Multiple sequence alignment - TraesCS1B01G327300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1B01G327300 chr1B 100.000 6426 0 0 1 6426 553552908 553559333 0.000000e+00 11867
1 TraesCS1B01G327300 chr1B 93.651 126 8 0 1 126 14629210 14629085 8.510000e-44 189
2 TraesCS1B01G327300 chr1B 92.800 125 9 0 1 125 615613926 615613802 1.420000e-41 182
3 TraesCS1B01G327300 chr1D 91.380 6183 302 80 125 6228 410738141 410744171 0.000000e+00 8251
4 TraesCS1B01G327300 chr1D 94.949 99 5 0 6328 6426 410744428 410744526 8.630000e-34 156
5 TraesCS1B01G327300 chr1A 90.341 6429 325 125 125 6426 506997697 507003956 0.000000e+00 8159
6 TraesCS1B01G327300 chr7D 88.620 1529 116 28 4356 5874 370516628 370518108 0.000000e+00 1807
7 TraesCS1B01G327300 chr7D 86.533 349 33 6 1026 1371 233910318 233909981 7.870000e-99 372
8 TraesCS1B01G327300 chrUn 88.000 350 28 6 1026 1375 102814447 102814112 1.000000e-107 401
9 TraesCS1B01G327300 chrUn 89.895 287 24 5 856 1138 49108228 49107943 1.320000e-96 364
10 TraesCS1B01G327300 chrUn 90.244 287 14 8 856 1135 238805830 238806109 4.740000e-96 363
11 TraesCS1B01G327300 chrUn 90.000 290 15 8 856 1138 299747759 299747477 4.740000e-96 363
12 TraesCS1B01G327300 chrUn 89.547 287 25 5 856 1138 49052742 49052457 6.130000e-95 359
13 TraesCS1B01G327300 chr3D 87.784 352 25 8 1027 1375 609865941 609866277 4.670000e-106 396
14 TraesCS1B01G327300 chr3B 87.606 355 27 8 1027 1375 820860385 820860042 4.670000e-106 396
15 TraesCS1B01G327300 chr3B 89.547 287 25 5 856 1138 673562882 673562597 6.130000e-95 359
16 TraesCS1B01G327300 chr4B 86.782 348 29 12 1031 1375 8269944 8269611 7.870000e-99 372
17 TraesCS1B01G327300 chr6A 90.459 283 22 3 856 1134 558130485 558130766 1.020000e-97 368
18 TraesCS1B01G327300 chr5D 89.189 296 24 5 845 1135 102639769 102639477 4.740000e-96 363
19 TraesCS1B01G327300 chr7A 87.188 320 30 5 3025 3341 49508998 49509309 2.850000e-93 353
20 TraesCS1B01G327300 chr3A 85.429 350 37 8 1026 1375 108076684 108076349 1.030000e-92 351
21 TraesCS1B01G327300 chr2A 85.552 353 31 10 1026 1375 31354095 31354430 1.030000e-92 351
22 TraesCS1B01G327300 chr7B 93.130 131 8 1 1 131 128868420 128868549 2.360000e-44 191
23 TraesCS1B01G327300 chr7B 92.857 126 9 0 1 126 516907102 516906977 3.960000e-42 183
24 TraesCS1B01G327300 chr7B 92.857 126 9 0 1 126 538205047 538205172 3.960000e-42 183
25 TraesCS1B01G327300 chr7B 89.781 137 14 0 1 137 653231248 653231112 6.620000e-40 176
26 TraesCS1B01G327300 chr7B 89.781 137 14 0 1 137 653236237 653236101 6.620000e-40 176
27 TraesCS1B01G327300 chr7B 89.781 137 14 0 1 137 653285985 653285849 6.620000e-40 176
28 TraesCS1B01G327300 chr6B 92.800 125 9 0 1 125 180658734 180658858 1.420000e-41 182


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G327300 chr1B 553552908 553559333 6425 False 11867.0 11867 100.0000 1 6426 1 chr1B.!!$F1 6425
1 TraesCS1B01G327300 chr1D 410738141 410744526 6385 False 4203.5 8251 93.1645 125 6426 2 chr1D.!!$F1 6301
2 TraesCS1B01G327300 chr1A 506997697 507003956 6259 False 8159.0 8159 90.3410 125 6426 1 chr1A.!!$F1 6301
3 TraesCS1B01G327300 chr7D 370516628 370518108 1480 False 1807.0 1807 88.6200 4356 5874 1 chr7D.!!$F1 1518

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
431 444 0.109827 CGATGCATTGGTCAACGCAA 60.110 50.000 8.48 0.0 42.92 4.85 F
1511 1600 0.267356 CCTTCCCATCTCCTCCTCCT 59.733 60.000 0.00 0.0 0.00 3.69 F
2316 2437 0.312102 GTTTCCTGCAGTGTCTTGGC 59.688 55.000 13.81 0.0 0.00 4.52 F
2896 3017 1.148273 TCCCACTGTGAACACCTGC 59.852 57.895 9.86 0.0 0.00 4.85 F
4236 4373 3.018856 TGGTAATGATGGCAGCAAAGAG 58.981 45.455 10.46 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2279 2400 0.250513 ACACGAAGAGGCTCCCAATC 59.749 55.000 11.71 4.11 0.0 2.67 R
3124 3255 0.316204 AGCAAGTTGACAAGGCATGC 59.684 50.000 9.90 9.90 0.0 4.06 R
3127 3258 2.098614 TGAAAGCAAGTTGACAAGGCA 58.901 42.857 7.16 0.00 0.0 4.75 R
4326 4463 0.393537 AGCTGCTATCAACACTGCCC 60.394 55.000 0.00 0.00 0.0 5.36 R
5496 5639 0.037326 TTAGCGGCGATCCATCCATC 60.037 55.000 12.98 0.00 0.0 3.51 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 8.514330 AACTATGTAAAGTTTGACTTTGACCA 57.486 30.769 14.50 9.45 46.83 4.02
88 89 8.514330 ACTATGTAAAGTTTGACTTTGACCAA 57.486 30.769 14.50 0.00 46.83 3.67
89 90 8.962679 ACTATGTAAAGTTTGACTTTGACCAAA 58.037 29.630 14.50 0.00 46.83 3.28
90 91 9.233232 CTATGTAAAGTTTGACTTTGACCAAAC 57.767 33.333 14.50 5.71 46.83 2.93
91 92 6.391537 TGTAAAGTTTGACTTTGACCAAACC 58.608 36.000 14.50 1.42 46.83 3.27
92 93 5.738619 AAAGTTTGACTTTGACCAAACCT 57.261 34.783 12.56 0.03 45.83 3.50
93 94 6.109156 AAAGTTTGACTTTGACCAAACCTT 57.891 33.333 12.56 5.50 45.83 3.50
94 95 7.234661 AAAGTTTGACTTTGACCAAACCTTA 57.765 32.000 12.56 0.00 45.83 2.69
95 96 7.847096 AAAGTTTGACTTTGACCAAACCTTAT 58.153 30.769 12.56 0.00 45.83 1.73
96 97 8.973182 AAAGTTTGACTTTGACCAAACCTTATA 58.027 29.630 12.56 0.00 45.83 0.98
