Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008138.1 Hibiscus syriacus cultivar Beakdansim tig00110694_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: 3838456
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 18
Found at i:521000 original size:60 final size:60
Alignment explanation
Indices: 520896--521031 Score: 177
Period size: 60 Copynumber: 2.3 Consensus size: 60
520886 TGCATCATAT
* * * *
520896 ATCCTCAAACTATAACTTTTATTCTAAATTAGCCCCTAAGCTTTTGAATATTCCAATTTC
1 ATCCTCAAACTATGACTTTCATTCTAAATTAGCCCCGAAGCTTTTGAATATTCCAAATTC
* *
520956 ATCCTCAAACTATGA-TTCTCATTCTAAATTGATCCTCGAA-CTTTTGAATATTCCAAATTC
1 ATCCTCAAACTATGACTT-TCATTCTAAATT-AGCCCCGAAGCTTTTGAATATTCCAAATTC
*
521016 ATCCCCAAACTATGAC
1 ATCCTCAAACTATGAC
521032 CCACAATCTA
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
59 2 0.03
60 58 0.88
61 6 0.09
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (60 bp):
ATCCTCAAACTATGACTTTCATTCTAAATTAGCCCCGAAGCTTTTGAATATTCCAAATTC
Found at i:521013 original size:29 final size:29
Alignment explanation
Indices: 520936--521026 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 29
520926 AGCCCCTAAG
*
520936 CTTTTGAATATTCCAATTTCATCCTCAAA
1 CTTTTGAATATTCCAAATTCATCCTCAAA
* * * * *
520965 C-TATGATTCTCATTCTAAATTGATCCTCGAA
1 CTTTTGA--AT-ATTCCAAATTCATCCTCAAA
*
520996 CTTTTGAATATTCCAAATTCATCCCCAAA
1 CTTTTGAATATTCCAAATTCATCCTCAAA
521025 CT
1 CT
521027 ATGACCCACA
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
28 4 0.09
29 19 0.41
30 2 0.04
31 17 0.37
32 4 0.09
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.38
Consensus pattern (29 bp):
CTTTTGAATATTCCAAATTCATCCTCAAA
Found at i:521058 original size:60 final size:60
Alignment explanation
Indices: 520936--521071 Score: 157
Period size: 60 Copynumber: 2.3 Consensus size: 60
520926 AGCCCCTAAG
* * ** * * * * *
520936 CTTTTGAATATTCCAATTTCATCCTCAAACTATGATTCTCATTCTAAATTGATCCTCGAA
1 CTTTTGAATATTCCAAATTCATCCCCAAACTATGACCCACAATCTAAAGTGATCCCCAAA
*
520996 CTTTTGAATATTCCAAATTCATCCCCAAACTATGACCCACAATCTAAAGTGGTCCCCAAA
1 CTTTTGAATATTCCAAATTCATCCCCAAACTATGACCCACAATCTAAAGTGATCCCCAAA
*
521056 CTTCTGAACT-TTCCAA
1 CTTTTGAA-TATTCCAA
521072 TCTCCTAAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 63 0.98
61 1 0.02
ACGTcount: A:0.32, C:0.27, G:0.07, T:0.34
Consensus pattern (60 bp):
CTTTTGAATATTCCAAATTCATCCCCAAACTATGACCCACAATCTAAAGTGATCCCCAAA
Found at i:521183 original size:60 final size:60
Alignment explanation
Indices: 521088--521235 Score: 172
Period size: 60 Copynumber: 2.5 Consensus size: 60
521078 AAAAGCATTC
** * ** * ** *
521088 AAAAGTTTGGGGGGTCAATATAGAATGAGGATCATAGTTTGTGGATGAATTTGGAATGTTT
1 AAAAGTTT-GGGGACCAATTTAGAATGAGGATCATAGTTTGAAGATGAAATTAAAAAGTTT
521149 AAAAGTTTGGGGACCAATTTAGAATGA-GAGTCATAGTTTGAAGATGAAATTAAAAAGTTT
1 AAAAGTTTGGGGACCAATTTAGAATGAGGA-TCATAGTTTGAAGATGAAATTAAAAAGTTT
* *
521209 AAAAGTTTGAGGACTAATTTAGAATGA
1 AAAAGTTTGGGGACCAATTTAGAATGA
521236 AGATTTTGAG
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
59 2 0.03
60 65 0.87
61 8 0.11
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (60 bp):
AAAAGTTTGGGGACCAATTTAGAATGAGGATCATAGTTTGAAGATGAAATTAAAAAGTTT
Found at i:526638 original size:12 final size:11
Alignment explanation
Indices: 526625--526676 Score: 50
Period size: 12 Copynumber: 4.4 Consensus size: 11
526615 TGCCATTTTA
526625 TTTATTTATTT
1 TTTATTTATTT
*
526636 ATTTATTCATTT
1 -TTTATTTATTT
*
526648 TGTTATTTTTATT
1 T-TTATTTAT-TT
526661 TTTATTTTATTT
1 TTTA-TTTATTT
526673 TTTA
1 TTTA
526677 GGGGTCCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 1 0.03
12 25 0.76
13 7 0.21
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (11 bp):
TTTATTTATTT
Found at i:527633 original size:18 final size:18
Alignment explanation
Indices: 527610--527652 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
527600 CTTTAGATTA
*
527610 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
527628 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
527646 TTTATTT
1 TTTATTT
527653 TTAAAAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:527728 original size:21 final size:21
Alignment explanation
Indices: 527704--527810 Score: 73
Period size: 20 Copynumber: 5.1 Consensus size: 21
527694 CTACTATTTC
527704 TTATTTTATTA-TATTTCCCTT
1 TTATTTTATTATTATTT-CCTT
**
527725 TTA-TTTATTATTATTTTGTT
1 TTATTTTATTATTATTTCCTT
*
527745 TTATTTTATTTTTATTTTCTCTT
1 TTATTTTATTATTA-TTTC-CTT
* *
527768 TTAATATTTTTTAATATTT--TT
1 TT-AT-TTTATTATTATTTCCTT
527789 TATATTTTATTATT-TTT-CTT
1 T-TATTTTATTATTATTTCCTT
527809 TT
1 TT
527811 CTGAAATTTA
Statistics
Matches: 68, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
19 4 0.06
20 22 0.32
21 22 0.32
22 4 0.06
23 4 0.06
24 5 0.07
25 7 0.10
ACGTcount: A:0.20, C:0.06, G:0.01, T:0.74
Consensus pattern (21 bp):
TTATTTTATTATTATTTCCTT
Found at i:527781 original size:10 final size:10
Alignment explanation
Indices: 527766--527796 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
527756 TTATTTTCTC
527766 TTTTAATATT
1 TTTTAATATT
527776 TTTTAATATT
1 TTTTAATATT
527786 TTTT-ATATT
1 TTTTAATATT
527795 TT
1 TT
527797 ATTATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.33
10 14 0.67
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTAATATT
Found at i:529868 original size:20 final size:23
Alignment explanation
Indices: 529843--529889 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
529833 CCTCTAATTC
529843 TCATGCA-T-CATGT-ATTATTT
1 TCATGCATTGCATGTCATTATTT
*
529863 TCATGCATTGCATGTCATTTTTT
1 TCATGCATTGCATGTCATTATTT
529886 TCAT
1 TCAT
529890 TTTCCCATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 1 0.04
22 5 0.22
23 10 0.43
ACGTcount: A:0.21, C:0.17, G:0.11, T:0.51
Consensus pattern (23 bp):
TCATGCATTGCATGTCATTATTT
Found at i:533945 original size:86 final size:86
Alignment explanation
Indices: 533796--534004 Score: 283
Period size: 86 Copynumber: 2.4 Consensus size: 86
533786 GAAGAACATT
* * * *
533796 TCACATGGCTTTCCCGTGAAGGAGAGCCACCCAAAGATCATGTCAATTGGTTCAGACCCGCGAAG
1 TCACATGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCAATTGGTTCAGACCCGCGAAG
533861 GGGAACCACCTGAGGAATATA
66 GGGAACCACCTGAGGAATATA
* * * *
533882 TCACATGGTTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCATACCTGCGAAG
1 TCACATGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCAATTGGTTCAGACCCGCGAAG
*
533947 GGGAACCATCTGAGGAATATA
66 GGGAACCACCTGAGGAATATA
* * * * * *
533968 CCACTTGGCTTTCCCGTAAATGGAAGTCATCTAAAGA
1 TCACATGGCTTTCCCGTGAAGGGGAGTCATCCAAAGA
534005 ATTATGACCT
Statistics
Matches: 107, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
86 107 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (86 bp):
TCACATGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCAATTGGTTCAGACCCGCGAAG
GGGAACCACCTGAGGAATATA
Found at i:533973 original size:44 final size:44
Alignment explanation
Indices: 533842--533975 Score: 114
Period size: 44 Copynumber: 3.1 Consensus size: 44
533832 ATCATGTCAA
* * *
533842 TTGGTTCAGACCCGCGAAGGGGAACCACCTGAGGAATATATCAC
1 TTGGTTCATACCCGCGAAGGGGAACCATCTGAGGAATATACCAC
* * * ** ** *
533886 ATGGTT--TTCCCGTGAAGGGGAGTCATCCAAAG-ATCAT-CTCAC
1 TTGGTTCATACCCGCGAAGGGGAACCATCTGAGGAAT-ATAC-CAC
*
533928 TTGGTTCATACCTGCGAAGGGGAACCATCTGAGGAATATACCAC
1 TTGGTTCATACCCGCGAAGGGGAACCATCTGAGGAATATACCAC
533972 TTGG
1 TTGG
533976 CTTTCCCGTA
Statistics
Matches: 64, Mismatches: 20, Indels: 12
0.67 0.21 0.12
Matches are distributed among these distances:
41 2 0.03
42 27 0.42
44 32 0.50
45 3 0.05
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (44 bp):
TTGGTTCATACCCGCGAAGGGGAACCATCTGAGGAATATACCAC
Found at i:534442 original size:202 final size:202
Alignment explanation
Indices: 534064--534445 Score: 478
Period size: 202 Copynumber: 1.9 Consensus size: 202
534054 AACCGTTCAC
* * *
534064 AGCATAGCTCAAGGTGAGAATGGCTATCTGTCAACAAAAAACTTTCGAGTTCGATTCCATTCAGT
1 AGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAAACTTTCGAGTTCGATTCCATTCAGC
* * * * * * * *
534129 TCGATGACATATTAACCGCATGGTAGCAACGGGGAATTACTTTCCGGTTGAAGCTTAAACTGAGG
66 TCGAGGACATATCAACCACATGGTAGCAACGAGGAACTACATTCAGGTTGAAGCTTAAACCGAGG
** * *** * *
534194 TCTTTAAGTCAAGAGGAAGACCTGTGTTGGCTGCAACTTAGCAACAAGAAACTATATCTCAGCAT
131 TCTTTAAACCAAGAAGAAGACCAAAGTTGACTACAACTTAGCAACAAGAAACTATATCTCAGCAT
534259 AATTTAT
196 AATTTAT
* *
534266 AGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAAACTTTCGAGTTTGATTCCATTCAGC
1 AGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAAACTTTCGAGTTCGATTCCATTCAGC
** * **
534330 TCGAGGGTATATCAACCACATGGTAGCATCGAGGAACTACATTCAGGTTGAATTTTCAAACCGAG
66 TCGAGGACATATCAACCACATGGTAGCAACGAGGAACTACATTCAGGTTGAAGCTT-AAACCGAG
* * * *
534395 GTCTTTAAACCGAGAAGAAGACCAAAGTTGACTACGATTTGGCAACAAGAA
130 GTCTTTAAACCAAGAAGAAGACCAAAGTTGACTACAACTTAGCAACAAGAA
534446 GTCACCTTCT
Statistics
Matches: 149, Mismatches: 30, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
201 71 0.48
202 78 0.52
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (202 bp):
AGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAAACTTTCGAGTTCGATTCCATTCAGC
TCGAGGACATATCAACCACATGGTAGCAACGAGGAACTACATTCAGGTTGAAGCTTAAACCGAGG
TCTTTAAACCAAGAAGAAGACCAAAGTTGACTACAACTTAGCAACAAGAAACTATATCTCAGCAT
AATTTAT
Found at i:534769 original size:9 final size:9
Alignment explanation
Indices: 534744--534776 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
534734 ACTTATTTAG
534744 TATATATAT
1 TATATATAT
534753 TA-ATATAT
1 TATATATAT
534761 TATATATAT
1 TATATATAT
*
534770 AATATAT
1 TATATAT
534777 GGTTTTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
TATATATAT
Found at i:534838 original size:21 final size:22
Alignment explanation
Indices: 534804--534844 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
534794 TCGAAAATAT
*
534804 ATATAATATTATTTT-TTTAAA
1 ATATAATATCATTTTATTTAAA
*
534825 ATATAATGTCATTTTATTTA
1 ATATAATATCATTTTATTTA
534845 TTTCTTTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
ATATAATATCATTTTATTTAAA
Found at i:534884 original size:22 final size:21
Alignment explanation
Indices: 534836--534892 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
534826 TATAATGTCA
*
534836 TTTTATTTATTTCTTTTCATT
1 TTTTATTTATTTATTTTCATT
534857 TATTTATTTATTTATTTTGC-TAT
1 T-TTTATTTATTTATTTT-CAT-T
534880 TTTTATTTCATTT
1 TTTTATTT-ATTT
534893 TTTAGGGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 1 0.03
22 23 0.74
23 7 0.23
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTTATTTATTTATTTTCATT
Found at i:535253 original size:12 final size:12
Alignment explanation
Indices: 535236--535260 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
535226 ATGCTTAACT
535236 AATTTTCTTTTA
1 AATTTTCTTTTA
535248 AATTTTCTTTTA
1 AATTTTCTTTTA
535260 A
1 A
535261 GCCGAAGGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (12 bp):
AATTTTCTTTTA
Found at i:535591 original size:18 final size:18
Alignment explanation
Indices: 535564--535606 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
535554 CTTTAAATTA
*
535564 TTTT-TTTAATTATTTTC
1 TTTTATTTAATTATTATC
*
535581 TTTTATTTAATTCTTATC
1 TTTTATTTAATTATTATC
535599 TTTTATTT
1 TTTTATTT
535607 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTATTTAATTATTATC
Found at i:535739 original size:24 final size:23
Alignment explanation
Indices: 535692--535739 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
535682 ATTATTTTTA
*
535692 TTTTTATTTTCTCTTTTAACATT
1 TTTTTATTTTCTCTTTTAAAATT
535715 TTTTTATTTT-TCTTTTCTAAAATT
1 TTTTTATTTTCTC-TTT-TAAAATT
535739 T
1 T
535740 AATATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 2 0.09
