Multiple sequence alignment - TraesCS6A01G033800

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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 TraesCS6A01G033800 chr6A 100.000 2806 0 0 1 2806 16461113 16463918 0.000000e+00 5182.0
1 TraesCS6A01G033800 chr6B 87.829 1709 128 37 969 2621 27946281 27947965 0.000000e+00 1930.0
2 TraesCS6A01G033800 chr6B 88.756 1005 77 23 1019 1992 27999868 27998869 0.000000e+00 1197.0
3 TraesCS6A01G033800 chr6B 79.924 264 35 14 421 676 28000286 28000033 7.990000e-41 178.0
4 TraesCS6A01G033800 chr6B 91.200 125 9 2 672 795 506295833 506295956 4.810000e-38 169.0
5 TraesCS6A01G033800 chr6B 86.014 143 9 7 420 561 27945941 27946073 2.910000e-30 143.0
6 TraesCS6A01G033800 chr2B 83.028 1691 116 58 1024 2633 46603566 46605166 0.000000e+00 1375.0
7 TraesCS6A01G033800 chr2B 97.436 39 1 0 94 132 46602509 46602547 1.800000e-07 67.6
8 TraesCS6A01G033800 chr6D 90.012 821 53 7 1990 2806 16202531 16203326 0.000000e+00 1035.0
9 TraesCS6A01G033800 chr6D 88.206 602 29 14 1434 1999 16198878 16199473 0.000000e+00 680.0
10 TraesCS6A01G033800 chr6D 92.035 452 25 9 976 1425 16198462 16198904 2.370000e-175 625.0
11 TraesCS6A01G033800 chr6D 93.985 133 6 2 421 552 16197988 16198119 1.700000e-47 200.0
12 TraesCS6A01G033800 chr6D 92.661 109 6 2 827 933 16198355 16198463 3.740000e-34 156.0
13 TraesCS6A01G033800 chr6D 86.066 122 12 3 15 131 16197098 16197219 2.930000e-25 126.0
14 TraesCS6A01G033800 chr6D 100.000 33 0 0 646 678 16198250 16198282 8.390000e-06 62.1
15 TraesCS6A01G033800 chr5B 80.545 807 128 21 1994 2790 666858088 666857301 6.690000e-166 593.0
16 TraesCS6A01G033800 chr5A 79.012 810 137 23 1994 2790 657271301 657270512 8.910000e-145 523.0
17 TraesCS6A01G033800 chr3B 80.612 294 55 2 1487 1779 786720611 786720903 2.810000e-55 226.0
18 TraesCS6A01G033800 chr3B 85.492 193 20 5 1185 1370 89375982 89376173 7.930000e-46 195.0
19 TraesCS6A01G033800 chr3B 92.437 119 7 2 678 795 32722914 32723031 4.810000e-38 169.0
20 TraesCS6A01G033800 chr3B 89.231 130 14 0 678 807 520452928 520452799 2.240000e-36 163.0
21 TraesCS6A01G033800 chr3B 76.207 290 66 3 1495 1781 786279644 786279933 1.740000e-32 150.0
22 TraesCS6A01G033800 chr3D 82.083 240 39 4 1487 1724 588315063 588315300 4.740000e-48 202.0
23 TraesCS6A01G033800 chr3D 84.974 193 21 5 1185 1370 56712086 56712277 3.690000e-44 189.0
24 TraesCS6A01G033800 chr3D 84.456 193 22 6 1186 1371 588078506 588078697 1.720000e-42 183.0
25 TraesCS6A01G033800 chr3D 76.630 368 63 21 1020 1373 588028595 588028237 6.170000e-42 182.0
26 TraesCS6A01G033800 chr3D 84.021 194 23 5 1185 1371 588155991 588155799 2.220000e-41 180.0
27 TraesCS6A01G033800 chr3D 92.500 120 6 2 676 795 460417844 460417960 4.810000e-38 169.0
28 TraesCS6A01G033800 chr4A 92.623 122 9 0 674 795 698264155 698264276 2.870000e-40 176.0
29 TraesCS6A01G033800 chr4B 93.043 115 8 0 684 798 660419663 660419549 4.810000e-38 169.0
30 TraesCS6A01G033800 chr4B 93.043 115 8 0 684 798 660448971 660448857 4.810000e-38 169.0
31 TraesCS6A01G033800 chr7A 89.844 128 13 0 671 798 32166975 32166848 6.220000e-37 165.0
32 TraesCS6A01G033800 chr1B 91.525 118 10 0 678 795 564788586 564788703 2.240000e-36 163.0
33 TraesCS6A01G033800 chr1B 81.507 146 27 0 2551 2696 4318197 4318342 1.370000e-23 121.0
34 TraesCS6A01G033800 chr1B 76.923 130 23 7 2549 2674 673700434 673700308 1.800000e-07 67.6


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 TraesCS6A01G033800 chr6A 16461113 16463918 2805 False 5182.000000 5182 100.000000 1 2806 1 chr6A.!!$F1 2805
1 TraesCS6A01G033800 chr6B 27945941 27947965 2024 False 1036.500000 1930 86.921500 420 2621 2 chr6B.!!$F2 2201
2 TraesCS6A01G033800 chr6B 27998869 28000286 1417 True 687.500000 1197 84.340000 421 1992 2 chr6B.!!$R1 1571
3 TraesCS6A01G033800 chr2B 46602509 46605166 2657 False 721.300000 1375 90.232000 94 2633 2 chr2B.!!$F1 2539
4 TraesCS6A01G033800 chr6D 16197098 16203326 6228 False 412.014286 1035 91.852143 15 2806 7 chr6D.!!$F1 2791
5 TraesCS6A01G033800 chr5B 666857301 666858088 787 True 593.000000 593 80.545000 1994 2790 1 chr5B.!!$R1 796
6 TraesCS6A01G033800 chr5A 657270512 657271301 789 True 523.000000 523 79.012000 1994 2790 1 chr5A.!!$R1 796

