Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 64 of 168
Found at i:18459973 original size:23 final size:23
Alignment explanation
Indices: 18459939--18460014 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
18459929 AGTGTTATTG
*
18459939 ATCAGTGCTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
18459962 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
18459985 ATCAGGGGTAGCTTCGACTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
18460008 ATCAGTG
1 ATCAGTG
18460015 TGGCACTTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:18462161 original size:28 final size:28
Alignment explanation
Indices: 18462125--18462179 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
18462115 AGTAACAGTA
*
18462125 CAGTATGGGCCTTAGCCCAATACAGAAT
1 CAGTATGGGCCTTAGCCCAATAAAGAAT
*
18462153 CAGTGTGGGCCTTAGCCCAATAAAGAA
1 CAGTATGGGCCTTAGCCCAATAAAGAA
18462180 ATGGTGGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (28 bp):
CAGTATGGGCCTTAGCCCAATAAAGAAT
Found at i:18471110 original size:22 final size:22
Alignment explanation
Indices: 18471047--18471120 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
18471037 CAGCAAAGCT
*
18471047 GCCAGTAACCAGAATGGCTAAGA
1 GCCA-TAAACAGAATGGCTAAGA
* * *
18471070 GCCGTAAACAGGATAGCTATA-A
1 GCCATAAACAGAATGGCTA-AGA
*
18471092 GCTATAAACAGAATGGCTACAG-
1 GCCATAAACAGAATGGCTA-AGA
18471114 GCCATAA
1 GCCATAA
18471121 GTACAGTAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
22 35 0.90
23 4 0.10
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (22 bp):
GCCATAAACAGAATGGCTAAGA
Found at i:18471161 original size:32 final size:32
Alignment explanation
Indices: 18471125--18471310 Score: 223
Period size: 32 Copynumber: 5.8 Consensus size: 32
18471115 CCATAAGTAC
* * *
18471125 AGTAATATGATTGGGACAAAGCCATCAGTAGT
1 AGTAATATGATCGGCACAAAGCCATCAGTAAT
** * * *
18471157 AGTAATAT-ATCAACACACAGCTATTAGTAAT
1 AGTAATATGATCGGCACAAAGCCATCAGTAAT
* *
18471188 AGTAGTATGATCGGCACAAAGCCATCAGTAGT
1 AGTAATATGATCGGCACAAAGCCATCAGTAAT
* *
18471220 AGTAATATGATCGGCACACATCCATCAGTAAT
1 AGTAATATGATCGGCACAAAGCCATCAGTAAT
*
18471252 GGTAATATGATCGGCACACAA-CCATCAGTAAT
1 AGTAATATGATCGGCACA-AAGCCATCAGTAAT
*
18471284 GGTAATATGATCGGCACAAAGCCATCA
1 AGTAATATGATCGGCACAAAGCCATCA
18471311 ATAACATCGT
Statistics
Matches: 130, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
31 24 0.18
32 105 0.81
33 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (32 bp):
AGTAATATGATCGGCACAAAGCCATCAGTAAT
Found at i:18471303 original size:96 final size:95
Alignment explanation
Indices: 18471125--18471310 Score: 246
Period size: 96 Copynumber: 1.9 Consensus size: 95
18471115 CCATAAGTAC
* * * * * *
18471125 AGTAATATGATTGGGACAAAGCCATCAGTAGTAGTAATATATCAACACACAGCTATTAGTAATAG
1 AGTAATATGATCGGCACAAAGCCATCAGTAATAGTAATATATCAACACACAACCATCAGTAATAG
*
18471190 TAGTATGATCGGCACAAAGCCATCAGTAGT
66 TAATATGATCGGCACAAAGCCATCAGTAGT
* * * ** *
18471220 AGTAATATGATCGGCACACATCCATCAGTAATGGTAATATGATCGGCACACAACCATCAGTAATG
1 AGTAATATGATCGGCACAAAGCCATCAGTAATAGTAATAT-ATCAACACACAACCATCAGTAATA
18471285 GTAATATGATCGGCACAAAGCCATCA
65 GTAATATGATCGGCACAAAGCCATCA
18471311 ATAACATCGT
Statistics
Matches: 77, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
95 34 0.44
96 43 0.56
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (95 bp):
AGTAATATGATCGGCACAAAGCCATCAGTAATAGTAATATATCAACACACAACCATCAGTAATAG
TAATATGATCGGCACAAAGCCATCAGTAGT
Found at i:18471363 original size:27 final size:27
Alignment explanation
Indices: 18471333--18471390 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
18471323 CAAAGCTGCT
18471333 AGTAACTGT-ATATGTGGTCA-AGCCACC
1 AGTAACTGTGAT-TGTGG-CAGAGCCACC
*
18471360 AGTAACTGTGATTGTGGCAGAGCTACC
1 AGTAACTGTGATTGTGGCAGAGCCACC
18471387 AGTA
1 AGTA
18471391 TAGTACTTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 2 0.07
27 24 0.86
28 2 0.07
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (27 bp):
AGTAACTGTGATTGTGGCAGAGCCACC
Found at i:18471500 original size:24 final size:24
Alignment explanation
Indices: 18471473--18471567 Score: 100
Period size: 24 Copynumber: 4.0 Consensus size: 24
18471463 AGTCATACGA
* *
18471473 ATCACAGACAAATCAACCATTTAT
1 ATCACAGACAAATCAATCATTTAC
* *
18471497 ATCACAAACAAATCAGTCATTTAC
1 ATCACAGACAAATCAATCATTTAC
* * ** *
18471521 ATCTCGGACAAATCCTTCATTTAG
1 ATCACAGACAAATCAATCATTTAC
*
18471545 ATCACAGGCAAATCAATCATTTA
1 ATCACAGACAAATCAATCATTTA
18471568 ACCCCGAGGA
Statistics
Matches: 56, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.27
Consensus pattern (24 bp):
ATCACAGACAAATCAATCATTTAC
Found at i:18471617 original size:27 final size:27
Alignment explanation
Indices: 18471586--18471678 Score: 134
Period size: 27 Copynumber: 3.5 Consensus size: 27
18471576 GAGTAAAATA
18471586 GTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
18471613 ATCATTTTACCATACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* **
18471640 GTCATTTTACCCTACAGAGGTGTTACG
1 GTCATTTTACCCTACAGGGGCATTACG
18471667 GTCA-TTTACCCT
1 GTCATTTTACCCT
18471679 TCGAGGGTAT
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
26 8 0.14
27 51 0.86
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:18471694 original size:26 final size:27
Alignment explanation
Indices: 18471586--18471715 Score: 106
Period size: 27 Copynumber: 4.9 Consensus size: 27
18471576 GAGTAAAATA
* *
18471586 GTCATTTTACCCTAC-AGGGGCATTACG
1 GTCATTTTACCCTTCGA-GGGTATTACG
* * * *
18471613 ATCATTTTACCATAC-AGGGGCATTACG
1 GTCATTTTACCCTTCGA-GGGTATTACG
* *
18471640 GTCATTTTACCCTAC-AGAGGTGTTACG
1 GTCATTTTACCCTTCGAG-GGTATTACG
*
18471667 GTCA-TTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTACG
* *
18471693 GTAATTTTACACTTCGAGGGTAT
1 GTCATTTTACCCTTCGAGGGTAT
18471716 CCCAGTAATT
Statistics
Matches: 89, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
26 20 0.22
27 69 0.78
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (27 bp):
GTCATTTTACCCTTCGAGGGTATTACG
Found at i:18471723 original size:27 final size:27
Alignment explanation
Indices: 18471671--18471727 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
18471661 GTTACGGTCA
* ** *
18471671 TTTACCCTTCGAGGGTATTTCGGTAAT
1 TTTACACTTCGAGGGTATCCCAGTAAT
18471698 TTTACACTTCGAGGGTATCCCAGTAAT
1 TTTACACTTCGAGGGTATCCCAGTAAT
18471725 TTT
1 TTT
18471728 TCAACCTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (27 bp):
TTTACACTTCGAGGGTATCCCAGTAAT
Found at i:18498757 original size:20 final size:18
Alignment explanation
Indices: 18498720--18498758 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
18498710 AATAATGTTT
*
18498720 TAAAAATAAAAGTACAAA
1 TAAAAATAAAACTACAAA
18498738 TAAAAATAACTAACTACAAA
1 TAAAAATAA--AACTACAAA
18498758 T
1 T
18498759 GCCATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
20 9 0.50
ACGTcount: A:0.67, C:0.10, G:0.03, T:0.21
Consensus pattern (18 bp):
TAAAAATAAAACTACAAA
Found at i:18507212 original size:18 final size:18
Alignment explanation
Indices: 18507189--18507223 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
18507179 GAAGAACAGG
18507189 AAGCATCAAAATAGTTTC
1 AAGCATCAAAATAGTTTC
*
18507207 AAGCATTAAAATAGTTT
1 AAGCATCAAAATAGTTT
18507224 GACACATCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (18 bp):
AAGCATCAAAATAGTTTC
Found at i:18511510 original size:18 final size:20
Alignment explanation
Indices: 18511468--18511511 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
18511458 TACACGCCCA
*
18511468 TGTG-GAAGAGGCACACACC
1 TGTGTGAAGAAGCACACACC
*
18511487 TGTGTGAAGAAGCACACACT
1 TGTGTGAAGAAGCACACACC
18511507 TGTGT
1 TGTGT
18511512 AAAATGAGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (20 bp):
TGTGTGAAGAAGCACACACC
Found at i:18511523 original size:22 final size:20
Alignment explanation
Indices: 18511473--18511525 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
18511463 GCCCATGTGG
*
18511473 AAGAGGCACACACCTGTGTG
1 AAGAGGCACACACCTGTGTA
* *
18511493 AAGAAGCACACACTTGTGTAA
1 AAGAGGCACACACCTGTGT-A
18511514 AATGAGGCACAC
1 AA-GAGGCACAC
18511526 GGTCGTGTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 17 0.63
21 2 0.07
22 8 0.30
ACGTcount: A:0.38, C:0.23, G:0.25, T:0.15
Consensus pattern (20 bp):
AAGAGGCACACACCTGTGTA
Found at i:18513864 original size:7 final size:7
Alignment explanation
Indices: 18513847--18513881 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
18513837 ATATCGGTTT
18513847 AATATAAA
1 AATA-AAA
18513855 AATAAAA
1 AATAAAA
18513862 AATAAAA
1 AATAAAA
18513869 AATAAAA
1 AATAAAA
18513876 AA-AAAA
1 AATAAAA
18513882 CCTCAAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 4 0.15
7 19 0.70
8 4 0.15
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AATAAAA
Found at i:18535000 original size:2 final size:2
Alignment explanation
Indices: 18534993--18535021 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18534983 AAGATTTAAT
18534993 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 T
18535022 CATTCACTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18550434 original size:23 final size:26
Alignment explanation
Indices: 18550408--18550466 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 26
18550398 CAGCTCTTAT
18550408 GAGCTTACCG-T-TTCAGCTCG-ATA
1 GAGCTTACCGTTCTTCAGCTCGAATA
*
18550431 GAGCTTACTGTTCTTCAGCTCGTAATA
1 GAGCTTACCGTTCTTCAGCTCG-AATA
18550458 -AGCTTACCG
1 GAGCTTACCG
18550467 ATCATGGCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 9 0.30
24 1 0.03
25 9 0.30
26 8 0.27
27 3 0.10
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (26 bp):
GAGCTTACCGTTCTTCAGCTCGAATA
Found at i:18556643 original size:17 final size:16
Alignment explanation
Indices: 18556587--18556647 Score: 51
Period size: 17 Copynumber: 3.9 Consensus size: 16
18556577 ATTGTTTGCC
18556587 TTTCTTTATTTTA-T-
1 TTTCTTTATTTTATTA
*
18556601 TTT-TTTA-TTTAGTA
1 TTTCTTTATTTTATTA
18556615 TTT-TATTAATTTTATTAA
1 TTTCT-TT-ATTTTATT-A
18556633 TTTCTTTATTTTATT
1 TTTCTTTATTTTATT
18556648 CCTCTGCTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
12 4 0.10
13 5 0.13
