Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008105.1 Hibiscus syriacus cultivar Beakdansim tig00110637_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: 5962497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 30
Found at i:2751327 original size:102 final size:99
Alignment explanation
Indices: 2751138--2751327 Score: 215
Period size: 102 Copynumber: 1.9 Consensus size: 99
2751128 CACAATAAAT
* * * * *
2751138 TTTAAACTAAACTTTCCAAGGTACTCAAATACGATTTAATCTGTAAAATAATAAATTAGTCTAAT
1 TTTAAACTAAACTTACCAAGGTACTCAAATACAACTTAATATGTAAAATAATAAATTAGTATAAT
*
2751203 AATTTATATTACTCAATAAAAAAATAATGTAATAA
66 AATTTATATTA-TAAATAAAAAAATAATGTAATAA
* *
2751238 TTTAAACTACACTTACCAAGTTTTACTCAAATACAACTTAATATGTAAAATTAAAATAAA-TAGT
1 TTTAAACTAAACTTACCAAG--GTACTCAAATACAACTTAATATGTAAAA-T--AATAAATTAGT
*
2751302 ATAATAA-TTATAATT-TAAATTAAAAA
61 ATAATAATTTAT-ATTATAAATAAAAAA
2751328 CAAAAATTAT
Statistics
Matches: 75, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
100 18 0.24
102 33 0.44
103 5 0.07
104 13 0.17
105 6 0.08
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (99 bp):
TTTAAACTAAACTTACCAAGGTACTCAAATACAACTTAATATGTAAAATAATAAATTAGTATAAT
AATTTATATTATAAATAAAAAAATAATGTAATAA
Found at i:2772775 original size:11 final size:11
Alignment explanation
Indices: 2772751--2772795 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
2772741 TTGGTGCTGG
2772751 AAACAAGATAA
1 AAACAAGATAA
* *
2772762 AAATAAGATTA
1 AAACAAGATAA
2772773 AAACAAGATAA
1 AAACAAGATAA
2772784 ACAA-AAGATAA
1 A-AACAAGATAA
2772795 A
1 A
2772796 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.07, G:0.09, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:2772779 original size:22 final size:22
Alignment explanation
Indices: 2772751--2772792 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2772741 TTGGTGCTGG
2772751 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAACAA-AAGATTA
2772773 AAACAAGATAAACAAAAGAT
1 AAACAAGATAAACAAAAGAT
2772793 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.07, G:0.10, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAACAAAAGATTA
Found at i:2780425 original size:19 final size:19
Alignment explanation
Indices: 2780403--2780439 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2780393 AATGGAGTAG
*
2780403 ATGAGAACGTGAGGAGCAT
1 ATGAGAACGTAAGGAGCAT
2780422 ATGAGAACGTAAGGAGCA
1 ATGAGAACGTAAGGAGCA
2780440 GATTTATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.11, G:0.35, T:0.14
Consensus pattern (19 bp):
ATGAGAACGTAAGGAGCAT
Found at i:2785665 original size:32 final size:32
Alignment explanation
Indices: 2785629--2785846 Score: 170
Period size: 32 Copynumber: 6.8 Consensus size: 32
2785619 CATAGTAGTA
* *
2785629 TCAACATTACATTCAGATAAAGCATAACAGGG
1 TCAACATTACATTCAGATAATGCATAACAGAG
2785661 TCAACATTACATTCAGATAATGCATAACAGAG
1 TCAACATTACATTCAGATAATGCATAACAGAG
* * * *
2785693 TCAATATTACATTTAGTTAATGCATAGCAGAG
1 TCAACATTACATTCAGATAATGCATAACAGAG
* * * **
2785725 TCAATATTGCATTCAGATAATCCA-AAGTGGAG
1 TCAACATTACATTCAGATAATGCATAA-CAGAG
* * * * *
2785757 TCAATATTATATTTAGTTAATGCA-CACTAGAG
1 TCAACATTACATTCAGATAATGCATAAC-AGAG
* **** * * *
2785789 TTAGTGCTGCATTCAGATAATGCACAACATAG
1 TCAACATTACATTCAGATAATGCATAACAGAG
* *
2785821 TCAATATTACATTAAGATAATGCATA
1 TCAACATTACATTCAGATAATGCATA
2785847 GCAAATTTAG
Statistics
Matches: 145, Mismatches: 38, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
31 1 0.01
32 142 0.98
33 2 0.01
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.30
Consensus pattern (32 bp):
TCAACATTACATTCAGATAATGCATAACAGAG
Found at i:2785718 original size:64 final size:63
Alignment explanation
Indices: 2785629--2785906 Score: 216
Period size: 64 Copynumber: 4.3 Consensus size: 63
2785619 CATAGTAGTA
* * * * * *
2785629 TCAACATTACATTCAGATAAAGCATAACAGGGTCAACATTACATTCAGATAATGCATAACAGAG
1 TCAATATTACATTTAGATAATGCATAACAGAGTCAATATTGCATTCAGATAATGCA-AACAGAG
* * * **
2785693 TCAATATTACATTTAGTTAATGCATAGCAGAGTCAATATTGCATTCAGATAATCCAAAGTGGAG
1 TCAATATTACATTTAGATAATGCATAACAGAGTCAATATTGCATTCAGATAATGCAAA-CAGAG
* * * * * ** *
2785757 TCAATATTATATTTAGTTAATGCA-CACTAGAGTTAGTGCTGCATTCAGATAATGCACAACATAG
1 TCAATATTACATTTAGATAATGCATAAC-AGAGTCAATATTGCATTCAGATAATGCA-AACAGAG
* * * * * * * * ** *
2785821 TCAATATTACATTAAGATAATGCATAGCAAATTTAGTGTTGCATTCAGACAATGCACATGAGCG
1 TCAATATTACATTTAGATAATGCATAACAGAGTCAATATTGCATTCAGATAATGCA-AACAGAG
* *
2785885 TCAGTATCACATTTAGATAATG
1 TCAATATTACATTTAGATAATG
2785907 AGTAGTATAT
Statistics
Matches: 172, Mismatches: 38, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
63 3 0.02
64 166 0.97
65 3 0.02
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (63 bp):
TCAATATTACATTTAGATAATGCATAACAGAGTCAATATTGCATTCAGATAATGCAAACAGAG
Found at i:2785899 original size:128 final size:128
Alignment explanation
Indices: 2785670--2785906 Score: 305
Period size: 128 Copynumber: 1.9 Consensus size: 128
2785660 GTCAACATTA
* * * *
2785670 CATTCAGATAATGCATAACAGAGTCAATATTACATTTAGTTAATGCATAGCAGAGTCAATATTGC
1 CATTCAGATAATGCACAACAGAGTCAATATTACATTAAGATAATGCATAGCAAAGTCAATATTGC
* * * *
2785735 ATTCAGATAATCCAAAGTGGAGTCAATATTATATTTAGTTAATGCACACTAGAGTTAGTGCTG
66 ATTCAGACAATCCAAAGTGGAGTCAATATCACATTTAGATAATGCACACTAGAGTTAGTGCTG
* * * * *
2785798 CATTCAGATAATGCACAACATAGTCAATATTACATTAAGATAATGCATAGCAAATTTAGTGTTGC
1 CATTCAGATAATGCACAACAGAGTCAATATTACATTAAGATAATGCATAGCAAAGTCAATATTGC
* * * *
2785863 ATTCAGACAATGCACA-TGAGCGTCAGTATCACATTTAGATAATG
66 ATTCAGACAATCCAAAGTG-GAGTCAATATCACATTTAGATAATG
2785907 AGTAGTATAT
Statistics
Matches: 91, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
127 2 0.02
128 89 0.98
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (128 bp):
CATTCAGATAATGCACAACAGAGTCAATATTACATTAAGATAATGCATAGCAAAGTCAATATTGC
ATTCAGACAATCCAAAGTGGAGTCAATATCACATTTAGATAATGCACACTAGAGTTAGTGCTG
Found at i:2791297 original size:64 final size:65
Alignment explanation
Indices: 2791212--2791521 Score: 278
Period size: 64 Copynumber: 4.8 Consensus size: 65
2791202 GTAGTATCAA
* * * * *
2791212 CATTGCATTCAAATAATGCATAATAGAGTTAAAATTGCCTTCAAATAATGCATAGCTGAGTCA-T
1 CATTGCATTCAGATAATGCATAACAGAGTTAATATTGCATTCAAATAATGCATAGCAGAGTCAGT
* * * * * * ** *
2791276 CATTGCATTCAGATAATGCATATCAAAGTCAGTATTGTATTTAGTTAATGCATAGCAGAGTC-GG
1 CATTGCATTCAGATAATGCATAACAGAGTTAATATTGCATTCAAATAATGCATAGCAGAGTCAGT
* *
2791340 CATTGCATTCAGATAATTCATAACAGA-TTCAATATTGCATTC-AATCAATGCATAGCAGAGTTA
1 CATTGCATTCAGATAATGCATAACAGAGTT-AATATTGCATTCAAAT-AATGCATAGCAGAGTCA
2791403 GT
64 GT
* * * * * * *
2791405 -GTTGCATTCA-ATTAATGCATAGCAGA-TTCAATATTACATTTAGATAATGCACAACAG-GTCA
1 CATTGCATTCAGA-TAATGCATAACAGAGTT-AATATTGCATTCAAATAATGCATAGCAGAGTCA
2791466 GT
64 GT
* * * *
2791468 -ATTGCATTCAGATAATGCATAACAGAGTTATTGTTGTATTCAGATAATGCATAG
1 CATTGCATTCAGATAATGCATAACAGAGTTAATATTGCATTCAAATAATGCATAG
2791522 GAATGTCACT
Statistics
Matches: 195, Mismatches: 43, Indels: 17
0.76 0.17 0.07
Matches are distributed among these distances:
63 48 0.25
64 144 0.74
65 3 0.02
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (65 bp):
CATTGCATTCAGATAATGCATAACAGAGTTAATATTGCATTCAAATAATGCATAGCAGAGTCAGT
Found at i:2791306 original size:32 final size:31
Alignment explanation
Indices: 2791213--2791521 Score: 237
Period size: 32 Copynumber: 9.7 Consensus size: 31
2791203 TAGTATCAAC
* ** * *
2791213 ATTGCATTCAAATAATGCATAATAGAGTTAAA
1 ATTGCATTCAGATAATGCATAGCAGAG-TCAT
* * *
2791245 ATTGCCTTCAAATAATGCATAGCTGAGTCAT
1 ATTGCATTCAGATAATGCATAGCAGAGTCAT
* *
2791276 CATTGCATTCAGATAATGCATATCAAAGTCAGT
1 -ATTGCATTCAGATAATGCATAGCAGAGTCA-T
* * * **
2791309 ATTGTATTTAGTTAATGCATAGCAGAGTCGGC
1 ATTGCATTCAGATAATGCATAGCAGAGTC-AT
* * *
2791341 ATTGCATTCAGATAATTCATAACAGATTCAAT
1 ATTGCATTCAGATAATGCATAGCAGAGTC-AT
*
2791373 ATTGCATTCA-ATCAATGCATAGCAGAGTTAGT
1 ATTGCATTCAGAT-AATGCATAGCAGAGTCA-T
* *
2791405 GTTGCATTCA-ATTAATGCATAGCAGATTCAAT
1 ATTGCATTCAGA-TAATGCATAGCAGAGTC-AT
* * * *
2791437 ATTACATTTAGATAATGCACAACAG-GTCAGT
1 ATTGCATTCAGATAATGCATAGCAGAGTCA-T
* *
2791468 ATTGCATTCAGATAATGCATAACAGAGTTATT
1 ATTGCATTCAGATAATGCATAGCAGAGTCA-T
* *
2791500 GTTGTATTCAGATAATGCATAG
1 ATTGCATTCAGATAATGCATAG
2791522 GAATGTCACT
Statistics
Matches: 219, Mismatches: 48, Indels: 20
0.76 0.17 0.07
Matches are distributed among these distances:
30 1 0.00
31 30 0.14
32 184 0.84
33 4 0.02
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Consensus pattern (31 bp):
ATTGCATTCAGATAATGCATAGCAGAGTCAT
Found at i:2791497 original size:95 final size:96
Alignment explanation
Indices: 2791269--2791549 Score: 293
Period size: 96 Copynumber: 2.9 Consensus size: 96
2791259 ATGCATAGCT
* * * * * *
2791269 GAGTC-ATCATTGCATTCAGATAATGCATATCAAAGTCAGTATTGTATTTAGTTAATGCATAGCA
1 GAGTCAAT-ATTGCATTCAGATAATGCATAACAGAGTTAGTGTTGTATTCAATTAATGCATAGCA
* *** * * * *
2791333 GAGTCGGCATTGCATTCAGATAATTCATAACA
65 GATTCAATATTACATTTAGATAATGCACAACA
* * *
2791365 GATTCAATATTGCATTCA-ATCAATGCATAGCAGAGTTAGTGTTGCATTCAATTAATGCATAGCA
1 GAGTCAATATTGCATTCAGAT-AATGCATAACAGAGTTAGTGTTGTATTCAATTAATGCATAGCA
2791429 GATTCAATATTACATTTAGATAATGCACAACA
65 GATTCAATATTACATTTAGATAATGCACAACA
* * *
2791461 G-GTCAGTATTGCATTCAGATAATGCATAACAGAGTTATTGTTGTATTCAGA-TAATGCATAGGA
1 GAGTCAATATTGCATTCAGATAATGCATAACAGAGTTAGTGTTGTATTCA-ATTAATGCATAGCA
* *
2791524 -ATGTCACTATCACATTTAGATAATGC
65 GAT-TCAATATTACATTTAGATAATGC
2791550 GTAGGAGATA
Statistics
Matches: 156, Mismatches: 24, Indels: 11
0.82 0.13 0.06
Matches are distributed among these distances:
94 2 0.01
95 74 0.47
96 78 0.50
97 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (96 bp):
GAGTCAATATTGCATTCAGATAATGCATAACAGAGTTAGTGTTGTATTCAATTAATGCATAGCAG
ATTCAATATTACATTTAGATAATGCACAACA
Found at i:2799296 original size:20 final size:20
Alignment explanation
Indices: 2799271--2799317 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
2799261 ATACACTTAT
*
2799271 TATCGATATCTTGCATGTAG
1 TATCGATATCTTGCAAGTAG
* *
2799291 TATCGA-CTCTTTCAAGTAG
1 TATCGATATCTTGCAAGTAG
2799310 TATCGATA
1 TATCGATA