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
167 192 0.029567 CGCTACTACAGAAGAGGGCG 59.970 60.0 0.00 0.0 35.87 6.13 F
696 1340 0.032813 TACCCTCTCCGTCCGGAAAT 60.033 55.0 5.23 0.0 44.66 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1123 1822 0.034380 GTAAACAGGAAGGGGGCCTC 60.034 60.0 0.84 0.0 32.12 4.70 R
2394 6356 0.528684 GATCGCTTCGGTGCTAGCTT 60.529 55.0 17.23 0.0 35.25 3.74 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
42 43 6.605471 TTCATGAGACAACATACCACTAGT 57.395 37.500 0.00 0.00 0.00 2.57
44 45 7.334844 TCATGAGACAACATACCACTAGTAG 57.665 40.000 0.00 0.00 33.42 2.57
86 92 2.107141 GCGAACAGGCGAGCCTAT 59.893 61.111 17.13 1.75 46.28 2.57
89 95 1.154205 CGAACAGGCGAGCCTATTGG 61.154 60.000 17.13 9.59 46.28 3.16
141 165 5.740224 GCACTATACCAGCACATGTATGAGT 60.740 44.000 10.94 9.48 0.00 3.41
149 173 0.179084 ACATGTATGAGTTCCCCGCG 60.179 55.000 0.00 0.00 0.00 6.46
155 179 0.754217 ATGAGTTCCCCGCGCTACTA 60.754 55.000 5.56 0.00 0.00 1.82
167 192 0.029567 CGCTACTACAGAAGAGGGCG 59.970 60.000 0.00 0.00 35.87 6.13
173 198 1.822990 CTACAGAAGAGGGCGGTGTAA 59.177 52.381 0.00 0.00 0.00 2.41
176 201 1.822990 CAGAAGAGGGCGGTGTAAGTA 59.177 52.381 0.00 0.00 0.00 2.24
188 213 4.682787 CGGTGTAAGTATTGAGCAGATGA 58.317 43.478 0.00 0.00 0.00 2.92
190 215 5.053145 GGTGTAAGTATTGAGCAGATGAGG 58.947 45.833 0.00 0.00 0.00 3.86
191 216 5.053145 GTGTAAGTATTGAGCAGATGAGGG 58.947 45.833 0.00 0.00 0.00 4.30
192 217 4.962362 TGTAAGTATTGAGCAGATGAGGGA 59.038 41.667 0.00 0.00 0.00 4.20
193 218 4.414337 AAGTATTGAGCAGATGAGGGAC 57.586 45.455 0.00 0.00 0.00 4.46
194 219 2.363680 AGTATTGAGCAGATGAGGGACG 59.636 50.000 0.00 0.00 0.00 4.79
195 220 1.198713 ATTGAGCAGATGAGGGACGT 58.801 50.000 0.00 0.00 0.00 4.34
196 221 0.247460 TTGAGCAGATGAGGGACGTG 59.753 55.000 0.00 0.00 0.00 4.49
197 222 1.142748 GAGCAGATGAGGGACGTGG 59.857 63.158 0.00 0.00 0.00 4.94
198 223 1.305297 AGCAGATGAGGGACGTGGA 60.305 57.895 0.00 0.00 0.00 4.02
199 224 1.142748 GCAGATGAGGGACGTGGAG 59.857 63.158 0.00 0.00 0.00 3.86
200 225 1.142748 CAGATGAGGGACGTGGAGC 59.857 63.158 0.00 0.00 0.00 4.70
202 227 0.689080 AGATGAGGGACGTGGAGCAT 60.689 55.000 0.00 0.00 0.00 3.79
203 228 0.249657 GATGAGGGACGTGGAGCATC 60.250 60.000 0.00 0.00 0.00 3.91
204 229 0.689080 ATGAGGGACGTGGAGCATCT 60.689 55.000 0.00 0.00 33.73 2.90
205 230 1.142748 GAGGGACGTGGAGCATCTG 59.857 63.158 0.00 0.00 33.73 2.90
206 231 2.512515 GGGACGTGGAGCATCTGC 60.513 66.667 0.00 0.00 42.49 4.26
207 232 2.265739 GGACGTGGAGCATCTGCA 59.734 61.111 4.79 0.00 45.16 4.41
213 238 4.536316 GGAGCATCTGCACCTGAG 57.464 61.111 10.88 0.00 46.30 3.35
215 240 1.221293 GAGCATCTGCACCTGAGCT 59.779 57.895 4.79 0.00 45.16 4.09
216 241 0.810823 GAGCATCTGCACCTGAGCTC 60.811 60.000 6.82 6.82 45.16 4.09
217 242 1.078637 GCATCTGCACCTGAGCTCA 60.079 57.895 17.19 17.19 41.59 4.26
218 243 0.675837 GCATCTGCACCTGAGCTCAA 60.676 55.000 18.85 0.48 41.59 3.02
220 245 2.366533 CATCTGCACCTGAGCTCAAAT 58.633 47.619 18.85 5.66 34.99 2.32
221 246 1.817357 TCTGCACCTGAGCTCAAATG 58.183 50.000 18.85 18.60 34.99 2.32
222 247 0.170561 CTGCACCTGAGCTCAAATGC 59.829 55.000 31.22 31.22 37.33 3.56
230 255 2.296920 AGCTCAAATGCTCCCGGTA 58.703 52.632 0.00 0.00 39.34 4.02
231 256 0.618458 AGCTCAAATGCTCCCGGTAA 59.382 50.000 0.00 0.00 39.34 2.85
232 257 1.004277 AGCTCAAATGCTCCCGGTAAA 59.996 47.619 0.00 0.00 39.34 2.01
233 258 1.132453 GCTCAAATGCTCCCGGTAAAC 59.868 52.381 0.00 0.00 0.00 2.01
234 259 2.432444 CTCAAATGCTCCCGGTAAACA 58.568 47.619 0.00 0.00 0.00 2.83
236 261 2.159382 CAAATGCTCCCGGTAAACAGT 58.841 47.619 0.00 0.00 0.00 3.55
238 263 3.706600 AATGCTCCCGGTAAACAGTAA 57.293 42.857 0.00 0.00 0.00 2.24
239 264 3.706600 ATGCTCCCGGTAAACAGTAAA 57.293 42.857 0.00 0.00 0.00 2.01
240 265 3.488778 TGCTCCCGGTAAACAGTAAAA 57.511 42.857 0.00 0.00 0.00 1.52
241 266 4.023726 TGCTCCCGGTAAACAGTAAAAT 57.976 40.909 0.00 0.00 0.00 1.82
242 267 4.004982 TGCTCCCGGTAAACAGTAAAATC 58.995 43.478 0.00 0.00 0.00 2.17
243 268 4.004982 GCTCCCGGTAAACAGTAAAATCA 58.995 43.478 0.00 0.00 0.00 2.57
245 270 5.124936 GCTCCCGGTAAACAGTAAAATCAAT 59.875 40.000 0.00 0.00 0.00 2.57
246 271 6.316890 GCTCCCGGTAAACAGTAAAATCAATA 59.683 38.462 0.00 0.00 0.00 1.90
247 272 7.148205 GCTCCCGGTAAACAGTAAAATCAATAA 60.148 37.037 0.00 0.00 0.00 1.40