98 99 8.742554 GTTTGACTTTGACCAAACCTTATATG 57.257 34.615 0.00 0.00 43.62 1.78
99 100 6.509418 TGACTTTGACCAAACCTTATATGC 57.491 37.500 0.00 0.00 0.00 3.14
100 101 6.007076 TGACTTTGACCAAACCTTATATGCA 58.993 36.000 0.00 0.00 0.00 3.96
101 102 6.150976 TGACTTTGACCAAACCTTATATGCAG 59.849 38.462 0.00 0.00 0.00 4.41
102 103 6.245408 ACTTTGACCAAACCTTATATGCAGA 58.755 36.000 0.00 0.00 0.00 4.26
103 104 6.151144 ACTTTGACCAAACCTTATATGCAGAC 59.849 38.462 0.00 0.00 0.00 3.51
104 105 5.435686 TGACCAAACCTTATATGCAGACT 57.564 39.130 0.00 0.00 0.00 3.24
105 106 6.553953 TGACCAAACCTTATATGCAGACTA 57.446 37.500 0.00 0.00 0.00 2.59
106 107 6.953101 TGACCAAACCTTATATGCAGACTAA 58.047 36.000 0.00 0.00 0.00 2.24
107 108 7.398829 TGACCAAACCTTATATGCAGACTAAA 58.601 34.615 0.00 0.00 0.00 1.85
108 109 7.885922 TGACCAAACCTTATATGCAGACTAAAA 59.114 33.333 0.00 0.00 0.00 1.52
109 110 8.644374 ACCAAACCTTATATGCAGACTAAAAA 57.356 30.769 0.00 0.00 0.00 1.94
110 111 8.739972 ACCAAACCTTATATGCAGACTAAAAAG 58.260 33.333 0.00 0.00 0.00 2.27
111 112 8.956426 CCAAACCTTATATGCAGACTAAAAAGA 58.044 33.333 0.00 0.00 0.00 2.52
115 116 8.665685 ACCTTATATGCAGACTAAAAAGAAACG 58.334 33.333 0.00 0.00 0.00 3.60
116 117 8.122952 CCTTATATGCAGACTAAAAAGAAACGG 58.877 37.037 0.00 0.00 0.00 4.44
117 118 8.780846 TTATATGCAGACTAAAAAGAAACGGA 57.219 30.769 0.00 0.00 0.00 4.69
118 119 5.613358 ATGCAGACTAAAAAGAAACGGAG 57.387 39.130 0.00 0.00 0.00 4.63
119 120 4.699637 TGCAGACTAAAAAGAAACGGAGA 58.300 39.130 0.00 0.00 0.00 3.71
120 121 4.750098 TGCAGACTAAAAAGAAACGGAGAG 59.250 41.667 0.00 0.00 0.00 3.20
121 122 4.989168 GCAGACTAAAAAGAAACGGAGAGA 59.011 41.667 0.00 0.00 0.00 3.10
122 123 5.119434 GCAGACTAAAAAGAAACGGAGAGAG 59.881 44.000 0.00 0.00 0.00 3.20
123 124 6.217294 CAGACTAAAAAGAAACGGAGAGAGT 58.783 40.000 0.00 0.00 0.00 3.24
128 129 4.422546 AAAGAAACGGAGAGAGTACGAG 57.577 45.455 0.00 0.00 0.00 4.18
137 138 5.087397 CGGAGAGAGTACGAGTTTAGTTTG 58.913 45.833 0.00 0.00 0.00 2.93
156 157 2.596346 TGCCTTGCAGGAAATCAGAAA 58.404 42.857 0.00 0.00 37.67 2.52
182 183 5.422214 AATATGGCCTCTAAATACGGGAG 57.578 43.478 3.32 0.00 0.00 4.30
201 202 2.408050 AGATCGCGGATAGAAATGCAC 58.592 47.619 6.13 0.00 0.00 4.57
208 209 2.096565 CGGATAGAAATGCACTGCGATG 60.097 50.000 0.00 0.00 0.00 3.84
218 219 0.376152 CACTGCGATGATTGCACTCC 59.624 55.000 2.57 0.00 37.44 3.85
219 220 0.251354 ACTGCGATGATTGCACTCCT 59.749 50.000 2.57 0.00 37.44 3.69
227 228 4.753610 CGATGATTGCACTCCTGTGATAAT 59.246 41.667 1.11 0.57 46.55 1.28
229 230 6.424812 CGATGATTGCACTCCTGTGATAATAA 59.575 38.462 1.11 0.00 46.55 1.40
231 232 9.440773 GATGATTGCACTCCTGTGATAATAATA 57.559 33.333 1.11 0.00 46.55 0.98
233 234 7.384932 TGATTGCACTCCTGTGATAATAATACG 59.615 37.037 1.11 0.00 46.55 3.06
234 235 6.156748 TGCACTCCTGTGATAATAATACGT 57.843 37.500 0.00 0.00 46.55 3.57
235 236 6.578944 TGCACTCCTGTGATAATAATACGTT 58.421 36.000 0.00 0.00 46.55 3.99
237 238 6.924060 GCACTCCTGTGATAATAATACGTTCT 59.076 38.462 0.00 0.00 46.55 3.01
238 239 7.438459 GCACTCCTGTGATAATAATACGTTCTT 59.562 37.037 0.00 0.00 46.55 2.52
239 240 8.969267 CACTCCTGTGATAATAATACGTTCTTC 58.031 37.037 0.00 0.00 46.55 2.87
243 244 7.148950 CCTGTGATAATAATACGTTCTTCGAGC 60.149 40.741 0.00 0.00 42.86 5.03
244 245 6.358822 TGTGATAATAATACGTTCTTCGAGCG 59.641 38.462 0.00 0.00 41.73 5.03
245 246 6.576313 GTGATAATAATACGTTCTTCGAGCGA 59.424 38.462 7.09 0.00 38.48 4.93
246 247 7.112565 GTGATAATAATACGTTCTTCGAGCGAA 59.887 37.037 7.09 5.14 38.48 4.70
248 249 5.807730 ATAATACGTTCTTCGAGCGAATG 57.192 39.130 5.73 13.86 38.48 2.67
249 250 1.265568 TACGTTCTTCGAGCGAATGC 58.734 50.000 14.85 0.00 38.48 3.56
265 266 3.814842 CGAATGCTGGCTGATAATAACCA 59.185 43.478 0.00 0.00 0.00 3.67
266 267 4.275689 CGAATGCTGGCTGATAATAACCAA 59.724 41.667 0.00 0.00 0.00 3.67
278 283 6.005823 TGATAATAACCAATGGCAGGATGAG 58.994 40.000 0.00 0.00 39.69 2.90
281 286 0.700564 ACCAATGGCAGGATGAGTGT 59.299 50.000 0.00 0.00 39.69 3.55
282 287 1.915489 ACCAATGGCAGGATGAGTGTA 59.085 47.619 0.00 0.00 39.69 2.90
283 288 2.511218 ACCAATGGCAGGATGAGTGTAT 59.489 45.455 0.00 0.00 39.69 2.29
284 289 3.144506 CCAATGGCAGGATGAGTGTATC 58.855 50.000 0.00 0.00 39.69 2.24
285 290 3.144506 CAATGGCAGGATGAGTGTATCC 58.855 50.000 0.00 0.00 45.71 2.59
296 301 7.164230 GGATGAGTGTATCCTACTATCCTTG 57.836 44.000 0.00 0.00 42.73 3.61
301 306 7.125792 AGTGTATCCTACTATCCTTGGTTTG 57.874 40.000 0.00 0.00 0.00 2.93
311 316 1.073125 TCCTTGGTTTGATCGAAGGCA 59.927 47.619 0.00 0.00 41.12 4.75
315 320 3.848272 TGGTTTGATCGAAGGCATTTC 57.152 42.857 0.00 0.00 0.00 2.17
342 352 5.763088 TCTCTTCCAATAGATCGACAATCG 58.237 41.667 0.00 0.00 42.10 3.34
355 366 1.062587 GACAATCGCTTGGATGGAACG 59.937 52.381 3.77 0.00 36.64 3.95
364 375 0.461870 TGGATGGAACGAGGCGAATG 60.462 55.000 0.00 0.00 0.00 2.67
376 387 4.684265 CGAATGGTCGTCGATCGT 57.316 55.556 15.94 0.00 42.53 3.73
