Multiple sequence alignment - TraesCS7D01G429200

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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 TraesCS7D01G429200 chr7D 100.000 2913 0 0 1 2913 549133753 549136665 0.000000e+00 5380.0
1 TraesCS7D01G429200 chr7D 91.959 1281 70 16 850 2123 549274160 549275414 0.000000e+00 1764.0
2 TraesCS7D01G429200 chr7D 85.525 829 91 20 1039 1847 548916088 548915269 0.000000e+00 839.0
3 TraesCS7D01G429200 chr7D 84.483 174 15 9 1041 1207 614535594 614535762 8.350000e-36 161.0
4 TraesCS7D01G429200 chr7D 79.630 216 42 2 2699 2913 8592951 8592737 1.400000e-33 154.0
5 TraesCS7D01G429200 chr7D 81.193 218 16 16 2419 2620 549276460 549276668 5.030000e-33 152.0
6 TraesCS7D01G429200 chr7A 92.510 1789 82 24 666 2435 634476566 634478321 0.000000e+00 2514.0
7 TraesCS7D01G429200 chr7A 94.468 1392 57 14 728 2114 634463688 634465064 0.000000e+00 2126.0
8 TraesCS7D01G429200 chr7A 91.174 1303 85 14 780 2068 634605253 634606539 0.000000e+00 1742.0
9 TraesCS7D01G429200 chr7A 85.622 772 77 22 1 742 634604118 634604885 0.000000e+00 780.0
10 TraesCS7D01G429200 chr7A 90.281 391 36 1 107 495 634462444 634462834 7.200000e-141 510.0
11 TraesCS7D01G429200 chr7A 83.542 559 56 15 112 667 634475718 634476243 9.380000e-135 490.0
12 TraesCS7D01G429200 chr7A 93.333 255 10 6 486 736 634463419 634463670 1.280000e-98 370.0
13 TraesCS7D01G429200 chr7A 83.659 410 33 16 2231 2620 634610112 634610507 3.570000e-94 355.0
14 TraesCS7D01G429200 chr7B 90.011 1842 108 30 728 2532 592807627 592809429 0.000000e+00 2313.0
15 TraesCS7D01G429200 chr7B 89.848 1842 112 29 728 2532 592867418 592869221 0.000000e+00 2296.0
16 TraesCS7D01G429200 chr7B 89.094 1843 105 42 817 2611 592718270 592720064 0.000000e+00 2202.0
17 TraesCS7D01G429200 chr7B 90.000 640 52 10 109 742 592866774 592867407 0.000000e+00 817.0
18 TraesCS7D01G429200 chr7B 84.994 813 92 13 1039 1828 592534853 592534048 0.000000e+00 798.0
19 TraesCS7D01G429200 chr7B 89.392 641 54 11 109 742 592806983 592807616 0.000000e+00 795.0
20 TraesCS7D01G429200 chr7B 87.372 586 33 13 279 827 592716561 592717142 4.100000e-178 634.0
21 TraesCS7D01G429200 chr7B 82.657 542 48 21 2119 2620 592912308 592912843 3.450000e-119 438.0
22 TraesCS7D01G429200 chr7B 83.113 302 24 9 1 275 592716093 592716394 1.730000e-62 250.0
23 TraesCS7D01G429200 chr7B 92.683 41 3 0 2580 2620 592810251 592810291 3.130000e-05 60.2
24 TraesCS7D01G429200 chr7B 92.683 41 3 0 2580 2620 592870043 592870083 3.130000e-05 60.2
25 TraesCS7D01G429200 chr2D 84.507 213 32 1 2701 2913 615577451 615577662 2.940000e-50 209.0
26 TraesCS7D01G429200 chr2B 84.038 213 34 0 2701 2913 793999754 793999966 3.810000e-49 206.0
27 TraesCS7D01G429200 chr2B 83.256 215 36 0 2699 2913 513249673 513249887 6.370000e-47 198.0
28 TraesCS7D01G429200 chr2B 80.645 217 37 4 2699 2913 641651835 641652048 2.320000e-36 163.0
29 TraesCS7D01G429200 chr6A 82.273 220 28 8 2699 2913 613659023 613659236 2.310000e-41 180.0
30 TraesCS7D01G429200 chr5D 81.019 216 31 9 2701 2913 108170508 108170716 2.320000e-36 163.0
31 TraesCS7D01G429200 chr5D 80.193 207 33 5 2712 2913 536281260 536281057 6.500000e-32 148.0
32 TraesCS7D01G429200 chr3A 80.465 215 39 3 2701 2913 78184341 78184128 8.350000e-36 161.0


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 TraesCS7D01G429200 chr7D 549133753 549136665 2912 False 5380.000000 5380 100.000000 1 2913 1 chr7D.!!$F1 2912
1 TraesCS7D01G429200 chr7D 549274160 549276668 2508 False 958.000000 1764 86.576000 850 2620 2 chr7D.!!$F3 1770
2 TraesCS7D01G429200 chr7D 548915269 548916088 819 True 839.000000 839 85.525000 1039 1847 1 chr7D.!!$R2 808
3 TraesCS7D01G429200 chr7A 634475718 634478321 2603 False 1502.000000 2514 88.026000 112 2435 2 chr7A.!!$F2 2323
4 TraesCS7D01G429200 chr7A 634462444 634465064 2620 False 1002.000000 2126 92.694000 107 2114 3 chr7A.!!$F1 2007
5 TraesCS7D01G429200 chr7A 634604118 634610507 6389 False 959.000000 1742 86.818333 1 2620 3 chr7A.!!$F3 2619
6 TraesCS7D01G429200 chr7B 592866774 592870083 3309 False 1057.733333 2296 90.843667 109 2620 3 chr7B.!!$F4 2511
7 TraesCS7D01G429200 chr7B 592806983 592810291 3308 False 1056.066667 2313 90.695333 109 2620 3 chr7B.!!$F3 2511
8 TraesCS7D01G429200 chr7B 592716093 592720064 3971 False 1028.666667 2202 86.526333 1 2611 3 chr7B.!!$F2 2610
