Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 84 of 89
Found at i:20240071 original size:11 final size:11
Alignment explanation
Indices: 20240055--20240079 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20240045 ACACTCAAGT
20240055 CAAACAATGAG
1 CAAACAATGAG
20240066 CAAACAATGAG
1 CAAACAATGAG
20240077 CAA
1 CAA
20240080 GAAAGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.20, G:0.16, T:0.08
Consensus pattern (11 bp):
CAAACAATGAG
Found at i:20242016 original size:21 final size:21
Alignment explanation
Indices: 20241964--20242010 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
20241954 GGAAGGTGGA
20241964 GGTCTCGGGTGCACGCGTTGG
1 GGTCTCGGGTGCACGCGTTGG
*
20241985 GGTCTCGGGTGCATGCGTTGG
1 GGTCTCGGGTGCACGCGTTGG
20242006 GGTCT
1 GGTCT
20242011 TCGGTGTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.04, C:0.21, G:0.47, T:0.28
Consensus pattern (21 bp):
GGTCTCGGGTGCACGCGTTGG
Found at i:20242254 original size:17 final size:18
Alignment explanation
Indices: 20242224--20242257 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
20242214 AGGAGGCGAC
20242224 AAGCGATGAACGACGATT
1 AAGCGATGAACGACGATT
*
20242242 AAGC-ATGACCGACGAT
1 AAGCGATGAACGACGAT
20242258 CTCGGGTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (18 bp):
AAGCGATGAACGACGATT
Found at i:20242715 original size:21 final size:21
Alignment explanation
Indices: 20242675--20242713 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20242665 GTGTTTAGAG
20242675 AAAAATAAAATAAAATAAATC
1 AAAAATAAAATAAAATAAATC
*
20242696 AAAAATAAAA-ATAATAAA
1 AAAAATAAAATAAAATAAA
20242714 ATAAAGTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (21 bp):
AAAAATAAAATAAAATAAATC
Found at i:20246223 original size:19 final size:19
Alignment explanation
Indices: 20246199--20246250 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
20246189 CTTAAGGGGT
20246199 TGCATCGATGCACTCATCA
1 TGCATCGATGCACTCATCA
*
20246218 TGCATCAATGCACTCATCA
1 TGCATCGATGCACTCATCA
*
20246237 TGCATCGATACACT
1 TGCATCGATGCACT
20246251 AATTGCATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.27
Consensus pattern (19 bp):
TGCATCGATGCACTCATCA
Found at i:20246239 original size:11 final size:11
Alignment explanation
Indices: 20246201--20246240 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
20246191 TAAGGGGTTG
20246201 CATCGATGCACT
1 CATC-ATGCACT
20246213 CATCATGCA-T
1 CATCATGCACT
20246223 CA--ATGCACT
1 CATCATGCACT
20246232 CATCATGCA
1 CATCATGCA
20246241 TCGATACACT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
8 5 0.20
9 3 0.12
10 3 0.12
11 10 0.40
12 4 0.16
ACGTcount: A:0.30, C:0.33, G:0.12, T:0.25
Consensus pattern (11 bp):
CATCATGCACT
Found at i:20251000 original size:14 final size:14
Alignment explanation
Indices: 20250981--20251010 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
20250971 TGAACCTACG
20250981 AGAAGAAGAAAGAA
1 AGAAGAAGAAAGAA
20250995 AGAAGAAGAAAGAA
1 AGAAGAAGAAAGAA
20251009 AG
1 AG
20251011 CTTACAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (14 bp):
AGAAGAAGAAAGAA
Found at i:20253828 original size:21 final size:21
Alignment explanation
Indices: 20253780--20253829 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
20253770 ATGCAATTAG
*
20253780 CTTTTCCTGGGACGTAACCAA
1 CTTTTCTTGGGACGTAACCAA
20253801 CTTTTCTTGGGACGTAACCAA
1 CTTTTCTTGGGACGTAACCAA
20253822 CTTTTCTT
1 CTTTTCTT
20253830 ATGAAATTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.26, G:0.16, T:0.38
Consensus pattern (21 bp):
CTTTTCTTGGGACGTAACCAA
Found at i:20255277 original size:4 final size:5
Alignment explanation
Indices: 20255250--20255274 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
20255240 AGATGAGAAG
20255250 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
20255275 TAATTATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:20256203 original size:24 final size:21
Alignment explanation
Indices: 20256176--20256227 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 21
20256166 AAATCCTAAT
*
20256176 TAAAATACTTAAAACTATTTAAAC
1 TAAAATACAT-AAA-TA-TTAAAC
*
20256200 TAAAATACATAAATATTAAAT
1 TAAAATACATAAATATTAAAC
20256221 TAAAATA
1 TAAAATA
20256228 ATATCCTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 12 0.46
22 2 0.08
23 3 0.12
24 9 0.35
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAATACATAAATATTAAAC
Found at i:20256688 original size:32 final size:32
Alignment explanation
Indices: 20256591--20256777 Score: 110
Period size: 32 Copynumber: 5.9 Consensus size: 32
20256581 ATTTTAAAAA
* * *
20256591 TTATAAAATATTTATT-AACTTTATCAAAATG
1 TTATAAAATAATCATTAAATTTTATCAAAATG
* * * ** **
20256622 TTATGAAATTATTATTAAATTTTATTGAGTTG
1 TTATAAAATAATCATTAAATTTTATCAAAATG
* * *
20256654 TTATAAAATGATCATTAATTTTTATCAAACTG
1 TTATAAAATAATCATTAAATTTTATCAAAATG
* * ** *
20256686 TTATAAAATAATCATTAAATTATATTAAGTTA
1 TTATAAAATAATCATTAAATTTTATCAAAATG
* * * * *
20256718 TTATTAAATAGTCATTAAGA-TTTATTAAATTA
1 TTATAAAATAATCATTAA-ATTTTATCAAAATG
* * *
20256750 TTACAAAATAATTATTTAA-TTTATCAAA
1 TTATAAAATAATCATTAAATTTTATCAAA
20256778 CTTATATTTA
Statistics
Matches: 121, Mismatches: 33, Indels: 4
0.77 0.21 0.03
Matches are distributed among these distances:
31 22 0.18
32 98 0.81
33 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (32 bp):
TTATAAAATAATCATTAAATTTTATCAAAATG
Found at i:20256688 original size:64 final size:64
Alignment explanation
Indices: 20256590--20256735 Score: 170
Period size: 64 Copynumber: 2.3 Consensus size: 64
20256580 AATTTTAAAA
* * * * * * * *
20256590 ATTATAAAATATTTATTAA-CTTTATCAAAATGTTATGAAATTATTATTAAATTTTATTGAGTT
1 ATTATAAAATAGTCATTAATTTTTATCAAAATGTTATAAAATAATCATTAAATTATATTAAGTT
* *
20256653 GTTATAAAAT-GATCATTAATTTTTATCAAACTGTTATAAAATAATCATTAAATTATATTAAGTT
1 ATTATAAAATAG-TCATTAATTTTTATCAAAATGTTATAAAATAATCATTAAATTATATTAAGTT
*
20256717 ATTATTAAATAGTCATTAA
1 ATTATAAAATAGTCATTAA
20256736 GATTTATTAA
Statistics
Matches: 68, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
63 15 0.22
64 52 0.76
65 1 0.01
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (64 bp):
ATTATAAAATAGTCATTAATTTTTATCAAAATGTTATAAAATAATCATTAAATTATATTAAGTT
Found at i:20256718 original size:10 final size:11
Alignment explanation
Indices: 20256622--20256752 Score: 58
Period size: 11 Copynumber: 12.3 Consensus size: 11
20256612 TATCAAAATG
*
20256622 TTATGAAATTA
1 TTATTAAATTA
20256633 TTATTAAATT-
1 TTATTAAATTA
* * *
20256643 TTATTGAGTTG
1 TTATTAAATTA
* *
20256654 TTATAAAATGA
1 TTATTAAATTA
* *
20256665 TCATT-AATTT
1 TTATTAAATTA
* * *
20256675 TTATCAAACTG
1 TTATTAAATTA
* *
20256686 TTATAAAATAA
1 TTATTAAATTA
*
20256697 TCATTAAATTA
1 TTATTAAATTA
*
20256708 -TATTAAGTTA
1 TTATTAAATTA
20256718 TTATTAAA-TA
1 TTATTAAATTA
*
20256728 GTCATTAAGA-T-
1 -TTATTAA-ATTA
20256739 TTATTAAATTA
1 TTATTAAATTA
20256750 TTA
1 TTA
20256753 CAAAATAATT
Statistics
Matches: 85, Mismatches: 28, Indels: 14
0.67 0.22 0.11
Matches are distributed among these distances:
9 1 0.01
10 31 0.36
11 51 0.60
12 2 0.02
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (11 bp):
TTATTAAATTA
Found at i:20256724 original size:21 final size:21
Alignment explanation
Indices: 20256699--20256750 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
20256689 TAAAATAATC
*
20256699 ATTAAATTAT-ATTAAGTTATT
1 ATTAAATTATCATTAAGAT-TT
20256720 ATTAAA-TAGTCATTAAGATTT
1 ATTAAATTA-TCATTAAGATTT
20256741 ATTAAATTAT
1 ATTAAATTAT
20256751 TACAAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.07
21 16 0.59
22 9 0.33
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (21 bp):
ATTAAATTATCATTAAGATTT
Found at i:20256742 original size:64 final size:64
Alignment explanation
Indices: 20256610--20256770 Score: 171
Period size: 64 Copynumber: 2.5 Consensus size: 64
20256600 ATTTATTAAC
* * * * * **
20256610 TTTATCAAAATGTTATGAAATTATTATTAAATTTTATTGAGTTGTTATAAAATGATCATTAATT
1 TTTATCAAAATGTTATAAAATAATTATTAAATTATATTAAGTTATTATAAAATGATCATTAAGA
* * *
20256674 TTTATCAAACTGTTATAAAATAATCATTAAATTATATTAAGTTATTATTAAAT-AGTCATTAAGA
1 TTTATCAAAATGTTATAAAATAATTATTAAATTATATTAAGTTATTATAAAATGA-TCATTAAGA
* * * * *
20256738 TTTATTAAATTATTACAAAATAATTATTTAATT
1 TTTATCAAAATGTTATAAAATAATTATTAAATT
20256771 TATCAAACTT
Statistics
Matches: 80, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
63 1 0.01
64 79 0.99
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (64 bp):
TTTATCAAAATGTTATAAAATAATTATTAAATTATATTAAGTTATTATAAAATGATCATTAAGA
Found at i:20258387 original size:21 final size:21
Alignment explanation
Indices: 20258364--20258409 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
20258354 TTTAAAATTT
*
20258364 AAATTTTAATATATATTTTTTA
1 AAATATTAATAT-TATTTTTTA
* *
20258386 AAATATTATTATTATTTTTAA
1 AAATATTAATATTATTTTTTA
20258407 AAA
1 AAA
20258410 ATTTTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AAATATTAATATTATTTTTTA
Found at i:20258389 original size:22 final size:22
Alignment explanation
Indices: 20258364--20258416 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
20258354 TTTAAAATTT
*
20258364 AAATTTTAATATATATTTTT-TA
1 AAATTTTAATAT-TATTTTTAAA
* *
20258386 AAATATTATTATTATTTTTAAA
1 AAATTTTAATATTATTTTTAAA
20258408 AAATTTTAA
1 AAATTTTAA
20258417 AAAAATTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AAATTTTAATATTATTTTTAAA
Found at i:20258646 original size:32 final size:31
Alignment explanation
Indices: 20258610--20258681 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 31
20258600 CTTTTAAAAC
* * *
20258610 TTGCAATTTAATC-CCCTAATATTTAGTCCGTT
1 TTGCAATATAATCACTC-AATATTTAATCCG-T
*
20258642 TTGCAATATGATCACTCAATATTTAATCCGT
1 TTGCAATATAATCACTCAATATTTAATCCGT
20258673 TTGCAATAT
1 TTGCAATAT
20258682 GGTCTCCGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 10 0.29
32 23 0.66
33 2 0.06
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (31 bp):
TTGCAATATAATCACTCAATATTTAATCCGT
Found at i:20260468 original size:20 final size:21
Alignment explanation
Indices: 20260423--20260469 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
20260413 CCTTCCATTA
*
20260423 ATTTATGTTTTTATTTTTTTC
1 ATTTATGTTTTGATTTTTTTC
*
20260444 TTTTATG-TTTGATTTTTTAT-
1 ATTTATGTTTTGATTTTTT-TC
20260464 ATTTAT
1 ATTTAT
20260470 TAATTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.74
Consensus pattern (21 bp):
ATTTATGTTTTGATTTTTTTC
Found at i:20260937 original size:75 final size:75
Alignment explanation
Indices: 20260814--20260958 Score: 263
Period size: 75 Copynumber: 1.9 Consensus size: 75
20260804 TTTTGACAAG
* *
20260814 ATAGAACTCCCTAATTTTATTTAAAAATATAAAATATTCAAATTACAGTAAAATTTTATAATCAT
1 ATAGAACTCCCTAATTTAATTTAAAAATATAAAATATTCAAATTACAGTAAAAGTTTATAATCAT
20260879 AATAAGAATA
66 AATAAGAATA
*
20260889 ATAGAACTTCCTAATTTAATTTAAAAATATAAAATATTCAAATTACAGTAAAAGTTTATAATCAT
1 ATAGAACTCCCTAATTTAATTTAAAAATATAAAATATTCAAATTACAGTAAAAGTTTATAATCAT
20260954 AATAA
66 AATAA
20260959 TAAACTAAAC
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (75 bp):
ATAGAACTCCCTAATTTAATTTAAAAATATAAAATATTCAAATTACAGTAAAAGTTTATAATCAT
AATAAGAATA
Found at i:20267581 original size:128 final size:128
Alignment explanation
Indices: 20267353--20267611 Score: 482
Period size: 128 Copynumber: 2.0 Consensus size: 128
20267343 AAAATTTCTT
*
