ACATAAACGAACATAACCG
1 AAC-ATAAATGAACGAACATAAACG
1645661 AAC
1 AAC
1645664 GTTCACGAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
23 3 0.07
24 37 0.86
25 3 0.07
ACGTcount: A:0.55, C:0.20, G:0.12, T:0.13
Consensus pattern (24 bp):
AACATAAATGAACGAACATAAACG
Found at i:1645644 original size:38 final size:38
Alignment explanation
Indices: 1645589--1645664 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
1645579 AGATTGGGTA
* *
1645589 AACATAAATGAATGAACATAAACGAACATAATCGAACG
1 AACATAAATGAACGAACATAAACGAACATAACCGAACG
1645627 AACAT-AATCGAACGAACATAAACGAACATAACCGAACG
1 AACATAAAT-GAACGAACATAAACGAACATAACCGAACG
1645665 TTCACGAACG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 3 0.09
38 32 0.91
ACGTcount: A:0.54, C:0.20, G:0.13, T:0.13
Consensus pattern (38 bp):
AACATAAATGAACGAACATAAACGAACATAACCGAACG
Found at i:1645664 original size:14 final size:14
Alignment explanation
Indices: 1645609--1645653 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
1645599 AATGAACATA
1645609 AACGAACATAATCG
1 AACGAACATAATCG
1645623 AACGAACATAATCG
1 AACGAACATAATCG
*
1645637 AACGAACATAAACG
1 AACGAACATAATCG
1645651 AAC
1 AAC
1645654 ATAACCGAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.53, C:0.22, G:0.13, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:1645674 original size:24 final size:24
Alignment explanation
Indices: 1645621--1645674 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1645611 CGAACATAAT
*
1645621 CGAACGAACATAATCGAACGAACA
1 CGAACGAACATAACCGAACGAACA
** **
1645645 TAAACGAACATAACCGAACGTTCA
1 CGAACGAACATAACCGAACGAACA
1645669 CGAACG
1 CGAACG
1645675 TAAATGAACG
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.46, C:0.26, G:0.17, T:0.11
Consensus pattern (24 bp):
CGAACGAACATAACCGAACGAACA
Found at i:1646195 original size:2 final size:2
Alignment explanation
Indices: 1646188--1646257 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
1646178 ACCGGTTGCA
1646188 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
1646230 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
1646258 CAATTTCTAG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1648738 original size:19 final size:19
Alignment explanation
Indices: 1648716--1648753 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1648706 TAACTTTTCC
1648716 AAATGAAATTGTACAAACT
1 AAATGAAATTGTACAAACT
**
1648735 AAATGTTATTGTACAAACT
1 AAATGAAATTGTACAAACT
1648754 TAAGCATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (19 bp):
AAATGAAATTGTACAAACT
Found at i:1652961 original size:29 final size:29
Alignment explanation
Indices: 1652940--1652997 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
1652930 AAACTTTGAA
* *
1652940 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAAATCAATTCAAGTACAAAAACA-TTTG
1652969 TAAAATCAATTCAAGTACAAAAACCATTT
1 TAAAATCAATTCAAGTACAAAAA-CATTT
1652998 TGCCTTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.40
30 13 0.52
31 2 0.08
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (29 bp):
TAAAATCAATTCAAGTACAAAAACATTTG
Found at i:1652992 original size:30 final size:30
Alignment explanation
Indices: 1652940--1652999 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
1652930 AAACTTTGAA
* *
1652940 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAAATCAATTAAGTACAAAAACCATTTTG
1652969 TAAAATCAATTCAAGTACAAAAACCATTTTG
1 TAAAATCAATT-AAGTACAAAAACCATTTTG
1653000 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 10 0.37
31 7 0.26
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.32
Consensus pattern (30 bp):
TAAAATCAATTAAGTACAAAAACCATTTTG
Found at i:1654250 original size:19 final size:20
Alignment explanation
Indices: 1654214--1654261 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1654204 TCTAAATCAT
*
1654214 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATTCCATTTTGG
*
1654234 TTTTCAAAA-TCCATTTTTG
1 TTTTCAAAATTCCATTTTGG
*
1654253 CTTTCAAAA
1 TTTTCAAAA
1654262 GAAAATCGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTGG
Found at i:1655430 original size:20 final size:22
Alignment explanation
Indices: 1655405--1655444 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1655395 AGTCGTTTAT
1655405 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
1655425 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
1655445 TCTGCTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:1655569 original size:19 final size:19
Alignment explanation
Indices: 1655545--1655612 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
1655535 GTTGCAGTCA
*
1655545 GGGGGTATTGATACCCCTG
1 GGGGGTATAGATACCCCTG
*
1655564 GGGGGTATCGATA-CCC--
1 GGGGGTATAGATACCCCTG
*
1655580 -GGGGTATGGATACCCCTG
1 GGGGGTATAGATACCCCTG
1655598 GGGGGTATAGATACC
1 GGGGGTATAGATACC
1655613 ATCCGAGCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
15 11 0.26
16 3 0.07
18 3 0.07
19 25 0.60
ACGTcount: A:0.19, C:0.21, G:0.38, T:0.22
Consensus pattern (19 bp):
GGGGGTATAGATACCCCTG
Found at i:1655585 original size:15 final size:15
Alignment explanation
Indices: 1655565--1655594 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1655555 ATACCCCTGG