9 TraesCS7D01G429200 chr7B 592534048 592534853 805 True 798.000000 798 84.994000 1039 1828 1 chr7B.!!$R1 789
10 TraesCS7D01G429200 chr7B 592912308 592912843 535 False 438.000000 438 82.657000 2119 2620 1 chr7B.!!$F1 501

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
709 1842 0.252012 CCCATGCCCCACTTGGTTTA 60.252 55.0 0.0 0.0 41.1 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2666 10365 0.033109 GGTCCCCTTTCTTCCATGGG 60.033 60.0 13.02 0.0 39.37 4.0 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
35 36 8.519492 AAACCGAAGATGAACATTGTATTTTG 57.481 30.769 0.00 0.00 0.00 2.44
39 40 8.427012 CCGAAGATGAACATTGTATTTTGTTTG 58.573 33.333 0.00 0.00 36.25 2.93
172 203 4.904253 TTTTTCTTAAGGAACACACCCG 57.096 40.909 1.85 0.00 33.13 5.28
189 220 3.399181 GGAGGGCATCGTGGACCA 61.399 66.667 3.86 0.00 38.98 4.02
217 248 6.149474 CGATTGTCTAGGAAAATGACCAGTTT 59.851 38.462 0.00 0.00 0.00 2.66
243 276 7.687941 ATGAAAAGATAACTGAACGTGGAAT 57.312 32.000 0.00 0.00 0.00 3.01
401 597 9.793259 TCTTTCACTTTAATTAACAGGACTGAT 57.207 29.630 6.29 0.00 0.00 2.90
477 673 4.282195 CCTTGTCCATCCCTATCTCTACAC 59.718 50.000 0.00 0.00 0.00 2.90
636 1445 1.626654 CCGTGCTACAAGGAACTGCG 61.627 60.000 0.00 0.00 40.86 5.18
639 1448 1.376037 GCTACAAGGAACTGCGCCT 60.376 57.895 4.18 0.00 40.86 5.52
640 1449 1.362406 GCTACAAGGAACTGCGCCTC 61.362 60.000 4.18 0.00 40.86 4.70
709 1842 0.252012 CCCATGCCCCACTTGGTTTA 60.252 55.000 0.00 0.00 41.10 2.01
736 1896 2.360600 GCACACGTTGGGCCCATA 60.361 61.111 29.23 14.31 41.97 2.74
756 1916 1.292992 AAGTTGGTGAAACGTCGTCC 58.707 50.000 0.00 0.00 44.04 4.79
763 1924 1.236616 TGAAACGTCGTCCTAGCGGA 61.237 55.000 0.00 0.00 36.83 5.54
808 2275 5.758924 AGAACCTAAAATTCGACTTGCAAC 58.241 37.500 0.00 0.00 0.00 4.17
825 3430 7.081976 ACTTGCAACCGTAAAAGCTAATTAAG 58.918 34.615 0.00 0.00 0.00 1.85
1035 3642 4.347000 AGGCCTCTCTAGTCTACAGTCTAG 59.653 50.000 0.00 4.68 35.88 2.43
1284 3915 0.040157 TGATATGCGCGTACGTACCC 60.040 55.000 19.67 10.22 42.83 3.69
1847 4488 2.267351 CCACGCCATGCTTGTTCCA 61.267 57.895 0.00 0.00 0.00 3.53
1965 4621 2.323447 TCGTGCTCGATCGCGTAG 59.677 61.111 20.09 3.87 41.35 3.51
1989 4645 8.225603 AGACAAGGCGTTATGATTTGATTTAT 57.774 30.769 0.00 0.00 0.00 1.40
2030 4694 7.554732 ACGATTTGATTTGAACAAATTTCACG 58.445 30.769 12.91 15.15 44.46 4.35
2094 4791 6.879458 ACTGAAAAAGAAGTATCCGTATGCTT 59.121 34.615 0.00 0.00 40.31 3.91
2098 4795 6.851222 AAAGAAGTATCCGTATGCTTGATG 57.149 37.500 0.00 0.00 38.06 3.07
2114 4811 7.692460 TGCTTGATGTGAAAATCTGTAGAAT 57.308 32.000 0.00 0.00 0.00 2.40
2116 4813 9.230122 TGCTTGATGTGAAAATCTGTAGAATTA 57.770 29.630 0.00 0.00 0.00 1.40
2117 4814 9.495754 GCTTGATGTGAAAATCTGTAGAATTAC 57.504 33.333 0.00 0.00 0.00 1.89
2334 8508 2.072298 CACTCTCTCTTTTTCTGCGGG 58.928 52.381 0.00 0.00 0.00 6.13
2346 8520 3.593442 TTCTGCGGGGAAATCCATTAT 57.407 42.857 1.22 0.00 37.91 1.28
2350 8524 4.288366 TCTGCGGGGAAATCCATTATCATA 59.712 41.667 1.22 0.00 37.91 2.15
2445 9345 9.530633 AGTTCCATATAACTAATCTCGTTGAAC 57.469 33.333 0.00 0.00 37.93 3.18
2453 9355 9.871238 ATAACTAATCTCGTTGAACATACTGTT 57.129 29.630 0.00 0.00 44.37 3.16
2454 9356 7.582435 ACTAATCTCGTTGAACATACTGTTG 57.418 36.000 0.00 0.00 41.28 3.33
2515 9450 6.823689 ACGGAGAAAGATTATTATGTTGTGCT 59.176 34.615 0.00 0.00 0.00 4.40
2579 9514 7.609056 ACTGATTTAAAAGATTGCATTGCTCT 58.391 30.769 10.49 2.29 0.00 4.09
2580 9515 7.544566 ACTGATTTAAAAGATTGCATTGCTCTG 59.455 33.333 10.49 1.56 0.00 3.35
2583 9518 3.482722 AAAGATTGCATTGCTCTGTCG 57.517 42.857 10.49 0.00 0.00 4.35
2622 10321 6.648879 TGGATACATCATCGTAGTCAATCA 57.351 37.500 0.00 0.00 46.17 2.57
2623 10322 7.049799 TGGATACATCATCGTAGTCAATCAA 57.950 36.000 0.00 0.00 46.17 2.57
2624 10323 7.147976 TGGATACATCATCGTAGTCAATCAAG 58.852 38.462 0.00 0.00 46.17 3.02
2625 10324 7.148641 GGATACATCATCGTAGTCAATCAAGT 58.851 38.462 0.00 0.00 34.12 3.16
2626 10325 8.297426 GGATACATCATCGTAGTCAATCAAGTA 58.703 37.037 0.00 0.00 34.12 2.24
2627 10326 9.678941 GATACATCATCGTAGTCAATCAAGTAA 57.321 33.333 0.00 0.00 0.00 2.24
2629 10328 8.186178 ACATCATCGTAGTCAATCAAGTAAAC 57.814 34.615 0.00 0.00 0.00 2.01
2630 10329 7.817478 ACATCATCGTAGTCAATCAAGTAAACA 59.183 33.333 0.00 0.00 0.00 2.83
2631 10330 8.655970 CATCATCGTAGTCAATCAAGTAAACAA 58.344 33.333 0.00 0.00 0.00 2.83