14 7 0.18
15 2 0.05
16 1 0.03
17 13 0.33
18 6 0.15
19 1 0.03
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (16 bp):
TTTCTTTATTTTATTA
Found at i:18558880 original size:14 final size:14
Alignment explanation
Indices: 18558861--18558887 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18558851 CAGTATATAG
18558861 ATTCATGAGATTCA
1 ATTCATGAGATTCA
18558875 ATTCATGAGATTC
1 ATTCATGAGATTC
18558888 CCGAACCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (14 bp):
ATTCATGAGATTCA
Found at i:18563493 original size:27 final size:27
Alignment explanation
Indices: 18563455--18563782 Score: 346
Period size: 27 Copynumber: 12.2 Consensus size: 27
18563445 GTAATGGGCC
18563455 TAAAATTA-TCGAAATACCCTCGAAGGG
1 TAAAATTACT-GAAATACCCTCGAAGGG
*
18563482 TAAAATTA-TCGAAATATCCTCGAAGGG
1 TAAAATTACT-GAAATACCCTCGAAGGG
* * * *
18563509 TAAACTTACTAAAATACCATCAAAGGG
1 TAAAATTACTGAAATACCCTCGAAGGG
*
18563536 TAAAATTGCTGAAATACCCTCGAAGGG
1 TAAAATTACTGAAATACCCTCGAAGGG
*
18563563 TAAAATTACCGAAATACCCTCGAAGGG
1 TAAAATTACTGAAATACCCTCGAAGGG
* * *
18563590 T--AATTACCGAAATACCCTCAAAGTG
1 TAAAATTACTGAAATACCCTCGAAGGG
*
18563615 TAAAATTACTGAAATACCCTCTAAGGG
1 TAAAATTACTGAAATACCCTCGAAGGG
*
18563642 TAAAATTACTGAAATACCCTTGAAGGG
1 TAAAATTACTGAAATACCCTCGAAGGG
* *
18563669 TAAAATGA-TCGAAATACCCTCGAAGTG
1 TAAAATTACT-GAAATACCCTCGAAGGG
* * *
18563696 TAAAATGACTGAAATAACCTAGAAGGG
1 TAAAATTACTGAAATACCCTCGAAGGG
* * * *
18563723 TAAACTAACTGAAATACCC-CTAAAAGG
1 TAAAATTACTGAAATACCCTC-GAAGGG
* * *
18563750 TAAAATGACTAAAATACCC-CTATAGGG
1 TAAAATTACTGAAATACCCTCGA-AGGG
18563777 TAAAAT
1 TAAAAT
18563783 AACCGTTATA
Statistics
Matches: 257, Mismatches: 37, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
25 23 0.09
26 2 0.01
27 230 0.89
28 2 0.01
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (27 bp):
TAAAATTACTGAAATACCCTCGAAGGG
Found at i:18564036 original size:26 final size:26
Alignment explanation
Indices: 18563991--18564050 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
18563981 TTACTGGTAG
* *
18563991 CTTTGCTACGTTAATGTTAT-TGGCAA
1 CTTTGCTACCTTAATATTATAT-GCAA
* *
18564017 CTTTGCTACCTTATTATTATATGTAA
1 CTTTGCTACCTTAATATTATATGCAA
18564043 CTTTGCTA
1 CTTTGCTA
18564051 TGATATTGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 28 0.97
27 1 0.03
ACGTcount: A:0.23, C:0.17, G:0.13, T:0.47
Consensus pattern (26 bp):
CTTTGCTACCTTAATATTATATGCAA
Found at i:18564202 original size:28 final size:28
Alignment explanation
Indices: 18564162--18564222 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
18564152 ATTGTACTAA
* **
18564162 TTACTTTATTGGGCGAAGGCTTACATTG
1 TTACTGTATTGGGCGAAGGCCCACATTG
*
18564190 TTACTGTATTGGGCTAAGGCCCACATTG
1 TTACTGTATTGGGCGAAGGCCCACATTG
18564218 TTACT
1 TTACT
18564223 ATAATGGGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (28 bp):
TTACTGTATTGGGCGAAGGCCCACATTG
Found at i:18564230 original size:28 final size:28
Alignment explanation
Indices: 18564184--18564250 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
18564174 GCGAAGGCTT
* *
18564184 ACATTGTTACTGTATTGGGCTAAGGCCC
1 ACATTGTTACTATAATGGGCTAAGGCCC
* *
18564212 ACATTGTTACTATAATGGGGTAAGGCTC
1 ACATTGTTACTATAATGGGCTAAGGCCC
*
18564240 ACACTG-TACTA
1 ACATTGTTACTA
18564251 ATACTGTACA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 5 0.15
28 29 0.85
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.31
Consensus pattern (28 bp):
ACATTGTTACTATAATGGGCTAAGGCCC
Found at i:18569306 original size:27 final size:27
Alignment explanation
Indices: 18569276--18569645 Score: 395
Period size: 27 Copynumber: 13.7 Consensus size: 27
18569266 ACTTCTCGGA
* *
18569276 TAAATTTACCGAAATACCCTCGAAGGC
1 TAAAATTACCGAAATACCCTCGAAGGG
* *
18569303 TAAAATTATCGAAATACTCTCGAAGGG
1 TAAAATTACCGAAATACCCTCGAAGGG
** *
18569330 TAAAATTACTAAAATACCATCGAAGGG
1 TAAAATTACCGAAATACCCTCGAAGGG
*
18569357 TAAAATTACTGAAATACCCTCGAAGGG
1 TAAAATTACCGAAATACCCTCGAAGGG
* *
18569384 TAAAATTATCGAAATACCCTCGAATGG
1 TAAAATTACCGAAATACCCTCGAAGGG
* **
18569411 TAAAATTACCAAAATACCCTCGAAGCA
1 TAAAATTACCGAAATACCCTCGAAGGG
* * * *
18569438 TAAAATTATCGAAATACGCTTGAAGAG
1 TAAAATTACCGAAATACCCTCGAAGGG
** * *
18569465 TAAAATTACTAAAATACCGTCGAGGGG
1 TAAAATTACCGAAATACCCTCGAAGGG
*
18569492 TAAAATTACCGAAATACCCTCAAAGGG
1 TAAAATTACCGAAATACCCTCGAAGGG
**
18569519 TAAAATTATTGAAATACCCTCGAAGGG
1 TAAAATTACCGAAATACCCTCGAAGGG
* * * *
18569546 TAAAATGACCGAAAGACTCC-CAAATGG
1 TAAAATTACCGAAATAC-CCTCGAAGGG
* *
18569573 TAAAATGACCGAAATA-CCTCTATAGGG
1 TAAAATTACCGAAATACCCTCGA-AGGG
* *
18569600 TAAAATGACCGAAATACTCC-CAAAGGG
1 TAAAATTACCGAAATAC-CCTCGAAGGG
*
18569627 TAAAATGACCGAAATACCC
1 TAAAATTACCGAAATACCC
18569646 CTATTGGCTA
Statistics
Matches: 287, Mismatches: 51, Indels: 11
0.82 0.15 0.03
Matches are distributed among these distances:
25 2 0.01
26 4 0.01
27 275 0.96
28 4 0.01
29 2 0.01
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.21
Consensus pattern (27 bp):
TAAAATTACCGAAATACCCTCGAAGGG
Found at i:18571858 original size:41 final size:39
Alignment explanation
Indices: 18571813--18571959 Score: 120
Period size: 41 Copynumber: 3.6 Consensus size: 39
18571803 GGTTCTGTAC
18571813 CTAGCAAGCTTAATGCCGGTGAAGTAATTCAGACTTTACGT
1 CTAGCAAGCTTAATGCCGGTGAA-TAATTCAGACTTTA-GT
* *
18571854 CTAGCAGGCTTAATGCCGGTG-ATACATTTCAGACTATATGT
1 CTAGCAAGCTTAATGCCGGTGAATA-A-TTCAGACTTTA-GT
* * * * *
18571895 CTAGCAGGC-TAAGTGCCGGTGTACTAAATCAGGCTTTGAGC
1 CTAGCAAGCTTAA-TGCCGGTG-AATAATTCAGACTTT-AGT
*
18571936 CTAGC-AGACTAAATGCCGGTGAAT
1 CTAGCAAG-CTTAATGCCGGTGAAT
18571960 CTGTTTAAAT
Statistics
Matches: 87, Mismatches: 11, Indels: 17
0.76 0.10 0.15
Matches are distributed among these distances:
39 2 0.02
40 8 0.09
41 71 0.82
42 4 0.05
43 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (39 bp):
CTAGCAAGCTTAATGCCGGTGAATAATTCAGACTTTAGT
Found at i:18579756 original size:41 final size:39
Alignment explanation
Indices: 18579706--18579852 Score: 145
Period size: 41 Copynumber: 3.6 Consensus size: 39
18579696 GGTTCTGTAC
18579706 CTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTACGT
1 CTAGCAGGCTTAATGCCGGTGAA-TAATTCAGACTTTA-GT
* *
18579747 CTAGGAGGCTTAATGCCGGTG-ATACATTTCAGACTATATGT
1 CTAGCAGGCTTAATGCCGGTGAATA-A-TTCAGACTTTA-GT
* * * *
18579788 CTAGCAGGC-TAAGTGCCGGTGTACTAAATCAGGCTTTGAGC
1 CTAGCAGGCTTAA-TGCCGGTG-AATAATTCAGACTTT-AGT
*
18579829 CTAGCAGGCTAAATGCCGGTGAAT
1 CTAGCAGGCTTAATGCCGGTGAAT
18579853 CTGTTTAAAT
Statistics
Matches: 88, Mismatches: 11, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
39 2 0.02
40 7 0.08
41 73 0.83
42 4 0.05
43 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (39 bp):
CTAGCAGGCTTAATGCCGGTGAATAATTCAGACTTTAGT
Found at i:18580011 original size:2 final size:2
Alignment explanation
Indices: 18580004--18580052 Score: 55
Period size: 2 Copynumber: 24.0 Consensus size: 2
18579994 TATGCATTTG
* *
18580004 AT AT AT AT AT AT AT AT AT AC AT GT ACT CAT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T -AT AT AT AT AT AT AT AT
18580047 AT AT AT
1 AT AT AT
18580053 TCGAATGTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
1 1 0.03
2 36 0.90
3 2 0.05
4 1 0.03
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:18582722 original size:28 final size:27
Alignment explanation
Indices: 18582682--18582770 Score: 117
Period size: 28 Copynumber: 3.2 Consensus size: 27
18582672 ATTGTACTGA
*
18582682 TTACCGTATTGGGCTAAGGCTCACATTG
1 TTACTGTATTGGGCTAAGGC-CACATTG
*
18582710 TTACTGTATTGGGCTAAGGCCCACAATG
1 TTACTGTATTGGGCTAAGG-CCACATTG
*
18582738 TTACTGTAATGGGCTAAGGCCTACATTG
1 TTACTGTATTGGGCTAAGGCC-ACATTG
18582766 -TACTG
1 TTACTG
18582771 ATACTATACA
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 7 0.13
28 47 0.85
29 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (27 bp):
TTACTGTATTGGGCTAAGGCCACATTG
Found at i:18584369 original size:22 final size:23
Alignment explanation
Indices: 18584339--18584382 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
18584329 ATAAAGAAAC
18584339 TACAGCTAGCTCAC-GAGTTTTTG
1 TACAGCTAG-TCACTGAGTTTTTG
*
18584362 TACA-CTAGTGACTGAGTTTTT
1 TACAGCTAGTCACTGAGTTTTT
18584383 TTCTACTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 3 0.16
22 12 0.63
23 4 0.21
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (23 bp):
TACAGCTAGTCACTGAGTTTTTG
Found at i:18592686 original size:21 final size:21
Alignment explanation
Indices: 18592662--18592702 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
18592652 AGGGATTTCA
18592662 CATTAATGTTCTTGAATGAGC
1 CATTAATGTTCTTGAATGAGC
18592683 CATTAATGTTCTTGAATGAG
1 CATTAATGTTCTTGAATGAG
18592703 TTTTGGTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (21 bp):
CATTAATGTTCTTGAATGAGC
Found at i:18595936 original size:29 final size:29
Alignment explanation
Indices: 18595892--18595952 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
18595882 GGTCTGAAAC
*
18595892 TACCGTAGTTTCTTGGGCCGAAGCTCTCT
1 TACCGTAGTTTATTGGGCCGAAGCTCTCT
* *
18595921 TACCGTAGTTTATTGGGCTGAAGCTCTTT
1 TACCGTAGTTTATTGGGCCGAAGCTCTCT
18595950 TAC
1 TAC
18595953 TCTTCCTAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (29 bp):
TACCGTAGTTTATTGGGCCGAAGCTCTCT
Found at i:18600980 original size:25 final size:25
Alignment explanation
Indices: 18600951--18601000 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
18600941 GCAAGTAAGT
18600951 AGGTTACAGATAATAGTGGCAAGGC
1 AGGTTACAGATAATAGTGGCAAGGC
18600976 AGGTTACAGATAATAGTGGCAAGGC
1 AGGTTACAGATAATAGTGGCAAGGC
18601001 TCACTCCTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.32, T:0.20
Consensus pattern (25 bp):
AGGTTACAGATAATAGTGGCAAGGC
Found at i:18602171 original size:67 final size:68
Alignment explanation
Indices: 18601962--18602224 Score: 298
Period size: 68 Copynumber: 3.9 Consensus size: 68
18601952 CAAAAGTCTG
* * * ** *
18601962 CCAGGACAATAAACA-GGGGTTACAGTATGTAAGAACATAGCTCAACTATCACAACATATGGAGT
1 CCAGGACAATAAACATGGGGTTACAATGTGTAAGACCATAGCTCAACTATGGCAACATATGAAGT
18602026 CCA
66 CCA
* * * *
18602029 CCAGGACAATAAACATGGGGTTATAATTTGTAAAACCATAGCTCAGCTATGGCAACATAT-AGAG