23 13 0.59
24 7 0.32
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTTTATTTTCTCTTTTAAAATT
Found at i:535770 original size:63 final size:64
Alignment explanation
Indices: 535688--535809 Score: 176
Period size: 63 Copynumber: 1.9 Consensus size: 64
535678 ATTTATTATT
* **
535688 TTTATTTTTATTTTCTCTTTTAACATTTTTTTATTTTTC-TTTTCTAAAATTTAATATTTTTTCA
1 TTTATTTTTATTTTCTCTTTTAACA-TTTTTTATGTAACATTTTCTAAAATTTAATATTTTTTCA
* *
535752 TTTA-TTTTATTTTTTCTTTTAACATTTTTTATGTAACATTTTTTAAAATTTAATATTT
1 TTTATTTTTATTTTCTCTTTTAACATTTTTTATGTAACATTTTCTAAAATTTAATATTT
535810 CCTTCTTTGA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
62 10 0.19
63 38 0.73
64 4 0.08
ACGTcount: A:0.25, C:0.07, G:0.01, T:0.67
Consensus pattern (64 bp):
TTTATTTTTATTTTCTCTTTTAACATTTTTTATGTAACATTTTCTAAAATTTAATATTTTTTCA
Found at i:535824 original size:63 final size:63
Alignment explanation
Indices: 535688--535829 Score: 173
Period size: 63 Copynumber: 2.2 Consensus size: 63
535678 ATTTATTATT
* * ** *
535688 TTTATTTTTATTTTCTCTTTTAACATTTTTTTATTTTTCTTTTCTAAAATTTAATATTTTTTCA
1 TTTA-TTTTATTTTTTCTTTTAACATTTTTTTATGTAACTTTTCTAAAATTTAATATTTCTTCA
*
535752 TTTATTTTATTTTTTCTTTTAACA-TTTTTTATGTAACATTTTTTAAAATTTAATATTTCCTTC-
1 TTTATTTTATTTTTTCTTTTAACATTTTTTTATGTAAC-TTTTCTAAAATTTAATATTT-CTTCA
535815 TTTGA-TTTATTTTTT
1 TTT-ATTTTATTTTTT
535830 AATTTAATTT
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
62 10 0.14
63 51 0.74
64 8 0.12
ACGTcount: A:0.23, C:0.08, G:0.01, T:0.68
Consensus pattern (63 bp):
TTTATTTTATTTTTTCTTTTAACATTTTTTTATGTAACTTTTCTAAAATTTAATATTTCTTCA
Found at i:541382 original size:20 final size:20
Alignment explanation
Indices: 541359--541422 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 20
541349 TAGTATTTAG
541359 ATAAAT-TTATTAATAATTTT
1 ATAAATATT-TTAATAATTTT
* *
541379 AT-AATCTTTTAATAAATTTA
1 ATAAATATTTTAAT-AATTTT
*
541399 ATAAGTATTTT-ATAATTTT
1 ATAAATATTTTAATAATTTT
*
541418 TTAAA
1 ATAAA
541423 CTTTATTGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
19 16 0.46
20 13 0.37
21 6 0.17
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
ATAAATATTTTAATAATTTT
Found at i:541392 original size:19 final size:20
Alignment explanation
Indices: 541368--541417 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
541358 GATAAATTTA
*
541368 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
541387 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
541408 TT-ATAATTTT
1 TTAATAATTTT
541418 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:541420 original size:31 final size:30
Alignment explanation
Indices: 541335--541421 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
541325 TTCGATAATA
* *
541335 TAATAATTATTTTAT-AGTATTTAGATAAATT
1 TAATAA-TATTTTATAATTTTTTA-ATAAATT
* *
541366 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATTTTTTAATAAATT
541397 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATTTTTTAA
541422 ACTTTATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 40 0.85
32 6 0.13
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAATTTTTTAATAAATT
Found at i:542180 original size:31 final size:30
Alignment explanation
Indices: 542145--542231 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
542135 TCAATAAAGT
542145 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
* *
542176 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAA-TATTATTAAATTTA
* *
542207 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAAT-ATTATTA
542232 TATTATCGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:542207 original size:20 final size:20
Alignment explanation
Indices: 542140--542207 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 20
542130 TTTCGTCAAT
*
542140 AAAG-TTTAAAAAATTA-TA
1 AAAGATTTATAAAATTATTA
* * *
542158 AAATACTTATTAAATTTATTA
1 AAAGATTTA-TAAAATTATTA
542179 AAAGA-TTATAAAATTATTA
1 AAAGATTTATAAAATTATTA
542198 ATAA-ATTTAT
1 A-AAGATTTAT
542208 CTAAATACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 3 0.08
19 15 0.38
20 15 0.38
21 6 0.15
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (20 bp):
AAAGATTTATAAAATTATTA
Found at i:543173 original size:21 final size:21
Alignment explanation
Indices: 543147--543200 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
543137 GCGTTGCATT
543147 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*
543168 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
543189 TCGCGTTGCGAT
1 TCGCGTTGCGAT
543201 TTTCCATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:543214 original size:20 final size:19
Alignment explanation
Indices: 543191--543376 Score: 98
Period size: 20 Copynumber: 9.5 Consensus size: 19
543181 GTTGAAAATC
*
543191 GCGTTGCGATTTTCCATTT
1 GCGTTGCGATTTTCCAATT
*
543210 CGCGTTGCGATTTTCCAGTT
1 -GCGTTGCGATTTTCCAATT
* * *
543230 CGCGTTGCGATAGTCTACAGTT
1 -GCGTTGCGAT--TTTCCAATT
*
543252 GTCGTTGTGATTTTCCAAATT
1 G-CGTTGCGATTTTCC-AATT
* * *
543273 -CGTTGCGATAGTCTACAGTT
1 GCGTTGCGAT--TTTCCAATT
543293 GTCGTTGCGATTTTCCAAATT
1 G-CGTTGCGATTTTCC-AATT
* *
543314 -CGTTGCGA-----AAATC
1 GCGTTGCGATTTTCCAATT
*
543327 GCGTTGCGATTTTCCATTT
1 GCGTTGCGATTTTCCAATT
*
543346 CGCGTTGCGATTTTCCAGTTT
1 -GCGTTGCGATTTTCCA-ATT
543367 GCGTTGCGAT
1 GCGTTGCGAT
543377 AGTTGAAAAT
Statistics
Matches: 130, Mismatches: 19, Indels: 34
0.71 0.10 0.19
Matches are distributed among these distances:
13 3 0.02
14 8 0.06
19 18 0.14
20 64 0.49
21 13 0.10
22 24 0.18
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.40
Consensus pattern (19 bp):
GCGTTGCGATTTTCCAATT
Found at i:543257 original size:22 final size:22
Alignment explanation
Indices: 543232--543303 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
543222 TTCCAGTTCG
543232 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * * **
543254 CGTTGTGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
543273 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
543295 CGTTGCGAT
1 CGTTGCGAT
543304 TTTCCAAATT
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 9 0.24
20 5 0.14
21 5 0.14
22 18 0.49
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:543277 original size:19 final size:19
Alignment explanation
Indices: 543253--543478 Score: 70
Period size: 20 Copynumber: 11.5 Consensus size: 19
543243 TCTACAGTTG
*
543253 TCGTTGTGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
543272 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
543293 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
543313 TCGTTGCGA------AAAT
1 TCGTTGCGATTTTCCAAAT
* *
543326 CGCGTTGCGATTTTCC-ATT
1 -TCGTTGCGATTTTCCAAAT
**
543345 TCGCGTTGCGATTTTCCAGTT
1 T--CGTTGCGATTTTCCAAAT
* **
543366 TGCGTTGCGATAGTTGAAAAT
1 T-CGTTGCGAT-TTTCCAAAT
* * * **
543387 CGCGTTGCGATAGTCTACAGTT
1 -TCGTTGCGAT--TTTCCAAAT
*
543409 GTCATTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
* * **
543429 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
543450 ATCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
543470 TCGTTGCGA
1 TCGTTGCGA
543479 AAATTCGTTG
Statistics
Matches: 146, Mismatches: 42, Indels: 38
0.65 0.19 0.17
Matches are distributed among these distances:
13 4 0.03
14 8 0.05
19 38 0.26
20 39 0.27
21 26 0.18
22 31 0.21
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.38
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:543286 original size:41 final size:41
Alignment explanation
Indices: 543212--543478 Score: 272
Period size: 41 Copynumber: 6.7 Consensus size: 41
543202 TTCCATTTCG
*
543212 CGTTGCGATTTTCC-AGTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGT
*
543254 CGTTGTGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
*
543295 CGTTGCGATTTTCCAAATTCGTTGCGA-A----A-A-TCG-
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
* * *
543328 CGTTGCGATTTTCC-ATTTCGCGTTGCGAT--TTTCCAGTT-T
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGT
* ** *
543367 GCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTCTACAGTTGT
1 -CGTTGCGAT-TTTCCAAAT-TCGTTGCGATAGTCTACAGTTGT
* *
543411 CATTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTAT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
543452 CGTTGCGATTTTCCAAATTCGTTGCGA
1 CGTTGCGATTTTCCAAATTCGTTGCGA
543479 AAATTCGTTG
Statistics
Matches: 187, Mismatches: 21, Indels: 35
0.77 0.09 0.14
Matches are distributed among these distances:
32 3 0.02
33 14 0.07
34 10 0.05
35 1 0.01
36 1 0.01
38 1 0.01
39 1 0.01
40 10 0.05
41 106 0.57
42 21 0.11
43 18 0.10
44 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
Found at i:543339 original size:116 final size:116
Alignment explanation
Indices: 543209--543437 Score: 329
Period size: 116 Copynumber: 2.0 Consensus size: 116
543199 ATTTTCCATT
* * *
543209 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTCTACAG-TTGTCGTTGTGAT-TTTCCAAAT
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGAT--TCTACAGTTTG-CGTTGCGATAGTTCAAAAT
* *
543272 -TCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGCGAAAA
63 CGCGTTGCGATAGTCTACAGTTGTCATTGCGATTTTCCAAATTCGTTGCGAAAA
* * * *
543325 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGTTTGCGTTGCGATAGTTGAAAATCGC
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATTCTACAGTTTGCGTTGCGATAGTTCAAAATCGC
543390 GTTGCGATAGTCTACAGTTGTCATTGCGATTTTCCAAATTCGTTGCGA
66 GTTGCGATAGTCTACAGTTGTCATTGCGATTTTCCAAATTCGTTGCGA
543438 TAGTCTACAG
Statistics
Matches: 101, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
114 13 0.13
115 9 0.09
116 79 0.78
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (116 bp):
TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATTCTACAGTTTGCGTTGCGATAGTTCAAAATCGC
GTTGCGATAGTCTACAGTTGTCATTGCGATTTTCCAAATTCGTTGCGAAAA
Found at i:543424 original size:157 final size:156
Alignment explanation
Indices: 543189--543482 Score: 491
Period size: 157 Copynumber: 1.9 Consensus size: 156
543179 TAGTTGAAAA
* * **
543189 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTCTACAGTTGT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATGTTCAAAATCGCGTTGCGATAGTCTACAGTTGT
* * *
543254 CGTTGTGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTG
66 CATTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTATCGTTGCGATTTTCCAAATTCGTTG
543319 CGAAAATCGCGTTGCGATTTTCCATT
131 CGAAAATCGCGTTGCGATTTTCCATT
*
543345 TCGCGTTGCGATTTTCCAGTTT-GCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTCTACAGTT
1 TCGCGTTGCGATTTTCCA-TTTCGCGTTGCGAT-GTTCAAAATCGCGTTGCGATAGTCTACAGTT
543409 GTCATTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTATCGTTGCGATTTTCCAAATTCGT
64 GTCATTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTATCGTTGCGATTTTCCAAATTCGT
543474 TGCGAAAAT
129 TGCGAAAAT
543483 TCGTTGTGAT
Statistics
Matches: 128, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
156 28 0.22
157 100 0.78
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.38
Consensus pattern (156 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATGTTCAAAATCGCGTTGCGATAGTCTACAGTTGT
CATTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTATCGTTGCGATTTTCCAAATTCGTTG
CGAAAATCGCGTTGCGATTTTCCATT
Found at i:543457 original size:22 final size:21
Alignment explanation
Indices: 543389--543460 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 21
543379 TTGAAAATCG
543389 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTT-T
* * * **
543411 CATTGCGAT--TTTCCAAATT
1 CGTTGCGATAGTCTACAGTTT
543430 CGTTGCGATAGTCTACAGTTAT
1 CGTTGCGATAGTCTACAGTT-T
543452 CGTTGCGAT
1 CGTTGCGAT
543461 TTTCCAAATT
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 9 0.24