20267353 CAAATTATGACCACTCCCTGAATCATCAAGCTGATTATTCTTATTTCCATGCATATATCTCCCAG
1 CAAATTATGACCACCCCCTGAATCATCAAGCTGATTATTCTTATTTCCATGCATATATCTCCCAG
*
20267418 CAAGCAAGATTTTAGACTCACTGACAGAGATAGAAACACTAACAGACCACTCATGCTGAACAA
66 CAAGCAAGATGTTAGACTCACTGACAGAGATAGAAACACTAACAGACCACTCATGCTGAACAA
20267481 CAAATTATGACCACCCCCTGAATCATCAAGCTGATTATTCTTATTTCCATGCATATATCTCCCAG
1 CAAATTATGACCACCCCCTGAATCATCAAGCTGATTATTCTTATTTCCATGCATATATCTCCCAG
* *
20267546 CAAGCAAGATGTTGGACTCACTGACAGAGATAGAAACACTAACAGACCTCTCATGCTGAACAA
66 CAAGCAAGATGTTAGACTCACTGACAGAGATAGAAACACTAACAGACCACTCATGCTGAACAA
20267609 CAA
1 CAA
20267612 TAGCAAAGAT
Statistics
Matches: 127, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
128 127 1.00
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (128 bp):
CAAATTATGACCACCCCCTGAATCATCAAGCTGATTATTCTTATTTCCATGCATATATCTCCCAG
CAAGCAAGATGTTAGACTCACTGACAGAGATAGAAACACTAACAGACCACTCATGCTGAACAA
Found at i:20267801 original size:216 final size:216
Alignment explanation
Indices: 20267427--20267861 Score: 870
Period size: 216 Copynumber: 2.0 Consensus size: 216
20267417 GCAAGCAAGA
20267427 TTTTAGACTCACTGACAGAGATAGAAACACTAACAGACCACTCATGCTGAACAACAAATTATGAC
1 TTTTAGACTCACTGACAGAGATAGAAACACTAACAGACCACTCATGCTGAACAACAAATTATGAC
20267492 CACCCCCTGAATCATCAAGCTGATTATTCTTATTTCCATGCATATATCTCCCAGCAAGCAAGATG
66 CACCCCCTGAATCATCAAGCTGATTATTCTTATTTCCATGCATATATCTCCCAGCAAGCAAGATG
20267557 TTGGACTCACTGACAGAGATAGAAACACTAACAGACCTCTCATGCTGAACAACAATAGCAAAGAT
131 TTGGACTCACTGACAGAGATAGAAACACTAACAGACCTCTCATGCTGAACAACAATAGCAAAGAT
20267622 TTCATTATTAGATCGCATGGG
196 TTCATTATTAGATCGCATGGG
20267643 TTTTAGACTCACTGACAGAGATAGAAACACTAACAGACCACTCATGCTGAACAACAAATTATGAC
1 TTTTAGACTCACTGACAGAGATAGAAACACTAACAGACCACTCATGCTGAACAACAAATTATGAC
20267708 CACCCCCTGAATCATCAAGCTGATTATTCTTATTTCCATGCATATATCTCCCAGCAAGCAAGATG
66 CACCCCCTGAATCATCAAGCTGATTATTCTTATTTCCATGCATATATCTCCCAGCAAGCAAGATG
20267773 TTGGACTCACTGACAGAGATAGAAACACTAACAGACCTCTCATGCTGAACAACAATAGCAAAGAT
131 TTGGACTCACTGACAGAGATAGAAACACTAACAGACCTCTCATGCTGAACAACAATAGCAAAGAT
20267838 TTCATTATTAGATCGCATGGG
196 TTCATTATTAGATCGCATGGG
20267859 TTT
1 TTT
20267862 CATCATCAGA
Statistics
Matches: 219, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
216 219 1.00
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (216 bp):
TTTTAGACTCACTGACAGAGATAGAAACACTAACAGACCACTCATGCTGAACAACAAATTATGAC
CACCCCCTGAATCATCAAGCTGATTATTCTTATTTCCATGCATATATCTCCCAGCAAGCAAGATG
TTGGACTCACTGACAGAGATAGAAACACTAACAGACCTCTCATGCTGAACAACAATAGCAAAGAT
TTCATTATTAGATCGCATGGG
Found at i:20275794 original size:38 final size:36
Alignment explanation
Indices: 20275674--20275796 Score: 112
Period size: 37 Copynumber: 3.4 Consensus size: 36
20275664 CAAGTTGGAA
* *
20275674 AATTTATCTTTAGTAGGTGGCCAACTTTTCACATGAG
1 AATTTATCTTTGGTAGGTGGCCAAC-TTTCATATGAG
* * *
20275711 AATTTCATC-TTGGTTGGTGACCAAC-TT-AT-TGAAA
1 AATTT-ATCTTTGGTAGGTGGCCAACTTTCATATG-AG
20275745 AATTTATCTTTGGTAGGTGGCCAACTTTGCATATG-G
1 AATTTATCTTTGGTAGGTGGCCAACTTT-CATATGAG
20275781 TAATTTCATCTTTGGT
1 -AATTT-ATCTTTGGT
20275797 CCCTAAAATA
Statistics
Matches: 69, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
33 5 0.07
34 21 0.30
35 4 0.06
37 25 0.36
38 14 0.20
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.41
Consensus pattern (36 bp):
AATTTATCTTTGGTAGGTGGCCAACTTTCATATGAG
Found at i:20277123 original size:22 final size:21
Alignment explanation
Indices: 20277084--20277124 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
20277074 ACATATGATG
*
20277084 TAAAATAAAATATTTACAATA
1 TAAAATAAAACATTTACAATA
20277105 TAAAATAACAACATTTACAA
1 TAAAATAA-AACATTTACAA
20277125 CATGTACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAATAAAACATTTACAATA
Found at i:20277275 original size:30 final size:29
Alignment explanation
Indices: 20277241--20277317 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 29
20277231 AAACAGGAGT
20277241 TTAAAGGACTAAAATGGCAAAAATAGAAAC
1 TTAAAGG-CTAAAATGGCAAAAATAGAAAC
* *
20277271 TTAAATGGCTAAAATAGTAAAAATAGAAAC
1 TTAAA-GGCTAAAATGGCAAAAATAGAAAC
*
20277301 TTAAGGGTCTAAAATGG
1 TTAAAGG-CTAAAATGG
20277318 TATTAACAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 2 0.05
30 37 0.90
31 2 0.05
ACGTcount: A:0.52, C:0.08, G:0.18, T:0.22
Consensus pattern (29 bp):
TTAAAGGCTAAAATGGCAAAAATAGAAAC
Found at i:20278805 original size:9 final size:9
Alignment explanation
Indices: 20278791--20278829 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
20278781 ATATGTAAAT
20278791 TAAAAATAA
1 TAAAAATAA
*
20278800 TAAAAAGAA
1 TAAAAATAA
*
20278809 TAATAATAA
1 TAAAAATAA
*
20278818 TAATAATAA
1 TAAAAATAA
20278827 TAA
1 TAA
20278830 TATAATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (9 bp):
TAAAAATAA
Found at i:20278813 original size:3 final size:3
Alignment explanation
Indices: 20278795--20278836 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
20278785 GTAAATTAAA
* *
20278795 AAT AAT AAA AAG AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
20278837 TTAACAAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:20279322 original size:130 final size:129
Alignment explanation
Indices: 20279150--20279384 Score: 380
Period size: 130 Copynumber: 1.8 Consensus size: 129
20279140 CTACACGATA
* *
20279150 AGGACAGCTGGTTATCTGGGGTAACATGACTCCTACGTGATGAGCTGGTCTGGTCAGGGGATGAC
1 AGGACAGCTAGTTATCTGGGGTAACATGACTCCTACGTGATGAGCAGGTCTGGTCAGGGGATGAC
* *
20279215 ACAGTTCCTACGTGATGAGGACGGCAGACCATCTTTTAGGGTGATAATATGGTTACTACGTGATG
66 ACAGTTCCTACGTGATGAGGACGGAAAACCAT-TTTTAGGGTGATAATATGGTTACTACGTGATG
* * *
20279280 AGGACGGCTAGTTATCTGGGGTGACATGACTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGAC
1 AGGACAGCTAGTTATCTGGGGTAACATGACTCCTACGTGATGAGCAGGTCTGGTCAGGGGATGAC
* *
20279345 ACGGTTCCTACGTGATGAGGATGGAAAACCATTTTTAGGG
66 ACAGTTCCTACGTGATGAGGACGGAAAACCATTTTTAGGG
20279385 ATATTGGTTT
Statistics
Matches: 96, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
129 8 0.08
130 88 0.92
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (129 bp):
AGGACAGCTAGTTATCTGGGGTAACATGACTCCTACGTGATGAGCAGGTCTGGTCAGGGGATGAC
ACAGTTCCTACGTGATGAGGACGGAAAACCATTTTTAGGGTGATAATATGGTTACTACGTGATG
Found at i:20279819 original size:64 final size:63
Alignment explanation
Indices: 20279653--20279834 Score: 202
Period size: 64 Copynumber: 2.8 Consensus size: 63
20279643 TGTTTTGAGG
* * * * * *** **
20279653 AAAATTTTCTCAAGTGAGACAACACTTTGTTTCAAATGAAACAAACTCAATTTTTTTTTTCAAA
1 AAAATTGTCTCAAGAGAGACAAAACTTTGTTTCTAA-GAAACAGACTCAAAGATTTTCATCAAA
* * *
20279717 AAAACTGTCTCAAAAGAGACAAAATTTTGTTTCCTAAGAAACAGACTCAAAGATTTTCATCAAA
1 AAAATTGTCTCAAGAGAGACAAAACTTTGTTT-CTAAGAAACAGACTCAAAGATTTTCATCAAA
* *
20279781 AGAAATTGTCTCAAGAGAGACAAAACTTTGTTTTTAAGAAACGGACTCAAAGAT
1 A-AAATTGTCTCAAGAGAGACAAAACTTTGTTTCTAAGAAACAGACTCAAAGAT
20279835 GATTTTTGTT
Statistics
Matches: 98, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
64 67 0.68
65 31 0.32
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (63 bp):
AAAATTGTCTCAAGAGAGACAAAACTTTGTTTCTAAGAAACAGACTCAAAGATTTTCATCAAA
Found at i:20279979 original size:36 final size:35
Alignment explanation
Indices: 20279886--20279989 Score: 120
Period size: 36 Copynumber: 2.9 Consensus size: 35
20279876 AGAACAAATG
* *
20279886 TCTCAAACGAGACGAAATTTG-TTTTACGAGAAATTG
1 TCTCAAGCGAGACGAAATTTGTTTTTA-GA-AAATTA
*
20279922 TCTCAAGCGAGACAAAATTTGTTTTTAGAAAATTA
1 TCTCAAGCGAGACGAAATTTGTTTTTAGAAAATTA
* * *
20279957 TCTTAAGTGGGACGAAACTTTGTTTTTAGAAAA
1 TCTCAAGCGAGACGAAA-TTTGTTTTTAGAAAA
20279990 ACACCCTCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
35 18 0.31
36 36 0.61
37 5 0.08
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.34
Consensus pattern (35 bp):
TCTCAAGCGAGACGAAATTTGTTTTTAGAAAATTA
Found at i:20285247 original size:30 final size:30
Alignment explanation
Indices: 20285153--20285274 Score: 82
Period size: 30 Copynumber: 4.0 Consensus size: 30
20285143 CTTGAAATTA
* *
20285153 AAAAGGACCAAAATGGAAAAAAACATAAACTT
1 AAAA-GACCAAAATAG-TAAAAACATAAACTT
* * * ** **
20285185 AAAGGACCAAAATAGTACAAATAGGAGTTT
1 AAAAGACCAAAATAGTAAAAACATAAACTT
* *
20285215 AAAAGACTAAAATGGTAAAAACATAAACTT
1 AAAAGACCAAAATAGTAAAAACATAAACTT
* * * * *
20285245 AAATGGCTAAAACAGTAAAAACAAAAACTT
1 AAAAGACCAAAATAGTAAAAACATAAACTT
20285275 GAGGGTATAA
Statistics
Matches: 67, Mismatches: 23, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
30 54 0.81
31 10 0.15
32 3 0.04
ACGTcount: A:0.58, C:0.11, G:0.13, T:0.17
Consensus pattern (30 bp):
AAAAGACCAAAATAGTAAAAACATAAACTT
Found at i:20286467 original size:3 final size:3
Alignment explanation
Indices: 20286459--20286484 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
20286449 ATATGTAAAT
20286459 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
20286485 TTAACAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:20299898 original size:20 final size:22
Alignment explanation
Indices: 20299849--20299903 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 22
20299839 AATTATTAAT
20299849 GGTAGTATCGATACCTGTTGAAG
1 GGTAGTATCGATA-CTGTTGAAG
*
20299872 AG-A-TATCGATACTG-T-AAG
1 GGTAGTATCGATACTGTTGAAG
20299890 GGTAGTATCGATAC
1 GGTAGTATCGATAC
20299904 CTGATGTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 4 0.14
19 2 0.07
20 12 0.43
21 8 0.29
22 1 0.04
23 1 0.04
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (22 bp):
GGTAGTATCGATACTGTTGAAG
Found at i:20301785 original size:19 final size:20
Alignment explanation
Indices: 20301747--20301785 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
20301737 AATGAAGAAA
* *
20301747 AATAATTTAAAGCGAATATT
1 AATAAATTAAAGCAAATATT
20301767 AATAAATTAAA-CAAATATT
1 AATAAATTAAAGCAAATATT
20301786 TGAAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (20 bp):
AATAAATTAAAGCAAATATT
Found at i:20302393 original size:12 final size:13
Alignment explanation
Indices: 20302376--20302409 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
20302366 AGCATGTTTA
20302376 AAAATAAAACTT-
1 AAAATAAAACTTG
20302388 AAAATAAAAACTTG
1 AAAAT-AAAACTTG
20302402 AAAATAAA
1 AAAATAAA
20302410 GAAAAGAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.25
13 10 0.50
14 5 0.25
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.21
Consensus pattern (13 bp):
AAAATAAAACTTG
Found at i:20302407 original size:14 final size:13
Alignment explanation
Indices: 20302376--20302409 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
20302366 AGCATGTTTA
20302376 AAAAT-AAAACTT
1 AAAATAAAAACTT
20302388 AAAATAAAAACTT
1 AAAATAAAAACTT
20302401 GAAAATAAA
1 -AAAATAAA
20302410 GAAAAGAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 7 0.35
14 8 0.40
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.21
Consensus pattern (13 bp):
AAAATAAAAACTT
Found at i:20310667 original size:45 final size:45
Alignment explanation
Indices: 20310085--20310654 Score: 854
Period size: 45 Copynumber: 12.7 Consensus size: 45
20310075 ATTATTCATT
*
20310085 ATTTTCATTTATGGCATCCTTCCATGCCTTTAATGCACCGTTATGC
1 ATTTT-ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
20310131 ATTTTATTTATGGCAT-CTTTTATGCCTTTATTGCACCGTTATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
20310175 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCATCGTTATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * *
20310220 ATTTTATTTATGGCATACTTTCATGCCTTTAATGCACCATTATGT
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* ** * *
20310265 ATTTTAGTTATTACATCCTTTCAGGCCTTTAATGCACCATTATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
20310310 ATTTTATTTATGACATCATTTCATGCCTTTAATGCACCGTTATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
20310355 ATTTTATTTATGGCATCCTTTCATGCTTTTAATGCACCGTTATAC
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
20310400 ATTTTATTTATTGCATCCTTTCATGCCTTTAATGCACCGTTATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
20310445 ATTTTATTTATGGCATCATTTCATGCCTTTAATGCATCGTTATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
** *
20310490 ATTTTATTTATGATATCCTTTCATGCCATTAATGCACCGTTATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * * * *
20310535 GTTTTAGTTATGTCATCCTTTTATTCCTTTAATGCACCGTTATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
20310580 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
20310625 ATTTTATATATGGCATGCTTTCATGCCTTT
1 ATTTTATTTATGGCATCCTTTCATGCCTTT
20310655 TGTGCACCAT
Statistics
Matches: 472, Mismatches: 51, Indels: 3
0.90 0.10 0.01
Matches are distributed among these distances:
44 41 0.09
45 426 0.90
46 5 0.01
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.46
Consensus pattern (45 bp):
ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:20313584 original size:45 final size:45
Alignment explanation
Indices: 20313529--20314324 Score: 789
Period size: 45 Copynumber: 18.0 Consensus size: 45
20313519 ACTATTCATT
* * *
20313529 ATTTTCATTTATGACATCCTTTCACATCTTTAATGCACCGTTATGT
1 ATTTT-ATTTATGACATCCTTTCATACCTTTAATGCACCGTTATGC
* *
20313575 ATTTTATTTATGGA-ATCCTTTCATGCCTTTAATGCACCGTTATAC
1 ATTTTATTTAT-GACATCCTTTCATACCTTTAATGCACCGTTATGC
* * * * *
20313620 ATTTTATTTATGGCATCCTTTCATGCCTTTAATACACTGGTATGC
1 ATTTTATTTATGACATCCTTTCATACCTTTAATGCACCGTTATGC
* * * * *
20313665 ATTTTATTTATGGA-ATCATTTCATGCTTTTAATGTACCATTATGC
1 ATTTTATTTAT-GACATCCTTTCATACCTTTAATGCACCGTTATGC
* * * *
20313710 ATTTTAGTTATGACATCCTTTAATGCCTTTAATGCACCATTATGC
1 ATTTTATTTATGACATCCTTTCATACCTTTAATGCACCGTTATGC
* * *
20313755 ATTTTATTCATG-C-T--TTT-A-A--TGT-A--C-CA-TTATGC
1 ATTTTATTTATGACATCCTTTCATACCTTTAATGCACCGTTATGC
* * * *
20313787 ATTTTAGTTATGACATCCTTTAATGCCTTTAATGCACCATTATGC
1 ATTTTATTTATGACATCCTTTCATACCTTTAATGCACCGTTATGC
* * * *
20313832 ATTTTAGTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGC
1 ATTTTATTTATGACATCCTTTCATACCTTTAATGCACCGTTATGC
* * * * * * *
20313877 ATTTTATTTATGGCATCCATTCATGCCTTTAACGCATCATTATAC
1 ATTTTATTTATGACATCCTTTCATACCTTTAATGCACCGTTATGC
* * *
20313922 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACTGTTATGC
1 ATTTTATTTATGACATCCTTTCATACCTTTAATGCACCGTTATGC
* * * * *
20313967 ATTTTATTTATGGCATCATTTCATGCGTTTAATGCAGCGTTATGC
1 ATTTTATTTATGACATCCTTTCATACCTTTAATGCACCGTTATGC
** * * *
20314012 ATTTTATTTATGGTATCCTTTAATGCCTTTAATACACCGTTATGC
1 ATTTTATTTATGACATCCTTTCATACCTTTAATGCACCGTTATGC
* * *
20314057 ATTTTATTTATGGCAACCTTTCA-AGTCTTTAATGCACCGTTATGC
1 ATTTTATTTATGACATCCTTTCATA-CCTTTAATGCACCGTTATGC
* * *
20314102 ATTTTATTTATGTCATCCTTTCATGCCTTTAATGCACTGTTATGC
1 ATTTTATTTATGACATCCTTTCATACCTTTAATGCACCGTTATGC
* * *
20314147 ATTTTATTTATGACATCTTTTCATGCCTTTAATGCACTGTTATGC
1 ATTTTATTTATGACATCCTTTCATACCTTTAATGCACCGTTATGC
* * * *
20314192 ATTTTAGTTATGACTTCCTTTCATGCCTTTAATGCACTGTTATGC
1 ATTTTATTTATGACATCCTTTCATACCTTTAATGCACCGTTATGC
* * * *
20314237 ATTTTATTTTTAGA-ATCCTTTCATGCCTTTAATGCACCATTATGT
1 ATTTTATTTAT-GACATCCTTTCATACCTTTAATGCACCGTTATGC
* * * *
20314282 ATTTTATTTATGGCATCCTTTCACACCTTTTATGCACCATTAT
1 ATTTTATTTATGACATCCTTTCATACCTTTAATGCACCGTTAT
20314325 TATATTAAAT
Statistics
Matches: 646, Mismatches: 83, Indels: 43
0.84 0.11 0.06
Matches are distributed among these distances:
32 16 0.02
33 2 0.00
34 2 0.00
36 4 0.01
37 3 0.00
40 3 0.00
41 4 0.01
43 2 0.00
44 6 0.01
45 594 0.92
46 10 0.02
ACGTcount: A:0.24, C:0.19, G:0.11, T:0.46
Consensus pattern (45 bp):
ATTTTATTTATGACATCCTTTCATACCTTTAATGCACCGTTATGC
Found at i:20313714 original size:135 final size:134
Alignment explanation
Indices: 20313529--20314304 Score: 886
Period size: 135 Copynumber: 5.8 Consensus size: 134
20313519 ACTATTCATT
*** *
20313529 ATTTTCATTTAT-GACATCCTTTCACATCTTTAATGCACCGTTATGTATTTTATTTATGGAATCC
1 ATTTT-ATTTATGGA-ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTTATTTATGGAATCC
* *
20313593 TTTCATGCCTTTAATGCACCGTTATACATTTTATTTATGGCATCCTTTCATGCCTTTAATACACT
64 TTTCATGCCTTTAATGCACCATTATGCATTTTATTTATGGCATCCTTTCATGCCTTTAATACACT
20313658 GGTATGC
129 -GTATGC
* * * * *
20313665 ATTTTATTTATGGAATCATTTCATGCTTTTAATGTACCATTATGCATTTTAGTTAT-GACATCCT
1 ATTTTATTTATGGAATCCTTTCATGCCTTTAATGCACCGTTATGCATTTTATTTATGGA-ATCCT
* * * *
20313729 TTAATGCCTTTAATGCACCATTATGCATTTTATTCAT-GC-T--TTTAATG----T-A-CCA-T-
65 TTCATGCCTTTAATGCACCATTATGCATTTTATTTATGGCATCCTTTCATGCCTTTAATACACTG
20313782 TATGC
130 TATGC
* * * * *
20313787 ATTTTAGTTAT-GACATCCTTTAATGCCTTTAATGCACCATTATGCATTTTAGTTATGGCATCCT
1 ATTTTATTTATGGA-ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTTATTTATGGAATCCT
* **
20313851 TTCATGCCTTTAATGCACCATTATGCATTTTATTTATGGCATCCATTCATGCCTTTAACGCATCA
65 TTCATGCCTTTAATGCACCATTATGCATTTTATTTATGGCATCCTTTCATGCCTTTAATACA-C-
*
20313916 T-TATAC
128 TGTATGC
* * * *
20313922 ATTTTATTTATGGCATCCTTTCATGCCTTTAATGCACTGTTATGCATTTTATTTATGGCATCATT
1 ATTTTATTTATGGAATCCTTTCATGCCTTTAATGCACCGTTATGCATTTTATTTATGGAATCCTT
* * * * * *
20313987 TCATGCGTTTAATGCAGCGTTATGCATTTTATTTATGGTATCCTTTAATGCCTTTAATACACCGT
66 TCATGCCTTTAATGCACCATTATGCATTTTATTTATGGCATCCTTTCATGCCTTTAATACACTG-
20314052 TATGC
130 TATGC
* * **
20314057 ATTTTATTTATGGCAA-CCTTTCAAGTCTTTAATGCACCGTTATGCATTTTATTTATGTCATCCT
1 ATTTTATTTATGG-AATCCTTTCATGCCTTTAATGCACCGTTATGCATTTTATTTATGGAATCCT
** * * *
20314121 TTCATGCCTTTAATGCACTGTTATGCATTTTATTTATGACATCTTTTCATGCCTTTAATGCACTG
65 TTCATGCCTTTAATGCACCATTATGCATTTTATTTATGGCATCCTTTCATGCCTTTAATACACTG
20314186 TTATGC
130 -TATGC
* * * * *
20314192 ATTTTAGTTAT-GACTTCCTTTCATGCCTTTAATGCACTGTTATGCATTTTATTTTTAGAATCCT
1 ATTTTATTTATGGA-ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTTATTTATGGAATCCT
*
20314256 TTCATGCCTTTAATGCACCATTATGTATTTTATTTATGGCATCCTTTCA
65 TTCATGCCTTTAATGCACCATTATGCATTTTATTTATGGCATCCTTTCA
20314305 CACCTTTTAT
Statistics
Matches: 544, Mismatches: 73, Indels: 47
0.82 0.11 0.07
Matches are distributed among these distances:
121 2 0.00
122 93 0.17
123 3 0.01
124 2 0.00
125 2 0.00
126 6 0.01
127 1 0.00
130 1 0.00
131 7 0.01
132 2 0.00
133 2 0.00
134 6 0.01
135 408 0.75
136 9 0.02
ACGTcount: A:0.24, C:0.19, G:0.12, T:0.46
Consensus pattern (134 bp):
ATTTTATTTATGGAATCCTTTCATGCCTTTAATGCACCGTTATGCATTTTATTTATGGAATCCTT
TCATGCCTTTAATGCACCATTATGCATTTTATTTATGGCATCCTTTCATGCCTTTAATACACTGT
ATGC
Found at i:20313765 original size:77 final size:77
Alignment explanation
Indices: 20313684--20313837 Score: 308
Period size: 77 Copynumber: 2.0 Consensus size: 77
20313674 ATGGAATCAT
20313684 TTCATGCTTTTAATGTACCATTATGCATTTTAGTTATGACATCCTTTAATGCCTTTAATGCACCA
1 TTCATGCTTTTAATGTACCATTATGCATTTTAGTTATGACATCCTTTAATGCCTTTAATGCACCA
20313749 TTATGCATTTTA
66 TTATGCATTTTA
20313761 TTCATGCTTTTAATGTACCATTATGCATTTTAGTTATGACATCCTTTAATGCCTTTAATGCACCA
1 TTCATGCTTTTAATGTACCATTATGCATTTTAGTTATGACATCCTTTAATGCCTTTAATGCACCA
20313826 TTATGCATTTTA
66 TTATGCATTTTA
20313838 GTTATGGCAT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.45
Consensus pattern (77 bp):
TTCATGCTTTTAATGTACCATTATGCATTTTAGTTATGACATCCTTTAATGCCTTTAATGCACCA
TTATGCATTTTA
Found at i:20313773 original size:32 final size:32
Alignment explanation
Indices: 20313732--20313792 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
20313722 ACATCCTTTA
20313732 ATGCCTTTAATGCACCATTATGCATTTTATTC
1 ATGCCTTTAATGCACCATTATGCATTTTATTC
* *
20313764 ATGCTTTTAATGTACCATTATGCATTTTA
1 ATGCCTTTAATGCACCATTATGCATTTTA
20313793 GTTATGACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (32 bp):
ATGCCTTTAATGCACCATTATGCATTTTATTC
Found at i:20313886 original size:24 final size:24
Alignment explanation
Indices: 20313814--20313886 Score: 57
Period size: 24 Copynumber: 3.2 Consensus size: 24
20313804 CTTTAATGCC
20313814 TTTAATGCACCATTATGCATTTTA
1 TTTAATGCACCATTATGCATTTTA
* ***
20313838 GTT-ATGGCATCC-TT-T-CA-TGCC
1 TTTAAT-GCA-CCATTATGCATTTTA
20313859 TTTAATGCACCATTATGCATTTTA
1 TTTAATGCACCATTATGCATTTTA
20313883 TTTA
1 TTTA
20313887 TGGCATCCAT
Statistics
Matches: 34, Mismatches: 8, Indels: 14
0.61 0.14 0.25
Matches are distributed among these distances:
20 2 0.06
21 8 0.24
22 5 0.15
23 5 0.15
24 12 0.35
25 2 0.06
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.45
Consensus pattern (24 bp):
TTTAATGCACCATTATGCATTTTA
Found at i:20315813 original size:24 final size:24
Alignment explanation
Indices: 20315776--20315822 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
20315766 TTAGCATGTT
*
20315776 TAAAAATAATACTT-AAAATAAAA
1 TAAAAATAAAACTTGAAAATAAAA
20315799 TAAAAATGAAAACTTGAAAATAAA
1 TAAAAAT-AAAACTTGAAAATAAA
20315823 GAAAAAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 6 0.29
25 8 0.38
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.23
Consensus pattern (24 bp):
TAAAAATAAAACTTGAAAATAAAA
Found at i:20315827 original size:24 final size:23
Alignment explanation
Indices: 20315777--20315828 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
20315767 TAGCATGTTT
* *
20315777 AAAAATAATACTTAAAATAAAAT
1 AAAAATAAAACTTAAAATAAAAG
20315800 AAAAATGAAAACTTGAAAAT-AAAG
1 AAAAAT-AAAACTT-AAAATAAAAG
20315824 AAAAA
1 AAAAA
20315829 ACAACTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.24
24 14 0.56
25 5 0.20
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.19
Consensus pattern (23 bp):
AAAAATAAAACTTAAAATAAAAG
Found at i:20323280 original size:127 final size:127
Alignment explanation
Indices: 20323106--20323362 Score: 498
Period size: 127 Copynumber: 2.0 Consensus size: 127
20323096 GACTACGAGT
20323106 GTTCAATAGAGTACTATCCTGGTAAGGTGAACATTGTTGCCGATGGTTTGAGTCGTAAGTCGTTA
1 GTTCAATAGAGTACTATCCTGGTAAGGTGAACATTGTTGCCGATGGTTTGAGTCGTAAGTCGTTA
20323171 GGTGAGTTGTGAGTTTTGTTTGCGAGCTTGAGTTTTGTCCGAGG-TGGAGCGTTAGTCACTGA
66 GGTGAGTTGTGAGTTTTGTTTGCGAGCTTGAG-TTTGTCCGAGGATGGAGCGTTAGTCACTGA
20323233 GTTCAATAGAGTACTATCCTGGTAAGGTGAACATTGTTGCCGATGGTTTGAGTCGTAAGTCGTTA
1 GTTCAATAGAGTACTATCCTGGTAAGGTGAACATTGTTGCCGATGGTTTGAGTCGTAAGTCGTTA
20323298 GGTGAGTTGTGAGTTTTGTTTGCGAGCTTGAGTTTGTCCGAGGATGGAGCGTTAGTCACTGA
66 GGTGAGTTGTGAGTTTTGTTTGCGAGCTTGAGTTTGTCCGAGGATGGAGCGTTAGTCACTGA
20323360 GTT
1 GTT
20323363 GCAAGTTAAG
Statistics
Matches: 129, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
126 11 0.09
127 118 0.91
ACGTcount: A:0.20, C:0.12, G:0.32, T:0.35
Consensus pattern (127 bp):
GTTCAATAGAGTACTATCCTGGTAAGGTGAACATTGTTGCCGATGGTTTGAGTCGTAAGTCGTTA
GGTGAGTTGTGAGTTTTGTTTGCGAGCTTGAGTTTGTCCGAGGATGGAGCGTTAGTCACTGA
Found at i:20325352 original size:27 final size:27
Alignment explanation
Indices: 20325320--20325376 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
20325310 CCTCGTTTGA
20325320 TTTCTTTTATTTTCCAAATTAATTCTC
1 TTTCTTTTATTTTCCAAATTAATTCTC
20325347 TTTCTTTTATTTTCCAAATTAATTCTC
1 TTTCTTTTATTTTCCAAATTAATTCTC
20325374 TTT
1 TTT
20325377 TTGTTTTCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.61