1655565 GGGGTATCGATACCC
1 GGGGTATCGATACCC
*
1655580 GGGGTATGGATACCC
1 GGGGTATCGATACCC
1655595 CTGGGGGGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.23, G:0.37, T:0.20
Consensus pattern (15 bp):
GGGGTATCGATACCC
Found at i:1655592 original size:34 final size:34
Alignment explanation
Indices: 1655546--1655612 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
1655536 TTGCAGTCAG
* *
1655546 GGGGTATTGATACCCCTGGGGGGTATCGATACCC
1 GGGGTATGGATACCCCTGGGGGGTATAGATACCC
1655580 GGGGTATGGATACCCCTGGGGGGTATAGATACC
1 GGGGTATGGATACCCCTGGGGGGTATAGATACC
1655613 ATCCGAGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.19, C:0.21, G:0.37, T:0.22
Consensus pattern (34 bp):
GGGGTATGGATACCCCTGGGGGGTATAGATACCC
Found at i:1662694 original size:31 final size:31
Alignment explanation
Indices: 1662656--1662732 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
1662646 TTAAAATACA
* *
1662656 TAAGATATGATCACCTTCGTTTTTAGTTAAT
1 TAAGATATGGTCACCTTCATTTTTAGTTAAT
* * * *
1662687 TAAGATATGGTCACTTTTATTTTTATTTATT
1 TAAGATATGGTCACCTTCATTTTTAGTTAAT
*
1662718 TAAGATTTGGTCACC
1 TAAGATATGGTCACC
1662733 ACAGGTTAAC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.27, C:0.12, G:0.13, T:0.48
Consensus pattern (31 bp):
TAAGATATGGTCACCTTCATTTTTAGTTAAT
Found at i:1663671 original size:18 final size:19
Alignment explanation
Indices: 1663634--1663675 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
1663624 TAAACTTATA
*
1663634 AAATTTTAGATGACGAAAAT
1 AAATTTTAAATGA-GAAAAT
1663654 AAATTTTAAATG-GAAAAT
1 AAATTTTAAATGAGAAAAT
1663672 AAAT
1 AAAT
1663676 AGAAAAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
20 11 0.52
ACGTcount: A:0.55, C:0.02, G:0.12, T:0.31
Consensus pattern (19 bp):
AAATTTTAAATGAGAAAAT
Found at i:1664245 original size:31 final size:31
Alignment explanation
Indices: 1664207--1664285 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
1664197 AGTTTTAAAA
* * *
1664207 ATAACAAATTGGTTACTAATGTTATCAATTT
1 ATAACAAATTGATCACTAACGTTATCAATTT
* * *
1664238 ATAACAAATCGATCATTAACGTTATCGATTT
1 ATAACAAATTGATCACTAACGTTATCAATTT
*
1664269 GTAACAAATTGATCACT
1 ATAACAAATTGATCACT
1664286 CGCCATCAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (31 bp):
ATAACAAATTGATCACTAACGTTATCAATTT
Found at i:1670728 original size:22 final size:22
Alignment explanation
Indices: 1670695--1670747 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
1670685 TAGGGTCGGA
1670695 TCACGGGGTGGAGAACCCTTTCT
1 TCAC-GGGTGGAGAACCCTTTCT
1670718 TCACGGGTGGAGAACCCTTTCT
1 TCACGGGTGGAGAACCCTTTCT
*
1670740 TCTCGGGT
1 TCACGGGT
1670748 CGGGTAACCC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 25 0.86
23 4 0.14
ACGTcount: A:0.15, C:0.26, G:0.30, T:0.28
Consensus pattern (22 bp):
TCACGGGTGGAGAACCCTTTCT
Found at i:1671206 original size:20 final size:19
Alignment explanation
Indices: 1671178--1671215 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1671168 ATATATATAT
1671178 ATTATAATAAATAATAAAA
1 ATTATAATAAATAATAAAA
*
1671197 ATTATGAATAAATATTAAA
1 ATTAT-AATAAATAATAAA
1671216 TTAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
ATTATAATAAATAATAAAA
Found at i:1671482 original size:37 final size:37
Alignment explanation
Indices: 1671432--1671510 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
1671422 TTTTTCCAGA
1671432 TACGAGCATTCTTGTCCGACCATGTTGCATTTATGTG
1 TACGAGCATTCTTGTCCGACCATGTTGCATTTATGTG
* * *
1671469 TACGAGCATTCTTGTCCGACTATGTTGCGTTTATTTG
1 TACGAGCATTCTTGTCCGACCATGTTGCATTTATGTG
1671506 TACGA
1 TACGA
1671511 ATATGTATGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (37 bp):
TACGAGCATTCTTGTCCGACCATGTTGCATTTATGTG
Found at i:1679544 original size:17 final size:16
Alignment explanation
Indices: 1679517--1679548 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1679507 TAATAATAAT
1679517 TATTATTATTAATATA
1 TATTATTATTAATATA
1679533 TATTATTTATTAATAT
1 TATTA-TTATTAATAT
1679549 TACAAAACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTATTAATATA
Found at i:1681585 original size:24 final size:23
Alignment explanation
Indices: 1681558--1681607 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
1681548 TTATTATACT
1681558 TTTTATT-ATAGTATTTATATTTCA
1 TTTTATTCA-AGTATTT-TATTTCA
1681582 TTTTATTGCAAGTATTTTATTTCA
1 TTTTATT-CAAGTATTTTATTTCA
1681606 TT
1 TT
1681608 ATTTATGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 16 0.67
25 7 0.29
26 1 0.04
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (23 bp):
TTTTATTCAAGTATTTTATTTCA
Found at i:1684874 original size:15 final size:15
Alignment explanation
Indices: 1684854--1684885 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1684844 ATCAATACCT
1684854 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
1684869 TTTTGCATACATTCA
1 TTTTGCATACATGCA
1684884 TT
1 TT
1684886 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:1692211 original size:11 final size:11
Alignment explanation
Indices: 1692195--1692263 Score: 68
Period size: 11 Copynumber: 6.3 Consensus size: 11
1692185 ATTATGCTTG
1692195 AAGAAAAAAAA
1 AAGAAAAAAAA