248 273 8.632906 TCCCGGTAAACAGTAAAATCAATAAA 57.367 30.769 0.00 0.00 0.00 1.40
249 274 9.075678 TCCCGGTAAACAGTAAAATCAATAAAA 57.924 29.630 0.00 0.00 0.00 1.52
299 579 9.058174 TCGAATCATTTTTGTAGTAACCTTTGA 57.942 29.630 0.00 0.00 0.00 2.69
300 580 9.113876 CGAATCATTTTTGTAGTAACCTTTGAC 57.886 33.333 0.00 0.00 0.00 3.18
301 581 9.959749 GAATCATTTTTGTAGTAACCTTTGACA 57.040 29.630 0.00 0.00 0.00 3.58
307 587 9.930693 TTTTTGTAGTAACCTTTGACAAATGTT 57.069 25.926 20.59 20.59 39.15 2.71
308 588 8.918961 TTTGTAGTAACCTTTGACAAATGTTG 57.081 30.769 23.71 5.21 35.63 3.33
310 590 8.734218 TGTAGTAACCTTTGACAAATGTTGTA 57.266 30.769 23.71 15.35 45.52 2.41
311 591 9.344772 TGTAGTAACCTTTGACAAATGTTGTAT 57.655 29.630 23.71 14.89 45.52 2.29
312 592 9.607285 GTAGTAACCTTTGACAAATGTTGTATG 57.393 33.333 23.71 3.06 45.52 2.39
313 593 7.145323 AGTAACCTTTGACAAATGTTGTATGC 58.855 34.615 23.71 12.69 45.52 3.14
314 594 4.545610 ACCTTTGACAAATGTTGTATGCG 58.454 39.130 0.05 0.00 45.52 4.73
315 595 3.364621 CCTTTGACAAATGTTGTATGCGC 59.635 43.478 0.00 0.00 45.52 6.09
317 597 3.469899 TGACAAATGTTGTATGCGCTC 57.530 42.857 9.73 0.00 45.52 5.03
318 598 2.159720 TGACAAATGTTGTATGCGCTCG 60.160 45.455 9.73 0.00 45.52 5.03
321 601 1.720805 AATGTTGTATGCGCTCGTGA 58.279 45.000 9.73 0.00 0.00 4.35
323 603 1.503294 TGTTGTATGCGCTCGTGAAA 58.497 45.000 9.73 0.00 0.00 2.69
324 604 1.867865 TGTTGTATGCGCTCGTGAAAA 59.132 42.857 9.73 0.00 0.00 2.29
326 606 3.058570 TGTTGTATGCGCTCGTGAAAATT 60.059 39.130 9.73 0.00 0.00 1.82
327 607 3.822594 TGTATGCGCTCGTGAAAATTT 57.177 38.095 9.73 0.00 0.00 1.82
329 609 5.478233 TGTATGCGCTCGTGAAAATTTAT 57.522 34.783 9.73 0.00 0.00 1.40
330 610 5.498159 TGTATGCGCTCGTGAAAATTTATC 58.502 37.500 9.73 0.00 0.00 1.75
331 611 4.614555 ATGCGCTCGTGAAAATTTATCA 57.385 36.364 9.73 0.00 0.00 2.15
332 612 3.742786 TGCGCTCGTGAAAATTTATCAC 58.257 40.909 9.73 16.84 42.94 3.06
351 631 8.890124 TTATCACGAACGGATATTTATGGAAA 57.110 30.769 0.00 0.00 0.00 3.13
353 633 7.416154 TCACGAACGGATATTTATGGAAATC 57.584 36.000 0.00 0.00 36.62 2.17
356 636 6.073980 ACGAACGGATATTTATGGAAATCGTG 60.074 38.462 0.00 0.00 34.85 4.35
357 637 6.554334 AACGGATATTTATGGAAATCGTGG 57.446 37.500 0.00 0.00 34.85 4.94
358 638 4.454504 ACGGATATTTATGGAAATCGTGGC 59.545 41.667 0.00 0.00 33.94 5.01
359 639 4.454161 CGGATATTTATGGAAATCGTGGCA 59.546 41.667 0.00 0.00 36.62 4.92
360 640 5.049060 CGGATATTTATGGAAATCGTGGCAA 60.049 40.000 0.00 0.00 36.62 4.52
361 641 6.514212 CGGATATTTATGGAAATCGTGGCAAA 60.514 38.462 0.00 0.00 36.62 3.68
362 642 7.206687 GGATATTTATGGAAATCGTGGCAAAA 58.793 34.615 0.00 0.00 36.62 2.44
363 643 7.708752 GGATATTTATGGAAATCGTGGCAAAAA 59.291 33.333 0.00 0.00 36.62 1.94
388 916 2.560542 AGACTCGATACTGCCCATCATC 59.439 50.000 0.00 0.00 0.00 2.92
402 930 1.170919 ATCATCTTCGCATGGCAGCC 61.171 55.000 3.66 3.66 0.00 4.85
404 932 1.822613 ATCTTCGCATGGCAGCCAG 60.823 57.895 21.51 12.99 36.75 4.85
405 933 2.547640 ATCTTCGCATGGCAGCCAGT 62.548 55.000 21.51 5.38 36.75 4.00
406 934 3.047718 CTTCGCATGGCAGCCAGTG 62.048 63.158 21.51 18.05 36.75 3.66
409 937 2.412323 CGCATGGCAGCCAGTGATT 61.412 57.895 21.51 0.00 36.75 2.57
410 938 1.895238 GCATGGCAGCCAGTGATTT 59.105 52.632 21.51 0.00 36.75 2.17
411 939 0.248289 GCATGGCAGCCAGTGATTTT 59.752 50.000 21.51 0.00 36.75 1.82
412 940 1.338389 GCATGGCAGCCAGTGATTTTT 60.338 47.619 21.51 0.00 36.75 1.94
585 1226 3.568007 TGTTATTGACCACTTTGTCTGCC 59.432 43.478 0.00 0.00 36.21 4.85
591 1232 3.265791 GACCACTTTGTCTGCCAGATAG 58.734 50.000 0.00 0.00 32.39 2.08
602 1243 1.134580 TGCCAGATAGTGCAAGAGAGC 60.135 52.381 0.00 0.00 33.87 4.09
612 1253 5.095145 AGTGCAAGAGAGCAGATCAAATA 57.905 39.130 0.00 0.00 46.69 1.40
614 1255 5.759273 AGTGCAAGAGAGCAGATCAAATATC 59.241 40.000 0.00 0.00 46.69 1.63
680 1324 9.401873 GTTATTTGTGTGGAATTACAAACTACC 57.598 33.333 12.35 0.00 46.01 3.18
681 1325 6.394025 TTTGTGTGGAATTACAAACTACCC 57.606 37.500 12.35 0.00 40.65 3.69
683 1327 5.310451 TGTGTGGAATTACAAACTACCCTC 58.690 41.667 12.35 0.00 31.36 4.30
685 1329 5.642491 GTGTGGAATTACAAACTACCCTCTC 59.358 44.000 3.47 0.00 31.36 3.20
686 1330 5.183969 GTGGAATTACAAACTACCCTCTCC 58.816 45.833 0.00 0.00 0.00 3.71
687 1331 4.081309 TGGAATTACAAACTACCCTCTCCG 60.081 45.833 0.00 0.00 0.00 4.63
689 1333 4.732672 ATTACAAACTACCCTCTCCGTC 57.267 45.455 0.00 0.00 0.00 4.79
