Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008527.1 Hibiscus syriacus cultivar Beakdansim tig00111402_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: 9057482
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 37
Found at i:1751185 original size:15 final size:15
Alignment explanation
Indices: 1751165--1751211 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
1751155 GAATTAATTG
*
1751165 ATTAATAAATTAAAT
1 ATTAATAAATTAAAA
1751180 ATTAAT-AATTATAAA
1 ATTAATAAATTA-AAA
1751195 ATTAAATAAATATAAAA
1 ATT-AATAAAT-TAAAA
1751212 TCGTACTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 5 0.19
15 11 0.41
16 3 0.11
17 6 0.22
18 2 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATTAATAAATTAAAA
Found at i:1751211 original size:16 final size:15
Alignment explanation
Indices: 1751165--1751212 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
1751155 GAATTAATTG
1751165 ATTAATAAAT-TAAA
1 ATTAATAAATATAAA
*
1751179 TATTAATAATTATAAA
1 -ATTAATAAATATAAA
1751195 ATTAAATAAATATAAA
1 ATT-AATAAATATAAA
1751211 AT
1 AT
1751213 CGTACTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTAATAAATATAAA
Found at i:1751347 original size:32 final size:32
Alignment explanation
Indices: 1751309--1751378 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
1751299 TTTATTCATC
1751309 TTGTTGTTATTATATGCATCTTTATGTTAATG
1 TTGTTGTTATTATATGCATCTTTATGTTAATG
*
1751341 TTGTTGTTATTATATGCATCTTTATGTTAATT
1 TTGTTGTTATTATATGCATCTTTATGTTAATG
1751373 TTGTTG
1 TTGTTG
1751379 GTGATTATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.20, C:0.06, G:0.16, T:0.59
Consensus pattern (32 bp):
TTGTTGTTATTATATGCATCTTTATGTTAATG
Found at i:1752221 original size:78 final size:78
Alignment explanation
Indices: 1752092--1752267 Score: 343
Period size: 78 Copynumber: 2.3 Consensus size: 78
1752082 CAGTTATGTG
1752092 GACCATTTTGTAACTTTTAAAATGATTGTCAAAATTTTAACTAAAAATTATGAGTTTCGAATATA
1 GACCATTTTGTAACTTTTAAAATGATTGTCAAAATTTTAACTAAAAATTATGAGTTTCGAATATA
1752157 TGAAAAATCAGGT
66 TGAAAAATCAGGT
1752170 GACCATTTTGTAACTTTTAAAATGATTGTCAAAATTTTAACTAAAAATTATGAGTTTCGAATATA
1 GACCATTTTGTAACTTTTAAAATGATTGTCAAAATTTTAACTAAAAATTATGAGTTTCGAATATA
*
1752235 TGAAAAGTCAGGT
66 TGAAAAATCAGGT
1752248 GACCATTTTGTAACTTTTAA
1 GACCATTTTGTAACTTTTAA
1752268 TAGTCAGGAA
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 97 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (78 bp):
GACCATTTTGTAACTTTTAAAATGATTGTCAAAATTTTAACTAAAAATTATGAGTTTCGAATATA
TGAAAAATCAGGT
Found at i:1759679 original size:26 final size:26
Alignment explanation
Indices: 1759649--1759727 Score: 158
Period size: 26 Copynumber: 3.0 Consensus size: 26
1759639 AATTAAACTA
1759649 AAACAAAATCAGAAATTTAGGTTCTT
1 AAACAAAATCAGAAATTTAGGTTCTT
1759675 AAACAAAATCAGAAATTTAGGTTCTT
1 AAACAAAATCAGAAATTTAGGTTCTT
1759701 AAACAAAATCAGAAATTTAGGTTCTT
1 AAACAAAATCAGAAATTTAGGTTCTT
1759727 A
1 A
1759728 CTCAACAGTC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.30
Consensus pattern (26 bp):
AAACAAAATCAGAAATTTAGGTTCTT
Found at i:1761167 original size:87 final size:87
Alignment explanation
Indices: 1761020--1761366 Score: 628
Period size: 87 Copynumber: 4.0 Consensus size: 87
1761010 TTCATAGTAC
* * *
1761020 GCCAATGAGAGTGGCGCCATATGAACAACCTGGATTAAGCTATTGCCCTTCATGGATTCTGCATT
1 GCCAATGAGAGTGGCGCCATATGAACAACCTAGATTAAGCTATTGCCATTCATGGGTTCTGCATT
1761085 CAAAAACATCTGCTTGTAGGAT
66 CAAAAACATCTGCTTGTAGGAT
1761107 GCCAATGAGAGTGGCGCCATATGAACAACCTAGATTAAGCTATTGCCATTCATGGGTTCTGCATT
1 GCCAATGAGAGTGGCGCCATATGAACAACCTAGATTAAGCTATTGCCATTCATGGGTTCTGCATT
1761172 CAAAAACATCTGCTTGTAGGAT
66 CAAAAACATCTGCTTGTAGGAT
1761194 GCCAAT--GAGTGGCGCCATATGAACAACCTAGATTAAGCTATTGCCATTCATGGGTTCTGCATT
1 GCCAATGAGAGTGGCGCCATATGAACAACCTAGATTAAGCTATTGCCATTCATGGGTTCTGCATT
1761257 CAAAAACATCTGCTTGTAGGAT
66 CAAAAACATCTGCTTGTAGGAT
*
1761279 GCCAATGAGAGTGGCGCCATATGAACAACCTGGATTAAGCTATTGCC-TCTCATGGGTTCTGCAT
1 GCCAATGAGAGTGGCGCCATATGAACAACCTAGATTAAGCTATTGCCAT-TCATGGGTTCTGCAT
1761343 TCAAAAACATCTGCTTGTAGGAT
65 TCAAAAACATCTGCTTGTAGGAT
1761366 G
1 G
1761367 GTGGTTCCAG
Statistics
Matches: 253, Mismatches: 4, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
85 85 0.34
86 1 0.00
87 167 0.66
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (87 bp):
GCCAATGAGAGTGGCGCCATATGAACAACCTAGATTAAGCTATTGCCATTCATGGGTTCTGCATT
CAAAAACATCTGCTTGTAGGAT
Found at i:1761317 original size:172 final size:172
Alignment explanation
Indices: 1761028--1761366 Score: 626
Period size: 172 Copynumber: 2.0 Consensus size: 172
1761018 ACGCCAATGA
* *
1761028 GAGTGGCGCCATATGAACAACCTGGATTAAGCTATTGCCCTTCATGGATTCTGCATTCAAAAACA
1 GAGTGGCGCCATATGAACAACCTAGATTAAGCTATTGCCATTCATGGATTCTGCATTCAAAAACA
1761093 TCTGCTTGTAGGATGCCAATGAGAGTGGCGCCATATGAACAACCTAGATTAAGCTATTGCCAT-T
66 TCTGCTTGTAGGATGCCAATGAGAGTGGCGCCATATGAACAACCTAGATTAAGCTATTGCC-TCT
1761157 CATGGGTTCTGCATTCAAAAACATCTGCTTGTAGGATGCCAAT
130 CATGGGTTCTGCATTCAAAAACATCTGCTTGTAGGATGCCAAT
*
1761200 GAGTGGCGCCATATGAACAACCTAGATTAAGCTATTGCCATTCATGGGTTCTGCATTCAAAAACA
1 GAGTGGCGCCATATGAACAACCTAGATTAAGCTATTGCCATTCATGGATTCTGCATTCAAAAACA
*
1761265 TCTGCTTGTAGGATGCCAATGAGAGTGGCGCCATATGAACAACCTGGATTAAGCTATTGCCTCTC
66 TCTGCTTGTAGGATGCCAATGAGAGTGGCGCCATATGAACAACCTAGATTAAGCTATTGCCTCTC
1761330 ATGGGTTCTGCATTCAAAAACATCTGCTTGTAGGATG
131 ATGGGTTCTGCATTCAAAAACATCTGCTTGTAGGATG
1761367 GTGGTTCCAG
Statistics
Matches: 162, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
171 1 0.01
172 161 0.99
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (172 bp):
GAGTGGCGCCATATGAACAACCTAGATTAAGCTATTGCCATTCATGGATTCTGCATTCAAAAACA
TCTGCTTGTAGGATGCCAATGAGAGTGGCGCCATATGAACAACCTAGATTAAGCTATTGCCTCTC
ATGGGTTCTGCATTCAAAAACATCTGCTTGTAGGATGCCAAT
Found at i:1766161 original size:2 final size:2
Alignment explanation
Indices: 1766154--1766194 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1766144 TAATAAAAAT
1766154 TA TA TA TA 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 TA TA TA TA T
1766195 GTGTGTTGCG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1766916 original size:17 final size:18
Alignment explanation
Indices: 1766894--1766928 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1766884 CAATCGAATC
1766894 TTTTTA-AGAATTTAAAA
1 TTTTTATAGAATTTAAAA
*
1766911 TTTTTATATAATTTAAAA
1 TTTTTATAGAATTTAAAA
1766929 AAAATTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTTTATAGAATTTAAAA
Found at i:1775237 original size:35 final size:35
Alignment explanation
Indices: 1775198--1775272 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
1775188 AAAATACTTC
1775198 AATTTAGGATTTAGAATGTAATTGAAATATTTTGG
1 AATTTAGGATTTAGAATGTAATTGAAATATTTTGG
* * *
1775233 AATTTAGGGTTTAGAATGTAATTGAAGTGTTTTGG
1 AATTTAGGATTTAGAATGTAATTGAAATATTTTGG
1775268 AATTT
1 AATTT
1775273 TGAACATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (35 bp):
AATTTAGGATTTAGAATGTAATTGAAATATTTTGG
Found at i:1785318 original size:58 final size:58
Alignment explanation
Indices: 1785217--1785332 Score: 142
Period size: 58 Copynumber: 2.0 Consensus size: 58
1785207 CCTTGGCCAC
* * **
1785217 CCCCAAGTTTGGTGGGTTCAATTACTTCCCAAGTCCCTACTAGTTTTGAAACCATGCA
1 CCCCAAATTTGCTGGGTTCAATTACTTCCCAAGTAACTACTAGTTTTGAAACCATGCA
* * * * * *
1785275 CCCCAAATTTGCTGGGTTCAGTTATTTCCTAAGTAACTGCTAGTTTTGGAACTATGCA
1 CCCCAAATTTGCTGGGTTCAATTACTTCCCAAGTAACTACTAGTTTTGAAACCATGCA
1785333 AAATAAGCTT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
58 48 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (58 bp):
CCCCAAATTTGCTGGGTTCAATTACTTCCCAAGTAACTACTAGTTTTGAAACCATGCA
Found at i:1791867 original size:15 final size:15
Alignment explanation
Indices: 1791839--1791877 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1791829 TGTTTTGATA
* *
1791839 AATCAGTCATCATTG
1 AATCATTCAACATTG
*
1791854 AATCATTCAACATTT
1 AATCATTCAACATTG
1791869 AATCATTCA
1 AATCATTCA
1791878 GAGGTGCGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (15 bp):
AATCATTCAACATTG
Found at i:1794876 original size:21 final size:20
Alignment explanation
Indices: 1794790--1794947 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1794780 AAATGACCAA
**
1794790 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1794809 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1794829 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1794849 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1794870 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1794891 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1794911 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1794932 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1794948 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1794963 original size:40 final size:40
Alignment explanation
Indices: 1794914--1795223 Score: 363
Period size: 40 Copynumber: 7.8 Consensus size: 40
1794904 CGATTTTCCA
* * * *
1794914 AAATCGCAACGCGAATATGAAAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATCTGTAAATCGCAACGAGAATC-CGT
* * * *
1794954 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCTGTAAATCGCAACGAGAATCCGT
* * * * * *
1794994 ATATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCTGTAAATCGCAACGAGAATCCGT
* * *
1795034 ATATCGCAACGC-ATATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGA-ATCTGTAAATCGCAACGAGAATCCGT
* *
1795074 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCTGTAAATCGCAACGAGAATCCGT
* *
1795114 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCTGTAAATCGCAACGAGAATCCGT
* *
1795154 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCTGTAAATCGCAACGAGAATCCGT
* *
1795194 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGCGAATCTGTAAATCGCAAC
1795224 ACTGAAATTT
Statistics
Matches: 248, Mismatches: 19, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
40 246 0.99
41 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (40 bp):
AAATCGCAACGCGAATCTGTAAATCGCAACGAGAATCCGT
Found at i:1794976 original size:20 final size:20
Alignment explanation
Indices: 1794914--1795223 Score: 288
Period size: 20 Copynumber: 15.5 Consensus size: 20
1794904 CGATTTTCCA
* ** *