1692206 AAGAAAAAAAA
1 AAGAAAAAAAA
*
1692217 AGAGAAGAAAAA
1 A-AGAAAAAAAA
* *
1692229 GAGAAAAAAGA
1 AAGAAAAAAAA
*
1692240 AA-TAAAAAAA
1 AAGAAAAAAAA
* *
1692250 GAGAAAAGAAA
1 AAGAAAAAAAA
1692261 AAG
1 AAG
1692264 GGGGTCAAGA
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
10 7 0.16
11 29 0.64
12 9 0.20
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.01
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:1692227 original size:21 final size:21
Alignment explanation
Indices: 1692195--1692263 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 21
1692185 ATTATGCTTG
*
1692195 AAGAAAAAAAAAAGAAAAAAA
1 AAGAGAAAAAAAAGAAAAAAA
1692216 AAGAGAAGAAAAAGAGAAAAAAGA
1 AAGAGAA-AAAAA-AGAAAAAA-A
* *
1692240 AATA-AAAAAAGAGAAAAGAAA
1 AAGAGAAAAAAAAGAAAA-AAA
1692261 AAG
1 AAG
1692264 GGGGTCAAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
21 15 0.38
22 11 0.28
23 10 0.25
24 4 0.10
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.01
Consensus pattern (21 bp):
AAGAGAAAAAAAAGAAAAAAA
Found at i:1692246 original size:19 final size:19
Alignment explanation
Indices: 1692212--1692260 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1692202 AAAAAAGAAA
*
1692212 AAAAAAGAGAAGAAAAAGAG
1 AAAAAAGA-AAGAAAAAAAG
*
1692232 AAAAAAGAAATAAAAAAAG
1 AAAAAAGAAAGAAAAAAAG
*
1692251 AGAAAAGAAA
1 AAAAAAGAAA
1692261 AAGGGGGTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (19 bp):
AAAAAAGAAAGAAAAAAAG
Found at i:1692247 original size:34 final size:34
Alignment explanation
Indices: 1692196--1692263 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
1692186 TTATGCTTGA
*
1692196 AGAAAAAAAAAAGAAAAAAAAAGAGAAGAAAAAG
1 AGAAAAAAAAAAGAAAAAAAAAGAAAAGAAAAAG
* * *
1692230 AGAAAAAAGAAATAAAAAAAGAGAAAAGAAAAAG
1 AGAAAAAAAAAAGAAAAAAAAAGAAAAGAAAAAG
1692264 GGGGTCAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (34 bp):
AGAAAAAAAAAAGAAAAAAAAAGAAAAGAAAAAG
Found at i:1693878 original size:92 final size:92
Alignment explanation
Indices: 1693521--1693871 Score: 580
Period size: 92 Copynumber: 3.8 Consensus size: 92
1693511 AGAAGACCCA
1693521 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAAT
* *
1693586 AATTGAATTTGAAAGATGAATGTGC-C
66 CATTGAATTTGAAAGATAAATGTGCTC
1693612 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAA
1 -ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAA
*
1693677 TCATTGAATTTGGAAGATAAATGTGCTC
65 TCATTGAATTTGAAAGATAAATGTGCTC
* *
1693705 ATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAAAACCAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAAT
1693770 CATTGAATTTGAAAGATAAATGTGCTC
66 CATTGAATTTGAAAGATAAATGTGCTC
* * * *
1693797 ATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTTGATATAAAACC-CAGAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT-GAACCACAGAACCAA
1693861 TCATTGGAATT
65 TCATT-GAATT
1693872 AAAAGATGAA
Statistics
Matches: 246, Mismatches: 10, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
92 236 0.96
93 10 0.04
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.36
Consensus pattern (92 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAAT
CATTGAATTTGAAAGATAAATGTGCTC
Found at i:1694331 original size:95 final size:95
Alignment explanation
Indices: 1694168--1694365 Score: 396
Period size: 95 Copynumber: 2.1 Consensus size: 95
1694158 TATTCTCCTC
1694168 ATCAGAATCAGAATTCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTG
1 ATCAGAATCAGAATTCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTG
1694233 AAAGATCACTTCATAATCAGATGAGTTGTT
66 AAAGATCACTTCATAATCAGATGAGTTGTT
1694263 ATCAGAATCAGAATTCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTG
1 ATCAGAATCAGAATTCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTG
1694328 AAAGATCACTTCATAATCAGATGAGTTGTT
66 AAAGATCACTTCATAATCAGATGAGTTGTT
1694358 ATCAGAAT
1 ATCAGAAT
1694366 TAACATGTTG
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 103 1.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (95 bp):
ATCAGAATCAGAATTCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTG
AAAGATCACTTCATAATCAGATGAGTTGTT
Found at i:1694887 original size:113 final size:113
Alignment explanation
Indices: 1694661--1695341 Score: 894
Period size: 113 Copynumber: 6.0 Consensus size: 113
1694651 TGGCAAAGAT
* *
1694661 TCAAATCCATCATTTGATGGATCAGTA-TTT-CCAG-GTAGAGTTCATAATGAGAAGAACTCCTC
1 TCAAATCCATCACTTGATGGATCA--ACTTTGCCAGAG-AAAGTTCATAATGAGAAGAA---CTC
*
1694723 ATCTG-A-AAGAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGC
60 ATCTGAAGAAG-GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** *
1694776 TTGAATCCATCACTTGATGGATTAACTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1694841 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
1694889 TCAAATCCATCATTTGATGGATCAGCTTTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATTAC
1 TCAAATCCATCACTTGATGGATCAACTTTGCCAGAG-AAAGTTCATAATGAGAAGAACTCA-T-C
*
1694953 TTGAAGGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
63 -TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
1695005 TCAAATCCATCACTTGATGGATTAACTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