690 1334 1.264295 ACAAACTACCCTCTCCGTCC 58.736 55.000 0.00 0.00 0.00 4.79
691 1335 0.172803 CAAACTACCCTCTCCGTCCG 59.827 60.000 0.00 0.00 0.00 4.79
692 1336 0.969409 AAACTACCCTCTCCGTCCGG 60.969 60.000 0.00 0.00 0.00 5.14
693 1337 1.856539 AACTACCCTCTCCGTCCGGA 61.857 60.000 0.00 0.00 42.90 5.14
694 1338 1.077212 CTACCCTCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
695 1339 0.682209 CTACCCTCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
696 1340 0.032813 TACCCTCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
697 1341 0.032813 ACCCTCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
698 1342 0.388294 CCCTCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
699 1343 1.400737 CCTCTCCGTCCGGAAATACT 58.599 55.000 5.23 0.00 44.66 2.12
702 1346 2.165845 CTCTCCGTCCGGAAATACTTGT 59.834 50.000 5.23 0.00 44.66 3.16
703 1347 2.165030 TCTCCGTCCGGAAATACTTGTC 59.835 50.000 5.23 0.00 44.66 3.18
706 1350 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
708 1352 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
709 1353 6.918800 CCGTCCGGAAATACTTGTCATCAAG 61.919 48.000 5.23 6.44 45.65 3.02
710 1354 8.994207 CCGTCCGGAAATACTTGTCATCAAGA 62.994 46.154 5.23 0.31 44.37 3.02
796 1440 9.894783 TTTTAATGACAAATATTTTCGGACGAA 57.105 25.926 2.62 2.62 0.00 3.85
797 1441 9.549509 TTTAATGACAAATATTTTCGGACGAAG 57.450 29.630 7.25 0.00 35.38 3.79
824 1468 0.108804 GATGCGTGGAAAGAGACGGA 60.109 55.000 0.00 0.00 40.32 4.69
826 1470 2.095252 GCGTGGAAAGAGACGGAGC 61.095 63.158 0.00 0.00 36.09 4.70
828 1472 1.671742 GTGGAAAGAGACGGAGCCA 59.328 57.895 0.00 0.00 0.00 4.75
830 1474 0.250234 TGGAAAGAGACGGAGCCATG 59.750 55.000 0.00 0.00 0.00 3.66
832 1476 0.107945 GAAAGAGACGGAGCCATGCT 60.108 55.000 0.00 0.00 43.88 3.79
864 1550 1.056660 AGATGGTTGGTGAGTCGGTT 58.943 50.000 0.00 0.00 0.00 4.44
916 1612 0.326264 AAGGACCACTGCACCAGATC 59.674 55.000 0.00 0.00 35.18 2.75
939 1638 7.026631 TCAACGTTTTCTTCATTCAGTCATT 57.973 32.000 0.00 0.00 0.00 2.57
940 1639 7.479980 TCAACGTTTTCTTCATTCAGTCATTT 58.520 30.769 0.00 0.00 0.00 2.32
942 1641 7.914537 ACGTTTTCTTCATTCAGTCATTTTC 57.085 32.000 0.00 0.00 0.00 2.29
943 1642 7.479980 ACGTTTTCTTCATTCAGTCATTTTCA 58.520 30.769 0.00 0.00 0.00 2.69
944 1643 8.137437 ACGTTTTCTTCATTCAGTCATTTTCAT 58.863 29.630 0.00 0.00 0.00 2.57
945 1644 9.611284 CGTTTTCTTCATTCAGTCATTTTCATA 57.389 29.630 0.00 0.00 0.00 2.15
950 1649 8.618677 TCTTCATTCAGTCATTTTCATATCTGC 58.381 33.333 0.00 0.00 0.00 4.26
951 1650 8.515695 TTCATTCAGTCATTTTCATATCTGCT 57.484 30.769 0.00 0.00 0.00 4.24
952 1651 8.515695 TCATTCAGTCATTTTCATATCTGCTT 57.484 30.769 0.00 0.00 0.00 3.91
953 1652 8.403236 TCATTCAGTCATTTTCATATCTGCTTG 58.597 33.333 0.00 0.00 0.00 4.01
954 1653 7.692460 TTCAGTCATTTTCATATCTGCTTGT 57.308 32.000 0.00 0.00 0.00 3.16
955 1654 7.080353 TCAGTCATTTTCATATCTGCTTGTG 57.920 36.000 0.00 0.00 0.00 3.33
956 1655 6.656270 TCAGTCATTTTCATATCTGCTTGTGT 59.344 34.615 0.00 0.00 0.00 3.72
957 1656 6.745907 CAGTCATTTTCATATCTGCTTGTGTG 59.254 38.462 0.00 0.00 0.00 3.82
958 1657 6.432162 AGTCATTTTCATATCTGCTTGTGTGT 59.568 34.615 0.00 0.00 0.00 3.72
959 1658 6.525628 GTCATTTTCATATCTGCTTGTGTGTG 59.474 38.462 0.00 0.00 0.00 3.82
960 1659 4.424061 TTTCATATCTGCTTGTGTGTGC 57.576 40.909 0.00 0.00 0.00 4.57
961 1660 3.339253 TCATATCTGCTTGTGTGTGCT 57.661 42.857 0.00 0.00 0.00 4.40
962 1661 3.264947 TCATATCTGCTTGTGTGTGCTC 58.735 45.455 0.00 0.00 0.00 4.26
963 1662 2.099141 TATCTGCTTGTGTGTGCTCC 57.901 50.000 0.00 0.00 0.00 4.70
964 1663 0.952497 ATCTGCTTGTGTGTGCTCCG 60.952 55.000 0.00 0.00 0.00 4.63
965 1664 2.591429 TGCTTGTGTGTGCTCCGG 60.591 61.111 0.00 0.00 0.00 5.14
966 1665 4.030452 GCTTGTGTGTGCTCCGGC 62.030 66.667 0.00 0.00 39.26 6.13
967 1666 3.716006 CTTGTGTGTGCTCCGGCG 61.716 66.667 0.00 0.00 42.25 6.46
990 1689 2.583520 CCTCTGCAGCTCCAGACC 59.416 66.667 9.47 0.00 36.96 3.85
996 1695 2.584418 CAGCTCCAGACCGCATCG 60.584 66.667 0.00 0.00 0.00 3.84
1123 1822 1.810030 GGTAAGTCCCTTGCGCTCG 60.810 63.158 9.73 0.00 0.00 5.03
1168 1888 2.029073 AGTTCGTGTGGCTGACGG 59.971 61.111 8.62 0.00 37.43 4.79
1245 1980 1.868251 GACCACGTCGACATCTCGC 60.868 63.158 17.16 0.00 39.96 5.03
1390 2131 2.958355 CCATTTCAGGTGCCCGATATTT 59.042 45.455 0.00 0.00 0.00 1.40