2632 10331 8.596271 TCATCGTAGTCAATCAAGTAAACAAA 57.404 30.769 0.00 0.00 0.00 2.83
2633 10332 8.492748 TCATCGTAGTCAATCAAGTAAACAAAC 58.507 33.333 0.00 0.00 0.00 2.93
2634 10333 6.869473 TCGTAGTCAATCAAGTAAACAAACG 58.131 36.000 0.00 0.00 0.00 3.60
2635 10334 5.558888 CGTAGTCAATCAAGTAAACAAACGC 59.441 40.000 0.00 0.00 0.00 4.84
2636 10335 5.751243 AGTCAATCAAGTAAACAAACGCT 57.249 34.783 0.00 0.00 0.00 5.07
2637 10336 5.510671 AGTCAATCAAGTAAACAAACGCTG 58.489 37.500 0.00 0.00 0.00 5.18
2638 10337 4.675114 GTCAATCAAGTAAACAAACGCTGG 59.325 41.667 0.00 0.00 0.00 4.85
2639 10338 4.336993 TCAATCAAGTAAACAAACGCTGGT 59.663 37.500 0.00 0.00 0.00 4.00
2640 10339 3.955771 TCAAGTAAACAAACGCTGGTC 57.044 42.857 0.00 0.00 0.00 4.02
2641 10340 2.285756 TCAAGTAAACAAACGCTGGTCG 59.714 45.455 0.00 0.00 45.38 4.79
2642 10341 2.228138 AGTAAACAAACGCTGGTCGA 57.772 45.000 0.00 0.00 41.67 4.20
2643 10342 2.762745 AGTAAACAAACGCTGGTCGAT 58.237 42.857 0.00 0.00 41.67 3.59
2644 10343 3.135994 AGTAAACAAACGCTGGTCGATT 58.864 40.909 0.00 0.00 41.67 3.34
2645 10344 2.681152 AAACAAACGCTGGTCGATTC 57.319 45.000 0.00 0.00 41.67 2.52
2646 10345 0.872388 AACAAACGCTGGTCGATTCC 59.128 50.000 0.00 0.00 41.67 3.01
2647 10346 0.250124 ACAAACGCTGGTCGATTCCA 60.250 50.000 0.00 0.00 41.67 3.53
2648 10347 0.165944 CAAACGCTGGTCGATTCCAC 59.834 55.000 0.00 0.00 41.67 4.02
2649 10348 1.289109 AAACGCTGGTCGATTCCACG 61.289 55.000 12.26 12.26 41.67 4.94
2650 10349 2.149803 AACGCTGGTCGATTCCACGA 62.150 55.000 17.47 0.00 41.67 4.35
2651 10350 1.874019 CGCTGGTCGATTCCACGAG 60.874 63.158 9.75 0.00 42.88 4.18
2652 10351 1.215647 GCTGGTCGATTCCACGAGT 59.784 57.895 0.00 0.00 42.88 4.18
2653 10352 0.802607 GCTGGTCGATTCCACGAGTC 60.803 60.000 0.00 0.00 42.88 3.36
2654 10353 0.523546 CTGGTCGATTCCACGAGTCG 60.524 60.000 11.85 11.85 42.88 4.18
2655 10354 1.239296 TGGTCGATTCCACGAGTCGT 61.239 55.000 13.56 13.56 41.37 4.34
2656 10355 0.109412 GGTCGATTCCACGAGTCGTT 60.109 55.000 17.16 0.28 41.37 3.85
2657 10356 1.668047 GGTCGATTCCACGAGTCGTTT 60.668 52.381 17.16 0.83 41.37 3.60
2658 10357 2.056577 GTCGATTCCACGAGTCGTTTT 58.943 47.619 17.16 0.43 41.37 2.43
2659 10358 2.090195 GTCGATTCCACGAGTCGTTTTC 59.910 50.000 17.16 9.34 41.37 2.29
2660 10359 2.030540 TCGATTCCACGAGTCGTTTTCT 60.031 45.455 17.16 1.02 41.37 2.52
2661 10360 2.729882 CGATTCCACGAGTCGTTTTCTT 59.270 45.455 17.16 0.00 38.32 2.52
2662 10361 3.183775 CGATTCCACGAGTCGTTTTCTTT 59.816 43.478 17.16 0.00 38.32 2.52
2663 10362 4.663389 CGATTCCACGAGTCGTTTTCTTTC 60.663 45.833 17.16 7.62 38.32 2.62
2664 10363 3.447918 TCCACGAGTCGTTTTCTTTCT 57.552 42.857 17.16 0.00 38.32 2.52
2665 10364 3.788937 TCCACGAGTCGTTTTCTTTCTT 58.211 40.909 17.16 0.00 38.32 2.52
2666 10365 3.800506 TCCACGAGTCGTTTTCTTTCTTC 59.199 43.478 17.16 0.00 38.32 2.87
2667 10366 3.059800 CCACGAGTCGTTTTCTTTCTTCC 60.060 47.826 17.16 0.00 38.32 3.46
2668 10367 3.059800 CACGAGTCGTTTTCTTTCTTCCC 60.060 47.826 17.16 0.00 38.32 3.97
2669 10368 3.128349 CGAGTCGTTTTCTTTCTTCCCA 58.872 45.455 3.82 0.00 0.00 4.37
2670 10369 3.746492 CGAGTCGTTTTCTTTCTTCCCAT 59.254 43.478 3.82 0.00 0.00 4.00
2671 10370 4.377431 CGAGTCGTTTTCTTTCTTCCCATG 60.377 45.833 3.82 0.00 0.00 3.66
2672 10371 3.821033 AGTCGTTTTCTTTCTTCCCATGG 59.179 43.478 4.14 4.14 0.00 3.66
2673 10372 3.818773 GTCGTTTTCTTTCTTCCCATGGA 59.181 43.478 15.22 0.00 0.00 3.41
2674 10373 4.277423 GTCGTTTTCTTTCTTCCCATGGAA 59.723 41.667 15.22 4.85 39.66 3.53
2683 10382 1.766951 TTCCCATGGAAGAAAGGGGA 58.233 50.000 15.22 0.00 45.84 4.81
2684 10383 0.999712 TCCCATGGAAGAAAGGGGAC 59.000 55.000 15.22 0.00 42.75 4.46
2704 10403 1.558233 CCTTTGACTAGGGACCTCGT 58.442 55.000 0.00 0.00 0.00 4.18
2705 10404 1.477295 CCTTTGACTAGGGACCTCGTC 59.523 57.143 14.24 14.24 38.67 4.20
2706 10405 2.448453 CTTTGACTAGGGACCTCGTCT 58.552 52.381 19.74 0.10 38.88 4.18
2707 10406 2.125773 TTGACTAGGGACCTCGTCTC 57.874 55.000 19.74 0.93 38.88 3.36
2708 10407 0.989602 TGACTAGGGACCTCGTCTCA 59.010 55.000 19.74 3.23 38.88 3.27
2709 10408 1.564818 TGACTAGGGACCTCGTCTCAT 59.435 52.381 19.74 0.00 38.88 2.90
2710 10409 1.950909 GACTAGGGACCTCGTCTCATG 59.049 57.143 13.93 0.00 35.11 3.07
2711 10410 1.285373 ACTAGGGACCTCGTCTCATGT 59.715 52.381 0.00 0.00 35.11 3.21
2712 10411 1.678627 CTAGGGACCTCGTCTCATGTG 59.321 57.143 0.00 0.00 35.11 3.21
2713 10412 0.972983 AGGGACCTCGTCTCATGTGG 60.973 60.000 0.00 0.00 35.11 4.17