1695070 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * **** *
1695118 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * * *
1695183 AGAAGGAAGAA-AAAGATCATAATGAGAAGAACTTGTTTAACCTTTTGT
66 AGAAGGAAGAAGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
1695231 TCAAATTCATCACTTGATGGATCAACATTT-CCAGAGAAAGTTCATAATAAGAAGAACTTATTTG
1 TCAAATCCATCACTTGATGGATCAAC-TTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* * **
1695295 AAG-AGGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTG
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
1695342 AATGACTCTA
Statistics
Matches: 504, Mismatches: 49, Indels: 29
0.87 0.08 0.05
Matches are distributed among these distances:
112 48 0.10
113 295 0.59
114 11 0.02
115 45 0.09
116 104 0.21
117 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAACTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:1695061 original size:229 final size:229
Alignment explanation
Indices: 1694661--1695341 Score: 1038
Period size: 229 Copynumber: 3.0 Consensus size: 229
1694651 TGGCAAAGAT
* *
1694661 TCAAATCCATCATTTGATGGATCAG-TATTTCCAGGTAGAGTTCATAATGAGAAGAACTCCTCA-
1 TCAAATCCATCATTTGATGGATCAGCT-TTTCCAGGTAGAGTTCATAATGAGAAGAACTCATTAC
* * **
1694724 TCTGAAAGA-GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTGAATCCATCA
65 T-TGAAGGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCA
1694788 CTTGATGGATTAACTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
129 CTTGATGGATTAACTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1694853 AAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
194 AAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
1694889 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGGTAGAGTTCATAATGAGAAGAACTCATTACT
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGGTAGAGTTCATAATGAGAAGAACTCATTACT
1694954 TGAAGGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACT
66 TGAAGGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACT
1695019 TGATGGATTAACTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
131 TGATGGATTAACTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
*
1695084 ATTCATAATGAGAAGAATTTGTTCAACCTTATGC
196 ATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
1695118 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCA-T-C-
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGGTAGAGTTCATAATGAGAAGAACTCATTACT
* * * * * *
1695180 TGAAGAAGGAAGAA-AAAGATCATAATGAGAAGAACTTGTTTAACCTTTTGTTCAAATTCATCAC
66 TGAAGGAGGAAGAAGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCAC
* * * *
1695244 TTGATGGATCAACATTT-CCAGAGAAAGTTCATAATAAGAAGAACTTATTTGAAG-AGGAAGAAG
130 TTGATGGATTAAC-TTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
* * **
1695307 AAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTG
194 AAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
1695342 AATGACTCTA
Statistics
Matches: 422, Mismatches: 26, Indels: 13
0.92 0.06 0.03
Matches are distributed among these distances:
225 42 0.10
226 100 0.24
227 4 0.01
228 66 0.16
229 210 0.50
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (229 bp):
TCAAATCCATCATTTGATGGATCAGCTTTTCCAGGTAGAGTTCATAATGAGAAGAACTCATTACT
TGAAGGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACT
TGATGGATTAACTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
ATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:1695288 original size:342 final size:337
Alignment explanation
Indices: 1694661--1695341 Score: 924
Period size: 342 Copynumber: 2.0 Consensus size: 337
1694651 TGGCAAAGAT
* *
1694661 TCAAATCCATCATTTGATGGATCAGTATTTCCAGGTAGAGTTCATAATGAGAAGAACTCCTCATC
1 TCAAATCCATCACTTGATGGATCAG-ATTTCCAGGTAAAGTTCATAATGAGAAGAA--CCTCATC
* * **
1694726 TGAAAGAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTGAATCCATCACTT
63 TGAAAGAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTCAAATCCATCACTT
*
1694791 GATGGATTAACTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA
128 GATGGATCAACTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA
* * * * *
1694856 TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCC
193 ATCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACATTTCC
* * *
1694921 AGGTAGAGTTCATAATGAGAAGAACTCATTACTTGAAGGAGGAAGAAGAAATTCATAATGAGAAG
258 AGGTAAAGTTCATAATAAGAAGAA--C-TTACTTGAA-GAGGAAGAAGAAATTCACAATGAGAAG
*
1694986 AATTTGTTCAACCTTTTGC
319 AACTTGTTCAACCTTTTGC
*
1695005 TCAAATCCATCACTTGATGGATTA-ACTTTGCCAGAG-AAAGTTCATAATGAGAAGAA-CTCATC
1 TCAAATCCATCACTTGATGGATCAGA-TTT-CCAG-GTAAAGTTCATAATGAGAAGAACCTCATC
1695067 TG-AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTCAAATCCATCAC
63 TGAAAG-A-GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTCAAATCCATCAC
* * **** *
1695131 TTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAA-A
126 TTGATGGATCAACTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *
1695195 AAGATCATAATGAGAAGAACTTGTTTAACCTTTTGTTCAAATTCATCACTTGATGGATCAACATT
191 AA-ATCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACATT
* *
1695260 TCCAGAG-AAAGTTCATAATAAGAAGAACTTATTTGAAGAGGAAGAAGAAGTTCACAATGAGAAG
