Multiple sequence alignment - TraesCS1A01G084200

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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 TraesCS1A01G084200 chr1A 100.000 4968 0 0 1 4968 69395403 69390436 0.000000e+00 9175.0
1 TraesCS1A01G084200 chr1A 100.000 554 0 0 5288 5841 69390116 69389563 0.000000e+00 1024.0
2 TraesCS1A01G084200 chr1A 92.405 158 11 1 54 211 69395194 69395038 2.120000e-54 224.0
3 TraesCS1A01G084200 chr1A 92.405 158 11 1 210 366 69395350 69395193 2.120000e-54 224.0
4 TraesCS1A01G084200 chr1D 97.631 3081 51 13 210 3275 69790569 69787496 0.000000e+00 5265.0
5 TraesCS1A01G084200 chr1D 97.546 1345 30 1 3624 4968 69786965 69785624 0.000000e+00 2298.0
6 TraesCS1A01G084200 chr1D 88.995 418 13 7 5288 5683 69785572 69785166 2.450000e-133 486.0
7 TraesCS1A01G084200 chr1D 95.222 293 6 4 3335 3627 69787500 69787216 1.920000e-124 457.0
8 TraesCS1A01G084200 chr1D 91.589 214 15 3 1 211 69790624 69790411 5.720000e-75 292.0
9 TraesCS1A01G084200 chr1D 92.424 66 5 0 3425 3490 69787474 69787409 1.730000e-15 95.3
10 TraesCS1A01G084200 chr1B 97.567 3082 51 14 210 3275 111372695 111369622 0.000000e+00 5254.0
11 TraesCS1A01G084200 chr1B 94.930 1637 55 10 3335 4968 111369626 111368015 0.000000e+00 2538.0
12 TraesCS1A01G084200 chr1B 90.847 437 24 10 5288 5719 111367963 111367538 6.570000e-159 571.0
13 TraesCS1A01G084200 chr1B 92.056 214 14 3 1 211 111372750 111372537 1.230000e-76 298.0
14 TraesCS1A01G084200 chr1B 89.524 105 11 0 210 314 111373162 111373058 3.670000e-27 134.0
15 TraesCS1A01G084200 chr1B 94.048 84 3 2 5743 5825 111365661 111365579 6.140000e-25 126.0
16 TraesCS1A01G084200 chr1B 90.909 66 6 0 3425 3490 111369600 111369535 8.060000e-14 89.8


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 TraesCS1A01G084200 chr1A 69389563 69395403 5840 True 2661.750000 9175 96.202500 1 5841 4 chr1A.!!$R1 5840
1 TraesCS1A01G084200 chr1D 69785166 69790624 5458 True 1482.216667 5265 93.901167 1 5683 6 chr1D.!!$R1 5682
2 TraesCS1A01G084200 chr1B 111365579 111373162 7583 True 1287.257143 5254 92.840143 1 5825 7 chr1B.!!$R1 5824

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
555 971 0.031010 GCCTCCTCCCCCTTCTTCTA 60.031 60.000 0.00 0.00 0.00 2.10 F
1332 1758 0.178953 ACCCAAATGAGGCACAGCTT 60.179 50.000 0.00 0.00 0.00 3.74 F
1593 2019 1.973281 GCTTGCTAGCCTGGTTGCA 60.973 57.895 13.29 1.48 41.74 4.08 F
2442 2868 2.200373 TGCCTTTACCTTCCTCAAGC 57.800 50.000 0.00 0.00 0.00 4.01 F
2694 3123 2.022718 AGGAGGAGCTTCAGTCACTT 57.977 50.000 0.00 0.00 0.00 3.16 F
3842 4525 2.287009 GCGTCTCTCCAACCTTTGTTTG 60.287 50.000 0.00 0.00 30.42 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 2246 0.536460 CACTGGGGTAAGTTTGCCGT 60.536 55.000 0.00 0.0 33.27 5.68 R
2661 3090 1.172175 CCTCCTTCTCTTTGGCAAGC 58.828 55.000 0.00 0.0 0.00 4.01 R
2694 3123 1.550976 GCCTCTTCCTTCTCTTTCCGA 59.449 52.381 0.00 0.0 0.00 4.55 R
4414 5097 0.879765 CAGCTTTGAGGTGCAGGAAG 59.120 55.000 0.00 0.0 36.88 3.46 R
4546 5229 3.241530 AGGGCGCAGGTCTTGTCA 61.242 61.111 10.83 0.0 0.00 3.58 R
5737 6456 0.034380 GAGTTAGGCCCCTTGGTTCC 60.034 60.000 0.00 0.0 0.00 3.62 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
32 445 2.289257 CCGATTAGATCATGCAGAGCCA 60.289 50.000 0.00 0.00 31.44 4.75
33 446 2.994578 CGATTAGATCATGCAGAGCCAG 59.005 50.000 0.00 0.00 31.44 4.85
56 471 3.463585 CCCGCCAAGCCATGCAAT 61.464 61.111 0.00 0.00 0.00 3.56
69 484 2.339418 CATGCAATCGCCACAACAAAT 58.661 42.857 0.00 0.00 37.32 2.32
70 485 2.522836 TGCAATCGCCACAACAAATT 57.477 40.000 0.00 0.00 37.32 1.82
71 486 3.650070 TGCAATCGCCACAACAAATTA 57.350 38.095 0.00 0.00 37.32 1.40
99 514 1.002990 TCGCCGACCACTCTCACTA 60.003 57.895 0.00 0.00 0.00 2.74
104 519 1.469308 CCGACCACTCTCACTACACTC 59.531 57.143 0.00 0.00 0.00 3.51
108 523 1.401670 CCACTCTCACTACACTCACGC 60.402 57.143 0.00 0.00 0.00 5.34
119 534 0.888736 CACTCACGCCAATCAACCCA 60.889 55.000 0.00 0.00 0.00 4.51
194 609 4.066139 GCCCCCATGTCAGCCCTT 62.066 66.667 0.00 0.00 0.00 3.95
195 610 2.043652 CCCCCATGTCAGCCCTTG 60.044 66.667 0.00 0.00 0.00 3.61
196 611 2.615465 CCCCCATGTCAGCCCTTGA 61.615 63.158 0.00 0.00 0.00 3.02
197 612 1.616921 CCCCATGTCAGCCCTTGAT 59.383 57.895 0.00 0.00 38.29 2.57
198 613 0.466922 CCCCATGTCAGCCCTTGATC 60.467 60.000 0.00 0.00 38.29 2.92
199 614 0.256752 CCCATGTCAGCCCTTGATCA 59.743 55.000 0.00 0.00 38.29 2.92
200 615 1.133575 CCCATGTCAGCCCTTGATCAT 60.134 52.381 0.00 0.00 38.29 2.45
201 616 1.954382 CCATGTCAGCCCTTGATCATG 59.046 52.381 0.00 0.00 38.29 3.07
202 617 1.954382 CATGTCAGCCCTTGATCATGG 59.046 52.381 18.61 18.61 38.29 3.66
203 618 0.994247 TGTCAGCCCTTGATCATGGT 59.006 50.000 22.43 6.00 38.29 3.55
204 619 1.340308 TGTCAGCCCTTGATCATGGTG 60.340 52.381 22.43 16.22 38.29 4.17
205 620 0.256752 TCAGCCCTTGATCATGGTGG 59.743 55.000 22.43 11.79 0.00 4.61
206 621 0.033796 CAGCCCTTGATCATGGTGGT 60.034 55.000 22.43 16.88 0.00 4.16
207 622 0.706433 AGCCCTTGATCATGGTGGTT 59.294 50.000 22.43 7.05 0.00 3.67
208 623 1.106285 GCCCTTGATCATGGTGGTTC 58.894 55.000 22.43 6.23 0.00 3.62
209 624 1.767759 CCCTTGATCATGGTGGTTCC 58.232 55.000 22.43 0.00 0.00 3.62
221 636 2.725641 GGTTCCAACCGCCACAAC 59.274 61.111 0.00 0.00 39.66 3.32
222 637 2.122167 GGTTCCAACCGCCACAACA 61.122 57.895 0.00 0.00 39.66 3.33
223 638 1.668101 GGTTCCAACCGCCACAACAA 61.668 55.000 0.00 0.00 39.66 2.83