1397 2138 1.947456 GGTGCCCGATATTTTCCTGAC 59.053 52.381 0.00 0.00 0.00 3.51
1398 2139 2.421529 GGTGCCCGATATTTTCCTGACT 60.422 50.000 0.00 0.00 0.00 3.41
1399 2140 2.614057 GTGCCCGATATTTTCCTGACTG 59.386 50.000 0.00 0.00 0.00 3.51
1400 2141 1.604278 GCCCGATATTTTCCTGACTGC 59.396 52.381 0.00 0.00 0.00 4.40
1401 2142 2.222027 CCCGATATTTTCCTGACTGCC 58.778 52.381 0.00 0.00 0.00 4.85
1402 2143 2.421388 CCCGATATTTTCCTGACTGCCA 60.421 50.000 0.00 0.00 0.00 4.92
1403 2144 3.278574 CCGATATTTTCCTGACTGCCAA 58.721 45.455 0.00 0.00 0.00 4.52
1404 2145 3.885297 CCGATATTTTCCTGACTGCCAAT 59.115 43.478 0.00 0.00 0.00 3.16
1405 2146 4.023707 CCGATATTTTCCTGACTGCCAATC 60.024 45.833 0.00 0.00 0.00 2.67
1406 2147 4.023707 CGATATTTTCCTGACTGCCAATCC 60.024 45.833 0.00 0.00 0.00 3.01
1407 2148 2.673775 TTTTCCTGACTGCCAATCCA 57.326 45.000 0.00 0.00 0.00 3.41
1408 2149 1.909700 TTTCCTGACTGCCAATCCAC 58.090 50.000 0.00 0.00 0.00 4.02
1409 2150 0.038166 TTCCTGACTGCCAATCCACC 59.962 55.000 0.00 0.00 0.00 4.61
1410 2151 1.746615 CCTGACTGCCAATCCACCG 60.747 63.158 0.00 0.00 0.00 4.94
1411 2152 1.746615 CTGACTGCCAATCCACCGG 60.747 63.158 0.00 0.00 0.00 5.28
1412 2153 2.184020 CTGACTGCCAATCCACCGGA 62.184 60.000 9.46 0.00 35.55 5.14
1413 2154 1.002624 GACTGCCAATCCACCGGAA 60.003 57.895 9.46 0.00 34.34 4.30
1441 2182 2.233431 CCTTCCTCTTCTCCTGTCACTG 59.767 54.545 0.00 0.00 0.00 3.66
1442 2183 2.685106 TCCTCTTCTCCTGTCACTGT 57.315 50.000 0.00 0.00 0.00 3.55
1469 2234 4.681483 GGAATTTTTCCTTCTCAAACTGCG 59.319 41.667 0.00 0.00 46.57 5.18
1473 2238 1.581934 TCCTTCTCAAACTGCGTGTG 58.418 50.000 0.00 0.00 0.00 3.82
1477 2242 2.124529 TCAAACTGCGTGTGCCCA 60.125 55.556 0.00 0.00 41.78 5.36
1480 2262 2.480610 AAACTGCGTGTGCCCACTG 61.481 57.895 0.00 0.00 41.78 3.66
1739 2569 4.648007 ACCAAGGAGCAGGTCAGA 57.352 55.556 1.20 0.00 30.79 3.27
1762 2592 2.047844 GCTCCTGTCGCTGCAAGA 60.048 61.111 0.00 0.00 34.07 3.02
1763 2593 1.669115 GCTCCTGTCGCTGCAAGAA 60.669 57.895 0.00 0.00 34.07 2.52
1767 2597 1.002430 TCCTGTCGCTGCAAGAATTCT 59.998 47.619 0.88 0.88 34.07 2.40
1790 2620 3.334054 AGGCTCCAGGGCAAGTCC 61.334 66.667 0.00 0.00 43.56 3.85
1791 2621 3.650950 GGCTCCAGGGCAAGTCCA 61.651 66.667 0.00 0.00 40.53 4.02
1824 2667 4.021719 ACTGATGCCTCCATTTGTTTCTTG 60.022 41.667 0.00 0.00 0.00 3.02
1832 2675 5.008613 CCTCCATTTGTTTCTTGAGACGAAA 59.991 40.000 0.00 0.00 0.00 3.46
1833 2676 6.294176 CCTCCATTTGTTTCTTGAGACGAAAT 60.294 38.462 0.00 0.00 33.45 2.17
1835 2678 5.630680 CCATTTGTTTCTTGAGACGAAATGG 59.369 40.000 19.89 19.89 37.66 3.16
1836 2679 3.896648 TGTTTCTTGAGACGAAATGGC 57.103 42.857 0.00 0.00 33.45 4.40
1837 2680 3.210227 TGTTTCTTGAGACGAAATGGCA 58.790 40.909 0.00 0.00 33.45 4.92
1870 2718 4.823989 TCATTAGATCGTCTGAGCAGATCA 59.176 41.667 15.53 0.00 42.21 2.92
1890 2757 5.497464 TCATCACAAACTCCACCTTGATA 57.503 39.130 0.00 0.00 0.00 2.15
1982 2858 3.017048 TCATTATCTTGCCCCTTGGTG 57.983 47.619 0.00 0.00 0.00 4.17
2021 5965 4.935205 AGTAACTATGCACGCTCAAAATGA 59.065 37.500 0.00 0.00 0.00 2.57
2089 6033 9.451002 TCGGTGAATTTACCAATTATTTGTCTA 57.549 29.630 18.58 0.00 40.89 2.59
2412 6374 0.744874 TAAGCTAGCACCGAAGCGAT 59.255 50.000 18.83 0.00 43.63 4.58
2509 6498 5.771153 TTCAACATTGAACATGAGCTTCA 57.229 34.783 0.00 0.00 41.88 3.02
2513 6502 6.039605 TCAACATTGAACATGAGCTTCAAAGA 59.960 34.615 15.32 8.89 40.22 2.52
2514 6503 6.395426 ACATTGAACATGAGCTTCAAAGAA 57.605 33.333 15.32 0.00 40.22 2.52
2532 6521 6.260050 TCAAAGAAGCTCACAAAACGAATACT 59.740 34.615 0.00 0.00 0.00 2.12
2583 6572 1.000385 CACCACAACCACGCATCAAAT 60.000 47.619 0.00 0.00 0.00 2.32
2593 6582 3.440173 CCACGCATCAAATAAGTCCACTT 59.560 43.478 0.00 0.00 39.85 3.16
2712 6704 7.419204 CGGATAAAACTAGAACAAAACAACCA 58.581 34.615 0.00 0.00 0.00 3.67
2800 6792 4.168760 GTTTGCCTTTAGTGTGATGCATC 58.831 43.478 20.14 20.14 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 7.116736 TCTACTAGTGGTATGTTGTCTCATGA 58.883 38.462 5.39 0.00 0.00 3.07
22 23 7.834681 TCTTCTACTAGTGGTATGTTGTCTCAT 59.165 37.037 5.39 0.00 0.00 2.90
132 138 1.227556 GCGCGGGGAACTCATACAT 60.228 57.895 8.83 0.00 0.00 2.29
134 158 0.596859 GTAGCGCGGGGAACTCATAC 60.597 60.000 8.83 0.00 0.00 2.39
141 165 0.966875 TTCTGTAGTAGCGCGGGGAA 60.967 55.000 8.83 0.00 0.00 3.97