255 TCCAG-GTAAAGTTCATAATAAGAAGAACTTACTTGAAGAGGAAGAAGAAATTCACAATGAGAAG
*
1695324 AGCTTGTTCAACCTTTTG
319 AACTTGTTCAACCTTTTG
1695342 AATGACTCTA
Statistics
Matches: 300, Mismatches: 30, Indels: 20
0.86 0.09 0.06
Matches are distributed among these distances:
338 41 0.14
339 8 0.03
340 4 0.01
341 12 0.04
342 185 0.62
343 4 0.01
344 45 0.15
345 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (337 bp):
TCAAATCCATCACTTGATGGATCAGATTTCCAGGTAAAGTTCATAATGAGAAGAACCTCATCTGA
AAGAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTCAAATCCATCACTTGAT
GGATCAACTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAAATC
ATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACATTTCCAGG
TAAAGTTCATAATAAGAAGAACTTACTTGAAGAGGAAGAAGAAATTCACAATGAGAAGAACTTGT
TCAACCTTTTGC
Found at i:1695575 original size:3 final size:3
Alignment explanation
Indices: 1695569--1695625 Score: 64
Period size: 3 Copynumber: 19.0 Consensus size: 3
1695559 TTACCCATTT
*
1695569 TTA TTA TTA TT- TT- TTA TAA TTA TTA TTA TTA TTA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
*
1695613 TTTA TTA ATA TTA
1 -TTA TTA TTA TTA
1695626 CAAAACCCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 4 0.09
3 37 0.79
4 6 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1695593 original size:19 final size:22
Alignment explanation
Indices: 1695569--1695625 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 22
1695559 TTACCCATTT
1695569 TTATTATTATT-TT-TTATA-A
1 TTATTATTATTATTATTATATA
1695588 TTATTATTATTATTATTATATA
1 TTATTATTATTATTATTATATA
*
1695610 TTATTTATTAATATTA
1 TTA-TTATTATTATTA
1695626 CAAAACCCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
19 11 0.33
20 2 0.06
21 5 0.15
22 4 0.12
23 11 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTATTATTATTATTATTATATA
Found at i:1695611 original size:13 final size:13
Alignment explanation
Indices: 1695570--1695625 Score: 62
Period size: 13 Copynumber: 4.4 Consensus size: 13
1695560 TACCCATTTT
* *
1695570 TATTATTATTTTT
1 TATTATTATTATA
*
1695583 TATAATTATTAT-
1 TATTATTATTATA
1695595 TATTATTATTATA
1 TATTATTATTATA
1695608 TATTATTTATTA-A
1 TATTA-TTATTATA
1695621 TATTA
1 TATTA
1695626 CAAAACCCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
12 11 0.29
13 21 0.55
14 6 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTATTATTATA
Found at i:1699809 original size:26 final size:26
Alignment explanation
Indices: 1699738--1699810 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
1699728 AATGATAAAT
1699738 AATAAA-AAATTATAATAAAAAAGTCC
1 AATAAACAAA-TATAATAAAAAAGTCC
* * *
1699764 AATAAACAACTATAGT-AAAAAGTACT
1 AATAAACAAATATAATAAAAAAGT-CC
*
1699790 AA-ATACAAATATAATAAAAAA
1 AATAAACAAATATAATAAAAAA
1699811 CAAAATCTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
25 17 0.45
26 19 0.50
27 2 0.05
ACGTcount: A:0.66, C:0.08, G:0.04, T:0.22
Consensus pattern (26 bp):
AATAAACAAATATAATAAAAAAGTCC
Found at i:1700290 original size:21 final size:21
Alignment explanation
Indices: 1700250--1700290 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1700240 CACGAGTCAG
*
1700250 GGGATGATGGTGCTGAGTCGA
1 GGGATGATGGTGATGAGTCGA
*
1700271 GGGATGATGGTGATGTGTCG
1 GGGATGATGGTGATGAGTCG
1700291 GTGAACGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.07, G:0.49, T:0.27
Consensus pattern (21 bp):
GGGATGATGGTGATGAGTCGA
Found at i:1701913 original size:25 final size:25
Alignment explanation
Indices: 1701860--1701924 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
1701850 TTATATCTGC
*
1701860 AAAA-AAATTAATTACGTAAAATATT
1 AAAATAAATTAAATACG-AAAATATT
1701885 -AAATAAATTAAATAC-AAAATATTT
1 AAAATAAATTAAATACGAAAATA-TT
*
1701909 AAAATATAATAAAATA
1 AAAATA-AATTAAATA
1701925 TACCTTAGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
23 6 0.18
24 5 0.15
25 15 0.44
26 8 0.24
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.31
Consensus pattern (25 bp):
AAAATAAATTAAATACGAAAATATT
Found at i:1701965 original size:10 final size:10
Alignment explanation
Indices: 1701952--1701980 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1701942 ATAAGAGTAT
1701952 TTGAGAGAAG
1 TTGAGAGAAG
1701962 TTGAGAGAAG
1 TTGAGAGAAG
1701972 TTGAGAGAA
1 TTGAGAGAA
1701981 TTTAGTGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.38, T:0.21
Consensus pattern (10 bp):
TTGAGAGAAG
Found at i:1706790 original size:43 final size:41
Alignment explanation
Indices: 1706669--1706876 Score: 265
Period size: 43 Copynumber: 4.9 Consensus size: 41
1706659 GGTCTGACCT
*
1706669 CTATAGGTCTGATCTTTTGCGGCGTTTGTATCTAAAAACGCCG
1 CTATAGGTCT-A-CTTTTGCGGCGTTTGTATCCAAAAACGCCG
* *
1706712 CTATAGGTCTATTTCTTGCGGCGTTTGTATTCAAAAACGCCG
1 CTATAGGTCTACTT-TTGCGGCGTTTGTATCCAAAAACGCCG
* *
1706754 CTATAGGTCTGACCTTTTGCGGTGTTTGTATCCAAAAATGCCG
1 CTATAGGTCT-A-CTTTTGCGGCGTTTGTATCCAAAAACGCCG
*
1706797 CTATAGGTCTAATCTTTTGCGGCGTTTGTATCCAAAAATGCCG
1 CTATAGGTCT-A-CTTTTGCGGCGTTTGTATCCAAAAACGCCG
* * *
1706840 TTATAGGTCTATTTTTGCGGCGTTTGT-TCAAAAAACG
1 CTATAGGTCTACTTTTGCGGCGTTTGTATCCAAAAACG
1706877 TTGCTATATA
Statistics
Matches: 148, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