224 639 0.173708 GTTCCAACCGCCACAACAAA 59.826 50.000 0.00 0.00 0.00 2.83
225 640 0.173708 TTCCAACCGCCACAACAAAC 59.826 50.000 0.00 0.00 0.00 2.93
226 641 1.227118 CCAACCGCCACAACAAACC 60.227 57.895 0.00 0.00 0.00 3.27
227 642 1.227118 CAACCGCCACAACAAACCC 60.227 57.895 0.00 0.00 0.00 4.11
228 643 1.380650 AACCGCCACAACAAACCCT 60.381 52.632 0.00 0.00 0.00 4.34
229 644 0.106619 AACCGCCACAACAAACCCTA 60.107 50.000 0.00 0.00 0.00 3.53
230 645 0.536460 ACCGCCACAACAAACCCTAG 60.536 55.000 0.00 0.00 0.00 3.02
231 646 0.250553 CCGCCACAACAAACCCTAGA 60.251 55.000 0.00 0.00 0.00 2.43
232 647 0.872388 CGCCACAACAAACCCTAGAC 59.128 55.000 0.00 0.00 0.00 2.59
233 648 0.872388 GCCACAACAAACCCTAGACG 59.128 55.000 0.00 0.00 0.00 4.18
234 649 1.812708 GCCACAACAAACCCTAGACGT 60.813 52.381 0.00 0.00 0.00 4.34
235 650 2.140717 CCACAACAAACCCTAGACGTC 58.859 52.381 7.70 7.70 0.00 4.34
236 651 1.790623 CACAACAAACCCTAGACGTCG 59.209 52.381 10.46 0.00 0.00 5.12
237 652 1.410153 ACAACAAACCCTAGACGTCGT 59.590 47.619 10.46 0.00 0.00 4.34
238 653 2.056577 CAACAAACCCTAGACGTCGTC 58.943 52.381 17.70 17.70 0.00 4.20
239 654 0.239347 ACAAACCCTAGACGTCGTCG 59.761 55.000 19.11 7.98 37.67 5.12
240 655 1.069378 CAAACCCTAGACGTCGTCGC 61.069 60.000 19.11 0.00 41.18 5.19
241 656 2.205243 AAACCCTAGACGTCGTCGCC 62.205 60.000 19.11 0.00 41.18 5.54
242 657 4.233635 CCCTAGACGTCGTCGCCG 62.234 72.222 19.11 11.30 41.18 6.46
243 658 3.190849 CCTAGACGTCGTCGCCGA 61.191 66.667 19.11 6.03 41.73 5.54
251 666 3.429141 TCGTCGCCGACCACTCTC 61.429 66.667 12.26 0.00 38.40 3.20
252 667 3.733960 CGTCGCCGACCACTCTCA 61.734 66.667 12.26 0.00 35.63 3.27
253 668 2.126424 GTCGCCGACCACTCTCAC 60.126 66.667 5.81 0.00 0.00 3.51
254 669 2.282251 TCGCCGACCACTCTCACT 60.282 61.111 0.00 0.00 0.00 3.41
255 670 2.126307 CGCCGACCACTCTCACTG 60.126 66.667 0.00 0.00 0.00 3.66
256 671 2.433318 GCCGACCACTCTCACTGC 60.433 66.667 0.00 0.00 0.00 4.40
257 672 3.051210 CCGACCACTCTCACTGCA 58.949 61.111 0.00 0.00 0.00 4.41
258 673 1.373497 CCGACCACTCTCACTGCAC 60.373 63.158 0.00 0.00 0.00 4.57
259 674 1.662608 CGACCACTCTCACTGCACT 59.337 57.895 0.00 0.00 0.00 4.40
260 675 0.387878 CGACCACTCTCACTGCACTC 60.388 60.000 0.00 0.00 0.00 3.51
261 676 0.676184 GACCACTCTCACTGCACTCA 59.324 55.000 0.00 0.00 0.00 3.41
262 677 0.390860 ACCACTCTCACTGCACTCAC 59.609 55.000 0.00 0.00 0.00 3.51
263 678 0.665670 CCACTCTCACTGCACTCACG 60.666 60.000 0.00 0.00 0.00 4.35
264 679 1.006805 ACTCTCACTGCACTCACGC 60.007 57.895 0.00 0.00 0.00 5.34
265 680 1.288439 CTCTCACTGCACTCACGCT 59.712 57.895 0.00 0.00 0.00 5.07
266 681 0.523519 CTCTCACTGCACTCACGCTA 59.476 55.000 0.00 0.00 0.00 4.26
267 682 0.958822 TCTCACTGCACTCACGCTAA 59.041 50.000 0.00 0.00 0.00 3.09
268 683 1.546029 TCTCACTGCACTCACGCTAAT 59.454 47.619 0.00 0.00 0.00 1.73
269 684 1.923204 CTCACTGCACTCACGCTAATC 59.077 52.381 0.00 0.00 0.00 1.75
270 685 1.272212 TCACTGCACTCACGCTAATCA 59.728 47.619 0.00 0.00 0.00 2.57
271 686 2.068519 CACTGCACTCACGCTAATCAA 58.931 47.619 0.00 0.00 0.00 2.57
272 687 2.674852 CACTGCACTCACGCTAATCAAT 59.325 45.455 0.00 0.00 0.00 2.57
273 688 3.125829 CACTGCACTCACGCTAATCAATT 59.874 43.478 0.00 0.00 0.00 2.32
274 689 3.753272 ACTGCACTCACGCTAATCAATTT 59.247 39.130 0.00 0.00 0.00 1.82
275 690 4.935205 ACTGCACTCACGCTAATCAATTTA 59.065 37.500 0.00 0.00 0.00 1.40
276 691 5.586243 ACTGCACTCACGCTAATCAATTTAT 59.414 36.000 0.00 0.00 0.00 1.40
277 692 6.048073 TGCACTCACGCTAATCAATTTATC 57.952 37.500 0.00 0.00 0.00 1.75
278 693 5.817296 TGCACTCACGCTAATCAATTTATCT 59.183 36.000 0.00 0.00 0.00 1.98
279 694 6.316140 TGCACTCACGCTAATCAATTTATCTT 59.684 34.615 0.00 0.00 0.00 2.40
280 695 6.848296 GCACTCACGCTAATCAATTTATCTTC 59.152 38.462 0.00 0.00 0.00 2.87
281 696 7.348201 CACTCACGCTAATCAATTTATCTTCC 58.652 38.462 0.00 0.00 0.00 3.46
282 697 6.483640 ACTCACGCTAATCAATTTATCTTCCC 59.516 38.462 0.00 0.00 0.00 3.97
283 698 6.353323 TCACGCTAATCAATTTATCTTCCCA 58.647 36.000 0.00 0.00 0.00 4.37
284 699 6.998074 TCACGCTAATCAATTTATCTTCCCAT 59.002 34.615 0.00 0.00 0.00 4.00
285 700 7.173218 TCACGCTAATCAATTTATCTTCCCATC 59.827 37.037 0.00 0.00 0.00 3.51
286 701 7.173907 CACGCTAATCAATTTATCTTCCCATCT 59.826 37.037 0.00 0.00 0.00 2.90
287 702 7.389053 ACGCTAATCAATTTATCTTCCCATCTC 59.611 37.037 0.00 0.00 0.00 2.75
288 703 7.388776 CGCTAATCAATTTATCTTCCCATCTCA 59.611 37.037 0.00 0.00 0.00 3.27
289 704 9.071276 GCTAATCAATTTATCTTCCCATCTCAA 57.929 33.333 0.00 0.00 0.00 3.02
292 707 8.827832 ATCAATTTATCTTCCCATCTCAAACA 57.172 30.769 0.00 0.00 0.00 2.83
293 708 8.055279 TCAATTTATCTTCCCATCTCAAACAC 57.945 34.615 0.00 0.00 0.00 3.32
294 709 7.669304 TCAATTTATCTTCCCATCTCAAACACA 59.331 33.333 0.00 0.00 0.00 3.72
295 710 8.472413 CAATTTATCTTCCCATCTCAAACACAT 58.528 33.333 0.00 0.00 0.00 3.21
296 711 7.630242 TTTATCTTCCCATCTCAAACACATC 57.370 36.000 0.00 0.00 0.00 3.06
297 712 4.639078 TCTTCCCATCTCAAACACATCA 57.361 40.909 0.00 0.00 0.00 3.07
298 713 5.183530 TCTTCCCATCTCAAACACATCAT 57.816 39.130 0.00 0.00 0.00 2.45
299 714 6.312141 TCTTCCCATCTCAAACACATCATA 57.688 37.500 0.00 0.00 0.00 2.15
300 715 6.115446 TCTTCCCATCTCAAACACATCATAC 58.885 40.000 0.00 0.00 0.00 2.39
301 716 4.780815 TCCCATCTCAAACACATCATACC 58.219 43.478 0.00 0.00 0.00 2.73
302 717 3.885297 CCCATCTCAAACACATCATACCC 59.115 47.826 0.00 0.00 0.00 3.69