149 173 0.386113 CCGCCCTCTTCTGTAGTAGC 59.614 60.000 0.00 0.00 0.00 3.58
155 179 0.608640 CTTACACCGCCCTCTTCTGT 59.391 55.000 0.00 0.00 0.00 3.41
167 192 5.053145 CCTCATCTGCTCAATACTTACACC 58.947 45.833 0.00 0.00 0.00 4.16
173 198 2.363680 CGTCCCTCATCTGCTCAATACT 59.636 50.000 0.00 0.00 0.00 2.12
176 201 1.134580 CACGTCCCTCATCTGCTCAAT 60.135 52.381 0.00 0.00 0.00 2.57
188 213 3.023949 GCAGATGCTCCACGTCCCT 62.024 63.158 0.00 0.00 38.21 4.20
190 215 2.103042 GTGCAGATGCTCCACGTCC 61.103 63.158 6.35 0.00 42.66 4.79
191 216 3.479370 GTGCAGATGCTCCACGTC 58.521 61.111 6.35 0.00 42.66 4.34
197 222 0.810823 GAGCTCAGGTGCAGATGCTC 60.811 60.000 9.40 10.04 42.66 4.26
198 223 1.221293 GAGCTCAGGTGCAGATGCT 59.779 57.895 9.40 0.00 42.66 3.79
199 224 0.675837 TTGAGCTCAGGTGCAGATGC 60.676 55.000 17.43 0.00 42.50 3.91
200 225 1.817357 TTTGAGCTCAGGTGCAGATG 58.183 50.000 17.43 0.00 34.99 2.90
202 227 1.817357 CATTTGAGCTCAGGTGCAGA 58.183 50.000 17.43 0.00 34.99 4.26
203 228 0.170561 GCATTTGAGCTCAGGTGCAG 59.829 55.000 32.97 17.92 37.72 4.41
204 229 0.251033 AGCATTTGAGCTCAGGTGCA 60.251 50.000 36.06 16.85 42.18 4.57
205 230 2.564471 AGCATTTGAGCTCAGGTGC 58.436 52.632 31.86 31.86 42.18 5.01
213 238 1.132453 GTTTACCGGGAGCATTTGAGC 59.868 52.381 6.32 0.00 0.00 4.26
215 240 2.224670 ACTGTTTACCGGGAGCATTTGA 60.225 45.455 6.32 0.00 0.00 2.69
216 241 2.159382 ACTGTTTACCGGGAGCATTTG 58.841 47.619 6.32 0.00 0.00 2.32
217 242 2.579410 ACTGTTTACCGGGAGCATTT 57.421 45.000 6.32 0.00 0.00 2.32
218 243 3.706600 TTACTGTTTACCGGGAGCATT 57.293 42.857 6.32 0.00 0.00 3.56
220 245 3.488778 TTTTACTGTTTACCGGGAGCA 57.511 42.857 6.32 0.90 0.00 4.26
221 246 4.004982 TGATTTTACTGTTTACCGGGAGC 58.995 43.478 6.32 0.00 0.00 4.70
222 247 6.753107 ATTGATTTTACTGTTTACCGGGAG 57.247 37.500 6.32 0.00 0.00 4.30
224 249 9.694137 TTTTTATTGATTTTACTGTTTACCGGG 57.306 29.630 6.32 0.00 0.00 5.73
272 552 9.840427 CAAAGGTTACTACAAAAATGATTCGAT 57.160 29.630 0.00 0.00 0.00 3.59
275 555 9.959749 TGTCAAAGGTTACTACAAAAATGATTC 57.040 29.630 0.00 0.00 0.00 2.52
281 561 9.930693 AACATTTGTCAAAGGTTACTACAAAAA 57.069 25.926 22.98 0.00 42.80 1.94
283 563 8.524487 ACAACATTTGTCAAAGGTTACTACAAA 58.476 29.630 23.58 5.56 42.75 2.83
284 564 8.057536 ACAACATTTGTCAAAGGTTACTACAA 57.942 30.769 23.58 0.00 42.75 2.41
285 565 7.633193 ACAACATTTGTCAAAGGTTACTACA 57.367 32.000 23.58 0.00 42.75 2.74
286 566 9.607285 CATACAACATTTGTCAAAGGTTACTAC 57.393 33.333 23.58 0.00 42.75 2.73
287 567 8.293867 GCATACAACATTTGTCAAAGGTTACTA 58.706 33.333 23.58 16.91 42.75 1.82
288 568 7.145323 GCATACAACATTTGTCAAAGGTTACT 58.855 34.615 23.58 15.63 42.75 2.24
290 570 6.146216 CGCATACAACATTTGTCAAAGGTTA 58.854 36.000 23.58 12.82 42.75 2.85
292 572 4.545610 CGCATACAACATTTGTCAAAGGT 58.454 39.130 9.73 9.73 44.12 3.50
294 574 4.229096 AGCGCATACAACATTTGTCAAAG 58.771 39.130 11.47 0.00 44.12 2.77
300 580 2.159720 TCACGAGCGCATACAACATTTG 60.160 45.455 11.47 0.00 0.00 2.32
301 581 2.073056 TCACGAGCGCATACAACATTT 58.927 42.857 11.47 0.00 0.00 2.32
302 582 1.720805 TCACGAGCGCATACAACATT 58.279 45.000 11.47 0.00 0.00 2.71
304 584 1.503294 TTTCACGAGCGCATACAACA 58.497 45.000 11.47 0.00 0.00 3.33
305 585 2.587612 TTTTCACGAGCGCATACAAC 57.412 45.000 11.47 0.00 0.00 3.32
306 586 3.822594 AATTTTCACGAGCGCATACAA 57.177 38.095 11.47 0.00 0.00 2.41
307 587 3.822594 AAATTTTCACGAGCGCATACA 57.177 38.095 11.47 0.00 0.00 2.29
308 588 5.392585 GTGATAAATTTTCACGAGCGCATAC 59.607 40.000 11.47 0.00 34.67 2.39
309 589 5.498159 GTGATAAATTTTCACGAGCGCATA 58.502 37.500 11.47 0.00 34.67 3.14
310 590 4.342772 GTGATAAATTTTCACGAGCGCAT 58.657 39.130 11.47 0.00 34.67 4.73
311 591 3.742786 GTGATAAATTTTCACGAGCGCA 58.257 40.909 11.47 0.00 34.67 6.09
318 598 9.498307 AAATATCCGTTCGTGATAAATTTTCAC 57.502 29.630 16.84 16.84 40.06 3.18
323 603 9.496873 TCCATAAATATCCGTTCGTGATAAATT 57.503 29.630 7.19 7.92 0.00 1.82
324 604 9.496873 TTCCATAAATATCCGTTCGTGATAAAT 57.503 29.630 7.19 3.94 0.00 1.40
326 606 8.890124 TTTCCATAAATATCCGTTCGTGATAA 57.110 30.769 7.19 0.00 0.00 1.75
327 607 9.146984 GATTTCCATAAATATCCGTTCGTGATA 57.853 33.333 6.11 6.11 35.41 2.15
329 609 6.144886 CGATTTCCATAAATATCCGTTCGTGA 59.855 38.462 0.00 0.00 35.41 4.35
330 610 6.073980 ACGATTTCCATAAATATCCGTTCGTG 60.074 38.462 0.00 0.00 35.41 4.35