1 CCAGGACAATAAACATGGGGTTACAATGTGTAAGACCATAGCTCAACTATGGCAACATATGA-AG
18602093 TCCA
65 TCCA
** * * *
18602097 CTGGGACATTAAACATGGGG-TAGAATGTGTAAGACCATAGCTCAACTATGGCAATATATGAAGT
1 CCAGGACAATAAACATGGGGTTACAATGTGTAAGACCATAGCTCAACTATGGCAACATATGAAGT
*
18602161 GCA
66 CCA
* * * * * *
18602164 CCAGGACAATGAACATGGGCTTTCAATGTGTAAGACCATAACTCGACTACGGCAACATATG
1 CCAGGACAATAAACATGGGGTTACAATGTGTAAGACCATAGCTCAACTATGGCAACATATG
18602225 GAGTTTGCAG
Statistics
Matches: 163, Mismatches: 29, Indels: 7
0.82 0.15 0.04
Matches are distributed among these distances:
67 69 0.42
68 94 0.58
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.22
Consensus pattern (68 bp):
CCAGGACAATAAACATGGGGTTACAATGTGTAAGACCATAGCTCAACTATGGCAACATATGAAGT
CCA
Found at i:18609394 original size:12 final size:12
Alignment explanation
Indices: 18609373--18609423 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
18609363 ATAAATAAAT
*
18609373 TTTATCTTTATC
1 TTTATTTTTATC
* **
18609385 TTTATGTTTAAG
1 TTTATTTTTATC
18609397 TTTATTTTTAT-
1 TTTATTTTTATC
18609408 TTTATTTTTTATC
1 TTTA-TTTTTATC
18609421 TTT
1 TTT
18609424 TTTGTTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
11 4 0.12
12 25 0.78
13 3 0.09
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.73
Consensus pattern (12 bp):
TTTATTTTTATC
Found at i:18613599 original size:21 final size:21
Alignment explanation
Indices: 18613573--18613617 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
18613563 TATATGTGAG
* * *
18613573 AAATTTACTTATGTTATGGAT
1 AAATTTACCTATGTCATGAAT
18613594 AAATTTACCTATGTCATGAAT
1 AAATTTACCTATGTCATGAAT
18613615 AAA
1 AAA
18613618 GACACTAATT
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:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (21 bp):
AAATTTACCTATGTCATGAAT
Found at i:18615045 original size:20 final size:20
Alignment explanation
Indices: 18615022--18615061 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
18615012 TCTTTATCGT
18615022 TTATTTTAATTCTATGTTTA
1 TTATTTTAATTCTATGTTTA
18615042 TTATTTTAATTCTATGTTTA
1 TTATTTTAATTCTATGTTTA
18615062 CGTTGCTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.65
Consensus pattern (20 bp):
TTATTTTAATTCTATGTTTA
Found at i:18631034 original size:26 final size:26
Alignment explanation
Indices: 18630996--18631062 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
18630986 CTTTATATCA
18630996 TTGCTCACACGAGCTGTGAAATGGG-
1 TTGCTCACACGAGCTGTGAAATGGGC
* *
18631021 TCTGCTCACTCGAGTTGTGAAATGGGC
1 T-TGCTCACACGAGCTGTGAAATGGGC
18631048 TTGCTCACACGAGCT
1 TTGCTCACACGAGCT
18631063 ATGGAGTATC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 1 0.03
26 34 0.94
27 1 0.03
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (26 bp):
TTGCTCACACGAGCTGTGAAATGGGC
Found at i:18631467 original size:17 final size:17
Alignment explanation
Indices: 18631420--18631466 Score: 76
Period size: 17 Copynumber: 2.7 Consensus size: 17
18631410 TCTTGATCTA
*
18631420 AATTAATAATTTTATTT
1 AATTTATAATTTTATTT
18631437 AATTTATAATTTTATTT
1 AATTTATAATTTTATTT
18631454 AATTTATTAATTT
1 AATTTA-TAATTT
18631467 AGATAGTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 22 0.79
18 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTTATAATTTTATTT
Found at i:18634925 original size:7 final size:7
Alignment explanation
Indices: 18634913--18634939 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
18634903 GACAAAATTG
18634913 AGTCTGA
1 AGTCTGA
18634920 AGTCTGA
1 AGTCTGA
18634927 AGTCTGA
1 AGTCTGA
18634934 AGTCTG
1 AGTCTG
18634940 TCGTACGTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (7 bp):
AGTCTGA
Found at i:18645505 original size:50 final size:49
Alignment explanation
Indices: 18645439--18645554 Score: 119
Period size: 50 Copynumber: 2.3 Consensus size: 49
18645429 CATGTATGCT
* * *
18645439 CATACGAGCTGTGAATCACTATGCTCTCACAAGCTGTA-AATCGGTAA-GC
1 CATACGAGTTGAGAATCACTAAGCTCTCACAAGC--TACAATCGGTAAGGC
* * ** *
18645488 TGATACGATTTGAGAATCGGTAAGCTCTCACGAGCTACAATCGGTAAGGC
1 -CATACGAGTTGAGAATCACTAAGCTCTCACAAGCTACAATCGGTAAGGC
18645538 CATACGAGTTGAGAATC
1 CATACGAGTTGAGAATC
18645555 GGTAATCTGT
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
48 2 0.04
49 24 0.44
50 28 0.52
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (49 bp):
CATACGAGTTGAGAATCACTAAGCTCTCACAAGCTACAATCGGTAAGGC
Found at i:18645520 original size:25 final size:24
Alignment explanation
Indices: 18645477--18645559 Score: 80
Period size: 25 Copynumber: 3.4 Consensus size: 24
18645467 ACAAGCTGTA
* *
18645477 AATCGGTAAGCTGATACGATTTGAG
1 AATCGGTAAGCT-CTACGAGTTGAG
* *
18645502 AATCGGTAAGCTCTCACGAGCT-AC
1 AATCGGTAAGCTCT-ACGAGTTGAG
18645526 AATCGGTAAGGC-CATACGAGTTGAG
1 AATCGGTAA-GCTC-TACGAGTTGAG
18645551 AATCGGTAA
1 AATCGGTAA
18645560 TCTGTAATGA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
24 18 0.38
25 30 0.62
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.23
Consensus pattern (24 bp):
AATCGGTAAGCTCTACGAGTTGAG
Found at i:18655988 original size:27 final size:27
Alignment explanation
Indices: 18655957--18656013 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
18655947 TCGTAATAAG
*
18655957 GACCGTAATGCCCCTATAAGGTAAAAT
1 GACCGTAATGACCCTATAAGGTAAAAT
* *
18655984 GACCGTAATGACCCTGTAGGGTAAAAT
1 GACCGTAATGACCCTATAAGGTAAAAT
18656011 GAC
1 GAC
18656014 TATTTTACCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (27 bp):
GACCGTAATGACCCTATAAGGTAAAAT
Found at i:18656061 original size:24 final size:24
Alignment explanation
Indices: 18656032--18656150 Score: 98
Period size: 24 Copynumber: 5.0 Consensus size: 24
18656022 CGATCGGGGT
*
18656032 TAAATGATTGATATGTCTGTGATG
1 TAAATGATTGATTTGTCTGTGATG
* *
18656056 TAAATGATTGATTTGT-TCGAGGTG
1 TAAATGATTGATTTGTCT-GTGATG
* * *
18656080 TAAATGACTGATTTTTCTGTGATT
1 TAAATGATTGATTTGTCTGTGATG
* * *
18656104 TAAATGACTAATTTGTCTATGAT-
1 TAAATGATTGATTTGTCTGTGATG
* * *
18656127 TGATATGAATGATTTGCCTGTGAT
1 T-AAATGATTGATTTGTCTGTGAT
18656151 TTGTATGACT
Statistics
Matches: 76, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
23 2 0.03
24 73 0.96
25 1 0.01
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.44
Consensus pattern (24 bp):
TAAATGATTGATTTGTCTGTGATG
Found at i:18656151 original size:24 final size:24
Alignment explanation
Indices: 18656083--18656164 Score: 76
Period size: 24 Copynumber: 3.4 Consensus size: 24
18656073 CGAGGTGTAA
** * *
18656083 ATGACTGATTTTTCTGTGATTTAA
1 ATGACTGATTTGCCTGTGATTGAT
* * *
18656107 ATGACTAATTTGTCTATGATTGAT
1 ATGACTGATTTGCCTGTGATTGAT
*
18656131 ATGAATGATTTGCCTGTGATTTG-T
1 ATGACTGATTTGCCTGTGA-TTGAT
18656155 ATGACTGATT
1 ATGACTGATT
18656165 CTGTGCATGG
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
24 44 0.94
25 3 0.06
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.46
Consensus pattern (24 bp):
ATGACTGATTTGCCTGTGATTGAT
Found at i:18656276 original size:27 final size:27
Alignment explanation
Indices: 18656233--18656287 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
18656223 GGAAGTACTG
*
18656233 TACTGGTGGCTCTGCCACA-ATCACTAT
1 TACTAGTGGCTCTGCCACATAT-ACTAT
18656260 TACTAGTGGCT-TGGCCACATATACTAT
1 TACTAGTGGCTCT-GCCACATATACTAT
18656287 T
1 T
18656288 GTTGGCAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 1 0.04
27 22 0.88
28 2 0.08
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (27 bp):
TACTAGTGGCTCTGCCACATATACTAT
Found at i:18656438 original size:22 final size:21
Alignment explanation
Indices: 18656408--18656471 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
18656398 ATTACTGTAC
18656408 TTATGGCTTGTAGCCATTCTAT
1 TTATGGCTT-TAGCCATTCTAT
* * * *
18656430 TTATAGCTTATAGCTATCCTGT
1 TTATGGCTT-TAGCCATTCTAT
18656452 TTATGGCTATTAGCCATTCT
1 TTATGGCT-TTAGCCATTCT
18656472 GATTACTGGC
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
22 32 0.97
23 1 0.03
ACGTcount: A:0.20, C:0.19, G:0.16, T:0.45
Consensus pattern (21 bp):
TTATGGCTTTAGCCATTCTAT
Found at i:18661381 original size:21 final size:21
Alignment explanation
Indices: 18661349--18661405 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
18661339 TGGTTTATTG
**
18661349 ATTTAGTTCATTTTTTATTTTT
1 ATTTA-TTCATTTTTTATCGTT
*
18661371 ATTTATTCATTTGTTATCGTT
1 ATTTATTCATTTTTTATCGTT
*
18661392 ATTTATTTATTTTT
1 ATTTATTCATTTTT
18661406 ATCTCATCAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 25 0.83
22 5 0.17
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.70
Consensus pattern (21 bp):
ATTTATTCATTTTTTATCGTT
Found at i:18662531 original size:34 final size:34
Alignment explanation
Indices: 18662493--18662576 Score: 107
Period size: 34 Copynumber: 2.5 Consensus size: 34
18662483 CACGGGTTAC
*
18662493 TACACCACACCAGAT-AGCTCAATAGAGCAAGAAG
1 TACACCACACCAAATGA-CTCAATAGAGCAAGAAG
* * * *
18662527 TACACCACACCAAATGACTCGATAGAGCGATAAT
1 TACACCACACCAAATGACTCAATAGAGCAAGAAG
18662561 TACACCACACCAAATG
1 TACACCACACCAAATG
18662577 GCTTGAGAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
34 43 0.98
35 1 0.02
ACGTcount: A:0.43, C:0.29, G:0.14, T:0.14
Consensus pattern (34 bp):
TACACCACACCAAATGACTCAATAGAGCAAGAAG
Found at i:18662592 original size:34 final size:34
Alignment explanation
Indices: 18662527--18662607 Score: 117
Period size: 34 Copynumber: 2.4 Consensus size: 34
18662517 GAGCAAGAAG
* * *
18662527 TACACCACACCAAATGACTCGATAGAGCGATAAT
1 TACACCACACCAAATGACTCGAGAGAACGATAAC
* *
18662561 TACACCACACCAAATGGCTTGAGAGAACGATAAC
1 TACACCACACCAAATGACTCGAGAGAACGATAAC
18662595 TACACCACACCAA
1 TACACCACACCAA
18662608 TACACGTAGT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.42, C:0.30, G:0.14, T:0.15
Consensus pattern (34 bp):
TACACCACACCAAATGACTCGAGAGAACGATAAC
Found at i:18663466 original size:16 final size:17
Alignment explanation
Indices: 18663435--18663467 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
18663425 ATAGAAAGGG
18663435 AGAAATGGAAAACATTT
1 AGAAATGGAAAACATTT
*
18663452 AGAAAT-GAAACCATTT
1 AGAAATGGAAAACATTT
18663468 GGGAATGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (17 bp):
AGAAATGGAAAACATTT