303 718 4.385643 CCCATCTCAAACACATCATACCCT 60.386 45.833 0.00 0.00 0.00 4.34
304 719 4.818546 CCATCTCAAACACATCATACCCTC 59.181 45.833 0.00 0.00 0.00 4.30
305 720 5.430886 CATCTCAAACACATCATACCCTCA 58.569 41.667 0.00 0.00 0.00 3.86
306 721 5.698741 TCTCAAACACATCATACCCTCAT 57.301 39.130 0.00 0.00 0.00 2.90
307 722 5.674525 TCTCAAACACATCATACCCTCATC 58.325 41.667 0.00 0.00 0.00 2.92
308 723 5.189539 TCTCAAACACATCATACCCTCATCA 59.810 40.000 0.00 0.00 0.00 3.07
309 724 5.430886 TCAAACACATCATACCCTCATCAG 58.569 41.667 0.00 0.00 0.00 2.90
310 725 5.045651 TCAAACACATCATACCCTCATCAGT 60.046 40.000 0.00 0.00 0.00 3.41
311 726 4.679373 ACACATCATACCCTCATCAGTC 57.321 45.455 0.00 0.00 0.00 3.51
312 727 3.068732 ACACATCATACCCTCATCAGTCG 59.931 47.826 0.00 0.00 0.00 4.18
313 728 2.630098 ACATCATACCCTCATCAGTCGG 59.370 50.000 0.00 0.00 0.00 4.79
314 729 2.454336 TCATACCCTCATCAGTCGGT 57.546 50.000 0.00 0.00 0.00 4.69
315 730 2.747177 TCATACCCTCATCAGTCGGTT 58.253 47.619 0.00 0.00 0.00 4.44
316 731 2.693591 TCATACCCTCATCAGTCGGTTC 59.306 50.000 0.00 0.00 0.00 3.62
317 732 1.100510 TACCCTCATCAGTCGGTTCG 58.899 55.000 0.00 0.00 0.00 3.95
318 733 1.519455 CCCTCATCAGTCGGTTCGC 60.519 63.158 0.00 0.00 0.00 4.70
319 734 1.519455 CCTCATCAGTCGGTTCGCC 60.519 63.158 0.00 0.00 0.00 5.54
320 735 1.215382 CTCATCAGTCGGTTCGCCA 59.785 57.895 0.00 0.00 37.00 5.69
321 736 1.078759 CTCATCAGTCGGTTCGCCAC 61.079 60.000 0.00 0.00 37.00 5.01
322 737 1.374125 CATCAGTCGGTTCGCCACA 60.374 57.895 0.00 0.00 37.00 4.17
323 738 0.740868 CATCAGTCGGTTCGCCACAT 60.741 55.000 0.00 0.00 37.00 3.21
324 739 0.460284 ATCAGTCGGTTCGCCACATC 60.460 55.000 0.00 0.00 37.00 3.06
325 740 1.374125 CAGTCGGTTCGCCACATCA 60.374 57.895 0.00 0.00 37.00 3.07
326 741 1.079819 AGTCGGTTCGCCACATCAG 60.080 57.895 0.00 0.00 37.00 2.90
327 742 2.434185 TCGGTTCGCCACATCAGC 60.434 61.111 0.00 0.00 37.00 4.26
328 743 3.499737 CGGTTCGCCACATCAGCC 61.500 66.667 0.00 0.00 37.00 4.85
329 744 3.499737 GGTTCGCCACATCAGCCG 61.500 66.667 0.00 0.00 37.19 5.52
330 745 4.166011 GTTCGCCACATCAGCCGC 62.166 66.667 0.00 0.00 0.00 6.53
406 821 2.880890 GGTCATCATGTAGGTGGCAATC 59.119 50.000 0.00 0.00 0.00 2.67
418 833 3.509517 GGCAATCTGGCATCCTTCT 57.490 52.632 0.00 0.00 43.14 2.85
419 834 1.772836 GGCAATCTGGCATCCTTCTT 58.227 50.000 0.00 0.00 43.14 2.52
420 835 1.407979 GGCAATCTGGCATCCTTCTTG 59.592 52.381 0.00 0.00 43.14 3.02
421 836 1.202382 GCAATCTGGCATCCTTCTTGC 60.202 52.381 0.00 0.00 39.41 4.01
422 837 2.097036 CAATCTGGCATCCTTCTTGCA 58.903 47.619 0.00 0.00 41.95 4.08
423 838 2.494471 CAATCTGGCATCCTTCTTGCAA 59.506 45.455 0.00 0.00 41.95 4.08
476 891 1.304464 GGCCAAGGAAGAAGGGTGG 60.304 63.158 0.00 0.00 0.00 4.61
555 971 0.031010 GCCTCCTCCCCCTTCTTCTA 60.031 60.000 0.00 0.00 0.00 2.10
780 1204 0.586010 GACTAGCGACGCACGAGTAC 60.586 60.000 23.70 11.51 45.77 2.73
899 1324 2.093869 TCAGTTTAATCCTTCCCGTCCG 60.094 50.000 0.00 0.00 0.00 4.79
918 1343 2.159627 CCGTGGAGAATTTTCCTTCGTG 59.840 50.000 21.37 14.04 38.12 4.35
932 1358 1.939934 CTTCGTGTTCTTGGCTGTTGA 59.060 47.619 0.00 0.00 0.00 3.18
1332 1758 0.178953 ACCCAAATGAGGCACAGCTT 60.179 50.000 0.00 0.00 0.00 3.74
1593 2019 1.973281 GCTTGCTAGCCTGGTTGCA 60.973 57.895 13.29 1.48 41.74 4.08
1820 2246 3.433031 CCACAGACTGGTGTTACTTTCCA 60.433 47.826 7.51 0.00 37.06 3.53
1946 2372 2.877975 GCAAGATGCATCCTGTGGT 58.122 52.632 23.06 0.04 44.26 4.16
2442 2868 2.200373 TGCCTTTACCTTCCTCAAGC 57.800 50.000 0.00 0.00 0.00 4.01
2694 3123 2.022718 AGGAGGAGCTTCAGTCACTT 57.977 50.000 0.00 0.00 0.00 3.16
2942 3371 5.006386 GGAGCTTTCAAAGAAGGATGAGAA 58.994 41.667 0.00 0.00 0.00 2.87
3298 3727 7.913674 AAACAGGAAAAAGTTAAACATTGCA 57.086 28.000 0.00 0.00 0.00 4.08
3299 3728 6.902224 ACAGGAAAAAGTTAAACATTGCAC 57.098 33.333 0.00 0.00 0.00 4.57
3300 3729 6.402222 ACAGGAAAAAGTTAAACATTGCACA 58.598 32.000 0.00 0.00 0.00 4.57
3301 3730 6.876257 ACAGGAAAAAGTTAAACATTGCACAA 59.124 30.769 0.00 0.00 0.00 3.33
3302 3731 7.389053 ACAGGAAAAAGTTAAACATTGCACAAA 59.611 29.630 0.00 0.00 0.00 2.83
3303 3732 8.233190 CAGGAAAAAGTTAAACATTGCACAAAA 58.767 29.630 0.00 0.00 0.00 2.44
3304 3733 8.233868 AGGAAAAAGTTAAACATTGCACAAAAC 58.766 29.630 0.00 0.00 0.00 2.43
3305 3734 8.233868 GGAAAAAGTTAAACATTGCACAAAACT 58.766 29.630 0.00 0.00 0.00 2.66
3306 3735 8.947304 AAAAAGTTAAACATTGCACAAAACTG 57.053 26.923 0.00 0.00 0.00 3.16
3307 3736 7.897575 AAAGTTAAACATTGCACAAAACTGA 57.102 28.000 0.00 0.00 0.00 3.41
3308 3737 8.491331 AAAGTTAAACATTGCACAAAACTGAT 57.509 26.923 0.00 0.00 0.00 2.90
3309 3738 7.467557 AGTTAAACATTGCACAAAACTGATG 57.532 32.000 0.00 0.00 0.00 3.07
3310 3739 7.041107 AGTTAAACATTGCACAAAACTGATGT 58.959 30.769 0.00 0.00 0.00 3.06
3311 3740 7.548780 AGTTAAACATTGCACAAAACTGATGTT 59.451 29.630 3.82 3.82 38.83 2.71
3312 3741 8.812329 GTTAAACATTGCACAAAACTGATGTTA 58.188 29.630 8.99 0.00 36.89 2.41
3313 3742 7.467557 AAACATTGCACAAAACTGATGTTAG 57.532 32.000 8.99 0.00 36.89 2.34
3314 3743 5.531634 ACATTGCACAAAACTGATGTTAGG 58.468 37.500 0.00 0.00 34.96 2.69
3315 3744 5.068987 ACATTGCACAAAACTGATGTTAGGT 59.931 36.000 0.00 0.00 34.96 3.08
3316 3745 5.590530 TTGCACAAAACTGATGTTAGGTT 57.409 34.783 0.00 0.00 34.96 3.50
3317 3746 4.930963 TGCACAAAACTGATGTTAGGTTG 58.069 39.130 0.00 0.00 34.96 3.77
3318 3747 3.735746 GCACAAAACTGATGTTAGGTTGC 59.264 43.478 0.00 0.00 34.96 4.17