377 388 3.812097 CGAATGGTCGTCGATCGTA 57.188 52.632 15.94 0.00 42.53 3.43
378 389 1.383120 CGAATGGTCGTCGATCGTAC 58.617 55.000 15.94 11.64 42.53 3.67
379 390 1.751552 GAATGGTCGTCGATCGTACC 58.248 55.000 21.90 21.90 40.80 3.34
381 392 0.749091 ATGGTCGTCGATCGTACCCA 60.749 55.000 24.11 20.47 38.22 4.51
421 434 1.536766 ACAACTCACACCGATGCATTG 59.463 47.619 6.99 6.99 0.00 2.82
431 444 0.109827 CGATGCATTGGTCAACGCAA 60.110 50.000 8.48 0.00 42.92 4.85
433 446 0.387112 ATGCATTGGTCAACGCAACG 60.387 50.000 8.48 0.00 42.92 4.10
502 515 4.840288 CGCGACGCACGTCCCATA 62.840 66.667 21.35 0.00 44.60 2.74
503 516 2.279252 GCGACGCACGTCCCATAT 60.279 61.111 16.42 0.00 44.60 1.78
504 517 2.585869 GCGACGCACGTCCCATATG 61.586 63.158 16.42 0.00 44.60 1.78
505 518 2.585869 CGACGCACGTCCCATATGC 61.586 63.158 16.81 0.00 41.76 3.14
506 519 1.520564 GACGCACGTCCCATATGCA 60.521 57.895 12.04 0.00 39.39 3.96
507 520 1.490693 GACGCACGTCCCATATGCAG 61.491 60.000 12.04 0.00 39.39 4.41
530 560 1.448013 CGGCTCCTCCTCGGAAAAC 60.448 63.158 0.00 0.00 42.53 2.43
545 575 2.788191 AAAACTCCTCCGGCTCAGCG 62.788 60.000 0.00 0.00 0.00 5.18
582 616 4.796231 CCGCCGTTGACCCGAGAG 62.796 72.222 0.00 0.00 0.00 3.20
637 675 2.438795 AGTCGAGCTCGTCCTCCC 60.439 66.667 33.33 15.95 40.80 4.30
688 733 4.084797 CGCAAGTTAAAAATTTGTTCCGGG 60.085 41.667 0.00 0.00 31.49 5.73
689 734 4.319190 GCAAGTTAAAAATTTGTTCCGGGC 60.319 41.667 0.00 0.00 31.49 6.13
690 735 3.997762 AGTTAAAAATTTGTTCCGGGCC 58.002 40.909 0.00 0.00 0.00 5.80
691 736 2.726832 TAAAAATTTGTTCCGGGCCG 57.273 45.000 21.46 21.46 0.00 6.13
692 737 0.601576 AAAAATTTGTTCCGGGCCGC 60.602 50.000 23.20 7.90 0.00 6.53
693 738 2.757155 AAAATTTGTTCCGGGCCGCG 62.757 55.000 23.20 14.51 0.00 6.46
918 977 1.075600 CCTCCCTCCCTCTCACTCC 60.076 68.421 0.00 0.00 0.00 3.85
919 978 1.589399 CCTCCCTCCCTCTCACTCCT 61.589 65.000 0.00 0.00 0.00 3.69
1164 1235 4.021925 GAGCTGGCCAAGGACGGT 62.022 66.667 7.01 0.00 0.00 4.83
1188 1265 1.153667 CGGTGAGAGCTCTGCTTCC 60.154 63.158 23.91 15.66 39.88 3.46
1223 1304 1.591703 GACTCATCTGCCACCGTCA 59.408 57.895 0.00 0.00 0.00 4.35
1329 1410 2.829458 GGGGAGGACGACGAGGAG 60.829 72.222 0.00 0.00 0.00 3.69
1506 1595 2.812619 CGCCCCTTCCCATCTCCTC 61.813 68.421 0.00 0.00 0.00 3.71
1507 1596 2.456443 GCCCCTTCCCATCTCCTCC 61.456 68.421 0.00 0.00 0.00 4.30
1508 1597 1.319799 CCCCTTCCCATCTCCTCCT 59.680 63.158 0.00 0.00 0.00 3.69
1509 1598 0.766288 CCCCTTCCCATCTCCTCCTC 60.766 65.000 0.00 0.00 0.00 3.71
1510 1599 0.766288 CCCTTCCCATCTCCTCCTCC 60.766 65.000 0.00 0.00 0.00 4.30
1511 1600 0.267356 CCTTCCCATCTCCTCCTCCT 59.733 60.000 0.00 0.00 0.00 3.69
1689 1793 0.815615 GCCATGGGATCTTCGTGGTC 60.816 60.000 15.13 13.47 41.91 4.02
1935 2039 4.337060 TCGATCGCCGCATACCCG 62.337 66.667 11.09 0.00 38.37 5.28
1971 2075 1.376424 CGCCAGCCACATCTGAACT 60.376 57.895 0.00 0.00 36.19 3.01
2010 2114 3.069729 GTGGTTCAGCTATCTACGGGAAT 59.930 47.826 0.00 0.00 0.00 3.01
2011 2115 4.280174 GTGGTTCAGCTATCTACGGGAATA 59.720 45.833 0.00 0.00 0.00 1.75
2012 2116 4.523173 TGGTTCAGCTATCTACGGGAATAG 59.477 45.833 0.00 0.00 0.00 1.73
2064 2169 2.429930 CCACGGCCAACTCTTCCA 59.570 61.111 2.24 0.00 0.00 3.53
2138 2253 3.478274 CTCCTGGCCAGCCTCTCC 61.478 72.222 28.39 0.00 36.94 3.71
2316 2437 0.312102 GTTTCCTGCAGTGTCTTGGC 59.688 55.000 13.81 0.00 0.00 4.52
2353 2474 5.048434 TGTCGTGCTCTGAATATCTATCTGG 60.048 44.000 0.00 0.00 0.00 3.86
2421 2542 6.646267 ACACTGTTTAGGTGTCTTAACTCAA 58.354 36.000 0.00 0.00 43.35 3.02
2426 2547 9.450807 CTGTTTAGGTGTCTTAACTCAATTTTG 57.549 33.333 0.00 0.00 34.63 2.44
2449 2570 3.727673 TGCAAATGCGTTCTTATTCTCGC 60.728 43.478 0.35 0.00 45.83 5.03
2673 2794 3.864583 CACACACACCTTTTCACATTTGG 59.135 43.478 0.00 0.00 0.00 3.28
2675 2796 4.020662 ACACACACCTTTTCACATTTGGTT 60.021 37.500 0.00 0.00 0.00 3.67
2773 2894 4.260170 CTGCTTAGATTTCTCAGCTGGTT 58.740 43.478 15.13 0.00 42.19 3.67
2811 2932 4.070716 ACTCTTCTTCTGCCTGTCAAATG 58.929 43.478 0.00 0.00 0.00 2.32
2857 2978 3.372566 CCCAAGGTGCTAATGGTTCCATA 60.373 47.826 4.67 0.00 32.13 2.74
2871 2992 4.589374 TGGTTCCATATTTCCCGTTGTTTT 59.411 37.500 0.00 0.00 0.00 2.43
2874 2995 5.890424 TCCATATTTCCCGTTGTTTTCTC 57.110 39.130 0.00 0.00 0.00 2.87
2896 3017 1.148273 TCCCACTGTGAACACCTGC 59.852 57.895 9.86 0.00 0.00 4.85
2989 3120 8.584157 AGTTGTTAATCAGTAATTGGAAATGCA 58.416 29.630 0.00 0.00 0.00 3.96
3045 3176 6.320944 AGCGAAACTAGTAGCTAAACAGTAC 58.679 40.000 15.87 0.00 38.29 2.73
3124 3255 5.482908 CAGTGCCCTATATGCTTAGGTAAG 58.517 45.833 7.04 0.00 37.62 2.34
3212 3343 5.569059 GTGTTGACAGCATTGCTTGTAATAC 59.431 40.000 8.83 8.65 36.40 1.89
3315 3446 6.671190 TCAAAGCTCACATGTTTCTGTTATG 58.329 36.000 0.00 0.00 0.00 1.90
3411 3542 6.530019 TGTCTGCTCAAACTGTGATATCTA 57.470 37.500 3.98 0.00 35.07 1.98
3433 3564 9.692325 ATCTAAGAATTTGCTTCTCTTATGGTT 57.308 29.630 0.00 0.00 43.60 3.67