2799318 CTCCCTTGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (20 bp):
TATCGATATCTTGCAAGTAG
Found at i:2800651 original size:131 final size:132
Alignment explanation
Indices: 2800448--2800692 Score: 429
Period size: 131 Copynumber: 1.9 Consensus size: 132
2800438 GGTGGTAATG
*
2800448 TAATATTACTAATAGTAAATAATATATGAGAATTTTCGTTATTATCTATTTCTTAGGTGCTTAAG
1 TAATATTACTAATAGTAAATAATATATGAGAATATTCGTTATTATCTATTTCTTAGGTGCTTAAG
2800513 ATCATTAATAATAAATATTATTTTGAATAATTTTATCTTTAAAATTTATGAGAATAAATATTATT
66 ATCATTAATAATAAATATTATTTTGAATAATTTTATCTTTAAAATTTATGAGAATAAATATTATT
2800578 AA
131 AA
* * *
2800580 TAATATTGCTAATAGTAATTAATATATGAGAATATTCG-TATTATCTATTTCTTTGGTGCTTAAG
1 TAATATTACTAATAGTAAATAATATATGAGAATATTCGTTATTATCTATTTCTTAGGTGCTTAAG
* *
2800644 ATTATTAATAATAAATATTATTTTGAATAATTTTGTCTTTAAAATTTAT
66 ATCATTAATAATAAATATTATTTTGAATAATTTTATCTTTAAAATTTAT
2800693 TTATTTATTT
Statistics
Matches: 107, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
131 72 0.67
132 35 0.33
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (132 bp):
TAATATTACTAATAGTAAATAATATATGAGAATATTCGTTATTATCTATTTCTTAGGTGCTTAAG
ATCATTAATAATAAATATTATTTTGAATAATTTTATCTTTAAAATTTATGAGAATAAATATTATT
AA
Found at i:2803824 original size:20 final size:21
Alignment explanation
Indices: 2803785--2803825 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2803775 TTTCGAAATT
*
2803785 AAGTATCGATACTGAGATGAA
1 AAGTATCAATACTGAGATGAA
2803806 AAGTATCAATACT-AGATGAA
1 AAGTATCAATACTGAGATGAA
2803826 TTGGGGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.24
Consensus pattern (21 bp):
AAGTATCAATACTGAGATGAA
Found at i:2822721 original size:16 final size:16
Alignment explanation
Indices: 2822700--2822731 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2822690 CCTTAATCCC
2822700 TACACATGACCGAGCA
1 TACACATGACCGAGCA
*
2822716 TACACATGACCTAGCA
1 TACACATGACCGAGCA
2822732 AGAGCTTGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.31, G:0.16, T:0.16
Consensus pattern (16 bp):
TACACATGACCGAGCA
Found at i:2825249 original size:11 final size:10
Alignment explanation
Indices: 2825233--2825393 Score: 56
Period size: 10 Copynumber: 16.2 Consensus size: 10
2825223 ATAACAAAAT
2825233 AAATAATATAA
1 AAATAATA-AA
2825244 AAATAATACAA
1 AAATAATA-AA
2825255 AAATAATAAA
1 AAATAATAAA
* *
2825265 AAGA-AAGAGA
1 AA-ATAATAAA
*
2825275 AAGTAA-AAA
1 AAATAATAAA
2825284 AAAT-AT-AA
1 AAATAATAAA
*
2825292 TAATAAT--A
1 AAATAATAAA
2825300 AAAT-ATAAA
1 AAATAATAAA
*
2825309 AAAT-ATACAT
1 AAATAATA-AA
* *
2825319 ATATAAT-AT
1 AAATAATAAA
2825328 AAATAAGTAGAA
1 AAATAA-TA-AA
*
2825340 TAAA-AAGAAA
1 -AAATAATAAA
*
2825350 ATATAATAGTAA
1 AAATAATA--AA
2825362 AAATAATAAA
1 AAATAATAAA
*
2825372 AATATAAT-AG
1 AA-ATAATAAA
*
2825382 TAATAATAAA
1 AAATAATAAA
2825392 AA
1 AA
2825394 TGCAAAGAAA
Statistics
Matches: 113, Mismatches: 20, Indels: 35
0.67 0.12 0.21
Matches are distributed among these distances:
7 2 0.02
8 10 0.09
9 29 0.26
10 30 0.27
11 27 0.24
12 12 0.11
13 3 0.03
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.23
Consensus pattern (10 bp):
AAATAATAAA
Found at i:2825377 original size:23 final size:23
Alignment explanation
Indices: 2825347--2825390 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2825337 GAATAAAAAG
2825347 AAAATATAATAGTAAAAATAATA
1 AAAATATAATAGTAAAAATAATA
*
2825370 AAAATATAATAGTAATAATAA
1 AAAATATAATAGTAAAAATAA
2825391 AAATGCAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (23 bp):
AAAATATAATAGTAAAAATAATA
Found at i:2825406 original size:20 final size:21
Alignment explanation
Indices: 2825347--2825407 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 21
2825337 GAATAAAAAG
*
2825347 AAAATATAATAGTAAAAATAATA
1 AAAATACAATAG--AAAATAATA
* *
2825370 AAAATATAATAG-TAATAATA
1 AAAATACAATAGAAAATAATA
*
2825390 AAAATGCAA-AGAAAATAA
1 AAAATACAATAGAAAATAA
2825408 ATATATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
19 2 0.06
20 19 0.58
23 12 0.36
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.23
Consensus pattern (21 bp):
AAAATACAATAGAAAATAATA
Found at i:2826011 original size:37 final size:37
Alignment explanation
Indices: 2825970--2826059 Score: 110
Period size: 37 Copynumber: 2.4 Consensus size: 37
2825960 GGATCCCATC
* *
2825970 TTTAGGAGTTTAAATCATAGT-AGAACTCTATCCTATT
1 TTTAGGAGTTTGAATCATA-TCAAAACTCTATCCTATT
* * *
2826007 TTTAGGAGTTTGAATCCTATCAAAATTCTATCTTATT
1 TTTAGGAGTTTGAATCATATCAAAACTCTATCCTATT
*
2826044 TTTATGAGTTTGAATC
1 TTTAGGAGTTTGAATC
2826060 CAAGTAGGAC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
36 1 0.02
37 45 0.98
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.44
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCATATCAAAACTCTATCCTATT
Found at i:2827115 original size:106 final size:106
Alignment explanation
Indices: 2826819--2828277 Score: 2108
Period size: 106 Copynumber: 13.8 Consensus size: 106
2826809 CTCCATCGTA
* * ** * * * * *
2826819 AAGTTGAAATTGGCTATGGAATCAGGAAATTTTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAA
1 AAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
* * *
2826884 GTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGTTGTG
66 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
* * * * *
2826925 AAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAATCAGCCG-CCCTTTCGTCGTGA
1 AAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCC-TTCGTCGTGA
* * * *
2826983 AGTTGAGCTTGTGTTGTCTTGG-GTCCAAGATCCTTCGCTGAG
65 AGTTGAACTTGCGTTGTC-TGGAGTCCAATATCCTTCGCTGTG
* * *
2827025 AAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACTAGCGATCCCTTCGTTGTGAA
1 AAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
* *
2827090 GTTGAACTTGCGTTGTCTTGAGTCCAATATCCTACGCTGTG
66 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
* * * * *
2827131 AAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTATTGACAACCAGCAGTCTCTTCTTCGTGAA
1 AAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
* **
2827196 GTTGAACTTGCGTTTTCTGGAGTCCAATATCCTTCATTGTG
66 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
* * *
2827237 AAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
1 AAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
*
2827302 GTTGAAATTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
66 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
* *
2827343 AAGTTGAAATTAGCTCTGAAATTGGGAAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
1 AAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
*
2827408 GTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTG
66 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
* * * *
2827449 AAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAACCAGCGGTCCCTTCATCGTGAA
1 AAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
*
2827514 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
66 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
* * *
2827555 AAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCAGTCCCTTCGTCGTGAA
1 AAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
* * *
2827620 CTTGAACTTGCGTTGTTTGGAGTCCAATATCCTTCGTTGTG
66 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
* * *
2827661 AAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAA
1 AAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
2827726 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
66 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
* * *
2827767 AAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTAATGACAACCAGCAGTCCCTTCGTTGTGAA
1 AAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
*
2827832 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
66 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
* * *
2827873 AAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCAGTCCCTTCGTCGTGAA
1 AAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
* * * *
2827938 GTTGAACTTGCATTGTTTAGAGTCCAATATCCTTTGCTGTG
66 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
* *
2827979 AAGTTGAAATTGGCTCTAAAATTGGAAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
1 AAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
* *
2828044 GTTGAACTTGTGTTATCTGGAGTCCAATATCCTTCGCTGTG
66 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
* *
2828085 AAGTTGAAATTGGCTCTGAAATTAGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
1 AAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
2828150 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
66 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
* * * * * * *
2828191 AAGTTGAAATTGGCTCCGAAATTAGAAAATTG-TTATTGTCAACCAGCCGTCCCTTCGTTGTGAA
1 AAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
* *
2828255 GTTGAACTTGTGTTGTCTTGAGT
66 GTTGAACTTGCGTTGTCTGGAGT
2828278 GGCACGATAT
Statistics
Matches: 1230, Mismatches: 113, Indels: 21
0.90 0.08 0.02
Matches are distributed among these distances:
99 3 0.00
100 77 0.06
101 5 0.00
102 4 0.00
104 3 0.00
105 55 0.04
106 1080 0.88
107 3 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (106 bp):
AAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
Found at i:2828680 original size:18 final size:19
Alignment explanation
Indices: 2828653--2828689 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2828643 TGTTGAATCC
*
2828653 CCAAATAATGTCCCAATAT
1 CCAAATAATGCCCCAATAT
2828672 CCAAA-AATGCCCCAATAT
1 CCAAATAATGCCCCAATAT
2828690 TTGATGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.43, C:0.30, G:0.05, T:0.22
Consensus pattern (19 bp):
CCAAATAATGCCCCAATAT
Found at i:2829127 original size:22 final size:22
Alignment explanation
Indices: 2829102--2829156 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
2829092 TTGTGTTTGG
*
2829102 TCAAAGATTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
2829124 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
2829146 TCAAAGGTTTG
1 TCAAAGGTTTG
2829157 ATGGGATAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:2829802 original size:16 final size:16