331 611 5.987347 ACGATTTCCATAAATATCCGTTCGT 59.013 36.000 0.00 0.00 35.41 3.85
332 612 6.296605 CACGATTTCCATAAATATCCGTTCG 58.703 40.000 0.00 0.00 35.41 3.95
333 613 6.599437 CCACGATTTCCATAAATATCCGTTC 58.401 40.000 0.00 0.00 35.41 3.95
336 616 4.454161 TGCCACGATTTCCATAAATATCCG 59.546 41.667 0.00 0.00 35.41 4.18
363 643 3.695830 TGGGCAGTATCGAGTCTTTTT 57.304 42.857 0.00 0.00 0.00 1.94
364 644 3.197766 TGATGGGCAGTATCGAGTCTTTT 59.802 43.478 0.00 0.00 0.00 2.27
365 645 2.766263 TGATGGGCAGTATCGAGTCTTT 59.234 45.455 0.00 0.00 0.00 2.52
367 647 2.073252 TGATGGGCAGTATCGAGTCT 57.927 50.000 0.00 0.00 0.00 3.24
368 648 2.560542 AGATGATGGGCAGTATCGAGTC 59.439 50.000 0.00 0.00 0.00 3.36
369 649 2.603021 AGATGATGGGCAGTATCGAGT 58.397 47.619 0.00 0.00 0.00 4.18
370 650 3.583806 GAAGATGATGGGCAGTATCGAG 58.416 50.000 0.00 0.00 0.00 4.04
371 651 2.029918 CGAAGATGATGGGCAGTATCGA 60.030 50.000 0.00 0.00 33.20 3.59
372 652 2.332104 CGAAGATGATGGGCAGTATCG 58.668 52.381 0.00 0.00 0.00 2.92
373 653 2.072298 GCGAAGATGATGGGCAGTATC 58.928 52.381 0.00 0.00 0.00 2.24
375 655 0.829990 TGCGAAGATGATGGGCAGTA 59.170 50.000 0.00 0.00 0.00 2.74
377 657 0.591659 CATGCGAAGATGATGGGCAG 59.408 55.000 0.00 0.00 37.01 4.85
379 659 1.954528 CCATGCGAAGATGATGGGC 59.045 57.895 0.00 0.00 34.14 5.36
380 660 0.820482 TGCCATGCGAAGATGATGGG 60.820 55.000 0.00 0.00 37.67 4.00
388 916 2.749044 ACTGGCTGCCATGCGAAG 60.749 61.111 23.64 11.87 30.82 3.79
418 946 9.185680 TGCTACACTATATCTGTACTTTCTGAA 57.814 33.333 0.00 0.00 0.00 3.02
428 959 7.604164 GCCATGTTTATGCTACACTATATCTGT 59.396 37.037 0.00 0.00 32.79 3.41
501 1033 0.734253 CTACACTCACTGTCTGCGCC 60.734 60.000 4.18 0.00 33.91 6.53
585 1226 3.797451 TCTGCTCTCTTGCACTATCTG 57.203 47.619 0.00 0.00 38.12 2.90
591 1232 5.333187 CGATATTTGATCTGCTCTCTTGCAC 60.333 44.000 0.00 0.00 38.12 4.57
612 1253 7.063898 CCAGAATGCTGATAATAATTCGACGAT 59.936 37.037 0.74 0.00 45.17 3.73
614 1255 6.146184 ACCAGAATGCTGATAATAATTCGACG 59.854 38.462 0.74 0.00 45.17 5.12
628 1269 2.733227 GCGGAAAATGACCAGAATGCTG 60.733 50.000 0.00 0.00 41.93 4.41
678 1322 0.032813 TATTTCCGGACGGAGAGGGT 60.033 55.000 13.64 0.00 46.06 4.34
679 1323 0.388294 GTATTTCCGGACGGAGAGGG 59.612 60.000 13.64 0.00 46.06 4.30
680 1324 1.400737 AGTATTTCCGGACGGAGAGG 58.599 55.000 13.64 0.00 46.06 3.69
681 1325 2.165845 ACAAGTATTTCCGGACGGAGAG 59.834 50.000 13.64 0.20 46.06 3.20
683 1327 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
685 1329 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
686 1330 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
687 1331 5.470845 CTTGATGACAAGTATTTCCGGAC 57.529 43.478 1.83 0.00 45.73 4.79
699 1343 9.690913 ATCTCCTTTTATTCATCTTGATGACAA 57.309 29.630 12.28 7.53 34.65 3.18
770 1414 9.894783 TTCGTCCGAAAATATTTGTCATTAAAA 57.105 25.926 0.39 0.00 0.00 1.52
771 1415 9.549509 CTTCGTCCGAAAATATTTGTCATTAAA 57.450 29.630 0.39 0.00 33.34 1.52
772 1416 8.937884 TCTTCGTCCGAAAATATTTGTCATTAA 58.062 29.630 0.39 0.00 33.34 1.40
773 1417 8.481974 TCTTCGTCCGAAAATATTTGTCATTA 57.518 30.769 0.39 0.00 33.34 1.90
774 1418 7.372451 TCTTCGTCCGAAAATATTTGTCATT 57.628 32.000 0.39 0.00 33.34 2.57
775 1419 6.978343 TCTTCGTCCGAAAATATTTGTCAT 57.022 33.333 0.39 0.00 33.34 3.06
776 1420 6.788684 TTCTTCGTCCGAAAATATTTGTCA 57.211 33.333 0.39 0.00 33.34 3.58
777 1421 8.669394 ATTTTCTTCGTCCGAAAATATTTGTC 57.331 30.769 15.21 1.54 44.69 3.18
784 1428 6.912591 GCATCATATTTTCTTCGTCCGAAAAT 59.087 34.615 18.41 18.41 46.76 1.82
785 1429 6.255215 GCATCATATTTTCTTCGTCCGAAAA 58.745 36.000 3.52 10.09 42.49 2.29
786 1430 5.501736 CGCATCATATTTTCTTCGTCCGAAA 60.502 40.000 3.52 0.00 33.34 3.46
787 1431 4.026062 CGCATCATATTTTCTTCGTCCGAA 60.026 41.667 1.81 1.81 0.00 4.30
788 1432 3.489416 CGCATCATATTTTCTTCGTCCGA 59.511 43.478 0.00 0.00 0.00 4.55
789 1433 3.245284 ACGCATCATATTTTCTTCGTCCG 59.755 43.478 0.00 0.00 0.00 4.79
790 1434 4.518217 CACGCATCATATTTTCTTCGTCC 58.482 43.478 0.00 0.00 0.00 4.79
791 1435 4.270084 TCCACGCATCATATTTTCTTCGTC 59.730 41.667 0.00 0.00 0.00 4.20
792 1436 4.188462 TCCACGCATCATATTTTCTTCGT 58.812 39.130 0.00 0.00 0.00 3.85
793 1437 4.794248 TCCACGCATCATATTTTCTTCG 57.206 40.909 0.00 0.00 0.00 3.79
794 1438 6.785191 TCTTTCCACGCATCATATTTTCTTC 58.215 36.000 0.00 0.00 0.00 2.87