3319 3748 4.736168 GCACAAAACTGATGTTAGGTTGCA 60.736 41.667 0.00 0.00 34.96 4.08
3320 3749 4.739716 CACAAAACTGATGTTAGGTTGCAC 59.260 41.667 0.00 0.00 34.96 4.57
3321 3750 4.644685 ACAAAACTGATGTTAGGTTGCACT 59.355 37.500 0.00 0.00 34.96 4.40
3322 3751 4.836125 AAACTGATGTTAGGTTGCACTG 57.164 40.909 0.00 0.00 34.96 3.66
3323 3752 2.783135 ACTGATGTTAGGTTGCACTGG 58.217 47.619 0.00 0.00 0.00 4.00
3324 3753 2.371841 ACTGATGTTAGGTTGCACTGGA 59.628 45.455 0.00 0.00 0.00 3.86
3325 3754 3.181445 ACTGATGTTAGGTTGCACTGGAA 60.181 43.478 0.00 0.00 0.00 3.53
3326 3755 4.012374 CTGATGTTAGGTTGCACTGGAAT 58.988 43.478 0.00 0.00 0.00 3.01
3327 3756 4.406456 TGATGTTAGGTTGCACTGGAATT 58.594 39.130 0.00 0.00 0.00 2.17
3328 3757 4.832266 TGATGTTAGGTTGCACTGGAATTT 59.168 37.500 0.00 0.00 0.00 1.82
3329 3758 4.846779 TGTTAGGTTGCACTGGAATTTC 57.153 40.909 0.00 0.00 0.00 2.17
3330 3759 4.469657 TGTTAGGTTGCACTGGAATTTCT 58.530 39.130 0.00 0.00 0.00 2.52
3331 3760 5.626142 TGTTAGGTTGCACTGGAATTTCTA 58.374 37.500 0.00 0.00 0.00 2.10
3332 3761 6.065374 TGTTAGGTTGCACTGGAATTTCTAA 58.935 36.000 0.00 0.00 0.00 2.10
3333 3762 6.547880 TGTTAGGTTGCACTGGAATTTCTAAA 59.452 34.615 0.00 0.00 0.00 1.85
3391 3820 6.827586 ATACGTGTTGATTTTGTTGGGTAT 57.172 33.333 0.00 0.00 0.00 2.73
3406 3835 6.350103 TGTTGGGTATGTTTAATAGATGCGA 58.650 36.000 0.00 0.00 0.00 5.10
3432 3861 7.259882 TCATGGTTATGCTTTTCATGCTTTAG 58.740 34.615 0.00 0.00 36.22 1.85
3440 3869 6.611381 TGCTTTTCATGCTTTAGTATGTGTC 58.389 36.000 7.54 0.00 38.89 3.67
3558 3987 6.070481 TGTTTCTGTGCATACTAATGAGGGTA 60.070 38.462 0.00 0.00 34.84 3.69
3609 4038 4.799564 AATTGGTTGTTATGCCGTGAAT 57.200 36.364 0.00 0.00 0.00 2.57
3803 4486 4.411256 ACAGAGTAAAAAGTCGGTTCCA 57.589 40.909 0.00 0.00 0.00 3.53
3842 4525 2.287009 GCGTCTCTCCAACCTTTGTTTG 60.287 50.000 0.00 0.00 30.42 2.93
3911 4594 9.942526 ATCTTTCAGAGGGTGGAATATAAAAAT 57.057 29.630 0.00 0.00 0.00 1.82
4033 4716 4.260948 GCTACTGAAACCAGCATCATAAGC 60.261 45.833 0.00 0.00 35.09 3.09
4112 4795 6.198650 TGACCAATTCATTCTATGTGCTTG 57.801 37.500 0.00 0.00 0.00 4.01
4142 4825 3.811722 ATCGTGTGTGCTTGTAACATG 57.188 42.857 0.00 0.00 33.10 3.21
4173 4856 6.528537 TTAGCTTTCATGGTTTGCATACAT 57.471 33.333 9.57 1.29 0.00 2.29
4414 5097 2.438411 TCTCTGAGGTCGGAAGAGAAC 58.562 52.381 4.59 0.00 42.60 3.01
4522 5205 2.659016 CTGGACGCTTCAGAGGCA 59.341 61.111 5.23 0.00 34.36 4.75
4556 5239 0.613777 GGGAACGGATGACAAGACCT 59.386 55.000 0.00 0.00 0.00 3.85
4663 5346 1.136774 CTTCGACGACATCCAGCGA 59.863 57.895 0.00 0.00 0.00 4.93
4761 5444 2.279918 GTGCAACGACCTCCACGT 60.280 61.111 0.00 0.00 45.89 4.49
4864 5547 6.108015 AGTGAGAAGAGAGAGATTTTGCATC 58.892 40.000 0.00 0.00 0.00 3.91
4926 5611 4.710865 TGATTGCCCAGCTTGAATTTGATA 59.289 37.500 0.00 0.00 0.00 2.15
4960 5645 3.655276 AGAATAACGAGTGTTGTCGGT 57.345 42.857 0.00 0.00 44.53 4.69
4961 5646 3.572584 AGAATAACGAGTGTTGTCGGTC 58.427 45.455 0.00 0.00 44.53 4.79
4962 5647 1.973138 ATAACGAGTGTTGTCGGTCG 58.027 50.000 0.00 0.00 44.53 4.79
4966 5651 1.002250 CGAGTGTTGTCGGTCGGAAG 61.002 60.000 0.00 0.00 36.26 3.46
5341 6034 2.158534 TGGATTGTGTGTTGCTAACCCT 60.159 45.455 0.00 0.00 0.00 4.34
5342 6035 2.488153 GGATTGTGTGTTGCTAACCCTC 59.512 50.000 0.00 0.00 0.00 4.30
5344 6037 2.543777 TGTGTGTTGCTAACCCTCTC 57.456 50.000 0.00 0.00 0.00 3.20
5346 6039 2.438021 TGTGTGTTGCTAACCCTCTCTT 59.562 45.455 0.00 0.00 0.00 2.85
5347 6040 3.118038 TGTGTGTTGCTAACCCTCTCTTT 60.118 43.478 0.00 0.00 0.00 2.52
5424 6126 2.176798 TGTTCATTTCTGGTTCCTGGGT 59.823 45.455 0.00 0.00 0.00 4.51
5425 6127 2.558359 GTTCATTTCTGGTTCCTGGGTG 59.442 50.000 0.00 0.00 0.00 4.61
5426 6128 2.061848 TCATTTCTGGTTCCTGGGTGA 58.938 47.619 0.00 0.00 0.00 4.02
5427 6129 2.445145 TCATTTCTGGTTCCTGGGTGAA 59.555 45.455 0.00 0.00 0.00 3.18
5428 6130 2.656947 TTTCTGGTTCCTGGGTGAAG 57.343 50.000 0.00 0.00 0.00 3.02
5429 6131 1.518367 TTCTGGTTCCTGGGTGAAGT 58.482 50.000 0.00 0.00 0.00 3.01
5430 6132 1.518367 TCTGGTTCCTGGGTGAAGTT 58.482 50.000 0.00 0.00 0.00 2.66
5431 6133 1.142870 TCTGGTTCCTGGGTGAAGTTG 59.857 52.381 0.00 0.00 0.00 3.16
5432 6134 0.184933 TGGTTCCTGGGTGAAGTTGG 59.815 55.000 0.00 0.00 0.00 3.77
5464 6166 0.474184 ATAAGGGAATGGGAGCCACG 59.526 55.000 0.00 0.00 35.80 4.94
5518 6220 1.607509 GCTGGATCTGGACATGGATCG 60.608 57.143 0.00 0.00 39.19 3.69
5653 6368 2.356793 CCGATGGATCTCTGGCGC 60.357 66.667 0.00 0.00 0.00 6.53
5683 6398 0.815615 CTGTCGCCCCAAGGATTAGC 60.816 60.000 0.00 0.00 33.47 3.09
5685 6400 0.533085 GTCGCCCCAAGGATTAGCTC 60.533 60.000 0.00 0.00 33.47 4.09
5687 6402 1.227973 GCCCCAAGGATTAGCTCGG 60.228 63.158 0.00 0.00 33.47 4.63
5704 6423 1.446272 GGTGCACTCGGCTCTACAC 60.446 63.158 17.98 0.00 45.15 2.90
5711 6430 4.320971 CGGCTCTACACCGTATGC 57.679 61.111 0.00 0.00 45.70 3.14
5719 6438 1.480954 CTACACCGTATGCCTTCACCT 59.519 52.381 0.00 0.00 0.00 4.00
5720 6439 0.036388 ACACCGTATGCCTTCACCTG 60.036 55.000 0.00 0.00 0.00 4.00
5721 6440 1.078426 ACCGTATGCCTTCACCTGC 60.078 57.895 0.00 0.00 0.00 4.85
5722 6441 1.078497 CCGTATGCCTTCACCTGCA 60.078 57.895 0.00 0.00 42.52 4.41
5723 6442 1.091771 CCGTATGCCTTCACCTGCAG 61.092 60.000 6.78 6.78 41.46 4.41
5724 6443 0.108186 CGTATGCCTTCACCTGCAGA 60.108 55.000 17.39 0.00 41.46 4.26
5725 6444 1.473965 CGTATGCCTTCACCTGCAGAT 60.474 52.381 17.39 0.00 41.46 2.90
5726 6445 1.945394 GTATGCCTTCACCTGCAGATG 59.055 52.381 17.39 9.11 41.46 2.90