Alignment explanation
Indices: 2829783--2829825 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
2829773 TTTTTGTTCT
2829783 TTTTTTTGTTTTCTTC
1 TTTTTTTGTTTTCTTC
*
2829799 -TTTTTTG-TTTCTTT
1 TTTTTTTGTTTTCTTC
2829813 TCTTTTTTGTTTT
1 T-TTTTTTGTTTT
2829826 TGCCCTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 6 0.26
15 7 0.30
16 7 0.30
17 3 0.13
ACGTcount: A:0.00, C:0.09, G:0.07, T:0.84
Consensus pattern (16 bp):
TTTTTTTGTTTTCTTC
Found at i:2829813 original size:19 final size:17
Alignment explanation
Indices: 2829782--2829826 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
2829772 ATTTTTGTTC
*
2829782 TTTTTTTTGTTTTCTTCT
1 TTTTTTTTCTTTTCTT-T
2829800 TTTTTGTTTCTTTTCTTT
1 TTTTT-TTTCTTTTCTTT
2829818 TTTGTTTTT
1 TTT-TTTTT
2829827 GCCCTTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.00, C:0.09, G:0.07, T:0.84
Consensus pattern (17 bp):
TTTTTTTTCTTTTCTTT
Found at i:2833126 original size:19 final size:20
Alignment explanation
Indices: 2833098--2833135 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2833088 TGCAGATGAT
*
2833098 GGAAATAAAAT-AAAAGAGA
1 GGAAAAAAAATGAAAAGAGA
2833117 GGAAAAAAAATGAAAAGAG
1 GGAAAAAAAATGAAAAGAG
2833136 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (20 bp):
GGAAAAAAAATGAAAAGAGA
Found at i:2834311 original size:26 final size:26
Alignment explanation
Indices: 2834260--2834344 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
2834250 TAAAATGAAG
*
2834260 AAAACAAAGATAAAATAGTAAGTAAA
1 AAAACAAAAATAAAATAGTAAGTAAA
2834286 AAAACAAATAATAAAATA-T-A-TATAA
1 AAAACAAA-AATAAAATAGTAAGTA-AA
* * * *
2834311 AAAAGAAAAAGAAAA-AGAAAATAAA
1 AAAACAAAAATAAAATAGTAAGTAAA
2834336 TAAAACAAA
1 -AAAACAAA
2834345 TAAACAAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
23 1 0.02
24 8 0.17
25 13 0.27
26 18 0.38
27 8 0.17
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (26 bp):
AAAACAAAAATAAAATAGTAAGTAAA
Found at i:2834383 original size:2 final size:2
Alignment explanation
Indices: 2834376--2834400 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2834366 AGTACGAATA
2834376 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 A
2834401 AAATAAATAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2834568 original size:2 final size:2
Alignment explanation
Indices: 2834561--2834587 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2834551 GAACATACGC
2834561 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 A
2834588 ACAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2834662 original size:16 final size:17
Alignment explanation
Indices: 2834643--2834692 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 17
2834633 GAGAAAGTAA
*
2834643 AAAATATAATAATA-AT
1 AAAATATAATAAAATAT
2834659 AAAATATAA-AAAATAT
1 AAAATATAATAAAATAT
2834675 ACAAATATAATATAAATA
1 A-AAATATAATA-AAATA
2834693 AGTAGAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 3 0.10
16 12 0.41
17 8 0.28
18 1 0.03
19 5 0.17
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAATATAATAAAATAT
Found at i:2835364 original size:37 final size:37
Alignment explanation
Indices: 2835323--2835427 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
2835313 GTGTTTGTGG
* * *
2835323 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* *
2835360 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
*
2835397 ATCCTATTTTTATGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
2835428 GACGAAAAGG
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:2842887 original size:7 final size:6
Alignment explanation
Indices: 2842870--2842903 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
2842860 AACATATTCG
2842870 ATAAAA ATAAAA AGTAAAA ATAAAAA ATAAAA AT
1 ATAAAA ATAAAA A-TAAAA AT-AAAA ATAAAA AT
2842904 TTAATGGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 14 0.54
7 12 0.46
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:2842889 original size:13 final size:13
Alignment explanation
Indices: 2842870--2842903 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2842860 AACATATTCG
2842870 ATAAAAATAAAAA
1 ATAAAAATAAAAA
*
2842883 GTAAAAATAAAAA
1 ATAAAAATAAAAA
2842896 ATAAAAAT
1 ATAAAAAT
2842904 TTAATGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (13 bp):
ATAAAAATAAAAA
Found at i:2851042 original size:117 final size:117
Alignment explanation
Indices: 2850822--2851043 Score: 286
Period size: 117 Copynumber: 1.9 Consensus size: 117
2850812 CTTTCAAATC
* *
2850822 GAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTT
1 GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
* * * *
2850887 CATTTTGATTTTCAAAATCCATTTTTGTTTTTAGAAGAAGTTTGTTTAATTT
66 CATTTTGATTTTCAAAATCCATTTTAGCTTTCAAAAGAAGTTTGTTTAATTT
* * * *
2850939 GAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTCCTT-TCTCAACAT
1 GAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCT-TCAACAT
* * **
2851002 TTCATTTTGATTTTCCAAGTCTGTTTTAGCTTTCAAAAGAAG
64 TTCATTTTGATTTTCAAAATCCATTTTAGCTTTCAAAAGAAG
2851044 ATCATTTTTA
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
116 2 0.02
117 87 0.98
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.48
Consensus pattern (117 bp):
GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
CATTTTGATTTTCAAAATCCATTTTAGCTTTCAAAAGAAGTTTGTTTAATTT
Found at i:2854050 original size:21 final size:21
Alignment explanation
Indices: 2854024--2854068 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2854014 TCCAGATTCC
2854024 CAACGCAAACATCGACTATCG
1 CAACGCAAACATCGACTATCG
* *
2854045 CAACGCGAACTTCGACTATCG
1 CAACGCAAACATCGACTATCG
2854066 CAA
1 CAA
2854069 TGCGATTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.33, G:0.16, T:0.16
Consensus pattern (21 bp):
CAACGCAAACATCGACTATCG
Found at i:2854126 original size:42 final size:39
Alignment explanation
Indices: 2854069--2854436 Score: 260
Period size: 42 Copynumber: 8.8 Consensus size: 39
2854059 ACTATCGCAA
*
2854069 TGCGATT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTATTCCAAGTTCGTTGCGATAGTCCAAGTT--CGT
* *
2854109 TGCGATTTATTCCAAATTCGCGTTGCGATAGTCCAAATTCGT
1 TGCGA-TTATTCCAAGTT--CGTTGCGATAGTCCAAGTTCGT
* * * *
2854151 TGCGA-TAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCGT
1 TGCGATTATTCCAAGTTCG--TTGCGA--TAGTCCAAGTTCGT
* * * *
2854193 TGCGA-TAGTCGAAGTTCGCATTGCAATTTATTCCAAGTTCGT
1 TGCGATTATTCCAAGTTCG--TTGCGA--TAGTCCAAGTTCGT
* * * * *
2854235 TGCGA-TAGTCGAAGTTTGCGTTGCGATTTATTCTAAATTCGT
1 TGCGATTATTCCAAG-TT-CGTTGCGA--TAGTCCAAGTTCGT
* * *
2854277 TGCGA-TAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGT
1 TGCGATTATTCCAAGTT--CGTTGCGA--TAGTCCAAGTTCGT
*
2854319 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGA-TTATTCCAAGTTCGTTGCGATAGTCCAAGTT--CGT
*
2854361 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCACGT
1 TGCGA-TTATTCCAAGTTCGTTGCGATAGTCCAAGTT--CGT
2854403 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAA
1 TGCGA-TTATTCCAAGTTCGTTGCGATAGTCCAA
2854437 AATCGCAACG
Statistics
Matches: 295, Mismatches: 18, Indels: 28
0.87 0.05 0.08
Matches are distributed among these distances:
38 2 0.01
40 28 0.09
41 4 0.01
42 230 0.78
43 2 0.01
44 29 0.10
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (39 bp):
TGCGATTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGT
Found at i:2854168 original size:63 final size:61
Alignment explanation
Indices: 2854077--2854391 Score: 359
Period size: 63 Copynumber: 5.0 Consensus size: 61
2854067 AATGCGATTT
* *
2854077 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGCGTTGCGATAG
1 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT--CGTTGCGATAG
* *
2854140 TCCAAATTCGTTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAG
* * * * * * *
2854201 TCGAAGTTCGCATTGCAATTTATTCCAAGTT--CGTTGCGA--TAGTCGAAGTTTGCGTTGCGAT
1 TCCAAATTCG--TTGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAAG-TT-CGTTGCGA-
*
2854262 TTAT
59 -TAG
* *
2854266 TCTAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATTTAT
1 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGA--TAG
*
2854329 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAG
2854390 TC
1 TC
2854392 GAAGTTCACG
Statistics
Matches: 218, Mismatches: 22, Indels: 26
0.82 0.08 0.10
Matches are distributed among these distances:
61 38 0.17
62 2 0.01
63 150 0.69
64 2 0.01
65 26 0.12
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (61 bp):
TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAG
Found at i:2854228 original size:84 final size:84
Alignment explanation
Indices: 2854140--2854324 Score: 316
Period size: 84 Copynumber: 2.2 Consensus size: 84
2854130 GTTGCGATAG
*
2854140 TCCAAATTCGTTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCGA
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCGA
2854205 AGTTCGCATTGCAATTTAT
66 AGTTCGCATTGCAATTTAT
* * *
2854224 TCCAAGTTCGTTGCGATAGTCGAAGTTTGCGTTGCGATTTATTCTAAATTCGTTGCGATAGTCGA
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCGA
* *
2854289 AGTTCGCGTTGCGATTTAT
66 AGTTCGCATTGCAATTTAT
2854308 TCCAAGTTCGTTGCGAT
1 TCCAAGTTCGTTGCGAT
2854325 TTATTCCAAG
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 95 1.00
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (84 bp):
TCCAAGTTCGTTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCGA
AGTTCGCATTGCAATTTAT
Found at i:2854367 original size:105 final size:105
Alignment explanation
Indices: 2854204--2854429 Score: 389
Period size: 105 Copynumber: 2.1 Consensus size: 105
2854194 GCGATAGTCG
* * *
2854204 AAGTTCGCATTGCAATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTTGCGTTGCGATTTATTCT
1 AAGTTCG--TTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCC
*
2854269 AAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCC
64 AAATTCGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCC
2854311 AAGTTCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAA
1 AAGTTCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAA
*
2854376 GTTCGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCC
66 ATTCGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCC
2854416 AAGTTCGTTGCGAT
1 AAGTTCGTTGCGAT
2854430 AGTCCAAAAT
Statistics
Matches: 114, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
105 107 0.94
107 7 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (105 bp):
AAGTTCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAA
ATTCGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCC
Found at i:2855087 original size:6 final size:6
Alignment explanation
Indices: 2855071--2855102 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
2855061 TCTCGGGTTG
2855071 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
2855103 AATACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:2855224 original size:21 final size:19
Alignment explanation
Indices: 2855192--2855392 Score: 132
Period size: 21 Copynumber: 9.7 Consensus size: 19
2855182 CATTGCGATT
*
2855192 TTGGACTATCGCAACGAAC
1 TTGGAATATCGCAACGAAC
2855211 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
* *
2855234 TTCGACTATCGCAACGAAC
1 TTGGAATATCGCAACGAAC
2855253 TTGGAATAAATCGCAACGCTAAC
1 TTGGAAT--ATCGCAACG--AAC
* *
2855276 TTCGACTATCGCAACGAAC
1 TTGGAATATCGCAACGAAC
2855295 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
* *
2855318 TTCGACTATCGCAACGAAC
1 TTGGAATATCGCAACGAAC
* * * *
2855337 TTAGACTATCACAACGAAT
1 TTGGAATATCGCAACGAAC
*
2855356 TTGTAATAAATCGCAACACGAAC
1 TTGGAAT--ATCGC-A-ACGAAC
* *
2855379 TTTGACTATCGCAA
1 TTGGAATATCGCAA
2855393 ATCAGTTTCC
Statistics
Matches: 144, Mismatches: 22, Indels: 32
0.73 0.11 0.16
Matches are distributed among these distances:
19 50 0.35
20 1 0.01
21 55 0.38
22 1 0.01
23 37 0.26
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (19 bp):
TTGGAATATCGCAACGAAC
Found at i:2855254 original size:42 final size:42
Alignment explanation
Indices: 2855195--2855338 Score: 279
Period size: 42 Copynumber: 3.4 Consensus size: 42
2855185 TGCGATTTTG
2855195 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
2855237 GACTATCGCAACGAACTTGGAATAAATCGCAACGCTAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
2855279 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
2855321 GACTATCGCAACGAACTT
1 GACTATCGCAACGAACTT
2855339 AGACTATCAC
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 100 1.00
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:2855352 original size:61 final size:62
Alignment explanation
Indices: 2855262--2855392 Score: 192
Period size: 61 Copynumber: 2.1 Consensus size: 62
2855252 CTTGGAATAA
* * *
2855262 ATCGCAACGCTAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGC-AACTTAGACTATCACAACGAACTTGGAATAAATCGCAACACGAACTTCGACT
* * *
2855325 ATCGCAACG-AACTTAGACTATCACAACGAATTTGTAATAAATCGCAACACGAACTTTGACT
1 ATCGCAACGCAACTTAGACTATCACAACGAACTTGGAATAAATCGCAACACGAACTTCGACT
2855386 ATCGCAA
1 ATCGCAA
2855393 ATCAGTTTCC
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
61 53 0.85
63 9 0.15
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.22
Consensus pattern (62 bp):
ATCGCAACGCAACTTAGACTATCACAACGAACTTGGAATAAATCGCAACACGAACTTCGACT
Found at i:2857992 original size:57 final size:57
Alignment explanation
Indices: 2857904--2858186 Score: 424
Period size: 57 Copynumber: 5.0 Consensus size: 57
2857894 GTTAGAGGAA
* *
2857904 GAATACTTGCAGGTTCCTC-GTTCTTGTGCTGAGAGCCTTACTGTTTGTGACGGGGTT
1 GAATACTTGCAGGTTCCTCGGCT-TTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
* *
2857961 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAACCTTACTGTTCGTGACGGAGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
* *
2858018 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAACCTTACTGTTCATGACGGGGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
* * * *
2858075 GAATACTTGCAGGTTCCTCAGCTTTGTGCTTAGAGCCTTACTGTTCATGACAGGGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
* * * *
2858132 GATTACTTGCAGGTTCCTTGGCTTTGTGCTTAGGGCCTTACTGTTCGTGACGGGG
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGG
2858187 GTTGTATGGT
Statistics
Matches: 209, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
57 207 0.99
58 2 0.01
ACGTcount: A:0.16, C:0.20, G:0.29, T:0.35
Consensus pattern (57 bp):
GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
Found at i:2859842 original size:37 final size:36
Alignment explanation
Indices: 2859767--2859842 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
2859757 TTTTTATATT
*
2859767 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* * *
2859803 TTTAATTTTTTAGAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTA-AAAAAATTATATAAATATTAT-CAA
2859840 TTT
1 TTT
2859843 GTAATATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 24 0.71
37 10 0.29
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:2860783 original size:5 final size:5
Alignment explanation
Indices: 2860773--2860801 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
2860763 GTTGTTTCGA
2860773 TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
2860802 TGTATGGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (5 bp):
TTTTG
Found at i:2873173 original size:27 final size:27
Alignment explanation
Indices: 2873138--2873189 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
2873128 CTAATATAAG
2873138 ATTTAAAAAATAAATTTAAGATTTTAT
1 ATTTAAAAAATAAATTTAAGATTTTAT
* * * *
2873165 ATTTTAAAAGTATATTTAATATTTT
1 ATTTAAAAAATAAATTTAAGATTTT
2873190 TCTTTTCTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (27 bp):
ATTTAAAAAATAAATTTAAGATTTTAT
Found at i:2881561 original size:2 final size:2
Alignment explanation
Indices: 2881554--2881603 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2881544 TCAATTTACA
2881554 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2881596 AT AT AT AT
1 AT AT AT AT
2881604 TTACGAAATA
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):
AT
Found at i:2881781 original size:13 final size:13
Alignment explanation
Indices: 2881757--2881810 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
2881747 AATGACACTC
*
2881757 AATGAACGTCATA
1 AATGAGCGTCATA
*
2881770 AATAAGCGTCATA
1 AATGAGCGTCATA
* *
2881783 AATGTGTGTCATA
1 AATGAGCGTCATA
*
2881796 AATGAGTGTCATA
1 AATGAGCGTCATA
2881809 AA
1 AA
2881811 AAAGAATAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.28
Consensus pattern (13 bp):
AATGAGCGTCATA
Found at i:2892750 original size:44 final size:44
Alignment explanation
Indices: 2892666--2892773 Score: 121
Period size: 44 Copynumber: 2.5 Consensus size: 44
2892656 GTGATGGATG
2892666 AACCCAACT-CTCTATGTGATGGAATCTAGAAAAATATTGATACT
1 AACCCAACTCCT-TATGTGATGGAATCTAGAAAAATATTGATACT
* * * *
2892710 GACCCAACTCCTTATGTGATGGAATCTA-ACGAAATGTTGATCCT
1 AACCCAACTCCTTATGTGATGGAATCTAGA-AAAATATTGATACT
* * *
2892754 AACCTAATTCCTTATATGAT
1 AACCCAACTCCTTATGTGAT
2892774 AGACGAGCCG
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
43 1 0.02
44 51 0.94
45 2 0.04
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (44 bp):
AACCCAACTCCTTATGTGATGGAATCTAGAAAAATATTGATACT
Found at i:2894469 original size:12 final size:12
Alignment explanation
Indices: 2894466--2894509 Score: 88
Period size: 12 Copynumber: 3.7 Consensus size: 12
2894456 TCATTTTTCA
2894466 TTTCATTTCATT
1 TTTCATTTCATT
2894478 TTTCATTTCATT
1 TTTCATTTCATT
2894490 TTTCATTTCATT
1 TTTCATTTCATT
2894502 TTTCATTT
1 TTTCATTT
2894510 TCTTTTCATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTCATTTCATT
Found at i:2894502 original size:17 final size:17
Alignment explanation
Indices: 2894450--2894490 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
2894440 ATATTTTCTT
2894450 TTTC-TTTCATTTTTCA
1 TTTCATTTCATTTTTCA
2894466 TTTCATTTCATTTTTCA
1 TTTCATTTCATTTTTCA
2894483 TTTCATTT
1 TTTCATTT
2894491 TTCATTTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.17
17 20 0.83
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTCATTTCATTTTTCA
Found at i:2894515 original size:12 final size:12
Alignment explanation
Indices: 2894466--2894573 Score: 63
Period size: 12 Copynumber: 9.2 Consensus size: 12
2894456 TCATTTTTCA
2894466 TTTCA-TTTCATT
1 TTTCATTTTC-TT
2894478 TTTCA-TTTCATT
1 TTTCATTTTC-TT
2894490 TTTCA-TTTCATT
1 TTTCATTTTC-TT
2894502 TTTCATTTTC-T
1 TTTCATTTTCTT
2894513 TTTCATCTTT-TCT
1 TTTCAT-TTTCT-T
2894526 TTTCATCTTTTCTT
1 TTTCA--TTTTCTT
2894540 TTT-ATTTT-TT
1 TTTCATTTTCTT
*
2894550 CTT-ATTTT-TT
1 TTTCATTTTCTT
* *
2894560 TCTCTTTTTCTT
1 TTTCATTTTCTT
2894572 TT
1 TT
2894574 CTCGTTTTTT
Statistics
Matches: 82, Mismatches: 5, Indels: 18
0.78 0.05 0.17
Matches are distributed among these distances:
10 12 0.15
11 15 0.18
12 35 0.43
13 11 0.13
14 7 0.09
15 2 0.02
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTCATTTTCTT
Found at i:2894523 original size:13 final size:13
Alignment explanation
Indices: 2894507--2894552 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
2894497 TCATTTTTCA
2894507 TTTTCTTTTCATC
1 TTTTCTTTTCATC
2894520 TTTTCTTTTCATC
1 TTTTCTTTTCATC
* *
2894533 TTTTCTTTTTATT
1 TTTTCTTTTCATC
2894546 TTTTCTT
1 TTTTCTT
2894553 ATTTTTTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTCTTTTCATC
Found at i:2894541 original size:18 final size:18
Alignment explanation
Indices: 2894438--2894531 Score: 77
Period size: 18 Copynumber: 4.9 Consensus size: 18
2894428 TGTTTATTTC
*
2894438 TCATATTTTCTTTTTC-TT
1 TCAT-TTTTCATTTTCATT
2894456 TCATTTTTCA-TTTCATT
1 TCATTTTTCATTTTCATT
2894473 TCATTTTTCATTTCATTTTTCATT
1 TCA---TT--TTTCA-TTTTCATT
*
2894497 TCATTTTTCATTTTCTTT
1 TCATTTTTCATTTTCATT
2894515 TCATCTTTTC-TTTTCAT
1 TCAT-TTTTCATTTTCAT
2894532 CTTTTCTTTT
Statistics
Matches: 64, Mismatches: 3, Indels: 18
0.75 0.04 0.21
Matches are distributed among these distances:
16 4 0.06
17 10 0.16
18 21 0.33
19 10 0.16
20 2 0.03
21 2 0.03
22 5 0.08
24 10 0.16
ACGTcount: A:0.14, C:0.18, G:0.00, T:0.68
Consensus pattern (18 bp):
TCATTTTTCATTTTCATT
Found at i:2894560 original size:13 final size:12
Alignment explanation
Indices: 2894533--2894595 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 12