Found at i:18665314 original size:19 final size:19
Alignment explanation
Indices: 18665290--18665327 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
18665280 CTAAAAGAGT
18665290 TGAGAGAATGATGA-ATGAG
1 TGAGAG-ATGATGAGATGAG
18665309 TGAGAGATGATGAGATGAG
1 TGAGAGATGATGAGATGAG
18665328 AGATGATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.21
Consensus pattern (19 bp):
TGAGAGATGATGAGATGAG
Found at i:18665317 original size:15 final size:16
Alignment explanation
Indices: 18665299--18665333 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
18665289 TTGAGAGAAT
18665299 GATGAATGAG-TGAGA
1 GATGAATGAGATGAGA
18665314 GATG-ATGAGATGAGA
1 GATGAATGAGATGAGA
18665329 GATGA
1 GATGA
18665334 TTGAAAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (16 bp):
GATGAATGAGATGAGA
Found at i:18667942 original size:28 final size:30
Alignment explanation
Indices: 18667885--18667957 Score: 105
Period size: 28 Copynumber: 2.5 Consensus size: 30
18667875 CCAGAGCTCT
*
18667885 ATACAGTAATAGTGTGTGGGCCTTAGCCCA
1 ATACAGTAATAGTGAGTGGGCCTTAGCCCA
18667915 ATACAGTAATAGT-AG-GGGCCTTAGCCCA
1 ATACAGTAATAGTGAGTGGGCCTTAGCCCA
*
18667943 ATACAATAATTAGTG
1 ATACAGTAA-TAGTG
18667958 CAATGCATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 21 0.54
29 5 0.13
30 13 0.33
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (30 bp):
ATACAGTAATAGTGAGTGGGCCTTAGCCCA
Found at i:18668123 original size:26 final size:26
Alignment explanation
Indices: 18668094--18668164 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 26
18668084 GTGACATAGC
*
18668094 AAAGCTACTAGTAACAGTAACGCAGT
1 AAAGCTACCAGTAACAGTAACGCAGT
* * *
18668120 AAAGCTGCCAGTAACAGTGACGTAGT
1 AAAGCTACCAGTAACAGTAACGCAGT
* *
18668146 AAAGCTGCCAATAACAGTA
1 AAAGCTACCAGTAACAGTA
18668165 TATGTAGCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.41, C:0.20, G:0.21, T:0.18
Consensus pattern (26 bp):
AAAGCTACCAGTAACAGTAACGCAGT
Found at i:18668161 original size:52 final size:52
Alignment explanation
Indices: 18668062--18668164 Score: 125
Period size: 52 Copynumber: 2.0 Consensus size: 52
18668052 ACACCAATAT
** * *
18668062 CGCAGCAAAGCTGCCAATAGTAGTGACATAGCAAAGCTACTAGTAACAGTAA
1 CGCAGCAAAGCTGCCAATAACAGTGACATAGCAAAGCTACCAATAACAGTAA
* * * * *
18668114 CGCAGTAAAGCTGCCAGTAACAGTGACGTAGTAAAGCTGCCAATAACAGTA
1 CGCAGCAAAGCTGCCAATAACAGTGACATAGCAAAGCTACCAATAACAGTA
18668165 TATGTAGCAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.39, C:0.21, G:0.22, T:0.17
Consensus pattern (52 bp):
CGCAGCAAAGCTGCCAATAACAGTGACATAGCAAAGCTACCAATAACAGTAA
Found at i:18668373 original size:27 final size:27
Alignment explanation
Indices: 18668342--18668639 Score: 287
Period size: 27 Copynumber: 11.0 Consensus size: 27
18668332 TATAATATTC
*
18668342 ATTTTACCCTAT-GGGGGTATTTCGGTT
1 ATTTTACCCT-TCGAGGGTATTTCGGTT
*
18668369 TTTTTACCCTTCGAGGGTATTTCGGTT
1 ATTTTACCCTTCGAGGGTATTTCGGTT
* * * *
18668396 ATTTTACCCTTCAAAGGTATTTTGGTC
1 ATTTTACCCTTCGAGGGTATTTCGGTT
* *
18668423 ATTTTACCCTTCGAAGGTATTTCGGTC
1 ATTTTACCCTTCGAGGGTATTTCGGTT
* * *
18668450 ATTGTACCCATCGAGGGTAATTT-GGTC
1 ATTTTACCCTTCGAGGGT-ATTTCGGTT
* * *
18668477 ATTTTACCCTTCGGGGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGGTT
* *
18668504 ATTTTACCCTTTG-GAGGTATTTCGGTC
1 ATTTTACCCTTCGAG-GGTATTTCGGTT
* * * * *
18668531 ATTTTATCCTTCAAGGATATTTTGGTC
1 ATTTTACCCTTCGAGGGTATTTCGGTT
*
18668558 ATTTTACCCTTCGAGGGTATTTCGGTC
1 ATTTTACCCTTCGAGGGTATTTCGGTT
* * *
18668585 ATTTTATCCTTCGAGAGTATTTCGGTC
1 ATTTTACCCTTCGAGGGTATTTCGGTT
*** *
18668612 ATTTCGTCCTTCGAGGGTATTTCAGTT
1 ATTTTACCCTTCGAGGGTATTTCGGTT
18668639 A
1 A
18668640 GTTGCCCATG
Statistics
Matches: 232, Mismatches: 34, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.03
27 221 0.95
28 5 0.02
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGGTT
Found at i:18668415 original size:54 final size:54
Alignment explanation
Indices: 18668340--18668634 Score: 324
Period size: 54 Copynumber: 5.5 Consensus size: 54
18668330 GGTATAATAT
** **
18668340 TCATTTTACCCTAT-GGGGGTATTTCGGTTTTTTTACCCTTCGAGGGTATTTCGG
1 TCATTTTACCCT-TCGAAGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCGG
* * * *
18668394 TTATTTTACCCTTCAAAGGTATTTTGGTCATTTTACCCTTCGAAGGTATTTCGG
1 TCATTTTACCCTTCGAAGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCGG
* * * * *
18668448 TCATTGTACCCATCGAGGGTAATTT-GGTCATTTTACCCTTCGGGGGTATTTCGA
1 TCATTTTACCCTTCGAAGGT-ATTTCGGTCATTTTACCCTTCGAGGGTATTTCGG
* * * * * *
18668502 TCATTTTACCCTTTGGAGGTATTTCGGTCATTTTATCCTTCAAGGATATTTTGG
1 TCATTTTACCCTTCGAAGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCGG
* * *
18668556 TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTATCCTTCGAGAGTATTTCGG
1 TCATTTTACCCTTCGAAGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCGG
*** *
18668610 TCATTTCGTCCTTCGAGGGTATTTC
1 TCATTTTACCCTTCGAAGGTATTTC
18668635 AGTTAGTTGC
Statistics
Matches: 201, Mismatches: 37, Indels: 6
0.82 0.15 0.02
Matches are distributed among these distances:
53 5 0.02
54 192 0.96
55 4 0.02
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (54 bp):
TCATTTTACCCTTCGAAGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCGG
Found at i:18668465 original size:81 final size:81
Alignment explanation
Indices: 18668340--18668634 Score: 353
Period size: 81 Copynumber: 3.6 Consensus size: 81
18668330 GGTATAATAT
* ** *
18668340 TCATTTTACCCTAT-GGGGGTATTTCGGTTTTTTTACCCTTCGAGGGTATTTCGGTTATTTTACC
1 TCATTTTACCCT-TCGGAGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACC
* * *
18668404 CTTCAAAGGTATTTTGG
65 CTTCGAGGGTATTTCGG
* * *
18668421 TCATTTTACCCTTCGAAGGTATTTCGGTCATTGTACCCATCGAGGGTAATTT-GGTCATTTTACC
1 TCATTTTACCCTTCGGAGGTATTTCGGTCATTTTACCCTTCGAGGGT-ATTTCGGTCATTTTACC
* *
18668485 CTTCGGGGGTATTTCGA
65 CTTCGAGGGTATTTCGG
* * * * *
18668502 TCATTTTACCCTTTGGAGGTATTTCGGTCATTTTATCCTTCAAGGATATTTTGGTCATTTTACCC
1 TCATTTTACCCTTCGGAGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCC
18668567 TTCGAGGGTATTTCGG
66 TTCGAGGGTATTTCGG
* ***
18668583 TCATTTTATCCTTC-GAGAGTATTTCGGTCATTTCGTCCTTCGAGGGTATTTC
1 TCATTTTACCCTTCGGAG-GTATTTCGGTCATTTTACCCTTCGAGGGTATTTC
18668635 AGTTAGTTGC
Statistics
Matches: 182, Mismatches: 28, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
80 8 0.04
81 170 0.93
82 4 0.02
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (81 bp):
TCATTTTACCCTTCGGAGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCC
TTCGAGGGTATTTCGG
Found at i:18673820 original size:14 final size:14
Alignment explanation
Indices: 18673801--18673828 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18673791 CCAATTTATT
18673801 AATGAATTATTAAA
1 AATGAATTATTAAA
18673815 AATGAATTATTAAA
1 AATGAATTATTAAA
18673829 TATAACTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AATGAATTATTAAA
Found at i:18687360 original size:12 final size:12
Alignment explanation
Indices: 18687345--18687373 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
18687335 TTTAAATAGA
18687345 ATTTTAAATTAT
1 ATTTTAAATTAT
18687357 ATTTTAAATTAT
1 ATTTTAAATTAT
18687369 ATTTT
1 ATTTT
18687374 TTTATAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATTTTAAATTAT
Found at i:18687544 original size:87 final size:87
Alignment explanation
Indices: 18687435--18687620 Score: 237
Period size: 87 Copynumber: 2.1 Consensus size: 87
18687425 TCATCGACCA
* * * * *
18687435 ATGAAAAGGGGTAGCTTCGGCTATCGATTATAAAAAGGGATAGTGATGACCGTCAACTATTAAAA
1 ATGAAAAGGGATAGCTTCGGCTATCGATTATAAAAAGGGACAGTGACGACCATCAACTATGAAAA
* *
18687500 GGGATGGGGACGACCATCGAAT
66 GAGATGGGGACGACCATCAAAT
* * * ** * *
18687522 ATGAAAAGGGATAGCTTTGGCTATTGATTATGAAAATTGACGGTGACGACCATGAACTATGAAAA
1 ATGAAAAGGGATAGCTTCGGCTATCGATTATAAAAAGGGACAGTGACGACCATCAACTATGAAAA
*
18687587 GAGATGGTGACGACCATCAAAT
66 GAGATGGGGACGACCATCAAAT
18687609 ATGAAAAGGGAT
1 ATGAAAAGGGAT
18687621 GGTTTCAACC
Statistics
Matches: 84, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
87 84 1.00
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (87 bp):
ATGAAAAGGGATAGCTTCGGCTATCGATTATAAAAAGGGACAGTGACGACCATCAACTATGAAAA
GAGATGGGGACGACCATCAAAT
Found at i:18687621 original size:29 final size:29
Alignment explanation
Indices: 18687467--18687623 Score: 109
Period size: 29 Copynumber: 5.4 Consensus size: 29
18687457 ATCGATTATA
* * * * *
18687467 AAAAGGGATAGTGATGACCGTCAACTATT
1 AAAAGGGATGGTGACGACCATCAAATATG
* *
18687496 AAAAGGGATGGGGACGACCATCGAATATG
1 AAAAGGGATGGTGACGACCATCAAATATG
* ** * * ** *
18687525 AAAAGGGATAGCT-TTGGCTATTGATTATG
1 AAAAGGGAT-GGTGACGACCATCAAATATG
** * * *
18687554 AAAATTGACGGTGACGACCATGAACTATG
1 AAAAGGGATGGTGACGACCATCAAATATG
*
18687583 AAAAGAGATGGTGACGACCATCAAATATG
1 AAAAGGGATGGTGACGACCATCAAATATG
18687612 AAAAGGGATGGT
1 AAAAGGGATGGT
18687624 TTCAACCATT
Statistics
Matches: 94, Mismatches: 32, Indels: 4
0.72 0.25 0.03
Matches are distributed among these distances:
28 2 0.02
29 91 0.97
30 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.22
Consensus pattern (29 bp):
AAAAGGGATGGTGACGACCATCAAATATG
Found at i:18687631 original size:29 final size:29
Alignment explanation
Indices: 18687570--18687663 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 29
18687560 GACGGTGACG
* * * * *
18687570 ACCATGAACTATGAAAAGAGATGGTGACG
1 ACCATCAAATATGAAAAGGGATGGTTACA
*
18687599 ACCATCAAATATGAAAAGGGATGGTTTCA
1 ACCATCAAATATGAAAAGGGATGGTTACA
** * * **
18687628 ACCATTGAACATGAAAAGGGACGGTTATG
1 ACCATCAAATATGAAAAGGGATGGTTACA
18687657 ACCATCA
1 ACCATCA
18687664 TTTAGCACAC
Statistics
Matches: 50, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.20
Consensus pattern (29 bp):
ACCATCAAATATGAAAAGGGATGGTTACA
Found at i:18687651 original size:87 final size:87
Alignment explanation
Indices: 18687489--18687661 Score: 204
Period size: 87 Copynumber: 2.0 Consensus size: 87
18687479 GATGACCGTC
* * * ** * **
18687489 AACTATTAAAAGGGATGGGGACGACCATCGAATATGAAAAGGGATAGCTTTGGCTATTGATTATG
1 AACTATGAAAAGAGATGGGGACGACCATCAAATATGAAAAGGGATAGCTTTAACCATTGAACATG
**
18687554 AAAATTGACGGTGACGACCATG
66 AAAAGGGACGGTGACGACCATG
* *