1794914 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1794934 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1794954 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1794974 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1794994 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1795014 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
1795034 ATATCGCAACGCATATCCGT
1 AAATCGCAACGCGTATCCGT
*
1795054 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1795074 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1795094 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1795114 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1795134 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1795154 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1795174 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1795194 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1795214 AAATCACAAC
1 AAATCGCAAC
1795224 ACTGAAATTT
Statistics
Matches: 242, Mismatches: 38, Indels: 20
0.81 0.13 0.07
Matches are distributed among these distances:
19 3 0.01
20 237 0.98
21 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1795000 original size:60 final size:60
Alignment explanation
Indices: 1794914--1795223 Score: 322
Period size: 60 Copynumber: 5.2 Consensus size: 60
1794904 CGATTTTCCA
* ** * * *
1794914 AAATCGCAACGCGAATATGAAAATCGCAACGCGAA-CACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGAGAATC-CGTAAATCGCAACGCGTATCCGT
* * * * *
1794974 AAATCGCAACGTGTATCCGTATATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGCGTATCCGT
* * * * * *
1795034 ATATCGCAACG-CATATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGA-ATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGCGTATCCGT
* *
1795094 AAATCGCAACGAT-AATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACG-ATAATCCGT
1 AAATCGCAACG-TGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGCGT-ATCCGT
* * * * * *
1795154 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGCGTATCCGT
*
1795214 AAATCACAAC
1 AAATCGCAAC
1795224 ACTGAAATTT
Statistics
Matches: 209, Mismatches: 34, Indels: 14
0.81 0.13 0.05
Matches are distributed among these distances:
60 207 0.99
61 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGTGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGCGTATCCGT
Found at i:1795945 original size:24 final size:24
Alignment explanation
Indices: 1795906--1795952 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1795896 AAATTTGGTC
1795906 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1795930 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1795953 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1798435 original size:33 final size:34
Alignment explanation
Indices: 1798384--1798548 Score: 183
Period size: 33 Copynumber: 4.7 Consensus size: 34
1798374 CGGAAATTAC
* *
1798384 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
1798417 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
1798451 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C--AATGAAAATCGCAATGCGAAATGAA
* *
1798489 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
1798522 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAA--C--AATGAAAATCGCAA
1798549 CGAGAGAATC
Statistics
Matches: 113, Mismatches: 7, Indels: 19
0.81 0.05 0.14
Matches are distributed among these distances:
32 1 0.01
33 50 0.44
34 16 0.14
35 1 0.01
36 2 0.02
37 1 0.01
38 26 0.23
39 16 0.14
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:1798467 original size:19 final size:19
Alignment explanation
Indices: 1798398--1798586 Score: 219
Period size: 19 Copynumber: 10.7 Consensus size: 19
1798388 GCAACGAGAG
1798398 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1798417 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1798431 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
1798451 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1798470 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1798489 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1798503 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1798522 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1798541 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
1798555 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
1798574 AATCGCATTGCGA
1 AATCGCAATGCGA
1798587 TTCTCCCGTT
Statistics
Matches: 146, Mismatches: 8, Indels: 32
0.78 0.04 0.17
Matches are distributed among these distances:
14 32 0.22
15 2 0.01
16 5 0.03
17 5 0.03
18 2 0.01
19 84 0.58
20 16 0.11
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1798525 original size:52 final size:52
Alignment explanation
Indices: 1798384--1798586 Score: 281
Period size: 52 Copynumber: 3.9 Consensus size: 52
1798374 CGGAAATTAC
*
1798384 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
1798431 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1798489 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* *
1798541 AATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCGCATTGCGA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
1798587 TTCTCCCGTT
Statistics
Matches: 140, Mismatches: 5, Indels: 17
0.86 0.03 0.10
Matches are distributed among these distances:
47 8 0.06
49 1 0.01
50 1 0.01
52 85 0.61
53 29 0.21
55 2 0.01
56 1 0.01
58 13 0.09
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:1798635 original size:19 final size:19
Alignment explanation
Indices: 1798595--1798692 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1798585 GATTCTCCCG
1798595 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1798615 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1798634 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1798648 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1798667 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1798686 TTGCGAT
1 TTGCGAT
1798693 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1798689 original size:52 final size:53
Alignment explanation
Indices: 1798576--1798692 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
1798566 GAAATTAAAA
1798576 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
*
1798629 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1798681 TCGCATTGCGAT
1 TCGCATTGCGAT
1798693 AGTCAATTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:1800832 original size:14 final size:14
Alignment explanation
Indices: 1800813--1800869 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1800803 GCGAAATGAA
*
1800813 AATCGCAACGACAG
1 AATCGCAACGAAAG
1800827 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1800844 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1800860 AATCGCAACG
1 AATCGCAACG
1800870 CGAAATAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1800840 original size:33 final size:33
Alignment explanation
Indices: 1800794--1800886 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1800784 GCGAAACCAA
*
1800794 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1800827 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1800860 AATCGCAACGCGAAATAAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1800887 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1800851 original size:19 final size:19
Alignment explanation
Indices: 1800757--1800891 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
1800747 TAGTTTACTT
* *
1800757 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1800777 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1800796 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1800815 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1800829 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1800848 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1800862 TCGCAACGCGAAATAAAAA
1 TCGCAACGCGAAATGAAAA
*
1800881 TCGCAATGCGA
1 TCGCAACGCGA
1800892 TTTTGGTTTC
Statistics
Matches: 96, Mismatches: 9, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
14 16 0.17
16 11 0.11
17 10 0.10
19 47 0.49
20 12 0.12
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1800909 original size:19 final size:19
Alignment explanation
Indices: 1800887--1801015 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1800877 AAAATCGCAA
1800887 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1800906 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1800920 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1800939 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1800953 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1800972 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1800991 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1801011 TGCGA
1 TGCGA
1801016 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1800929 original size:33 final size:33
Alignment explanation
Indices: 1800887--1800978 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1800877 AAAATCGCAA
1800887 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1800920 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1800953 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1800979 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1801179 original size:93 final size:93
Alignment explanation
Indices: 1801067--1801717 Score: 1284
Period size: 93 Copynumber: 7.0 Consensus size: 93
1801057 ATTGCATTGC
1801067 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
1 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
1801132 GAATTGGCAGCAACCGAACAAATTTACT
66 GAATTGGCAGCAACCGAACAAATTTACT
1801160 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
1 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
1801225 GAATTGGCAGCAACCGAACAAATTTACT
66 GAATTGGCAGCAACCGAACAAATTTACT
1801253 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
1 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
1801318 GAATTGGCAGCAACCGAACAAATTTACT
66 GAATTGGCAGCAACCGAACAAATTTACT
1801346 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
1 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
1801411 GAATTGGCAGCAACCGAACAAATTTACT
66 GAATTGGCAGCAACCGAACAAATTTACT
1801439 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
1 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