2714 10413 1.258445 GGGACCTCGTCTCATGTGGT 61.258 60.000 0.00 0.00 32.50 4.16
2715 10414 0.608640 GGACCTCGTCTCATGTGGTT 59.391 55.000 0.00 0.00 32.47 3.67
2716 10415 1.002087 GGACCTCGTCTCATGTGGTTT 59.998 52.381 0.00 0.00 32.47 3.27
2717 10416 2.550208 GGACCTCGTCTCATGTGGTTTT 60.550 50.000 0.00 0.00 32.47 2.43
2718 10417 3.306502 GGACCTCGTCTCATGTGGTTTTA 60.307 47.826 0.00 0.00 32.47 1.52
2719 10418 3.926616 ACCTCGTCTCATGTGGTTTTAG 58.073 45.455 0.00 0.00 0.00 1.85
2720 10419 3.262420 CCTCGTCTCATGTGGTTTTAGG 58.738 50.000 0.00 0.00 0.00 2.69
2721 10420 3.262420 CTCGTCTCATGTGGTTTTAGGG 58.738 50.000 0.00 0.00 0.00 3.53
2722 10421 1.737793 CGTCTCATGTGGTTTTAGGGC 59.262 52.381 0.00 0.00 0.00 5.19
2723 10422 2.092323 GTCTCATGTGGTTTTAGGGCC 58.908 52.381 0.00 0.00 0.00 5.80
2724 10423 1.707989 TCTCATGTGGTTTTAGGGCCA 59.292 47.619 6.18 0.00 0.00 5.36
2725 10424 2.311542 TCTCATGTGGTTTTAGGGCCAT 59.688 45.455 6.18 0.00 37.09 4.40
2726 10425 2.428171 CTCATGTGGTTTTAGGGCCATG 59.572 50.000 6.18 0.00 37.09 3.66
2727 10426 1.481772 CATGTGGTTTTAGGGCCATGG 59.518 52.381 7.63 7.63 37.09 3.66
2728 10427 0.780637 TGTGGTTTTAGGGCCATGGA 59.219 50.000 18.40 0.00 37.09 3.41
2729 10428 1.148027 TGTGGTTTTAGGGCCATGGAA 59.852 47.619 18.40 0.00 37.09 3.53
2730 10429 2.252714 GTGGTTTTAGGGCCATGGAAA 58.747 47.619 18.40 3.79 37.09 3.13
2731 10430 2.028476 GTGGTTTTAGGGCCATGGAAAC 60.028 50.000 18.40 16.02 37.09 2.78
2732 10431 1.203758 GGTTTTAGGGCCATGGAAACG 59.796 52.381 18.40 0.00 32.50 3.60
2733 10432 1.890489 GTTTTAGGGCCATGGAAACGT 59.110 47.619 18.40 8.87 0.00 3.99
2746 10445 3.521560 TGGAAACGTGATAGATGTCTGC 58.478 45.455 0.00 0.00 0.00 4.26
2747 10446 2.866762 GGAAACGTGATAGATGTCTGCC 59.133 50.000 0.00 0.00 0.00 4.85
2748 10447 2.604046 AACGTGATAGATGTCTGCCC 57.396 50.000 0.00 0.00 0.00 5.36
2749 10448 1.781786 ACGTGATAGATGTCTGCCCT 58.218 50.000 0.00 0.00 0.00 5.19
2750 10449 2.111384 ACGTGATAGATGTCTGCCCTT 58.889 47.619 0.00 0.00 0.00 3.95
2751 10450 3.296854 ACGTGATAGATGTCTGCCCTTA 58.703 45.455 0.00 0.00 0.00 2.69
2752 10451 3.068307 ACGTGATAGATGTCTGCCCTTAC 59.932 47.826 0.00 0.00 0.00 2.34
2753 10452 3.553096 CGTGATAGATGTCTGCCCTTACC 60.553 52.174 0.00 0.00 0.00 2.85
2754 10453 2.628178 TGATAGATGTCTGCCCTTACCG 59.372 50.000 0.00 0.00 0.00 4.02
2755 10454 2.154567 TAGATGTCTGCCCTTACCGT 57.845 50.000 0.00 0.00 0.00 4.83
2756 10455 0.824759 AGATGTCTGCCCTTACCGTC 59.175 55.000 0.00 0.00 0.00 4.79
2757 10456 0.527817 GATGTCTGCCCTTACCGTCG 60.528 60.000 0.00 0.00 0.00 5.12
2758 10457 1.956629 ATGTCTGCCCTTACCGTCGG 61.957 60.000 10.48 10.48 0.00 4.79
2759 10458 3.072468 TCTGCCCTTACCGTCGGG 61.072 66.667 17.28 0.00 43.60 5.14
2760 10459 3.072468 CTGCCCTTACCGTCGGGA 61.072 66.667 17.28 3.30 43.44 5.14
2761 10460 3.072468 TGCCCTTACCGTCGGGAG 61.072 66.667 17.28 12.68 43.44 4.30
2762 10461 3.846430 GCCCTTACCGTCGGGAGG 61.846 72.222 22.51 22.51 43.44 4.30
2763 10462 3.152400 CCCTTACCGTCGGGAGGG 61.152 72.222 29.66 29.66 43.44 4.30
2764 10463 3.846430 CCTTACCGTCGGGAGGGC 61.846 72.222 21.99 0.00 39.85 5.19
2765 10464 2.758737 CTTACCGTCGGGAGGGCT 60.759 66.667 17.28 0.00 39.85 5.19
2766 10465 2.284112 TTACCGTCGGGAGGGCTT 60.284 61.111 17.28 0.00 39.85 4.35
2767 10466 2.294132 CTTACCGTCGGGAGGGCTTC 62.294 65.000 17.28 0.00 39.85 3.86
2770 10469 4.065281 CGTCGGGAGGGCTTCGTT 62.065 66.667 0.00 0.00 0.00 3.85
2771 10470 2.703798 CGTCGGGAGGGCTTCGTTA 61.704 63.158 0.00 0.00 0.00 3.18
2772 10471 1.821258 GTCGGGAGGGCTTCGTTAT 59.179 57.895 0.00 0.00 0.00 1.89
2773 10472 0.177373 GTCGGGAGGGCTTCGTTATT 59.823 55.000 0.00 0.00 0.00 1.40
2774 10473 0.906775 TCGGGAGGGCTTCGTTATTT 59.093 50.000 0.00 0.00 0.00 1.40
2775 10474 1.134610 TCGGGAGGGCTTCGTTATTTC 60.135 52.381 0.00 0.00 0.00 2.17
2776 10475 1.406341 CGGGAGGGCTTCGTTATTTCA 60.406 52.381 0.00 0.00 0.00 2.69
2777 10476 2.745152 CGGGAGGGCTTCGTTATTTCAT 60.745 50.000 0.00 0.00 0.00 2.57
2778 10477 3.493699 CGGGAGGGCTTCGTTATTTCATA 60.494 47.826 0.00 0.00 0.00 2.15
2779 10478 4.652822 GGGAGGGCTTCGTTATTTCATAT 58.347 43.478 0.00 0.00 0.00 1.78
2780 10479 5.070685 GGGAGGGCTTCGTTATTTCATATT 58.929 41.667 0.00 0.00 0.00 1.28
2781 10480 5.535030 GGGAGGGCTTCGTTATTTCATATTT 59.465 40.000 0.00 0.00 0.00 1.40
2782 10481 6.040504 GGGAGGGCTTCGTTATTTCATATTTT 59.959 38.462 0.00 0.00 0.00 1.82
2783 10482 7.417456 GGGAGGGCTTCGTTATTTCATATTTTT 60.417 37.037 0.00 0.00 0.00 1.94