3608 3741 3.767902 TGGGGCTTTGAAAAATCCAAG 57.232 42.857 0.00 0.00 0.00 3.61
3673 3806 5.417754 TTTGCAGAAATAATGAATGCCCA 57.582 34.783 0.00 0.00 36.04 5.36
3803 3936 3.763097 TGCATAATTTCTCCAGTTGCG 57.237 42.857 0.00 0.00 0.00 4.85
3963 4100 3.437049 GCTGTCTTATGTCTGGTGGAAAC 59.563 47.826 0.00 0.00 0.00 2.78
4020 4157 9.409312 TCTTGTTATTGACATTTGCTGTATTTG 57.591 29.630 0.00 0.00 38.54 2.32
4062 4199 3.922240 CCATTGCTGAAACATTTCGAAGG 59.078 43.478 0.00 0.00 40.01 3.46
4218 4355 3.256136 ACGACGAGAGAGAAGAAAATGGT 59.744 43.478 0.00 0.00 0.00 3.55
4236 4373 3.018856 TGGTAATGATGGCAGCAAAGAG 58.981 45.455 10.46 0.00 0.00 2.85
4326 4463 4.381398 CGATCATCCCCTGCTAAGACTATG 60.381 50.000 0.00 0.00 0.00 2.23
4494 4632 0.681243 GTGGAAGGATGGTCAAGGGC 60.681 60.000 0.00 0.00 0.00 5.19
4521 4659 1.000274 GTTGCCAAGTTGGTGGATCAC 60.000 52.381 22.85 5.20 41.65 3.06
4709 4848 3.801594 GTCCTTTTGTCCGTACGTGTTAA 59.198 43.478 15.21 1.10 0.00 2.01
4712 4851 4.143052 CCTTTTGTCCGTACGTGTTAATCC 60.143 45.833 15.21 0.00 0.00 3.01
4809 4948 1.228429 TTGTACAAGCAGTGGCCCC 60.228 57.895 3.59 0.00 42.56 5.80
4885 5024 0.662085 GTACCTCGCTCTAACTCCGG 59.338 60.000 0.00 0.00 0.00 5.14
5019 5158 3.623863 CCGTTTGTAATGTGACACAACC 58.376 45.455 13.23 4.08 34.52 3.77
5028 5167 0.395173 GTGACACAACCTTGGTGGGT 60.395 55.000 0.00 0.00 40.54 4.51
5040 5179 4.141779 ACCTTGGTGGGTATAGATCGAAAC 60.142 45.833 0.00 0.00 41.11 2.78
5117 5260 3.052082 CTGTCACGGCAAGCCCAG 61.052 66.667 5.34 3.19 0.00 4.45
5150 5293 2.351276 TTCAGGAAGAAGGCCGGC 59.649 61.111 21.18 21.18 0.00 6.13
5174 5317 3.144657 GGGTCCCTTAAAACCGAAGAA 57.855 47.619 0.00 0.00 36.35 2.52
5176 5319 3.890756 GGGTCCCTTAAAACCGAAGAAAA 59.109 43.478 0.00 0.00 36.35 2.29
5185 5328 1.207593 CCGAAGAAAACAGCGCAGG 59.792 57.895 11.47 3.29 0.00 4.85
5296 5439 3.506067 GGTGTTGGAGACCTGGTAATTTG 59.494 47.826 0.00 0.00 0.00 2.32
5303 5446 4.142160 GGAGACCTGGTAATTTGCATTTCC 60.142 45.833 0.00 0.00 31.79 3.13
5311 5454 4.929211 GGTAATTTGCATTTCCAGTTGACC 59.071 41.667 0.00 0.00 31.53 4.02
5365 5508 3.188873 GCTTCAGCATCCTAATGATCTGC 59.811 47.826 0.00 0.00 41.59 4.26
5495 5638 5.564063 CGTCAAATTGATGGATGGATGGATG 60.564 44.000 7.29 0.00 29.96 3.51
5496 5639 4.836175 TCAAATTGATGGATGGATGGATGG 59.164 41.667 0.00 0.00 0.00 3.51
5497 5640 4.752621 AATTGATGGATGGATGGATGGA 57.247 40.909 0.00 0.00 0.00 3.41
5498 5641 4.967209 ATTGATGGATGGATGGATGGAT 57.033 40.909 0.00 0.00 0.00 3.41
5499 5642 3.732048 TGATGGATGGATGGATGGATG 57.268 47.619 0.00 0.00 0.00 3.51
5500 5643 2.310647 TGATGGATGGATGGATGGATGG 59.689 50.000 0.00 0.00 0.00 3.51
5501 5644 2.136974 TGGATGGATGGATGGATGGA 57.863 50.000 0.00 0.00 0.00 3.41
5502 5645 2.651190 TGGATGGATGGATGGATGGAT 58.349 47.619 0.00 0.00 0.00 3.41
5503 5646 2.310647 TGGATGGATGGATGGATGGATG 59.689 50.000 0.00 0.00 0.00 3.51
5504 5647 2.357881 GGATGGATGGATGGATGGATGG 60.358 54.545 0.00 0.00 0.00 3.51
5505 5648 2.136974 TGGATGGATGGATGGATGGA 57.863 50.000 0.00 0.00 0.00 3.41
5506 5649 2.651190 TGGATGGATGGATGGATGGAT 58.349 47.619 0.00 0.00 0.00 3.41
5526 5669 1.600916 GCCGCTAATCCCATGACCC 60.601 63.158 0.00 0.00 0.00 4.46
5563 5706 1.136085 CGCCGTGAAAACCTGTACATG 60.136 52.381 0.00 0.00 0.00 3.21
5632 5777 8.594881 AGATTTATCATCCGTGTCTTAATGTC 57.405 34.615 0.00 0.00 0.00 3.06
5777 5929 7.988937 TGGCTGGTTCATTCCTTATTCTATAT 58.011 34.615 0.00 0.00 0.00 0.86
5778 5930 9.111519 TGGCTGGTTCATTCCTTATTCTATATA 57.888 33.333 0.00 0.00 0.00 0.86
5849 6003 4.625607 AATTCTTCTTGGACTCCGTCTT 57.374 40.909 0.00 0.00 32.47 3.01
5874 6028 0.528470 GAACCCGTCTGAGGAGTGAG 59.472 60.000 0.00 0.00 0.00 3.51
5875 6029 0.900647 AACCCGTCTGAGGAGTGAGG 60.901 60.000 0.00 0.00 0.00 3.86
5876 6030 1.000771 CCCGTCTGAGGAGTGAGGA 60.001 63.158 0.00 0.00 0.00 3.71
5877 6031 1.034838 CCCGTCTGAGGAGTGAGGAG 61.035 65.000 0.00 0.00 0.00 3.69
5878 6032 1.034838 CCGTCTGAGGAGTGAGGAGG 61.035 65.000 0.00 0.00 0.00 4.30
5879 6033 0.034960 CGTCTGAGGAGTGAGGAGGA 60.035 60.000 0.00 0.00 0.00 3.71
5880 6034 1.762708 GTCTGAGGAGTGAGGAGGAG 58.237 60.000 0.00 0.00 0.00 3.69
5881 6035 1.005450 GTCTGAGGAGTGAGGAGGAGT 59.995 57.143 0.00 0.00 0.00 3.85
5882 6036 1.005332 TCTGAGGAGTGAGGAGGAGTG 59.995 57.143 0.00 0.00 0.00 3.51
5883 6037 1.005332 CTGAGGAGTGAGGAGGAGTGA 59.995 57.143 0.00 0.00 0.00 3.41
5884 6038 1.429299 TGAGGAGTGAGGAGGAGTGAA 59.571 52.381 0.00 0.00 0.00 3.18
5885 6039 2.099405 GAGGAGTGAGGAGGAGTGAAG 58.901 57.143 0.00 0.00 0.00 3.02
5897 6051 0.804989 GAGTGAAGGTGAATTGGCCG 59.195 55.000 0.00 0.00 0.00 6.13
5898 6052 1.212751 GTGAAGGTGAATTGGCCGC 59.787 57.895 0.00 0.00 0.00 6.53
5902 6056 3.810896 GGTGAATTGGCCGCCGTC 61.811 66.667 4.58 2.78 0.00 4.79
5921 6076 0.040958 CCTGCGTGTTTTGACAGCTC 60.041 55.000 0.00 0.00 0.00 4.09
5967 6122 3.052082 CACAGAAGCCACCGCCAG 61.052 66.667 0.00 0.00 34.57 4.85
5969 6124 4.711949 CAGAAGCCACCGCCAGCT 62.712 66.667 0.00 0.00 42.40 4.24