795 1439 6.599244 TCTCTTTCCACGCATCATATTTTCTT 59.401 34.615 0.00 0.00 0.00 2.52
796 1440 6.037610 GTCTCTTTCCACGCATCATATTTTCT 59.962 38.462 0.00 0.00 0.00 2.52
797 1441 6.195165 GTCTCTTTCCACGCATCATATTTTC 58.805 40.000 0.00 0.00 0.00 2.29
801 1445 3.384668 CGTCTCTTTCCACGCATCATAT 58.615 45.455 0.00 0.00 0.00 1.78
824 1468 0.750850 GCATCCAATCAAGCATGGCT 59.249 50.000 0.00 0.00 42.56 4.75
826 1470 1.068588 CTGGCATCCAATCAAGCATGG 59.931 52.381 0.00 0.00 38.09 3.66
828 1472 2.447408 TCTGGCATCCAATCAAGCAT 57.553 45.000 0.00 0.00 30.80 3.79
830 1474 1.340248 CCATCTGGCATCCAATCAAGC 59.660 52.381 0.00 0.00 30.80 4.01
832 1476 2.761767 CAACCATCTGGCATCCAATCAA 59.238 45.455 0.00 0.00 39.32 2.57
864 1550 0.539986 GCCTTATCGGACAAGACCCA 59.460 55.000 0.00 0.00 33.16 4.51
916 1612 7.684062 AAATGACTGAATGAAGAAAACGTTG 57.316 32.000 0.00 0.00 0.00 4.10
939 1638 4.074259 AGCACACACAAGCAGATATGAAA 58.926 39.130 0.00 0.00 0.00 2.69
940 1639 3.678289 AGCACACACAAGCAGATATGAA 58.322 40.909 0.00 0.00 0.00 2.57
942 1641 2.353889 GGAGCACACACAAGCAGATATG 59.646 50.000 0.00 0.00 0.00 1.78
943 1642 2.636830 GGAGCACACACAAGCAGATAT 58.363 47.619 0.00 0.00 0.00 1.63
944 1643 1.672737 CGGAGCACACACAAGCAGATA 60.673 52.381 0.00 0.00 0.00 1.98
945 1644 0.952497 CGGAGCACACACAAGCAGAT 60.952 55.000 0.00 0.00 0.00 2.90
946 1645 1.595109 CGGAGCACACACAAGCAGA 60.595 57.895 0.00 0.00 0.00 4.26
947 1646 2.610694 CCGGAGCACACACAAGCAG 61.611 63.158 0.00 0.00 0.00 4.24
948 1647 2.591429 CCGGAGCACACACAAGCA 60.591 61.111 0.00 0.00 0.00 3.91
949 1648 4.030452 GCCGGAGCACACACAAGC 62.030 66.667 5.05 0.00 39.53 4.01
950 1649 3.716006 CGCCGGAGCACACACAAG 61.716 66.667 5.05 0.00 39.83 3.16
951 1650 4.228567 TCGCCGGAGCACACACAA 62.229 61.111 5.05 0.00 39.83 3.33
952 1651 4.961511 GTCGCCGGAGCACACACA 62.962 66.667 5.05 0.00 39.83 3.72
1123 1822 0.034380 GTAAACAGGAAGGGGGCCTC 60.034 60.000 0.84 0.00 32.12 4.70
1168 1888 2.674380 CTGGCTTCACACCCAGGC 60.674 66.667 0.00 0.00 43.87 4.85
1390 2131 0.038166 GGTGGATTGGCAGTCAGGAA 59.962 55.000 12.30 0.00 0.00 3.36
1397 2138 1.185315 AAATTCCGGTGGATTGGCAG 58.815 50.000 0.00 0.00 0.00 4.85
1398 2139 1.638529 AAAATTCCGGTGGATTGGCA 58.361 45.000 0.00 0.00 0.00 4.92
1399 2140 2.760634 AAAAATTCCGGTGGATTGGC 57.239 45.000 0.00 0.00 0.00 4.52
1739 2569 1.580845 GCAGCGACAGGAGCATGTTT 61.581 55.000 0.00 0.00 37.01 2.83
1762 2592 1.211456 CTGGAGCCTGAGGGAGAATT 58.789 55.000 0.00 0.00 33.58 2.17
1763 2593 0.693767 CCTGGAGCCTGAGGGAGAAT 60.694 60.000 0.00 0.00 33.58 2.40
1790 2620 0.890683 GGCATCAGTTCCCCTGTTTG 59.109 55.000 0.00 0.00 42.19 2.93
1791 2621 0.779997 AGGCATCAGTTCCCCTGTTT 59.220 50.000 0.00 0.00 42.19 2.83
1824 2667 0.723981 GAGCACTGCCATTTCGTCTC 59.276 55.000 0.00 0.00 0.00 3.36
1836 2679 3.051327 CGATCTAATGAGCAGAGCACTG 58.949 50.000 6.80 6.80 45.91 3.66
1837 2680 2.692557 ACGATCTAATGAGCAGAGCACT 59.307 45.455 0.00 0.00 0.00 4.40
1856 2704 2.573941 TGTGATGATCTGCTCAGACG 57.426 50.000 1.15 0.00 40.75 4.18
1870 2718 5.491982 GAGTATCAAGGTGGAGTTTGTGAT 58.508 41.667 0.00 0.00 33.17 3.06
1963 2839 3.017048 TCACCAAGGGGCAAGATAATG 57.983 47.619 0.00 0.00 37.90 1.90
2009 5953 1.210155 GGCGCTTCATTTTGAGCGT 59.790 52.632 17.43 0.00 42.03 5.07
2021 5965 2.665603 GAGTGAAGGAGGGCGCTT 59.334 61.111 7.64 0.00 0.00 4.68
2359 6320 9.332301 CGGCTAACGTTTATTATTTGAAAAAGA 57.668 29.630 5.91 0.00 37.93 2.52
2394 6356 0.528684 GATCGCTTCGGTGCTAGCTT 60.529 55.000 17.23 0.00 35.25 3.74
2509 6498 6.260050 TGAGTATTCGTTTTGTGAGCTTCTTT 59.740 34.615 0.00 0.00 0.00 2.52
2513 6502 4.814234 TGTGAGTATTCGTTTTGTGAGCTT 59.186 37.500 0.00 0.00 0.00 3.74
2514 6503 4.377021 TGTGAGTATTCGTTTTGTGAGCT 58.623 39.130 0.00 0.00 0.00 4.09
2522 6511 3.067106 CAGTGCCTGTGAGTATTCGTTT 58.933 45.455 0.00 0.00 0.00 3.60
2532 6521 4.662961 CGACGCCAGTGCCTGTGA 62.663 66.667 2.18 0.00 0.00 3.58
2544 6533 2.063266 TGTCCTTACATGTTTCGACGC 58.937 47.619 2.30 0.00 0.00 5.19
2583 6572 4.414182 TCTTTTGGGAGGAAAGTGGACTTA 59.586 41.667 0.00 0.00 35.95 2.24
2593 6582 8.115384 TGAAGATGATATTTCTTTTGGGAGGAA 58.885 33.333 4.04 0.00 33.65 3.36
2661 6653 9.601971 GCGTTGATTTGAGTTTTAGTAATGTTA 57.398 29.630 0.00 0.00 0.00 2.41
2667 6659 4.989797 TCCGCGTTGATTTGAGTTTTAGTA 59.010 37.500 4.92 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.