Consensus pattern (27 bp):
TTTCTTTTATTTTCCAAATTAATTCTC
Found at i:20330427 original size:5 final size:5
Alignment explanation
Indices: 20330417--20330443 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
20330407 GTGTAAACAT
20330417 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
20330444 GTTGGGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:20331038 original size:12 final size:12
Alignment explanation
Indices: 20331003--20331045 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
20330993 TTTTCTTCTC
20331003 TTTTCAAGTTTTCA
1 TTTT-AAGTTTT-A
*
20331017 TTTTTA-TTTTA
1 TTTTAAGTTTTA
20331028 TTTTAAGTTTTA
1 TTTTAAGTTTTA
20331040 TTTTAA
1 TTTTAA
20331046 AACATGCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 6 0.23
12 15 0.58
13 1 0.04
14 4 0.15
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (12 bp):
TTTTAAGTTTTA
Found at i:20331696 original size:20 final size:20
Alignment explanation
Indices: 20331671--20331722 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
20331661 AGGTAAGGGA
20331671 AGTATCGATACTCACTAGGT
1 AGTATCGATACTCACTAGGT
20331691 AGTATCGATACTCACTAGGT
1 AGTATCGATACTCACTAGGT
20331711 AGTATCGATACT
1 AGTATCGATACT
20331723 ACCAACATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTATCGATACTCACTAGGT
Found at i:20336813 original size:41 final size:41
Alignment explanation
Indices: 20336756--20336845 Score: 180
Period size: 41 Copynumber: 2.2 Consensus size: 41
20336746 TTGTTCATAA
20336756 AAAATCCAATGCCAGGCCTTGTCAGAGTAACGTATTCACAG
1 AAAATCCAATGCCAGGCCTTGTCAGAGTAACGTATTCACAG
20336797 AAAATCCAATGCCAGGCCTTGTCAGAGTAACGTATTCACAG
1 AAAATCCAATGCCAGGCCTTGTCAGAGTAACGTATTCACAG
20336838 AAAATCCA
1 AAAATCCA
20336846 TAATGCTGGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (41 bp):
AAAATCCAATGCCAGGCCTTGTCAGAGTAACGTATTCACAG
Found at i:20337732 original size:36 final size:36
Alignment explanation
Indices: 20337651--20337867 Score: 296
Period size: 36 Copynumber: 6.1 Consensus size: 36
20337641 AGATGAACAA
* * *
20337651 TTGAATCGAAAGTGCGGATACTTCCTTCCGTTC-AC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCTTC
*
20337686 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCTTC
20337722 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCATT-
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC-TTC
* *
20337758 TTGAATCGAAAGTGCTGATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCTTC
* * *
20337794 TTGAATCGAAAGTGTCGATGTTTCCTTCCGTTC-AC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCTTC
* *
20337829 TTTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTTC
1 -TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCTTC
20337866 TT
1 TT
20337868 CCTCACCTTC
Statistics
Matches: 162, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
35 33 0.20
36 126 0.78
37 3 0.02
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (36 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCTTC
Found at i:20337787 original size:72 final size:71
Alignment explanation
Indices: 20337651--20337867 Score: 346
Period size: 72 Copynumber: 3.0 Consensus size: 71
20337641 AGATGAACAA
* * * *
20337651 TTGAATCGAAAGTGCGGATACTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTCCTTTCG
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCATTTGAATCGAAAGTGCTGATGCTTCCTTTCG
20337716 TTCTTC
66 TTCTTC
20337722 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCATTTTGAATCGAAAGTGCTGATGCTTCCTTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCA-TTTGAATCGAAAGTGCTGATGCTTCCTTTC
20337787 GTTCTTC
65 GTTCTTC
* *
20337794 TTGAATCGAAAGTGTCGATGTTTCCTTCCGTTCACTTTGAATCGAAAGTG-TCGATGCTTCCTTT
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCA-TTTGAATCGAAAGTGCT-GATGCTTCCTTT
20337858 CGTTCTTC
64 CGTTCTTC
20337866 TT
1 TT
20337868 CCTCACCTTC
Statistics
Matches: 137, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
71 33 0.24
72 104 0.76
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (71 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCATTTGAATCGAAAGTGCTGATGCTTCCTTTCG
TTCTTC
Found at i:20339712 original size:45 final size:45
Alignment explanation
Indices: 20339653--20339838 Score: 192
Period size: 45 Copynumber: 4.1 Consensus size: 45
20339643 TGGTGAAGCA
* * * *
20339653 TGATGTTATAGAGATGATGATGAATGTTAAGGTGGAGATGGTAAG
1 TGATGTAATGGAGATGATGATGAATGTTGAGGTGAAGATGGTAAG
* * * * * * *
20339698 TGATTTATTGGAGATGGTAACGAATGTTGAGGTGGAGATGATAAG
1 TGATGTAATGGAGATGATGATGAATGTTGAGGTGAAGATGGTAAG
* * * *
20339743 TGACGAAATGGAGATAATGATGAATGCTGAGGTGAAGATGGTAAG
1 TGATGTAATGGAGATGATGATGAATGTTGAGGTGAAGATGGTAAG
* * * *
20339788 TGATGTAGTGGATATGATTATGAATGTTGAGGTGAAAATGGTAAG
1 TGATGTAATGGAGATGATGATGAATGTTGAGGTGAAGATGGTAAG
*
20339833 CGATGT
1 TGATGT
20339839 GTGGATTGAG
Statistics
Matches: 112, Mismatches: 29, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
45 112 1.00
ACGTcount: A:0.33, C:0.02, G:0.35, T:0.30
Consensus pattern (45 bp):
TGATGTAATGGAGATGATGATGAATGTTGAGGTGAAGATGGTAAG
Found at i:20340358 original size:40 final size:40
Alignment explanation
Indices: 20340287--20340363 Score: 91
Period size: 40 Copynumber: 1.9 Consensus size: 40
20340277 CTGTACAAGT
* * * *
20340287 AGTACTGATACTGTTCTTACAGTATCGATACCTAAGGAAC
1 AGTACTAATACTGTTCTTACAGTACCAATACCAAAGGAAC
* **
20340327 AGTACTAATATTGTTCTTATGGTACCAATACCAAAGG
1 AGTACTAATACTGTTCTTACAGTACCAATACCAAAGG
20340364 TAACTACTAG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (40 bp):
AGTACTAATACTGTTCTTACAGTACCAATACCAAAGGAAC
Found at i:20342400 original size:19 final size:19
Alignment explanation
Indices: 20342364--20342400 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20342354 TGAAAATGAT
*
20342364 TTGATTTTGAAAGCCAAAG
1 TTGATTTTGAAAACCAAAG
*
20342383 TTGATTTTGAAAATCAAA
1 TTGATTTTGAAAACCAAA
20342401 ATGAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (19 bp):
TTGATTTTGAAAACCAAAG
Found at i:20342692 original size:18 final size:18
Alignment explanation
Indices: 20342668--20342710 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
20342658 ACGGAATGTG
*
20342668 AGATTACCAGTGGGAATA
1 AGATTACCAGTGAGAATA
* *
20342686 TGATTACCGGTGAGAATA
1 AGATTACCAGTGAGAATA
20342704 AGATTAC
1 AGATTAC
20342711 TGGGAATGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.26
Consensus pattern (18 bp):
AGATTACCAGTGAGAATA
Found at i:20348300 original size:7 final size:8
Alignment explanation
Indices: 20348282--20348371 Score: 58
Period size: 8 Copynumber: 10.8 Consensus size: 8
20348272 GAAGATAAAG
20348282 AAAATATA
1 AAAATATA
20348290 AAAATATA
1 AAAATATA
20348298 AAAATTATGA
1 AAAA-TAT-A
*
20348308 AAAATAAA
1 AAAATATA
*
20348316 GAAAATAAA
1 -AAAATATA
20348325 AGAAATA-A
1 A-AAATATA
* *
20348333 AAGAAGAAA
1 AA-AATATA
20348342 AAAATAATA
1 AAAAT-ATA
*
20348351 ATAA-ATA
1 AAAATATA
20348358 AAAATATA
1 AAAATATA
*
20348366 GAAATA
1 AAAATA
20348372 GAAATAAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
7 7 0.10
8 29 0.43
9 26 0.39
10 5 0.07
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (8 bp):
AAAATATA
Found at i:20348320 original size:9 final size:8
Alignment explanation
Indices: 20348276--20348361 Score: 64
Period size: 9 Copynumber: 9.9 Consensus size: 8
20348266 ATAAGTGAAG
20348276 ATAAAGAAA
1 ATAAA-AAA
*
20348285 ATATAAAA
1 ATAAAAAA
20348293 ATATAAAAA
1 ATA-AAAAA
* *
20348302 TTATGAAAA
1 ATA-AAAAA
20348311 ATAAAGAAA
1 ATAAA-AAA
20348320 ATAAAAGAA
1 ATAAAA-AA
*
20348329 ATAAAAGA
1 ATAAAAAA
*
20348337 AGAAAAAA
1 ATAAAAAA
20348345 ATAATAATAA
1 ATAA-AA-AA
20348355 ATAAAAA
1 ATAAAAA
20348362 TATAGAAATA
Statistics
Matches: 62, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
8 19 0.31
9 37 0.60
10 6 0.10
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (8 bp):
ATAAAAAA
Found at i:20348334 original size:14 final size:14
Alignment explanation
Indices: 20348317--20348390 Score: 50
Period size: 14 Copynumber: 5.4 Consensus size: 14
20348307 AAAAATAAAG
20348317 AAAATAAAAGAAAT
1 AAAATAAAAGAAAT
*
20348331 -AAA-AGAAGAAA-
1 AAAATAAAAGAAAT
*
20348342 AAAATAATAATAAAT
1 AAAATAA-AAGAAAT
*
20348357 AAAA-ATATAGAAAT
1 AAAATA-AAAGAAAT
*
20348371 AGAAATAAAA-AAGT
1 A-AAATAAAAGAAAT
20348385 AAAATA
1 AAAATA
20348391 TATAAGTTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 15
0.68 0.10 0.22
Matches are distributed among these distances:
12 10 0.22
13 9 0.20
14 16 0.35
15 10 0.22
16 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (14 bp):
AAAATAAAAGAAAT
Found at i:20350919 original size:249 final size:248
Alignment explanation
Indices: 20350265--20351012 Score: 1140
Period size: 247 Copynumber: 3.0 Consensus size: 248
20350255 CTAGAGATGG
* * *
20350265 ATGCTGCTTGTGGGAACGATATCCTTCGTTGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTG
1 ATGCTGCTTGTGAGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTG
* * *
20350330 AAGTTGAGCCTTAAATTGGGTATCCTTCGTCATGAAGTTGAAATCCAATCTTGTTTGTTATATTG
66 AAGTTGAGCCTTGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAATCTTGTTTGTTGTATTG
* * * *
20350395 TTTCAAGTCCAATATCCTTCGCCATGAAGTTTAAATTGGCCCTGAATGAAATTGGGAAGCCACTT
131 TTTCAAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCC-CTT
* *
20350460 CGCTGTGAAGTTGAGCTTTGAATTCGATATCCTTCGTTGTGAAGTTGAAATCCA
195 CGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCA
* * * * * * *
20350514 ATGCTGTTTGTGAGCACGATATTCTTCGTC--GAAGTTAAAATCGTGGATGGCCCCTTCGCTGTA
1 ATGCTGCTTGTGAGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTG
* *
20350577 AAGTTGAGCCTTGAATTGAATATCCTTCGTCATGAAGTTGAAATCTAATCTTGTTTGTTGTATTG
66 AAGTTGAGCCTTGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAATCTTGTTTGTTGTATTG
*** * *
20350642 TTTCAAGTCCAATATCCTTTTTCGTGAAGTTGAAATTGGCTCTGAATTAAACTAGGAAGCCCTTT
131 TTTCAAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCCC-TT
*
20350707 CGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCATTGTGAAGTTGAAATCCA
195 CGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCA
*
20350761 ATGCTGCTTGTGAGCACGTTATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTG
1 ATGCTGCTTGTGAGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTG
* * *
20350826 AAGTTGAACCTTGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAATCTTGTTTGTTGTATTG
66 AAGTTGAGCCTTGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAATCTTGTTTGTTGTATTG
*
20350891 TTTCAAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGCGCTTTGAATGAAACTGGGAAGCCCAT
131 TTTCAAGTCCAATATCCTTCGCCGTGAAGTTGAAATTG-GCTCTGAATGAAACTGGGAAGCCC-T
* *
20350956 TCGTTGTGAAATTGAGCTTTGAATTGGATATCCTTCGTTGTGAAGTTGTAATCCA
194 TCGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCA
20351011 AT
1 AT
20351013 CTCGAGTAAA
Statistics
Matches: 445, Mismatches: 50, Indels: 7
0.89 0.10 0.01
Matches are distributed among these distances:
246 1 0.00
247 220 0.49
249 148 0.33
250 76 0.17
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (248 bp):
ATGCTGCTTGTGAGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTG
AAGTTGAGCCTTGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAATCTTGTTTGTTGTATTG
TTTCAAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCTTC
GTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCA
Found at i:20362874 original size:23 final size:23