1801504 GAATTGGCAGCAACCGAACAAATTTACT
66 GAATTGGCAGCAACCGAACAAATTTACT
1801532 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
1 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
1801597 GAATTGGCAGCAACCGAACAAATTTACT
66 GAATTGGCAGCAACCGAACAAATTTACT
*
1801625 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCAAAGTGTTAAAGAATACACAGTTTAGCA
1 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
*
1801690 GAATTGGCAGCAACCGAATAAATTTACT
66 GAATTGGCAGCAACCGAACAAATTTACT
1801718 AAGCAATCTA
Statistics
Matches: 556, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 556 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
GAATTGGCAGCAACCGAACAAATTTACT
Found at i:1803442 original size:14 final size:14
Alignment explanation
Indices: 1803423--1803512 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
1803413 TTGAAATGAA
1803423 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1803437 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1803456 AATCGCAACTAGAG
1 AATCGCAACGAGAG
*
1803470 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1803489 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1803503 AATCGCAACG
1 AATCGCAACG
1803513 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 30 0.50
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 20 0.33
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1803455 original size:33 final size:33
Alignment explanation
Indices: 1803415--1803529 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
1803405 TCTTTTGGTT
1803415 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1803448 GAAATGAAAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1803481 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1803514 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1803530 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1803461 original size:19 final size:19
Alignment explanation
Indices: 1803437--1803534 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
1803427 GCAACGAGAG
1803437 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
1803456 AATCGCAA--C--TA-GAG
1 AATCGCAACGCGAAATGAA
1803470 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1803489 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
1803503 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1803522 AATCGCAATGCGA
1 AATCGCAACGCGA
1803535 TTTTGGTTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 32 0.52
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1803565 original size:14 final size:14
Alignment explanation
Indices: 1803546--1803602 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1803536 TTTGGTTTCG
1803546 CGTTGCGATTCTCA
1 CGTTGCGATTCTCA
*
1803560 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCA
*
1803579 CGTTGCGATTCTCT
1 CGTTGCGATTCTCA
1803593 CGTTGCGATT
1 CGTTGCGATT
1803603 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCA
Found at i:1803578 original size:33 final size:33
Alignment explanation
Indices: 1803530--1803610 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
1803520 AAAATCGCAA
**
1803530 TGCGATTTTGGTTTCGCGTTGCGATTCTCACGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCACGT
*
1803563 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCACGT
1803596 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
1803611 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCACGT
Found at i:1803643 original size:41 final size:41
Alignment explanation
Indices: 1803586--1803663 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
1803576 TCGCGTTGCG
*
1803586 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
1803627 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1803664 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:1803648 original size:20 final size:21
Alignment explanation
Indices: 1803587--1803662 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1803577 CGCGTTGCGA
1803587 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1803608 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1803628 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
1803649 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
1803663 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1803784 original size:33 final size:33
Alignment explanation
Indices: 1803742--1803812 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1803732 AATACTAACT
*
1803742 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1803775 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1803808 TGAAA
1 TGAAA
1803813 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1804046 original size:22 final size:22
Alignment explanation
Indices: 1803994--1804048 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1803984 TGGTTGTGAG
**
1803994 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1804016 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1804038 GGATTTCTTCG
1 GGATTTCTTCG
1804049 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1804220 original size:20 final size:20
Alignment explanation
Indices: 1804195--1804348 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
1804185 CTTTAAATAT
1804195 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1804215 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1804237 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1804256 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
1804276 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1804296 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1804316 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1804336 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1804349 TGGAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1804322 original size:40 final size:40
Alignment explanation
Indices: 1804194--1804348 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
1804184 GCTTTAAATA
*
1804194 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
1804235 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
1804275 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
1804315 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
1804349 TGGAAAATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:1804365 original size:21 final size:21
Alignment explanation
Indices: 1804335--1804417 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1804325 ATTTTCATAT
*
1804335 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1804356 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1804377 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1804398 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1804418 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1804408 original size:42 final size:43
Alignment explanation
Indices: 1804315--1804413 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1804305 ATTTATGTGT
* *
1804315 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1804356 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1804398 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1804414 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1818563 original size:33 final size:33
Alignment explanation
Indices: 1818521--1818584 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
1818511 GCACGTTAAG
1818521 TCTCGTCTCTTTGAAGAGCGCTTCCGGATGAAT
1 TCTCGTCTCTTTGAAGAGCGCTTCCGGATGAAT
*
1818554 TCTCGTCTCTTTGAGGAGCGCTTCCGGATGA
1 TCTCGTCTCTTTGAAGAGCGCTTCCGGATGA
1818585 GAACAAGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.33
Consensus pattern (33 bp):
TCTCGTCTCTTTGAAGAGCGCTTCCGGATGAAT
Found at i:1820892 original size:43 final size:45
Alignment explanation
Indices: 1820821--1820906 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 45
1820811 AAAATTTATA
* * *
1820821 TTTTATTGAAACTCGTCACCTCGGCGTGACGAGTTCAAATAATTG
1 TTTTATTGAAACTAGTCAACTCAGCGTGACGAGTTCAAATAATTG
* *
1820866 TTTT-TTG-AACTAGTCAACTCAGCGTGATGAGTTCCAATAAT
1 TTTTATTGAAACTAGTCAACTCAGCGTGACGAGTTCAAATAAT
1820907 ACTGTAGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
43 29 0.81
44 3 0.08
45 4 0.11
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (45 bp):
TTTTATTGAAACTAGTCAACTCAGCGTGACGAGTTCAAATAATTG
Found at i:1835343 original size:19 final size:18
Alignment explanation
Indices: 1835311--1835346 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1835301 GTTTTTTATA
1835311 TGAAGGGTGAGAGGGTTT
1 TGAAGGGTGAGAGGGTTT
*
1835329 TGAAGTGGTGGGAGGGTT
1 TGAAG-GGTGAGAGGGTT
1835347 GTCTCTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.19, C:0.00, G:0.53, T:0.28
Consensus pattern (18 bp):
TGAAGGGTGAGAGGGTTT
Found at i:1848201 original size:7 final size:7
Alignment explanation
Indices: 1848180--1848211 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1848170 CCGACCCGAC
1848180 CCGTTGA
1 CCGTTGA
1848187 CTCGTTGA
1 C-CGTTGA
1848195 CCGTTGA
1 CCGTTGA
1848202 CCGTTGA
1 CCGTTGA
1848209 CCG
1 CCG
1848212 GTGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.31, G:0.28, T:0.28
Consensus pattern (7 bp):
CCGTTGA
Found at i:1848911 original size:36 final size:36
Alignment explanation
Indices: 1848864--1848936 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
1848854 AGTTCTGGAA
*
1848864 TTAAGTGATAAAAGAATCAGCCATGGATATATAGAT
1 TTAAGTGATAAAAGAATCAACCATGGATATATAGAT
*
1848900 TTAAGTGATAAAAGAATCAACCATGGATATGTAGAT
1 TTAAGTGATAAAAGAATCAACCATGGATATATAGAT
1848936 T
1 T
1848937 ATAATTTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.29
Consensus pattern (36 bp):
TTAAGTGATAAAAGAATCAACCATGGATATATAGAT
Found at i:1849651 original size:29 final size:29
Alignment explanation
Indices: 1849619--1849729 Score: 93
Period size: 29 Copynumber: 3.8 Consensus size: 29
1849609 CAGTGTTGTC
*
1849619 GTAGGTCGCCAGGGCATC-CCA-GTGACATG
1 GTAGGTCGCCA-GGCA-CGCCAGGCGACATG
*
1849648 GTAGGTCGCCATGCACGCCAGGCGACATG
1 GTAGGTCGCCAGGCACGCCAGGCGACATG
* * * *
1849677 GTAGGTCGTCATGCACGCCCA-GCGACCTT
1 GTAGGTCGCCAGGCACG-CCAGGCGACATG
* * *
1849706 ATAGGTCGCCATGCACGCCCGGCG
1 GTAGGTCGCCAGGCACGCCAGGCG
1849730 TCCAATGTTC
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
27 1 0.01
28 8 0.11
29 58 0.83
30 3 0.04
ACGTcount: A:0.19, C:0.32, G:0.32, T:0.16