20 5 0.14
21 5 0.14
22 18 0.49
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTTT
Found at i:543562 original size:6 final size:6
Alignment explanation
Indices: 543551--543575 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
543541 GACACGTATT
543551 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
543576 GACGAGACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:543582 original size:5 final size:5
Alignment explanation
Indices: 543572--543603 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
543562 GACCACGACC
543572 ACGAG ACGAG ACGAG ACGAG ACGAG ACG-G ACG
1 ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACG
543604 GCGGAGGCGG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.38, C:0.22, G:0.41, T:0.00
Consensus pattern (5 bp):
ACGAG
Found at i:544099 original size:6 final size:6
Alignment explanation
Indices: 544088--544125 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
544078 GTCTCGGGTC
544088 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
544126 AATACGTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.34
Consensus pattern (6 bp):
GTCGTG
Found at i:544250 original size:21 final size:19
Alignment explanation
Indices: 544198--544251 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
544188 AAATCTTTTT
544198 TTTA-ACTATCGCAACGAA
1 TTTAGACTATCGCAACGAA
* **
544216 TTTGGAAAATCGCAACGACA
1 TTTAGACTATCGCAACGA-A
544236 TTGTAGACTATCGCAA
1 TT-TAGACTATCGCAA
544252 TGCGAAATGA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
18 3 0.11
19 11 0.41
20 3 0.11
21 10 0.37
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (19 bp):
TTTAGACTATCGCAACGAA
Found at i:544270 original size:20 final size:20
Alignment explanation
Indices: 544245--544561 Score: 256
Period size: 20 Copynumber: 15.5 Consensus size: 20
544235 ATTGTAGACT
* *
544245 ATCGCAATGCGAAATGAAAA
1 ATCGCAACGCGAAATGGAAA
544265 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
544285 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
544305 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
544326 ATAGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
544346 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
544367 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
544387 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
544408 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*** ** *
544428 ATCGCAACGCGGTTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
544449 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
544469 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
544490 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
544510 ATCGCAACGCGATTTTTCAACT
1 ATCGCAACGCGA-AATGGAA-A
544532 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
544552 ATCGCAACGC
1 ATCGCAACGC
544562 AATTTCCAAC
Statistics
Matches: 224, Mismatches: 66, Indels: 14
0.74 0.22 0.05
Matches are distributed among these distances:
20 133 0.59
21 79 0.35
22 12 0.05
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:544305 original size:41 final size:41
Alignment explanation
Indices: 544196--544588 Score: 571
Period size: 41 Copynumber: 9.6 Consensus size: 41
544186 CAAAATCTTT
* *
544196 TTTTTAACTATCGCAA--CGAATTTGGAAAATCGCAACGAC-A
1 TTTTCAACTATCGCAACGCGAA-ATGGAAAATCGCAACG-CGA
* * *
544236 TTGT-AGACTATCGCAATGCGAAATGAAAAATCGCAACGCGA
1 TTTTCA-ACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
** ** *
544277 AATGGAA-AATCGCAACGCGAAATGGAAAATCGCAACGCGA
1 TTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
*
544317 TTTTCAACTATAGCAACGCGAAATGGAAAATCGCAACGCGA
1 TTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
544358 TTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
1 TTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
*
544399 TTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGG
1 TTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
544440 TTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
1 TTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
*
544481 TTTTCAACTATCGCAACGCGAAATGAAAAATCGCAACGCGA
1 TTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
*
544522 TTTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCAA
1 -TTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
* *
544564 TTTCCAACTATCGCAATGCGAAATG
1 TTTTCAACTATCGCAACGCGAAATG
544589 CAACGCGAAT
Statistics
Matches: 322, Mismatches: 24, Indels: 13
0.90 0.07 0.04
Matches are distributed among these distances:
39 1 0.00
40 47 0.15
41 230 0.71
42 44 0.14
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (41 bp):
TTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
Found at i:545173 original size:18 final size:18
Alignment explanation
Indices: 545150--545186 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
545140 TCTTTTCTTC
545150 AATATTAATAAATA-AATA
1 AATATTAA-AAATATAATA
545168 AATATTAAAAATATAATA
1 AATATTAAAAATATAATA
545186 A
1 A
545187 TTTTTCCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATATTAAAAATATAATA
Found at i:545747 original size:2 final size:2
Alignment explanation
Indices: 545740--545768 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
545730 ATCTAAAGGA
545740 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 A
545769 CGAGATAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:548350 original size:14 final size:14
Alignment explanation
Indices: 548331--548361 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
548321 GTAATTATGC
*
548331 AAAAATGCAAATGT
1 AAAAATGAAAATGT
548345 AAAAATGAAAATGT
1 AAAAATGAAAATGT
548359 AAA
1 AAA
548362 TACAATCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.13, T:0.19
Consensus pattern (14 bp):
AAAAATGAAAATGT
Found at i:552088 original size:2 final size:2
Alignment explanation
Indices: 552081--552130 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
552071 TCCTATCTCG
552081 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
552123 TA TA TA TA
1 TA TA TA TA
552131 CGAGATAGGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:553316 original size:3 final size:3
Alignment explanation
Indices: 553308--553383 Score: 88
Period size: 3 Copynumber: 25.7 Consensus size: 3
553298 TATTTATTTA
553308 AAT AAT AAT AAT -AT ATAT AAT AAT -AT AAGT AAT AAT AAT AAT -AT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
*
553352 ATT AAT AAT AAAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AA
553384 AAAAATAAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 14
0.80 0.03 0.17
Matches are distributed among these distances:
2 8 0.12
3 47 0.73
4 9 0.14
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:553341 original size:27 final size:25
Alignment explanation
Indices: 553306--553391 Score: 106
Period size: 27 Copynumber: 3.4 Consensus size: 25
553296 AATATTTATT
553306 TAAATAATAATAATATATATAATAA
1 TAAATAATAATAATATATATAATAA
553331 TATAAGTAATAATAATAATATATTAATAA
1 TA-AA-TAATAATAAT-ATATA-TAATAA
*
553360 TAAATAATAATAATA-ATAAAATAA
1 TAAATAATAATAATATATATAATAA
553384 -AAA-AATAA
1 TAAATAATAA
553392 AAAAACTAGT
Statistics
Matches: 56, Mismatches: 1, Indels: 11
0.82 0.01 0.16
Matches are distributed among these distances:
22 5 0.09
23 3 0.05
24 5 0.09
25 5 0.09
26 3 0.05
27 20 0.36
28 7 0.12
29 8 0.14
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (25 bp):
TAAATAATAATAATATATATAATAA
Found at i:553378 original size:30 final size:30
Alignment explanation
Indices: 553308--553377 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
553298 TATTTATTTA
553308 AATAATAATAATATATATAATAATATAAGT
1 AATAATAATAATATATATAATAATATAAGT
553338 AATAATAATAATATAT-TAATAATA-AA-T
1 AATAATAATAATATATATAATAATATAAGT
553365 AATAATAATAATA
1 AATAATAATAATA
553378 AAATAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
27 14 0.35
28 2 0.05
29 8 0.20
30 16 0.40
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (30 bp):
AATAATAATAATATATATAATAATATAAGT
Found at i:553390 original size:16 final size:17
Alignment explanation
Indices: 553307--553395 Score: 67
Period size: 18 Copynumber: 5.2 Consensus size: 17
553297 ATATTTATTT
*
553307 AAATAATAATAATATATA
1 AAATAATAAAAATA-ATA
* * *
553325 TAATAATATAAGTAATA
1 AAATAATAAAAATAATA
*
553342 ATAATAATATATTAATAAT-
1 A-AATAATA-A-AAATAATA
*
553361 AAATAATAATAATAATA
1 AAATAATAAAAATAATA
553378 AAATAA-AAAAATAA-A
1 AAATAATAAAAATAATA
553393 AAA
1 AAA
553396 ACTAGTGTCT
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
15 4 0.07
16 14 0.24
17 10 0.17
18 24 0.41
19 1 0.02
20 5 0.09
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (17 bp):
AAATAATAAAAATAATA
Found at i:554462 original size:19 final size:18
Alignment explanation
Indices: 554420--554466 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
554410 TTAAATAACT
* * *
554420 ATTTAAATAATCATTTAT
1 ATTTAATTAATCATTAAA
554438 ATTTAATTAATCAATTAAA
1 ATTTAATTAATC-ATTAAA
554457 ATTTAATTAA
1 ATTTAATTAA
554467 AATTTTCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTAATTAATCATTAAA
Found at i:554591 original size:47 final size:48
Alignment explanation
Indices: 554537--554698 Score: 121
Period size: 57 Copynumber: 3.1 Consensus size: 48
554527 ATTTGCTTTC
*
554537 ATAAATAATTATAAAATATAAATGTATATTTAAATTTT-AATAATTAA
1 ATAAATAATTATAAAATTTAAATGTATATTTAAATTTTAAATAATTAA
** * *
554584 ATAAATAAAAAT-AATTTTAAACTGTATTTTTTTCAAATTTTAAATAATTAAA
1 ATAAATAATTATAAAATTTAAA-TGTA--TATTT-AAATTTTAAATAATT-AA
* * *
554636 ATAATCATAAATAATATAAACAATTTAAAATATTTATTTAAATTTTGAATAATTAA
1 ATAA--AT-AAT--TAT-AA-AATTT-AAATGTATATTTAAATTTTAAATAATTAA
554692 ATAAATA
1 ATAAATA
554699 TAATTTGAAA
Statistics
Matches: 88, Mismatches: 12, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
46 7 0.08
47 14 0.16
49 4 0.05
50 7 0.08
51 7 0.08
52 6 0.07
53 1 0.01
54 4 0.05
55 2 0.02
56 6 0.07
57 16 0.18
58 4 0.05
59 1 0.01
60 6 0.07
61 3 0.03
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (48 bp):
ATAAATAATTATAAAATTTAAATGTATATTTAAATTTTAAATAATTAA
Found at i:555441 original size:60 final size:59
Alignment explanation
Indices: 555325--555469 Score: 141
Period size: 60 Copynumber: 2.4 Consensus size: 59
555315 CTTAAACTTA
* * * *
555325 TAAATATTCTAATTTCATCCCTAAACTATGATTACCATTCTAAATTAGTTCTCAAAC-TTC
1 TAAACATTCAAATTTCATCCC-AAACTATGATTA-CATTCTAAATTAGTCCCCAAACTTTC
* * * * *
555385 TGAACATTTAAATTTCATCTCCAAACTATGAACTT-CATTTTAAATTGGTCCCCAAACTTTT
1 TAAACATTCAAATTTCATC-CCAAACTATG-A-TTACATTCTAAATTAGTCCCCAAACTTTC
*
555446 TAAACATTCCAATTTCATCCCAAA
1 TAAACATTCAAATTTCATCCCAAA
555470 ATCTACATAT
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
60 46 0.67
61 21 0.30
62 2 0.03
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (59 bp):
TAAACATTCAAATTTCATCCCAAACTATGATTACATTCTAAATTAGTCCCCAAACTTTC
Found at i:556132 original size:25 final size:25
Alignment explanation
Indices: 556101--556161 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
556091 ACAAAAAGAT
556101 ATAAAAAAGGAAGATAAATAA-A-TAA
1 ATAAAAAAGGAAGA-AAA-AACATTAA
556126 ATAAAAATA-GAAGAAAAAACATTAA
1 ATAAAAA-AGGAAGAAAAAACATTAA
556151 AT-AAAAAGGAA
1 ATAAAAAAGGAA
556162 AACCAAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
23 3 0.09
24 11 0.34
25 17 0.53
26 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (25 bp):
ATAAAAAAGGAAGAAAAAACATTAA
Found at i:556259 original size:26 final size:26
Alignment explanation
Indices: 556230--556285 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
556220 TTAAATTAAG
*
556230 TAAAAAATAATGAA-AAAAATAAAGAA
1 TAAAAAATAAT-AAGAAAAATAAAAAA
*