Alignment explanation
Indices: 20362844--20362934 Score: 112
Period size: 23 Copynumber: 4.0 Consensus size: 23
20362834 ATTATTATAT
*
20362844 GGCACTACGGTTCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
*
20362867 GGCACTACGGTTCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
**
20362890 GGCACT-CTGGTGCAATTCTACTT
1 GGCACTAC-GGTGCAATTCTACGC
* *
20362913 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
20362935 AACTGTGGTG
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
22 1 0.02
23 59 0.97
24 1 0.02
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:20366811 original size:28 final size:27
Alignment explanation
Indices: 20366770--20366831 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
20366760 AATAAGTGAA
20366770 AATAAAGAAAATAAA-AGAAGAAAAAAAT
1 AATAAA-AAAATAAATAGAA-AAAAAAAT
*
20366798 AATAAAAAATATAAATAGAAATAAAAAT
1 AATAAAAAA-ATAAATAGAAAAAAAAAT
20366826 AA-AAAA
1 AATAAAA
20366832 GTAAAATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 7 0.23
28 20 0.65
29 4 0.13
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (27 bp):
AATAAAAAAATAAATAGAAAAAAAAAT
Found at i:20366838 original size:25 final size:24
Alignment explanation
Indices: 20366768--20366838 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 24
20366758 AAAATAAGTG
*
20366768 AAAATAAAGAAAATAAAAGAAGAAAAA
1 AAAAT-AA-AAAATAAAA-TAGAAAAA
*
20366795 AATAATAAAAAATATAAATAGAAATA
1 AA-AATAAAAAATA-AAATAGAAAAA
20366821 AAAATAAAAAAGTAAAAT
1 AAAATAAAAAA-TAAAAT
20366839 TTATAAATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
25 13 0.33
26 16 0.41
27 7 0.18
28 3 0.08
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.15
Consensus pattern (24 bp):
AAAATAAAAAATAAAATAGAAAAA
Found at i:20366943 original size:9 final size:9
Alignment explanation
Indices: 20366931--20366972 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
20366921 TAAATAAGGT
20366931 ATATAAAAA
1 ATATAAAAA
20366940 ATATAAAAA
1 ATATAAAAA
20366949 ATA-AAAAA
1 ATATAAAAA
20366957 ATA-AAATAA
1 ATATAAA-AA
20366966 A-ATAAAA
1 ATATAAAA
20366973 TAAAATCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 13 0.42
9 18 0.58
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
ATATAAAAA
Found at i:20366957 original size:17 final size:18
Alignment explanation
Indices: 20366935--20366972 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
20366925 TAAGGTATAT
*
20366935 AAAAAATATAA-AAAATA
1 AAAAAATAAAATAAAATA
20366952 AAAAAATAAAATAAAATA
1 AAAAAATAAAATAAAATA
20366970 AAA
1 AAA
20366973 TAAAATCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (18 bp):
AAAAAATAAAATAAAATA
Found at i:20367002 original size:18 final size:17
Alignment explanation
Indices: 20366933--20367002 Score: 56
Period size: 18 Copynumber: 4.0 Consensus size: 17
20366923 AATAAGGTAT
20366933 ATAAAA-AAT-ATAAAAA
1 ATAAAATAATAAT-AAAA
* *
20366949 ATAAAAAAATAAAATAAA
1 ATAAAATAATAATA-AAA
20366967 ATAAAATAA-AATCCAAAA
1 ATAAAATAATAAT--AAAA
20366985 ATAATAATAATAATAAAA
1 ATAA-AATAATAATAAAA
20367003 GGATTAAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
16 6 0.14
17 6 0.14
18 23 0.52
19 6 0.14
20 3 0.07
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (17 bp):
ATAAAATAATAATAAAA
Found at i:20374320 original size:49 final size:49
Alignment explanation
Indices: 20374263--20374361 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
20374253 AATTTTAATC
20374263 CTTTAGAAGTGTTTTAAAACCTTTCTTAATCTCTAAATTCAGTTAGTAA
1 CTTTAGAAGTGTTTTAAAACCTTTCTTAATCTCTAAATTCAGTTAGTAA
20374312 CTTTAGAAGTGTTTTAAAACCTTTCTTAATCTCTAAATTCAGTTAGTAA
1 CTTTAGAAGTGTTTTAAAACCTTTCTTAATCTCTAAATTCAGTTAGTAA
20374361 C
1 C
20374362 CCATTCTTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.42
Consensus pattern (49 bp):
CTTTAGAAGTGTTTTAAAACCTTTCTTAATCTCTAAATTCAGTTAGTAA
Found at i:20383214 original size:56 final size:56
Alignment explanation
Indices: 20383128--20383239 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
20383118 AGAGTTAGTC
20383128 ACATATATGTTATGACGAATCATGACTTCCCGTAACTTAGATCACAATGACATATT
1 ACATATATGTTATGACGAATCATGACTTCCCGTAACTTAGATCACAATGACATATT
*
20383184 ACATATATGTTATGATGAATCATGACTTCCCGTAACTTAGATCACAATGACATATT
1 ACATATATGTTATGACGAATCATGACTTCCCGTAACTTAGATCACAATGACATATT
20383240 GCTAGATGTC
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:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (56 bp):
ACATATATGTTATGACGAATCATGACTTCCCGTAACTTAGATCACAATGACATATT
Found at i:20383441 original size:21 final size:21
Alignment explanation
Indices: 20383399--20383441 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20383389 TGTGTATTTA
* **
20383399 ATATATATATATGTATGTATG
1 ATATATATATATATATACATG
20383420 ATATATATATATATATACATG
1 ATATATATATATATATACATG
20383441 A
1 A
20383442 ATACTGAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (21 bp):
ATATATATATATATATACATG
Found at i:20388937 original size:20 final size:20
Alignment explanation
Indices: 20388889--20388985 Score: 103
Period size: 18 Copynumber: 5.0 Consensus size: 20
20388879 CACTGAATAT
*
20388889 TTGTCCCAAAGGACCACT-A
1 TTGTCCCGAAGGACCACTGA
20388908 -TGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* *
20388927 TTGTTCCGAAGAACCACT-A
1 TTGTCCCGAAGGACCACTGA
* * *
20388946 -TGTCCCAAAGAACCACTGT
1 TTGTCCCGAAGGACCACTGA
*
20388965 TTGTCCCGAAAGACCACTGA
1 TTGTCCCGAAGGACCACTGA
20388985 T
1 T
20388986 AATCCCTTGA
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
18 31 0.48
19 2 0.03
20 31 0.48
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.22
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:20388944 original size:38 final size:38
Alignment explanation
Indices: 20388889--20388982 Score: 120
Period size: 38 Copynumber: 2.5 Consensus size: 38
20388879 CACTGAATAT
* *
20388889 TTGTCCC-AAAGGACCACTATGTCCCGAAGGACCACTGA
1 TTGTCCCGAAA-GACCACTATGTCCCAAAGAACCACTGA
* *
20388927 TTGTTCCG-AAGAACCACTATGTCCCAAAGAACCACTGT
1 TTGTCCCGAAAG-ACCACTATGTCCCAAAGAACCACTGA
20388965 TTGTCCCGAAAGACCACT
1 TTGTCCCGAAAGACCACT
20388983 GATAATCCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
37 1 0.02
38 44 0.92
39 3 0.06
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.21
Consensus pattern (38 bp):
TTGTCCCGAAAGACCACTATGTCCCAAAGAACCACTGA
Found at i:20390577 original size:24 final size:20
Alignment explanation
Indices: 20390524--20390581 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
20390514 TCCCCTTTGA
*
20390524 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
20390544 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
20390567 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
20390582 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:20398173 original size:20 final size:20
Alignment explanation
Indices: 20398087--20398159 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
20398077 AAGATATGCT
* * *
20398087 AGTATCGATACTAAGCATCAT
1 AGTATCGATACTAACCCT-AG
20398108 AGTATCGATACTAACCCTAG
1 AGTATCGATACTAACCCTAG
20398128 AGTATCGATACTAACCCTAG
1 AGTATCGATACTAACCCTAG
20398148 AGTATCGATACT
1 AGTATCGATACT
20398160 CCTCCTAGGG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 33 0.67
21 16 0.33
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (20 bp):
AGTATCGATACTAACCCTAG
Found at i:20398178 original size:20 final size:20
Alignment explanation
Indices: 20398108--20398180 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
20398098 TAAGCATCAT
*
20398108 AGTATCGATACTAAC-CCTAG
1 AGTATCGATACT-CCTCCTAG
*
20398128 AGTATCGATACTAAC-CCTAG
1 AGTATCGATACT-CCTCCTAG
20398148 AGTATCGATACTCCTCCTAG
1 AGTATCGATACTCCTCCTAG
* *
20398168 GGTATCTATACTC
1 AGTATCGATACTC
20398181 ATTAGCTAGT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
19 1 0.02
20 48 0.98
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (20 bp):
AGTATCGATACTCCTCCTAG
Found at i:20403227 original size:247 final size:246
Alignment explanation
Indices: 20402781--20403259 Score: 832
Period size: 247 Copynumber: 1.9 Consensus size: 246
20402771 CTCTACCCAT
* * *
20402781 TTGGCTTTTGATATGTTTTAAGGCTTCATGGTCGGTATGTACAACGAATTCCTTTGGTAATAGAT
1 TTGGCCTTTGATATGTTTTAAGGCTTCATGGTCGGTATGTACAACAAATTCCTTTAGTAATAGAT
* *
20402846 AATGCTACCAAACTCAAGTACCCTTATGAGAGAATACATCTCTTTTTCATAAGTTGGATAGTTTA
66 AATGCTACCAAACTCAAGTACCCTTATGAGACAATACATCTCTTTGTCATAAGTTGGATAGTTTA
* *
20402911 GCAAAGCACCATTCAATTTTTCACTAAAGTATGCAGTGGGTCGTCCTTCTTGAGTCAAAACAGCC
131 GCAAAGCACCATTCAATTTTTCACTAAAGTATGCAATGGGTCGTCCTTCTTGAGTCAAAACAACC
** *
20402976 CTAATTCTGATTCTAGAAGCATCACATTCCACTTCAACCAATTAACTTGTG
196 CTAATTCCAATTCCAGAAGCATCACATTCCACTTCAACCAATTAACTTGTG
20403027 TTGGCCTTTGATATGTTTTAAGGCTTCATGGTCGGTATGTACAACAAATTCCTTTAGTAATAGAT
1 TTGGCCTTTGATATGTTTTAAGGCTTCATGGTCGGTATGTACAACAAATTCCTTTAGTAATAGAT
*
20403092 AATGCTACCAAACTTCAAGTGCCCTTATGAGACAATACATCTCTTTGTCATAAGTTGGATAGTTT
66 AATGCTACCAAAC-TCAAGTACCCTTATGAGACAATACATCTCTTTGTCATAAGTTGGATAGTTT
* *
20403157 AGCAAAGCACCATTCAATTTTTCACTAAAGTATGTAATGGGTCGTTCTTCTTGAGTCAAAACAAC
130 AGCAAAGCACCATTCAATTTTTCACTAAAGTATGCAATGGGTCGTCCTTCTTGAGTCAAAACAAC
20403222 CCTAATTCCAATTCCAGAAGCATCACATTCCACTTCAA
195 CCTAATTCCAATTCCAGAAGCATCACATTCCACTTCAA
20403260 AAGTCTTATC
Statistics
Matches: 219, Mismatches: 13, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
246 75 0.34
247 144 0.66
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (246 bp):
TTGGCCTTTGATATGTTTTAAGGCTTCATGGTCGGTATGTACAACAAATTCCTTTAGTAATAGAT
AATGCTACCAAACTCAAGTACCCTTATGAGACAATACATCTCTTTGTCATAAGTTGGATAGTTTA
GCAAAGCACCATTCAATTTTTCACTAAAGTATGCAATGGGTCGTCCTTCTTGAGTCAAAACAACC
CTAATTCCAATTCCAGAAGCATCACATTCCACTTCAACCAATTAACTTGTG
Found at i:20407872 original size:3 final size:3
Alignment explanation
Indices: 20407864--20407892 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
20407854 TGCAAGGAAA
20407864 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
20407893 CTATGCAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:20410435 original size:18 final size:18
Alignment explanation
Indices: 20410412--20410451 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
20410402 TCATTTAAAT
20410412 AAATTCAATTATGTCCAA
1 AAATTCAATTATGTCCAA
20410430 AAATTCAATTATGTCCAA
1 AAATTCAATTATGTCCAA
20410448 AAAT
1 AAAT
20410452 ATTTTGTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.33
Consensus pattern (18 bp):
AAATTCAATTATGTCCAA
Found at i:20411106 original size:118 final size:119
Alignment explanation
Indices: 20410905--20411161 Score: 313
Period size: 118 Copynumber: 2.2 Consensus size: 119
20410895 TTTTAATATT
* *
20410905 TAAACTTTCATTTTTTTTAAACCATATATAACGTTAATTTTTATTTTATTTTAGTACCCACCGTT
1 TAAACTTTCATTTTTTTTAAACCATACATAACGTTAATTTTTATTTTATTTTAGTACCCACCATT
* * * ** **
20410970 AGAAACTTAACACGTTTAATACCTAGATTATCGGTTTTGGTCTGTTTTAGCACC
66 AAAAACTTAACACGTTTAATACCTAAAATATCAATTTTGGTCCATTTTAGCACC
* * * * *
20411024 TAAACTTTTA-TTTTTTT-AACTATACCTAATGTTTATTTTT-TTTTCATTTTAGTATCCCACCA
1 TAAACTTTCATTTTTTTTAAACCATACATAACGTTAATTTTTATTTT-ATTTTAGTA-CCCACCA
* *
20411086 TTAAAAACTTAACACGTTTAATACCTAAAATATCAATTTTTGTCCATTTTAGTACC
64 TTAAAAACTTAACACGTTTAATACCTAAAATATCAATTTTGGTCCATTTTAGCACC
20411142 TAAACTTTCATATATTTTTT
1 TAAACTTTCAT-T-TTTTTT
20411162 TCAAAAATTA
Statistics
Matches: 116, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