2894523 TCTTTTCATC
2894533 TTTTCTTTTTATT
1 TTTTCTTTTT-TT
2894546 TTTTCTTATTTTT
1 TTTTCTT-TTTTT
*
2894559 TTCTCTTTTTCTT
1 TTTTCTTTTT-TT
*
2894572 TTCTCGTTTTTTT
1 TTTTC-TTTTTTT
2894585 TCTTTCTTTTT
1 T-TTTCTTTTT
2894596 CTTTCTTATG
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
12 3 0.07
13 30 0.68
14 11 0.25
ACGTcount: A:0.03, C:0.14, G:0.02, T:0.81
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:2894561 original size:37 final size:34
Alignment explanation
Indices: 2894520--2894599 Score: 88
Period size: 37 Copynumber: 2.2 Consensus size: 34
2894510 TCTTTTCATC
** *
2894520 TTTTCTTTTCATCTTTTCTTTTTATTTTTTCTTATTT
1 TTTTCTTTT-ATCTTTTCTCGTT-TTTTTTCTT-TCT
*
2894557 TTTTCTCTTTTTCTTTTCTCGTTTTTTTTCTTTCT
1 TTTTCT-TTTATCTTTTCTCGTTTTTTTTCTTTCT
2894592 TTTTCTTT
1 TTTTCTTT
2894600 CTTATGAACT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
34 2 0.05
35 8 0.21
36 9 0.24
37 16 0.42
38 3 0.08
ACGTcount: A:0.04, C:0.16, G:0.01, T:0.79
Consensus pattern (34 bp):
TTTTCTTTTATCTTTTCTCGTTTTTTTTCTTTCT
Found at i:2894565 original size:26 final size:25
Alignment explanation
Indices: 2894536--2894604 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 25
2894526 TTTCATCTTT
2894536 TCTTTTTATTTTTTCTTATTTTTTTC
1 TCTTTTT-TTTTTTCTTATTTTTTTC
* *
2894562 TCTTTTTCTTTTCTCGT-TTTTTTTC
1 TCTTTTT-TTTTTTCTTATTTTTTTC
*
2894587 T-TTCTTTTTCTTTCTTAT
1 TCTT-TTTTTTTTTCTTAT
2894605 GAACTTGGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
24 8 0.23
25 13 0.37
26 14 0.40
ACGTcount: A:0.04, C:0.16, G:0.01, T:0.78
Consensus pattern (25 bp):
TCTTTTTTTTTTTCTTATTTTTTTC
Found at i:2894584 original size:27 final size:26
Alignment explanation
Indices: 2894534--2894599 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
2894524 CTTTTCATCT
* *
2894534 TTTCTTTTTATTTTTTCTTATTTTT-
1 TTTCTTTTTCTTTTCTCTTATTTTTC
*
2894559 TTCTCTTTTTCTTTTCTCGTTTTTTTTC
1 TT-TCTTTTTCTTTTCTC-TTATTTTTC
2894587 TTTCTTTTTCTTT
1 TTTCTTTTTCTTT
2894600 CTTATGAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 2 0.06
26 13 0.37
27 18 0.51
28 2 0.06
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.80
Consensus pattern (26 bp):
TTTCTTTTTCTTTTCTCTTATTTTTC
Found at i:2899577 original size:13 final size:14
Alignment explanation
Indices: 2899543--2899579 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
2899533 GATAAATAGG
2899543 ATAAATAAA-GGAA
1 ATAAATAAAGGGAA
2899556 ATTAAATAAAGGGAA
1 A-TAAATAAAGGGAA
2899571 A-AAATAAAG
1 ATAAATAAAG
2899580 CATATACTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.41
14 8 0.36
15 5 0.23
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (14 bp):
ATAAATAAAGGGAA
Found at i:2899649 original size:22 final size:23
Alignment explanation
Indices: 2899616--2899683 Score: 68
Period size: 25 Copynumber: 2.9 Consensus size: 23
2899606 GTGAATAGTA
*
2899616 ATAAAAGA-AAAGAAAAGCAAAC-
1 ATAAAA-ACAAAGAAAAGAAAACT
*
2899638 ATAAAAACAAAGAAATGAAAACTAT
1 ATAAAAACAAAGAAAAGAAAAC--T
*
2899663 ATAAAAACAAAGAAAATAAAA
1 ATAAAAACAAAGAAAAGAAAA
2899684 ATAAATAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
21 1 0.03
22 18 0.47
25 19 0.50
ACGTcount: A:0.74, C:0.07, G:0.09, T:0.10
Consensus pattern (23 bp):
ATAAAAACAAAGAAAAGAAAACT
Found at i:2899683 original size:25 final size:25
Alignment explanation
Indices: 2899638--2899692 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
2899628 AAAAGCAAAC
* *
2899638 ATAAAAACAAAGAAATGAAAACTAT
1 ATAAAAACAAAGAAATGAAAAATAA
2899663 ATAAAAACAAAGAAAAT-AAAAATAA
1 ATAAAAACAAAG-AAATGAAAAATAA
2899688 ATAAA
1 ATAAA
2899693 CTAAATGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 23 0.85
26 4 0.15
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (25 bp):
ATAAAAACAAAGAAATGAAAAATAA
Found at i:2904527 original size:17 final size:17
Alignment explanation
Indices: 2904502--2904549 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
2904492 TGTAATATTA
*
2904502 TGTTGGTTGGTTTAGTT
1 TGTTTGTTGGTTTAGTT
*
2904519 TGTTTGTT-GTCTTATTT
1 TGTTTGTTGGT-TTAGTT
2904536 TGTATTGTTGGTTT
1 TGT-TTGTTGGTTT
2904550 TTTACTCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 2 0.08
17 15 0.58
18 7 0.27
19 2 0.08
ACGTcount: A:0.06, C:0.02, G:0.27, T:0.65
Consensus pattern (17 bp):
TGTTTGTTGGTTTAGTT
Found at i:2905818 original size:43 final size:43
Alignment explanation
Indices: 2905747--2905828 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
2905737 ATAAATATCA
* *
2905747 AACCTATTACGGTGTTTGTGCCCAAAAACACCGCTATATGGCG
1 AACCTATTACGGTGTTTGTACACAAAAACACCGCTATATGGCG
* * * *
2905790 AACCTATTGCGGTGTTTGTATACTAAAACGCCGCTATAT
1 AACCTATTACGGTGTTTGTACACAAAAACACCGCTATAT
2905829 AACATGAACT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (43 bp):
AACCTATTACGGTGTTTGTACACAAAAACACCGCTATATGGCG
Found at i:2910044 original size:3 final size:3
Alignment explanation
Indices: 2910025--2910077 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
2910015 GTAACCTGAA
* *
2910025 AAT AA- AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT TAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
2910072 TAT AAT
1 AAT AAT
2910078 TATTATTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:2910078 original size:6 final size:6
Alignment explanation
Indices: 2910038--2910116 Score: 68
Period size: 6 Copynumber: 13.2 Consensus size: 6
2910028 AAAATAATAG
* * * * *
2910038 TAATAA TAATAA TAATAA TAATAA TAATTA TAATTA TAATTA TTATTA
1 TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA
* * * * *
2910086 TTATTA TTATTA TTATTA TTATTA TTATTA T
1 TAATTA TAATTA TAATTA TAATTA TAATTA T
2910117 TATTGGTAAA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TAATTA
Found at i:2910082 original size:3 final size:3
Alignment explanation
Indices: 2910064--2910120 Score: 96
Period size: 3 Copynumber: 19.0 Consensus size: 3
2910054 AATAATAATA
* *
2910064 ATT ATA ATT ATA ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2910112 ATT ATT ATT
1 ATT ATT ATT
2910121 GGTAAAAATG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:2914060 original size:43 final size:43
Alignment explanation
Indices: 2913914--2914251 Score: 496
Period size: 43 Copynumber: 7.8 Consensus size: 43
2913904 ATCGTTACAG
*
2913914 CAGGCTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCC
* **
2913958 CAGGTCCCTTTTTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCC
* * *
2914002 CAGATCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAATTTCCC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* *
2914045 CAAGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTATAGTTTCCC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
*
2914088 CAGGTTCCTTTACTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* *
2914131 CAGGTTCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCT
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
*
2914174 CAGGTTCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* * * *
2914217 CAGGCTCTTTTGCTATGTGCAAGGATAAGACCTTA
1 CAGGTTCCTTTGCTGTGTGCAAGGGTAAG-CCTTA
2914252 TCGTTTTTGC
Statistics
Matches: 270, Mismatches: 23, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
43 189 0.70
44 81 0.30
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.33
Consensus pattern (43 bp):
CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
Found at i:2919284 original size:43 final size:43
Alignment explanation
Indices: 2919141--2919418 Score: 389
Period size: 43 Copynumber: 6.4 Consensus size: 43
2919131 TACAGCATGC
*
2919141 TCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCATG-
1 TCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCCCAGGT
*
2919184 TCTCTTTGCTGTGTGTAAGGGTAAGCCTTACAGTTTCCCCCAGGT
1 TC-CTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCCCAGGT
* * *
2919229 CCCTTTGCTGTGTGCAAGGGTAAACCTTATAGTTTCCCCAGGT
1 TCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGT
* *
2919272 TCCTTTGTTGTGTGCAAGGGTAAGCCTGACAGTTTCCCCAGGT
1 TCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGT
* *
2919315 TCTTTTGCTGTGTGAAAGGGTAAGCCTTA-AGTTTCCCCAGGT
1 TCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGT
* * *
2919357 TCCTTTACTGTATGCAAGGGTAAGCCTTACAGTTTCCCCAGGC
1 TCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGT
* *
2919400 TCTTTTGCTTTGTGCAAGG
1 TCCTTTGCTGTGTGCAAGG
2919419 ATAATACCTT
Statistics
Matches: 208, Mismatches: 24, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
42 38 0.18
43 100 0.48
44 69 0.33
45 1 0.00
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.34
Consensus pattern (43 bp):
TCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGT
Found at i:2919381 original size:85 final size:86
Alignment explanation
Indices: 2919144--2919418 Score: 392
Period size: 85 Copynumber: 3.2 Consensus size: 86
2919134 AGCATGCTCC
* *
2919144 TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCATG-TCTCTTTGCTGTGTGTAAGGGTAA
1 TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCCCAGGTTC-CTTTGCTGTGTGCAAGGGTAA
* *
2919208 GCCTTACAGTTTCCCCCAGGTCCC
64 GCCTTACAGTTT-CCCCAGGTTCT
* * *
2919232 TTTGCTGTGTGCAAGGGTAAACCTTATAGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGC
1 TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGC
*
2919297 CTGACAGTTTCCCCAGGTTCT
66 CTTACAGTTTCCCCAGGTTCT
* * *
2919318 TTTGCTGTGTGAAAGGGTAAGCCTTA-AGTTTCCCCAGGTTCCTTTACTGTATGCAAGGGTAAGC
1 TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGC
*
2919382 CTTACAGTTTCCCCAGGCTCT
66 CTTACAGTTTCCCCAGGTTCT
*
2919403 TTTGCTTTGTGCAAGG
1 TTTGCTGTGTGCAAGG
2919419 ATAATACCTT
Statistics
Matches: 169, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
85 68 0.40
86 33 0.20
87 36 0.21
88 32 0.19
ACGTcount: A:0.17, C:0.24, G:0.25, T:0.34
Consensus pattern (86 bp):
TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGC
CTTACAGTTTCCCCAGGTTCT
Found at i:2923883 original size:21 final size:22
Alignment explanation
Indices: 2923853--2923934 Score: 78
Period size: 23 Copynumber: 3.7 Consensus size: 22