556256 TAAAAAATCATAAGAAAAATAAAAAA
1 TAAAAAATAATAAGAAAAATAAAAAA
556282 TAAA
1 TAAA
556286 TAAAAACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 2 0.07
26 25 0.93
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (26 bp):
TAAAAAATAATAAGAAAAATAAAAAA
Found at i:556260 original size:13 final size:12
Alignment explanation
Indices: 556231--556310 Score: 51
Period size: 12 Copynumber: 6.5 Consensus size: 12
556221 TAAATTAAGT
*
556231 AAAAAATAATGA
1 AAAAAATAAAGA
556243 AAAAAATAAAGAA
1 AAAAAATAAAG-A
556256 TAAAAAATCATAAG-
1 -AAAAAAT-A-AAGA
556270 -AAAAATAAA-A
1 AAAAAATAAAGA
*
556280 AATAAATAAA-A
1 AAAAAATAAAGA
*
556291 ACAAATAATAAATA
1 A-AAA-AATAAAGA
556305 AAAAAA
1 AAAAAA
556311 AGTTAAATTT
Statistics
Matches: 56, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
10 2 0.04
11 11 0.20
12 20 0.36
13 10 0.18
14 9 0.16
15 1 0.02
16 3 0.05
ACGTcount: A:0.79, C:0.03, G:0.04, T:0.15
Consensus pattern (12 bp):
AAAAAATAAAGA
Found at i:556270 original size:16 final size:14
Alignment explanation
Indices: 556230--556309 Score: 51
Period size: 14 Copynumber: 5.5 Consensus size: 14
556220 TTAAATTAAG
*
556230 TAAAAAATAATG-A
1 TAAAAAATAAAGAA
556243 -AAAAAATAAAGAA
1 TAAAAAATAAAGAA
556256 TAAAAAATCATAAGAAAAA
1 TAAAAAAT-A-AAG---AA
*
556275 TAAAAAATAAATAA
1 TAAAAAATAAAGAA
556289 -AAACAAATAATA-AA
1 TAAA-AAATAA-AGAA
556303 TAAAAAA
1 TAAAAAA
556310 AAGTTAAATT
Statistics
Matches: 55, Mismatches: 2, Indels: 19
0.72 0.03 0.25
Matches are distributed among these distances:
12 10 0.18
13 4 0.07
14 20 0.36
15 5 0.09
16 3 0.05
17 2 0.04
18 1 0.02
19 10 0.18
ACGTcount: A:0.78, C:0.03, G:0.04, T:0.16
Consensus pattern (14 bp):
TAAAAAATAAAGAA
Found at i:556282 original size:7 final size:7
Alignment explanation
Indices: 556243--556309 Score: 50
Period size: 7 Copynumber: 9.9 Consensus size: 7
556233 AAAATAATGA
556243 AAAAAAT
1 AAAAAAT
*
556250 AAAGAAT
1 AAAAAAT
556257 AAAAAAT
1 AAAAAAT
* *
556264 -CATAA-
1 AAAAAAT
*
556269 GAAAAAT
1 AAAAAAT
556276 AAAAAAT
1 AAAAAAT
556283 AAATAAA-
1 AAA-AAAT
*
556290 AACAAAT
1 AAAAAAT
*
556297 AATAAAT
1 AAAAAAT
556304 AAAAAA
1 AAAAAA
556310 AAGTTAAATT
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
6 9 0.20
7 34 0.74
8 3 0.07
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (7 bp):
AAAAAAT
Found at i:556290 original size:17 final size:17
Alignment explanation
Indices: 556232--556308 Score: 75
Period size: 17 Copynumber: 4.3 Consensus size: 17
556222 AAATTAAGTA
556232 AAAAATAATGAAAA-AAAT
1 AAAAATAA--AAAATAAAT
*
556250 AAAGAATAAAAAATCATAAG
1 AAA-AATAAAAAAT-A-AAT
556270 AAAAATAAAAAATAAAT
1 AAAAATAAAAAATAAAT
* *
556287 AAAAACAAATAATAAAT
1 AAAAATAAAAAATAAAT
556304 AAAAA
1 AAAAA
556309 AAAGTTAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
17 26 0.51
18 4 0.08
19 16 0.31
20 5 0.10
ACGTcount: A:0.78, C:0.03, G:0.04, T:0.16
Consensus pattern (17 bp):
AAAAATAAAAAATAAAT
Found at i:556296 original size:21 final size:20
Alignment explanation
Indices: 556254--556311 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 20
556244 AAAAATAAAG
* *
556254 AATAAAAAAT-CATAAGAAA
1 AATAAAAAATAAATAAAAAA
556273 AATAAAAAATAAATAAAAACA
1 AATAAAAAATAAATAAAAA-A
*
556294 AATAATAAATAAA-AAAAA
1 AATAAAAAATAAATAAAAA
556312 GTTAAATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 10 0.29
20 11 0.32
21 13 0.38
ACGTcount: A:0.79, C:0.03, G:0.02, T:0.16
Consensus pattern (20 bp):
AATAAAAAATAAATAAAAAA
Found at i:556671 original size:14 final size:14
Alignment explanation
Indices: 556654--556683 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
556644 TCATCTTCAT
556654 CGGCCTATCTCCAC
1 CGGCCTATCTCCAC
556668 CGGCCTATCTCCAC
1 CGGCCTATCTCCAC
556682 CG
1 CG
556684 CACCGTCACT
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:0.13, C:0.50, G:0.17, T:0.20
Consensus pattern (14 bp):
CGGCCTATCTCCAC
Found at i:557682 original size:2 final size:2
Alignment explanation
Indices: 557675--557699 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
557665 TTTCAAAAAT
557675 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
557700 TTTCAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:557689 original size:47 final size:46
Alignment explanation
Indices: 557638--557735 Score: 121
Period size: 47 Copynumber: 2.2 Consensus size: 46
557628 ATTTTCAAAC
* *
557638 TATATAT-TATACATA-TTT-AAAAAGTGTTTTCAAAAATTATATAT
1 TATATATATATACATATTTTCAAAAA-TATTTTCAAAAACTATATAT
* *
557682 ATATATATATATATATATTTTCAAAAATATTTTTAAAAACTATATAT
1 -TATATATATATACATATTTTCAAAAATATTTTCAAAAACTATATAT
557729 TATATAT
1 TATATAT
557736 GTTTTCAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
45 7 0.15
46 14 0.30
47 20 0.43
48 5 0.11
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (46 bp):
TATATATATATACATATTTTCAAAAATATTTTCAAAAACTATATAT
Found at i:557753 original size:37 final size:37
Alignment explanation
Indices: 557683--557998 Score: 302
Period size: 37 Copynumber: 8.7 Consensus size: 37
557673 ATTATATATA
* *
557683 TATATATATATATATATTTTCAAAAATATTTTTAAAAAC
1 TATATAT-TATATATGTTTTCAAAAAT-GTTTTAAAAAC
557722 TATATATTATATATGTTTTCAAAAATGTTTTAAAAAC
1 TATATATTATATATGTTTTCAAAAATGTTTTAAAAAC
* * *
557759 TATATAATATATATGTTTTCGAAAATGTTTTCAAAAC
1 TATATATTATATATGTTTTCAAAAATGTTTTAAAAAC
* *
557796 T-TATATT-TATATGTTTTCAAAATTGTTTTGAAAAAT
1 TATATATTATATATGTTTTCAAAAATGTTTT-AAAAAC
*
557832 TATATA-T-TATATGTTTTCAAAAATGTTTT--TAA-
1 TATATATTATATATGTTTTCAAAAATGTTTTAAAAAC
* **
557864 -A-A-ATTATATA--TTTT-ACAAATGTTTTTTAAAC
1 TATATATTATATATGTTTTCAAAAATGTTTTAAAAAC
*
557895 TATATAATATATAAATGTTTTCAAAAATGTTTTTAAAAAAC
1 TATAT-AT-TATATATGTTTTCAAAAATG-TTTT-AAAAAC
* *
557936 TATA-ATTATATAAGTTTT-GAAAATGATTTTAAAAAC
1 TATATATTATATATGTTTTCAAAAATG-TTTTAAAAAC
*
557972 TATATATTATATACGTATTTTCAAAAA
1 TATATATTATATA--TGTTTTCAAAAA
557999 CCATTTGCAA
Statistics
Matches: 231, Mismatches: 25, Indels: 41
0.78 0.08 0.14
Matches are distributed among these distances:
28 10 0.04
29 5 0.02
30 4 0.02
31 5 0.02
32 1 0.00
33 3 0.01
35 22 0.10
36 47 0.20
37 67 0.29
38 32 0.14
39 19 0.08
40 8 0.03
41 8 0.03
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (37 bp):
TATATATTATATATGTTTTCAAAAATGTTTTAAAAAC
Found at i:557898 original size:27 final size:28
Alignment explanation
Indices: 557852--557921 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
557842 ATGTTTTCAA
* * *
557852 AAATGTTTTTAAAAATTATATATTTTAC
1 AAATGTTTTTAAAAACTATATAATATAC
* *
557880 AAATGTTTTT-TAAACTATATAATATAT
1 AAATGTTTTTAAAAACTATATAATATAC
*
557907 AAATGTTTTCAAAAA
1 AAATGTTTTTAAAAA
557922 TGTTTTTAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
27 21 0.62
28 13 0.38
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (28 bp):
AAATGTTTTTAAAAACTATATAATATAC
Found at i:557925 original size:39 final size:39
Alignment explanation
Indices: 557880--557998 Score: 102
Period size: 39 Copynumber: 3.1 Consensus size: 39
557870 TATATTTTAC
557880 AAATGTTTTTTAAACTATATAATATATAAATGTTTTCAA
1 AAATGTTTTTTAAACTATATAATATATAAATGTTTTCAA
** *
557919 AAATG-TTTTTAAAAAACTATAAT-TATATAA-GTTTT-GA
1 AAATGTTTTTTAAACTA-TATAATATATA-AATGTTTTCAA
** * ** *
557956 AAATGATTTTAAAAACTATATATTATATACGTATTTTCAA
1 AAATG-TTTTTTAAACTATATAATATATAAATGTTTTCAA
557996 AAA
1 AAA
557999 CCATTTGCAA
Statistics
Matches: 61, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
37 6 0.10
38 23 0.38
39 28 0.46
40 4 0.07
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (39 bp):
AAATGTTTTTTAAACTATATAATATATAAATGTTTTCAA
Found at i:558794 original size:84 final size:82
Alignment explanation
Indices: 558509--559655 Score: 1137
Period size: 84 Copynumber: 13.8 Consensus size: 82
558499 ATTTTATTGA
* * * * * *
558509 CAGATAACCCTTCTTGCTTTGAGCTATGCTGTAAATTTGATTTCCCTCT-GAGCTGAGTGTAATC
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA--TGATGTGCCT-TGGAGCTGAGTGTAATC
* * *
558573 AAACTTGAAGGTCTTTGATG
63 GAACTCGAAGGTCTTTGTTG
* * ** * * * * * *
558593 ACAGATAGCCCTTCTCGATTTAAGCTATGCTGCAAATAATATGCCTTTGAACTGAGTGTAATCGA
1 -CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGA
*
558658 ACTCGAAGGTCATTGTTG
65 ACTCGAAGGTCTTTGTTG
* * * *
558676 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGCGCCTTGGAGCTGAGTGTCATCAA
1 -CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGA
558741 ACTC-AGAGGTCTTTAGTTAG
65 ACTCGA-AGGTCTTT-GTT-G
* * * * * * * * *
558761 CAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTGCAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGAA
558826 CTCGAAGGTCTTTTGTTGG
66 CTCGAAGGTC-TTTGTT-G
* *
558845 CAGGTAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGGTGCCTTTGAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT-GTGCCTTGGAGCTGAGTGTAATCGA
558910 ACTCGAAGGTCTTTG--G
65 ACTCGAAGGTCTTTGTTG
* * * *
558926 CAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGGTACCTTTGAGCTGAGTATAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT-GTGCCTTGGAGCTGAGTGTAATCGA
*
558991 ACTAGAAGGTCTTTG--G
65 ACTCGAAGGTCTTTGTTG
* * * * * * * *
559007 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGAA
559072 CTCGAAGGTCTTTTGTTGG
66 CTCGAAGGTC-TTTGTT-G
* * * ** * * *
559091 CAAATAACCCTTCTTGCCTTGAGCTATATTGCAAATGATGTGCCCTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGAA
*
559156 CTCGAAGGTATTTTGTTGG
66 CTCGAAGGT-CTTTGTT-G
* * *
559175 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGTGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGTGTAATCGA
*
559240 ACTCGAGGGTCTTTG--G
65 ACTCGAAGGTCTTTGTTG
* * * * *
559256 CAGATATCCCTTCTAGCCTTGAGTTGTACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGAA
*
559321 CTTGAAGGTCTTTTGTTGG
66 CTCGAAGGTC-TTTGTT-G
* * * * ** ** * * ** * *
559340 TAAATAGCCCTTCTTGCCTTGAGTTATATTGCATTTGATGTGCCTTAGAGCTAAGCATAGTCAAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGAA
559405 CTCGAAGGTCTTTTGTTG
66 CTCGAAGGTC-TTTGTTG
* * *
559423 ACAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 -CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGTGTAATCG
*
559488 AACTCGAGGGTCTTTG--G
64 AACTCGAAGGTCTTTGTTG
* * * *
559505 CAGATATCCCTTCTAGCCTTGAGTTGTACTGCAAATGATGTGCCGT-GAGCTGAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGAA
* *
559569 CTCAAAGGTCTTTTATTGG
66 CTCGAAGGTC-TTTGTT-G
* * * *
559588 CAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGTCCTCGAAGTTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGTGTAATCGA
559653 ACT
65 ACT
559656 GTCAGATAGC
Statistics
Matches: 889, Mismatches: 148, Indels: 50
0.82 0.14 0.05
Matches are distributed among these distances:
79 25 0.03
80 61 0.07
81 198 0.22
82 3 0.00
83 139 0.16
84 329 0.37
85 134 0.15
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (82 bp):
CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGAA
CTCGAAGGTCTTTGTTG
Found at i:559290 original size:249 final size:246
Alignment explanation
Indices: 558509--559939 Score: 1500
Period size: 249 Copynumber: 5.8 Consensus size: 246
558499 ATTTTATTGA
* * * * * * * * * *
558509 CAGATAACCCTTCTTGCTTTGAGCTATGCTGTAAATTTGATTTCCCTCTGAGCTGAGTGTAATCA
1 CAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAA--TGATGTGCCT-TGAGCTGAGCGTAGTCG
* * * * * * ** * * * * *
558574 AACTTGAAGGTC-TTTGATGACAGATAGCCCTTCTCGATTTAAGCTATGCTGCAAATAATATGCC
63 AACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGTTATGTTGCAAATGATGTGCC
* * * * *
558638 TTTGAACTGAGTGTAATCGAACTCGAAGGTCA-TTGTTGACAGATAACCCTTCTAGCCTTGAGTT
128 TTGGAGCTGAGCGTAGTCGAACTCGAAGGT-ATTTGTTGGCAGATAACCCTTCTAGCCTTGAGTT
* * * *
558702 ATGCTGTAAATGATGCG-CCTTGGAGCTGAGTGTCATCAAACTC-AGAGGTCTTTAGTTAG