116 4 0.03
117 27 0.23
118 69 0.59
119 9 0.08
120 1 0.01
121 6 0.05
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.47
Consensus pattern (119 bp):
TAAACTTTCATTTTTTTTAAACCATACATAACGTTAATTTTTATTTTATTTTAGTACCCACCATT
AAAAACTTAACACGTTTAATACCTAAAATATCAATTTTGGTCCATTTTAGCACC
Found at i:20412231 original size:2 final size:2
Alignment explanation
Indices: 20412180--20412216 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
20412170 ACAAATAAGA
20412180 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20412217 AACATAAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20412698 original size:23 final size:23
Alignment explanation
Indices: 20412672--20412719 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
20412662 TATCGTATTT
20412672 GTGTTCGTTATTTATTT-TTGAAC
1 GTGTTCG-TATTTATTTATTGAAC
*
20412695 GTGTTCGTATTTATTTATTTAAC
1 GTGTTCGTATTTATTTATTGAAC
20412718 GT
1 GT
20412720 TCGTAAACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.19, C:0.08, G:0.17, T:0.56
Consensus pattern (23 bp):
GTGTTCGTATTTATTTATTGAAC
Found at i:20416063 original size:14 final size:14
Alignment explanation
Indices: 20416044--20416102 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
20416034 GTAATTGGTT
*
20416044 TTCTGGAAATTGAA
1 TTCTGGAAAATGAA
20416058 TTCTGGAAAATGAA
1 TTCTGGAAAATGAA
** **
20416072 TTACTCTAATTTGAA
1 TT-CTGGAAAATGAA
20416087 TTCTGGAAAATGAA
1 TTCTGGAAAATGAA
20416101 TT
1 TT
20416103 ACATTTCTGG
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
14 25 0.71
15 10 0.29
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.37
Consensus pattern (14 bp):
TTCTGGAAAATGAA
Found at i:20419169 original size:29 final size:29
Alignment explanation
Indices: 20419130--20419200 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 29
20419120 TAAAGGGTTA
* *
20419130 AAATAGCAAAAATAGAAAGTTAAAGGACT
1 AAATAGAAAAAATAGAAACTTAAAGGACT
20419159 AAATAGAAAAAATAGAAACTTAAAGGACT
1 AAATAGAAAAAATAGAAACTTAAAGGACT
* *
20419188 TAATA-AATAAATA
1 AAATAGAAAAAATA
20419201 TGAACAAATC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
28 7 0.18
29 31 0.82
ACGTcount: A:0.62, C:0.06, G:0.13, T:0.20
Consensus pattern (29 bp):
AAATAGAAAAAATAGAAACTTAAAGGACT
Found at i:20420873 original size:131 final size:131
Alignment explanation
Indices: 20420580--20421159 Score: 653
Period size: 131 Copynumber: 4.4 Consensus size: 131
20420570 GTTCGAGTCG
* * * * * * * * *
20420580 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGTGGATGACACTGCTCATACGT
1 TCTAGGGGTGACATGACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACAGTTCCTACGC
** ** * * * **
20420645 GATGAAAAGTTCTTGGTCATCTTTAAGAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGTT
66 GATGAGGA-TGGTAGGCCATCTTT-AG--GGATGATAACACGGTTCCTACGTGATGAGGACGACT
*
20420710 GGTTA
127 AGTTA
* * * * *
20420715 TCT-GAGGGTGGCACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGTTCCTACA
1 TCTAG-GGGTGACATGACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACAGTTCCTACG
* * *
20420779 CAATGAGGATGGTAGGCCATCTTTAGGGATGATAACACGGTTCCTACGTGATAAGGATGACTAGT
65 CGATGAGGATGGTAGGCCATCTTTAGGGATGATAACACGGTTCCTACGTGATGAGGACGACTAGT
20420844 TA
130 TA
* * *
20420846 TCTAGGGGTGACATGACCCCTATGTGATGAGGAGGTCTGGTCGGGGGATGACACAGTTCCTACGC
1 TCTAGGGGTGACATGACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACAGTTCCTACGC
* * *
20420911 GATGAGAATGGCAGGCCATCTTTAGGGATGATAACACGGTTCCTACGTGATGAGGACGACTGGTT
66 GATGAGGATGGTAGGCCATCTTTAGGGATGATAACACGGTTCCTACGTGATGAGGACGACTAGTT
20420976 A
131 A
* * * * * * * * * * *
20420977 TCTAGAGGTGTCAGGGCTCCAACATGATGAGGAGGTCTTGTAGGGGGATGACATAGTTCCTACGT
1 TCTAGGGGTGACATGACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACAGTTCCTACGC
* * * *
20421042 GATGAGGATGGTAGGCCATCTTTAGGAATGATAACACGATTCCTACGTGATGAGGACGATTAATT
66 GATGAGGATGGTAGGCCATCTTTAGGGATGATAACACGGTTCCTACGTGATGAGGACGACTAGTT
20421107 A
131 A
*
20421108 TCTA-GGGTGACATGACTCCTACGTGATGAGGAGATCTGGTC-AGGGATGACAC
1 TCTAGGGGTGACATGACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACAC
20421160 TGCTCATACT
Statistics
Matches: 377, Mismatches: 66, Indels: 10
0.83 0.15 0.02
Matches are distributed among these distances:
129 9 0.02
130 28 0.07
131 266 0.71
132 1 0.00
133 2 0.01
134 11 0.03
135 60 0.16
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (131 bp):
TCTAGGGGTGACATGACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACAGTTCCTACGC
GATGAGGATGGTAGGCCATCTTTAGGGATGATAACACGGTTCCTACGTGATGAGGACGACTAGTT
A
Found at i:20421054 original size:262 final size:259
Alignment explanation
Indices: 20420584--20421159 Score: 724
Period size: 262 Copynumber: 2.2 Consensus size: 259
20420574 GAGTCGTCTA
* * * * * * *
20420584 AGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGTGGATGACACTGCTCATACGTGATG
1 AGGGTGACATGACCCCTACGTGATGAGGAGATCTGGTCAG-GGATGACACAGTTCCTACGCGATG
* * * * **
20420649 A-AAAGTTCTTGGTCATCTTTAAGAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGTTGGT
65 AGAATG-GC-AGGCCATCTTT----AGGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGT
* * * *
20420713 TATCTGAGGGTGGCACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGTTCCTAC
124 TATCTGAGGGTGGCACGGCTCCAACATGATGAGGAGATCTGGTAGGGGGATGACACAGTTCCTAC
* * * *
20420778 ACAATGAGGATGGTAGGCCATCTTTAGGGATGATAACACGGTTCCTACGTGATAAGGATGACTAG
189 ACAATGAGGATGGTAGGCCATCTTTAGGAATGATAACACGATTCCTACGTGATAAGGACGACTAA
20420843 TTATCT
254 TTATCT
* * *
20420849 AGGGGTGACATGACCCCTATGTGATGAGGAGGTCTGGTCGGGGGATGACACAGTTCCTACGCGAT
1 A-GGGTGACATGACCCCTACGTGATGAGGAGATCTGGTC-AGGGATGACACAGTTCCTACGCGAT
20420914 GAGAATGGCAGGCCATCTTTAGGGATGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATC
64 GAGAATGGCAGGCCATCTTTAGGG-TGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATC
* * * * * ***
20420979 T-AGAGGTGTCAGGGCTCCAACATGATGAGGAGGTCTTGTAGGGGGATGACATAGTTCCTACGTG
128 TGAG-GGTGGCACGGCTCCAACATGATGAGGAGATCTGGTAGGGGGATGACACAGTTCCTACACA
* *
20421043 ATGAGGATGGTAGGCCATCTTTAGGAATGATAACACGATTCCTACGTGATGAGGACGATTAATTA
192 ATGAGGATGGTAGGCCATCTTTAGGAATGATAACACGATTCCTACGTGATAAGGACGACTAATTA
20421108 TCT
257 TCT
*
20421111 AGGGTGACATGACTCCTACGTGATGAGGAGATCTGGTCAGGGATGACAC
1 AGGGTGACATGACCCCTACGTGATGAGGAGATCTGGTCAGGGATGACAC
20421160 TGCTCATACT
Statistics
Matches: 268, Mismatches: 38, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
260 10 0.04
261 40 0.15
262 150 0.56
265 10 0.04
266 54 0.20
267 4 0.01
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (259 bp):
AGGGTGACATGACCCCTACGTGATGAGGAGATCTGGTCAGGGATGACACAGTTCCTACGCGATGA
GAATGGCAGGCCATCTTTAGGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTGA
GGGTGGCACGGCTCCAACATGATGAGGAGATCTGGTAGGGGGATGACACAGTTCCTACACAATGA
GGATGGTAGGCCATCTTTAGGAATGATAACACGATTCCTACGTGATAAGGACGACTAATTATCT
Found at i:20421233 original size:43 final size:40
Alignment explanation
Indices: 20421156--20421270 Score: 122
Period size: 40 Copynumber: 2.8 Consensus size: 40
20421146 GTCAGGGATG
** *
20421156 ACACTGCTCATACTATGATGAATCTTGGCCATCTAAGGGTGATA
1 ACACTGCTCATA-TGCGATGAGTCTTGGCCATCT-AGGGT--TA
** *
20421200 ACACTGCTCATATGCGATGAGTCTTGGTTATCTAGGGTTG
1 ACACTGCTCATATGCGATGAGTCTTGGCCATCTAGGGTTA
* *
20421240 ACACGGCTCATATGCGATGAGTCTTAGCCAT
1 ACACTGCTCATATGCGATGAGTCTTGGCCAT
20421271 GGGATAGTAA
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
40 28 0.46
42 5 0.08
43 16 0.26
44 12 0.20
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.30
Consensus pattern (40 bp):
ACACTGCTCATATGCGATGAGTCTTGGCCATCTAGGGTTA
Found at i:20421360 original size:123 final size:117
Alignment explanation
Indices: 20421224--20421460 Score: 330
Period size: 123 Copynumber: 2.0 Consensus size: 117
20421214 CGATGAGTCT
* *
20421224 TGGTTATCTAGGGTTGACACGGCTCATATGCGATGAGTCTTAGCCATGGGATAGTAATGCTCATA
1 TGGTTATCAAGGGTTGACACGGCTCATATGCGATGAGTCTTAGCCAGGGGATAGTAATGCTCATA
*
20421289 TGAGATGAGTCTTAACCATATAACGGTGATAACACGGTTCCTACGTGATGAGGATAGA
66 TGAGATGACTCTTAACC--AT----GTGATAACACGGTTCCTACGTGATGAGGATAGA
* * * *
20421347 TGGTTATCAAGGGTTGACACTGCTCATATGCGATGAGTCTTGGCCAGGGGATGGTACTGCTCATA
1 TGGTTATCAAGGGTTGACACGGCTCATATGCGATGAGTCTTAGCCAGGGGATAGTAATGCTCATA
* * *
20421412 TGCGATGACTCTTGACCATGTGATAACACGGTTCCTACGTTATGAGGAT
66 TGAGATGACTCTTAACCATGTGATAACACGGTTCCTACGTGATGAGGAT
20421461 GCCTAGTTAT
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
117 29 0.28
121 2 0.02
123 73 0.70
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (117 bp):
TGGTTATCAAGGGTTGACACGGCTCATATGCGATGAGTCTTAGCCAGGGGATAGTAATGCTCATA
TGAGATGACTCTTAACCATGTGATAACACGGTTCCTACGTGATGAGGATAGA
Found at i:20421807 original size:65 final size:65
Alignment explanation
Indices: 20421682--20421864 Score: 190
Period size: 65 Copynumber: 2.8 Consensus size: 65
20421672 GTTTATTTTA
* * * * ** *
20421682 TTTCAAGGGAAACAAACTCAAAGATAGGTATTTCATAATAAACTGTCTCAAGGGATACAAAACTT
1 TTTCAAGGAAAAC-AACTCAAAGATAGGTGTTTCAAAAGAAACTGTCTCAAAAGAGACAAAA-TT
20421747 -G
64 CG
* * *
20421748 TTTCATA-TAAAATAACTCAAAGATAGGTGTTTCAAAAGAAACTGTCTTAAAAGAGACAAAATTC
1 TTTCA-AGGAAAACAACTCAAAGATAGGTGTTTCAAAAGAAACTGTCTCAAAAGAGACAAAATTC
20421812 G
65 G
** * *
20421813 TTTCAAGGAAAACAATCTCAAAGATATTTGTTTCAATAGAAACAGTCTCAAA
1 TTTCAAGGAAAACAA-CTCAAAGATAGGTGTTTCAAAAGAAACTGTCTCAAA
20421865 GATGGGTATT
Statistics
Matches: 96, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
64 3 0.03
65 53 0.55
66 39 0.41
67 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.27
Consensus pattern (65 bp):
TTTCAAGGAAAACAACTCAAAGATAGGTGTTTCAAAAGAAACTGTCTCAAAAGAGACAAAATTCG
Found at i:20421928 original size:36 final size:36
Alignment explanation
Indices: 20421888--20421998 Score: 104
Period size: 36 Copynumber: 3.2 Consensus size: 36
20421878 CGAGAAATTG
*
20421888 TCTCAAGGAAAATAAGAATTGTTTCAAGAGAAACGA
1 TCTCAAGGAAAATAAGAATTGTTTCAAGAGAAACAA
** ** *
20421924 TCTCAA--ATATTTTTG--TTGTTTCATGAGAAACAA
1 TCTCAAGGA-AAATAAGAATTGTTTCAAGAGAAACAA
* * *
20421957 TCTCAAGGAAAATAATAATTGTTTCAAGAAAAATAA
1 TCTCAAGGAAAATAAGAATTGTTTCAAGAGAAACAA
20421993 TCTCAA
1 TCTCAA
20421999 AGATAATTGT
Statistics
Matches: 56, Mismatches: 14, Indels: 10
0.70 0.17 0.12
Matches are distributed among these distances:
33 22 0.39
34 3 0.05
35 4 0.07
36 27 0.48
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.31
Consensus pattern (36 bp):
TCTCAAGGAAAATAAGAATTGTTTCAAGAGAAACAA
Found at i:20422009 original size:69 final size:69
Alignment explanation
Indices: 20421888--20422031 Score: 182
Period size: 69 Copynumber: 2.1 Consensus size: 69
20421878 CGAGAAATTG
* * * **
20421888 TCTCAAGGAAAATAAGAATTGTTTCAAGAGAAACGATCTCAAATATTTTTG-TTGTTTCATGAGA
1 TCTCAAGGAAAATAAGAATTGTTTCAAGAAAAACAATCTCAAAGATAATTGTTTGTTTCA-GAGA
20421952 AACAA
65 AACAA
* * * *
20421957 TCTCAAGGAAAATAATAATTGTTTCAAGAAAAATAATCTCAAAGATAATTGTTTTTTTCAGTGAA
1 TCTCAAGGAAAATAAGAATTGTTTCAAGAAAAACAATCTCAAAGATAATTGTTTGTTTCAGAGAA
20422022 ACAA
66 ACAA
*
20422026 ACTCAA
1 TCTCAA
20422032 AGGTTTTTCT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
69 57 0.89
70 7 0.11
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (69 bp):
TCTCAAGGAAAATAAGAATTGTTTCAAGAAAAACAATCTCAAAGATAATTGTTTGTTTCAGAGAA
ACAA
Found at i:20422262 original size:34 final size:34
Alignment explanation
Indices: 20422207--20422274 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