2804 10503 6.361768 TTTTTGAGTTTGGTTAGGGTTTGT 57.638 33.333 0.00 0.00 0.00 2.83
2805 10504 4.993029 TTGAGTTTGGTTAGGGTTTGTG 57.007 40.909 0.00 0.00 0.00 3.33
2806 10505 3.970842 TGAGTTTGGTTAGGGTTTGTGT 58.029 40.909 0.00 0.00 0.00 3.72
2807 10506 3.949113 TGAGTTTGGTTAGGGTTTGTGTC 59.051 43.478 0.00 0.00 0.00 3.67
2808 10507 3.293337 AGTTTGGTTAGGGTTTGTGTCC 58.707 45.455 0.00 0.00 0.00 4.02
2809 10508 3.053170 AGTTTGGTTAGGGTTTGTGTCCT 60.053 43.478 0.00 0.00 37.18 3.85
2810 10509 2.649531 TGGTTAGGGTTTGTGTCCTG 57.350 50.000 0.00 0.00 34.75 3.86
2811 10510 1.847737 TGGTTAGGGTTTGTGTCCTGT 59.152 47.619 0.00 0.00 34.75 4.00
2812 10511 2.242708 TGGTTAGGGTTTGTGTCCTGTT 59.757 45.455 0.00 0.00 34.75 3.16
2813 10512 2.882761 GGTTAGGGTTTGTGTCCTGTTC 59.117 50.000 0.00 0.00 34.75 3.18
2814 10513 3.547746 GTTAGGGTTTGTGTCCTGTTCA 58.452 45.455 0.00 0.00 34.75 3.18
2815 10514 2.348411 AGGGTTTGTGTCCTGTTCAG 57.652 50.000 0.00 0.00 31.11 3.02
2816 10515 1.843851 AGGGTTTGTGTCCTGTTCAGA 59.156 47.619 1.00 0.00 31.11 3.27
2817 10516 2.158755 AGGGTTTGTGTCCTGTTCAGAG 60.159 50.000 1.00 0.00 31.11 3.35
2818 10517 2.158813 GGGTTTGTGTCCTGTTCAGAGA 60.159 50.000 1.00 0.00 0.00 3.10
2819 10518 3.134458 GGTTTGTGTCCTGTTCAGAGAG 58.866 50.000 1.00 0.00 0.00 3.20
2820 10519 3.181465 GGTTTGTGTCCTGTTCAGAGAGA 60.181 47.826 1.00 0.00 0.00 3.10
2821 10520 3.735237 TTGTGTCCTGTTCAGAGAGAC 57.265 47.619 1.00 6.53 0.00 3.36
2822 10521 1.609072 TGTGTCCTGTTCAGAGAGACG 59.391 52.381 1.00 0.00 0.00 4.18
2823 10522 1.880675 GTGTCCTGTTCAGAGAGACGA 59.119 52.381 1.00 0.00 0.00 4.20
2824 10523 2.095466 GTGTCCTGTTCAGAGAGACGAG 60.095 54.545 1.00 0.00 0.00 4.18
2825 10524 1.470890 GTCCTGTTCAGAGAGACGAGG 59.529 57.143 1.00 0.00 0.00 4.63
2826 10525 0.172352 CCTGTTCAGAGAGACGAGGC 59.828 60.000 1.00 0.00 0.00 4.70
2827 10526 0.179176 CTGTTCAGAGAGACGAGGCG 60.179 60.000 0.00 0.00 0.00 5.52
2828 10527 1.137825 GTTCAGAGAGACGAGGCGG 59.862 63.158 0.00 0.00 0.00 6.13
2829 10528 2.701780 TTCAGAGAGACGAGGCGGC 61.702 63.158 0.00 0.00 33.59 6.53
2830 10529 4.544689 CAGAGAGACGAGGCGGCG 62.545 72.222 0.51 0.51 41.28 6.46
2831 10530 4.779966 AGAGAGACGAGGCGGCGA 62.780 66.667 12.98 0.00 41.28 5.54
2832 10531 3.587933 GAGAGACGAGGCGGCGAT 61.588 66.667 12.98 0.00 41.28 4.58
2833 10532 3.815569 GAGAGACGAGGCGGCGATG 62.816 68.421 12.98 0.00 41.28 3.84
2834 10533 4.933064 GAGACGAGGCGGCGATGG 62.933 72.222 12.98 1.38 41.28 3.51
2840 10539 4.101448 AGGCGGCGATGGCTCTTT 62.101 61.111 12.98 0.00 41.54 2.52
2841 10540 2.203015 GGCGGCGATGGCTCTTTA 60.203 61.111 12.98 0.00 39.81 1.85
2842 10541 1.817941 GGCGGCGATGGCTCTTTAA 60.818 57.895 12.98 0.00 39.81 1.52
2843 10542 1.373590 GGCGGCGATGGCTCTTTAAA 61.374 55.000 12.98 0.00 39.81 1.52
2844 10543 0.028110 GCGGCGATGGCTCTTTAAAG 59.972 55.000 12.98 9.04 39.81 1.85
2845 10544 1.651987 CGGCGATGGCTCTTTAAAGA 58.348 50.000 16.85 16.85 39.81 2.52
2846 10545 2.213499 CGGCGATGGCTCTTTAAAGAT 58.787 47.619 18.02 3.56 39.81 2.40
2847 10546 2.032549 CGGCGATGGCTCTTTAAAGATG 60.033 50.000 18.02 12.85 39.81 2.90
2848 10547 2.291741 GGCGATGGCTCTTTAAAGATGG 59.708 50.000 18.02 8.98 39.81 3.51
2849 10548 3.206150 GCGATGGCTCTTTAAAGATGGA 58.794 45.455 18.02 5.64 33.93 3.41
2850 10549 3.627577 GCGATGGCTCTTTAAAGATGGAA 59.372 43.478 18.02 5.59 33.93 3.53
2851 10550 4.276926 GCGATGGCTCTTTAAAGATGGAAT 59.723 41.667 18.02 9.76 33.93 3.01
2852 10551 5.470098 GCGATGGCTCTTTAAAGATGGAATA 59.530 40.000 18.02 3.39 33.93 1.75
2853 10552 6.017109 GCGATGGCTCTTTAAAGATGGAATAA 60.017 38.462 18.02 1.70 33.93 1.40
2854 10553 7.579726 CGATGGCTCTTTAAAGATGGAATAAG 58.420 38.462 18.02 5.54 33.93 1.73
2855 10554 7.308229 CGATGGCTCTTTAAAGATGGAATAAGG 60.308 40.741 18.02 4.87 33.93 2.69
2856 10555 6.731467 TGGCTCTTTAAAGATGGAATAAGGT 58.269 36.000 18.02 0.00 33.93 3.50
2857 10556 7.182060 TGGCTCTTTAAAGATGGAATAAGGTT 58.818 34.615 18.02 0.00 33.93 3.50
2858 10557 7.339466 TGGCTCTTTAAAGATGGAATAAGGTTC 59.661 37.037 18.02 2.40 33.93 3.62
2859 10558 7.558081 GGCTCTTTAAAGATGGAATAAGGTTCT 59.442 37.037 18.02 0.00 33.93 3.01
2860 10559 8.616942 GCTCTTTAAAGATGGAATAAGGTTCTC 58.383 37.037 18.02 0.00 33.93 2.87
2861 10560 9.114952 CTCTTTAAAGATGGAATAAGGTTCTCC 57.885 37.037 18.02 0.00 33.93 3.71
2862 10561 8.053355 TCTTTAAAGATGGAATAAGGTTCTCCC 58.947 37.037 13.99 0.00 0.00 4.30