5983 6138 1.301244 CAGCTCTCAAGTGCGGTGT 60.301 57.895 0.00 0.00 39.31 4.16
5984 6139 1.301244 AGCTCTCAAGTGCGGTGTG 60.301 57.895 0.00 0.00 39.31 3.82
5985 6140 2.320587 GCTCTCAAGTGCGGTGTGG 61.321 63.158 0.00 0.00 0.00 4.17
5986 6141 2.280797 TCTCAAGTGCGGTGTGGC 60.281 61.111 0.00 0.00 0.00 5.01
5987 6142 3.357079 CTCAAGTGCGGTGTGGCC 61.357 66.667 0.00 0.00 0.00 5.36
6042 6198 1.910722 CACCCCATGGAGTCTGAGG 59.089 63.158 15.22 6.34 34.81 3.86
6091 6247 1.022735 ATCTACTACAGCGGTGGTCG 58.977 55.000 20.20 3.87 39.64 4.79
6105 6261 3.725490 GGTGGTCGTAAAGTTGTCTTCT 58.275 45.455 0.00 0.00 32.90 2.85
6129 6285 2.667199 GTCGTTGTTGACCCCGGG 60.667 66.667 15.80 15.80 32.61 5.73
6130 6286 4.629523 TCGTTGTTGACCCCGGGC 62.630 66.667 17.73 2.17 0.00 6.13
6232 6521 4.974438 ACGGGGCTCCAGGTTCCA 62.974 66.667 1.96 0.00 0.00 3.53
6233 6522 4.410400 CGGGGCTCCAGGTTCCAC 62.410 72.222 1.96 0.00 0.00 4.02
6269 6564 2.998097 GGTCTATGGCTGGCACCA 59.002 61.111 5.88 10.50 45.82 4.17
6271 6566 1.452108 GTCTATGGCTGGCACCACC 60.452 63.158 5.88 0.67 44.17 4.61
6279 6574 3.259314 TGGCACCACCCAGCTCAT 61.259 61.111 0.00 0.00 37.83 2.90
6291 6586 0.656259 CAGCTCATGTCCAATCAGCG 59.344 55.000 0.00 0.00 0.00 5.18
6296 6591 1.831106 TCATGTCCAATCAGCGGTACT 59.169 47.619 0.00 0.00 0.00 2.73
6318 6613 0.250252 GATGCTTCTCTAGGCCTGCC 60.250 60.000 17.99 0.00 0.00 4.85
6356 6685 6.206180 TCTTGGGGAAGAAGAAGAAGAAAT 57.794 37.500 0.00 0.00 0.00 2.17
6357 6686 6.241645 TCTTGGGGAAGAAGAAGAAGAAATC 58.758 40.000 0.00 0.00 0.00 2.17
6369 6698 2.361438 AGAAGAAATCGGGCCGTACTAG 59.639 50.000 27.32 0.00 0.00 2.57
6414 6747 0.234106 CAGCAGTGAGTGAAGTTGCG 59.766 55.000 0.00 0.00 39.63 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 8.962679 TGGTCAAAGTCAAACTTTACATAGTTT 58.037 29.630 4.86 0.00 45.84 2.66
62 63 8.514330 TGGTCAAAGTCAAACTTTACATAGTT 57.486 30.769 4.86 0.00 45.84 2.24
63 64 8.514330 TTGGTCAAAGTCAAACTTTACATAGT 57.486 30.769 4.86 0.00 45.84 2.12
64 65 9.233232 GTTTGGTCAAAGTCAAACTTTACATAG 57.767 33.333 4.86 0.00 45.84 2.23
65 66 8.192110 GGTTTGGTCAAAGTCAAACTTTACATA 58.808 33.333 15.43 0.00 45.84 2.29
66 67 7.039270 GGTTTGGTCAAAGTCAAACTTTACAT 58.961 34.615 15.43 0.00 45.84 2.29
67 68 6.209788 AGGTTTGGTCAAAGTCAAACTTTACA 59.790 34.615 15.43 3.14 45.84 2.41
68 69 6.627243 AGGTTTGGTCAAAGTCAAACTTTAC 58.373 36.000 15.43 4.82 45.84 2.01
69 70 6.844097 AGGTTTGGTCAAAGTCAAACTTTA 57.156 33.333 15.43 0.00 45.84 1.85
71 72 5.738619 AAGGTTTGGTCAAAGTCAAACTT 57.261 34.783 15.43 7.93 46.86 2.66
72 73 8.576442 CATATAAGGTTTGGTCAAAGTCAAACT 58.424 33.333 15.43 3.50 46.86 2.66
73 74 7.328493 GCATATAAGGTTTGGTCAAAGTCAAAC 59.672 37.037 9.59 9.59 46.92 2.93
74 75 7.014711 TGCATATAAGGTTTGGTCAAAGTCAAA 59.985 33.333 0.00 0.00 0.00 2.69
75 76 6.491745 TGCATATAAGGTTTGGTCAAAGTCAA 59.508 34.615 0.00 0.00 0.00 3.18
76 77 6.007076 TGCATATAAGGTTTGGTCAAAGTCA 58.993 36.000 0.00 0.00 0.00 3.41
77 78 6.374333 TCTGCATATAAGGTTTGGTCAAAGTC 59.626 38.462 0.00 0.00 0.00 3.01
78 79 6.151144 GTCTGCATATAAGGTTTGGTCAAAGT 59.849 38.462 0.00 0.00 0.00 2.66
79 80 6.375455 AGTCTGCATATAAGGTTTGGTCAAAG 59.625 38.462 0.00 0.00 0.00 2.77
80 81 6.245408 AGTCTGCATATAAGGTTTGGTCAAA 58.755 36.000 0.00 0.00 0.00 2.69
81 82 5.815581 AGTCTGCATATAAGGTTTGGTCAA 58.184 37.500 0.00 0.00 0.00 3.18
82 83 5.435686 AGTCTGCATATAAGGTTTGGTCA 57.564 39.130 0.00 0.00 0.00 4.02
83 84 7.859325 TTTAGTCTGCATATAAGGTTTGGTC 57.141 36.000 0.00 0.00 0.00 4.02
84 85 8.644374 TTTTTAGTCTGCATATAAGGTTTGGT 57.356 30.769 0.00 0.00 0.00 3.67
85 86 8.956426 TCTTTTTAGTCTGCATATAAGGTTTGG 58.044 33.333 0.00 0.00 0.00 3.28
89 90 8.665685 CGTTTCTTTTTAGTCTGCATATAAGGT 58.334 33.333 0.00 0.00 0.00 3.50
90 91 8.122952 CCGTTTCTTTTTAGTCTGCATATAAGG 58.877 37.037 0.00 0.00 0.00 2.69
91 92 8.879759 TCCGTTTCTTTTTAGTCTGCATATAAG 58.120 33.333 0.00 0.00 0.00 1.73
92 93 8.780846 TCCGTTTCTTTTTAGTCTGCATATAA 57.219 30.769 0.00 0.00 0.00 0.98
93 94 8.255206 TCTCCGTTTCTTTTTAGTCTGCATATA 58.745 33.333 0.00 0.00 0.00 0.86
94 95 7.103641 TCTCCGTTTCTTTTTAGTCTGCATAT 58.896 34.615 0.00 0.00 0.00 1.78
95 96 6.460781 TCTCCGTTTCTTTTTAGTCTGCATA 58.539 36.000 0.00 0.00 0.00 3.14
96 97 5.305585 TCTCCGTTTCTTTTTAGTCTGCAT 58.694 37.500 0.00 0.00 0.00 3.96
97 98 4.699637 TCTCCGTTTCTTTTTAGTCTGCA 58.300 39.130 0.00 0.00 0.00 4.41
98 99 4.989168 TCTCTCCGTTTCTTTTTAGTCTGC 59.011 41.667 0.00 0.00 0.00 4.26
99 100 6.217294 ACTCTCTCCGTTTCTTTTTAGTCTG 58.783 40.000 0.00 0.00 0.00 3.51
100 101 6.408107 ACTCTCTCCGTTTCTTTTTAGTCT 57.592 37.500 0.00 0.00 0.00 3.24
101 102 6.305160 CGTACTCTCTCCGTTTCTTTTTAGTC 59.695 42.308 0.00 0.00 0.00 2.59
102 103 6.016777 TCGTACTCTCTCCGTTTCTTTTTAGT 60.017 38.462 0.00 0.00 0.00 2.24
103 104 6.376978 TCGTACTCTCTCCGTTTCTTTTTAG 58.623 40.000 0.00 0.00 0.00 1.85
104 105 6.016777 ACTCGTACTCTCTCCGTTTCTTTTTA 60.017 38.462 0.00 0.00 0.00 1.52
105 106 5.192327 TCGTACTCTCTCCGTTTCTTTTT 57.808 39.130 0.00 0.00 0.00 1.94