2923843 AGAACCCGTG
*
2923853 GGGGGTATCGATTCCCCT-AAA
1 GGGGGAATCGATTCCCCTCAAA
*
2923874 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCC-TCAAA
* *
2923897 GGGAGAATCGGTTCCCCTGC-AA
1 GGGGGAATCGATTCCCCT-CAAA
* *
2923919 GGAGGTATCGATTCCC
1 GGGGGAATCGATTCCC
2923935 TCTGCACCAA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
21 15 0.29
22 16 0.31
23 20 0.39
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.22
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTCAAA
Found at i:2923897 original size:23 final size:22
Alignment explanation
Indices: 2923853--2923914 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
2923843 AGAACCCGTG
* *
2923853 GGGGGTATCGATTCCCC-TAAA
1 GGGGGAATCGGTTCCCCTTAAA
2923874 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTT-AAA
*
2923897 GGGAGAATCGGTTCCCCT
1 GGGGGAATCGGTTCCCCT
2923915 GCAAGGAGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 15 0.42
22 1 0.03
23 20 0.56
ACGTcount: A:0.21, C:0.26, G:0.31, T:0.23
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCCTTAAA
Found at i:2927233 original size:22 final size:21
Alignment explanation
Indices: 2927191--2927230 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2927181 GAGTTTATTT
*
2927191 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2927212 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2927231 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:2930004 original size:16 final size:15
Alignment explanation
Indices: 2929983--2930093 Score: 57
Period size: 16 Copynumber: 7.0 Consensus size: 15
2929973 AATTTAATCC
2929983 TATTATTATTATTTTT
1 TATTATT-TTATTTTT
2929999 TATTATTTT-TTTATT
1 TATTATTTTATTT-TT
*
2930014 TGTTCATTTTATTTTT
1 TATT-ATTTTATTTTT
*
2930030 ATTTTATTTCCTATTTTTT
1 -TATTATTT--TA-TTTTT
* * *
2930049 TAATATTTT-GTTTA
1 TATTATTTTATTTTT
* *
2930063 TACGTTATTATATATTT
1 TA--TTATTTTATTTTT
2930080 T-TTATTTTATTTTT
1 TATTATTTTATTTTT
2930094 ATTTTACATC
Statistics
Matches: 72, Mismatches: 13, Indels: 22
0.67 0.12 0.21
Matches are distributed among these distances:
14 19 0.26
15 7 0.10
16 24 0.33
17 9 0.12
18 8 0.11
19 5 0.07
ACGTcount: A:0.21, C:0.04, G:0.03, T:0.73
Consensus pattern (15 bp):
TATTATTTTATTTTT
Found at i:2930035 original size:11 final size:11
Alignment explanation
Indices: 2929983--2930099 Score: 57
Period size: 11 Copynumber: 10.6 Consensus size: 11
2929973 AATTTAATCC
*
2929983 TATTATTATTAT
1 TATT-TTATTTT
2929995 T-TTTTATTATT
1 TATTTTATT-TT
2930006 T-TTTTATTTGT
1 TATTTTATTT-T
2930017 TCATTTTATTTT
1 T-ATTTTATTTT
*
2930029 TATTTTATTTCC
1 TATTTTATTT-T
*
2930041 TATTTT-TTTAA
1 TATTTTATTT-T
* *
2930052 TATTTTGTTTA
1 TATTTTATTTT
** *
2930063 TACGTTA-TTA
1 TATTTTATTTT
*
2930073 TA-TAT-TTTT
1 TATTTTATTTT
2930082 TATTTTATTTT
1 TATTTTATTTT
2930093 TATTTTA
1 TATTTTA
2930100 CATCTTATAT
Statistics
Matches: 85, Mismatches: 11, Indels: 19
0.74 0.10 0.17
Matches are distributed among these distances:
9 5 0.06
10 13 0.15
11 47 0.55
12 12 0.14
13 8 0.09
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.73
Consensus pattern (11 bp):
TATTTTATTTT
Found at i:2930047 original size:24 final size:25
Alignment explanation
Indices: 2929995--2930047 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
2929985 TTATTATTAT
**
2929995 TTTTTATTATTTTTTTATTTGTTCA
1 TTTTTATTATTTTTTTATTTCCTCA
2930020 -TTTTATT-TTTATTTTATTTCCT-A
1 TTTTTATTATTT-TTTTATTTCCTCA
2930043 TTTTT
1 TTTTT
2930048 TTAATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (25 bp):
TTTTTATTATTTTTTTATTTCCTCA
Found at i:2930148 original size:3 final size:3
Alignment explanation
Indices: 2930134--2930177 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
2930124 TTTCTTTCTT
* * *
2930134 TTA TTT TTA TTA TTA CTA TTA TTA TTA TTA TTA CTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2930178 TTCTTTTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2930175 original size:18 final size:18
Alignment explanation
Indices: 2930134--2930177 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
2930124 TTTCTTTCTT
*
2930134 TTATTTTTATTATTACTA
1 TTATTATTATTATTACTA
2930152 TTATTATTATTATTACTA
1 TTATTATTATTATTACTA
2930170 TTATTATT
1 TTATTATT
2930178 TTCTTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (18 bp):
TTATTATTATTATTACTA
Found at i:2930200 original size:2 final size:2
Alignment explanation
Indices: 2930193--2930219 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2930183 TTATTCTACT
2930193 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2930220 TGTTTTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2930784 original size:13 final size:13
Alignment explanation
Indices: 2930761--2930802 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
2930751 GTTTCCCTTA
2930761 TATTATTTTATTTT
1 TATT-TTTTATTTT
*
2930775 TATTTTTTATTAT
1 TATTTTTTATTTT
*
2930788 TATTTTTTCTTTT
1 TATTTTTTATTTT
2930801 TA
1 TA
2930803 CGAATTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 21 0.84
14 4 0.16
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:2930787 original size:21 final size:20
Alignment explanation
Indices: 2930761--2930801 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2930751 GTTTCCCTTA
*
2930761 TATTATTTTATTTTTATTTTT
1 TATTATTAT-TTTTTATTTTT
*
2930782 TATTATTATTTTTTCTTTTT
1 TATTATTATTTTTTATTTTT
2930802 ACGAATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (20 bp):
TATTATTATTTTTTATTTTT
Found at i:2931503 original size:10 final size:11
Alignment explanation
Indices: 2931454--2931696 Score: 81
Period size: 12 Copynumber: 21.1 Consensus size: 11
2931444 ATTATAAGTC
2931454 AATTATAAAAT
1 AATTATAAAAT
*
2931465 ATTTATAAAAAT
1 AATTAT-AAAAT
* *
2931477 AACTAAAAAAT
1 AATTATAAAAT
2931488 CAATTATAAAAT
1 -AATTATAAAAT
2931500 -ATTATAAAAAT
1 AATTAT-AAAAT
**
2931511 ATATTTATATTAT
1 A-A-TTATAAAAT
* *
2931524 CAAGTATACAAT
1 -AATTATAAAAT
*
2931536 AAATTAT-AATT
1 -AATTATAAAAT
* *
2931547 AA-AATATAAT
1 AATTATAAAAT
2931557 AATTAT-AAAT
1 AATTATAAAAT
**
2931567 --TTATAATTT
1 AATTATAAAAT
2931576 AAATTATAAAA-
1 -AATTATAAAAT
*
2931587 GATTATAAAAT
1 AATTATAAAAT
**
2931598 AAAATTTATTTAAT
1 --AA-TTATAAAAT
*
2931612 AATTA-ATAAT
1 AATTATAAAAT
2931622 AATTTATAAAAAT
1 AA-TTAT-AAAAT
*
2931635 ATTTATAAAAT
1 AATTATAAAAT
2931646 CAATTATAAAAT
1 -AATTATAAAAT
*
2931658 AAATCAATAAAAGT
1 -AAT-TATAAAA-T
2931672 AATTTATAAAATT
1 AA-TTATAAAA-T
2931685 ATATT-TAAAAT
1 A-ATTATAAAAT
2931696 A
1 A
2931697 TCAACTATTA
Statistics
Matches: 171, Mismatches: 36, Indels: 50
0.67 0.14 0.19
Matches are distributed among these distances:
8 4 0.02
9 4 0.02
10 29 0.17
11 32 0.19
12 58 0.34
13 29 0.17
14 15 0.09
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (11 bp):
AATTATAAAAT
Found at i:2931573 original size:28 final size:29
Alignment explanation
Indices: 2931534--2931605 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
2931524 CAAGTATACA
*
2931534 ATAAATTATAA-TTAAAATATAATA-ATT
1 ATAAATTATAATTTAAAATATAAAAGATT
*
2931561 ATAAATTTATAATTTAAATTATAAAAGATT
1 ATAAA-TTATAATTTAAAATATAAAAGATT
* *
2931591 ATAAAATAAAATTTA
1 ATAAATTATAATTTA
2931606 TTTAATAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
27 5 0.13
28 6 0.16
29 19 0.50
30 8 0.21
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (29 bp):
ATAAATTATAATTTAAAATATAAAAGATT
Found at i:2931650 original size:25 final size:26
Alignment explanation
Indices: 2931622--2931700 Score: 76
Period size: 25 Copynumber: 3.1 Consensus size: 26
2931612 AATTAATAAT
2931622 AATTTATAAAA-ATATTTATAAAATC
1 AATTTATAAAATATATTTATAAAATC
* **
2931647 AA-TTATAAAATAAATCAATAAAAGT-
1 AATTTATAAAATATATTTATAAAA-TC
2931672 AATTTATAAAATTATATTTA-AAATATC
1 AATTTATAAAA-TATATTTATAAA-ATC
2931699 AA
1 AA
2931701 CTATTAAATC
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
24 8 0.19
25 13 0.31
26 13 0.31
27 8 0.19
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (26 bp):
AATTTATAAAATATATTTATAAAATC
Found at i:2931918 original size:26 final size:26
Alignment explanation
Indices: 2931889--2931946 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
2931879 TTGTCATGAG
*
2931889 AATATCAAATCAGTTTTTTATATTAA
1 AATATCAAATCAATTTTTTATATTAA
2931915 AATATCAAATCAATTTTTTATATTAA
1 AATATCAAATCAATTTTTTATATTAA
2931941 AATATC
1 AATATC
2931947 CAGAACCCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.45
Consensus pattern (26 bp):
AATATCAAATCAATTTTTTATATTAA
Found at i:2935597 original size:32 final size:30
Alignment explanation
Indices: 2935542--2935602 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
2935532 TTTTTGAAGT
*
2935542 TTTTTTGTCAAAATAGATATTAAAAGTATTA
1 TTTTTTATCAAAATAGATATT-AAAGTATTA
2935573 TTTTTTATCAAAATATG-TACTTAAAGTATT
1 TTTTTTATCAAAATA-GATA-TTAAAGTATT
2935603 CAAATTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 24 0.89
32 3 0.11
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (30 bp):
TTTTTTATCAAAATAGATATTAAAGTATTA
Found at i:2937217 original size:34 final size:35
Alignment explanation
Indices: 2937179--2937261 Score: 114
Period size: 34 Copynumber: 2.4 Consensus size: 35
2937169 TTACGGAAGA
* * * *
2937179 CAATTCACGTTTTATGTGCATTTTAG-CCATAGCT
1 CAATTCACGTTTTATGTGCACTTAAGTCCAAAGCC
*
2937213 CAATTCACGTTTTATGTGCACTTAAGTCTAAAGCC
1 CAATTCACGTTTTATGTGCACTTAAGTCCAAAGCC
2937248 CAATTCACGTTTTA
1 CAATTCACGTTTTA
2937262 ATTTGATGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 24 0.56
35 19 0.44
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.39
Consensus pattern (35 bp):
CAATTCACGTTTTATGTGCACTTAAGTCCAAAGCC
Found at i:2938423 original size:16 final size:17
Alignment explanation
Indices: 2938399--2938434 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
2938389 ATTTTAAAAT
2938399 TTAATTTTTTTTATTAA
1 TTAATTTTTTTTATTAA
2938416 TTAA-TTTTTTTATTAA
1 TTAATTTTTTTTATTAA
2938432 TTA
1 TTA
2938435 TGTTTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTAATTTTTTTTATTAA
Found at i:2939753 original size:41 final size:41
Alignment explanation