Consensus pattern (29 bp):
GTAGGTCGCCAGGCACGCCAGGCGACATG
Found at i:1850473 original size:30 final size:28
Alignment explanation
Indices: 1850422--1850478 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
1850412 TAATTAGTAG
*
1850422 TTTGTTAGTTTAAGTTATATTATATTAA
1 TTTGTTAGTTTAAGTTATATTAGATTAA
1850450 TTTGTTAGTTTAAGTTATATATTAGATTA
1 TTTGTTAGTTTAAG-T-TATATTAGATTA
1850479 TATAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 14 0.54
29 1 0.04
30 11 0.42
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (28 bp):
TTTGTTAGTTTAAGTTATATTAGATTAA
Found at i:1856361 original size:30 final size:28
Alignment explanation
Indices: 1856310--1856366 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
1856300 TAATTAGTAG
*
1856310 TTTGTTAGTTTAAGTTATATTATATTAA
1 TTTGTTAGTTTAAGTTATATTAGATTAA
1856338 TTTGTTAGTTTAAGTTATATATTAGATTA
1 TTTGTTAGTTTAAG-T-TATATTAGATTA
1856367 TATAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 14 0.54
29 1 0.04
30 11 0.42
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (28 bp):
TTTGTTAGTTTAAGTTATATTAGATTAA
Found at i:1857777 original size:15 final size:15
Alignment explanation
Indices: 1857754--1857787 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1857744 AAAGAAACAA
*
1857754 GAAAGGAAAAGAAAG
1 GAAAAGAAAAGAAAG
*
1857769 GAAAAGAAATGAAAG
1 GAAAAGAAAAGAAAG
1857784 GAAA
1 GAAA
1857788 TGAGCAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (15 bp):
GAAAAGAAAAGAAAG
Found at i:1857790 original size:10 final size:10
Alignment explanation
Indices: 1857741--1857787 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
1857731 TATTGATTCG
*
1857741 AAGAAAGAAA
1 AAGAAAGGAA
1857751 CAAGAAAGGAA
1 -AAGAAAGGAA
1857762 AAGAAAGGAA
1 AAGAAAGGAA
*
1857772 AAGAAATGAA
1 AAGAAAGGAA
*
1857782 AGGAAA
1 AAGAAA
1857788 TGAGCAACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
10 24 0.73
11 9 0.27
ACGTcount: A:0.70, C:0.02, G:0.26, T:0.02
Consensus pattern (10 bp):
AAGAAAGGAA
Found at i:1860567 original size:49 final size:49
Alignment explanation
Indices: 1860514--1860749 Score: 409
Period size: 49 Copynumber: 4.8 Consensus size: 49
1860504 TAACTAATAT
* *
1860514 TAATGAAATTATTATTAATTTTTAATCATTTGATAGTAATGATTAGTAA
1 TAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAA
1860563 TAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAA
1 TAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAA
* * *
1860612 TAATGAAATTATTATTATTTTTTAATGATTTAATAGTAATGATTAGTAA
1 TAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAA
*
1860661 TAATGAAATTATTACTAATATTTAATGATTTGATAGTAATGATTAGTAA
1 TAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAA
*
1860710 TAATGAAATTATTATTAATATTTAATGATTTGATAATAAT
1 TAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
1860750 AATGATTTAA
Statistics
Matches: 176, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 176 1.00
ACGTcount: A:0.42, C:0.01, G:0.11, T:0.46
Consensus pattern (49 bp):
TAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAA
Found at i:1860918 original size:12 final size:12
Alignment explanation
Indices: 1860897--1860951 Score: 69
Period size: 12 Copynumber: 4.7 Consensus size: 12
1860887 CATAAAAATG
1860897 ATTTAATAAT-A
1 ATTTAATAATAA
*
1860908 ATTTAAATAAT-G
1 ATTT-AATAATAA
1860920 ATTTAATAATAA
1 ATTTAATAATAA
*
1860932 ATTTAATAATGA
1 ATTTAATAATAA
1860944 ATTTAATA
1 ATTTAATA
1860952 TTTAATGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
11 10 0.26
12 29 0.74
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (12 bp):
ATTTAATAATAA
Found at i:1860919 original size:23 final size:24
Alignment explanation
Indices: 1860889--1860951 Score: 96
Period size: 23 Copynumber: 2.7 Consensus size: 24
1860879 CAATTAACCA
1860889 TAAA-AATGATTTAATAAT-AATT
1 TAAATAATGATTTAATAATAAATT
1860911 TAAATAATGATTTAATAATAAATT
1 TAAATAATGATTTAATAATAAATT
1860935 T-AATAATGAATTTAATA
1 TAAATAATG-ATTTAATA
1860952 TTTAATGAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
22 4 0.11
23 21 0.55
24 13 0.34
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (24 bp):
TAAATAATGATTTAATAATAAATT
Found at i:1861295 original size:12 final size:12
Alignment explanation
Indices: 1861252--1861456 Score: 109
Period size: 12 Copynumber: 16.5 Consensus size: 12
1861242 TAATGATTAG
1861252 ATAATAATCATT
1 ATAATAATCATT
* *
1861264 ATAGTAATGATTT
1 ATAATAATCA-TT
*
1861277 GATAATAATCAGT
1 -ATAATAATCATT
*
1861290 ATAATAATGATTT
1 ATAATAATCA-TT
1861303 AGTAATAATCATT
1 A-TAATAATCATT
*
1861316 ATAATAATGATT
1 ATAATAATCATT
*
1861328 -TAATAATGATT
1 ATAATAATCATT
1861339 -T-A-AAT-ATTT
1 ATAATAATCA-TT
*
1861348 AATAATTTAATGATT
1 -ATAA--TAATCATT
* *
1861363 -TAGTAATGATTT
1 ATAATAATCA-TT
1861375 GATAATAATCATT
1 -ATAATAATCATT
*
1861388 ATAATAATGATTT
1 ATAATAATCA-TT
1861401 AGTAATAATCATT
1 A-TAATAATCATT
*
1861414 ATAATAATGATTT
1 ATAATAATCA-TT
* *
1861427 AATAATAATAATG
1 -ATAATAATCATT
*
1861440 ATAATAATGATT
1 ATAATAATCATT
1861452 -TAATA
1 ATAATA
1861457 GTAATTATTT
Statistics
Matches: 155, Mismatches: 19, Indels: 39
0.73 0.09 0.18
Matches are distributed among these distances:
8 1 0.01
9 5 0.03
10 1 0.01
11 24 0.15
12 57 0.37
13 21 0.14
14 40 0.26
15 5 0.03
16 1 0.01
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.42
Consensus pattern (12 bp):
ATAATAATCATT
Found at i:1861333 original size:11 final size:11
Alignment explanation
Indices: 1861291--1861511 Score: 84
Period size: 14 Copynumber: 17.6 Consensus size: 11
1861281 ATAATCAGTA
1861291 TAATAATGATTT
1 TAATAATGA-TT
*
1861303 AGTAATAATCATT
1 --TAATAATGATT
1861316 ATAATAATGATT
1 -TAATAATGATT
1861328 TAATAATGATT
1 TAATAATGATT
* * *
1861339 TAAATATTTA-A
1 T-AATAATGATT
1861350 TAATTTAATGATT
1 TAA--TAATGATT
*
1861363 TAGTAATGATTT
1 TAATAATGA-TT
*
1861375 GATAATAATCATT
1 --TAATAATGATT
1861388 ATAATAATGATTT
1 -TAATAATGA-TT
*
1861401 AGTAATAATCATT
1 --TAATAATGATT
1861414 ATAATAATGATT
1 -TAATAATGATT
*
1861426 TAATAATAATAAT
1 TAATAATGAT--T
1861439 GATAATAATGATT
1 --TAATAATGATT
*
1861452 TAATAGTAATTATT
1 T-A-A-TAATGATT
* *
1861466 TAGTAATTATTTT
1 TAATAATGA--TT
1861479 ATAATAATGATT
1 -TAATAATGATT
1861491 TAATACTAATGATT
1 T-A-A-TAATGATT
1861505 TAATAAT
1 TAATAAT
1861512 TATTACTAAT
Statistics
Matches: 162, Mismatches: 23, Indels: 47
0.70 0.10 0.20
Matches are distributed among these distances:
10 2 0.01
11 40 0.25
12 46 0.28
13 18 0.11
14 47 0.29
15 9 0.06
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.45
Consensus pattern (11 bp):
TAATAATGATT
Found at i:1861452 original size:26 final size:26
Alignment explanation
Indices: 1861242--1861511 Score: 263
Period size: 26 Copynumber: 10.6 Consensus size: 26
1861232 GATGATTTAG
*
1861242 TAATGA-TTAGATAATAATCATTATAG
1 TAATGATTTA-ATAATAATCATTATAA
* *
1861268 TAATGATTTGATAATAATCAGTATAA
1 TAATGATTTAATAATAATCATTATAA
*
1861294 TAATGATTTAGTAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
*
1861320 TAATGA-TT--TAATAATGATT-T-A
1 TAATGATTTAATAATAATCATTATAA
* *
1861341 -AAT-ATTTAATAATTTAATGATT-TAG
1 TAATGATTTAATAA--TAATCATTATAA
*
1861366 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
*
1861392 TAATGATTTAGTAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
* *
1861418 TAATGATTTAATAATAATAATGATAA
1 TAATGATTTAATAATAATCATTATAA
* * *
1861444 TAATGATTTAATAGTAATTATT-TAG
1 TAATGATTTAATAATAATCATTATAA
* * * *
1861469 TAATTATTTTATAATAATGATTTAATAC
1 TAATGATTTAATAATAATCA-TT-ATAA
1861497 TAATGATTTAATAAT
1 TAATGATTTAATAAT
1861512 TATTACTAAT
Statistics
Matches: 204, Mismatches: 27, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.00
20 5 0.02
21 1 0.00
22 4 0.02
23 10 0.05
24 9 0.04
25 27 0.13
26 122 0.60
27 10 0.05
28 15 0.07
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.44
Consensus pattern (26 bp):
TAATGATTTAATAATAATCATTATAA
Found at i:1861453 original size:124 final size:124
Alignment explanation
Indices: 1861228--1861456 Score: 379
Period size: 124 Copynumber: 1.8 Consensus size: 124
1861218 ATTATGATAG
* *
1861228 ATTTGATGATTTAGTAATGATTAGATAATAATCATTATAGTAATGATTTGATAATAATCAGTATA
1 ATTTAATGATTTAGTAATGATTAGATAATAATCATTATAATAATGATTTGATAATAATCAGTATA
* * *
1861293 ATAATGATTTAGTAATAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATA
66 ATAATGATTTAATAATAATAATGATAATAATGATTTAATAATGATTTAAATATTTAATA
* *
1861352 ATTTAATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATTT-AGTAATAATCATTAT
1 ATTTAATGATTTAGTAATGATTAGATAATAATCATTATAATAATGATTTGA-TAATAATCAGTAT
1861416 AATAATGATTTAATAATAATAATGATAATAATGATTTAATA
65 AATAATGATTTAATAATAATAATGATAATAATGATTTAATA
1861457 GTAATTATTT
Statistics
Matches: 97, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
123 1 0.01
124 96 0.99
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (124 bp):
ATTTAATGATTTAGTAATGATTAGATAATAATCATTATAATAATGATTTGATAATAATCAGTATA
ATAATGATTTAATAATAATAATGATAATAATGATTTAATAATGATTTAAATATTTAATA
Found at i:1861676 original size:24 final size:24
Alignment explanation
Indices: 1861628--1861672 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1861618 GATTTGATAC
*
1861628 TAATGATTTACTAATTATTATTAA
1 TAATGATTTACTAATTAATATTAA
*
1861652 TAATGATTTA-TTATTAATATT
1 TAATGATTTACTAATTAATATT
1861673 TAATTATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (24 bp):
TAATGATTTACTAATTAATATTAA
Found at i:1861679 original size:17 final size:17
Alignment explanation
Indices: 1861639--1861680 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1861629 AATGATTTAC
1861639 TAATTATTATTAATAAT
1 TAATTATTATTAATAAT
* * *
1861656 GATTTATTATTAATATT
1 TAATTATTATTAATAAT
1861673 TAATTATT
1 TAATTATT
1861681 TGATACTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TAATTATTATTAATAAT
Found at i:1861759 original size:22 final size:23
Alignment explanation
Indices: 1861706--1861759 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
1861696 AAAATATTAT
1861706 TTAATATATATTTTTAAATAAAAA
1 TTAATA-ATATTTTTAAATAAAAA
* * *
1861730 ATAA-AATATTTTTAAAT-TAAG
1 TTAATAATATTTTTAAATAAAAA
1861751 TTAATAATA
1 TTAATAATA
1861760 AAATATATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 5 0.20
22 16 0.64
23 1 0.04
24 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TTAATAATATTTTTAAATAAAAA