106 107 4.277921 ACTCGTACTCTCTCCGTTTCTTTT 59.722 41.667 0.00 0.00 0.00 2.27
107 108 3.819902 ACTCGTACTCTCTCCGTTTCTTT 59.180 43.478 0.00 0.00 0.00 2.52
108 109 3.410508 ACTCGTACTCTCTCCGTTTCTT 58.589 45.455 0.00 0.00 0.00 2.52
109 110 3.056588 ACTCGTACTCTCTCCGTTTCT 57.943 47.619 0.00 0.00 0.00 2.52
110 111 3.828060 AACTCGTACTCTCTCCGTTTC 57.172 47.619 0.00 0.00 0.00 2.78
111 112 4.759183 ACTAAACTCGTACTCTCTCCGTTT 59.241 41.667 0.00 0.00 0.00 3.60
112 113 4.322567 ACTAAACTCGTACTCTCTCCGTT 58.677 43.478 0.00 0.00 0.00 4.44
113 114 3.936564 ACTAAACTCGTACTCTCTCCGT 58.063 45.455 0.00 0.00 0.00 4.69
114 115 4.943142 AACTAAACTCGTACTCTCTCCG 57.057 45.455 0.00 0.00 0.00 4.63
115 116 4.858140 GCAAACTAAACTCGTACTCTCTCC 59.142 45.833 0.00 0.00 0.00 3.71
116 117 4.858140 GGCAAACTAAACTCGTACTCTCTC 59.142 45.833 0.00 0.00 0.00 3.20
117 118 4.523558 AGGCAAACTAAACTCGTACTCTCT 59.476 41.667 0.00 0.00 0.00 3.10
118 119 4.807443 AGGCAAACTAAACTCGTACTCTC 58.193 43.478 0.00 0.00 0.00 3.20
119 120 4.868314 AGGCAAACTAAACTCGTACTCT 57.132 40.909 0.00 0.00 0.00 3.24
120 121 4.377124 GCAAGGCAAACTAAACTCGTACTC 60.377 45.833 0.00 0.00 0.00 2.59
121 122 3.497262 GCAAGGCAAACTAAACTCGTACT 59.503 43.478 0.00 0.00 0.00 2.73
122 123 3.249080 TGCAAGGCAAACTAAACTCGTAC 59.751 43.478 0.00 0.00 34.76 3.67
123 124 3.468770 TGCAAGGCAAACTAAACTCGTA 58.531 40.909 0.00 0.00 34.76 3.43
156 157 6.043938 TCCCGTATTTAGAGGCCATATTTCTT 59.956 38.462 5.01 0.00 0.00 2.52
182 183 2.156504 CAGTGCATTTCTATCCGCGATC 59.843 50.000 8.23 0.00 0.00 3.69
191 192 3.242837 GCAATCATCGCAGTGCATTTCTA 60.243 43.478 16.83 0.00 36.97 2.10
201 202 0.656259 CAGGAGTGCAATCATCGCAG 59.344 55.000 16.99 0.00 40.78 5.18
208 209 7.385205 ACGTATTATTATCACAGGAGTGCAATC 59.615 37.037 5.38 5.38 45.49 2.67
218 219 7.408395 CGCTCGAAGAACGTATTATTATCACAG 60.408 40.741 0.00 0.00 41.61 3.66
219 220 6.358822 CGCTCGAAGAACGTATTATTATCACA 59.641 38.462 0.00 0.00 41.61 3.58
243 244 3.814842 TGGTTATTATCAGCCAGCATTCG 59.185 43.478 0.00 0.00 0.00 3.34
244 245 5.772825 TTGGTTATTATCAGCCAGCATTC 57.227 39.130 0.00 0.00 32.09 2.67
245 246 5.011329 CCATTGGTTATTATCAGCCAGCATT 59.989 40.000 0.00 0.00 32.09 3.56
246 247 4.525487 CCATTGGTTATTATCAGCCAGCAT 59.475 41.667 0.00 0.00 32.09 3.79
248 249 3.305608 GCCATTGGTTATTATCAGCCAGC 60.306 47.826 4.26 0.00 32.09 4.85
249 250 3.890756 TGCCATTGGTTATTATCAGCCAG 59.109 43.478 4.26 0.00 32.09 4.85
250 251 3.890756 CTGCCATTGGTTATTATCAGCCA 59.109 43.478 4.26 0.00 0.00 4.75
251 252 3.256631 CCTGCCATTGGTTATTATCAGCC 59.743 47.826 4.26 0.00 0.00 4.85
253 254 6.005823 TCATCCTGCCATTGGTTATTATCAG 58.994 40.000 4.26 1.21 0.00 2.90
255 256 6.006449 ACTCATCCTGCCATTGGTTATTATC 58.994 40.000 4.26 0.00 0.00 1.75
257 258 5.132502 CACTCATCCTGCCATTGGTTATTA 58.867 41.667 4.26 0.00 0.00 0.98
258 259 3.956199 CACTCATCCTGCCATTGGTTATT 59.044 43.478 4.26 0.00 0.00 1.40
259 260 3.053395 ACACTCATCCTGCCATTGGTTAT 60.053 43.478 4.26 0.00 0.00 1.89
260 261 2.308570 ACACTCATCCTGCCATTGGTTA 59.691 45.455 4.26 0.00 0.00 2.85
262 263 0.700564 ACACTCATCCTGCCATTGGT 59.299 50.000 4.26 0.00 0.00 3.67
265 266 3.498774 GGATACACTCATCCTGCCATT 57.501 47.619 0.00 0.00 41.24 3.16
278 283 7.120923 TCAAACCAAGGATAGTAGGATACAC 57.879 40.000 0.00 0.00 46.26 2.90
281 286 7.008332 TCGATCAAACCAAGGATAGTAGGATA 58.992 38.462 0.00 0.00 0.00 2.59
282 287 5.839063 TCGATCAAACCAAGGATAGTAGGAT 59.161 40.000 0.00 0.00 0.00 3.24
283 288 5.205821 TCGATCAAACCAAGGATAGTAGGA 58.794 41.667 0.00 0.00 0.00 2.94
284 289 5.531122 TCGATCAAACCAAGGATAGTAGG 57.469 43.478 0.00 0.00 0.00 3.18
285 290 5.986135 CCTTCGATCAAACCAAGGATAGTAG 59.014 44.000 0.00 0.00 38.15 2.57
286 291 5.684030 GCCTTCGATCAAACCAAGGATAGTA 60.684 44.000 0.00 0.00 38.15 1.82
287 292 4.770795 CCTTCGATCAAACCAAGGATAGT 58.229 43.478 0.00 0.00 38.15 2.12
288 293 3.561725 GCCTTCGATCAAACCAAGGATAG 59.438 47.826 0.00 0.00 38.15 2.08
296 301 3.691609 AGAGAAATGCCTTCGATCAAACC 59.308 43.478 0.00 0.00 39.22 3.27
301 306 4.692228 AGAGAAGAGAAATGCCTTCGATC 58.308 43.478 0.00 0.00 42.52 3.69
311 316 8.141268 GTCGATCTATTGGAAGAGAAGAGAAAT 58.859 37.037 0.00 0.00 29.01 2.17
315 320 6.384258 TGTCGATCTATTGGAAGAGAAGAG 57.616 41.667 0.00 0.00 29.01 2.85
342 352 2.464459 CGCCTCGTTCCATCCAAGC 61.464 63.158 0.00 0.00 0.00 4.01
364 375 1.063166 GTGGGTACGATCGACGACC 59.937 63.158 24.34 22.95 45.77 4.79
421 434 1.287041 GGTACTCCGTTGCGTTGACC 61.287 60.000 0.00 0.00 0.00 4.02
578 612 4.500116 GTCGCCGGTGAGCCTCTC 62.500 72.222 20.25 0.90 0.00 3.20
620 655 2.438795 GGGAGGACGAGCTCGACT 60.439 66.667 40.58 33.70 43.02 4.18
637 675 3.427573 AGGAAAAATAAAGACCGTGGGG 58.572 45.455 0.00 0.00 40.11 4.96
932 991 4.437587 GGGAGAGGACGGACGGGA 62.438 72.222 0.00 0.00 0.00 5.14
1329 1410 4.087892 TTCCGCTGCTGCTCCTCC 62.088 66.667 14.03 0.00 36.97 4.30
1506 1595 1.152567 ATGCGAGAGGAGGAGGAGG 60.153 63.158 0.00 0.00 32.19 4.30