Indices: 2939708--2939939 Score: 123
Period size: 41 Copynumber: 5.7 Consensus size: 41
2939698 AATTTGGCGT
* *
2939708 TGCGATTTTCCCAATTCGCAATGTGAATAAGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* *** * * *
2939749 TGCGAATTTGGAAAATCGCAATGCG-AT-ACTGACTATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGT-A-AATCGCAA
* * * * * **
2939790 TGCAATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCCTAATTCGCAATGCGA-ATAAGTAAATCGCAA
* *
2939831 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* *** * * * *
2939872 CGCGA-TTAAGTAAATCGCAATGCGAATTAGGAAAATCGTAA
1 TGCGATTTTCCTAATTCGCAATGCGAA-TAAGTAAATCGCAA
* * * *
2939913 TGCGA-ATACGTAAATCGCAATGCGAAT
1 TGCGATTTTCCTAATTCGCAATGCGAAT
2939940 CTTACTATCG
Statistics
Matches: 144, Mismatches: 40, Indels: 15
0.72 0.20 0.08
Matches are distributed among these distances:
39 2 0.01
40 26 0.18
41 114 0.79
43 1 0.01
44 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (41 bp):
TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
Found at i:2939818 original size:21 final size:21
Alignment explanation
Indices: 2939784--2939856 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
2939774 ATACTGACTA
* *
2939784 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
2939805 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
2939825 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
2939846 TCGCAATGCGA
1 TCGCAATGCGA
2939857 ATACGTAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:2939871 original size:20 final size:20
Alignment explanation
Indices: 2939846--2939957 Score: 127
Period size: 20 Copynumber: 5.5 Consensus size: 20
2939836 TTTTCATAAT
2939846 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
2939866 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
2939886 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
2939907 TCGTAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
2939927 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
2939947 TCGCAATGCGA
1 TCGCAATGCGA
2939958 TTTACATAGC
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 3 0.04
20 57 0.74
21 17 0.22
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:2940532 original size:19 final size:19
Alignment explanation
Indices: 2940508--2940552 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
2940498 GCAACGAGAG
*
2940508 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
2940527 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
2940546 AATCGCA
1 AATCGCA
2940553 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:2940636 original size:53 final size:53
Alignment explanation
Indices: 2940548--2940665 Score: 184
Period size: 53 Copynumber: 2.2 Consensus size: 53
2940538 GAAACCAAAA
* **
2940548 TCGCATTGCGA-TTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
*
2940600 TCGCGTTGTGATTTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
*
2940653 TCGTGTTGCGATT
1 TCGCGTTGCGATT
2940666 CTCTCGTTGC
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
52 9 0.15
53 50 0.85
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.46
Consensus pattern (53 bp):
TCGCGTTGCGATTTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
Found at i:2940642 original size:14 final size:14
Alignment explanation
Indices: 2940623--2940678 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
2940613 TTTCATTTCG
2940623 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2940637 CGTTGCGATAGTCATTT
1 CGTTGCGAT--TC-TCT
2940654 CGTGTTGCGATTCTCT
1 C--GTTGCGATTCTCT
2940670 CGTTGCGAT
1 CGTTGCGAT
2940679 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 17 0.49
16 5 0.14
17 5 0.14
19 8 0.23
ACGTcount: A:0.11, C:0.23, G:0.25, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2940652 original size:33 final size:33
Alignment explanation
Indices: 2940615--2940702 Score: 158
Period size: 33 Copynumber: 2.6 Consensus size: 33
2940605 TTGTGATTTT
2940615 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
*
2940648 TCATTTCGTGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
2940681 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
2940703 ATTATCTCGT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
33 38 0.73
34 14 0.27
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.41
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
Found at i:2940704 original size:20 final size:19
Alignment explanation
Indices: 2940548--2940727 Score: 120
Period size: 20 Copynumber: 10.1 Consensus size: 19
2940538 GAAACCAAAA
* *
2940548 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTCTCATT
2940567 TCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTCTCATT
*
2940583 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTCTCATT
* *
2940600 TCGCGTTGTGATTTTTCATT
1 TCGCGTTGCGA-TTCTCATT
2940620 TCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTCTCATT
**
2940636 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTCTCATT
*
2940653 TCGTGTTGCGATTCTC---
1 TCGCGTTGCGATTCTCATT
**
2940669 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTCTCATT
2940686 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTCTCATT
* *
2940706 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTCTCATT
2940726 TC
1 TC
2940728 AACCAAAAGA
Statistics
Matches: 125, Mismatches: 18, Indels: 36
0.70 0.10 0.20
Matches are distributed among these distances:
14 33 0.26
16 3 0.02
17 3 0.02
19 37 0.30
20 48 0.38
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTCTCATT
Found at i:2940705 original size:86 final size:87
Alignment explanation
Indices: 2940553--2940719 Score: 239
Period size: 86 Copynumber: 1.9 Consensus size: 87
2940543 CAAAATCGCA
** ** * *
2940553 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATTTCGCGTTGTGATTTTTCA
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCGCGTTGCGATTTCTCA
2940618 TT-TCGCGTTGCGATTCTCTCG
66 TTATCGCGTTGCGATTCTCTCG
*
2940639 TTGCGATAGTCATTTCGTGTTGCGATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGA-TTCTC
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTT-CGCGTTGCGATTTCTC
*
2940703 ATTATCTCGTTGCGATT
65 ATTATCGCGTTGCGATT
2940720 TTCATTTCAA
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
86 50 0.70
87 21 0.30
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.45
Consensus pattern (87 bp):
TTGCGATAGTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCGCGTTGCGATTTCTCA
TTATCGCGTTGCGATTCTCTCG
Found at i:2942896 original size:21 final size:21
Alignment explanation
Indices: 2942872--2942938 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2942862 TCATTCCTCG
2942872 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
2942893 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
2942914 AGAAGT-CCCTCCCACCATTCA
1 AG-AGTCCCCTCCCACCGTTCA
2942935 AGAG
1 AGAG
2942939 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:2942896 original size:42 final size:41
Alignment explanation
Indices: 2942825--2942938 Score: 104
Period size: 42 Copynumber: 2.7 Consensus size: 41
2942815 GCCTGCCATC
* * * * * *
2942825 CCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATT
1 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCA-T
*
2942867 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTGTCAT
1 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCAT
* * *
2942908 CGTTGAAGAAGT-CCCTCCCACCATTCAAGAG
1 CCTCG-AG-AGTCCCCTCCCACCGTTCAAGAG
2942939 CCCGATTCAC
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.07
42 53 0.88
43 3 0.05
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.22
Consensus pattern (41 bp):
CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCAT
Found at i:2944308 original size:14 final size:14
Alignment explanation
Indices: 2944289--2944324 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
2944279 ATTGTTTAAT
2944289 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
2944303 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
2944317 TGATTTGT
1 TGATTTGT
2944325 TTAATTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.42
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:2944478 original size:33 final size:33
Alignment explanation
Indices: 2944431--2944543 Score: 181
Period size: 33 Copynumber: 3.4 Consensus size: 33
2944421 AAAAAGTACT
* *
2944431 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAAA
*
2944464 ATCGCAACGTGAAATGAAAATCGCAACGAGAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAAA
* *
2944497 ATCGTAACGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAAA
2944530 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
2944544 CTAAATTCGC
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 73 1.00
ACGTcount: A:0.47, C:0.20, G:0.21, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAAA
Found at i:2944498 original size:14 final size:14
Alignment explanation
Indices: 2944446--2944543 Score: 70
Period size: 14 Copynumber: 6.3 Consensus size: 14
2944436 AATGCGAAAT
2944446 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
2944460 GAGAATCGCAACGTGAAA
1 GAAAATCGCAAC--G--A
2944478 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
*
2944493 GAAAATCGTAACGCGAAA
1 GAAAATCGCAA--CG--A
2944511 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
2944526 CAAAATCGCAACGC
1 GAAAATCGCAACGA
2944540 GAAA
1 GAAA
2944544 CTAAATTCGC
Statistics
Matches: 67, Mismatches: 7, Indels: 20
0.71 0.07 0.21
Matches are distributed among these distances:
14 36 0.54
15 2 0.03
16 3 0.04
17 3 0.04
18 2 0.03
19 21 0.31
ACGTcount: A:0.48, C:0.20, G:0.21, T:0.10
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:2944524 original size:19 final size:19
Alignment explanation
Indices: 2944431--2944524 Score: 82
Period size: 19 Copynumber: 5.5 Consensus size: 19
2944421 AAAAAGTACT
*
2944431 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
2944450 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
2944464 ATCGCAACGTGAAATGAAA
1 ATCGCAACGCGAAATGAAA