Found at i:1864040 original size:15 final size:16
Alignment explanation
Indices: 1864020--1864053 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
1864010 CAAAAAAATT
1864020 TAATATAAT-AACTTA
1 TAATATAATAAACTTA
1864035 TAATATAATAAACTTA
1 TAATATAATAAACTTA
1864051 TAA
1 TAA
1864054 AGTAACAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATATAATAAACTTA
Found at i:1864140 original size:30 final size:30
Alignment explanation
Indices: 1864106--1864211 Score: 142
Period size: 30 Copynumber: 3.5 Consensus size: 30
1864096 TTTCTTTAAA
1864106 CAACTAATAAACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
1864136 CAACTAATAAACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
* * *
1864166 AAACTAATAAACGATTTTTTAATTATAA-TT
1 CAACTAATAAACTATTCTTTAA-TATAACTT
*
1864196 CACTACTAAAAAACTA
1 CA--ACTAATAAACTA
1864212 ATTAACTAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
30 52 0.78
31 5 0.07
32 10 0.15
ACGTcount: A:0.46, C:0.15, G:0.01, T:0.38
Consensus pattern (30 bp):
CAACTAATAAACTATTCTTTAATATAACTT
Found at i:1864158 original size:15 final size:16
Alignment explanation
Indices: 1864110--1864164 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
1864100 TTTAAACAAC
1864110 TAATA-AACTATTCTT
1 TAATATAACTATTCTT
**
1864125 TAATATAAC--TTCAAC
1 TAATATAACTATTC-TT
1864140 TAATA-AACTATTCTT
1 TAATATAACTATTCTT
1864155 TAATATAACT
1 TAATATAACT
1864165 TAAACTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 6 0.19
15 15 0.48
16 10 0.32
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATATAACTATTCTT
Found at i:1864704 original size:22 final size:22
Alignment explanation
Indices: 1864676--1864724 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1864666 ATGGAGCAAC
*
1864676 GGGAGCAGGCGAGCATGCAGTG
1 GGGAGCAGGCGAGCATGCAGCG
1864698 GGGAGCAGGCGAGCATGCAGCG
1 GGGAGCAGGCGAGCATGCAGCG
1864720 GGGAG
1 GGGAG
1864725 TATGGCCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.22, C:0.18, G:0.53, T:0.06
Consensus pattern (22 bp):
GGGAGCAGGCGAGCATGCAGCG
Found at i:1864772 original size:29 final size:29
Alignment explanation
Indices: 1864751--1864822 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
1864741 GTCGCGGGGC
*
1864751 GTGCATGGCGACCTCCTTGGTCGCCCAGA
1 GTGCATGGCAACCTCCTTGGTCGCCCAGA
1864780 GTGCATGGCAACCTCCTTGGTCGCCC-GAA
1 GTGCATGGCAACCTCCTTGGTCGCCCAG-A
* *
1864809 GGGCATGGCGACCT
1 GTGCATGGCAACCT
1864823 ATGTTTTGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
28 1 0.03
29 38 0.97
ACGTcount: A:0.15, C:0.33, G:0.32, T:0.19
Consensus pattern (29 bp):
GTGCATGGCAACCTCCTTGGTCGCCCAGA
Found at i:1864865 original size:15 final size:15
Alignment explanation
Indices: 1864845--1864875 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1864835 GTGCATGTCC
1864845 CATGCGACGTTAATT
1 CATGCGACGTTAATT
1864860 CATGCGACGTTAATT
1 CATGCGACGTTAATT
1864875 C
1 C
1864876 GATCTTTGAT
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:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (15 bp):
CATGCGACGTTAATT
Found at i:1865848 original size:27 final size:27
Alignment explanation
Indices: 1865813--1865876 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
1865803 AATACCATTG
1865813 GAAGATCTATTCAGCGATGATTCTGAA
1 GAAGATCTATTCAGCGATGATTCTGAA
1865840 GAAGATCTATTCAGCGATGATTCTGAA
1 GAAGATCTATTCAGCGATGATTCTGAA
*
1865867 GATGATCTAT
1 GAAGATCTAT
1865877 GGACAAGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (27 bp):
GAAGATCTATTCAGCGATGATTCTGAA
Found at i:1866316 original size:12 final size:12
Alignment explanation
Indices: 1866296--1866365 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
1866286 GATACATGAC
*
1866296 CTGAATTCTGTT
1 CTGATTTCTGTT
*
1866308 CTGATTTCTGAT
1 CTGATTTCTGTT
1866320 CTGGA-TTCTGTT
1 CT-GATTTCTGTT
*
1866332 CTGATATCTGTT
1 CTGATTTCTGTT
* *
1866344 ATGAATTCTGTT
1 CTGATTTCTGTT
*
1866356 TTGATTTCTG
1 CTGATTTCTG
1866366 ATATCTCCAT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 43 0.91
13 2 0.04
ACGTcount: A:0.16, C:0.14, G:0.19, T:0.51
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:1866327 original size:24 final size:24
Alignment explanation
Indices: 1866297--1866369 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
1866287 ATACATGACC
*
1866297 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATTTCTGATA
* * *
1866321 TGGATTCTGTTCTGATATCTGTTA
1 TGAATTCTGTTCTGATTTCTGATA
*
1866345 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
1866369 T
1 T
1866370 CTCCATTTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATA
Found at i:1866330 original size:48 final size:49
Alignment explanation
Indices: 1866259--1866367 Score: 125
Period size: 48 Copynumber: 2.3 Consensus size: 49
1866249 AAATATTTTA
* *
1866259 TCTGATTTCCGA-CTTGAATTCTGTTATGATA-CATGACCTGAATTCTGT
1 TCTGATTTCTGATCTTGAATTCTGTTATGATATC-TGACATGAATTCTGT
* * **
1866307 TCTGATTTCTGATC-TGGATTCTGTTCTGATATCTGTTATGAATTCTGT
1 TCTGATTTCTGATCTTGAATTCTGTTATGATATCTGACATGAATTCTGT
*
1866355 TTTGATTTCTGAT
1 TCTGATTTCTGAT
1866368 ATCTCCATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
48 50 0.96
49 2 0.04
ACGTcount: A:0.19, C:0.16, G:0.17, T:0.48
Consensus pattern (49 bp):
TCTGATTTCTGATCTTGAATTCTGTTATGATATCTGACATGAATTCTGT
Found at i:1872000 original size:23 final size:23
Alignment explanation
Indices: 1871974--1872061 Score: 108
Period size: 23 Copynumber: 3.8 Consensus size: 23
1871964 AGCTCATATA
1871974 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1871997 AATTTGTC-CCGAAG-GACCGCGTAG
1 AA-TTG-CACCGAAGTG-CCACGTAG
*
1872021 AAATGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1872044 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1872062 TATAAGATTG
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
22 1 0.02
23 34 0.62
24 19 0.35
25 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.18
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1876225 original size:2 final size:2
Alignment explanation
Indices: 1876218--1876248 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1876208 TTATAAATGT
1876218 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1876249 ATTTCCATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1879941 original size:3 final size:3
Alignment explanation
Indices: 1879926--1879979 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
1879916 ATTTGGAATT
* * *
1879926 ATA ATA AT- TTA ATA ATA ATA ATA ATA AGTA ATA CTA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA
1879971 ATA ATA ATA
1 ATA ATA ATA
1879980 TATTAATATG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
2 1 0.02
3 39 0.91
4 3 0.07
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1881445 original size:13 final size:13
Alignment explanation
Indices: 1881427--1881451 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1881417 TTTGATATTA
1881427 TTTTACATAAAAT
1 TTTTACATAAAAT
1881440 TTTTACATAAAA
1 TTTTACATAAAA
1881452 AAAAATCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTTACATAAAAT
Found at i:1881797 original size:87 final size:87
Alignment explanation
Indices: 1881696--1881866 Score: 270
Period size: 87 Copynumber: 2.0 Consensus size: 87
1881686 AATAGTATTA
* * ** *
1881696 AGTTTTTATATCGTGTCATATGGCACAATTATTTTTAAGTTATATATATTTGGTTTTCTTATGTT
1 AGTTTTTATATCGTGTCACATGGCACAATTATATTTAAGTTATATATATTTGGAGTTCTTACGTT
1881761 ATGATAATGTCTAACCTACGTT
66 ATGATAATGTCTAACCTACGTT
* *
1881783 AGTTTTTATGTCGTGTCACATGTCACAATTATATTTAAGTTATATATATTTGGAGTTCTTACGTT
1 AGTTTTTATATCGTGTCACATGGCACAATTATATTTAAGTTATATATATTTGGAGTTCTTACGTT
*
1881848 ATGATAATGTCTAATCTAC
66 ATGATAATGTCTAACCTAC
1881867 ATTATATATA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 76 1.00
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.47
Consensus pattern (87 bp):
AGTTTTTATATCGTGTCACATGGCACAATTATATTTAAGTTATATATATTTGGAGTTCTTACGTT
ATGATAATGTCTAACCTACGTT
Found at i:1882047 original size:215 final size:215
Alignment explanation
Indices: 1881795--1882320 Score: 713
Period size: 219 Copynumber: 2.4 Consensus size: 215
1881785 TTTTTATGTC
* * * *
1881795 GTGTCACATGTCACAATTATATTTAAGTTATATATATTTGGAGTTCTTACGTTATGATAATGTCT
1 GTGTCATATGTCACAATTATGTTTAAGTTATATATATTTGGTGTTCTTATGTTATGATAATGTCT
* *
1881860 AATCTACATTATATATATAT-T-T-GA-T-TAGAGTTATATATTATATTTGAATAATCTTGTCTA
66 AAGCTATATTATATATATATATATAGATTATAGAGTTATATATTA-ATTTGAATAATCTTGTC--
* * * * *
1881920 TTGATGTCACTGAAAATCATTAATATATATTTTACTTGTTGAATTAATTTTAAACTAA-TTTAGT
128 -T-ATGTCACTAAAAACCATTAATATATATTTTACTCGTCG-ATTAATTTTAAACTAATTTTAAT
*
1881984 TTCCAGTAATATTAAATTTTTATACT
190 TTACAGTAATATTAAATTTTTATACT
* *
1882010 GTGTCATATGTCACGATTATGTTTAAGTTATATATATTTGGTGTTCTTATGTTATGATTATGTCT
1 GTGTCATATGTCACAATTATGTTTAAGTTATATATATTTGGTGTTCTTATGTTATGATAATGTCT
*
1882075 AAGCTTATTATATATATATATATATATATATTAATAGAGTTATATATTAATTTGAATAATCTTGT
66 AAGC-TA-TAT-TATATATATATATATAGATT-ATAGAGTTATATATTAATTTGAATAATCTTGT
1882140 CTATGTCACTAAAAACCATTAATATATATTTTACTCGTCGATTAATTTTAAACTAATTTTAATTT
127 CTATGTCACTAAAAACCATTAATATATATTTTACTCGTCGATTAATTTTAAACTAATTTTAATTT
* *
1882205 ATAGTAATATTAAATTTTTATATT
192 ACAGTAATATTAAATTTTTATACT
* * *
1882229 GTGCCATATGTTACTATTATGTTTAAGTTATATATATATTTGGTGTTCTTATGTTATGATAATGT
1 GTGTCATATGTCACAATTATGTTTAAG-T-TATATATATTTGGTGTTCTTATGTTATGATAATGT
*
1882294 CTAAGCAATATTATATATATATATATA
64 CTAAGCTATATTATATATATATATATA
1882321 TTGAATAATT
Statistics
Matches: 277, Mismatches: 22, Indels: 21
0.87 0.07 0.07
Matches are distributed among these distances:
215 62 0.22
216 2 0.01
217 2 0.01
218 43 0.16
219 90 0.32
220 4 0.01
221 41 0.15
222 1 0.00
223 17 0.06
224 15 0.05
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.48
Consensus pattern (215 bp):
GTGTCATATGTCACAATTATGTTTAAGTTATATATATTTGGTGTTCTTATGTTATGATAATGTCT
AAGCTATATTATATATATATATATAGATTATAGAGTTATATATTAATTTGAATAATCTTGTCTAT
GTCACTAAAAACCATTAATATATATTTTACTCGTCGATTAATTTTAAACTAATTTTAATTTACAG
TAATATTAAATTTTTATACT
Found at i:1888289 original size:10 final size:11
Alignment explanation
Indices: 1888274--1888312 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1888264 CGATTGCATC
1888274 ATTTGTTT-TG
1 ATTTGTTTATG
1888284 ATTTGTTTATG
1 ATTTGTTTATG
* *
1888295 TTTTTTTTATG
1 ATTTGTTTATG
1888306 ATTTGTT
1 ATTTGTT