20422197 GTATCTCAGA
* * * *
20422207 GAGAAATTGTCTTAAGCGAGACGAAATTTGTTTT
1 GAGAAATTATCTCAAGCGAGACAAAATTTATTTT
*
20422241 GAGAAATTATCTCAAGTGAGACAAAATTTATTTT
1 GAGAAATTATCTCAAGCGAGACAAAATTTATTTT
20422275 TTTAAGAGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (34 bp):
GAGAAATTATCTCAAGCGAGACAAAATTTATTTT
Found at i:20422407 original size:32 final size:32
Alignment explanation
Indices: 20422366--20422438 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
20422356 TTCGCATCAG
* *
20422366 GATGTTGAATC-CACAATGATGCCCCAATATTC
1 GATGTTGAATCTCAAAAT-ATGCCCCAACATTC
*
20422398 GATGTTGAATCTCAAAATATGCCCCAACATTT
1 GATGTTGAATCTCAAAATATGCCCCAACATTC
20422430 GATGTTGAA
1 GATGTTGAA
20422439 ACTTCAAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 32 0.86
33 5 0.14
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (32 bp):
GATGTTGAATCTCAAAATATGCCCCAACATTC
Found at i:20422452 original size:32 final size:32
Alignment explanation
Indices: 20422366--20422453 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 32
20422356 TTCGCATCAG
* * *
20422366 GATGTTGAATC-CACAATGATGCCCCAATATTC
1 GATGTTGAAACTCA-AAAGATGCCCCAACATTC
* * *
20422398 GATGTTGAATCTCAAAATATGCCCCAACATTT
1 GATGTTGAAACTCAAAAGATGCCCCAACATTC
20422430 GATGTTGAAACTTC-AAAGATGCCC
1 GATGTTGAAAC-TCAAAAGATGCCC
20422454 TTATTGTTCC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
32 44 0.92
33 4 0.08
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (32 bp):
GATGTTGAAACTCAAAAGATGCCCCAACATTC
Found at i:20423498 original size:15 final size:15
Alignment explanation
Indices: 20423474--20423513 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
20423464 TTCTTGTCCC
20423474 TTTT-TCTTTGTTTA
1 TTTTCTCTTTGTTTA
*
20423488 TTTTCTCTTTGTTTC
1 TTTTCTCTTTGTTTA
*
20423503 TTTTCTTTTTG
1 TTTTCTCTTTG
20423514 ATTTTTGTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.03, C:0.12, G:0.07, T:0.78
Consensus pattern (15 bp):
TTTTCTCTTTGTTTA
Found at i:20424749 original size:18 final size:20
Alignment explanation
Indices: 20424726--20424763 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
20424716 AAAATGCTTA
20424726 AAAATG-AA-ATGCAGATGC
1 AAAATGAAAGATGCAGATGC
20424744 AAAATGCAAAGATGCAGATG
1 AAAATG-AAAGATGCAGATG
20424764 TAGATGCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.50, C:0.11, G:0.24, T:0.16
Consensus pattern (20 bp):
AAAATGAAAGATGCAGATGC
Found at i:20425291 original size:198 final size:199
Alignment explanation
Indices: 20424943--20425301 Score: 438
Period size: 198 Copynumber: 1.8 Consensus size: 199
20424933 CCCCAATAGT
* *
20424943 TCTGTAACCTAACTCAGTTAATGCCCCGTGCAGTGCAGAAGTCAGTGTGTCGCTCCTTGATAACT
1 TCTGTAAACTAACTCAGTTAATGCCCCGTGCAGTACAGAAGTCAGTGTGTCGCTCCTTGATAACT
* * * *
20425008 AGCGATTAGATGATCATAGATAAGAATCCACTGATGTGTTACTCCTCGGATCAATGAATCATAAT
66 AGCAATGAAATGATCATAGATAAGAATCCACTGATGTGTTACTCCTCGAATCAATGAATCATAAT
* ** *
20425073 TTTAGTTTTGAATGTTGCACGATCGTCGAGCTTACTGGTTCGTCTCAGATCTTTGATGCCCCTCA
131 TTCAGTCCTGAATATTGCACGATCGTCGAGCTTACTGGTTCGTCTCAGATCTTTGATGCCCCTCA
20425138 ATGC
196 ATGC
* * * * **
20425142 TCTGTAAACTAACTCCA-TTAATGCCTCG-GCGGTACTGAAGTCAGTTTGTCGCTCCTTGATGGC
1 TCTGTAAACTAACT-CAGTTAATGCCCCGTGCAGTACAGAAGTCAGTGTGTCGCTCCTTGATAAC
* * * * * * * *
20425205 TAGCAATGAAATGATCATAGATGATACTCCATTGTTG-GATTACTCCTCGAATCAGTGGATCATC
65 TAGCAATGAAATGATCATAGATAAGAATCCACTGATGTG-TTACTCCTCGAATCAATGAATCATA
*
20425269 ATTTCAGTCCCT-AATATTGCACGATCTTCGAGC
129 ATTTCAGT-CCTGAATATTGCACGATCGTCGAGC
20425302 AAGTCTCATT
Statistics
Matches: 132, Mismatches: 25, Indels: 7
0.80 0.15 0.04
Matches are distributed among these distances:
197 1 0.01
198 105 0.80
199 24 0.18
200 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (199 bp):
TCTGTAAACTAACTCAGTTAATGCCCCGTGCAGTACAGAAGTCAGTGTGTCGCTCCTTGATAACT
AGCAATGAAATGATCATAGATAAGAATCCACTGATGTGTTACTCCTCGAATCAATGAATCATAAT
TTCAGTCCTGAATATTGCACGATCGTCGAGCTTACTGGTTCGTCTCAGATCTTTGATGCCCCTCA
ATGC
Found at i:20428904 original size:9 final size:9
Alignment explanation
Indices: 20428890--20428918 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
20428880 GATTACATAC
20428890 ATATGTGAT
1 ATATGTGAT
20428899 ATATGTGAT
1 ATATGTGAT
20428908 ATATGTGAT
1 ATATGTGAT
20428917 AT
1 AT
20428919 GATATGACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (9 bp):
ATATGTGAT
Found at i:20428997 original size:33 final size:33
Alignment explanation
Indices: 20428955--20429019 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
20428945 TATGAAAAGG
20428955 GATCTATTAGATCATACAAGAATGTTACACAAT
1 GATCTATTAGATCATACAAGAATGTTACACAAT
* *
20428988 GATCTATTAGATCATATAAGAATGTTATACAA
1 GATCTATTAGATCATACAAGAATGTTACACAA
20429020 GCTACATGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (33 bp):
GATCTATTAGATCATACAAGAATGTTACACAAT
Found at i:20429898 original size:64 final size:64
Alignment explanation
Indices: 20429824--20429986 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 64
20429814 CGGTGCACCA
*
20429824 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * * **
20429888 CTTGTGCATCGATGCATCAAATGCATTCAATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
20429953 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
20429987 CAATTAATTC
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
64 38 0.46
65 45 0.54
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:20429958 original size:19 final size:19
Alignment explanation
Indices: 20429934--20429984 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
20429924 GAAAATATTC
20429934 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
20429953 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
20429972 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
20429985 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:20438550 original size:64 final size:65
Alignment explanation
Indices: 20438445--20438590 Score: 206
Period size: 64 Copynumber: 2.3 Consensus size: 65
20438435 CGGTGCACCA
* *
20438445 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAAATAGCCAGAGTGCATCGATGCATGG
** **
20438509 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATG
1 AGTGTGCATCGATGCATCAAATGCATTCGATG-TTTGAAAAATAGCCAGAGTGCATCGATGCATG
20438573 G
65 G
*
20438574 AGAGTGCATCGATGCAT
1 AGTGTGCATCGATGCAT
20438591 GGAGAGTGCA
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
64 37 0.52
65 34 0.48
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (65 bp):
AGTGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:20438579 original size:19 final size:19
Alignment explanation
Indices: 20438555--20438624 Score: 108
Period size: 19 Copynumber: 3.7 Consensus size: 19
20438545 GAAAATATTC
20438555 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
20438574 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
20438593 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
20438612 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
20438625 TTCAATTAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
17 4 0.08
18 6 0.12
19 38 0.79
ACGTcount: A:0.26, C:0.16, G:0.36, T:0.23
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:20438666 original size:84 final size:83
Alignment explanation
Indices: 20438493--20438675 Score: 203
Period size: 84 Copynumber: 2.2 Consensus size: 83
20438483 AAATAGCCTG
*** *
20438493 GTGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGA
1 GTGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATG-TTTCAAAATATTCAGA
20438558 GTGCATCGATGCATGGAGA
65 GTGCATCGATGCATGGAGA
* ** *
20438577 GTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATG-TTC-AATTAATTCATC
1 GTGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT-ATTCA--
20438640 GA-TGCATCGATGCATGGACTGA
63 GAGTGCATCGATGCATGGA--GA
*
20438662 -TGCATCGGTGCATG
1 GTGCATCGATGCATG
20438676 CCTTTTGAAT
Statistics
Matches: 85, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
81 3 0.04
82 7 0.08
83 16 0.19
84 57 0.67
85 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (83 bp):
GTGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATTCAGAG
TGCATCGATGCATGGAGA
Found at i:20439250 original size:31 final size:31
Alignment explanation
Indices: 20439093--20439246 Score: 236
Period size: 31 Copynumber: 5.0 Consensus size: 31
20439083 GAGTCGAGGG
20439093 TTACCTATGTTCTTCGGGACATATGGACAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGT
* * * *
20439124 TTACATATGTTCTTCTGGAAATATGGATAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGT
20439155 TTACCTATGTTCTTCGGGACATATGGACAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGT
* * *
20439186 TTACCTGTGTTCTTCGGGATATATGGACAGA
1 TTACCTATGTTCTTCGGGACATATGGACAGT
*
20439217 TTACCTATGTTCTTCGGGATATATGGACAG
1 TTACCTATGTTCTTCGGGACATATGGACAG
20439247 ATTATTATAC
Statistics
Matches: 111, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 111 1.00
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACAGT
Found at i:20439454 original size:31 final size:31
Alignment explanation
Indices: 20439415--20439546 Score: 174
Period size: 31 Copynumber: 4.3 Consensus size: 31
20439405 TCTATATGTT
* *
20439415 ACAGATTACCTATGTTCTTCGTGACATATGG
1 ACAGATTACCTATATTCTTCGGGACATATGG
* * **
20439446 ACAAATTACCTATGTTCTTCAAGACATATGG
1 ACAGATTACCTATATTCTTCGGGACATATGG
* * *
20439477 ACATATTACCTATATTATTTGGGACATATGG
1 ACAGATTACCTATATTCTTCGGGACATATGG
*
20439508 ACAGATTACCTATATTCTTTGGGACATATGG
1 ACAGATTACCTATATTCTTCGGGACATATGG
20439539 ACAGATTA
1 ACAGATTA
20439547 TTATATGAGC
Statistics
Matches: 90, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 90 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (31 bp):
ACAGATTACCTATATTCTTCGGGACATATGG
Found at i:20444010 original size:576 final size:576
Alignment explanation
Indices: 20442911--20444061 Score: 2113
Period size: 576 Copynumber: 2.0 Consensus size: 576
20442901 GAAATATGCA
*
20442911 CATATTAGAAGTTTGAAAAAATTGGTGATTTAAGTGCAACATTCACATAGTTGGGGTGCTTAAAG
1 CATATTAGAAGTTTGAAAAAATTGGTGATTTAAGTGCAACATTCACATAGTTGGGGTACTTAAAG
* * *
20442976 GTAATTGTACCTTTGTAAAAGTAGTTGGTTGGTAATAATTCCAGTACTGGAATTTGTGGTATTTA
66 GTAATTGTACCTTTGTAAAAGTAATTGGCTGGTAATAATTCCAGTACTGGAATTTGTAGTATTTA
*
20443041 AAATTTAAGTGATAAAATGGTGAATGACCATTTTGTATAAATTGGAAAAGTTGGTGCCAATGTTA
131 AAATTTAAGTGATAAAATGGTGAATAACCATTTTGTATAAATTGGAAAAGTTGGTGCCAATGTTA
20443106 AAAGGAATTATTAAGTGTTAAGTATTTTGATAGAAAATGAGTTTCAAGTATATTATGGATTTGTT
196 AAAGGAATTATTAAGTGTTAAGTATTTTGATAGAAAATGAGTTTCAAGTATATTATGGATTTGTT
*
20443171 GTGGGGATTTGTTTATGTTAGTACAATACTAACATATGTATTGTTATGAAATTGTGATTTGTACA
261 GTGGGGATTTGTTCATGTTAGTACAATACTAACATATGTATTGTTATGAAATTGTGATTTGTACA
20443236 GATCGTGATTGATTTGTGACTAAGACAAGTCAAGTATAAAAGGGTTGTTGTGGATTATATTGAGG
326 GATCGTGATTGATTTGTGACTAAGACAAGTCAAGTATAAAAGGGTTGTTGTGGATTATATTGAGG
20443301 AATGTCGTTTGGATATATAAAGTGTCAAGGTAAGTGCAAATTTAATTTGTACTTATGTTATAGAA
391 AATGTCGTTTGGATATATAAAGTGTCAAGGTAAGTGCAAATTTAATTTGTACTTATGTTATAGAA
* * * *
20443366 TAAACATTGGCTTGTGATGAGCCATTGACGGAGTTACTATGGTGAGAAGTAACTCCTAAATTAAT
456 TAAAAATTGGCTTGTAATGAGCCAGTGACGGAGTTACTATGGTAAGAAGTAACTCCTAAATTAAT
20443431 GTTATTTGATTTGTGATGCATGCATAACGTTATACATGGATGTTTGAATACATGAC
521 GTTATTTGATTTGTGATGCATGCATAACGTTATACATGGATGTTTGAATACATGAC
* *
20443487 CATATTGGAAGTTTGAAAAGATTGGTGATTTAAGTGCAACATTCACATAGTTGGGGTACTTAAAG