2864 10563 8.632731 TTAAAGATGGAATAAGGTTCTCCCTA 57.367 34.615 0.00 0.00 45.47 3.53
2865 10564 6.502074 AAGATGGAATAAGGTTCTCCCTAC 57.498 41.667 0.00 0.00 45.47 3.18
2866 10565 4.908481 AGATGGAATAAGGTTCTCCCTACC 59.092 45.833 0.00 0.00 45.47 3.18
2867 10566 4.363546 TGGAATAAGGTTCTCCCTACCT 57.636 45.455 0.00 0.00 45.47 3.08
2868 10567 5.492565 TGGAATAAGGTTCTCCCTACCTA 57.507 43.478 0.00 0.00 45.47 3.08
2869 10568 5.464984 TGGAATAAGGTTCTCCCTACCTAG 58.535 45.833 0.00 0.00 45.47 3.02
2870 10569 5.042827 TGGAATAAGGTTCTCCCTACCTAGT 60.043 44.000 0.00 0.00 45.47 2.57
2871 10570 5.539574 GGAATAAGGTTCTCCCTACCTAGTC 59.460 48.000 0.00 0.00 45.47 2.59
2872 10571 3.401589 AAGGTTCTCCCTACCTAGTCC 57.598 52.381 0.00 0.00 45.47 3.85
2873 10572 1.574821 AGGTTCTCCCTACCTAGTCCC 59.425 57.143 0.00 0.00 44.11 4.46
2874 10573 1.290130 GGTTCTCCCTACCTAGTCCCA 59.710 57.143 0.00 0.00 32.75 4.37
2875 10574 2.668625 GTTCTCCCTACCTAGTCCCAG 58.331 57.143 0.00 0.00 0.00 4.45
2876 10575 1.997340 TCTCCCTACCTAGTCCCAGT 58.003 55.000 0.00 0.00 0.00 4.00
2877 10576 1.851653 TCTCCCTACCTAGTCCCAGTC 59.148 57.143 0.00 0.00 0.00 3.51
2878 10577 0.932211 TCCCTACCTAGTCCCAGTCC 59.068 60.000 0.00 0.00 0.00 3.85
2879 10578 0.105607 CCCTACCTAGTCCCAGTCCC 60.106 65.000 0.00 0.00 0.00 4.46
2880 10579 0.467659 CCTACCTAGTCCCAGTCCCG 60.468 65.000 0.00 0.00 0.00 5.14
2881 10580 0.549950 CTACCTAGTCCCAGTCCCGA 59.450 60.000 0.00 0.00 0.00 5.14
2882 10581 1.145325 CTACCTAGTCCCAGTCCCGAT 59.855 57.143 0.00 0.00 0.00 4.18
2883 10582 0.397254 ACCTAGTCCCAGTCCCGATG 60.397 60.000 0.00 0.00 0.00 3.84
2884 10583 0.106167 CCTAGTCCCAGTCCCGATGA 60.106 60.000 0.00 0.00 0.00 2.92
2885 10584 1.481428 CCTAGTCCCAGTCCCGATGAT 60.481 57.143 0.00 0.00 0.00 2.45
2886 10585 1.615883 CTAGTCCCAGTCCCGATGATG 59.384 57.143 0.00 0.00 0.00 3.07
2887 10586 0.325671 AGTCCCAGTCCCGATGATGT 60.326 55.000 0.00 0.00 0.00 3.06
2888 10587 0.541863 GTCCCAGTCCCGATGATGTT 59.458 55.000 0.00 0.00 0.00 2.71
2889 10588 1.065418 GTCCCAGTCCCGATGATGTTT 60.065 52.381 0.00 0.00 0.00 2.83
2890 10589 1.209504 TCCCAGTCCCGATGATGTTTC 59.790 52.381 0.00 0.00 0.00 2.78
2891 10590 1.210478 CCCAGTCCCGATGATGTTTCT 59.790 52.381 0.00 0.00 0.00 2.52
2892 10591 2.434336 CCCAGTCCCGATGATGTTTCTA 59.566 50.000 0.00 0.00 0.00 2.10
2893 10592 3.493350 CCCAGTCCCGATGATGTTTCTAG 60.493 52.174 0.00 0.00 0.00 2.43
2894 10593 3.126831 CAGTCCCGATGATGTTTCTAGC 58.873 50.000 0.00 0.00 0.00 3.42
2895 10594 2.766263 AGTCCCGATGATGTTTCTAGCA 59.234 45.455 0.00 0.00 0.00 3.49
2896 10595 3.389329 AGTCCCGATGATGTTTCTAGCAT 59.611 43.478 0.00 0.00 0.00 3.79
2897 10596 3.743396 GTCCCGATGATGTTTCTAGCATC 59.257 47.826 0.00 0.00 42.10 3.91
2901 10600 4.621526 GATGATGTTTCTAGCATCGTCG 57.378 45.455 12.46 0.00 44.36 5.12
2902 10601 2.809446 TGATGTTTCTAGCATCGTCGG 58.191 47.619 0.00 0.00 44.02 4.79
2903 10602 2.425668 TGATGTTTCTAGCATCGTCGGA 59.574 45.455 0.00 0.00 44.02 4.55
2904 10603 2.561733 TGTTTCTAGCATCGTCGGAG 57.438 50.000 0.00 0.00 0.00 4.63
2905 10604 1.134367 TGTTTCTAGCATCGTCGGAGG 59.866 52.381 0.00 0.00 0.00 4.30
2906 10605 0.744874 TTTCTAGCATCGTCGGAGGG 59.255 55.000 0.00 0.00 0.00 4.30
2907 10606 1.735376 TTCTAGCATCGTCGGAGGGC 61.735 60.000 0.00 0.00 0.00 5.19
2908 10607 3.544167 CTAGCATCGTCGGAGGGCG 62.544 68.421 0.00 0.00 33.15 6.13
2911 10610 4.129737 CATCGTCGGAGGGCGTGT 62.130 66.667 0.00 0.00 0.00 4.49
2912 10611 4.129737 ATCGTCGGAGGGCGTGTG 62.130 66.667 0.00 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 9.179552 TCAAACAAAATACAATGTTCATCTTCG 57.820 29.630 0.00 0.00 38.75 3.79
60 61 4.046286 AGGGAAAAAGTCATGTATGCCA 57.954 40.909 0.00 0.00 0.00 4.92
162 192 3.268103 ATGCCCTCCGGGTGTGTTC 62.268 63.158 0.00 0.00 46.51 3.18
172 203 3.391665 CTGGTCCACGATGCCCTCC 62.392 68.421 0.00 0.00 0.00 4.30
217 248 8.610248 TTCCACGTTCAGTTATCTTTTCATTA 57.390 30.769 0.00 0.00 0.00 1.90
277 310 6.642707 ATCGGAGGAATAAGAAGACTAGTG 57.357 41.667 0.00 0.00 0.00 2.74
518 1318 6.795593 GTGTGTTTATTTTTCGCTTCTACTCC 59.204 38.462 0.00 0.00 0.00 3.85
636 1445 1.528129 CTGTTGAGGAAAGTGGAGGC 58.472 55.000 0.00 0.00 0.00 4.70
639 1448 2.297701 GTTGCTGTTGAGGAAAGTGGA 58.702 47.619 0.00 0.00 30.29 4.02
640 1449 1.338020 GGTTGCTGTTGAGGAAAGTGG 59.662 52.381 0.00 0.00 30.29 4.00
709 1842 2.552315 CCCAACGTGTGCTTACAAGAAT 59.448 45.455 0.00 0.00 0.00 2.40