5728 6447 1.001641 GCCTTCACCTGCAGATGGT 60.002 57.895 17.39 1.92 38.53 3.55
5729 6448 1.028868 GCCTTCACCTGCAGATGGTC 61.029 60.000 17.39 0.85 35.28 4.02
5730 6449 0.325933 CCTTCACCTGCAGATGGTCA 59.674 55.000 17.39 0.00 35.28 4.02
5731 6450 1.064906 CCTTCACCTGCAGATGGTCAT 60.065 52.381 17.39 0.00 35.28 3.06
5732 6451 2.286872 CTTCACCTGCAGATGGTCATC 58.713 52.381 17.39 2.92 35.28 2.92
5733 6452 1.278537 TCACCTGCAGATGGTCATCA 58.721 50.000 17.39 0.00 40.22 3.07
5742 6461 1.884235 GATGGTCATCATCGGGAACC 58.116 55.000 6.12 0.00 42.29 3.62
5743 6462 1.140852 GATGGTCATCATCGGGAACCA 59.859 52.381 6.12 0.00 45.37 3.67
5744 6463 2.421388 GATGGTCATCATCGGGAACCAA 60.421 50.000 6.12 0.00 45.37 3.67
5745 6464 4.300045 GATGGTCATCATCGGGAACCAAG 61.300 52.174 6.12 0.00 45.37 3.61
5758 8329 0.838987 AACCAAGGGGCCTAACTCGA 60.839 55.000 0.84 0.00 37.90 4.04
5759 8330 0.620700 ACCAAGGGGCCTAACTCGAT 60.621 55.000 0.84 0.00 37.90 3.59
5764 8335 1.133009 AGGGGCCTAACTCGATCAGAT 60.133 52.381 0.84 0.00 0.00 2.90
5825 8397 1.302431 GCCAAACCAAACATGGGGC 60.302 57.895 0.00 0.00 34.71 5.80
5826 8398 1.767654 GCCAAACCAAACATGGGGCT 61.768 55.000 0.00 0.00 37.00 5.19
5827 8399 1.638529 CCAAACCAAACATGGGGCTA 58.361 50.000 0.00 0.00 0.00 3.93
5828 8400 1.974236 CCAAACCAAACATGGGGCTAA 59.026 47.619 0.00 0.00 0.00 3.09
5829 8401 2.289382 CCAAACCAAACATGGGGCTAAC 60.289 50.000 0.00 0.00 0.00 2.34
5830 8402 2.632512 CAAACCAAACATGGGGCTAACT 59.367 45.455 0.00 0.00 0.00 2.24
5831 8403 2.215942 ACCAAACATGGGGCTAACTC 57.784 50.000 0.00 0.00 0.00 3.01
5832 8404 1.094785 CCAAACATGGGGCTAACTCG 58.905 55.000 0.00 0.00 0.00 4.18
5833 8405 1.094785 CAAACATGGGGCTAACTCGG 58.905 55.000 0.00 0.00 0.00 4.63
5834 8406 0.696501 AAACATGGGGCTAACTCGGT 59.303 50.000 0.00 0.00 0.00 4.69
5835 8407 0.696501 AACATGGGGCTAACTCGGTT 59.303 50.000 0.00 0.00 0.00 4.44
5836 8408 0.696501 ACATGGGGCTAACTCGGTTT 59.303 50.000 0.00 0.00 0.00 3.27
5837 8409 1.094785 CATGGGGCTAACTCGGTTTG 58.905 55.000 0.00 0.00 0.00 2.93
5838 8410 0.696501 ATGGGGCTAACTCGGTTTGT 59.303 50.000 0.00 0.00 0.00 2.83
5839 8411 1.350071 TGGGGCTAACTCGGTTTGTA 58.650 50.000 0.00 0.00 0.00 2.41
5840 8412 1.276989 TGGGGCTAACTCGGTTTGTAG 59.723 52.381 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 433 0.179054 GAGATGCTGGCTCTGCATGA 60.179 55.000 19.10 0.00 46.13 3.07
32 445 4.496336 GGCTTGGCGGGAGATGCT 62.496 66.667 0.00 0.00 0.00 3.79
33 446 4.802051 TGGCTTGGCGGGAGATGC 62.802 66.667 0.00 0.00 0.00 3.91
35 448 2.194056 CATGGCTTGGCGGGAGAT 59.806 61.111 0.00 0.00 0.00 2.75
56 471 4.247258 ACGTCTATAATTTGTTGTGGCGA 58.753 39.130 0.00 0.00 0.00 5.54
99 514 0.889186 GGGTTGATTGGCGTGAGTGT 60.889 55.000 0.00 0.00 0.00 3.55
104 519 1.133025 GAAGATGGGTTGATTGGCGTG 59.867 52.381 0.00 0.00 0.00 5.34
108 523 2.530460 TGGGAAGATGGGTTGATTGG 57.470 50.000 0.00 0.00 0.00 3.16
119 534 5.183530 TGATGTGTTTGAGATGGGAAGAT 57.816 39.130 0.00 0.00 0.00 2.40
183 598 1.567649 ACCATGATCAAGGGCTGACAT 59.432 47.619 20.54 0.00 36.69 3.06
184 599 0.994247 ACCATGATCAAGGGCTGACA 59.006 50.000 20.54 0.00 36.69 3.58
185 600 1.386533 CACCATGATCAAGGGCTGAC 58.613 55.000 20.54 0.00 36.69 3.51
186 601 0.256752 CCACCATGATCAAGGGCTGA 59.743 55.000 20.54 0.00 38.81 4.26
187 602 0.033796 ACCACCATGATCAAGGGCTG 60.034 55.000 20.54 10.68 0.00 4.85
188 603 0.706433 AACCACCATGATCAAGGGCT 59.294 50.000 20.54 0.00 0.00 5.19
189 604 1.106285 GAACCACCATGATCAAGGGC 58.894 55.000 20.54 1.85 0.00 5.19
190 605 1.005805 TGGAACCACCATGATCAAGGG 59.994 52.381 20.54 16.91 44.64 3.95
191 606 2.512692 TGGAACCACCATGATCAAGG 57.487 50.000 15.39 15.39 44.64 3.61
204 619 1.668101 TTGTTGTGGCGGTTGGAACC 61.668 55.000 0.00 0.00 45.76 3.62
205 620 0.173708 TTTGTTGTGGCGGTTGGAAC 59.826 50.000 0.00 0.00 0.00 3.62
206 621 0.173708 GTTTGTTGTGGCGGTTGGAA 59.826 50.000 0.00 0.00 0.00 3.53
207 622 1.668101 GGTTTGTTGTGGCGGTTGGA 61.668 55.000 0.00 0.00 0.00 3.53
208 623 1.227118 GGTTTGTTGTGGCGGTTGG 60.227 57.895 0.00 0.00 0.00 3.77
209 624 1.227118 GGGTTTGTTGTGGCGGTTG 60.227 57.895 0.00 0.00 0.00 3.77
210 625 0.106619 TAGGGTTTGTTGTGGCGGTT 60.107 50.000 0.00 0.00 0.00 4.44
211 626 0.536460 CTAGGGTTTGTTGTGGCGGT 60.536 55.000 0.00 0.00 0.00 5.68
212 627 0.250553 TCTAGGGTTTGTTGTGGCGG 60.251 55.000 0.00 0.00 0.00 6.13
213 628 0.872388 GTCTAGGGTTTGTTGTGGCG 59.128 55.000 0.00 0.00 0.00 5.69
214 629 0.872388 CGTCTAGGGTTTGTTGTGGC 59.128 55.000 0.00 0.00 0.00 5.01
215 630 2.140717 GACGTCTAGGGTTTGTTGTGG 58.859 52.381 8.70 0.00 0.00 4.17
216 631 1.790623 CGACGTCTAGGGTTTGTTGTG 59.209 52.381 14.70 0.00 0.00 3.33
217 632 1.410153 ACGACGTCTAGGGTTTGTTGT 59.590 47.619 14.70 0.00 0.00 3.32
218 633 2.056577 GACGACGTCTAGGGTTTGTTG 58.943 52.381 20.52 0.00 0.00 3.33
219 634 1.335324 CGACGACGTCTAGGGTTTGTT 60.335 52.381 24.36 0.00 34.56 2.83
220 635 0.239347 CGACGACGTCTAGGGTTTGT 59.761 55.000 24.36 0.66 34.56 2.83
221 636 1.069378 GCGACGACGTCTAGGGTTTG 61.069 60.000 24.36 8.44 41.98 2.93
222 637 1.211190 GCGACGACGTCTAGGGTTT 59.789 57.895 24.36 0.00 41.98 3.27
223 638 2.694760 GGCGACGACGTCTAGGGTT 61.695 63.158 24.36 0.00 41.20 4.11
224 639 3.130160 GGCGACGACGTCTAGGGT 61.130 66.667 24.36 3.51 41.20 4.34
236 651 2.126424 GTGAGAGTGGTCGGCGAC 60.126 66.667 30.72 30.72 0.00 5.19
237 652 2.282251 AGTGAGAGTGGTCGGCGA 60.282 61.111 4.99 4.99 0.00 5.54