192 ATGCTGCAAATGATGTGCCCTT-GAGCTGAGTGTAATCGAACTCGAG-GGTCTTT-G---G
* * * * *
558761 CAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTGCAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTG-AGCTGAGCGTAGTCGAA
** * *
558826 CTCGAAGGTCTTTTGTTGGCAGGTAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGGTGCCT
65 CTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGTTATGTTGCAAATGAT-GTGCCT
* * * * *
558891 TTGAGCTGAGTGTAATCGAACTCGAAGG--TCT-TTGGCAGATAACCCTTCTCGCCTTGAGTTAT
129 TGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
* * * * *
558953 GCTGCAAATGATGGTACCTTTGAGCTGAGTATAATCGAACTAGAAGGTCTTTGG
194 GCTGCAAATGAT-GTGCCCTTGAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
* * * *
559007 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAA
* * *
559072 CTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATATTGCAAATGATGTGCCCT
65 CTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGTTATGTTGCAAATGATGTGCCTT
559137 GGAGCTGAGCGTAGTCGAACTCGAAGGTATTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
130 GGAGCTGAGCGTAGTCGAACTCGAAGGTA-TTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
* *
559202 GCTGCAAATGATGTGCCCTCGAAGCTGTGTGTAATCGAACTCGAGGGTCTTTGG
194 GCTGCAAATGATGTGCCCTTG-AGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
* * *
559256 CAGATATCCCTTCTAGCCTTGAGTTGTACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAA
* * * * **
559321 CTTGAAGGTCTTTTGTTGGTAAATAGCCCTTCTTGCCTTGAGTTATATTGCATTTGATGTGCCTT
65 CTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGTTATGTTGCAAATGATGTGCCTT
* * * * * *
559386 AGAGCTAAGCATAGTCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTAT
130 GGAGCTGAGCGTAGTCGAACTCGAAGGT-ATTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
* *
559451 GCTACAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
194 GCTGCAAATGATGTGCCCTTG-AGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
* * * * * *
559505 CAGATATCCCTTCTAGCCTTGAGTTGTACTGCAAATGATGTGCCGTGAGCTGAGTGTAATCGAAC
1 CAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGAGCTGAGCGTAGTCGAAC
* * * * *
559570 TCAAAGGTCTTTTATTGGCAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGTCCTC
66 TCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGTTATGTTGCAAATGATGTG-CCTT
* * * * * * * *
559635 GAAGTTGA--GT-GT--AA-TCG-A---A-CTG-T--CAGATAGCCCTTATAGCCATGAGCTATA
130 GGAGCTGAGCGTAGTCGAACTCGAAGGTATTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATG
* * * *
559686 CTGCAAATGATGTGCCGTTGAGCTGAGTGTAATCGAACTCAAAGGTATTTTGTTGG
195 CTGCAAATGATGTGCCCTTGAGCTGAGTGTAATCGAACTC-GAGG--GTCT-TTGG
* * * * *
559742 TAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATTATGTGCCTTGGAGCTGAGCATAGTCAAA
1 CAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAA
* * *
559807 CTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTACAAATGATGTGCCTT
65 CTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGTTATGTTGCAAATGATGTGCCTT
*
559872 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
130 GGAGCTGAGCGTAGTCGAACTCGAAGGT-ATTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
559937 GCT
194 GCT
559940 AATAATAATT
Statistics
Matches: 1007, Mismatches: 137, Indels: 70
0.83 0.11 0.06
Matches are distributed among these distances:
233 20 0.02
234 43 0.04
236 3 0.00
237 55 0.05
238 68 0.07
239 2 0.00
240 2 0.00
242 3 0.00
243 6 0.01
244 3 0.00
245 30 0.03
246 117 0.12
247 2 0.00
248 75 0.07
249 392 0.39
250 58 0.06
251 41 0.04
252 87 0.09
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (246 bp):
CAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGAGCTGAGCGTAGTCGAAC
TCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGTTATGTTGCAAATGATGTGCCTTG
GAGCTGAGCGTAGTCGAACTCGAAGGTATTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGC
TGCAAATGATGTGCCCTTGAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
Found at i:559290 original size:330 final size:329
Alignment explanation
Indices: 558499--559939 Score: 1481
Period size: 330 Copynumber: 4.4 Consensus size: 329
558489 GAACTCAACA
* * * * * * *
558499 ATTTTATTGACAGATAACCCTTCTTGCTTTGAGCTATGCTGTAAATTTGAT-TTCCCTCTGAGCT
1 ATTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA--TGATGTGCCCTC-GAGCT
* * * * ** * *
558563 GAGTGTAATCAAACTTGAAGGTCTTTGATGACAGATAGCCCTTCTCGATTTAAGCTATGCTGCAA
63 GAGTGTAATCGAACTCGAAGGTCTTTG--G-CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAA
* * * * *
558628 ATAATATGCCTTTGAACTGAGTGTAATCGAACTCGAAGGTCATTGTTGACAGATAACCCTTCTAG
125 ATGATGTGCCTTTGAGCTGAGTGTAATCGAACT-GAAGGTC-TTGTTGGCAGATAGCCCTTCTAG
* * * * * * *
558693 CCTTGAGTTATGCTGTAAATGATGCGCCTTGGAGCTGAGTGTCA-TCAAACTC-AGAGGTCTTTA
188 CCTTGAGCTATACTGCAAATGATGTGCCTTAGAGCTGAGCGT-AGTCAAACTCGA-AGGTCTTTT
* * * * * * * *
558756 GTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTGCAGCTGAGCGTAG
251 GTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCCTGGAGCTGAGCGTAG
558821 TCGAACTCGAAGGT
316 TCGAACTCGAAGGT
* * * *
558835 CTTTTGTTGGCAGGTAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGGTGCCTTTGAGCTGA
1 ATTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT-GTGCCCTCGAGCTGA
*
558900 GTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGAT
65 GTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
* * * * *
558965 GGTACCTTTGAGCTGAGTATAATCGAACTAGAAGGTC-T-TTGGCAGATAGCCCTTCTCGACTTA
130 -GTGCCTTTGAGCTGAGTGTAATCGAACT-GAAGGTCTTGTTGGCAGATAGCCCTTCTAGCCTTG
* *
559028 AGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCA
193 AGCTATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCA
* * **
559093 AATAACCCTTCTTGCCTTGAGCTATATTGCAAATGATGTGCCCTGGAGCTGAGCGTAGTCGAACT
258 GATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCCTGGAGCTGAGCGTAGTCGAACT
559158 CGAAGGT
323 CGAAGGT
*
559165 ATTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGT
1 ATTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCG-AGCTGA
* * * *
559230 GTGTAATCGAACTCGAGGGTCTTTGGCAGATATCCCTTCTAGCCTTGAGTTGTACTGCAAATGAT
65 GTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
* * * * * *
559295 GTGCCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGTTGGTAAATAGCCCTTCTTGCCTT
130 GTGCCTTTGAGCTGAGTGTAATCGAAC-TGAAGGTC--TTGTTGGCAGATAGCCCTTCTAGCCTT
* * ** * * *
559360 GAGTTATATTGCATTTGATGTGCCTTAGAGCTAAGCATAGTCAAACTCGAAGGTCTTTTGTTGAC
192 GAGCTATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGC
* * * * *
559425 AGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAA
257 AGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCCT-GGAGCTGAGCGTAGTCGAA
559490 CTCG-AGG-
321 CTCGAAGGT
* * * * * *
559497 -GTCT-TTGGCAGATATCCCTTCTAGCCTTGAGTTGTACTGCAAATGATGTGCCGT-GAGCTGAG
1 ATTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAGCTGAG
* *
559559 TGTAATCGAACTCAAAGGTCTTTTATTGGCAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
66 TGTAATCGAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
* * *
559624 GATGTGTCC-TCGAAGTTGAGTGTAAT----C-GAA---C-TG-T--CAGATAGCCCTTATAGCC
127 GATGTG-CCTTTG-AGCTGAGTGTAATCGAACTGAAGGTCTTGTTGGCAGATAGCCCTTCTAGCC
* * * * * *
559676 ATGAGCTATACTGCAAATGATGTGCCGTT-GAGCTGAGTGTAATCGAACTCAAAGGTATTTTGTT
190 TTGAGCTATACTGCAAATGATGTGCC-TTAGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTT
* * * * * *
559740 GGTAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATTATGTGCCTTGGAGCTGAGCATAGTCA
254 GGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCCTGGAGCTGAGCGTAGTCG
559805 AACTCGAAGGT
319 AACTCGAAGGT
* * * * * * * * *
559816 CTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTACAAATGATGTGCCTTGGAGCTGAG
1 ATTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAGCTGAG
* *
559881 CGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCT
66 TGTAATCGAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCT
559940 AATAATAATT
Statistics
Matches: 937, Mismatches: 144, Indels: 62
0.82 0.13 0.05
Matches are distributed among these distances:
317 18 0.02
318 109 0.12
319 2 0.00
320 3 0.00
321 43 0.05
322 62 0.07
324 1 0.00
327 3 0.00
328 24 0.03
329 39 0.04
330 294 0.31
331 5 0.01
332 78 0.08
333 161 0.17
334 24 0.03
335 30 0.03
336 41 0.04
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (329 bp):
ATTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAGCTGAG
TGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATG
TGCCTTTGAGCTGAGTGTAATCGAACTGAAGGTCTTGTTGGCAGATAGCCCTTCTAGCCTTGAGC
TATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAGAT
AACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCCTGGAGCTGAGCGTAGTCGAACTCGA
AGGT
Found at i:559809 original size:84 final size:84
Alignment explanation
Indices: 559658--559939 Score: 377
Period size: 84 Copynumber: 3.4 Consensus size: 84
559648 ATCGAACTGT
* * * * * *
559658 CAGATAGCCCTTATAGCCATGAGCTATACTGCAAATGATGTGCCGTT-GAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGA
* *
559722 ACTCAAAGGTATTTTGTTGG
65 ACTCGAAGGTCTTTTGTTGG
* * * * *
559742 TAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATTATGTGCCTTGGAGCTGAGCATAGTCAAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
559807 CTCGAAGGTCTTTTGTTGG
66 CTCGAAGGTCTTTTGTTGG
* * * * *
559826 CAAATAGCCCTTCTTGCCTTGAGCTATGTTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
559891 CTCGAAGGTCTTTTGTTGG
66 CTCGAAGGTCTTTTGTTGG
*
559910 CAGATAACCCTTCTAGCCTTGAGTTATGCT
1 CAGATAACCCTTCTAGCCTTGAGCTATGCT
559940 AATAATAATT
Statistics
Matches: 169, Mismatches: 28, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
83 2 0.01
84 167 0.99
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (84 bp):
CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTTGTTGG
Found at i:561256 original size:95 final size:94
Alignment explanation
Indices: 561054--561316 Score: 348
Period size: 95 Copynumber: 2.7 Consensus size: 94
561044 GGCCAACTGA
* * * * *
561054 ATCCATAAAGCCGGGGCGTTTAACCAATTGTTCTAGAGGGATAACTTAA-TATCATTGTGTAGAT
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGT-TTA-T-TGT--AT
*
561118 ATTATAATCACCTTTATCAGGTTAGCTGAATATT
61 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
561152 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAG-TTTATTGTATATTA
* *
561217 TAATCACCTTTATCAGGCTAGTTGAATCTT
65 TAATCACCTTTATCAGGCTAGCTGAATATT
* * *
561247 ATCTATAAAGTCGGGGCATTTAACCAATTGCTTTAGAGGGACAACTCAAGTTTTATTGTATATAT
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAG-TTTATTGTATAT-T
561312 ATAAT
64 ATAAT
561317 ATTATAATCT
Statistics
Matches: 150, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
95 92 0.61
96 6 0.04
97 3 0.02
98 46 0.31
99 2 0.01
100 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (94 bp):
ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGTTTATTGTATATTAT
AATCACCTTTATCAGGCTAGCTGAATATT
Found at i:563655 original size:24 final size:24
Alignment explanation
Indices: 563624--563670 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
563614 ATTTCTCTAA
*
563624 AAATGTAAACAAATGTT-AATAAT
1 AAATGTAAACAAATATTGAATAAT
563647 AAATAGTAAACAAATATTGAATAA
1 AAAT-GTAAACAAATATTGAATAA
563671 ATTAAAGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 12 0.57
25 5 0.24
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.28
Consensus pattern (24 bp):
AAATGTAAACAAATATTGAATAAT
Found at i:563706 original size:18 final size:17
Alignment explanation
Indices: 563685--563735 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
563675 AAGGAAAAAG
* *
563685 AAAAATAATAAAATAATA
1 AAAAACAATAAAA-AACA
563703 AAAAACAATAAAAAACA
1 AAAAACAATAAAAAACA
*
563720 AAAAAGATATAAAAAA
1 AAAAACA-ATAAAAAA
563736 GAAGATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 9 0.31