736 1896 1.667212 GGACGACGTTTCACCAACTTT 59.333 47.619 0.13 0.00 32.53 2.66
763 1924 0.519961 GGGACGTTTTGCGCAATAGT 59.480 50.000 25.64 22.48 46.11 2.12
1035 3642 3.973267 GAGCGACGAGTGCAGGGTC 62.973 68.421 0.00 0.00 33.85 4.46
1284 3915 3.767230 CCGTTCTCGTGCACTGCG 61.767 66.667 16.19 11.14 35.01 5.18
1368 3999 4.617520 TTGCTCGTCTTGCCGCCA 62.618 61.111 0.00 0.00 0.00 5.69
1785 4419 0.178995 TTGCCTTGATGGTCTGCACA 60.179 50.000 0.00 0.00 38.35 4.57
1836 4477 5.999044 AGAATACAGATCTGGAACAAGCAT 58.001 37.500 26.08 4.88 38.70 3.79
1905 4551 9.421806 CCAAGTATTTCATGTTTATTGCAAAGA 57.578 29.630 1.71 0.00 0.00 2.52
1960 4616 1.917273 TCATAACGCCTTGTCTACGC 58.083 50.000 0.00 0.00 0.00 4.42
1965 4621 8.856490 AATAAATCAAATCATAACGCCTTGTC 57.144 30.769 0.00 0.00 0.00 3.18
2065 4729 9.529325 CATACGGATACTTCTTTTTCAGTGATA 57.471 33.333 0.00 0.00 0.00 2.15
2066 4730 7.011482 GCATACGGATACTTCTTTTTCAGTGAT 59.989 37.037 0.00 0.00 0.00 3.06
2085 4782 5.163723 ACAGATTTTCACATCAAGCATACGG 60.164 40.000 0.00 0.00 0.00 4.02
2086 4783 5.872635 ACAGATTTTCACATCAAGCATACG 58.127 37.500 0.00 0.00 0.00 3.06
2117 4814 9.950680 ACACAAAGTTTTTCTTACATCAGTATG 57.049 29.630 0.00 0.00 35.84 2.39
2243 8416 7.330700 GCGAAAAAGGAATGAAAATGGATTGTA 59.669 33.333 0.00 0.00 0.00 2.41
2267 8440 8.614994 AAAGAATGAAAATAGATTTTACCGCG 57.385 30.769 0.00 0.00 39.86 6.46
2311 8484 3.999663 CCGCAGAAAAAGAGAGAGTGAAT 59.000 43.478 0.00 0.00 0.00 2.57
2316 8489 1.276421 TCCCCGCAGAAAAAGAGAGAG 59.724 52.381 0.00 0.00 0.00 3.20
2328 8501 2.862541 TGATAATGGATTTCCCCGCAG 58.137 47.619 0.00 0.00 34.29 5.18
2414 8614 9.530633 ACGAGATTAGTTATATGGAACTTGAAC 57.469 33.333 0.00 0.00 40.22 3.18
2445 9345 4.974275 GCTGCATGAATTAGCAACAGTATG 59.026 41.667 0.00 0.00 40.73 2.39
2449 9351 3.497297 TGCTGCATGAATTAGCAACAG 57.503 42.857 0.00 0.61 43.77 3.16
2453 9355 4.524316 AACTTTGCTGCATGAATTAGCA 57.476 36.364 1.84 3.49 44.92 3.49
2454 9356 6.267817 TGATAACTTTGCTGCATGAATTAGC 58.732 36.000 1.84 4.21 37.93 3.09
2579 9514 0.678950 TCATGTTGGCTCAGTCGACA 59.321 50.000 19.50 0.57 0.00 4.35
2580 9515 1.662629 CATCATGTTGGCTCAGTCGAC 59.337 52.381 7.70 7.70 0.00 4.20
2583 9518 2.408271 TCCATCATGTTGGCTCAGTC 57.592 50.000 16.72 0.00 36.66 3.51
2620 10319 2.285756 CGACCAGCGTTTGTTTACTTGA 59.714 45.455 0.00 0.00 34.64 3.02
2621 10320 2.285756 TCGACCAGCGTTTGTTTACTTG 59.714 45.455 0.00 0.00 41.80 3.16
2622 10321 2.553086 TCGACCAGCGTTTGTTTACTT 58.447 42.857 0.00 0.00 41.80 2.24
2623 10322 2.228138 TCGACCAGCGTTTGTTTACT 57.772 45.000 0.00 0.00 41.80 2.24
2624 10323 3.476181 GAATCGACCAGCGTTTGTTTAC 58.524 45.455 0.00 0.00 41.80 2.01
2625 10324 2.481185 GGAATCGACCAGCGTTTGTTTA 59.519 45.455 0.00 0.00 41.80 2.01
2626 10325 1.265905 GGAATCGACCAGCGTTTGTTT 59.734 47.619 0.00 0.00 41.80 2.83
2627 10326 0.872388 GGAATCGACCAGCGTTTGTT 59.128 50.000 0.00 0.00 41.80 2.83
2628 10327 0.250124 TGGAATCGACCAGCGTTTGT 60.250 50.000 0.00 0.00 41.80 2.83
2629 10328 0.165944 GTGGAATCGACCAGCGTTTG 59.834 55.000 0.00 0.00 40.85 2.93
2630 10329 1.289109 CGTGGAATCGACCAGCGTTT 61.289 55.000 0.00 0.00 40.85 3.60
2631 10330 1.736645 CGTGGAATCGACCAGCGTT 60.737 57.895 0.00 0.00 40.85 4.84
2632 10331 2.126071 CGTGGAATCGACCAGCGT 60.126 61.111 0.00 0.00 40.85 5.07
2633 10332 1.874019 CTCGTGGAATCGACCAGCG 60.874 63.158 0.00 3.44 40.85 5.18
2634 10333 0.802607 GACTCGTGGAATCGACCAGC 60.803 60.000 0.00 0.00 40.85 4.85
2635 10334 0.523546 CGACTCGTGGAATCGACCAG 60.524 60.000 0.00 0.00 40.85 4.00
2636 10335 1.239296 ACGACTCGTGGAATCGACCA 61.239 55.000 2.53 0.00 39.18 4.02
2637 10336 0.109412 AACGACTCGTGGAATCGACC 60.109 55.000 4.50 0.00 39.99 4.79
2638 10337 1.694639 AAACGACTCGTGGAATCGAC 58.305 50.000 4.50 0.00 39.99 4.20
2639 10338 2.030540 AGAAAACGACTCGTGGAATCGA 60.031 45.455 4.50 0.00 39.99 3.59
2640 10339 2.325761 AGAAAACGACTCGTGGAATCG 58.674 47.619 4.50 0.00 39.99 3.34
2641 10340 4.448060 AGAAAGAAAACGACTCGTGGAATC 59.552 41.667 4.50 1.95 39.99 2.52
2642 10341 4.377897 AGAAAGAAAACGACTCGTGGAAT 58.622 39.130 4.50 0.00 39.99 3.01
2643 10342 3.788937 AGAAAGAAAACGACTCGTGGAA 58.211 40.909 4.50 0.00 39.99 3.53
2644 10343 3.447918 AGAAAGAAAACGACTCGTGGA 57.552 42.857 4.50 0.00 39.99 4.02
2645 10344 3.059800 GGAAGAAAGAAAACGACTCGTGG 60.060 47.826 4.50 0.00 39.99 4.94
2646 10345 3.059800 GGGAAGAAAGAAAACGACTCGTG 60.060 47.826 4.50 0.00 39.99 4.35