40 8 0.05
41 17 0.11
42 37 0.25
43 84 0.57
44 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (41 bp):
CTATAGGTCTACTTTTGCGGCGTTTGTATCCAAAAACGCCG
Found at i:1707933 original size:33 final size:33
Alignment explanation
Indices: 1707891--1707955 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1707881 TTTGTGAAGA
*
1707891 TAAACAAGATGGAGTAGAGAATGCTGAAGGTAG
1 TAAAAAAGATGGAGTAGAGAATGCTGAAGGTAG
**
1707924 TAAAAAAGATGGAGTAGAGTCTGCTGAAGGTA
1 TAAAAAAGATGGAGTAGAGAATGCTGAAGGTA
1707956 CTGAAGGTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.06, G:0.32, T:0.20
Consensus pattern (33 bp):
TAAAAAAGATGGAGTAGAGAATGCTGAAGGTAG
Found at i:1710486 original size:20 final size:20
Alignment explanation
Indices: 1710461--1710501 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1710451 ATCAATTTAA
1710461 ATTGCTAATACAACAATTAC
1 ATTGCTAATACAACAATTAC
1710481 ATTGCTAATACAACAATTAC
1 ATTGCTAATACAACAATTAC
1710501 A
1 A
1710502 AAGAATCACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.20, G:0.05, T:0.29
Consensus pattern (20 bp):
ATTGCTAATACAACAATTAC
Found at i:1717264 original size:24 final size:24
Alignment explanation
Indices: 1717188--1717257 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
1717178 CCCAATTAAT
* * * *
1717188 TTTATGTTCATTCATTTATATTCA
1 TTTATGTTCGTTCGTTTGTGTTCA
*
1717212 TTTATGTTCTTTCGTTTGTGTTCA
1 TTTATGTTCGTTCGTTTGTGTTCA
1717236 TTTATGTTCGTTCGTTTGTGTT
1 TTTATGTTCGTTCGTTTGTGTT
1717258 TGTTTATCAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.13, C:0.11, G:0.14, T:0.61
Consensus pattern (24 bp):
TTTATGTTCGTTCGTTTGTGTTCA
Found at i:1733562 original size:2 final size:2
Alignment explanation
Indices: 1733555--1733600 Score: 76
Period size: 2 Copynumber: 23.0 Consensus size: 2
1733545 AACATATTAA
1733555 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
1733597 AT AT
1 AT AT
1733601 TTTAAAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 39 0.93
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1735074 original size:29 final size:29
Alignment explanation
Indices: 1735037--1735124 Score: 106
Period size: 29 Copynumber: 3.0 Consensus size: 29
1735027 AAGGCGCAGG
*
1735037 ACAAGGTCGCCCAACGTGCATGGCGACCT
1 ACAAGGTCGCCCGACGTGCATGGCGACCT
* * * *
1735066 ACCATGTCGCCTGGCGTGCATGGCGACCT
1 ACAAGGTCGCCCGACGTGCATGGCGACCT
*
1735095 ACAAGGTCGCCCGGA-GGGCATGGCGACCT
1 ACAAGGTCGCCC-GACGTGCATGGCGACCT
1735124 A
1 A
1735125 TGCTGGGAAG
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
29 47 0.98
30 1 0.02
ACGTcount: A:0.20, C:0.33, G:0.32, T:0.15
Consensus pattern (29 bp):
ACAAGGTCGCCCGACGTGCATGGCGACCT
Found at i:1736071 original size:31 final size:30
Alignment explanation
Indices: 1736036--1736102 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 30
1736026 AGAACTATGT
* *
1736036 CGACGACAGTGGTCATGGCCGGAGAGGGTGG
1 CGACGAC-GCGGTCATGGCCGAAGAGGGTGG
1736067 CGACG--GCGGTCATGGCCGAAGAGGGTGG
1 CGACGACGCGGTCATGGCCGAAGAGGGTGG
*
1736095 CAACGACG
1 CGACGACG
1736103 GATTAAGGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 25 0.81
30 1 0.03
31 5 0.16
ACGTcount: A:0.21, C:0.22, G:0.46, T:0.10
Consensus pattern (30 bp):
CGACGACGCGGTCATGGCCGAAGAGGGTGG
Found at i:1737012 original size:2 final size:2
Alignment explanation
Indices: 1737005--1737041 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1736995 TTGAGAAGAA
1737005 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1737042 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1737046 original size:2 final size:2
Alignment explanation
Indices: 1737041--1737088 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
1737031 ATATATATAT
1737041 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1737082 AG AG AG A
1 AG AG AG A
1737089 TGAGGCTCGA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1739598 original size:535 final size:535
Alignment explanation
Indices: 1738584--1739630 Score: 1645
Period size: 535 Copynumber: 2.0 Consensus size: 535
1738574 AAAAGGGAAC
* **
1738584 TTGTTGGGATTTCAAATAAAGCTTAATGATTAACCGAATGATTTGCCAAGATAGGGTGAATTGGT
1 TTGTTGGGATTTCAAATAAAGCTTAATGATCAACCGAATGATTTGCCAAGATAGGGTGAATTGAC
1738649 TTTTTGAGTTTAGGGAGTAAGGAGTATAAAAATATAGACAATTTCCACAAGGATTTATAGTGGTT
66 TTTTTGAGTTTAGGGAGTAAGGAGTATAAAAATATAGACAATTTCCACAAGGATTTATAGTGGTT
* * * *
1738714 CGACTTCTCAACCAAGTCTACATCCACTACCTAAGGTCATCACTTAGGCTTTCTAACAAATTCAC
131 CAACTTCTCAACCAAATCTACATCCACTACCTAAGCTCATCACGTAGGCTTTCTAACAAATTCAC
* * *
1738779 TAATTTGTTCTTTCTTTTTACTGGATCAAGAGATAACATTCACAACTCCCTAGCTTTTCAAAGGC
196 TAATTTGTTCTTTCTTTTTACAGAATCAAGAGATAACATTCACAACTCCCTAACTTTTCAAAGGC
*
1738844 TAAGCTAGAACCAATCCCCTTTACACAAAGGATAAGAAATGTAAACAAGAAAACCTCTCAAAGGA
261 TAAGCTAGAACCAATCCCCTTTACACAAAGGATAAGAAATGTAAACAAGAAAACATCTCAAAGGA
1738909 AGGTGTTTACAAAAGTTAAACTCACTAAAACACTAATATTTACAAGACAAAGGAAAATAAGAATG
326 AGGTGTTTACAAAAGTTAAACTCACTAAAACACTAATATTTACAAGACAAAGGAAAATAAGAATG
* * * *
1738974 ACAAATTCTTCTCTTGTGTTTGATTGCTTGGATAGGTGTTTATTAACCTTATTCAAGTGTCCTCA
391 AAAAAATCTTCTCTTGTGTTTGATTGCTTGGATAGGTGTTCATTAACCTTATTCAAGTGTCATCA
* * * *