18 20 0.69
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.14
Consensus pattern (17 bp):
AAAAACAATAAAAAACA
Found at i:563778 original size:20 final size:20
Alignment explanation
Indices: 563719--563778 Score: 57
Period size: 23 Copynumber: 2.8 Consensus size: 20
563709 AATAAAAAAC
* *
563719 AAAAAAGATATAAAAAAGAAG
1 AAAAAA-ATATTAAATAGAAG
*
563740 ATAAATAAATAAATAAATAGAAG
1 A-AAA-AAAT-ATTAAATAGAAG
563763 AAAAAAATATTAAATA
1 AAAAAAATATTAAATA
563779 AAAAGGAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
20 7 0.22
21 5 0.16
22 8 0.25
23 12 0.38
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.18
Consensus pattern (20 bp):
AAAAAAATATTAAATAGAAG
Found at i:565188 original size:29 final size:29
Alignment explanation
Indices: 565133--565188 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
565123 AAACCAAAAG
* **
565133 AAATAAAATAAATTATAAAAAGGAATAAA
1 AAATAAAATAAATAATAAAAACAAATAAA
*
565162 AAATAAACTAAATAATAAAAACAAATA
1 AAATAAAATAAATAATAAAAACAAATA
565189 TATATTATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.20
Consensus pattern (29 bp):
AAATAAAATAAATAATAAAAACAAATAAA
Found at i:565320 original size:37 final size:37
Alignment explanation
Indices: 565222--565699 Score: 384
Period size: 36 Copynumber: 13.0 Consensus size: 37
565212 GTTTTCAAAA
* * * *
565222 TTTCAAAAACA-TTTT-CAAACTATATATTTATACAT
1 TTTCAAAAATATTTTTAAAAACTATATATATATATAT
* *
565257 ATTT-AAAAATGTTTTCAAAAA-T-TATATATATATAT
1 -TTTCAAAAATATTTTTAAAAACTATATATATATATAT
*
565292 TTTCAAAAATATTTTTAAAAACTATATATTATATATGT
1 TTTCAAAAATATTTTTAAAAACTATATA-TATATATAT
*
565330 TTTCAAAAAT-GTTTTAAAAACTATATA-ATATATAT
1 TTTCAAAAATATTTTTAAAAACTATATATATATATAT
* * * * *
565365 GTTTTAGAAAAT-GTTTTCAAAACT-TATATTTATATGT
1 -TTTCA-AAAATATTTTTAAAAACTATATATATATATAT
* * * *
565402 TTTCAAAAATGTTTTGAAAAATTATATAT-TATATGT
1 TTTCAAAAATATTTTTAAAAACTATATATATATATAT
* * *
565438 TTTTAAAAATGTTTTTAAAAATTATATAT-TATATAT
1 TTTCAAAAATATTTTTAAAAACTATATATATATATAT
** * *
565474 TTT-AAAAATATTTTTAAAAGTTATATAATATAAATGT
1 TTTCAAAAATATTTTTAAAAACTATAT-ATATATATAT
*
565511 TTTCAAAAATGTTTTTAAAAAACTATATAT-TATATAAGT
1 TTTCAAAAATATTTTT-AAAAACTATATATATATAT-A-T
565550 TTTC-AAAATGA-TTTTAAAAACTATATAATATATATAT
1 TTTCAAAAAT-ATTTTTAAAAACTATAT-ATATATATAT
*** *
565587 TTTCTAAAAA-AAAATTCAAAACTATATAT-TATATAGT
1 TTTC-AAAAATATTTTTAAAAACTATATATATATATA-T
565624 TTTCAAAAATA-TTTTAAAAACTATATATTATATACGTAT
1 TTTCAAAAATATTTTTAAAAACTATATA-TATATA--TAT
* *
565663 TTTCAAAAACCA--TTTACAAACTATAATATATATATAT
1 TTTCAAAAA-TATTTTTAAAAACTAT-ATATATATATAT
565700 ATATATGGAC
Statistics
Matches: 370, Mismatches: 41, Indels: 61
0.78 0.09 0.13
Matches are distributed among these distances:
34 3 0.01
35 64 0.17
36 97 0.26
37 91 0.25
38 59 0.16
39 50 0.14
40 6 0.02
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.45
Consensus pattern (37 bp):
TTTCAAAAATATTTTTAAAAACTATATATATATATAT
Found at i:565458 original size:13 final size:12
Alignment explanation
Indices: 565398--565459 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
565388 TTATATTTAT
*
565398 ATGTTTTCAAAA
1 ATGTTTTTAAAA
*
565410 ATGTTTTGAAAA
1 ATGTTTTTAAAA
* * * *
565422 AT-TATATATTAT
1 ATGTTTTTA-AAA
565434 ATGTTTTTAAAA
1 ATGTTTTTAAAA
565446 ATGTTTTTAAAA
1 ATGTTTTTAAAA
565458 AT
1 AT
565460 TATATATTAT
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
11 3 0.08
12 31 0.82
13 4 0.11
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (12 bp):
ATGTTTTTAAAA
Found at i:569134 original size:18 final size:18
Alignment explanation
Indices: 569110--569152 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
569100 ATGATATGTA
*
569110 TTATATGTTATGTGATATG
1 TTATATGTTATAT-ATATG
569129 -TATATGTTATATATATG
1 TTATATGTTATATATATG
569146 TTATATG
1 TTATATG
569153 ATGATGATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.53
Consensus pattern (18 bp):
TTATATGTTATATATATG
Found at i:569908 original size:21 final size:21
Alignment explanation
Indices: 569865--569908 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
569855 CAAATGATAC
* *
569865 TAATAATAATAATAGTGTGAA
1 TAATAATAATAATAGTATAAA
*
569886 TAATAATAATGATAGTATAAA
1 TAATAATAATAATAGTATAAA
569907 TA
1 TA
569909 TATGCATGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (21 bp):
TAATAATAATAATAGTATAAA
Found at i:570322 original size:16 final size:17
Alignment explanation
Indices: 570295--570327 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
570285 ATTTTAGTCA
570295 CTTTGTAAAAGTAAATG
1 CTTTGTAAAAGTAAATG
*
570312 CTTTG-AAAAGTCAATG
1 CTTTGTAAAAGTAAATG
570328 TTACACATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.33
Consensus pattern (17 bp):
CTTTGTAAAAGTAAATG
Found at i:576437 original size:21 final size:23
Alignment explanation
Indices: 576411--576462 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
576401 AGGGAATCAA
576411 TCCCCCCATG-A-GGGAACCGAT
1 TCCCCCCATGAAGGGGAACCGAT
**
576432 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCCCATGAAGGGGAACCGAT
576455 TCCCCCCA
1 TCCCCCCA
576463 CAGGGGAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 8 0.32
22 1 0.04
23 16 0.64
ACGTcount: A:0.21, C:0.40, G:0.21, T:0.17
Consensus pattern (23 bp):
TCCCCCCATGAAGGGGAACCGAT
Found at i:576469 original size:21 final size:21
Alignment explanation
Indices: 576443--576482 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
576433 CCCCCTTTGA
*
576443 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
576464 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
576483 TGGGGTACTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:580929 original size:29 final size:28
Alignment explanation
Indices: 580896--581027 Score: 117
Period size: 29 Copynumber: 4.7 Consensus size: 28
580886 TTTTTTAAAA
*
580896 TAATTACCAAAATAACACCCTTTTCGAAT
1 TAATTACCAAAATAACA-CCATTTCGAAT
*
580925 TAATT-CTCAAAATAGCACCAATTTCGAAT
1 TAATTAC-CAAAATAACACC-ATTTCGAAT
* * * *
580954 TAATTCCCATAATATCA-CTTTTCGAA-
1 TAATTACCAAAATAACACCATTTCGAAT
* *
580980 AAATTACCAAAATAGCACCATTTCGAAT
1 TAATTACCAAAATAACACCATTTCGAAT
* * *
581008 TAATTCCCAGAATAATACCA
1 TAATTACCAAAATAACACCA
581028 AAACTGAATT
Statistics
Matches: 83, Mismatches: 15, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
26 13 0.16
27 15 0.18
28 19 0.23
29 35 0.42
30 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.30
Consensus pattern (28 bp):
TAATTACCAAAATAACACCATTTCGAAT
Found at i:581006 original size:54 final size:56
Alignment explanation
Indices: 580915--581021 Score: 166
Period size: 54 Copynumber: 1.9 Consensus size: 56
580905 AAATAACACC
* *
580915 CTTTTCGAATTAATTCTCAAAATAGCACCAATTTCGAATTAATTCCCATAATATCA
1 CTTTTCGAATAAATTCTCAAAATAGCACCAATTTCGAATTAATTCCCAGAATATCA
580971 CTTTTCGAA-AAATTAC-CAAAATAGCACC-ATTTCGAATTAATTCCCAGAATA
1 CTTTTCGAATAAATT-CTCAAAATAGCACCAATTTCGAATTAATTCCCAGAATA
581022 ATACCAAAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
54 22 0.46
55 16 0.33
56 10 0.21
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (56 bp):
CTTTTCGAATAAATTCTCAAAATAGCACCAATTTCGAATTAATTCCCAGAATATCA
Found at i:581091 original size:13 final size:13
Alignment explanation
Indices: 581073--581104 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
581063 TGTCAACGGT
*
581073 CGGGTCGGGTTAA
1 CGGGTCGGGTCAA
581086 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
581099 CGGGTC
1 CGGGTC
581105 ATGACCGGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.12, C:0.22, G:0.47, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:583497 original size:64 final size:63
Alignment explanation
Indices: 583413--583617 Score: 191
Period size: 64 Copynumber: 3.2 Consensus size: 63
583403 CATTCATAAG
* * *
583413 TGCATCGATGCAT-TCCTTTAAAAGAAGAACATCGAATGCCTTTGATGCATCGATGCAT-AGCTA
1 TGCATCGATGCATCT-CTTTAAAAGAA-AACATCGAATGCATTTAATGCATCGATGCATAAG-GA
583476 A
63 A
* * * * * *
583477 TGCATCTATGCATCAT-TTTAAAATAATAACATCAAATGCAATCAATGCATCGATGCATAAGGAG
1 TGCATCGATGCATC-TCTTTAAAAGAA-AACATCGAATGCATTTAATGCATCGATGCATAAGGAA
* * * * * * *
583541 TGCATCGATGCATCTCATTAATAAGGAAACATCGAATGCATTTTATGCACCGATGCACAAGTAG
1 TGCATCGATGCATCTCTTTAA-AAGAAAACATCGAATGCATTTAATGCATCGATGCATAAGGAA
583605 TGCATCGATGCAT
1 TGCATCGATGCAT
583618 ACCTTCATTG
Statistics
Matches: 115, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
63 1 0.01
64 108 0.94
65 5 0.04
66 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.28
Consensus pattern (63 bp):
TGCATCGATGCATCTCTTTAAAAGAAAACATCGAATGCATTTAATGCATCGATGCATAAGGAA
Found at i:583966 original size:18 final size:18
Alignment explanation
Indices: 583931--583966 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
583921 AAAATGGGTA
* *
583931 CATATGTTATATGTATTG
1 CATATGTTACATGAATTG
583949 CATATGTTACATGAATTG
1 CATATGTTACATGAATTG
583967 AATGAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (18 bp):
CATATGTTACATGAATTG
Found at i:585136 original size:18 final size:20
Alignment explanation
Indices: 585122--585164 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
585112 TTTGGGACAT
585122 AGTGGTCCTACGGGACATATA
1 AGTGGTCCTACGGGACA-ATA
585143 CAGTGGTCCTACGGGACGAATA
1 -AGTGGTCCTACGGGAC-AATA
585165 CTGAACTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (20 bp):
AGTGGTCCTACGGGACAATA
Found at i:588504 original size:64 final size:62
Alignment explanation
Indices: 588418--588629 Score: 212
Period size: 64 Copynumber: 3.3 Consensus size: 62
588408 CACATTCATA
* *
588418 AGTGCATCGATGCATTCC-TTTAAAAGAAGAACATCGAATGCCTTTGATGCATCGATGCATAGCT
1 AGTGCATCGATGCA-TCCTTTTAAAAGAA-AACATCGAATGCATTTAATGCATCGATGCATAG-T
* * * * * *
588482 AATGCATCGATGCATCCTTTTAAAATAATAACATCAAATGCAATCAATGCATCGATGCATAAGG
1 AGTGCATCGATGCATCCTTTTAAAAGAA-AACATCGAATGCATTTAATGCATCGATGCAT-AGT
* * * * *
588546 AGTGCATCGATGCAT-CTCATTAATAAGGAAACATCGAATGCATTTTATGCACCGATGCACAAGT
1 AGTGCATCGATGCATCCT-TTTAA-AAGAAAACATCGAATGCATTTAATGCATCGATGCA-TAGT
588610 AGTGCATCGATGCATACCTT
1 AGTGCATCGATGCAT-CCTT
588630 AATTGAAAGA
Statistics
Matches: 120, Mismatches: 21, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
63 5 0.04
64 108 0.90
65 5 0.04
66 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (62 bp):
AGTGCATCGATGCATCCTTTTAAAAGAAAACATCGAATGCATTTAATGCATCGATGCATAGT
Found at i:588973 original size:18 final size:18
Alignment explanation
Indices: 588938--588973 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
588928 AAAATGGGTA
* *
588938 CATATGTTATATGTATTG
1 CATATGTTACATGAATTG
588956 CATATGTTACATGAATTG
1 CATATGTTACATGAATTG
588974 AATGAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (18 bp):
CATATGTTACATGAATTG
Found at i:596344 original size:29 final size:29
Alignment explanation
Indices: 596308--596460 Score: 98
Period size: 29 Copynumber: 5.3 Consensus size: 29
596298 CATTTTACAC
*
596308 AAATAGCACCCTTTTTAAAATAATTAC-CA
1 AAATAGCACCCTTTTCAAAATAATT-CTCA
* *
596337 AAATAGCACCCTTTTCGAATTAATTCTCA
1 AAATAGCACCCTTTTCAAAATAATTCTCA
** * * *
596366 AAATAGCACCAATTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTCAAAATAATTCTCA
* * * * *
596395 GAATATCA--TTATTTCGAAA-AATTATCA
1 AAATAGCACCCT-TTTCAAAATAATTCTCA
* * * *
596422 AAATAGCACCCATTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTCAAAATAATTCTCA
*
596451 GAATAGCACC
1 AAATAGCACC
596461 AAAACCGAAT
Statistics
Matches: 98, Mismatches: 21, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
27 12 0.12
28 15 0.15
29 71 0.72
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (29 bp):
AAATAGCACCCTTTTCAAAATAATTCTCA
Found at i:596429 original size:85 final size:85
Alignment explanation