18687576 AACTATGAAAAGAGATGGTGACGACCATCAAATATGAAAAGGGAT-GGTTTCAACCATTGAACAT
1 AACTATGAAAAGAGATGGGGACGACCATCAAATATGAAAAGGGATAGCTTT-AACCATTGAACAT
* *
18687640 GAAAAGGGACGGTTATGACCAT
65 GAAAAGGGACGGTGACGACCAT
18687662 CATTTAGCAC
Statistics
Matches: 71, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
86 4 0.06
87 67 0.94
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (87 bp):
AACTATGAAAAGAGATGGGGACGACCATCAAATATGAAAAGGGATAGCTTTAACCATTGAACATG
AAAAGGGACGGTGACGACCATG
Found at i:18698097 original size:45 final size:45
Alignment explanation
Indices: 18698018--18698108 Score: 114
Period size: 45 Copynumber: 2.0 Consensus size: 45
18698008 ATAGAAATAA
18698018 AGAAATGGAAATCATTTAGAAATAATTATAGTTTTCTCCAAAATGG
1 AGAAATGGAAATCATTTAGAAATAATTATAGTTTTCT-CAAAATGG
* * * *
18698064 AGAAAT-GAAATCATTT-GAAAATTATTGTGGTTTTCTCAGAATGG
1 AGAAATGGAAATCATTTAG-AAATAATTATAGTTTTCTCAAAATGG
18698108 A
1 A
18698109 AATAGAAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
44 9 0.22
45 25 0.62
46 6 0.15
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.34
Consensus pattern (45 bp):
AGAAATGGAAATCATTTAGAAATAATTATAGTTTTCTCAAAATGG
Found at i:18701542 original size:79 final size:79
Alignment explanation
Indices: 18701411--18701569 Score: 300
Period size: 79 Copynumber: 2.0 Consensus size: 79
18701401 CTGCGGTTCA
*
18701411 TCAAGAAGTGTCAAAAGGCTCAAAATTGGTACTAAAGGTGAAGTATAAATAGGATAGTTTTTTAG
1 TCAAGAAGTGTCAAAAGCCTCAAAATTGGTACTAAAGGTGAAGTATAAATAGGATAGTTTTTTAG
18701476 CTCTGGGATGTGTT
66 CTCTGGGATGTGTT
18701490 TCAAGAAGTGTCAAAAGCCTCAAAATTGGTACTAAAGGTGAAGTATAAATAGGATAGTTTTTTAG
1 TCAAGAAGTGTCAAAAGCCTCAAAATTGGTACTAAAGGTGAAGTATAAATAGGATAGTTTTTTAG
*
18701555 CTCTTGGATGTGTT
66 CTCTGGGATGTGTT
18701569 T
1 T
18701570 TAAACAATGC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.34, C:0.09, G:0.24, T:0.33
Consensus pattern (79 bp):
TCAAGAAGTGTCAAAAGCCTCAAAATTGGTACTAAAGGTGAAGTATAAATAGGATAGTTTTTTAG
CTCTGGGATGTGTT
Found at i:18709481 original size:19 final size:20
Alignment explanation
Indices: 18709457--18709504 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
18709447 CTAAAAGAGT
**
18709457 TGAGAGAATGA-TGAATGAG
1 TGAGAGAATGATTGAAACAG
18709476 TGAGAG-ATGATTGAAACAG
1 TGAGAGAATGATTGAAACAG
18709495 TGAGA-AATGA
1 TGAGAGAATGA
18709505 GCTCTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.44, C:0.02, G:0.33, T:0.21
Consensus pattern (20 bp):
TGAGAGAATGATTGAAACAG
Found at i:18710836 original size:3 final size:3
Alignment explanation
Indices: 18710828--18710859 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
18710818 TTCTTTGTCT
18710828 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
18710860 TTAAGCATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:18722210 original size:35 final size:32
Alignment explanation
Indices: 18722173--18722259 Score: 99
Period size: 33 Copynumber: 2.7 Consensus size: 32
18722163 CATGCACACA
18722173 TATATATATTATTATATATATAACACCAAAACCC
1 TATATATATTATTATATATATAA-A-CAAAACCC
*
18722207 -ATATATATTA-TATATAAAT-AACAAAACCCC
1 TATATATATTATTATATATATAAACAAAA-CCC
*
18722237 TATACATATATATTATATATATA
1 TATATATAT-TATTATATATATA
18722260 CACATACCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
29 5 0.11
30 4 0.09
31 8 0.18
32 10 0.22
33 18 0.40
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (32 bp):
TATATATATTATTATATATATAAACAAAACCC
Found at i:18722213 original size:37 final size:36
Alignment explanation
Indices: 18722142--18722259 Score: 108
Period size: 37 Copynumber: 3.4 Consensus size: 36
18722132 ACCCACACAA
* ** *
18722142 ATATATTATACATATAACACCCATGCACACATATATAT
1 ATATATTATATATATAACA-CCA-AAACCCATATATAT
18722180 AT-TATTATATATATAACACCAAAACCCATATATAT
1 ATATATTATATATATAACACCAAAACCCATATATAT
* *
18722215 -TATA-TATA-A-AT-A-A-CAAAACCCCTATACAT
1 ATATATTATATATATAACACCAAAACCCATATATAT
18722244 ATATATTATATATATA
1 ATATATTATATATATA
18722260 CACATACCTT
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
29 14 0.21
30 5 0.07
31 5 0.07
32 3 0.04
33 3 0.04
34 5 0.07
35 13 0.19
36 3 0.04
37 15 0.22
38 2 0.03
ACGTcount: A:0.48, C:0.17, G:0.01, T:0.34
Consensus pattern (36 bp):
ATATATTATATATATAACACCAAAACCCATATATAT
Found at i:18722218 original size:30 final size:30
Alignment explanation
Indices: 18722176--18722255 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 30
18722166 GCACACATAT
*
18722176 ATATATTATTATATATATAACACCAAAACCC
1 ATATA-TATTATATATATAACAACAAAACCC
*
18722207 ATATATATTATATATA-AATAACAAAACCC
1 ATATATATTATATATATAACAACAAAACCC
* *
18722236 CTATACATATATATTATATA
1 ATATATAT-TATA-TATATA
18722256 TATACACATA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 17 0.40
30 15 0.36
31 9 0.21
32 1 0.02
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (30 bp):
ATATATATTATATATATAACAACAAAACCC
Found at i:18724345 original size:40 final size:39
Alignment explanation
Indices: 18724293--18724407 Score: 126
Period size: 40 Copynumber: 2.9 Consensus size: 39
18724283 GTTTGGATAA
*
18724293 AAAACAACGCTAAAGATCGAGCATTAGCGGCGCTTTTTGG
1 AAAAC-ACGCTAAAGATCAAGCATTAGCGGCGCTTTTTGG
* * *
18724333 AAAACACTGCTAAAGATCTAGCATTAGCGGCGCATTATGG
1 AAAACAC-GCTAAAGATCAAGCATTAGCGGCGCTTTTTGG
* * *
18724373 AAAACGCCACTAAAAAT-AAGCATTAGCGGCG-TTTT
1 AAAAC-ACGCTAAAGATCAAGCATTAGCGGCGCTTTT
18724408 CTAGAAAGCC
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.03
39 15 0.23
40 46 0.72
41 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.23
Consensus pattern (39 bp):
AAAACACGCTAAAGATCAAGCATTAGCGGCGCTTTTTGG
Found at i:18724521 original size:41 final size:40
Alignment explanation
Indices: 18724462--18724673 Score: 246
Period size: 41 Copynumber: 5.2 Consensus size: 40
18724452 TGAGCTTTCG
* *
18724462 GGGATTTAACGGCGTTTTTAATAAAGCGCCGCTAATGCTCA
1 GGGATTTAGCGGCGTTTTTGA-AAAGCGCCGCTAATGCTCA
* *
18724503 GGGATTTAGCGGCATTTTTGGAAAAGCACCGCTAATGCTCA
1 GGGATTTAGCGGCGTTTTT-GAAAAGCGCCGCTAATGCTCA
*
18724544 GGGATTTAGCGGCGTTTTTGGAAAAGTGCCGCTAATGCTCA
1 GGGATTTAGCGGCGTTTTT-GAAAAGCGCCGCTAATGCTCA
* * * * *
18724585 GGGCTATAGCAGCGTTTTTGAGAAAGCACCGTTAATGCTC-
1 GGGATTTAGCGGCGTTTTTGA-AAAGCGCCGCTAATGCTCA
* * * *
18724625 GGGGTTTAGCGGCATTTTCTAAAAAGCGCCGCTAATGCTTA
1 GGGATTTAGCGGCGTTTT-TGAAAAGCGCCGCTAATGCTCA
18724666 GGGATTTA
1 GGGATTTA
18724674 AAATAATTTA
Statistics
Matches: 145, Mismatches: 22, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
40 31 0.21
41 113 0.78
42 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (40 bp):
GGGATTTAGCGGCGTTTTTGAAAAGCGCCGCTAATGCTCA
Found at i:18725722 original size:7 final size:7
Alignment explanation
Indices: 18725710--18725763 Score: 72
Period size: 7 Copynumber: 7.7 Consensus size: 7
18725700 TGGGGTTTAA
18725710 GGGTTAG
1 GGGTTAG
18725717 GGGTTAG
1 GGGTTAG
* *
18725724 AGGTTAA
1 GGGTTAG
*
18725731 AGGTTAG
1 GGGTTAG
18725738 GGGTTAG
1 GGGTTAG
18725745 GGGTTAG
1 GGGTTAG
*
18725752 GGGCTAG
1 GGGTTAG
18725759 GGGTT
1 GGGTT
18725764 TATGTTTTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.19, C:0.02, G:0.52, T:0.28
Consensus pattern (7 bp):
GGGTTAG
Found at i:18730699 original size:43 final size:43
Alignment explanation
Indices: 18730612--18730903 Score: 354
Period size: 43 Copynumber: 6.8 Consensus size: 43
18730602 TTTTTGCGAG
* * * *
18730612 AAGCGTCGCTAAAGGT-TTGTTCTACAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAA
** ** * * *
18730654 AAGCGTTGCTAAAGGTCTCCAGCTATAGCGGTGTTTGTAGAAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAA
* * *
18730697 AAGAGCCGTTAAATGTCTTGATCTATAGCGGCGTTTGTGGAAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAA
* *
18730740 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGCTTGT-GCAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAA
* * *
18730782 AAGCGCCGCTAAAGGTCCTGATCTATAGCGGCATTTGTGGAGA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAA
* * *
18730825 AGGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAA
* *
18730868 AGGCGCCGCTAAAGGTCATGATCTATAGCGGCGTTT
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTT
18730904 ATTTCTAAAA
Statistics
Matches: 214, Mismatches: 34, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
42 53 0.25
43 161 0.75
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.26
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAA
Found at i:18730847 original size:128 final size:129
Alignment explanation
Indices: 18730612--18730900 Score: 359
Period size: 128 Copynumber: 2.3 Consensus size: 129
18730602 TTTTTGCGAG
* * * * * **
18730612 AAGCGTCGCTAAAGGT-TTGTTCTACAGCGGCGTTTGTGGGAAAAGCGTTGCTAAAGGTCTCCAG
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGCTTGTGGCAAAAGCGCCGCTAAAGGTCTCCAG
** * * *
18730676 CTATAGCGGTGTTTGTAGAAAAAGAGCCGTTAAATGTCTTGATCTATAGCGGCGTTTGTGGAAA
66 CTATAGCGGCATTTGTAGAAAAAGAGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGAAA
*
18730740 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGCTTGT-GCAAAAGCGCCGCTAAAGGTC-CTGA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGCTTGTGGCAAAAGCGCCGCTAAAGGTCTC-CA
* * * * * *
18730803 TCTATAGCGGCATTTGTGGAGAAGGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAA
65 GCTATAGCGGCATTTGTAGAAAAAGAGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGAAA
* *
18730868 AGGCGCCGCTAAAGGTCATGATCTATAGCGGCG
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCG
18730901 TTTATTTCTA
Statistics
Matches: 138, Mismatches: 21, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
127 1 0.01
128 119 0.86
129 18 0.13
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (129 bp):
AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGCTTGTGGCAAAAGCGCCGCTAAAGGTCTCCAG
CTATAGCGGCATTTGTAGAAAAAGAGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGAAA
Found at i:18734563 original size:12 final size:12
Alignment explanation
Indices: 18734546--18734571 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18734536 GAAAAATCAG
18734546 TTTTATTTAATA
1 TTTTATTTAATA
18734558 TTTTATTTAATA
1 TTTTATTTAATA
18734570 TT
1 TT
18734572 ATTTACTTAT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTATTTAATA
Found at i:18736281 original size:24 final size:24
Alignment explanation
Indices: 18736250--18736299 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
18736240 TAAATAGTAG
*
18736250 CTTTAATTATTA-TTTCTTG-TATA
1 CTTTAATT-TTAGTTTATTGTTATA
18736273 CTTTGAATTTTAGTTTATTGTTATA
1 CTTT-AATTTTAGTTTATTGTTATA
18736298 CT
1 CT
18736300 GACTTGCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 7 0.30
24 10 0.43
25 6 0.26
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (24 bp):
CTTTAATTTTAGTTTATTGTTATA
Found at i:18740536 original size:219 final size:219
Alignment explanation
Indices: 18740150--18740590 Score: 812
Period size: 219 Copynumber: 2.0 Consensus size: 219
18740140 ATCAGGACCA
18740150 GACGTGACAGGGAATCCGTTACCCAATCATCTTGATAAAGGGGTAAATGCGATAATCGAGAGTGG
1 GACGTGACAGGGAATCCGTTACCCAATCATCTTGATAAAGGGGTAAATGCGATAATCGAGAGTGG
* *
18740215 GAGAAAGAGAATCAAGGTCTACATTTCAGAGATAAAAACCCCCCTGAGTTGGGTTTGGAAACAAA
66 GAGAAAAAGAATCAAGGTCTACATTTCAGAGATAAAAACCCCACTGAGTTGGGTTTGGAAACAAA
18740280 TGATAGAGGGAGGTCTCATCAAACAAGATTTAAAGGAAAGGCCCGAAGGAATGAGGACGTAGTGT
131 TGATAGAGGGAGGTCTCATCAAACAAGATTTAAAGGAAAGGCCCGAAGGAATGAGGACGTAGTGT
18740345 GAGTTTCATGCCGAAGAGAGCCAT
196 GAGTTTCATGCCGAAGAGAGCCAT
* *
18740369 GACGTGGCAGGGAATCCGTTACCCAATCAT-TCTGATAAAGGGGTAAATGTGATAATCGAGAGTG
1 GACGTGACAGGGAATCCGTTACCCAATCATCT-TGATAAAGGGGTAAATGCGATAATCGAGAGTG
* *
18740433 GGAGAAAAAGAATCAGGGTCTACATTTCAGAGATAAAAACCCCACTGAGTTGGGTTTGGAGACAA
65 GGAGAAAAAGAATCAAGGTCTACATTTCAGAGATAAAAACCCCACTGAGTTGGGTTTGGAAACAA
18740498 ATGATAGAGGGAGGTCTCATCAAACAAGATTTAAAGGAAAGGCCCGAAGGAATGAGGACGTAGTG
130 ATGATAGAGGGAGGTCTCATCAAACAAGATTTAAAGGAAAGGCCCGAAGGAATGAGGACGTAGTG
18740563 TGAGTTTCATGCCGAAGAGAGCCAT
195 TGAGTTTCATGCCGAAGAGAGCCAT
18740588 GAC
1 GAC
18740591 ATCCAAAAAT
Statistics
Matches: 215, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
218 1 0.00
219 214 1.00
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.20
Consensus pattern (219 bp):
GACGTGACAGGGAATCCGTTACCCAATCATCTTGATAAAGGGGTAAATGCGATAATCGAGAGTGG
GAGAAAAAGAATCAAGGTCTACATTTCAGAGATAAAAACCCCACTGAGTTGGGTTTGGAAACAAA
TGATAGAGGGAGGTCTCATCAAACAAGATTTAAAGGAAAGGCCCGAAGGAATGAGGACGTAGTGT
GAGTTTCATGCCGAAGAGAGCCAT
Found at i:18747077 original size:43 final size:43
Alignment explanation
Indices: 18746990--18747293 Score: 226
Period size: 43 Copynumber: 7.0 Consensus size: 43
18746980 GTATTGGCGT
* * *
18746990 GAAGTAGATCGAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG
1 GAAGTGGATCGAAGA-AGCAAGTCATGTCTTCCTATATTGGTAG
*
18747034 GAAGTGGATCGAAGAAGCAAGTCATGTCTTCCTATATTAGTAG
1 GAAGTGGATCGAAGAAGCAAGTCATGTCTTCCTATATTGGTAG
*
18747077 GAAGTGGATCGAAGATGC-AGAT-ATCGTCTTCCTATATTGGTAG
1 GAAGTGGATCGAAGAAGCAAG-TCAT-GTCTTCCTATATTGGTAG
* * *
18747120 GAAGTGGATCGAAGATA-C-AGATCTTG-CTTTCCCATATTGGTGG
1 GAAGTGGATCGAAGA-AGCAAG-TCATGTC-TTCCTATATTGGTAG
* * * * * * *
18747163 CGGAGTAGATCGAAGAAAGC-AGATCTTGTCTTCGTGTGTTGGCAG
1 -GAAGTGGATCGAAG-AAGCAAG-TCATGTCTTCCTATATTGGTAG
* * ** *
18747208 TGAAGTAGATCGAAGATAGCAGGTTTTGTCTTCTTATATTGGTAG
1 -GAAGTGGATCGAAGA-AGCAAGTCATGTCTTCCTATATTGGTAG
* * * * *
18747253 GAAGTGGATCAAAGATGC-AGATCTTGTCTTCCCATACTGGT
1 GAAGTGGATCGAAGAAGCAAG-TCATGTCTTCCTATATTGGT
18747294 GGCGAAGTAG
Statistics
Matches: 214, Mismatches: 34, Indels: 25
0.78 0.12 0.09
Matches are distributed among these distances:
42 6 0.03
43 112 0.52
44 42 0.20
45 52 0.24
46 2 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (43 bp):
GAAGTGGATCGAAGAAGCAAGTCATGTCTTCCTATATTGGTAG
Found at i:18747256 original size:133 final size:132
Alignment explanation
Indices: 18747077--18747327 Score: 362
Period size: 133 Copynumber: 1.9 Consensus size: 132
18747067 ATATTAGTAG
* *
18747077 GAAGTGGATCGAAGATGCAGATATCGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATACAGAT
1 GAAGTAGATCGAAGATGCAGATATCGTCTTCCTATATTGGTAGGAAGTGGATCAAAGATACAGAT
* * * *
18747142 CTTG-CTTTCCCATATTGGTGGCGGAGTAG-ATCGAAGAAAGCAGATCTTGTCTTCGTGTGTTGG
66 CTTGTC-TTCCCATACTGGTGGCGAAGTAGAAT-GAAGAAAACAGATCTTATCTTCGTGTGTTGG
18747205 CAGT
129 CAGT
* * * * *
18747209 GAAGTAGATCGAAGATAGCAGGTTTTGTCTTCTTATATTGGTAGGAAGTGGATCAAAGATGCAGA
1 GAAGTAGATCGAAGAT-GCAGATATCGTCTTCCTATATTGGTAGGAAGTGGATCAAAGATACAGA
18747274 TCTTGTCTTCCCATACTGGTGGCGAAGTAGAATGAAGAAAACAGATCTTATCTT
65 TCTTGTCTTCCCATACTGGTGGCGAAGTAGAATGAAGAAAACAGATCTTATCTT
18747328 TCTGAAGTTG
Statistics
Matches: 105, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
132 15 0.14
133 87 0.83
134 3 0.03
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.30
Consensus pattern (132 bp):
GAAGTAGATCGAAGATGCAGATATCGTCTTCCTATATTGGTAGGAAGTGGATCAAAGATACAGAT
CTTGTCTTCCCATACTGGTGGCGAAGTAGAATGAAGAAAACAGATCTTATCTTCGTGTGTTGGCA
GT
Found at i:18747311 original size:88 final size:86
Alignment explanation
Indices: 18746967--18747327 Score: 309
Period size: 88 Copynumber: 4.1 Consensus size: 86
18746957 ATTAAAACAT
* * * * * *
18746967 ATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAGCAGGTCCTGTCTTCCTATATTGG
1 ATCTTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAGAT-GCAGATCTTGTCTTCCTATATTGG
*
18747031 TAGGAAGTGGATCGAAGA-AGCA-
64 TAGGAAGTAGATCGAAGATA-CAG
* * * *
18747053 AGTCATGTCTTCCTATATTAGTAGGAAGTGGATCGAAGATGCAGATATCGTCTTCCTATATTGGT
1 A-TCTTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCTATATTGGT
*
18747118 AGGAAGTGGATCGAAGATACAG
65 AGGAAGTAGATCGAAGATACAG
* * * * * * * *
18747140 ATCTTG-CTTTCCCATATTGGTGGCGGAGTAGATCGAAGAAAGCAGATCTTGTCTTCGTGTGTTG
1 ATCTTGTC-TTCCTATATTGGTAG-GAAGTGGATCGAAG-ATGCAGATCTTGTCTTCCTATATTG
*
18747204 GCAGTGAAGTAGATCGAAGATAGCAG
63 GTAG-GAAGTAGATCGAAGATA-CAG
* * * * * * *
18747230 GTTTTGTCTTCTTATATTGGTAGGAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATACTGGTG
1 ATCTTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCTATATTGGTA
*
18747295 GCGAAGTAGAAT-GAAGAAAACAG
66 G-GAAGTAG-ATCGAAG-ATACAG
*
18747318 ATCTTATCTT
1 ATCTTGTCTT
18747328 TCTGAAGTTG
Statistics
Matches: 218, Mismatches: 45, Indels: 22
0.76 0.16 0.08
Matches are distributed among these distances:
85 1 0.00
86 57 0.26
87 44 0.20
88 65 0.30
89 31 0.14
90 19 0.09
91 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.31
Consensus pattern (86 bp):
ATCTTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCTATATTGGTA
GGAAGTAGATCGAAGATACAG
Found at i:18747469 original size:50 final size:50
Alignment explanation
Indices: 18747388--18747567 Score: 182
Period size: 50 Copynumber: 3.6 Consensus size: 50
18747378 GCAGTGGAAC
** * *
18747388 AGATTGAAGCTACAACGGTGAATCTTGCTTCCCTGACATTGCAATTAAAA
1 AGATTGAAGCCGCAACGGCGAATCTTACTTCCCTGACATTGCAATTAAAA
* * * * * ** **
18747438 AGATTGAATCCGCAACGGTGAATTTTACTTCCCTGGCGA-TGCAGTGGATT
1 AGATTGAAGCCGCAACGGCGAATCTTACTTCCCTGAC-ATTGCAATTAAAA
** * *
18747488 AGATTGAAGCTACGACGGCGAATCTTGCTTCCCTGACATTGCAATTAAAA
1 AGATTGAAGCCGCAACGGCGAATCTTACTTCCCTGACATTGCAATTAAAA
*
18747538 AGATTGAAGCCGCAACAGCGAATCTTACTT
1 AGATTGAAGCCGCAACGGCGAATCTTACTT
18747568 TTCTAGCAGT
Statistics
Matches: 99, Mismatches: 29, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
49 1 0.01
50 97 0.98
51 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (50 bp):
AGATTGAAGCCGCAACGGCGAATCTTACTTCCCTGACATTGCAATTAAAA
Found at i:18747543 original size:100 final size:100
Alignment explanation
Indices: 18747370--18747567 Score: 324
Period size: 100 Copynumber: 2.0 Consensus size: 100
18747360 CCTTATCTCT
*
18747370 CTGGCGATGCAGTGGAACAGATTGAAGCTACAACGGTGAATCTTGCTTCCCTGACATTGCAATTA
1 CTGGCGATGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTGCTTCCCTGACATTGCAATTA
* * * *
18747435 AAAAGATTGAATCCGCAACGGTGAATTTTACTTCC
66 AAAAGATTGAAGCCGCAACAGCGAATCTTACTTCC
** *
18747470 CTGGCGATGCAGTGGATTAGATTGAAGCTACGACGGCGAATCTTGCTTCCCTGACATTGCAATTA
1 CTGGCGATGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTGCTTCCCTGACATTGCAATTA
18747535 AAAAGATTGAAGCCGCAACAGCGAATCTTACTT
66 AAAAGATTGAAGCCGCAACAGCGAATCTTACTT
18747568 TTCTAGCAGT
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 90 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (100 bp):
CTGGCGATGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTGCTTCCCTGACATTGCAATTA
AAAAGATTGAAGCCGCAACAGCGAATCTTACTTCC
Found at i:18749160 original size:12 final size:12
Alignment explanation
Indices: 18749143--18749168 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18749133 GAAAAATCAG
18749143 TTTTATTTAATA
1 TTTTATTTAATA
18749155 TTTTATTTAATA
1 TTTTATTTAATA
18749167 TT
1 TT
18749169 ATTTACTTAT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTATTTAATA
Found at i:18751644 original size:60 final size:63
Alignment explanation
Indices: 18751555--18751673 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 63
18751545 TGAAAAAGGA
18751555 AAAGATAAAAACAATATATATTAAATACTTTG-TTTTATT-TT-TTATTTTTAAAA-AAACCCCT
1 AAAGATAAAAACAATATATATTAAATAC-TTGATTTTATTATTATTA-TTTTAAAACAAACCCCT
** * *
18751616 AAAGAT-AAAACCTTATATATTTATTACTTGATTTTATTATTATTATTTTAAAACAAAC
1 AAAGATAAAAACAATATATATTAAATACTTGATTTTATTATTATTATTTTAAAACAAAC
18751674 TCATTTAAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
59 3 0.06
60 24 0.48
61 16 0.32
62 7 0.14
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (63 bp):
AAAGATAAAAACAATATATATTAAATACTTGATTTTATTATTATTATTTTAAAACAAACCCCT
Found at i:18754274 original size:17 final size:17
Alignment explanation
Indices: 18754252--18754286 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
18754242 AGATCCATGA
18754252 CTAAGAACTCATAGTGC
1 CTAAGAACTCATAGTGC
18754269 CTAAGAACTCATAGTGC
1 CTAAGAACTCATAGTGC
18754286 C
1 C
18754287 CACAACAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (17 bp):
CTAAGAACTCATAGTGC
Found at i:18765973 original size:56 final size:56
Alignment explanation
Indices: 18765903--18766014 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
18765893 TAAATTAAAA
18765903 AATGTTTTTGTTCATTGTGCATTCACATACCACTACAATCATGATACTACAAGAAT
1 AATGTTTTTGTTCATTGTGCATTCACATACCACTACAATCATGATACTACAAGAAT
*
18765959 AATGTTTTTGTTCATTGTGCATTCACATACCACTACAATCATGATACTGCAAGAAT