1507 1596 1.178534 GGATGCGAGAGGAGGAGGAG 61.179 65.000 0.00 0.00 32.19 3.69
1508 1597 1.152652 GGATGCGAGAGGAGGAGGA 60.153 63.158 0.00 0.00 32.19 3.71
1509 1598 2.560119 CGGATGCGAGAGGAGGAGG 61.560 68.421 0.00 0.00 32.19 4.30
1510 1599 1.388065 AACGGATGCGAGAGGAGGAG 61.388 60.000 15.49 0.00 32.19 3.69
1511 1600 1.379977 AACGGATGCGAGAGGAGGA 60.380 57.895 15.49 0.00 32.19 3.71
1689 1793 1.756375 GCCAGCATACGAAGCACGAG 61.756 60.000 10.05 0.00 45.77 4.18
1935 2039 1.726533 CGACTCCGGGGTAAGAGCTC 61.727 65.000 7.16 5.27 33.18 4.09
1940 2044 3.072468 TGGCGACTCCGGGGTAAG 61.072 66.667 7.16 5.89 37.80 2.34
1971 2075 2.431771 CGACGAACATGACCGCCA 60.432 61.111 0.00 0.00 0.00 5.69
2010 2114 4.348168 AGAAGCAAGAGAAACAGGGAACTA 59.652 41.667 0.00 0.00 40.21 2.24
2011 2115 3.137360 AGAAGCAAGAGAAACAGGGAACT 59.863 43.478 0.00 0.00 46.44 3.01
2012 2116 3.251972 CAGAAGCAAGAGAAACAGGGAAC 59.748 47.826 0.00 0.00 0.00 3.62
2186 2306 6.509418 TGAATAGTGTTTGCCATAAGAACC 57.491 37.500 0.00 0.00 0.00 3.62
2279 2400 0.250513 ACACGAAGAGGCTCCCAATC 59.749 55.000 11.71 4.11 0.00 2.67
2353 2474 3.060602 GTCAGGACAGCAACAGTAGAAC 58.939 50.000 0.00 0.00 0.00 3.01
2421 2542 6.646240 AGAATAAGAACGCATTTGCACAAAAT 59.354 30.769 3.13 0.00 42.21 1.82
2426 2547 3.780801 CGAGAATAAGAACGCATTTGCAC 59.219 43.478 3.13 0.00 42.21 4.57
2643 2764 5.008217 GTGAAAAGGTGTGTGTGCTACAATA 59.992 40.000 0.00 0.00 41.89 1.90
2673 2794 6.378280 ACACAATTATCTGGATCAAAGGGAAC 59.622 38.462 0.00 0.00 0.00 3.62
2675 2796 6.078456 ACACAATTATCTGGATCAAAGGGA 57.922 37.500 0.00 0.00 0.00 4.20
2811 2932 4.156008 ACAACTTGAACACTGGAAACTCAC 59.844 41.667 0.00 0.00 0.00 3.51
2857 2978 5.001874 GGACTAGAGAAAACAACGGGAAAT 58.998 41.667 0.00 0.00 0.00 2.17
2871 2992 2.891580 GTGTTCACAGTGGGACTAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
2874 2995 1.971357 AGGTGTTCACAGTGGGACTAG 59.029 52.381 0.00 0.00 0.00 2.57
2982 3113 8.496707 AATCTTCCATTACCAATTTGCATTTC 57.503 30.769 0.00 0.00 0.00 2.17
2989 3120 9.710900 GAAAGTCAAATCTTCCATTACCAATTT 57.289 29.630 0.00 0.00 0.00 1.82
3045 3176 7.383102 AGTATAAACCTGCATGAGAAAACAG 57.617 36.000 0.00 0.00 0.00 3.16
3124 3255 0.316204 AGCAAGTTGACAAGGCATGC 59.684 50.000 9.90 9.90 0.00 4.06
3125 3256 2.806608 AAGCAAGTTGACAAGGCATG 57.193 45.000 7.16 0.00 0.00 4.06
3126 3257 2.694628 TGAAAGCAAGTTGACAAGGCAT 59.305 40.909 7.16 0.00 0.00 4.40
3127 3258 2.098614 TGAAAGCAAGTTGACAAGGCA 58.901 42.857 7.16 0.00 0.00 4.75
3128 3259 2.869233 TGAAAGCAAGTTGACAAGGC 57.131 45.000 7.16 0.00 0.00 4.35
3226 3357 8.862325 AAAAGATGTACAGAACACATTATCCA 57.138 30.769 0.33 0.00 42.09 3.41
3268 3399 5.710513 TGAATGTGCTAGCTTCAACATTT 57.289 34.783 24.04 13.12 0.00 2.32
3382 3513 3.562973 CACAGTTTGAGCAGACATTCTGT 59.437 43.478 5.14 0.00 45.94 3.41
3383 3514 3.811497 TCACAGTTTGAGCAGACATTCTG 59.189 43.478 0.00 0.00 46.90 3.02
3433 3564 2.742856 CGGATAATGCCTGCAACAGAGA 60.743 50.000 0.00 0.00 32.44 3.10
3568 3699 3.435601 CCAATCAGGCTGGGCTATACTTT 60.436 47.826 15.73 0.00 0.00 2.66
3673 3806 2.745100 CAGTGAGTGCGGCATGCT 60.745 61.111 18.92 0.00 46.63 3.79
3803 3936 3.381949 AGCGACAAGACAACTAAGTGTC 58.618 45.455 0.00 0.00 46.90 3.67
3822 3955 7.363431 ACAACAAAAGCTAGATAAACAAGAGC 58.637 34.615 0.00 0.00 0.00 4.09
3963 4100 2.954318 CCAAATGACCAGGGCAGATAAG 59.046 50.000 0.00 0.00 0.00 1.73
4020 4157 7.222224 GCAATGGAATCTTGAATCTTTCATGAC 59.778 37.037 0.00 0.00 43.71 3.06
4062 4199 2.849880 TCACAAGTGCTTCTGTTTGC 57.150 45.000 0.00 0.00 0.00 3.68
4218 4355 2.938451 CGACTCTTTGCTGCCATCATTA 59.062 45.455 0.00 0.00 0.00 1.90
4236 4373 3.502920 ACGATCATCAACAGAAGACGAC 58.497 45.455 0.00 0.00 0.00 4.34
4326 4463 0.393537 AGCTGCTATCAACACTGCCC 60.394 55.000 0.00 0.00 0.00 5.36
4446 4584 3.479370 GCACTGCCATGTCGAGTC 58.521 61.111 0.00 0.00 0.00 3.36
4521 4659 4.576053 TCAAATTCATCAGCATTACGGAGG 59.424 41.667 0.00 0.00 0.00 4.30
4628 4766 9.211485 CTGAATCTTCCAAAGCACAAATAAAAT 57.789 29.630 0.00 0.00 0.00 1.82
4709 4848 3.202829 ACACTACAAAACACACCGGAT 57.797 42.857 9.46 0.00 0.00 4.18
4712 4851 2.159503 TGCAACACTACAAAACACACCG 60.160 45.455 0.00 0.00 0.00 4.94
4809 4948 4.379082 GCAAACCTAATGGACGTAAACCAG 60.379 45.833 0.68 0.00 40.89 4.00
4885 5024 1.547372 AGGCATGCTTTGTCCATCAAC 59.453 47.619 18.92 0.00 35.61 3.18
5019 5158 4.049186 CGTTTCGATCTATACCCACCAAG 58.951 47.826 0.00 0.00 0.00 3.61
5028 5167 7.533222 GTCTTCGCTTATTCGTTTCGATCTATA 59.467 37.037 0.00 0.00 35.23 1.31
5040 5179 0.931005 GCAGGGTCTTCGCTTATTCG 59.069 55.000 0.00 0.00 34.60 3.34
5117 5260 4.742012 TCCTGAAGTATATCTCCACCTCC 58.258 47.826 0.00 0.00 0.00 4.30
5148 5291 0.599558 GTTTTAAGGGACCCGTTGCC 59.400 55.000 3.59 0.00 35.35 4.52
5149 5292 0.599558 GGTTTTAAGGGACCCGTTGC 59.400 55.000 3.59 0.00 0.00 4.17
5150 5293 0.876399 CGGTTTTAAGGGACCCGTTG 59.124 55.000 3.59 0.00 34.10 4.10
5159 5302 3.972502 CGCTGTTTTCTTCGGTTTTAAGG 59.027 43.478 0.00 0.00 0.00 2.69