1739039 ACTTGTTTTTATATATTTGAATGAGTTTGTGG-CTATTTTTAGCCGTTTGG-GATGTTTGGAGTC
456 ACTTGCTTTTACATATTGGAATGAGTTTGTGGTC-ATTTCTAGCCG-TTGGAGATGTTTGGAGTC
1739102 GTTAGGGCTGATACCAA
519 GTTAGGGCTGATACCAA
* * *
1739119 TTGTTGGTATTTCAAATGAAGCTTAAATGATCAACCGAATGATTTGCCACA-ATGGGGTGAATTG
1 TTGTTGGGATTTCAAATAAAGCTT-AATGATCAACCGAATGATTTGCCA-AGATAGGGTGAATTG
* *
1739183 ACTTTTTGAGTTTAGGGAGTAAGGAGTAT-AAAATATAGATAATTTGCACAAGGATTTATAGTGG
64 ACTTTTTGAGTTTAGGGAGTAAGGAGTATAAAAATATAGACAATTTCCACAAGGATTTATAGTGG
* * * *
1739247 TTCAACTTTTCAACCAAATCTACATCCTCTACCTAAGCTCCTCACGTAGGATTT-TCAACAAATT
129 TTCAACTTCTCAACCAAATCTACATCCACTACCTAAGCTCATCACGTAGGCTTTCT-AACAAATT
*
1739311 CACTAATTTGTTCTTTCTTTTTACAGAATCAAGAGATAACCTTCACAACTCCCTAACTTTTCAAA
193 CACTAATTTGTTCTTTCTTTTTACAGAATCAAGAGATAACATTCACAACTCCCTAACTTTTCAAA
* * *
1739376 GGCTAATCTAGAACCAATTCTCTTTACACAAAGGATAAGAAATGTAAACAAGAAAACATCTCAAA
258 GGCTAAGCTAGAACCAATCCCCTTTACACAAAGGATAAGAAATGTAAACAAGAAAACATCTCAAA
* * * * *
1739441 GGAATGTGTTTATAAAAGTTGAGCTCACTAAAACACTAATATTTACAAGAGAAAGGAAAATAAGA
323 GGAAGGTGTTTACAAAAGTTAAACTCACTAAAACACTAATATTTACAAGACAAAGGAAAATAAGA
* *
1739506 ATGAAAAAATCTTCTCTTGTGTTTGATTGTTTGGATAGGTGTTCATTAACCTTCTTCAAGTGTCA
388 ATGAAAAAATCTTCTCTTGTGTTTGATTGCTTGGATAGGTGTTCATTAACCTTATTCAAGTGTCA
* *
1739571 TCAACTTGCTTTTACATGTTGGAATGAGTTTGTGGTCGTTTCTAGCCGTTGGAGATGTTT
453 TCAACTTGCTTTTACATATTGGAATGAGTTTGTGGTCATTTCTAGCCGTTGGAGATGTTT
1739631 TAGAGCCATT
Statistics
Matches: 466, Mismatches: 41, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
534 5 0.01
535 397 0.85
536 63 0.14
537 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (535 bp):
TTGTTGGGATTTCAAATAAAGCTTAATGATCAACCGAATGATTTGCCAAGATAGGGTGAATTGAC
TTTTTGAGTTTAGGGAGTAAGGAGTATAAAAATATAGACAATTTCCACAAGGATTTATAGTGGTT
CAACTTCTCAACCAAATCTACATCCACTACCTAAGCTCATCACGTAGGCTTTCTAACAAATTCAC
TAATTTGTTCTTTCTTTTTACAGAATCAAGAGATAACATTCACAACTCCCTAACTTTTCAAAGGC
TAAGCTAGAACCAATCCCCTTTACACAAAGGATAAGAAATGTAAACAAGAAAACATCTCAAAGGA
AGGTGTTTACAAAAGTTAAACTCACTAAAACACTAATATTTACAAGACAAAGGAAAATAAGAATG
AAAAAATCTTCTCTTGTGTTTGATTGCTTGGATAGGTGTTCATTAACCTTATTCAAGTGTCATCA
ACTTGCTTTTACATATTGGAATGAGTTTGTGGTCATTTCTAGCCGTTGGAGATGTTTGGAGTCGT
TAGGGCTGATACCAA
Found at i:1740770 original size:19 final size:19
Alignment explanation
Indices: 1740748--1740797 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
1740738 ACCTCGGAAT
1740748 GGTATCGTTACCTTGAGGA
1 GGTATCGTTACCTTGAGGA
1740767 GGTATCGTTACCTTGAGGA
1 GGTATCGTTACCTTGAGGA
*
1740786 GGTATCGATACC
1 GGTATCGTTACC
1740798 CTGAAGGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (19 bp):
GGTATCGTTACCTTGAGGA
Found at i:1743215 original size:22 final size:22
Alignment explanation
Indices: 1743185--1743235 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1743175 CGAGACATAT
*
1743185 ACAATATACAGAGGTCCTTCGGG
1 ACAA-ATACAGAGGTCATTCGGG
* *
1743208 ACAAATACATAGGTTATTCGGG
1 ACAAATACAGAGGTCATTCGGG
*
1743230 AAAAAT
1 ACAAAT
1743236 TTCACATGCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.24
Consensus pattern (22 bp):
ACAAATACAGAGGTCATTCGGG
Found at i:1744119 original size:21 final size:22
Alignment explanation
Indices: 1744084--1744126 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
1744074 GACCGAAATT
1744084 ACTGTAGCAAGGGTATCGATAC
1 ACTGTAGCAAGGGTATCGATAC
*
1744106 ACTGTAG-TAGGGTATCGATAC
1 ACTGTAGCAAGGGTATCGATAC
1744127 CCCTATAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (22 bp):
ACTGTAGCAAGGGTATCGATAC
Found at i:1744427 original size:21 final size:21
Alignment explanation
Indices: 1744403--1744452 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1744393 GTCGAGGGTT
*
1744403 TTATGTGGTCCTCCGAGACAA
1 TTATGTGGTCATCCGAGACAA
* * *
1744424 TTATATGGTCATTCGAGATAA
1 TTATGTGGTCATCCGAGACAA
*
1744445 ATATGTGG
1 TTATGTGG
1744453 CACTTCGGTG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (21 bp):
TTATGTGGTCATCCGAGACAA
Found at i:1746517 original size:20 final size:20
Alignment explanation
Indices: 1746480--1746518 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1746470 CTAAAAATCA
* * *
1746480 TTTTTTAAAATTTCATTTTG
1 TTTTTCAAAATCTAATTTTG
1746500 TTTTTCAAAATCTAATTTT
1 TTTTTCAAAATCTAATTTT
1746519 TCTTTCATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTTCAAAATCTAATTTTG
Found at i:1749608 original size:31 final size:31
Alignment explanation
Indices: 1749570--1749694 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
1749560 CCCGAAGGAC
* * *
1749570 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
1749601 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1749632 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1749663 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1749694 C
1 C
1749695 CCTCGAACCT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1750522 original size:21 final size:21
Alignment explanation
Indices: 1750498--1750542 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1750488 TGTTGTTCGT
* *
1750498 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1750519 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1750540 TTG
1 TTG