238 653 2.126307 CAGTGAGAGTGGTCGGCG 60.126 66.667 0.00 0.00 0.00 6.46
239 654 2.433318 GCAGTGAGAGTGGTCGGC 60.433 66.667 0.00 0.00 0.00 5.54
240 655 1.373497 GTGCAGTGAGAGTGGTCGG 60.373 63.158 0.00 0.00 0.00 4.79
241 656 0.387878 GAGTGCAGTGAGAGTGGTCG 60.388 60.000 0.00 0.00 0.00 4.79
242 657 0.676184 TGAGTGCAGTGAGAGTGGTC 59.324 55.000 0.00 0.00 0.00 4.02
243 658 0.390860 GTGAGTGCAGTGAGAGTGGT 59.609 55.000 0.00 0.00 0.00 4.16
244 659 0.665670 CGTGAGTGCAGTGAGAGTGG 60.666 60.000 0.00 0.00 0.00 4.00
245 660 1.280886 GCGTGAGTGCAGTGAGAGTG 61.281 60.000 0.00 0.00 34.15 3.51
246 661 1.006805 GCGTGAGTGCAGTGAGAGT 60.007 57.895 0.00 0.00 34.15 3.24
247 662 0.523519 TAGCGTGAGTGCAGTGAGAG 59.476 55.000 0.00 0.00 37.31 3.20
248 663 0.958822 TTAGCGTGAGTGCAGTGAGA 59.041 50.000 0.00 0.00 37.31 3.27
249 664 1.923204 GATTAGCGTGAGTGCAGTGAG 59.077 52.381 0.00 0.00 37.31 3.51
250 665 1.272212 TGATTAGCGTGAGTGCAGTGA 59.728 47.619 0.00 0.00 37.31 3.41
251 666 1.713597 TGATTAGCGTGAGTGCAGTG 58.286 50.000 0.00 0.00 37.31 3.66
252 667 2.455674 TTGATTAGCGTGAGTGCAGT 57.544 45.000 0.00 0.00 37.31 4.40
253 668 4.346734 AAATTGATTAGCGTGAGTGCAG 57.653 40.909 0.00 0.00 37.31 4.41
254 669 5.817296 AGATAAATTGATTAGCGTGAGTGCA 59.183 36.000 0.00 0.00 35.06 4.57
255 670 6.292389 AGATAAATTGATTAGCGTGAGTGC 57.708 37.500 0.00 0.00 35.06 4.40
256 671 7.348201 GGAAGATAAATTGATTAGCGTGAGTG 58.652 38.462 0.00 0.00 35.06 3.51
257 672 6.483640 GGGAAGATAAATTGATTAGCGTGAGT 59.516 38.462 0.00 0.00 35.06 3.41
258 673 6.483307 TGGGAAGATAAATTGATTAGCGTGAG 59.517 38.462 0.00 0.00 35.06 3.51
259 674 6.353323 TGGGAAGATAAATTGATTAGCGTGA 58.647 36.000 0.00 0.00 35.06 4.35
260 675 6.618287 TGGGAAGATAAATTGATTAGCGTG 57.382 37.500 0.00 0.00 35.06 5.34
261 676 7.227156 AGATGGGAAGATAAATTGATTAGCGT 58.773 34.615 0.00 0.00 35.06 5.07
262 677 7.388776 TGAGATGGGAAGATAAATTGATTAGCG 59.611 37.037 0.00 0.00 35.06 4.26
263 678 8.627208 TGAGATGGGAAGATAAATTGATTAGC 57.373 34.615 0.00 0.00 0.00 3.09
266 681 9.258629 TGTTTGAGATGGGAAGATAAATTGATT 57.741 29.630 0.00 0.00 0.00 2.57
267 682 8.689972 GTGTTTGAGATGGGAAGATAAATTGAT 58.310 33.333 0.00 0.00 0.00 2.57
268 683 7.669304 TGTGTTTGAGATGGGAAGATAAATTGA 59.331 33.333 0.00 0.00 0.00 2.57
269 684 7.829725 TGTGTTTGAGATGGGAAGATAAATTG 58.170 34.615 0.00 0.00 0.00 2.32
270 685 8.599624 ATGTGTTTGAGATGGGAAGATAAATT 57.400 30.769 0.00 0.00 0.00 1.82
271 686 7.835682 TGATGTGTTTGAGATGGGAAGATAAAT 59.164 33.333 0.00 0.00 0.00 1.40
272 687 7.174413 TGATGTGTTTGAGATGGGAAGATAAA 58.826 34.615 0.00 0.00 0.00 1.40
273 688 6.720309 TGATGTGTTTGAGATGGGAAGATAA 58.280 36.000 0.00 0.00 0.00 1.75
274 689 6.312141 TGATGTGTTTGAGATGGGAAGATA 57.688 37.500 0.00 0.00 0.00 1.98
275 690 5.183530 TGATGTGTTTGAGATGGGAAGAT 57.816 39.130 0.00 0.00 0.00 2.40
276 691 4.639078 TGATGTGTTTGAGATGGGAAGA 57.361 40.909 0.00 0.00 0.00 2.87
277 692 5.297776 GGTATGATGTGTTTGAGATGGGAAG 59.702 44.000 0.00 0.00 0.00 3.46
278 693 5.192927 GGTATGATGTGTTTGAGATGGGAA 58.807 41.667 0.00 0.00 0.00 3.97
279 694 4.385199 GGGTATGATGTGTTTGAGATGGGA 60.385 45.833 0.00 0.00 0.00 4.37
280 695 3.885297 GGGTATGATGTGTTTGAGATGGG 59.115 47.826 0.00 0.00 0.00 4.00
281 696 4.785301 AGGGTATGATGTGTTTGAGATGG 58.215 43.478 0.00 0.00 0.00 3.51
282 697 5.430886 TGAGGGTATGATGTGTTTGAGATG 58.569 41.667 0.00 0.00 0.00 2.90
283 698 5.698741 TGAGGGTATGATGTGTTTGAGAT 57.301 39.130 0.00 0.00 0.00 2.75
284 699 5.189539 TGATGAGGGTATGATGTGTTTGAGA 59.810 40.000 0.00 0.00 0.00 3.27
285 700 5.430886 TGATGAGGGTATGATGTGTTTGAG 58.569 41.667 0.00 0.00 0.00 3.02
286 701 5.045651 ACTGATGAGGGTATGATGTGTTTGA 60.046 40.000 0.00 0.00 0.00 2.69
287 702 5.188434 ACTGATGAGGGTATGATGTGTTTG 58.812 41.667 0.00 0.00 0.00 2.93
288 703 5.431765 GACTGATGAGGGTATGATGTGTTT 58.568 41.667 0.00 0.00 0.00 2.83
289 704 4.442052 CGACTGATGAGGGTATGATGTGTT 60.442 45.833 0.00 0.00 0.00 3.32
290 705 3.068732 CGACTGATGAGGGTATGATGTGT 59.931 47.826 0.00 0.00 0.00 3.72
291 706 3.553715 CCGACTGATGAGGGTATGATGTG 60.554 52.174 0.00 0.00 0.00 3.21
292 707 2.630098 CCGACTGATGAGGGTATGATGT 59.370 50.000 0.00 0.00 0.00 3.06
293 708 2.630098 ACCGACTGATGAGGGTATGATG 59.370 50.000 0.00 0.00 0.00 3.07
294 709 2.964209 ACCGACTGATGAGGGTATGAT 58.036 47.619 0.00 0.00 0.00 2.45
295 710 2.454336 ACCGACTGATGAGGGTATGA 57.546 50.000 0.00 0.00 0.00 2.15
296 711 2.543861 CGAACCGACTGATGAGGGTATG 60.544 54.545 0.00 0.00 31.18 2.39
297 712 1.681793 CGAACCGACTGATGAGGGTAT 59.318 52.381 0.00 0.00 31.18 2.73
298 713 1.100510 CGAACCGACTGATGAGGGTA 58.899 55.000 0.00 0.00 31.18 3.69
299 714 1.890894 CGAACCGACTGATGAGGGT 59.109 57.895 0.00 0.00 0.00 4.34
300 715 1.519455 GCGAACCGACTGATGAGGG 60.519 63.158 0.00 0.00 0.00 4.30
301 716 1.519455 GGCGAACCGACTGATGAGG 60.519 63.158 0.00 0.00 0.00 3.86
302 717 1.078759 GTGGCGAACCGACTGATGAG 61.079 60.000 0.00 0.00 39.70 2.90
303 718 1.080093 GTGGCGAACCGACTGATGA 60.080 57.895 0.00 0.00 39.70 2.92
304 719 0.740868 ATGTGGCGAACCGACTGATG 60.741 55.000 0.00 0.00 39.70 3.07
305 720 0.460284 GATGTGGCGAACCGACTGAT 60.460 55.000 0.00 0.00 39.70 2.90
306 721 1.080093 GATGTGGCGAACCGACTGA 60.080 57.895 0.00 0.00 39.70 3.41
307 722 1.354337 CTGATGTGGCGAACCGACTG 61.354 60.000 0.00 0.00 39.70 3.51
308 723 1.079819 CTGATGTGGCGAACCGACT 60.080 57.895 0.00 0.00 39.70 4.18
309 724 2.740714 GCTGATGTGGCGAACCGAC 61.741 63.158 0.00 0.00 39.70 4.79