5174 5317 4.961511 TCGTCGCCTGCGCTGTTT 62.962 61.111 9.73 0.00 39.59 2.83
5255 5398 0.315568 CAGAGGCGAGCATAGGGTAC 59.684 60.000 0.00 0.00 0.00 3.34
5296 5439 1.212751 GGCGGTCAACTGGAAATGC 59.787 57.895 0.00 0.00 0.00 3.56
5303 5446 4.569564 GGTTAGTTATTAGGCGGTCAACTG 59.430 45.833 7.54 0.00 32.09 3.16
5305 5448 3.553105 CGGTTAGTTATTAGGCGGTCAAC 59.447 47.826 0.00 0.00 0.00 3.18
5311 5454 3.714391 AGAAGCGGTTAGTTATTAGGCG 58.286 45.455 0.00 0.00 0.00 5.52
5365 5508 1.261938 TGGGAGGGACACGGTACATG 61.262 60.000 0.00 0.00 0.00 3.21
5454 5597 1.142748 CGGCCAGGAGAGTTAGCTG 59.857 63.158 2.24 0.00 0.00 4.24
5495 5638 1.888436 TAGCGGCGATCCATCCATCC 61.888 60.000 12.98 0.00 0.00 3.51
5496 5639 0.037326 TTAGCGGCGATCCATCCATC 60.037 55.000 12.98 0.00 0.00 3.51
5497 5640 0.615331 ATTAGCGGCGATCCATCCAT 59.385 50.000 12.98 0.00 0.00 3.41
5498 5641 0.037326 GATTAGCGGCGATCCATCCA 60.037 55.000 12.98 0.00 0.00 3.41
5499 5642 0.741221 GGATTAGCGGCGATCCATCC 60.741 60.000 24.29 17.36 41.21 3.51
5500 5643 0.741221 GGGATTAGCGGCGATCCATC 60.741 60.000 27.74 15.90 42.94 3.51
5501 5644 1.296715 GGGATTAGCGGCGATCCAT 59.703 57.895 27.74 8.69 42.94 3.41
5502 5645 1.480212 ATGGGATTAGCGGCGATCCA 61.480 55.000 27.74 15.51 42.94 3.41
5503 5646 1.021390 CATGGGATTAGCGGCGATCC 61.021 60.000 22.37 22.37 40.90 3.36
5504 5647 0.037326 TCATGGGATTAGCGGCGATC 60.037 55.000 12.98 4.54 0.00 3.69
5505 5648 0.320771 GTCATGGGATTAGCGGCGAT 60.321 55.000 12.98 7.15 0.00 4.58
5506 5649 1.069090 GTCATGGGATTAGCGGCGA 59.931 57.895 12.98 0.00 0.00 5.54
5526 5669 0.318275 GCGAGTAGATCCTTCCTGCG 60.318 60.000 0.00 0.00 0.00 5.18
5603 5747 9.698309 ATTAAGACACGGATGATAAATCTACTG 57.302 33.333 0.00 0.00 0.00 2.74
5713 5861 4.503296 CCTGTTTTACACACTGCTACTCCT 60.503 45.833 0.00 0.00 0.00 3.69
5714 5862 3.746492 CCTGTTTTACACACTGCTACTCC 59.254 47.826 0.00 0.00 0.00 3.85
5715 5863 4.377897 ACCTGTTTTACACACTGCTACTC 58.622 43.478 0.00 0.00 0.00 2.59
5780 5932 9.280174 CCAAACACTCCATTATAATTATACGGT 57.720 33.333 15.24 5.28 0.00 4.83
5797 5949 1.360192 GCAGCACCACCAAACACTC 59.640 57.895 0.00 0.00 0.00 3.51
5799 5951 1.226945 GTGCAGCACCACCAAACAC 60.227 57.895 15.27 0.00 0.00 3.32
5849 6003 1.171308 CCTCAGACGGGTTCGAGTTA 58.829 55.000 0.00 0.00 40.11 2.24
5874 6028 2.716217 CCAATTCACCTTCACTCCTCC 58.284 52.381 0.00 0.00 0.00 4.30
5875 6029 2.087646 GCCAATTCACCTTCACTCCTC 58.912 52.381 0.00 0.00 0.00 3.71
5876 6030 1.272147 GGCCAATTCACCTTCACTCCT 60.272 52.381 0.00 0.00 0.00 3.69
5877 6031 1.177401 GGCCAATTCACCTTCACTCC 58.823 55.000 0.00 0.00 0.00 3.85
5878 6032 0.804989 CGGCCAATTCACCTTCACTC 59.195 55.000 2.24 0.00 0.00 3.51
5879 6033 1.244019 GCGGCCAATTCACCTTCACT 61.244 55.000 2.24 0.00 0.00 3.41
5880 6034 1.212751 GCGGCCAATTCACCTTCAC 59.787 57.895 2.24 0.00 0.00 3.18
5881 6035 1.976474 GGCGGCCAATTCACCTTCA 60.976 57.895 15.62 0.00 0.00 3.02
5882 6036 2.885113 GGCGGCCAATTCACCTTC 59.115 61.111 15.62 0.00 0.00 3.46
5883 6037 3.061848 CGGCGGCCAATTCACCTT 61.062 61.111 20.71 0.00 0.00 3.50
5884 6038 4.344865 ACGGCGGCCAATTCACCT 62.345 61.111 20.71 0.00 0.00 4.00
5885 6039 3.810896 GACGGCGGCCAATTCACC 61.811 66.667 20.71 0.00 0.00 4.02
5902 6056 0.040958 GAGCTGTCAAAACACGCAGG 60.041 55.000 0.00 0.00 34.18 4.85
5906 6060 1.082756 GCCGAGCTGTCAAAACACG 60.083 57.895 0.00 0.00 0.00 4.49
5907 6061 1.282875 GGCCGAGCTGTCAAAACAC 59.717 57.895 0.00 0.00 0.00 3.32
5909 6064 0.884704 TCTGGCCGAGCTGTCAAAAC 60.885 55.000 0.00 0.00 0.00 2.43
5961 6116 3.123620 GCACTTGAGAGCTGGCGG 61.124 66.667 0.00 0.00 0.00 6.13
5963 6118 3.123620 CCGCACTTGAGAGCTGGC 61.124 66.667 0.00 0.00 0.00 4.85
5964 6119 2.031516 CACCGCACTTGAGAGCTGG 61.032 63.158 0.00 8.71 34.03 4.85
5965 6120 1.301244 ACACCGCACTTGAGAGCTG 60.301 57.895 0.00 0.00 0.00 4.24
5966 6121 1.301244 CACACCGCACTTGAGAGCT 60.301 57.895 0.00 0.00 0.00 4.09
5967 6122 2.320587 CCACACCGCACTTGAGAGC 61.321 63.158 0.00 0.00 0.00 4.09
5968 6123 2.320587 GCCACACCGCACTTGAGAG 61.321 63.158 0.00 0.00 0.00 3.20
5969 6124 2.280797 GCCACACCGCACTTGAGA 60.281 61.111 0.00 0.00 0.00 3.27
6042 6198 1.194896 GAGCGCATACGTGTCGAGAC 61.195 60.000 11.47 1.88 42.83 3.36
6091 6247 2.662156 CCGAGCGAGAAGACAACTTTAC 59.338 50.000 0.00 0.00 36.39 2.01
6105 6261 1.659335 GTCAACAACGACCGAGCGA 60.659 57.895 3.95 0.00 34.83 4.93
6254 6543 2.998097 GGTGGTGCCAGCCATAGA 59.002 61.111 9.10 0.00 41.08 1.98
6269 6564 0.994247 TGATTGGACATGAGCTGGGT 59.006 50.000 0.00 0.00 0.00 4.51
6271 6566 1.022735 GCTGATTGGACATGAGCTGG 58.977 55.000 0.00 0.00 0.00 4.85
6318 6613 2.289694 CCCAAGATTCCATACTAGGCCG 60.290 54.545 0.00 0.00 0.00 6.13
6326 6621 5.731187 TCTTCTTCTTCCCCAAGATTCCATA 59.269 40.000 0.00 0.00 38.50 2.74
6356 6685 2.475466 CGCTTCTAGTACGGCCCGA 61.475 63.158 11.71 0.00 0.00 5.14
6357 6686 2.025727 CGCTTCTAGTACGGCCCG 59.974 66.667 0.00 0.00 0.00 6.13


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.