1750543 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1757430 original size:46 final size:46
Alignment explanation
Indices: 1757377--1757470 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
1757367 AAAATTTATC
1757377 AAGTGGCTATGATGATTAATTTGCTATATTTTTCAATGAAAAAGAT
1 AAGTGGCTATGATGATTAATTTGCTATATTTTTCAATGAAAAAGAT
1757423 AAGTGGCTATGATGATTAATTTGCTATATTTTTCAATGAAAAAGAT
1 AAGTGGCTATGATGATTAATTTGCTATATTTTTCAATGAAAAAGAT
1757469 AA
1 AA
1757471 ATCTTTTTCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (46 bp):
AAGTGGCTATGATGATTAATTTGCTATATTTTTCAATGAAAAAGAT
Found at i:1763332 original size:13 final size:13
Alignment explanation
Indices: 1763279--1763339 Score: 54
Period size: 13 Copynumber: 4.6 Consensus size: 13
1763269 ATTTTTATTT
*
1763279 ATATGTTAATAAA
1 ATATATTAATAAA
1763292 ATA-A-TAATAAAA
1 ATATATTAAT-AAA
*
1763304 ATATCATGACATAAA
1 ATAT-ATTA-ATAAA
*
1763319 ATTTATTAATAAA
1 ATATATTAATAAA
1763332 ATATATTA
1 ATATATTA
1763340 GATTGATTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
11 4 0.11
12 6 0.16
13 15 0.39
14 4 0.11
15 7 0.18
16 2 0.05
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.36
Consensus pattern (13 bp):
ATATATTAATAAA
Found at i:1764935 original size:13 final size:13
Alignment explanation
Indices: 1764917--1764990 Score: 87
Period size: 13 Copynumber: 5.6 Consensus size: 13
1764907 GTCATAAATC
1764917 TATGACGCACATT
1 TATGACGCACATT
1764930 TATGACGCACATT
1 TATGACGCACATT
1764943 TATGA-GACACATT
1 TATGACG-CACATT
* *
1764956 TATAACACACATT
1 TATGACGCACATT
* *
1764969 TATGATGCTCATTT
1 TATGACGCACA-TT
1764983 TATGACGC
1 TATGACGC
1764991 GTATTGAGCG
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
12 1 0.02
13 41 0.80
14 9 0.18
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (13 bp):
TATGACGCACATT
Found at i:1770694 original size:22 final size:22
Alignment explanation
Indices: 1770669--1770714 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1770659 TTTGTTTGGT
*
1770669 AACAT-TTCTGAACATGTTCACG
1 AACATGTTC-GAACATGCTCACG
1770691 AACATGTTCGAACATGCTCACG
1 AACATGTTCGAACATGCTCACG
1770713 AA
1 AA
1770715 TGTTAAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (22 bp):
AACATGTTCGAACATGCTCACG
Found at i:1770695 original size:12 final size:12
Alignment explanation
Indices: 1770678--1770714 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1770668 TAACATTTCT
1770678 GAACATGTTCAC
1 GAACATGTTCAC
1770690 GAACATGTT--C
1 GAACATGTTCAC
*
1770700 GAACATGCTCAC
1 GAACATGTTCAC
1770712 GAA
1 GAA
1770715 TGTTAAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
10 9 0.41
12 13 0.59
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (12 bp):
GAACATGTTCAC
Found at i:1770813 original size:24 final size:24
Alignment explanation
Indices: 1770785--1770842 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
1770775 TAAACAAAAG
* *
1770785 TTAAACGAATATGTTCGCAAACAT
1 TTAAACGAACATGTTCACAAACAT
* *
1770809 TTAAATGAACATGTTCACGAACA-
1 TTAAACGAACATGTTCACAAACAT
*
1770832 TTAAATGAACA
1 TTAAACGAACA
1770843 CATTCATGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 11 0.37
24 19 0.63
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.28
Consensus pattern (24 bp):
TTAAACGAACATGTTCACAAACAT
Found at i:1770839 original size:23 final size:23
Alignment explanation
Indices: 1770677--1770864 Score: 82
Period size: 23 Copynumber: 8.2 Consensus size: 23
1770667 GTAACATTTC
1770677 TGAACATGTTCACGAACATGT---
1 TGAACATGTTCACGAACAT-TAAA
* **
1770698 TCGAACATGCTCACGAATGTTAAA
1 T-GAACATGTTCACGAACATTAAA
* **
1770722 TGAACATATT-AGCGAACGCTAAA
1 TGAACATGTTCA-CGAACATTAAA
** *
1770745 CAAACATGTTCATGAACATTAAA
1 TGAACATGTTCACGAACATTAAA
** * ** *
1770768 CAAACA-CTAAAC-AAAAGTTAAA
1 TGAACATGTTCACGAACA-TTAAA
* * * *
1770790 CGAATATGTTCGCAAACATTTAAA
1 TGAACATGTTCACGAACA-TTAAA
1770814 TGAACATGTTCACGAACATTAAA
1 TGAACATGTTCACGAACATTAAA
** * *
1770837 TGAACACATTCATGAACGTTAAA
1 TGAACATGTTCACGAACATTAAA
1770860 TGAAC
1 TGAAC
1770865 GAACACTAAC
Statistics
Matches: 124, Mismatches: 34, Indels: 16
0.71 0.20 0.09
Matches are distributed among these distances:
21 5 0.04
22 27 0.22
23 68 0.55
24 24 0.19
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.24
Consensus pattern (23 bp):
TGAACATGTTCACGAACATTAAA
Found at i:1773583 original size:12 final size:12
Alignment explanation
Indices: 1773566--1773591 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1773556 TTTACCCCCT
1773566 TACAATATCTCG
1 TACAATATCTCG
1773578 TACAATATCTCG
1 TACAATATCTCG
1773590 TA
1 TA
1773592 TGTTTCGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.35
Consensus pattern (12 bp):
TACAATATCTCG
Found at i:1777028 original size:17 final size:19
Alignment explanation
Indices: 1777006--1777040 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
1776996 AATATTTTTA
1777006 AATATTT-TAAAA-AAAAT
1 AATATTTATAAAATAAAAT
1777023 AATATTTATAAAATAAAA
1 AATATTTATAAAATAAAA
1777041 AATCGATGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 5 0.31
19 4 0.25
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AATATTTATAAAATAAAAT
Done.