310 725 2.434185 GCTGATGTGGCGAACCGA 60.434 61.111 0.00 0.00 39.70 4.69
311 726 3.499737 GGCTGATGTGGCGAACCG 61.500 66.667 0.00 0.00 39.70 4.44
332 747 4.431131 AAGGGCTGACATGGGGCG 62.431 66.667 0.00 0.00 0.00 6.13
333 748 2.578586 ATCAAGGGCTGACATGGGGC 62.579 60.000 0.00 0.00 36.69 5.80
334 749 0.466922 GATCAAGGGCTGACATGGGG 60.467 60.000 0.00 0.00 36.69 4.96
335 750 0.256752 TGATCAAGGGCTGACATGGG 59.743 55.000 0.00 0.00 36.69 4.00
336 751 1.954382 CATGATCAAGGGCTGACATGG 59.046 52.381 0.00 0.00 38.53 3.66
390 805 1.408683 GCCAGATTGCCACCTACATGA 60.409 52.381 0.00 0.00 0.00 3.07
406 821 3.389925 TTTTTGCAAGAAGGATGCCAG 57.610 42.857 0.00 0.00 43.16 4.85
423 838 4.899457 CCCCCTCCAGTTTTCTTAGTTTTT 59.101 41.667 0.00 0.00 0.00 1.94
476 891 2.022240 GAGGGAGGAGTCACGCCATC 62.022 65.000 0.00 0.00 0.00 3.51
555 971 0.030603 GTGGGAGGGAGGAGGAGATT 60.031 60.000 0.00 0.00 0.00 2.40
780 1204 4.331443 TCAACGAATCACGAACCCAATATG 59.669 41.667 0.00 0.00 45.77 1.78
899 1324 4.515567 AGAACACGAAGGAAAATTCTCCAC 59.484 41.667 0.00 0.00 38.02 4.02
918 1343 5.240403 AGAAAATCTCTCAACAGCCAAGAAC 59.760 40.000 0.00 0.00 0.00 3.01
932 1358 2.568623 AACGGCACCAGAAAATCTCT 57.431 45.000 0.00 0.00 33.23 3.10
1347 1773 5.639931 GTCAAAGGTTGTATCCAGACTCTTC 59.360 44.000 0.00 0.00 0.00 2.87
1593 2019 1.687612 CTGGGCCTCATTGACCACT 59.312 57.895 4.53 0.00 0.00 4.00
1820 2246 0.536460 CACTGGGGTAAGTTTGCCGT 60.536 55.000 0.00 0.00 33.27 5.68
1946 2372 6.981559 GTGTTCTTTTGGCTTAACATTTGGTA 59.018 34.615 0.00 0.00 34.62 3.25
2043 2469 2.295885 CTCTTGCTAGGGAATGGCTTG 58.704 52.381 0.00 0.00 36.12 4.01
2442 2868 2.099141 TCAAAGGAGCAGAACCATCG 57.901 50.000 0.00 0.00 0.00 3.84
2661 3090 1.172175 CCTCCTTCTCTTTGGCAAGC 58.828 55.000 0.00 0.00 0.00 4.01
2694 3123 1.550976 GCCTCTTCCTTCTCTTTCCGA 59.449 52.381 0.00 0.00 0.00 4.55
2942 3371 2.441750 TGCTGGGACCTTTTAAGACTGT 59.558 45.455 0.00 0.00 0.00 3.55
3272 3701 9.436957 TGCAATGTTTAACTTTTTCCTGTTTAA 57.563 25.926 0.00 0.00 0.00 1.52
3273 3702 8.874816 GTGCAATGTTTAACTTTTTCCTGTTTA 58.125 29.630 0.00 0.00 0.00 2.01
3274 3703 7.389053 TGTGCAATGTTTAACTTTTTCCTGTTT 59.611 29.630 0.00 0.00 0.00 2.83
3275 3704 6.876257 TGTGCAATGTTTAACTTTTTCCTGTT 59.124 30.769 0.00 0.00 0.00 3.16
3276 3705 6.402222 TGTGCAATGTTTAACTTTTTCCTGT 58.598 32.000 0.00 0.00 0.00 4.00
3277 3706 6.900568 TGTGCAATGTTTAACTTTTTCCTG 57.099 33.333 0.00 0.00 0.00 3.86
3278 3707 7.913674 TTTGTGCAATGTTTAACTTTTTCCT 57.086 28.000 0.00 0.00 0.00 3.36
3279 3708 8.233868 AGTTTTGTGCAATGTTTAACTTTTTCC 58.766 29.630 0.00 0.00 0.00 3.13
3280 3709 9.049974 CAGTTTTGTGCAATGTTTAACTTTTTC 57.950 29.630 0.00 0.00 0.00 2.29
3281 3710 8.778358 TCAGTTTTGTGCAATGTTTAACTTTTT 58.222 25.926 0.00 0.00 0.00 1.94
3282 3711 8.316640 TCAGTTTTGTGCAATGTTTAACTTTT 57.683 26.923 0.00 0.00 0.00 2.27
3283 3712 7.897575 TCAGTTTTGTGCAATGTTTAACTTT 57.102 28.000 0.00 0.00 0.00 2.66
3284 3713 7.548780 ACATCAGTTTTGTGCAATGTTTAACTT 59.451 29.630 0.00 0.00 0.00 2.66
3285 3714 7.041107 ACATCAGTTTTGTGCAATGTTTAACT 58.959 30.769 0.00 0.00 0.00 2.24
3286 3715 7.232945 ACATCAGTTTTGTGCAATGTTTAAC 57.767 32.000 0.00 0.00 0.00 2.01
3287 3716 7.840342 AACATCAGTTTTGTGCAATGTTTAA 57.160 28.000 3.82 0.00 34.60 1.52
3288 3717 7.651304 CCTAACATCAGTTTTGTGCAATGTTTA 59.349 33.333 12.80 2.00 38.11 2.01
3289 3718 6.479660 CCTAACATCAGTTTTGTGCAATGTTT 59.520 34.615 12.80 1.12 38.11 2.83
3290 3719 5.984926 CCTAACATCAGTTTTGTGCAATGTT 59.015 36.000 12.34 12.34 39.75 2.71
3291 3720 5.068987 ACCTAACATCAGTTTTGTGCAATGT 59.931 36.000 0.00 0.00 39.15 2.71
3292 3721 5.531634 ACCTAACATCAGTTTTGTGCAATG 58.468 37.500 0.00 0.00 39.15 2.82
3293 3722 5.789643 ACCTAACATCAGTTTTGTGCAAT 57.210 34.783 0.00 0.00 39.15 3.56
3294 3723 5.347342 CAACCTAACATCAGTTTTGTGCAA 58.653 37.500 0.00 0.00 39.15 4.08
3295 3724 4.736168 GCAACCTAACATCAGTTTTGTGCA 60.736 41.667 0.00 0.00 39.15 4.57
3296 3725 3.735746 GCAACCTAACATCAGTTTTGTGC 59.264 43.478 0.00 0.00 39.15 4.57
3297 3726 4.739716 GTGCAACCTAACATCAGTTTTGTG 59.260 41.667 0.00 0.00 39.15 3.33
3298 3727 4.644685 AGTGCAACCTAACATCAGTTTTGT 59.355 37.500 0.00 0.00 36.95 2.83
3299 3728 4.977963 CAGTGCAACCTAACATCAGTTTTG 59.022 41.667 0.00 0.00 36.95 2.44
3300 3729 4.037923 CCAGTGCAACCTAACATCAGTTTT 59.962 41.667 0.00 0.00 36.95 2.43
3301 3730 3.569701 CCAGTGCAACCTAACATCAGTTT 59.430 43.478 0.00 0.00 36.95 2.66
3302 3731 3.149196 CCAGTGCAACCTAACATCAGTT 58.851 45.455 0.00 0.00 38.76 3.16
3303 3732 2.371841 TCCAGTGCAACCTAACATCAGT 59.628 45.455 0.00 0.00 37.80 3.41
3304 3733 3.057969 TCCAGTGCAACCTAACATCAG 57.942 47.619 0.00 0.00 37.80 2.90
3305 3734 3.500448 TTCCAGTGCAACCTAACATCA 57.500 42.857 0.00 0.00 37.80 3.07
3306 3735 5.183904 AGAAATTCCAGTGCAACCTAACATC 59.816 40.000 0.00 0.00 37.80 3.06
3307 3736 5.079643 AGAAATTCCAGTGCAACCTAACAT 58.920 37.500 0.00 0.00 37.80 2.71
3308 3737 4.469657 AGAAATTCCAGTGCAACCTAACA 58.530 39.130 0.00 0.00 37.80 2.41
3309 3738 6.569179 TTAGAAATTCCAGTGCAACCTAAC 57.431 37.500 0.00 0.00 37.80 2.34
3310 3739 7.775053 ATTTAGAAATTCCAGTGCAACCTAA 57.225 32.000 0.00 0.00 37.80 2.69
3311 3740 9.474313 AATATTTAGAAATTCCAGTGCAACCTA 57.526 29.630 0.00 0.00 37.80 3.08
3312 3741 7.961326 ATATTTAGAAATTCCAGTGCAACCT 57.039 32.000 0.00 0.00 37.80 3.50
3313 3742 9.736023 CTAATATTTAGAAATTCCAGTGCAACC 57.264 33.333 0.00 0.00 37.80 3.77