Indices: 596329--596484 Score: 249
Period size: 85 Copynumber: 1.8 Consensus size: 85
596319 TTTTTAAAAT
* * ***
596329 AATTACCAAAATAGCACCCTTTTCGAATTAATTCTCAAAATAGCACCAATTTCGAATTAATTCCC
1 AATTACCAAAATAGCACCCATTTCGAATTAATTCCCAAAATAGCACCAAAACCGAATTAATTCCC
596394 AGAATATCATTATTTCGAAA
66 AGAATATCATTATTTCGAAA
* *
596414 AATTATCAAAATAGCACCCATTTCGAATTAATTCCCAGAATAGCACCAAAACCGAATTAATTCCC
1 AATTACCAAAATAGCACCCATTTCGAATTAATTCCCAAAATAGCACCAAAACCGAATTAATTCCC
596479 AGAATA
66 AGAATA
596485 ACACAGGTCA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
85 64 1.00
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (85 bp):
AATTACCAAAATAGCACCCATTTCGAATTAATTCCCAAAATAGCACCAAAACCGAATTAATTCCC
AGAATATCATTATTTCGAAA
Found at i:596437 original size:56 final size:57
Alignment explanation
Indices: 596349--596455 Score: 180
Period size: 56 Copynumber: 1.9 Consensus size: 57
596339 ATAGCACCCT
* *
596349 TTTCGAATTAATTCTCAAAATAGCACCAATTTCGAATTAATTCCCAGAATATCATTA
1 TTTCGAATAAATTATCAAAATAGCACCAATTTCGAATTAATTCCCAGAATATCATTA
*
596406 TTTCGAA-AAATTATCAAAATAGCACCCATTTCGAATTAATTCCCAGAATA
1 TTTCGAATAAATTATCAAAATAGCACCAATTTCGAATTAATTCCCAGAATA
596456 GCACCAAAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
56 40 0.85
57 7 0.15
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (57 bp):
TTTCGAATAAATTATCAAAATAGCACCAATTTCGAATTAATTCCCAGAATATCATTA
Found at i:603416 original size:6 final size:6
Alignment explanation
Indices: 603374--603414 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
603364 ATATATGTGT
* * *
603374 ATATGC ATATAC ATATAC ATATAC ATATAT ATATAT ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
603415 TACCAGCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (6 bp):
ATATAC
Found at i:604975 original size:11 final size:11
Alignment explanation
Indices: 604932--604970 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
604922 AAAAACTCAA
604932 AATTAAAAATT
1 AATTAAAAATT
*
604943 AGTTAAAAATT
1 AATTAAAAATT
604954 AATTAAATAA-T
1 AATTAAA-AATT
604965 AATTAA
1 AATTAA
604971 TTAATGGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 23 0.92
12 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
AATTAAAAATT
Found at i:610414 original size:157 final size:158
Alignment explanation
Indices: 610128--610444 Score: 600
Period size: 157 Copynumber: 2.0 Consensus size: 158
610118 ATAACCATCC
610128 AGCCTAGTGTTTTCTTCTTTTGTTTAGAAGATGAAAGTGAAGGTGAAAGTTTGAGCCTAGGCATT
1 AGCCTAGTGTTTTCTTCTTTTGTTTAGAAGATGAAAGTGAAGGTGAAAGTTTGAGCCTAGGCATT
610193 AGTGTAGAGTGCATAAAGGATAAGGCGAAGTGTATGTTACACTCTAAGCGAGAAATGAATAAAAC
66 AGTGTAGAGTGCATAAAGGATAAGGCGAAGTGTATGTTACACTCTAAGCGAGAAATGAATAAAAC
610258 AGG-CAACTTGAAAATAGAATCAGGGTG
131 AGGACAACTTGAAAATAGAATCAGGGTG
*
610285 AGCCTAGTGTTTTCTTCTTTTGTTTAGAAGATGAAAGTGAAGGTGAAAGTTTGAGCCTAGGCGTT
1 AGCCTAGTGTTTTCTTCTTTTGTTTAGAAGATGAAAGTGAAGGTGAAAGTTTGAGCCTAGGCATT
*
610350 AGTGTAGAGTGCATAAAGGATAAGGCGAGGTGTATGTTACACTCTAAGCGAGAAATGAATAAAAC
66 AGTGTAGAGTGCATAAAGGATAAGGCGAAGTGTATGTTACACTCTAAGCGAGAAATGAATAAAAC
*
610415 AGGACAACTTGAAAATAGAATTAGGGTG
131 AGGACAACTTGAAAATAGAATCAGGGTG
610443 AG
1 AG
610445 TTTCAGTACC
Statistics
Matches: 156, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
157 131 0.84
158 25 0.16
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.27
Consensus pattern (158 bp):
AGCCTAGTGTTTTCTTCTTTTGTTTAGAAGATGAAAGTGAAGGTGAAAGTTTGAGCCTAGGCATT
AGTGTAGAGTGCATAAAGGATAAGGCGAAGTGTATGTTACACTCTAAGCGAGAAATGAATAAAAC
AGGACAACTTGAAAATAGAATCAGGGTG
Found at i:617572 original size:14 final size:14
Alignment explanation
Indices: 617553--617582 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
617543 ACACATATAT
*
617553 ATATATATACTTAC
1 ATATATATACATAC
617567 ATATATATACATAC
1 ATATATATACATAC
617581 AT
1 AT
617583 GATCATAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATATATACATAC
Found at i:618059 original size:55 final size:55
Alignment explanation
Indices: 617865--618066 Score: 237
Period size: 55 Copynumber: 3.7 Consensus size: 55
617855 TGTCCTCTCC
* * ** *
617865 CTATTCTTTTAGAGAGTATAAGACTCGAATGATCTTCGATC-ATCGTGTCTGCTCT
1 CTATTCGTTCAGAGAGTATAAGACTCGAACAATCTTC-AACAATCGTGTCTGCTCT
* * ** *
617920 CTATTCGTTCAGAGAATATAAGACTCGAATAATCTTCAGTAATCGTGTCTGCTCC
1 CTATTCGTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCT
* *
617975 CTATTTC-TTTAGAGAGTATAAGACTCGAACAATCTTCAACAATCATGTCTGCTCT
1 CTA-TTCGTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCT
* * *
618030 TTATTCGTTCAGAGAGTACAAGACTCGAACAACCTTC
1 CTATTCGTTCAGAGAGTATAAGACTCGAACAATCTTC
618067 TGTAAACAGG
Statistics
Matches: 126, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
54 4 0.03
55 119 0.94
56 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.34
Consensus pattern (55 bp):
CTATTCGTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCT
Found at i:618084 original size:55 final size:55
Alignment explanation
Indices: 617865--618105 Score: 224
Period size: 55 Copynumber: 4.4 Consensus size: 55
617855 TGTCCTCTCC
* * ** *
617865 CTATTCTTTTAGAGAGTATAAGACTCGAATGATCTTC-GATCATC-GTGTCTGCTCT
1 CTATTCGTTCAGAGAGTATAAGACTCGAACAATCTTCAG-TAATCAGT-TCTGCTCT
* * *
617920 CTATTCGTTCAGAGAATATAAGACTCGAATAATCTTCAGTAATC-GTGTCTGCTCC
1 CTATTCGTTCAGAGAGTATAAGACTCGAACAATCTTCAGTAATCAGT-TCTGCTCT
* **
617975 CTATTTC-TTTAGAGAGTATAAGACTCGAACAATCTTCAACAATCA-TGTCTGCTCT
1 CTA-TTCGTTCAGAGAGTATAAGACTCGAACAATCTTCAGTAATCAGT-TCTGCTCT
* * * * *
618030 TTATTCGTTCAGAGAGTACAAGACTCGAACAACCTTCTGTAAACAGGTTC-GCTCT
1 CTATTCGTTCAGAGAGTATAAGACTCGAACAATCTTCAGTAATCA-GTTCTGCTCT
*
618085 CTATTCCTTTCAGAGAGTATA
1 CTATT-CGTTCAGAGAGTATA
618106 GAACTTGAGA
Statistics
Matches: 156, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
54 3 0.02
55 133 0.85
56 19 0.12
57 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (55 bp):
CTATTCGTTCAGAGAGTATAAGACTCGAACAATCTTCAGTAATCAGTTCTGCTCT
Found at i:618089 original size:110 final size:110
Alignment explanation
Indices: 617861--618105 Score: 307
Period size: 110 Copynumber: 2.2 Consensus size: 110
617851 AGCATGTCCT
* ** * *
617861 CTCCCTATTCTTTTAGAGAGTATAAGACTCGAATGATCTTCGATCATCGTGTCTGCTCTCTATTC
1 CTCCCTATTCCTTTAGAGAGTATAAGACTCGAACAATCTTCGAACATCATGTCTGCTCTCTATTC
* * * *
617926 GTTCAGAGAATATAAGACTCGAATAATCTTCAGTAATCGTGTCTG
66 GTTCAGAGAATACAAGACTCGAACAACCTTCAGTAAACGTGTCTG
* *
617971 CTCCCTATTTCTTTAGAGAGTATAAGACTCGAACAATCTTC-AACAATCATGTCTGCTCTTTATT
1 CTCCCTATTCCTTTAGAGAGTATAAGACTCGAACAATCTTCGAAC-ATCATGTCTGCTCTCTATT
* *
618035 CGTTCAGAGAGTACAAGACTCGAACAACCTTCTGTAAACAG-GT-TCG
65 CGTTCAGAGAATACAAGACTCGAACAACCTTCAGTAAAC-GTGTCT-G
*
618081 CTCTCTATTCCTTTCAGAGAGTATA
1 CTCCCTATTCCTTT-AGAGAGTATA
618106 GAACTTGAGA
Statistics
Matches: 116, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
109 3 0.03
110 102 0.88
111 11 0.09
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (110 bp):
CTCCCTATTCCTTTAGAGAGTATAAGACTCGAACAATCTTCGAACATCATGTCTGCTCTCTATTC
GTTCAGAGAATACAAGACTCGAACAACCTTCAGTAAACGTGTCTG
Found at i:618189 original size:54 final size:54
Alignment explanation
Indices: 618130--619087 Score: 1434
Period size: 54 Copynumber: 17.9 Consensus size: 54
618120 TTTTGAAAAA
* *
618130 GGGTTCGCTCCGTCTTTCTTTAGGAAGTATAGAACTCGAAAATCTTCTTCTTAC
1 GGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTAC
* * *
618184 AGGTTCGCTCCCTCTTTCTTCAGGAAGTATAAAACTCAAAAAATCTTCTTCTTAC
1 GGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTC-GAAAATCTTCTTCTTAC
*
618239 GGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAGAATCTTCTTCTTAC
1 GGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTAC
*
618293 GGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAGAATCTTCTTCTTAC
1 GGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTAC
* *
618347 GGGTTCGCTCCCTTTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTTCTTAC
1 GGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTAC
* * *
618401 GGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAAATCGAAAATCTTTTTCTTAC
1 GGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTAC
**
618455 GGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCAAAC
1 GGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTAC
618509 GGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAAAA---TCTTCTTAC
1 GGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTAC
* **
618560 GGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTTCAAAC
1 GGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTAC
* *
618614 GGGTTCGATCCCTCTTTCTTCAGGAAGTATAGAACTCGAGAATCTTCTTCTTAC
1 GGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTAC
* * *
618668 -GGTTTGCTCCCTCTTTCTTCAAGAAGTATAGAACTCGAGAATCTTCTTCTTAC
1 GGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTAC
* * *
618721 GGGTTCGCTCCCTCTATCTTCAGGGAGTATAGAACTCGAAAGTCTTCTTCTTAC
1 GGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTAC
* * *
618775 GGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCAAAAATCTTTTTCTTAC
1 GGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTAC
**
618829 GGGTTCGCTCCCTCTTTCTTCAGGAAGTATA-AACTCGAAAATCTTCTTCAAAC
1 GGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTAC
* * * **
618882 GGGTTCGCTCCCTCTTTCTTCAGAAAGTATATAACTCGAAAATCTTTTTCAAAC
1 GGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTAC
* * *
618936 GGGTTCGATCCCTCTTTCTTCAAGAAGTATA-AACTC-AAGGATCTTCTTCTTAC
1 GGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAA-AATCTTCTTCTTAC
* * **
618989 GGGTTCGCTTCCTCTTTCTTCAGGAAGTATGGAACTCGAAAA---TCTTCAAAC
1 GGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTAC
*
619040 GGGTTC-CTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTT
1 GGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAAAATCTTCTT
619088 TTGCTTCACT
Statistics
Matches: 825, Mismatches: 67, Indels: 25
0.90 0.07 0.03
Matches are distributed among these distances:
50 32 0.04
51 61 0.07
52 2 0.00
53 144 0.17
54 533 0.65
55 53 0.06
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (54 bp):
GGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTAC
Found at i:622288 original size:16 final size:16
Alignment explanation
Indices: 622269--622333 Score: 71
Period size: 16 Copynumber: 4.1 Consensus size: 16
622259 TCCAATTTTT
622269 TTCTTTTCTTTCTTTC
1 TTCTTTTCTTTCTTTC
622285 TTCTTTTCTTTTCTTT-
1 TTCTTTTC-TTTCTTTC
*
622301 TTCTTTT-TCTCTTTC
1 TTCTTTTCTTTCTTTC
* *
622316 TACATTTCTCTTCTTTC
1 TTCTTTTCT-TTCTTTC
622333 T
1 T
622334 CTTCACGATG
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
14 6 0.15
15 5 0.12
16 16 0.39
17 14 0.34
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (16 bp):
TTCTTTTCTTTCTTTC
Found at i:622294 original size:12 final size:11
Alignment explanation
Indices: 622266--622307 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
622256 ATTTCCAATT
622266 TTTTTCTTTTC
1 TTTTTCTTTTC
*
622277 TTTCTT-TCTTC
1 TTT-TTCTTTTC
622288 -TTTTCTTTTC
1 TTTTTCTTTTC
622298 TTTTTCTTTT
1 TTTTTCTTTT
622308 TCTCTTTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 2 0.08
10 6 0.23
11 16 0.62
12 2 0.08
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:622314 original size:31 final size:32
Alignment explanation
Indices: 622266--622336 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
622256 ATTTCCAATT
* * * *
622266 TTTTTCTTTTCTTTCTTTCTTCTTTTCTTTTC
1 TTTTTCTTTTCTCTCTTTCTACATTTCTCTTC
622298 TTTTTCTTTT-TCTCTTTCTACATTTCTCTTC
1 TTTTTCTTTTCTCTCTTTCTACATTTCTCTTC
*
622329 TTTCTCTT
1 TTTTTCTT
622337 CACGATGTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 24 0.71
32 10 0.29