1 CATATTAGAAGTTTGAAAAAATTGGTGATTTAAGTGCAACATTCACATAGTTGGGGTACTTAAAG
*
20443552 GTAATTGTACCTTTGTAATAGTAATTGGCTGGTAATAATTCCAGTACTGGAATTTGTAGTATTTA
66 GTAATTGTACCTTTGTAAAAGTAATTGGCTGGTAATAATTCCAGTACTGGAATTTGTAGTATTTA
* *
20443617 AAATTTAAGTGATAAAATGGTGAATAACCATTTTGTATAAATTGTAAAGGTTGGTGCCAATGTTA
131 AAATTTAAGTGATAAAATGGTGAATAACCATTTTGTATAAATTGGAAAAGTTGGTGCCAATGTTA
20443682 AAAGGAATTATTAAGTGTTAAGTATTTTGATAGAAAATGAGTTTCAAGTATATTATGGATTTGTT
196 AAAGGAATTATTAAGTGTTAAGTATTTTGATAGAAAATGAGTTTCAAGTATATTATGGATTTGTT
20443747 GTGGGGATTTGTTCATGTTAGTACAATACTAACATATGTATTGTTATGAAATTGTGATTTGTACA
261 GTGGGGATTTGTTCATGTTAGTACAATACTAACATATGTATTGTTATGAAATTGTGATTTGTACA
*
20443812 GATCGTGATTGATTTGTGACTAAGACAAGTCAAGTATAAAAGGGTTGTTGTGGATTATATTGATG
326 GATCGTGATTGATTTGTGACTAAGACAAGTCAAGTATAAAAGGGTTGTTGTGGATTATATTGAGG
* *
20443877 AATGTTGTTTGGATATATAAAGTGTCAAGGTGAGTGCAAATTTAATTTGTACTTATGTTATAGAA
391 AATGTCGTTTGGATATATAAAGTGTCAAGGTAAGTGCAAATTTAATTTGTACTTATGTTATAGAA
* * *
20443942 TAAAAATTGGCTTGTAATGAGCCAGTGATGGAGTTACTATGGTAAGAAGTGATTCCTAAATTAAT
456 TAAAAATTGGCTTGTAATGAGCCAGTGACGGAGTTACTATGGTAAGAAGTAACTCCTAAATTAAT
20444007 GTTATTTGATTTGTGATGCATGCATAACGTTATACATGGATGTTTGAATACATGA
521 GTTATTTGATTTGTGATGCATGCATAACGTTATACATGGATGTTTGAATACATGA
20444062 TTCCATAAGT
Statistics
Matches: 554, Mismatches: 21, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
576 554 1.00
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.37
Consensus pattern (576 bp):
CATATTAGAAGTTTGAAAAAATTGGTGATTTAAGTGCAACATTCACATAGTTGGGGTACTTAAAG
GTAATTGTACCTTTGTAAAAGTAATTGGCTGGTAATAATTCCAGTACTGGAATTTGTAGTATTTA
AAATTTAAGTGATAAAATGGTGAATAACCATTTTGTATAAATTGGAAAAGTTGGTGCCAATGTTA
AAAGGAATTATTAAGTGTTAAGTATTTTGATAGAAAATGAGTTTCAAGTATATTATGGATTTGTT
GTGGGGATTTGTTCATGTTAGTACAATACTAACATATGTATTGTTATGAAATTGTGATTTGTACA
GATCGTGATTGATTTGTGACTAAGACAAGTCAAGTATAAAAGGGTTGTTGTGGATTATATTGAGG
AATGTCGTTTGGATATATAAAGTGTCAAGGTAAGTGCAAATTTAATTTGTACTTATGTTATAGAA
TAAAAATTGGCTTGTAATGAGCCAGTGACGGAGTTACTATGGTAAGAAGTAACTCCTAAATTAAT
GTTATTTGATTTGTGATGCATGCATAACGTTATACATGGATGTTTGAATACATGAC
Found at i:20445266 original size:31 final size:31
Alignment explanation
Indices: 20445228--20445382 Score: 222
Period size: 31 Copynumber: 5.0 Consensus size: 31
20445218 AAGAGTCGAG
20445228 GGTTACCTATGTTCTTCGAGACATATGGACA
1 GGTTACCTATGTTCTTCGAGACATATGGACA
* *
20445259 GGTTACCTATGTTCTTCGGGACATATGGATA
1 GGTTACCTATGTTCTTCGAGACATATGGACA
*
20445290 GTTTACCTATGTTCTTCGAGACATATGGACA
1 GGTTACCTATGTTCTTCGAGACATATGGACA
* *
20445321 GTTTACCTATGTTATTC-AGGACATATGGACA
1 GGTTACCTATGTTCTTCGA-GACATATGGACA
** *
20445352 TATTACCTATGTTCTTCGGGACATATGGACA
1 GGTTACCTATGTTCTTCGAGACATATGGACA
20445383 TATTATTATA
Statistics
Matches: 112, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
30 1 0.01
31 111 0.99
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (31 bp):
GGTTACCTATGTTCTTCGAGACATATGGACA
Found at i:20445306 original size:62 final size:62
Alignment explanation
Indices: 20445230--20445382 Score: 245
Period size: 62 Copynumber: 2.5 Consensus size: 62
20445220 GAGTCGAGGG
* * *
20445230 TTACCTATGTTCTTCGAGACATATGGACAGGTTACCTATGTTCTTCGGGACATATGGATAGT-
1 TTACCTATGTTCTTCGAGACATATGGACAGGTTACCTATGTTATTCAGGACATATGGACA-TA
*
20445292 TTACCTATGTTCTTCGAGACATATGGACAGTTTACCTATGTTATTCAGGACATATGGACATA
1 TTACCTATGTTCTTCGAGACATATGGACAGGTTACCTATGTTATTCAGGACATATGGACATA
*
20445354 TTACCTATGTTCTTCGGGACATATGGACA
1 TTACCTATGTTCTTCGAGACATATGGACA
20445383 TATTATTATA
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
61 1 0.01
62 84 0.99
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (62 bp):
TTACCTATGTTCTTCGAGACATATGGACAGGTTACCTATGTTATTCAGGACATATGGACATA
Found at i:20445586 original size:31 final size:31
Alignment explanation
Indices: 20445551--20445618 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
20445541 TATATGTTAC
* *
20445551 AGATTACATATGTTCTTTGGGACATATGGAT
1 AGATTACATATGTTATTCGGGACATATGGAT
*
20445582 AGATTACCTATGTTATTCGGGACATATGGAT
1 AGATTACATATGTTATTCGGGACATATGGAT
20445613 AGATTA
1 AGATTA
20445619 TGTTGAGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (31 bp):
AGATTACATATGTTATTCGGGACATATGGAT
Found at i:20446462 original size:65 final size:65
Alignment explanation
Indices: 20446330--20446488 Score: 207
Period size: 65 Copynumber: 2.5 Consensus size: 65
20446320 GCACTAAGTC
* *
20446330 TGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGG
1 TGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGG
** * *
20446394 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATTCTCAGTGCATCGGTGCATGG-TA
1 TGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT-
*
20446457 TG
64 GG
*
20446459 TGCATCGATGCATGAAATGCATTCGATGTT
1 TGCATCGATGCATCAAATGCATTCGATGTT
20446489 CAATTTAATT
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 28 0.33
65 53 0.63
66 3 0.04
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (65 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGG
Found at i:20446965 original size:2 final size:2
Alignment explanation
Indices: 20446958--20446988 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20446948 TAGCCAATTG
20446958 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20446989 GCTTAAGCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20453085 original size:22 final size:21
Alignment explanation
Indices: 20453043--20453082 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20453033 GAGTTTATTT
*
20453043 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
20453064 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
20453083 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:20455492 original size:31 final size:31
Alignment explanation
Indices: 20455451--20455509 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
20455441 TTTTCAACAG
20455451 ATTACCTATGTTCTTCGGGACATATGGATAT
1 ATTACCTATGTTCTTCGGGACATATGGATAT
*
20455482 ATTACTTATGTTCTTCGGGACATATGGA
1 ATTACCTATGTTCTTCGGGACATATGGA
20455510 CAAATTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.39
Consensus pattern (31 bp):
ATTACCTATGTTCTTCGGGACATATGGATAT
Found at i:20457540 original size:30 final size:29
Alignment explanation
Indices: 20457479--20457560 Score: 74
Period size: 30 Copynumber: 2.7 Consensus size: 29
20457469 AAATAAAATT
* * * *
20457479 AACAGGAATTTAAAGGGTTAAAATAGCAAA
1 AACAGAAACTTAAAGGATT-AAACAGCAAA
* *
20457509 AATAGAAAGTTAAAGGATTAAACAGCAAAA
1 AACAGAAACTTAAAGGATTAAACAGC-AAA
*
20457539 AACATAAACTTAAAGGACTTAA
1 AACAGAAACTTAAAGGA-TTAA
20457561 TAAACAAATA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 6 0.14
30 32 0.76
31 4 0.10
ACGTcount: A:0.56, C:0.09, G:0.16, T:0.20
Consensus pattern (29 bp):
AACAGAAACTTAAAGGATTAAACAGCAAA
Found at i:20458783 original size:3 final size:3
Alignment explanation
Indices: 20458769--20458806 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
20458759 CATAAAATGC
20458769 AAT AATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
20458807 TATTTTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:20463538 original size:30 final size:30
Alignment explanation
Indices: 20463475--20463539 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
20463465 ATTTAATGTG
*
20463475 TTTAGCACCTAAATTATCAGTTTTGTTCCT
1 TTTAGCACCTAAATTATCAGTTTTGGTCCT
*
20463505 TTTAGCACTTAAATTA-C-GATTTTGGTCCGT
1 TTTAGCACCTAAATTATCAG-TTTTGGTCC-T
20463535 TTTAG
1 TTTAG
20463540 TACCATAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 1 0.03
29 9 0.29
30 21 0.68
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (30 bp):
TTTAGCACCTAAATTATCAGTTTTGGTCCT
Found at i:20470353 original size:33 final size:33
Alignment explanation
Indices: 20470311--20470373 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
20470301 CTTATAGATG
20470311 CATCCGTACTACTTGTTCTGCTTGAAGGAGCTT
1 CATCCGTACTACTTGTTCTGCTTGAAGGAGCTT
20470344 CATCCGTACTACTTGTTCTGCTTGAAGGAG
1 CATCCGTACTACTTGTTCTGCTTGAAGGAG
20470374 TATTATCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (33 bp):
CATCCGTACTACTTGTTCTGCTTGAAGGAGCTT
Found at i:20470632 original size:14 final size:14
Alignment explanation
Indices: 20470613--20470665 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
20470603 TAACTACAAT
20470613 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
20470627 AATAAATCAATTCATACT
1 AATAAAT-TATT--TA-A
20470645 AATAAATTATTTAA
1 AATAAATTATTTAA
20470659 AATAAAT
1 AATAAAT
20470666 CAATCTATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 14 0.45
15 5 0.16
17 5 0.16
18 7 0.23
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:20470749 original size:54 final size:53
Alignment explanation
Indices: 20470685--20471172 Score: 246
Period size: 54 Copynumber: 9.2 Consensus size: 53
20470675 CAACTACAAT
20470685 AATAAATCAATCCATATTTTAAAATAAATCAATATATACTAATAAATTGTTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATATATACTAATAAATT-TTTAA
20470739 AATAAATCAATCCATATTTTAAAATAAATCAAT-TCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATAT-ATACTAATAAATT-TTTAA
* * * * **
20470793 AATAAATCAATACATA----CAACTACAAT-AATAAAT-C-AATCTATATTTTAA
1 AATAAATCAATCCATATTTTAAAATA-AATCAATATATACTAATAAAT-TTTTAA
** * ** * * * * * **
20470841 AATAAATCAATCCATAATAATAAATTATTTAAAATAAATCAATTCATACAA-CTACAA
1 AATAAATCAATCCAT-ATTTTAAAATAAAT-CAATATAT--ACTAATA-AATTTTTAA
* ** *
20470898 TAACAAATCAATCCATATTTTAAAATAAATCAATCCATAATAATAAATTATTTAA
1 -AATAAATCAATCCATATTTTAAAATAAATCAATATATACTAATAAATT-TTTAA
* * * * * * * * *
20470953 AATAAATCAATTCATA-CTAATAAATTATTTAAAATA-AATCAATACATATTTTAA
1 AATAAATCAATCCATATTTTA-AAATAAATCAATATATACT-AATAAAT-TTTTAA
* *
20471007 AATAAATTAATTCATATGATTTAAAATAAATC---A-AT-CT-AT--A-TTTTAA
1 AATAAATCAATCCATAT--TTTAAAATAAATCAATATATACTAATAAATTTTTAA
* * * * * * * **
20471053 AATAAATCAATCCATA-CTAATAAATTATTTAAAATA-AATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTA-AAATAAATCAATATATACT-AATAAAT-TTTTAA
*
20471107 AATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATATATACTAATAAATT-TTTAA
20471161 AATAAATCAATC
1 AATAAATCAATC
20471173 TATACAACTA
Statistics
Matches: 324, Mismatches: 69, Indels: 82
0.68 0.15 0.17
Matches are distributed among these distances:
43 2 0.01
44 6 0.02
46 20 0.06
47 1 0.00
48 27 0.08
49 3 0.01
50 13 0.04
51 3 0.01
52 4 0.01
53 14 0.04
54 181 0.56
55 8 0.02
56 11 0.03
57 14 0.04
58 16 0.05
59 1 0.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.35
Consensus pattern (53 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATATATACTAATAAATTTTTAA
Found at i:20470759 original size:22 final size:22
Alignment explanation
Indices: 20470734--20470776 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
20470724 TAATAAATTG
20470734 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
20470756 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
20470777 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:20470785 original size:22 final size:22
Alignment explanation
Indices: 20470736--20470784 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
20470726 ATAAATTGTT
**
20470736 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
20470758 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
20470781 TAAA
1 TAAA
20470785 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Done.