2944483 ATCGCAA--CG--A-GAAA
1 ATCGCAACGCGAAATGAAA
*
2944497 ATCGTAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
2944516 ATCGCAACG
1 ATCGCAACG
2944525 ACAAAATCGC
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 20 0.34
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 29 0.49
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:2944571 original size:19 final size:19
Alignment explanation
Indices: 2944549--2944699 Score: 107
Period size: 19 Copynumber: 8.7 Consensus size: 19
2944539 CGAAACTAAA
*
2944549 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
2944568 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
2944584 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
2944601 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
*
2944615 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
2944634 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
2944650 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
** *
2944667 TTCGCATTGCGATAGTAAT
1 TTCGCATTGCGATTTTCAT
2944686 TTCCGCATTGCGAT
1 TT-CGCATTGCGAT
2944700 AGACATTAAG
Statistics
Matches: 102, Mismatches: 14, Indels: 31
0.69 0.10 0.21
Matches are distributed among these distances:
14 24 0.24
16 13 0.13
17 13 0.13
19 41 0.40
20 11 0.11
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:2944595 original size:33 final size:32
Alignment explanation
Indices: 2944553--2944679 Score: 202
Period size: 33 Copynumber: 3.9 Consensus size: 32
2944543 ACTAAATTCG
2944553 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
*
2944586 CGTTGCGATTTTCATTTCGCATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
2944619 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
2944652 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2944680 AGTAATTTCC
Statistics
Matches: 88, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
31 3 0.03
33 82 0.93
35 3 0.03
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:2944642 original size:66 final size:66
Alignment explanation
Indices: 2944546--2944678 Score: 257
Period size: 66 Copynumber: 2.0 Consensus size: 66
2944536 ACGCGAAACT
2944546 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
2944611 G
66 G
*
2944612 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
2944677 G
66 G
2944678 A
1 A
2944679 TAGTAATTTC
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:2946987 original size:12 final size:12
Alignment explanation
Indices: 2946970--2946994 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2946960 TCTTCGGGGA
2946970 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2946982 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2946994 C
1 C
2946995 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2948081 original size:20 final size:20
Alignment explanation
Indices: 2948056--2948112 Score: 114
Period size: 20 Copynumber: 2.9 Consensus size: 20
2948046 TAATACAAAA
2948056 TCGCAACGAGATTCTGACTT
1 TCGCAACGAGATTCTGACTT
2948076 TCGCAACGAGATTCTGACTT
1 TCGCAACGAGATTCTGACTT
2948096 TCGCAACGAGATTCTGA
1 TCGCAACGAGATTCTGA
2948113 AAATCACAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAACGAGATTCTGACTT
Found at i:2948431 original size:20 final size:20
Alignment explanation
Indices: 2948335--2948423 Score: 108
Period size: 20 Copynumber: 4.4 Consensus size: 20
2948325 CAACGGGGAA
2948335 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
2948355 ATCGCAACGCGAAAAATGGCT
1 ATCGCAACGCG-AAAATGGCT
** ***
2948376 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
2948396 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
2948416 ATCGCAAC
1 ATCGCAAC
2948424 TAGAAAATCA
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 5 0.09
20 28 0.50
21 23 0.41
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:2948474 original size:14 final size:14
Alignment explanation
Indices: 2948455--2948508 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
2948445 GAAAATCGCA
2948455 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
2948469 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
2948486 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
2948502 TTGCGAT
1 TTGCGAT
2948509 AGTCAGTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:2948474 original size:33 final size:33
Alignment explanation
Indices: 2948437--2948507 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
2948427 AAAATCACAA
2948437 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
2948470 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
2948503 TGCGA
1 TGCGA
2948508 TAGTCAGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:2950137 original size:41 final size:42
Alignment explanation
Indices: 2950083--2950173 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
2950073 CCTCTTCAAC
* * *
2950083 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTAAGG
* *
2950124 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTAAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTAAGG
*
2950166 AATGACAG
1 GATGACAG
2950174 TTGAGTCGGG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 20 0.48
42 22 0.52
ACGTcount: A:0.23, C:0.15, G:0.40, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTAAGG
Found at i:2950537 original size:20 final size:20
Alignment explanation
Indices: 2950512--2950564 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2950502 GAAGAATAGT
*
2950512 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
*
2950532 TTACTTTCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
* *
2950552 TGACTATCGCAAC
1 TTACTTTCGCAAC
2950565 GCGGAAATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:2950565 original size:20 final size:20
Alignment explanation
Indices: 2950518--2950604 Score: 86
Period size: 20 Copynumber: 4.4 Consensus size: 20
2950508 TAGTTTACTT
* * * *
2950518 TCGCAACACGAAACTTACTT
1 TCGCAACGCGAAAATGACTA
2950538 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* *
2950558 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGACTA
* **
2950578 TCGCAATGCG-AAATGAAAA
1 TCGCAACGCGAAAATGACTA
2950597 TCGCAACG
1 TCGCAACG
2950605 ATAAAATCGC
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
19 13 0.23
20 43 0.77
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:2950652 original size:19 final size:19
Alignment explanation
Indices: 2950630--2950726 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
2950620 GAAACACAAA
2950630 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
2950649 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
* *
2950665 TCG--TTACGGTTTTCATT
1 TCGCATTGCGATTTTCATT
*
2950682 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
2950698 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2950715 TCGCATTGCGAT
1 TCGCATTGCGAT
2950727 AGCCATTTTC
Statistics
Matches: 59, Mismatches: 9, Indels: 20
0.67 0.10 0.23
Matches are distributed among these distances:
14 10 0.17
15 6 0.10
16 8 0.14
17 8 0.14
18 6 0.10
19 21 0.36
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2950683 original size:33 final size:33
Alignment explanation
Indices: 2950638--2950726 Score: 151
Period size: 33 Copynumber: 2.7 Consensus size: 33
2950628 AATCGCATTG
*
2950638 CGATTTTCATTTCGCGTTGCGATTTTGTCGTTA
1 CGATTTTCATTTCGCATTGCGATTTTGTCGTTA
* *
2950671 CGGTTTTCATTTCGCATTGCGATTTTGTCGTTG
1 CGATTTTCATTTCGCATTGCGATTTTGTCGTTA
2950704 CGATTTTCATTTCGCATTGCGAT
1 CGATTTTCATTTCGCATTGCGAT
2950727 AGCCATTTTC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
CGATTTTCATTTCGCATTGCGATTTTGTCGTTA
Found at i:2950733 original size:19 final size:19
Alignment explanation
Indices: 2950711--2950754 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
2950701 TTGCGATTTT
*
2950711 CATTTCGCATTGCGATAGC
1 CATTTCACATTGCGATAGC
* *
2950730 CATTTTCACGTTGCGATAGT
1 CA-TTTCACATTGCGATAGC
2950750 CATTT
1 CATTT
2950755 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (19 bp):
CATTTCACATTGCGATAGC
Found at i:2951329 original size:18 final size:18
Alignment explanation
Indices: 2951306--2951353 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
2951296 CGGGTCGATC
2951306 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
2951324 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
2951342 AGGTGATGGCTC
1 AGGTGATGGCTC
2951354 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:2952698 original size:20 final size:20
Alignment explanation
Indices: 2952673--2952715 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
2952663 AATAGTTTCT
2952673 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
2952693 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
2952713 GAA
1 GAA
2952716 TTTGACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:2953030 original size:22 final size:22
Alignment explanation
Indices: 2953003--2953046 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2952993 GATGGAGATA
2953003 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
2953025 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
2953047 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:2953264 original size:20 final size:20
Alignment explanation
Indices: 2953239--2953303 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
2953229 GTATTATCTC
*
2953239 GTTGCGAAAGTCAGTATTGA
1 GTTGCGAAAGTCAGTATCGA
* *
2953259 GTTGCGAAATTAAGTATCGA
1 GTTGCGAAAGTCAGTATCGA
*
2953279 GTTGCGAAAGTCAGTATCGC
1 GTTGCGAAAGTCAGTATCGA
2953299 GTTGC
1 GTTGC
2953304 AGTTTTGTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (20 bp):
GTTGCGAAAGTCAGTATCGA
Found at i:2953340 original size:21 final size:21
Alignment explanation
Indices: 2953316--2953371 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
2953306 TTTTGTATTA
*
2953316 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
2953337 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
2953358 TCGCATTGCGATTT
1 TCGCATTGCGATTT
2953372 ACTTATTTGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Done.