1888313 CAGGTTTGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.13, C:0.00, G:0.15, T:0.72
Consensus pattern (11 bp):
ATTTGTTTATG
Found at i:1908960 original size:356 final size:356
Alignment explanation
Indices: 1908307--1909020 Score: 1383
Period size: 356 Copynumber: 2.0 Consensus size: 356
1908297 AACACTTTTT
1908307 GCTTAAAACAAAATACAATTACAAACTACACACTTACCCCACTATTTTTCTATTCTCCATCTCTA
1 GCTTAAAACAAAATACAATTACAAACTACACACTTACCCCACTATTTTTCTATTCTCCATCTCTA
*
1908372 AGCTCTCTTTCTTTAACTCACACTCTTGACACTCTTTTCTCCTTTTTCATTCTTATTACAATAGT
66 AGCTCTCTTTCTTTAACTCACACTCTTGACACTCTTTTCCCCTTTTTCATTCTTATTACAATAGT
1908437 AAAACCTACCTTTATTTATAGATTTTAGTGGTCATTGGATTGTTGACACATGTCAATATCTTAAC
131 AAAACCTACCTTTATTTATAGATTTTAGTGGTCATTGGATTGTTGACACATGTCAATATCTTAAC
* *
1908502 CATTTAATATTACAAATATCTAGATCATTCTAATAGATAATTCTAGATATAACATTAAATATTAT
196 CATTTAATATTACAAATATCTAGATCATTCTAATAGATAATTCTAGATATAACATTAAATACTAC
1908567 AAATATTTAAATTATTTTATGAATACTTCTACACATCTATTATTTTCATATTATTCTAGATTATT
261 AAATATTTAAATTATTTTATGAATACTTCTACACATCTATTATTTTCATATTATTCTAGATTATT
1908632 CTTAATAAATACCCTTGATTTAAAAATAAAA
326 CTTAATAAATACCCTTGATTTAAAAATAAAA
1908663 GCTTAAAACAAAATACAATTACAAACTACACACTTACCCCACTATTTTTCTATTCTCCATCTCTA
1 GCTTAAAACAAAATACAATTACAAACTACACACTTACCCCACTATTTTTCTATTCTCCATCTCTA
*
1908728 AGCTCTCTTTCTTTAACTCACACTCTTGACACTCTTTTCCCCTTTTTCATTCTTATTACAATGGT
66 AGCTCTCTTTCTTTAACTCACACTCTTGACACTCTTTTCCCCTTTTTCATTCTTATTACAATAGT
*
1908793 AAAACCTACCTTTATTTATAGATTTTAGTGGTCATTGGATTGTTGACACATGTCAATATCTTGAC
131 AAAACCTACCTTTATTTATAGATTTTAGTGGTCATTGGATTGTTGACACATGTCAATATCTTAAC
1908858 CATTTAATATTACAAATATCTAGATCATTCTAATAGATAATTCTAGATATAACATTAAATACTAC
196 CATTTAATATTACAAATATCTAGATCATTCTAATAGATAATTCTAGATATAACATTAAATACTAC
1908923 AAATATTTAAATTATTTTATGAATACTTCTACACATCTATTATTTTCATATTATTCTAGATTATT
261 AAATATTTAAATTATTTTATGAATACTTCTACACATCTATTATTTTCATATTATTCTAGATTATT
1908988 CTTAATAAATACCCTTGATTTAAAAATAAAA
326 CTTAATAAATACCCTTGATTTAAAAATAAAA
1909019 GC
1 GC
1909021 AATCCACTTA
Statistics
Matches: 353, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
356 353 1.00
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.41
Consensus pattern (356 bp):
GCTTAAAACAAAATACAATTACAAACTACACACTTACCCCACTATTTTTCTATTCTCCATCTCTA
AGCTCTCTTTCTTTAACTCACACTCTTGACACTCTTTTCCCCTTTTTCATTCTTATTACAATAGT
AAAACCTACCTTTATTTATAGATTTTAGTGGTCATTGGATTGTTGACACATGTCAATATCTTAAC
CATTTAATATTACAAATATCTAGATCATTCTAATAGATAATTCTAGATATAACATTAAATACTAC
AAATATTTAAATTATTTTATGAATACTTCTACACATCTATTATTTTCATATTATTCTAGATTATT
CTTAATAAATACCCTTGATTTAAAAATAAAA
Found at i:1909058 original size:3 final size:3
Alignment explanation
Indices: 1909045--1909107 Score: 81
Period size: 3 Copynumber: 20.7 Consensus size: 3
1909035 TCATATCTCT
* *
1909045 AGG AGG AAGG AGG AGG AGG AGG AGG ATG AGG AGG AGG AGA AGG AGG
1 AGG AGG -AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
* *
1909091 AGA AGG AGG AGA AGG AG
1 AGG AGG AGG AGG AGG AG
1909108 AAAAAGAATG
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 48 0.94
4 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.59, T:0.02
Consensus pattern (3 bp):
AGG
Found at i:1909107 original size:18 final size:18
Alignment explanation
Indices: 1909076--1909209 Score: 156
Period size: 18 Copynumber: 7.8 Consensus size: 18
1909066 GAGGATGAGG
* *
1909076 AGGAGGAGAAGGAGGAGA
1 AGGAGAAGAAGAAGGAGA
1909094 AGGAG--G-AGAAGGAGA
1 AGGAGAAGAAGAAGGAGA
**
1909109 AAAAGAATG-AGAAGGAGA
1 AGGAGAA-GAAGAAGGAGA
1909127 AGGAGAAGAAGAAGGAGA
1 AGGAGAAGAAGAAGGAGA
*
1909145 ATGAGAAGAAGAAGGAGA
1 AGGAGAAGAAGAAGGAGA
1909163 AGGAGAAGAAG-A--AGA
1 AGGAGAAGAAGAAGGAGA
*
1909178 AGAAGAAGAAGAAGGAGA
1 AGGAGAAGAAGAAGGAGA
1909196 AGGAGAAGAAGAAG
1 AGGAGAAGAAGAAG
1909210 AAGGAGAAGG
Statistics
Matches: 100, Mismatches: 9, Indels: 14
0.81 0.07 0.11
Matches are distributed among these distances:
15 24 0.24
16 2 0.02
17 2 0.02
18 72 0.72
ACGTcount: A:0.55, C:0.00, G:0.43, T:0.01
Consensus pattern (18 bp):
AGGAGAAGAAGAAGGAGA
Found at i:1909108 original size:6 final size:6
Alignment explanation
Indices: 1909045--1909220 Score: 136
Period size: 6 Copynumber: 27.7 Consensus size: 6
1909035 TCATATCTCT
* * * * * *
1909045 AGGAGGA AGGAGG AGGAGG AGGAGGA TGAGGAGG AGGAGA AGGAGG AGAAGG
1 AGGA-GA AGGAGA AGGAGA AGGA-GA --AGGAGA AGGAGA AGGAGA AGGAGA
** * *
1909097 AGGAGA AGGAGA AAAAGA ATGAGA AGGAGA AGGAGA AGAAGA AGGAGA
1 AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA
* * * *
1909145 ATGAGA AGAAGA AGGAGA AGGAGA AGAAGAAGA AGAAGA AGAAGA AGGAGA
1 AGGAGA AGGAGA AGGAGA AGGAGA AG--G-AGA AGGAGA AGGAGA AGGAGA
1909196 AGGAGA AGAAGAAGA AGGAGA AGGA
1 AGGAGA AG--G-AGA AGGAGA AGGA
1909221 CCATCCGTAT
Statistics
Matches: 139, Mismatches: 21, Indels: 19
0.78 0.12 0.11
Matches are distributed among these distances:
6 116 0.83
7 6 0.04
8 3 0.02
9 14 0.10
ACGTcount: A:0.52, C:0.00, G:0.47, T:0.02
Consensus pattern (6 bp):
AGGAGA
Found at i:1909384 original size:9 final size:9
Alignment explanation
Indices: 1909374--1909471 Score: 76
Period size: 9 Copynumber: 11.2 Consensus size: 9
1909364 CTTGTTGAGG
*
1909374 AGGAGGAGG
1 AGGAGGAGA
1909383 AGGAGGAGA
1 AGGAGGAGA
*
1909392 ATGAGGAGA
1 AGGAGGAGA
* *
1909401 AGGAGAAAA
1 AGGAGGAGA
*
1909410 AGAAGGAG-
1 AGGAGGAGA
1909418 A--AGGAGA
1 AGGAGGAGA
*
1909425 AGGAGAAGA
1 AGGAGGAGA
*
1909434 AGAAGGAGA
1 AGGAGGAGA
* *
1909443 ATGAGAAGA
1 AGGAGGAGA
*
1909452 AGAAGGAGA
1 AGGAGGAGA
*
1909461 AGGAGAAGA
1 AGGAGGAGA
1909470 AG
1 AG
1909472 AAGAAGAAGA
Statistics
Matches: 67, Mismatches: 19, Indels: 6
0.73 0.21 0.07
Matches are distributed among these distances:
6 5 0.07
7 1 0.01
8 1 0.01
9 60 0.90
ACGTcount: A:0.52, C:0.00, G:0.46, T:0.02
Consensus pattern (9 bp):
AGGAGGAGA
Found at i:1909406 original size:6 final size:6
Alignment explanation
Indices: 1909395--1909492 Score: 115
Period size: 6 Copynumber: 16.3 Consensus size: 6
1909385 GAGGAGAATG
** *
1909395 AGGAGA AGGAGA AAAAGA AGGAGA AGGAGA AGGAGA AGAAGA AGGAGA
1 AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA
* * * * * *
1909443 ATGAGA AGAAGA AGGAGA AGGAGA AGAAGA AGAAGA AGAAGA AGAAGA
1 AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA
1909491 AG
1 AG
1909493 AAGGACCATC
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 81 1.00
ACGTcount: A:0.58, C:0.00, G:0.41, T:0.01
Consensus pattern (6 bp):
AGGAGA
Found at i:1909495 original size:18 final size:18
Alignment explanation
Indices: 1909398--1909492 Score: 129
Period size: 18 Copynumber: 5.3 Consensus size: 18
1909388 GAGAATGAGG
* *
1909398 AGAAGGAGAAAAAGAAGG
1 AGAAGGAGAAGAAGAAGA
*
1909416 AGAAGGAGAAGGAGAAGA
1 AGAAGGAGAAGAAGAAGA
1909434 AGAAGGAGAATG-AGAAGA
1 AGAAGGAGAA-GAAGAAGA
*
1909452 AGAAGGAGAAGGAGAAGA
1 AGAAGGAGAAGAAGAAGA
*
1909470 AGAAGAAGAAGAAGAAGA
1 AGAAGGAGAAGAAGAAGA
1909488 AGAAG
1 AGAAG
1909493 AAGGACCATC
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
17 1 0.01
18 68 0.97
19 1 0.01
ACGTcount: A:0.59, C:0.00, G:0.40, T:0.01
Consensus pattern (18 bp):
AGAAGGAGAAGAAGAAGA
Found at i:1909588 original size:277 final size:279
Alignment explanation
Indices: 1909117--1909647 Score: 940
Period size: 277 Copynumber: 1.9 Consensus size: 279
1909107 GAAAAAGAAT
** *
1909117 GAGAAGGAGAAGGAGAAGAAGAAGGAGAATGAGAAGAAGAAGGAGAAGGAGAAGAAGAAGAAGAA
1 GAGAAGGAGAAAAAGAAGAAGAAGGAGAAGGAGAAGAAGAAGGAGAAGGAGAAGAAGAAG-AGAA
* * *
1909182 GAAGAAGAAGGAGAAGGAGAAGAAGAAGAAGGAGAAGGACCATCCGTATAGTTCACCATTGATTT
65 GAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGGACCATCCGTATAGTTCACCATTGATTT
*
1909247 AAAAATAAAAGCAATCCACTTGCCCATCATATCCTTAGAAAGAATAATTAAGCTCAAATCAATCC
130 AAAAATAAAAGCAATCCACTTGCCCATCATATCCCTAGAAAGAATAATTAAGCTCAAATCAATCC
1909312 CTTTTTGTTCTTGCTCGATCTCAGACATGGAAGATGAATTTGTAGGGACAACCTTGTTGAGGAGG
195 CTTTTTGTTCTTGCTCGATCTCAGACATGGAAGATGAATTTGTAGGGACAACCTTGTTGAGGAGG
1909377 AGGAGGAGGAGGAGAATGAG
260 AGGAGGAGGAGGAGAATGAG
* *
1909397 GAGAAGGAGAAAAAGAAGGAGAAGGAGAAGGAGAAGAAGAAGGAGAATGAGAAGAAGAAG-G-AG
1 GAGAAGGAGAAAAAGAAGAAGAAGGAGAAGGAGAAGAAGAAGGAGAAGGAGAAGAAGAAGAGAAG
*
1909460 AAGGAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGGACCATCCGTATAGTTCACCATTGATTTA
66 AAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGGACCATCCGTATAGTTCACCATTGATTTA
*
1909525 AAAATAAAATCAATCCACTTGCCCATCATATCCCTAGAAAGAATAATTAAGCTCAAATCAATCCC
131 AAAATAAAAGCAATCCACTTGCCCATCATATCCCTAGAAAGAATAATTAAGCTCAAATCAATCCC
1909590 TTTTTGTTCTTGCTCGATCTCAGACATGGAAGATGAATTTGTAGGGACAACCTTGTTG
196 TTTTTGTTCTTGCTCGATCTCAGACATGGAAGATGAATTTGTAGGGACAACCTTGTTG
1909648 TACGTTCTTC
Statistics
Matches: 240, Mismatches: 11, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
277 184 0.77
278 1 0.00
280 55 0.23
ACGTcount: A:0.43, C:0.12, G:0.27, T:0.18
Consensus pattern (279 bp):
GAGAAGGAGAAAAAGAAGAAGAAGGAGAAGGAGAAGAAGAAGGAGAAGGAGAAGAAGAAGAGAAG
AAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGGACCATCCGTATAGTTCACCATTGATTTA
AAAATAAAAGCAATCCACTTGCCCATCATATCCCTAGAAAGAATAATTAAGCTCAAATCAATCCC
TTTTTGTTCTTGCTCGATCTCAGACATGGAAGATGAATTTGTAGGGACAACCTTGTTGAGGAGGA
GGAGGAGGAGGAGAATGAG
Found at i:1912104 original size:13 final size:13
Alignment explanation
Indices: 1912088--1912114 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1912078 TATACAACTT
1912088 TTTCTGAAAGTAA
1 TTTCTGAAAGTAA
1912101 TTTCTGAAAGTAA
1 TTTCTGAAAGTAA
1912114 T
1 T
1912115 CACCTCTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (13 bp):
TTTCTGAAAGTAA
Found at i:1916213 original size:37 final size:37
Alignment explanation
Indices: 1916168--1916260 Score: 141
Period size: 37 Copynumber: 2.5 Consensus size: 37
1916158 TTTTATTAAG
* * *
1916168 ATTCAAACTCTTAAAAATATGATAGAGTTTTACTAGA
1 ATTCAAACTCCTAAAAATAGGATAGAGTTCTACTAGA
* *
1916205 ATTTAAACTCCTAAAAATAGGATAGAGTTCTACTATA
1 ATTCAAACTCCTAAAAATAGGATAGAGTTCTACTAGA
1916242 ATTCAAACTCCTAAAAATA
1 ATTCAAACTCCTAAAAATA
1916261 AGATCCACAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (37 bp):
ATTCAAACTCCTAAAAATAGGATAGAGTTCTACTAGA
Found at i:1916781 original size:23 final size:21
Alignment explanation
Indices: 1916724--1916781 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 21
1916714 TTTTCATGTA
1916724 ATATTTTTTTTTACATTTTAT
1 ATATTTTTTTTTACATTTTAT
*
1916745 ACATTTTCTTTTTTAC-TTTAGTAT
1 ATA-TTT-TTTTTTACATTT--TAT