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (32 bp):
TTTTTCTTTTCTCTCTTTCTACATTTCTCTTC
Found at i:623029 original size:20 final size:21
Alignment explanation
Indices: 623004--623050 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
622994 AAAATCCTTT
*
623004 CAAAAAGTTGA-GAAAAACAA
1 CAAAAAGTTGATAAAAAACAA
623024 CAAAAAGTTGATAAAAAACAA
1 CAAAAAGTTGATAAAAAACAA
623045 CAAAAA
1 CAAAAA
623051 CATTTTCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.68, C:0.11, G:0.11, T:0.11
Consensus pattern (21 bp):
CAAAAAGTTGATAAAAAACAA
Found at i:624880 original size:22 final size:21
Alignment explanation
Indices: 624858--624931 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
624848 TCCAATGTGA
624858 AATGGTCTTCATGTCTTTATG
1 AATGGTCTTCATGTCTTTATG
624879 AAATGGTCTTCATGTCTTTATG
1 -AATGGTCTTCATGTCTTTATG
* * *
624901 AACGGTCCTC-TCGTCCTTATG
1 AATGGTCTTCAT-GTCTTTATG
624922 AATGGTCTTC
1 AATGGTCTTC
624932 TCGTCCTCTG
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 1 0.02
21 24 0.52
22 21 0.46
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.42
Consensus pattern (21 bp):
AATGGTCTTCATGTCTTTATG
Found at i:624920 original size:21 final size:21
Alignment explanation
Indices: 624896--624938 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
624886 CTTCATGTCT
624896 TTATGAACGGTCCTCTCGTCC
1 TTATGAACGGTCCTCTCGTCC
* *
624917 TTATGAATGGTCTTCTCGTCC
1 TTATGAACGGTCCTCTCGTCC
624938 T
1 T
624939 CTGTATGACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.28, G:0.19, T:0.40
Consensus pattern (21 bp):
TTATGAACGGTCCTCTCGTCC
Found at i:629299 original size:29 final size:29
Alignment explanation
Indices: 629253--629316 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
629243 ATTTGGAATC
*
629253 TAAATTAATTAAATTAAATTATTCATTTT
1 TAAATTAATTAAATTAAATAATTCATTTT
* *
629282 TAAATTAATT-TATATAAATAATTTATTTT
1 TAAATTAATTAAAT-TAAATAATTCATTTT
*
629311 TTAATT
1 TAAATT
629317 TAGATTAGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 2 0.07
29 28 0.93
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (29 bp):
TAAATTAATTAAATTAAATAATTCATTTT
Found at i:630023 original size:18 final size:17
Alignment explanation
Indices: 629986--630028 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
629976 CTAAAATTTT
*
629986 AATCTATATAGATATAA
1 AATCTATTTAGATATAA
*
630003 AATCTATTTAGAATATGA
1 AATCTATTTAG-ATATAA
*
630021 AATTTATT
1 AATCTATT
630029 AAATTCTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (17 bp):
AATCTATTTAGATATAA
Found at i:630351 original size:18 final size:18
Alignment explanation
Indices: 630324--630367 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
630314 TGTGTTTGTT
* *
630324 TGTTTGTTTTTTTGAATG
1 TGTTTATTTTTTTGAAGG
630342 TGTTTATTTTTTTTGAAGG
1 TGTTTA-TTTTTTTGAAGG
630361 TGTTTAT
1 TGTTTAT
630368 GTTTAGTTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.14, C:0.00, G:0.20, T:0.66
Consensus pattern (18 bp):
TGTTTATTTTTTTGAAGG
Found at i:630354 original size:19 final size:19
Alignment explanation
Indices: 630330--630367 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
630320 TGTTTGTTTG
*
630330 TTTTTTTGAATGTGTTTAT
1 TTTTTTTGAAGGTGTTTAT
630349 TTTTTTTGAAGGTGTTTAT
1 TTTTTTTGAAGGTGTTTAT
630368 GTTTAGTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.18, T:0.66
Consensus pattern (19 bp):
TTTTTTTGAAGGTGTTTAT
Found at i:630382 original size:17 final size:18
Alignment explanation
Indices: 630360--630398 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
630350 TTTTTTGAAG
630360 GTGTTTATGTTT-AGTTC
1 GTGTTTATGTTTGAGTTC
*
630377 GTGTTTATGTTTGTGTTC
1 GTGTTTATGTTTGAGTTC
630395 GTGT
1 GTGT
630399 ATTTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.08, C:0.05, G:0.28, T:0.59
Consensus pattern (18 bp):
GTGTTTATGTTTGAGTTC
Found at i:631507 original size:50 final size:50
Alignment explanation
Indices: 631435--631535 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
631425 TCAAATATTA
*
631435 ATGAATATGACTAAAACATTAAGTGTCATTTCGATTGAAGTTACTATAAT
1 ATGAATATGACTAAAAAATTAAGTGTCATTTCGATTGAAGTTACTATAAT
631485 ATGAATATGACTAAAAAATTAAGTGTCATTTCGATTGAAGTTACTATAAT
1 ATGAATATGACTAAAAAATTAAGTGTCATTTCGATTGAAGTTACTATAAT
631535 A
1 A
631536 CAATCATTAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.36
Consensus pattern (50 bp):
ATGAATATGACTAAAAAATTAAGTGTCATTTCGATTGAAGTTACTATAAT
Found at i:632981 original size:23 final size:22
Alignment explanation
Indices: 632953--633006 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
632943 AAATTATAAT
*
632953 AATAATAAACAAATATTAAA-AA
1 AATAATAAACAAAGA-TAAAGAA
*
632975 AACTAATCAAATAAAGATAAAGAA
1 AA-TAAT-AAACAAAGATAAAGAA
632999 AATAATAA
1 AATAATAA
633007 TAATAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 4 0.15
23 12 0.44
24 11 0.41
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (22 bp):
AATAATAAACAAAGATAAAGAA
Found at i:633046 original size:55 final size:54
Alignment explanation
Indices: 632942--633046 Score: 124
Period size: 55 Copynumber: 1.9 Consensus size: 54
632932 AGAGAGGAGA
* * *
632942 AAAATTATAATAATAATAAACAAATATTAAAAAAACTAATCAAATAAAGATAAAG
1 AAAATAATAATAATAATAAACAAATATTAAAAAAAC-AATAAAAGAAAGATAAAG
*
632997 AAAATAATAATAATAATAAA-AAATAAGTTGAAAAATA-AATAAAAGAAAGA
1 AAAATAATAATAATAATAAACAAAT-A-TT-AAAAAAACAATAAAAGAAAGA
633047 GAATAAGTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
54 4 0.09
55 31 0.72
56 2 0.05
57 6 0.14
ACGTcount: A:0.70, C:0.03, G:0.06, T:0.22
Consensus pattern (54 bp):
AAAATAATAATAATAATAAACAAATATTAAAAAAACAATAAAAGAAAGATAAAG
Found at i:634395 original size:3 final size:3
Alignment explanation
Indices: 634389--634428 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
634379 AACAAAAATA
634389 AAT AAT AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
634429 AGAATAAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:634459 original size:16 final size:17
Alignment explanation
Indices: 634383--634477 Score: 83
Period size: 17 Copynumber: 5.5 Consensus size: 17
634373 AAAAAAAACA
634383 AAAATAAATAAT-AATAAT
1 AAAATAAA-AATGAA-AAT
*
634401 AAAATAATAAT-AATAAT
1 AAAATAAAAATGAA-AAT
634418 AATAATAATAAA-GAATAA-
1 AA-AATAA-AAATGAA-AAT
*
634436 AGAATAAAAATGAAAAT
1 AAAATAAAAATGAAAAT
634453 -AAATAAAAATGAAAAT
1 AAAATAAAAATGAAAAT
634469 AAAATAAAA
1 AAAATAAAA
634478 TAAAAAAATG
Statistics
Matches: 67, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
16 20 0.30
17 27 0.40
18 13 0.19
19 7 0.10
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (17 bp):
AAAATAAAAATGAAAAT
Found at i:634467 original size:7 final size:6
Alignment explanation
Indices: 634376--634483 Score: 80
Period size: 6 Copynumber: 17.8 Consensus size: 6
634366 TGGACCCAAA
* * * * *
634376 AAAAAC AAAAAT AAATAAT AATAAT AAAATAAT AATAAT AATAAT AATAAT
1 AAAAAT AAAAAT AAA-AAT AAAAAT -AAA-AAT AAAAAT AAAAAT AAAAAT
* *
634427 AAAGAAT AAAGAAT AAAAAT GAAAAT --AAAT AAAAAT GAAAAT -AAAAT
1 AAA-AAT AAA-AAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
634474 -AAAAT AAAAA
1 AAAAAT AAAAA
634484 AATGTTTTCA
Statistics
Matches: 88, Mismatches: 7, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
4 4 0.05
5 10 0.11
6 49 0.56
7 22 0.25
8 3 0.03
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (6 bp):
AAAAAT
Found at i:634477 original size:26 final size:26
Alignment explanation
Indices: 634388--634486 Score: 91
Period size: 26 Copynumber: 3.7 Consensus size: 26
634378 AAACAAAAAT
*
634388 AAATAATAATAAT-AAAATAATAATA
1 AAATAATAATAATAAAAATAAGAATA
634413 ATAATAATAATAATAAAGAATAAAGAATAA
1 A-AATAATAATAATAAA-AAT-AAGAAT-A
634443 AAATGAA-AATAAATAAAAATGAA-AATA
1 AAAT-AATAAT-AATAAAAAT-AAGAATA
634470 AAATAA-AATAA-AAAAAT
1 AAATAATAATAATAAAAAT
634487 GTTTTCAAAA
Statistics
Matches: 65, Mismatches: 2, Indels: 15
0.79 0.02 0.18
Matches are distributed among these distances:
24 6 0.09
25 3 0.05
26 17 0.26
27 7 0.11
28 6 0.09
29 16 0.25
30 10 0.15
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (26 bp):
AAATAATAATAATAAAAATAAGAATA
Found at i:634478 original size:16 final size:16
Alignment explanation
Indices: 634398--634482 Score: 61
Period size: 16 Copynumber: 5.1 Consensus size: 16
634388 AAATAATAAT
634398 AATAAAATAATAAT-AA
1 AATAAAATAA-AATGAA
*
634414 TAATAATAATAATAAAGAA
1 -AATAA-AATAA-AATGAA
*
634433 TAA-AGAATAAAAATGAA
1 -AATAAAAT-AAAATGAA
634450 AAT-AAATAAAAATGAA
1 AATAAAAT-AAAATGAA
634466 AATAAAATAAAAT-AA
1 AATAAAATAAAATGAA
634481 AA
1 AA
634483 AAATGTTTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
15 4 0.07
16 22 0.37
17 17 0.29
18 11 0.19
19 5 0.08
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (16 bp):
AATAAAATAAAATGAA
Found at i:634519 original size:14 final size:14
Alignment explanation
Indices: 634480--634538 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 14
634470 AAATAAAATA
634480 AAAAAATG-TTTTC
1 AAAAAATGTTTTTC
** *
634493 AAAACCT-TATTTC
1 AAAAAATGTTTTTC
634506 AAAAAATGTTTTTC
1 AAAAAATGTTTTTC
*
634520 AAAATAATATATTTTC
1 AAAA-AATGT-TTTTC
634536 AAA
1 AAA
634539 TTTTTTTTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
13 14 0.40
14 9 0.26
15 4 0.11
16 8 0.23
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.39
Consensus pattern (14 bp):
AAAAAATGTTTTTC
Found at i:634590 original size:37 final size:38
Alignment explanation
Indices: 634549--634786 Score: 259
Period size: 37 Copynumber: 6.5 Consensus size: 38
634539 TTTTTTTTAA
634549 AAAAACTATATATTATATATGTTTTCAAAAATGTTTT-
1 AAAAACTATATATTATATATGTTTTCAAAAATGTTTTC
*
634586 AAAAACTATATA--ATGT-T-TTTT-AAAAATGTTTTC
1 AAAAACTATATATTATATATGTTTTCAAAAATGTTTTC
*
634619 AAAAACTATATA--ATATATGTTTTTTAAAAATGTTTTC
1 AAAAACTATATATTATATATG-TTTTCAAAAATGTTTTC
* *
634656 AAAAACTATAT-TATATATATATTTT-AAAAATATTTTC
1 AAAAACTATATAT-TATATATGTTTTCAAAAATGTTTTC
* * ***
634693 AAAAACTATATATTATAGATTTTTTTCAAAAGCATTTTC
1 AAAAACTATATATTATATA-TGTTTTCAAAAATGTTTTC
*
634732 AAAAACTATATATTATATATGTTTTCAAAAA--ATTTC
1 AAAAACTATATATTATATATGTTTTCAAAAATGTTTTC
*
634768 -AAAACTATATAATATATAT
1 AAAAACTATATATTATATAT
634787 ATATTTTTGA
Statistics
Matches: 177, Mismatches: 13, Indels: 24
0.83 0.06 0.11
Matches are distributed among these distances:
32 11 0.06
33 19 0.11
34 2 0.01
35 21 0.12
36 8 0.05
37 62 0.35
38 20 0.11
39 34 0.19
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (38 bp):
AAAAACTATATATTATATATGTTTTCAAAAATGTTTTC
Found at i:634822 original size:39 final size:37
Alignment explanation
Indices: 634549--634825 Score: 238
Period size: 37 Copynumber: 7.6 Consensus size: 37
634539 TTTTTTTTAA
* *
634549 AAAAACTATATAT-TATATATGTTTTCAAAA-ATGTTTT
1 AAAAACTATATATATATATAT-TTTTTAAAATAT-TTTC
* * *
634586 AAAAAC--TATATA-ATGT-TTTTTAAAAATGTTTTC
1 AAAAACTATATATATATATATTTTTTAAAATATTTTC
* *
634619 AAAAACTATATA-ATATATGTTTTTTAAAAATGTTTTC
1 AAAAACTATATATATATATATTTTTT-AAAATATTTTC
*
634656 AAAAACTATAT-TATATATATATTTTAAAAATATTTTC
1 AAAAACTATATATATATATAT-TTTTTAAAATATTTTC
* *
634693 AAAAACTATATAT-TATAGATTTTTTTCAAAAGCATTTTC
1 AAAAACTATATATATATATA-TTTTTT-AAAA-TATTTTC
* *
634732 AAAAACTATATAT-TATATATGTTTTCAAAA-AATTTC
1 AAAAACTATATATATATATAT-TTTTTAAAATATTTTC
*
634768 -AAAACTATATAATATATATATATTTTTGAAATATTTTC
1 AAAAACTATAT-ATATATATAT-TTTTTAAAATATTTTC
**
634806 -AAAACTGCATATATATATAT
1 AAAAACTATATATATATATAT
634826 CCGAAAACCA
Statistics
Matches: 202, Mismatches: 21, Indels: 34
0.79 0.08 0.13
Matches are distributed among these distances:
33 17 0.08
34 3 0.01
35 25 0.12
36 12 0.06
37 89 0.44
38 28 0.14
39 28 0.14
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (37 bp):
AAAAACTATATATATATATATTTTTTAAAATATTTTC
Done.