1 AATGTTTTTGTTCATTGTGCATTCACATACCACTACAATCATGATACTACAAGAAT
18766015 GACTATTAGT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.36
Consensus pattern (56 bp):
AATGTTTTTGTTCATTGTGCATTCACATACCACTACAATCATGATACTACAAGAAT
Found at i:18771565 original size:17 final size:17
Alignment explanation
Indices: 18771538--18771572 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
18771528 GTATCATGAA
18771538 TTAACTTAAAATATCAAC
1 TTAACTTAAAATAT-AAC
18771556 TTAA-TTAAAATATAAC
1 TTAACTTAAAATATAAC
18771572 T
1 T
18771573 AAAAATAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 9 0.53
18 4 0.24
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (17 bp):
TTAACTTAAAATATAAC
Found at i:18772513 original size:14 final size:14
Alignment explanation
Indices: 18772417--18772514 Score: 63
Period size: 14 Copynumber: 7.0 Consensus size: 14
18772407 TTCTTTTCAA
* *
18772417 CTCAATACTCAATA
1 CTCAATCCTCAATT
* *
18772431 CTGATTCCTCAATT
1 CTCAATCCTCAATT
* ** *
18772445 TTCAATTTTCAAAT
1 CTCAATCCTCAATT
*
18772459 CTCAAAT-CTCAAAT
1 CTC-AATCCTCAATT
* *
18772473 CTCAATCATCAATC
1 CTCAATCCTCAATT
*
18772487 CTCAATCCTCAATC
1 CTCAATCCTCAATT
*
18772501 CTCAATTCTCAATT
1 CTCAATCCTCAATT
18772515 ATTTCTTTAA
Statistics
Matches: 64, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
13 3 0.05
14 58 0.91
15 3 0.05
ACGTcount: A:0.34, C:0.30, G:0.01, T:0.36
Consensus pattern (14 bp):
CTCAATCCTCAATT
Found at i:18772513 original size:21 final size:20
Alignment explanation
Indices: 18772417--18772513 Score: 70
Period size: 21 Copynumber: 4.7 Consensus size: 20
18772407 TTCTTTTCAA
* * *
18772417 CTCAATACTCAATACTGATTC
1 CTCAATTCTCAAT-CTCAATC
* *
18772438 CTCAATTTTCAATTTTCAAAT-
1 CTCAATTCTCAA-TCTC-AATC
*
18772459 CTCAAATCTCAAATCTCAATC
1 CTCAATTCTC-AATCTCAATC
* *
18772480 ATCAATCCTCAATCCTCAATC
1 CTCAATTCTCAAT-CTCAATC
18772501 CTCAATTCTCAAT
1 CTCAATTCTCAAT
18772514 TATTTCTTTA
Statistics
Matches: 58, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
20 6 0.10
21 47 0.81
22 5 0.09
ACGTcount: A:0.34, C:0.30, G:0.01, T:0.35
Consensus pattern (20 bp):
CTCAATTCTCAATCTCAATC
Found at i:18772514 original size:7 final size:7
Alignment explanation
Indices: 18772438--18772514 Score: 66
Period size: 7 Copynumber: 11.0 Consensus size: 7
18772428 ATACTGATTC
18772438 CTCAATT
1 CTCAATT
*
18772445 TTCAATT
1 CTCAATT
* *
18772452 TTCAAAT
1 CTCAATT
*
18772459 CTCAAAT
1 CTCAATT
*
18772466 CTCAAAT
1 CTCAATT
18772473 CTCAA-T
1 CTCAATT
*
18772479 CATCAATC
1 C-TCAATT
*
18772487 CTCAATC
1 CTCAATT
*
18772494 CTCAATC
1 CTCAATT
18772501 CTCAATT
1 CTCAATT
18772508 CTCAATT
1 CTCAATT
18772515 ATTTCTTTAA
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
6 2 0.03
7 60 0.95
8 1 0.02
ACGTcount: A:0.34, C:0.30, G:0.00, T:0.36
Consensus pattern (7 bp):
CTCAATT
Found at i:18777294 original size:21 final size:22
Alignment explanation
Indices: 18777268--18777314 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
18777258 ATGGGTAGGA
18777268 ATTGTTTTCTGAAAAA-TA-TGC
1 ATTGTTTT-TGAAAAAGTATTGC
18777289 ATTGTTTTTGAAAAAGTATTGC
1 ATTGTTTTTGAAAAAGTATTGC
18777311 ATTG
1 ATTG
18777315 ACATCGTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 7 0.29
21 10 0.42
22 7 0.29
ACGTcount: A:0.32, C:0.06, G:0.17, T:0.45
Consensus pattern (22 bp):
ATTGTTTTTGAAAAAGTATTGC
Found at i:18777754 original size:21 final size:21
Alignment explanation
Indices: 18777722--18777767 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
18777712 TGCCAAAGTC
*
18777722 AACTCATCACTT-GTATTTTTA
1 AACTCATCACTTCGT-TTTTGA
18777743 AACTCAAT-ACTTCGTTTTTGA
1 AACTC-ATCACTTCGTTTTTGA
18777764 AACT
1 AACT
18777768 TAACACTACC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (21 bp):
AACTCATCACTTCGTTTTTGA
Found at i:18779096 original size:17 final size:18
Alignment explanation
Indices: 18779064--18779098 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
18779054 TCAAATGAAC
18779064 ATAAATGGATAGAAATGGT
1 ATAAATGGA-AGAAATGGT
18779083 ATAAATGG-AGAAATGG
1 ATAAATGGAAGAAATGG
18779099 GAAACATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.23
Consensus pattern (18 bp):
ATAAATGGAAGAAATGGT
Found at i:18785441 original size:24 final size:24
Alignment explanation
Indices: 18785410--18785455 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
18785400 CAAAAATACT
18785410 AAAAAATT-AAAATAAATATTTACC
1 AAAAAATTGAAAATAAAT-TTTACC
18785434 AAAAAATTGAAAATAAATTTTA
1 AAAAAATTGAAAATAAATTTTA
18785456 AAAAATATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.30
Consensus pattern (24 bp):
AAAAAATTGAAAATAAATTTTACC
Found at i:18785537 original size:30 final size:30
Alignment explanation
Indices: 18785496--18785563 Score: 127
Period size: 30 Copynumber: 2.2 Consensus size: 30
18785486 TATATGCAAC
18785496 TTAAGCAAATGCCTCTAAAATAATAACAAAA
1 TTAA-CAAATGCCTCTAAAATAATAACAAAA
18785527 TTAACAAATGCCTCTAAAATAATAACAAAA
1 TTAACAAATGCCTCTAAAATAATAACAAAA
18785557 TTAACAA
1 TTAACAA
18785564 TAAAATAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 33 0.89
31 4 0.11
ACGTcount: A:0.56, C:0.16, G:0.04, T:0.24
Consensus pattern (30 bp):
TTAACAAATGCCTCTAAAATAATAACAAAA
Found at i:18786953 original size:22 final size:21
Alignment explanation
Indices: 18786917--18786969 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 21
18786907 ATTAATGTTT
*
18786917 AAAATTTAAAAATTTA---AA
1 AAAATTCAAAAATTTATTTAA
18786935 AAAATTCAAAAATTTATTTAA
1 AAAATTCAAAAATTTATTTAA
*
18786956 AAAATTTAAAAATT
1 AAAATTCAAAAATT
18786970 CTTAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 15 0.50
21 15 0.50
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAATTCAAAAATTTATTTAA
Found at i:18788160 original size:11 final size:11
Alignment explanation
Indices: 18788144--18788230 Score: 51
Period size: 11 Copynumber: 8.3 Consensus size: 11
18788134 TCAATTATTT
18788144 TCTCAATTTCC
1 TCTCAATTTCC
* *
18788155 TCTCAAATTGC
1 TCTCAATTTCC
18788166 TCTCAATTTCC
1 TCTCAATTTCC
18788177 T-TCCAAATTT-C
1 TCT-C-AATTTCC
*
18788188 TCTCAA-ATCC
1 TCTCAATTTCC
* **
18788198 -AT--ATTTAA
1 TCTCAATTTCC
*
18788206 TCTCAATTTGC
1 TCTCAATTTCC
18788217 TCTCAATTTCC
1 TCTCAATTTCC
18788228 TCT
1 TCT
18788231 TTAATTTCTC
Statistics
Matches: 55, Mismatches: 13, Indels: 16
0.65 0.15 0.19
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.05
10 4 0.07
11 40 0.73
12 6 0.11
ACGTcount: A:0.24, C:0.30, G:0.02, T:0.44
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:18788171 original size:22 final size:22
Alignment explanation
Indices: 18788144--18788193 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
18788134 TCAATTATTT
18788144 TCTCAATTTCC-TCTCAAATTGC
1 TCTCAATTTCCTTC-CAAATTGC
*
18788166 TCTCAATTTCCTTCCAAATTTC
1 TCTCAATTTCCTTCCAAATTGC
18788188 TCTCAA
1 TCTCAA
18788194 ATCCATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 24 0.92
23 2 0.08
ACGTcount: A:0.24, C:0.32, G:0.02, T:0.42
Consensus pattern (22 bp):
TCTCAATTTCCTTCCAAATTGC
Found at i:18788265 original size:51 final size:51
Alignment explanation
Indices: 18788155--18788254 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
18788145 CTCAATTTCC
*
18788155 TCTCAAATTGCTCTCAATTTCCTTCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAATTTGCTCTCAATTTCCTTCCAAATTTCTCTCAAATCCATATTTAA
** * *
18788206 TCTCAATTTGCTCTCAATTTCC-TCTTTAATTTCTCTTAAATCCCTATTT
1 TCTCAATTTGCTCTCAATTTCCTTC-CAAATTTCTCTCAAATCCATATTT
18788255 TTAATTAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 2 0.05
51 41 0.95
ACGTcount: A:0.25, C:0.27, G:0.02, T:0.46
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAATTTCCTTCCAAATTTCTCTCAAATCCATATTTAA
Found at i:18790363 original size:21 final size:20
Alignment explanation
Indices: 18790339--18790379 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
18790329 AGATACCCTA
* *
18790339 CCGGAGGAACCAGAATCCCCG
1 CCGGAGCAACCACAA-CCCCG
18790360 CCGGAGCAACCACAACCCCG
1 CCGGAGCAACCACAACCCCG
18790380 ACCGAAAGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.29, C:0.44, G:0.24, T:0.02
Consensus pattern (20 bp):
CCGGAGCAACCACAACCCCG
Found at i:18790595 original size:26 final size:26
Alignment explanation
Indices: 18790566--18790617 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
18790556 AACCCTAAAC
18790566 TAATTTATTAA-T-AATTTATAAATTTA
1 TAATTTA-TAATTAAATTTAT-AATTTA
18790592 TAATTTATAATTAAATTTATAATTTA
1 TAATTTATAATTAAATTTATAATTTA
18790618 ATTGAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 3 0.12
26 14 0.58
27 7 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TAATTTATAATTAAATTTATAATTTA
Found at i:18790596 original size:7 final size:7
Alignment explanation
Indices: 18790576--18790617 Score: 61
Period size: 7 Copynumber: 6.1 Consensus size: 7
18790566 TAATTTATTA
18790576 ATAATTT
1 ATAATTT
18790583 ATAAATTT
1 AT-AATTT
18790591 ATAATTT
1 ATAATTT
18790598 ATAA-TT
1 ATAATTT
18790604 A-AATTT
1 ATAATTT
18790610 ATAATTT
1 ATAATTT
18790617 A
1 A
18790618 ATTGAAAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 2 0.06
6 6 0.19
7 17 0.53
8 7 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
ATAATTT
Found at i:18790596 original size:15 final size:14
Alignment explanation
Indices: 18790576--18790617 Score: 61
Period size: 12 Copynumber: 3.1 Consensus size: 14
18790566 TAATTTATTA
18790576 ATAATTTATAAATTT
1 ATAATTTAT-AATTT
18790591 ATAATTTATAA-TT
1 ATAATTTATAATTT
18790604 A-AATTTATAATTT
1 ATAATTTATAATTT
18790617 A
1 A
18790618 ATTGAAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 9 0.35
13 6 0.23
14 2 0.08
15 9 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAATTTATAATTT
Found at i:18790648 original size:18 final size:18
Alignment explanation
Indices: 18790625--18790699 Score: 60
Period size: 18 Copynumber: 3.9 Consensus size: 18
18790615 TTAATTGAAA
*
18790625 AACCCTAACAAAAACCTT
1 AACCCTAACAAAAACCAT
* * *
18790643 AACCCTAACCATAACCCT
1 AACCCTAACAAAAACCAT
*
18790661 AACCCTTAACTTAAAAACACCAA
1 AACCC-TAAC---AAAA-ACCAT
18790684 AACCCTAACAAAAACC
1 AACCCTAACAAAAACC
18790700 CTAGCCCTAG