1916769 ATATTTTTATTTT
1 ATATTTTT-TTTT
1916782 TTTAGATTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
21 2 0.07
22 8 0.27
23 15 0.50
24 5 0.17
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.69
Consensus pattern (21 bp):
ATATTTTTTTTTACATTTTAT
Found at i:1916797 original size:2 final size:2
Alignment explanation
Indices: 1916792--1916829 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1916782 TTTAGATTAC
1916792 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
1916830 GTATGTTACT
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:1916891 original size:37 final size:38
Alignment explanation
Indices: 1916852--1916956 Score: 112
Period size: 38 Copynumber: 2.9 Consensus size: 38
1916842 TTATTATCTG
*
1916852 TTTTATTAATT-TTTATATATATATACTATTTTTTATGT
1 TTTTATTAATTATATATATATATATA-TATTTTTTATGT
* * *
1916890 TTTTATTTATTATATATATATATATATATTTTTTTTAT
1 TTTTATTAATTATATATATATATATATATTTTTTATGT
* *
1916928 TTTT-TTTATTAT-T-TAT-TATTTATATTTTT
1 TTTTATTAATTATATATATATATATATATTTTT
1916957 CTTCTTCTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
34 12 0.20
35 3 0.05
36 1 0.02
37 8 0.13
38 24 0.39
39 13 0.21
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.70
Consensus pattern (38 bp):
TTTTATTAATTATATATATATATATATATTTTTTATGT
Found at i:1916930 original size:9 final size:9
Alignment explanation
Indices: 1916916--1917003 Score: 56
Period size: 9 Copynumber: 9.7 Consensus size: 9
1916906 TATATATATA
1916916 TATTTTTTT
1 TATTTTTTT
1916925 TATTTTTTT
1 TATTTTTTT
*
1916934 TATTATTTAT
1 TATT-TTTTT
*
1916944 TATTTATATT
1 TATTT-TTTT
* *
1916954 T-TTCTTCT
1 TATTTTTTT
*
1916962 TCTTTTTCTT
1 TATTTTT-TT
1916972 TATTTTTCTT
1 TATTTTT-TT
*
1916982 TA-TTTATT
1 TATTTTTTT
*
1916990 TA-TTTATT
1 TATTTTTTT
1916998 TATTTT
1 TATTTT
1917004 ACTTACTATT
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
8 15 0.23
9 26 0.41
10 23 0.36
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (9 bp):
TATTTTTTT
Found at i:1916933 original size:12 final size:12
Alignment explanation
Indices: 1916918--1917003 Score: 50
Period size: 12 Copynumber: 7.1 Consensus size: 12
1916908 TATATATATA
1916918 TTTTTTTTATTT
1 TTTTTTTTATTT
*
1916930 TTTTTATTA-TT
1 TTTTTTTTATTT
* *
1916941 TATTATTTATATT
1 TTTTTTTTAT-TT
* * *
1916954 TTTCTTCT-TCT
1 TTTTTTTTATTT
*
1916965 TTTTCTTTATTT
1 TTTTTTTTATTT
1916977 TTCTTTATTTATTT
1 TT-TTT-TTTATTT
* *
1916991 ATTTATTTATTT
1 TTTTTTTTATTT
1917003 T
1 T
1917004 ACTTACTATT
Statistics
Matches: 52, Mismatches: 17, Indels: 10
0.66 0.22 0.13
Matches are distributed among these distances:
11 14 0.27
12 20 0.38
13 10 0.19
14 8 0.15
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTTTTATTT
Found at i:1916968 original size:34 final size:37
Alignment explanation
Indices: 1916865--1916968 Score: 99
Period size: 34 Copynumber: 2.8 Consensus size: 37
1916855 TATTAATTTT
* *
1916865 TATATATATATACTATTTTT-TATGTTTTTATTTATTATA
1 TATATATATATA-TATTTTTCT-TATTCTT-TTTATTATA
* *
1916904 TATATATATATATATTTTTTTTATTTTTTTTATTAT-
1 TATATATATATATATTTTTCTTATTCTTTTTATTATA
* *
1916940 T-TAT-TATTTATATTTTTCTTCTTCTTTTT
1 TATATATATATATATTTTTCTTATTCTTTTT
1916969 CTTTATTTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
34 21 0.36
35 3 0.05
36 1 0.02
37 8 0.14
38 13 0.22
39 13 0.22
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.70
Consensus pattern (37 bp):
TATATATATATATATTTTTCTTATTCTTTTTATTATA
Found at i:1916974 original size:38 final size:36
Alignment explanation
Indices: 1916863--1917003 Score: 108
Period size: 38 Copynumber: 3.8 Consensus size: 36
1916853 TTTATTAATT
* * *
1916863 TTTATATATATATACTATTTTTTATGTTTTTATTTATTA
1 TTTAT-TATTTATA-TATTTTTTTTATTTTT-TTTATTA
* *
1916902 TATATATATATATATATTTTTTTTATTTTTTTTATTA
1 TTTAT-TATTTATATATTTTTTTTATTTTTTTTATTA
*
1916939 TTTATTATTTATAT-TTTTCTTCTTCTTTTTCTTTATT-
1 TTTATTATTTATATATTTT-TT-TTATTTTT-TTTATTA
* * *
1916976 TTTCTTTATTTATTTA-TTTATTTATTTT
1 TTT-ATTATTTATATATTTTTTTTATTTT
1917004 ACTTACTATT
Statistics
Matches: 87, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
35 4 0.05
36 16 0.18
37 22 0.25
38 32 0.37
39 13 0.15
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (36 bp):
TTTATTATTTATATATTTTTTTTATTTTTTTTATTA
Found at i:1916984 original size:34 final size:34
Alignment explanation
Indices: 1916889--1916984 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 34
1916879 ATTTTTTATG
* *
1916889 TTTTTATTTATTATATATATATATATATATTTTTTTTA
1 TTTTT-TTTATTAT-T-TAT-TATTTATATTTTTCTTA
*
1916927 TTTTTTTTATTATTTATTATTTATATTTTTCTTC
1 TTTTTTTTATTATTTATTATTTATATTTTTCTTA
*
1916961 TTCTTTTTCT-TTATTT-TTCTTTAT
1 TT-TTTTT-TATTATTTATTATTTAT
1916985 TTATTTATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
34 23 0.44
35 14 0.27
36 2 0.04
37 8 0.15
38 5 0.10
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (34 bp):
TTTTTTTTATTATTTATTATTTATATTTTTCTTA
Found at i:1916995 original size:22 final size:22
Alignment explanation
Indices: 1916923--1916998 Score: 63
Period size: 22 Copynumber: 3.5 Consensus size: 22
1916913 ATATATTTTT
*
1916923 TTTATTT-TTTTT-ATTATTTA
1 TTTATTTATTTTTCTTTATTTA
1916943 -TTATTTATATTTTTCTTCT-TCTT-
1 TTTA-TT-TATTTTTCTT-TAT-TTA
*
1916966 TTTCTTTATTTTTCTTTATTTA
1 TTTATTTATTTTTCTTTATTTA
1916988 TTTATTTATTT
1 TTTATTTATTT
1916999 ATTTTACTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
19 3 0.07
20 2 0.05
21 4 0.09
22 26 0.59
23 4 0.09
24 5 0.11
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTATTTATTTTTCTTTATTTA
Found at i:1917021 original size:49 final size:47
Alignment explanation
Indices: 1916916--1917052 Score: 124
Period size: 48 Copynumber: 2.9 Consensus size: 47
1916906 TATATATATA
*
1916916 TATTTTT-TTTATTTTT-TTTA-TTATTTA-TTATTTATATTTTTCTTC
1 TATTTTTCTTTATTTTTCTTTATTTATTTATTTA-TT-TATTTTACTTC
*
1916961 TTCTTTTTCTTTATTTTTCTTTATTTATTTATTTATTTATTTTACTTAC
1 -TATTTTTCTTTATTTTTCTTTATTTATTTATTTATTTATTTTACTT-C
* * *
1917010 TATTTTATCTTT-GTTTTCTATATCTTATCT-TTTATTTAATTTT
1 TATTTT-TCTTTATTTTTCTTTAT-TTATTTATTTATTT-ATTTT
1917053 TTTCTTCATT
Statistics
Matches: 77, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
46 6 0.08
47 9 0.12
48 34 0.44
49 25 0.32
50 3 0.04
ACGTcount: A:0.18, C:0.08, G:0.01, T:0.74
Consensus pattern (47 bp):
TATTTTTCTTTATTTTTCTTTATTTATTTATTTATTTATTTTACTTC
Found at i:1917086 original size:23 final size:22
Alignment explanation
Indices: 1917039--1917086 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
1917029 ATATCTTATC
* *
1917039 TTTTATTTAATTTTTTTCTTCA
1 TTTTATTTAATTTATTTATTCA
*
1917061 TTTTAATTTAATTTATTTATTTA
1 TTTT-ATTTAATTTATTTATTCA
1917084 TTT
1 TTT
1917087 CTTACCTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTATTTAATTTATTTATTCA
Found at i:1920131 original size:14 final size:15
Alignment explanation
Indices: 1920085--1920131 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 15
1920075 ACGAAGAAAA
1920085 AAACAAAGACAAAGAG
1 AAACAAA-ACAAAGAG
1920101 AAA-ATAAA-AAAGAG
1 AAACA-AAACAAAGAG
1920115 AAACAAAACAAAG-G
1 AAACAAAACAAAGAG
1920129 AAA
1 AAA
1920132 AAGTGAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 16 0.57
15 7 0.25
16 5 0.18
ACGTcount: A:0.74, C:0.09, G:0.15, T:0.02
Consensus pattern (15 bp):
AAACAAAACAAAGAG
Found at i:1921684 original size:43 final size:43
Alignment explanation
Indices: 1921636--1921718 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
1921626 CGAAGGGGCC
*
1921636 ATCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCACAA
1 ATCCACGATTTCAACTCCACGACGAAGGATATCGTGCCCACAA
* * *
1921679 ATCCACGTTTTCAAGTTCACGACGAAGGATATCGTGCCCA
1 ATCCACGATTTCAACTCCACGACGAAGGATATCGTGCCCA
1921719 TTTACACAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (43 bp):
ATCCACGATTTCAACTCCACGACGAAGGATATCGTGCCCACAA
Found at i:1922187 original size:37 final size:36
Alignment explanation
Indices: 1922146--1922433 Score: 288
Period size: 36 Copynumber: 8.1 Consensus size: 36
1922136 AATTTACTCA
* **
1922146 AAACAAAGTTTTGTCTCTCTTGAGACAATTTCTTTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
1922183 AAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1922219 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * * *
1922255 AAACAAA----AT-T-T-TTGA-ATATTTTTACATT-
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCCCTTG
* * * **
1922283 AAACAAATTTTGTCTCCCTTGAGGCAATTTCTTTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * ** *
1922319 GAACTAAGTTTTGTCTCTCTTGAGACAACTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
1922356 AAACAAATTTTGTCTCTATTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
1922392 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
1922429 AAACA
1 AAACA
1922434 CCAATCTTTG
Statistics
Matches: 207, Mismatches: 32, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
28 9 0.04
29 10 0.05
30 1 0.00
31 1 0.00
32 2 0.01
33 1 0.00
35 9 0.04
36 105 0.51
37 69 0.33
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:1922199 original size:36 final size:36
Alignment explanation
Indices: 1922121--1922266 Score: 170
Period size: 36 Copynumber: 4.0 Consensus size: 36
1922111 ACAAGGGGTC
* *
1922121 GTCTCGCTTGAGACTAATTTACTC--AAAACAAAGTTTT
1 GTCTCTCTTGAGAC-AATTT-CTCTTGAAACAAA-TTTT
*
1922158 GTCTCTCTTGAGACAATTTCTTTTGAAACAAATTTT
1 GTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTT
* * *
1922194 ATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTT
1 GTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTT
* *
1922230 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTT
1 GTCTCTCTTGAGACAATTTCTCTTGAAAC-AAATTTT
1922267 TGAATATTTT
Statistics
Matches: 98, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
35 2 0.02
36 69 0.70
37 27 0.28
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (36 bp):
GTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTT
Found at i:1922356 original size:137 final size:137
Alignment explanation
Indices: 1922146--1922403 Score: 410
Period size: 137 Copynumber: 1.9 Consensus size: 137
1922136 AATTTACTCA
* **
1922146 AAACAAAGTTTTGTCTCTCTTGAGACAATTTCTTTTGAAACAAATTTTATCTCTCTTGAGACAGT
1 AAACAAAGTTTTGTCTCCCTTGAGACAATTTCTTTTGAAACAAATTTTATCTCTCTTGAGACAAC
*
1922211 TTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTGAATATTT
66 TTCCCTTGAAACAAATTTTGTCTCTATTGAGACAGTTTCCCTTGAAACAAAATTTTTGAATATTT
1922276 TTACATT
131 TTACATT
* * * *
1922283 AAACAAA-TTTTGTCTCCCTTGAGGCAATTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAA
1 AAACAAAGTTTTGTCTCCCTTGAGACAATTTCTTTTGAAAC-AAATTTTATCTCTCTTGAGACAA
* *
1922347 CTTCTCTTGAAACAAATTTTGTCTCTATTGAGACAGTTTCCCTTGAAACAAAGTTTT
65 CTTCCCTTGAAACAAATTTTGTCTCTATTGAGACAGTTTCCCTTGAAACAAAATTTT
1922404 GTCTCTCTTG
Statistics
Matches: 110, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
136 30 0.27
137 80 0.73
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (137 bp):
AAACAAAGTTTTGTCTCCCTTGAGACAATTTCTTTTGAAACAAATTTTATCTCTCTTGAGACAAC
TTCCCTTGAAACAAATTTTGTCTCTATTGAGACAGTTTCCCTTGAAACAAAATTTTTGAATATTT
TTACATT
Found at i:1922357 original size:101 final size:99
Alignment explanation
Indices: 1922183--1922366 Score: 251
Period size: 100 Copynumber: 1.8 Consensus size: 99
1922173 ATTTCTTTTG
* * **
1922183 AAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
1 AAACAAATTTTATCTCCCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAACT
1922248 TCCCTTGAAACAAAATTTTTGAATATTTTTACATT
66 TCCCTTGAAAC-AAATTTTTGAATATTTTTACATT
* * ** * *
1922283 AAACAAATTTTGTCTCCCTTGAGGCAATTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAAC
1 AAACAAATTTTATCTCCCTTGAGACAATTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAAC
*
1922348 TTCTCTTGAAACAAATTTT
65 TTCCCTTGAAACAAATTTT
1922367 GTCTCTATTG
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
100 40 0.56
101 32 0.44
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.41
Consensus pattern (99 bp):
AAACAAATTTTATCTCCCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAACT
TCCCTTGAAACAAATTTTTGAATATTTTTACATT
Found at i:1922372 original size:36 final size:36
Alignment explanation
Indices: 1922283--1922433 Score: 194
Period size: 37 Copynumber: 4.1 Consensus size: 36
1922273 TTTTTACATT
* * *
1922283 AAACAAATTTTGTCTCCCTTGAGGCAATTTCTTTTG
1 AAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTG
* * *
1922319 GAACTAAGTTTTGTCTCTCTTGAGACAACTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAATTTCTCTTG
* * *
1922356 AAACAAATTTTGTCTCTATTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTG
*
1922392 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAATTTCTCTTG
1922429 AAACA
1 AAACA
1922434 CCAATCTTTG
Statistics
Matches: 99, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
36 37 0.37
37 62 0.63
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTG
Found at i:1922402 original size:73 final size:73
Alignment explanation
Indices: 1922283--1922433 Score: 212
Period size: 73 Copynumber: 2.1 Consensus size: 73
1922273 TTTTTACATT
* * ** * *
1922283 AAACAAATTTTGTCTCCCTTGAGGCAATTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAAC
1 AAACAAATTTTGTCTCCATTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAAC
1922348 TTCTCTTG
66 TTCTCTTG
* * **
1922356 AAACAAATTTTGTCTCTATTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGT
1 AAACAAATTTTGTCTCCATTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAAC
1922421 TTCTCTTG
66 TTCTCTTG
1922429 AAACA
1 AAACA
1922434 CCAATCTTTG
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (73 bp):
AAACAAATTTTGTCTCCATTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAAC
TTCTCTTG
Found at i:1922532 original size:35 final size:35
Alignment explanation
Indices: 1922486--1922603 Score: 150
Period size: 34 Copynumber: 3.3 Consensus size: 35
1922476 CCTTGAGACA
1922486 GTTTCTCTTGAAACAAAAAAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACAAAAAAAAAACCTTTGAAATT
* *
1922521 GTTTCTCTTGAAAC-ACAAAAAAACATTTGAAATT
1 GTTTCTCTTGAAACAAAAAAAAAACCTTTGAAATT
* *
1922555 GTTTTTCTTGAAACACAAAAAAAAAACCTGTT-AAAAT
1 GTTTCTCTTG-AA-ACAAAAAAAAAACCT-TTGAAATT
*
1922592 ATTTCTCTTGAA
1 GTTTCTCTTGAA
1922604 TCCCAAGACC
Statistics
Matches: 71, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
34 27 0.38
35 16 0.23
36 4 0.06
37 22 0.31
38 2 0.03
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.33
Consensus pattern (35 bp):
GTTTCTCTTGAAACAAAAAAAAAACCTTTGAAATT
Found at i:1923243 original size:37 final size:37
Alignment explanation
Indices: 1923197--1923308 Score: 181
Period size: 37 Copynumber: 3.0 Consensus size: 37
1923187 AACATAACGT
* *
1923197 TAGAATTTTACTATGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
1923234 TAGAGTTTTACTA-GAATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATG-ATTCAAACTCCTAAAAATAGGA
*
1923271 TAGAGTTCTACTATGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
1923308 T
1 T
1923309 CCACAAGTGT
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
36 1 0.01
37 68 0.97
38 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (37 bp):
TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
Found at i:1923835 original size:20 final size:20
Alignment explanation
Indices: 1923793--1923835 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1923783 TTTCATGTAA
*
1923793 TATTTTTTTTATATTTTATG
1 TATTTTTTTTATACTTTATG
*
1923813 TATTTTCTTTTTTACTTTA-G
1 TATTTT-TTTTATACTTTATG
1923833 TAT
1 TAT
1923836 ATATTTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.72
Consensus pattern (20 bp):
TATTTTTTTTATACTTTATG
Found at i:1923861 original size:25 final size:25
Alignment explanation
Indices: 1923796--1923864 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
1923786 CATGTAATAT
* * *
1923796 TTTTTTTATATTTTATGTA-TTTTC
1 TTTTTTTAAATTATATATATTTTTC
**
1923820 -TTTTTTACTTTAGTATATATTTTTC
1 TTTTTTTAAATTA-TATATATTTTTC
1923845 TTTTTTTAAATTATATATAT
1 TTTTTTTAAATTATATATAT
1923865 ATATATATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
23 9 0.25
24 5 0.14
25 12 0.33
26 10 0.28
ACGTcount: A:0.23, C:0.04, G:0.03, T:0.70
Consensus pattern (25 bp):
TTTTTTTAAATTATATATATTTTTC
Found at i:1928967 original size:17 final size:18
Alignment explanation
Indices: 1928934--1928967 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1928924 TCAATTATGT
*
1928934 CTTATTATTTAATTCCAA
1 CTTATCATTTAATTCCAA
1928952 CTTATCATTT-ATTCCA
1 CTTATCATTTAATTCCA
1928968 GACCTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTATCATTTAATTCCAA
Found at i:1937025 original size:15 final size:15
Alignment explanation
Indices: 1937005--1937037 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1936995 TAAAATCTTT
*
1937005 TTTTCCCGTTCTTGA
1 TTTTCCCGTTCTGGA
1937020 TTTTCCCGTTCTGGA
1 TTTTCCCGTTCTGGA
1937035 TTT
1 TTT
1937038 CGATCTGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.24, G:0.15, T:0.55
Consensus pattern (15 bp):
TTTTCCCGTTCTGGA
Found at i:1938396 original size:16 final size:16
Alignment explanation
Indices: 1938375--1938431 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
1938365 ATATTATTAA
1938375 TAATATTATCACTTTG
1 TAATATTATCACTTTG
* * **
1938391 TAATATTTTACAAATTAA
1 TAATATTAT-C-ACTTTG
1938409 TAATATTATCACTTTG
1 TAATATTATCACTTTG
1938425 TAATATT
1 TAATATT
1938432 TTACAAATTA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
16 18 0.58
17 2 0.06
18 11 0.35
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.49
Consensus pattern (16 bp):
TAATATTATCACTTTG
Found at i:1938413 original size:34 final size:34
Alignment explanation
Indices: 1938370--1938449 Score: 160
Period size: 34 Copynumber: 2.4 Consensus size: 34
1938360 AAATTATATT
1938370 ATTAATAATATTATCACTTTGTAATATTTTACAA
1 ATTAATAATATTATCACTTTGTAATATTTTACAA
1938404 ATTAATAATATTATCACTTTGTAATATTTTACAA
1 ATTAATAATATTATCACTTTGTAATATTTTACAA
1938438 ATTAATAATATT
1 ATTAATAATATT
1938450 TATACAATCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (34 bp):
ATTAATAATATTATCACTTTGTAATATTTTACAA
Found at i:1938414 original size:18 final size:18
Alignment explanation
Indices: 1938391--1938456 Score: 73
Period size: 18 Copynumber: 3.7 Consensus size: 18
1938381 TATCACTTTG
1938391 TAATATTTTACAAATTAA
1 TAATATTTTACAAATTAA
* * **
1938409 TAATATTAT-C-ACTTTG
1 TAATATTTTACAAATTAA
1938425 TAATATTTTACAAATTAA
1 TAATATTTTACAAATTAA
1938443 TAATATTTATACAA
1 TAATATTT-TACAA
1938457 TCAAGATATT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
16 11 0.30
17 2 0.05
18 19 0.51
19 5 0.14
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (18 bp):
TAATATTTTACAAATTAA
Found at i:1940032 original size:31 final size:31
Alignment explanation
Indices: 1939992--1940066 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
1939982 ATAAGATTAG
*
1939992 GATCATTTTATAATAATTCAATAA-ATTTAAT
1 GATCATTTTATAATAATTCAA-AATATATAAT
* * * *
1940023 GATTATTTTATTATTATTTAAAATATATAAT
1 GATCATTTTATAATAATTCAAAATATATAAT
1940054 GATCATTTTATAA
1 GATCATTTTATAA
1940067 ATTGTAAAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 2 0.06
31 34 0.94
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (31 bp):
GATCATTTTATAATAATTCAAAATATATAAT
Found at i:1946502 original size:21 final size:21
Alignment explanation
Indices: 1946467--1946527 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 21
1946457 AGAACCCGTG
* *
1946467 GGGGGTATCGATTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
1946487 GGAGGGAATCGGTTCCCATTCAAA
1 GG-GGGAATCGGTTCCC--TCAAA
1946511 GGGGGAATCGGTTCCCT
1 GGGGGAATCGGTTCCCT
1946528 TATGGGGGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
20 2 0.06
21 13 0.37
23 16 0.46
24 4 0.11
ACGTcount: A:0.21, C:0.23, G:0.33, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:1954832 original size:2 final size:2
Alignment explanation
Indices: 1954821--1954860 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1954811 TTAAAAATAA
*
1954821 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1954861 AGACTAAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1956287 original size:3 final size:3
Alignment explanation
Indices: 1956281--1956340 Score: 74
Period size: 3 Copynumber: 21.0 Consensus size: 3
1956271 AAATTTATTT
*
1956281 TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAG TAA TAA -ACA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
1956324 TAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
1956341 AAAACAAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 6 0.12
3 45 0.88
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
TAA
Done.