3314 3743 9.736023 CCTAATATTTAGAAATTCCAGTGCAAC 57.264 33.333 0.00 0.00 0.00 4.17
3315 3744 9.693739 TCCTAATATTTAGAAATTCCAGTGCAA 57.306 29.630 0.00 0.00 0.00 4.08
3316 3745 9.342308 CTCCTAATATTTAGAAATTCCAGTGCA 57.658 33.333 0.00 0.00 0.00 4.57
3317 3746 8.787852 CCTCCTAATATTTAGAAATTCCAGTGC 58.212 37.037 0.00 0.00 0.00 4.40
3320 3749 9.225436 GCTCCTCCTAATATTTAGAAATTCCAG 57.775 37.037 0.00 0.00 0.00 3.86
3321 3750 8.164070 GGCTCCTCCTAATATTTAGAAATTCCA 58.836 37.037 0.00 0.00 0.00 3.53
3322 3751 8.387039 AGGCTCCTCCTAATATTTAGAAATTCC 58.613 37.037 0.00 0.00 45.41 3.01
3391 3820 8.720562 CATAACCATGATCGCATCTATTAAACA 58.279 33.333 0.00 0.00 33.67 2.83
3406 3835 5.864418 AGCATGAAAAGCATAACCATGAT 57.136 34.783 0.00 0.00 37.41 2.45
3432 3861 2.747446 ACCCAGCAAAATCGACACATAC 59.253 45.455 0.00 0.00 0.00 2.39
3440 3869 2.981400 AAACGTACCCAGCAAAATCG 57.019 45.000 0.00 0.00 0.00 3.34
3842 4525 9.113838 ACTTAAATCACATGATATGAGTCAACC 57.886 33.333 0.00 0.00 33.73 3.77
3911 4594 6.887013 TGTTTTGTACTGAAGTGGTAACCTA 58.113 36.000 0.00 0.00 0.00 3.08
4089 4772 5.945191 TCAAGCACATAGAATGAATTGGTCA 59.055 36.000 0.00 0.00 41.67 4.02
4112 4795 3.952535 AGCACACACGATTTCTGTTTTC 58.047 40.909 0.00 0.00 0.00 2.29
4142 4825 7.071414 GCAAACCATGAAAGCTAATGAAAAAC 58.929 34.615 0.00 0.00 0.00 2.43
4414 5097 0.879765 CAGCTTTGAGGTGCAGGAAG 59.120 55.000 0.00 0.00 36.88 3.46
4546 5229 3.241530 AGGGCGCAGGTCTTGTCA 61.242 61.111 10.83 0.00 0.00 3.58
4761 5444 0.914644 CTCCTTCATCCCCTGCTTGA 59.085 55.000 0.00 0.00 0.00 3.02
5296 5981 3.408237 AGGGAGGGGTACATGTCCATATA 59.592 47.826 0.00 0.00 0.00 0.86
5297 5982 2.184565 AGGGAGGGGTACATGTCCATAT 59.815 50.000 0.00 0.00 0.00 1.78
5298 5983 1.583611 AGGGAGGGGTACATGTCCATA 59.416 52.381 0.00 0.00 0.00 2.74
5299 5984 0.346932 AGGGAGGGGTACATGTCCAT 59.653 55.000 0.00 0.00 0.00 3.41
5341 6034 3.159472 ACATTGCCTGCATCAAAAGAGA 58.841 40.909 5.76 0.00 0.00 3.10
5342 6035 3.192844 AGACATTGCCTGCATCAAAAGAG 59.807 43.478 5.76 1.07 0.00 2.85
5344 6037 3.250744 CAGACATTGCCTGCATCAAAAG 58.749 45.455 5.76 4.95 0.00 2.27
5346 6039 1.546923 CCAGACATTGCCTGCATCAAA 59.453 47.619 5.76 0.00 0.00 2.69
5347 6040 1.179152 CCAGACATTGCCTGCATCAA 58.821 50.000 4.33 4.33 0.00 2.57
5424 6126 2.192861 CCAACCGCTGCCAACTTCA 61.193 57.895 0.00 0.00 0.00 3.02
5425 6127 2.193536 ACCAACCGCTGCCAACTTC 61.194 57.895 0.00 0.00 0.00 3.01
5426 6128 2.123897 ACCAACCGCTGCCAACTT 60.124 55.556 0.00 0.00 0.00 2.66
5427 6129 2.697147 ATCACCAACCGCTGCCAACT 62.697 55.000 0.00 0.00 0.00 3.16
5428 6130 0.958382 TATCACCAACCGCTGCCAAC 60.958 55.000 0.00 0.00 0.00 3.77
5429 6131 0.250945 TTATCACCAACCGCTGCCAA 60.251 50.000 0.00 0.00 0.00 4.52
5430 6132 0.676466 CTTATCACCAACCGCTGCCA 60.676 55.000 0.00 0.00 0.00 4.92
5431 6133 1.376609 CCTTATCACCAACCGCTGCC 61.377 60.000 0.00 0.00 0.00 4.85
5432 6134 1.376609 CCCTTATCACCAACCGCTGC 61.377 60.000 0.00 0.00 0.00 5.25
5464 6166 2.273449 CTGACAGGGGCCACATCC 59.727 66.667 8.31 0.00 0.00 3.51
5518 6220 1.009829 CAGTATTCCGGCAAGCTCAC 58.990 55.000 0.00 0.00 0.00 3.51
5672 6387 0.107703 TGCACCGAGCTAATCCTTGG 60.108 55.000 0.00 0.00 45.94 3.61
5683 6398 2.407428 TAGAGCCGAGTGCACCGAG 61.407 63.158 23.58 16.12 44.83 4.63
5685 6400 2.202623 GTAGAGCCGAGTGCACCG 60.203 66.667 14.63 16.36 44.83 4.94
5687 6402 1.446272 GGTGTAGAGCCGAGTGCAC 60.446 63.158 9.40 9.40 44.83 4.57
5704 6423 1.078497 TGCAGGTGAAGGCATACGG 60.078 57.895 0.00 0.00 34.58 4.02
5708 6427 0.395311 CCATCTGCAGGTGAAGGCAT 60.395 55.000 28.75 1.02 39.65 4.40
5711 6430 0.325933 TGACCATCTGCAGGTGAAGG 59.674 55.000 28.75 14.43 40.09 3.46
5723 6442 1.140852 TGGTTCCCGATGATGACCATC 59.859 52.381 3.17 3.17 46.36 3.51
5724 6443 1.212375 TGGTTCCCGATGATGACCAT 58.788 50.000 0.00 0.00 35.58 3.55
5725 6444 0.988063 TTGGTTCCCGATGATGACCA 59.012 50.000 0.00 0.00 38.54 4.02
5726 6445 1.668419 CTTGGTTCCCGATGATGACC 58.332 55.000 0.00 0.00 0.00 4.02
5728 6447 0.546122 CCCTTGGTTCCCGATGATGA 59.454 55.000 0.00 0.00 0.00 2.92
5729 6448 0.466189 CCCCTTGGTTCCCGATGATG 60.466 60.000 0.00 0.00 0.00 3.07
5730 6449 1.922821 CCCCTTGGTTCCCGATGAT 59.077 57.895 0.00 0.00 0.00 2.45
5731 6450 2.978946 GCCCCTTGGTTCCCGATGA 61.979 63.158 0.00 0.00 0.00 2.92
5732 6451 2.440247 GCCCCTTGGTTCCCGATG 60.440 66.667 0.00 0.00 0.00 3.84
5733 6452 2.850851 TAGGCCCCTTGGTTCCCGAT 62.851 60.000 0.00 0.00 0.00 4.18
5735 6454 2.608550 TTAGGCCCCTTGGTTCCCG 61.609 63.158 0.00 0.00 0.00 5.14
5736 6455 1.000019 GTTAGGCCCCTTGGTTCCC 60.000 63.158 0.00 0.00 0.00 3.97
5737 6456 0.034380 GAGTTAGGCCCCTTGGTTCC 60.034 60.000 0.00 0.00 0.00 3.62
5739 6458 0.838987 TCGAGTTAGGCCCCTTGGTT 60.839 55.000 0.00 0.00 0.00 3.67
5740 6459 0.620700 ATCGAGTTAGGCCCCTTGGT 60.621 55.000 0.00 0.00 0.00 3.67
5741 6460 0.106894 GATCGAGTTAGGCCCCTTGG 59.893 60.000 0.00 0.00 0.00 3.61
5742 6461 0.830648 TGATCGAGTTAGGCCCCTTG 59.169 55.000 0.00 0.00 0.00 3.61
5743 6462 1.123928 CTGATCGAGTTAGGCCCCTT 58.876 55.000 0.00 0.00 0.00 3.95
5744 6463 0.261991 TCTGATCGAGTTAGGCCCCT 59.738 55.000 0.00 0.00 0.00 4.79
5745 6464 1.343069 ATCTGATCGAGTTAGGCCCC 58.657 55.000 0.00 0.00 0.00 5.80
5749 8320 4.054671 GAGGCAAATCTGATCGAGTTAGG 58.945 47.826 0.00 0.00 0.00 2.69
5758 8329 3.087031 CCACAAGTGAGGCAAATCTGAT 58.913 45.455 0.94 0.00 0.00 2.90
5759 8330 2.507484 CCACAAGTGAGGCAAATCTGA 58.493 47.619 0.94 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.