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
18 23 0.51
19 8 0.18
22 6 0.13
23 8 0.18
ACGTcount: A:0.49, C:0.36, G:0.00, T:0.15
Consensus pattern (18 bp):
AACCCTAACAAAAACCAT
Found at i:18790652 original size:12 final size:12
Alignment explanation
Indices: 18790637--18790670 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
18790627 CCCTAACAAA
18790637 AACCTTAACCCT
1 AACCTTAACCCT
*
18790649 AACCATAACCCT
1 AACCTTAACCCT
18790661 AACCCTTAAC
1 AA-CCTTAAC
18790671 TTAAAAACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (12 bp):
AACCTTAACCCT
Found at i:18790731 original size:33 final size:33
Alignment explanation
Indices: 18790693--18790800 Score: 129
Period size: 33 Copynumber: 3.5 Consensus size: 33
18790683 AAACCCTAAC
*
18790693 AAAAACCCTAGCCCTAGCCCTAACCCTTAACTT
1 AAAAACCCTAACCCTAGCCCTAACCCTTAACTT
* * *
18790726 AAAAACCCTAACCATAGCCTTAACACTTAACTT
1 AAAAACCCTAACCCTAGCCCTAACCCTTAACTT
*
18790759 AAAAA--CT----CTAACCCTAACCCTTAACTT
1 AAAAACCCTAACCCTAGCCCTAACCCTTAACTT
18790786 AAAAACCCTAACCCT
1 AAAAACCCTAACCCT
18790801 TAACTTAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
27 21 0.34
29 2 0.03
31 2 0.03
33 36 0.59
ACGTcount: A:0.40, C:0.35, G:0.03, T:0.22
Consensus pattern (33 bp):
AAAAACCCTAACCCTAGCCCTAACCCTTAACTT
Found at i:18790770 original size:21 final size:21
Alignment explanation
Indices: 18790768--18790812 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
18790758 TAAAAACTCT
*
18790768 AACCCTAACCCTTAACTTAAA
1 AACCCTAACACTTAACTTAAA
*
18790789 AACCCTAACCCTTAACTTAAA
1 AACCCTAACACTTAACTTAAA
18790810 AAC
1 AAC
18790813 ACCAAAACGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.22
Consensus pattern (21 bp):
AACCCTAACACTTAACTTAAA
Found at i:18790781 original size:27 final size:27
Alignment explanation
Indices: 18790704--18790911 Score: 123
Period size: 27 Copynumber: 7.7 Consensus size: 27
18790694 AAAACCCTAG
*
18790704 CCCTAGCCCTAACCCTTAACTTAAAAA
1 CCCTAACCCTAACCCTTAACTTAAAAA
*
18790731 CCCTAACCATAGCCTTAACACTTAACTTAAAAA
1 CCCTAA-C----CC-TAACCCTTAACTTAAAAA
*
18790764 CTCTAACCCTAACCCTTAACTT--AAA
1 CCCTAACCCTAACCCTTAACTTAAAAA
18790789 ----AACCCTAACCCTTAACTTAAAAA
1 CCCTAACCCTAACCCTTAACTTAAAAA
* * *** * * *
18790812 CACCAAAACGCTAA-CAAAAAC--CATAG
1 C-CC-TAACCCTAACCCTTAACTTAAAAA
*
18790838 CCCTAACCCTAAACCTTAACTTAAAAA
1 CCCTAACCCTAACCCTTAACTTAAAAA
*
18790865 CCCTAACCATAACCC-TAACCCTT-AAAA
1 CCCTAACCCTAACCCTTAA--CTTAAAAA
18790892 CCCTAACCCTAACCCCTTAA
1 CCCTAACCCTAA-CCCTTAA
18790912 AAACCCTTAA
Statistics
Matches: 138, Mismatches: 22, Indels: 40
0.69 0.11 0.20
Matches are distributed among these distances:
21 18 0.13
23 3 0.02
24 7 0.05
25 9 0.07
26 6 0.04
27 47 0.34
28 13 0.09
29 10 0.07
32 3 0.02
33 22 0.16
ACGTcount: A:0.42, C:0.36, G:0.02, T:0.21
Consensus pattern (27 bp):
CCCTAACCCTAACCCTTAACTTAAAAA
Found at i:18790877 original size:6 final size:6
Alignment explanation
Indices: 18790863--18790906 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
18790853 TTAACTTAAA
*
18790863 AACCCT AACCAT AACCCT AACCCTT AAAACCCT AACCCT AACCC
1 AACCCT AACCCT AACCCT AACCC-T --AACCCT AACCCT AACCC
18790907 CTTAAAAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 26 0.79
7 1 0.03
8 1 0.03
9 5 0.15
ACGTcount: A:0.39, C:0.45, G:0.00, T:0.16
Consensus pattern (6 bp):
AACCCT
Found at i:18790898 original size:21 final size:23
Alignment explanation
Indices: 18790869--18790918 Score: 77
Period size: 21 Copynumber: 2.3 Consensus size: 23
18790859 TAAAAACCCT
*
18790869 AACCATAACCCTAA-CCCTT-AA
1 AACCCTAACCCTAACCCCTTAAA
18790890 AACCCTAACCCTAACCCCTTAAA
1 AACCCTAACCCTAACCCCTTAAA
18790913 AACCCT
1 AACCCT
18790919 TAACTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 13 0.50
22 5 0.19
23 8 0.31
ACGTcount: A:0.40, C:0.42, G:0.00, T:0.18
Consensus pattern (23 bp):
AACCCTAACCCTAACCCCTTAAA
Found at i:18790904 original size:134 final size:137
Alignment explanation
Indices: 18790655--18790929 Score: 385
Period size: 134 Copynumber: 2.0 Consensus size: 137
18790645 CCCTAACCAT
* * *
18790655 AACCCTAACCCTTAACTTAAAAACACCAAAACCCTAACAAAAACCCTAGCCCTAGCCCTAACCCT
1 AACCCTAACCCTTAACTTAAAAACACCAAAACCCTAACAAAAACCATAGCCCTAACCCTAAACCT
* * *** *
18790720 TAACTTAAAAACCCTAACCATAGCCTTAACACTTAACTTAAAAACTCTAA-CCC-T-AACCCTTA
66 TAACTTAAAAACCCTAACCATAACCCTAACACTTAAAACAAAAACCCTAACCCCTTAAACCCTTA
18790782 ACTTAAA
131 ACTTAAA
*
18790789 AACCCTAACCCTTAACTTAAAAACACCAAAACGCTAACAAAAACCATAGCCCTAACCCTAAACCT
1 AACCCTAACCCTTAACTTAAAAACACCAAAACCCTAACAAAAACCATAGCCCTAACCCTAAACCT
* ***
18790854 TAACTTAAAAACCCTAACCATAACCCTAACCCTTAAAACCCTAACCCTAACCCCTTAAAAACCCT
66 TAACTTAAAAACCCTAACCATAACCCTAACACTTAAAACAAAAACCCTAACCCCTT--AAACCCT
18790919 TAACTTAAA
129 TAACTTAAA
18790928 AA
1 AA
18790930 TACCAAAACC
Statistics
Matches: 122, Mismatches: 14, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
134 101 0.83
135 3 0.02
136 1 0.01
139 17 0.14
ACGTcount: A:0.44, C:0.35, G:0.02, T:0.20
Consensus pattern (137 bp):
AACCCTAACCCTTAACTTAAAAACACCAAAACCCTAACAAAAACCATAGCCCTAACCCTAAACCT
TAACTTAAAAACCCTAACCATAACCCTAACACTTAAAACAAAAACCCTAACCCCTTAAACCCTTA
ACTTAAA
Found at i:18791052 original size:56 final size:56
Alignment explanation
Indices: 18790991--18791165 Score: 162
Period size: 56 Copynumber: 3.1 Consensus size: 56
18790981 TAATTTGATA
*
18790991 ATTTTACTAACATTTAATACAATTAACAATTAATAATTTGACTAACAAAATGTTAG
1 ATTTTACTAACATTTAATACAATTAACAATTAATAATTTGACTAAAAAAATGTTAG
* * * * * * ** *
18791047 ATTTTAC-AAAATGTT-TTGACTGGTACTAACAATTAATCATTTGA-T-ATAATTTGATA-
1 ATTTTACTAACAT-TTAAT-AC---AATTAACAATTAATAATTTGACTAAAAAAATGTTAG
* *
18791103 ATTTTACTAACAATTAATACAATTAACAATTAATAATTTTACTAAAAAAATGTTAG
1 ATTTTACTAACATTTAATACAATTAACAATTAATAATTTGACTAAAAAAATGTTAG
18791159 ATTTTAC
1 ATTTTAC
18791166 AAAATATTTT
Statistics
Matches: 89, Mismatches: 20, Indels: 20
0.69 0.16 0.16
Matches are distributed among these distances:
53 17 0.19
54 1 0.01
55 12 0.13
56 29 0.33
57 11 0.12
58 1 0.01
59 18 0.20
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (56 bp):
ATTTTACTAACATTTAATACAATTAACAATTAATAATTTGACTAAAAAAATGTTAG
Found at i:18791146 original size:35 final size:36
Alignment explanation
Indices: 18790988--18791147 Score: 92
Period size: 35 Copynumber: 4.4 Consensus size: 36
18790978 ATATAATTTG
*
18790988 ATAATTTTACTAACATTTAATACAATTA-ACAATTA
1 ATAATTTTACTAACAATTAATACAATTACACAATTA
* * ** * * * *
18791023 ATAATTTGACTAACAAAATGTTAGATTTTACAAAATGTT
1 ATAATTTTACTAAC-AATTAATACA-ATTACACAAT-TA
* * ** * * * *
18791062 TTGACTGGTACTAACAATTAAT-CATTTGATATAATTTG
1 AT-AATTTTACTAACAATTAATACAATT-ACACAA-TTA
18791100 ATAATTTTACTAACAATTAATACAATTA-ACAATTA
1 ATAATTTTACTAACAATTAATACAATTACACAATTA
18791135 ATAATTTTACTAA
1 ATAATTTTACTAA
18791148 AAAAATGTTA
Statistics
Matches: 89, Mismatches: 28, Indels: 16
0.67 0.21 0.12
Matches are distributed among these distances:
35 28 0.31
36 8 0.09
37 23 0.26
38 15 0.17
39 7 0.08
40 8 0.09
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (36 bp):
ATAATTTTACTAACAATTAATACAATTACACAATTA
Found at i:18791204 original size:112 final size:112
Alignment explanation
Indices: 18790971--18791210 Score: 374
Period size: 112 Copynumber: 2.1 Consensus size: 112
18790961 ACCCTAACCC
*
18790971 TAATCTGATATAATTTGATAATTTTACTAACATTTAATACAATTAACAATTAATAATTTGACTAA
1 TAATCTGATATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTGACTAA
* * * * *
18791036 CAAAATGTTAGATTTTACAAAATGTTTTGACTGGTACTAACAATTAA
66 AAAAATGTTAGATTTTACAAAATATTTTGACTGGTACAAAAAAATAA
* * *
18791083 TCATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTACTAA
1 TAATCTGATATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTGACTAA
*
18791148 AAAAATGTTAGATTTTACAAAATATTTTGATTGGTACAAAAAAA-ATA
66 AAAAATGTTAGATTTTACAAAATATTTTGACTGGTACAAAAAAATA-A
18791195 TAATCTGATATAATTT
1 TAATCTGATATAATTT
18791211 TAATAACAAG
Statistics
Matches: 115, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
111 1 0.01
112 114 0.99
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (112 bp):
TAATCTGATATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTGACTAA
AAAAATGTTAGATTTTACAAAATATTTTGACTGGTACAAAAAAATAA
Found at i:18791445 original size:22 final size:22
Alignment explanation
Indices: 18791417--18791465 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
18791407 AACCCTACTT
18791417 TAATTTATTTTTTCTTAAAAAA
1 TAATTTATTTTTTCTTAAAAAA
18791439 TAATTTATTTTTTCTTAAAAAA
1 TAATTTATTTTTTCTTAAAAAA
18791461 TAATT
1 TAATT
18791466 AACACGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATTTATTTTTTCTTAAAAAA
Found at i:18791978 original size:8 final size:8
Alignment explanation
Indices: 18791965--18791996 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
18791955 TTTAATTCTT
18791965 AACCCTAA
1 AACCCTAA
18791973 AACCCTAA
1 AACCCTAA
18791981 AA-CCT-A
1 AACCCTAA
18791987 AACCCTAA
1 AACCCTAA
18791995 AA
1 AA
18791997 GTGCAGGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 3 0.14
7 6 0.27
8 13 0.59
ACGTcount: A:0.53, C:0.34, G:0.00, T:0.12
Consensus pattern (8 bp):
AACCCTAA
Found at i:18793171 original size:31 final size:30
Alignment explanation
Indices: 18793107--18793184 Score: 95
Period size: 31 Copynumber: 2.6 Consensus size: 30
18793097 AAGTTGTGGG
* * *
18793107 TTTAGTCATTGTAC-TTTAATTTGATTAAT
1 TTTAGTCACTGTACTTTTAAGTTGATCAAT
*
18793136 TTTAGTCACTGTACTTTTAAAGTTGGTCAAT
1 TTTAGTCACTGTACTTTT-AAGTTGATCAAT
*
18793167 TTTAGTCTCTGTACTTTT
1 TTTAGTCACTGTACTTTT
18793185 TGAATTTTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 13 0.31
30 3 0.07
31 26 0.62
ACGTcount: A:0.23, C:0.12, G:0.13, T:0.53
Consensus pattern (30 bp):
TTTAGTCACTGTACTTTTAAGTTGATCAAT
Found at i:18794310 original size:18 final size:18
Alignment explanation
Indices: 18794264--18794304 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
18794254 GATAAAAATT
*
18794264 AATATATTAATTAAACTA
1 AATAAATTAATTAAACTA
* *
18794282 ATTAAATTAATTAACCTA
1 AATAAATTAATTAAACTA
18794300 AATAA
1 AATAA
18794305 CATAATGGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (18 bp):
AATAAATTAATTAAACTA
Done.