2647 10346 3.129109 GGGAAGAAAGAAAACGACTCGT 58.871 45.455 0.00 0.00 43.97 4.18
2648 10347 3.128349 TGGGAAGAAAGAAAACGACTCG 58.872 45.455 0.00 0.00 0.00 4.18
2649 10348 4.083271 CCATGGGAAGAAAGAAAACGACTC 60.083 45.833 2.85 0.00 0.00 3.36
2650 10349 3.821033 CCATGGGAAGAAAGAAAACGACT 59.179 43.478 2.85 0.00 0.00 4.18
2651 10350 3.818773 TCCATGGGAAGAAAGAAAACGAC 59.181 43.478 13.02 0.00 0.00 4.34
2652 10351 4.093472 TCCATGGGAAGAAAGAAAACGA 57.907 40.909 13.02 0.00 0.00 3.85
2653 10352 4.846779 TTCCATGGGAAGAAAGAAAACG 57.153 40.909 13.02 0.00 36.71 3.60
2664 10363 1.357761 GTCCCCTTTCTTCCATGGGAA 59.642 52.381 13.02 5.56 46.47 3.97
2665 10364 0.999712 GTCCCCTTTCTTCCATGGGA 59.000 55.000 13.02 0.69 42.95 4.37
2666 10365 0.033109 GGTCCCCTTTCTTCCATGGG 60.033 60.000 13.02 0.00 39.37 4.00
2667 10366 0.033109 GGGTCCCCTTTCTTCCATGG 60.033 60.000 4.97 4.97 0.00 3.66
2668 10367 1.002857 AGGGTCCCCTTTCTTCCATG 58.997 55.000 3.51 0.00 45.70 3.66
2669 10368 3.540354 AGGGTCCCCTTTCTTCCAT 57.460 52.632 3.51 0.00 45.70 3.41
2685 10384 1.477295 GACGAGGTCCCTAGTCAAAGG 59.523 57.143 18.29 0.00 44.43 3.11
2686 10385 2.424246 GAGACGAGGTCCCTAGTCAAAG 59.576 54.545 23.11 0.00 46.41 2.77
2687 10386 2.224942 TGAGACGAGGTCCCTAGTCAAA 60.225 50.000 23.11 11.50 46.41 2.69
2688 10387 1.353358 TGAGACGAGGTCCCTAGTCAA 59.647 52.381 23.11 11.78 46.41 3.18
2689 10388 0.989602 TGAGACGAGGTCCCTAGTCA 59.010 55.000 23.11 6.62 46.41 3.41
2690 10389 1.950909 CATGAGACGAGGTCCCTAGTC 59.049 57.143 16.20 16.20 45.05 2.59
2691 10390 1.285373 ACATGAGACGAGGTCCCTAGT 59.715 52.381 0.00 0.00 34.69 2.57
2692 10391 1.678627 CACATGAGACGAGGTCCCTAG 59.321 57.143 0.00 0.00 32.18 3.02
2693 10392 1.685180 CCACATGAGACGAGGTCCCTA 60.685 57.143 0.00 0.00 32.18 3.53
2694 10393 0.972983 CCACATGAGACGAGGTCCCT 60.973 60.000 0.00 0.00 32.18 4.20
2695 10394 1.258445 ACCACATGAGACGAGGTCCC 61.258 60.000 0.00 0.00 32.18 4.46
2696 10395 0.608640 AACCACATGAGACGAGGTCC 59.391 55.000 0.00 0.00 32.18 4.46
2697 10396 2.457366 AAACCACATGAGACGAGGTC 57.543 50.000 0.00 0.00 0.00 3.85
2698 10397 2.930826 AAAACCACATGAGACGAGGT 57.069 45.000 0.00 0.00 0.00 3.85
2699 10398 3.262420 CCTAAAACCACATGAGACGAGG 58.738 50.000 0.00 0.00 0.00 4.63
2700 10399 3.262420 CCCTAAAACCACATGAGACGAG 58.738 50.000 0.00 0.00 0.00 4.18
2701 10400 2.614481 GCCCTAAAACCACATGAGACGA 60.614 50.000 0.00 0.00 0.00 4.20
2702 10401 1.737793 GCCCTAAAACCACATGAGACG 59.262 52.381 0.00 0.00 0.00 4.18
2703 10402 2.092323 GGCCCTAAAACCACATGAGAC 58.908 52.381 0.00 0.00 0.00 3.36
2704 10403 1.707989 TGGCCCTAAAACCACATGAGA 59.292 47.619 0.00 0.00 0.00 3.27
2705 10404 2.214376 TGGCCCTAAAACCACATGAG 57.786 50.000 0.00 0.00 0.00 2.90
2706 10405 2.455557 CATGGCCCTAAAACCACATGA 58.544 47.619 0.00 0.00 39.19 3.07
2707 10406 1.481772 CCATGGCCCTAAAACCACATG 59.518 52.381 0.00 0.00 39.19 3.21
2708 10407 1.360852 TCCATGGCCCTAAAACCACAT 59.639 47.619 6.96 0.00 39.19 3.21
2709 10408 0.780637 TCCATGGCCCTAAAACCACA 59.219 50.000 6.96 0.00 39.19 4.17
2710 10409 1.931635 TTCCATGGCCCTAAAACCAC 58.068 50.000 6.96 0.00 39.19 4.16
2711 10410 2.252714 GTTTCCATGGCCCTAAAACCA 58.747 47.619 6.96 0.00 41.06 3.67
2712 10411 1.203758 CGTTTCCATGGCCCTAAAACC 59.796 52.381 16.31 4.04 0.00 3.27
2713 10412 1.890489 ACGTTTCCATGGCCCTAAAAC 59.110 47.619 6.96 11.14 0.00 2.43
2714 10413 1.889829 CACGTTTCCATGGCCCTAAAA 59.110 47.619 6.96 0.00 0.00 1.52
2715 10414 1.074084 TCACGTTTCCATGGCCCTAAA 59.926 47.619 6.96 0.00 0.00 1.85
2716 10415 0.693622 TCACGTTTCCATGGCCCTAA 59.306 50.000 6.96 0.00 0.00 2.69
2717 10416 0.916086 ATCACGTTTCCATGGCCCTA 59.084 50.000 6.96 0.00 0.00 3.53
2718 10417 0.916086 TATCACGTTTCCATGGCCCT 59.084 50.000 6.96 0.00 0.00 5.19
2719 10418 1.134220 TCTATCACGTTTCCATGGCCC 60.134 52.381 6.96 0.00 0.00 5.80
2720 10419 2.325583 TCTATCACGTTTCCATGGCC 57.674 50.000 6.96 0.00 0.00 5.36
2721 10420 3.206150 ACATCTATCACGTTTCCATGGC 58.794 45.455 6.96 0.00 0.00 4.40
2722 10421 4.509230 CAGACATCTATCACGTTTCCATGG 59.491 45.833 4.97 4.97 0.00 3.66
2723 10422 4.025396 GCAGACATCTATCACGTTTCCATG 60.025 45.833 0.00 0.00 0.00 3.66
2724 10423 4.122776 GCAGACATCTATCACGTTTCCAT 58.877 43.478 0.00 0.00 0.00 3.41
2725 10424 3.521560 GCAGACATCTATCACGTTTCCA 58.478 45.455 0.00 0.00 0.00 3.53
2726 10425 2.866762 GGCAGACATCTATCACGTTTCC 59.133 50.000 0.00 0.00 0.00 3.13
2727 10426 2.866762 GGGCAGACATCTATCACGTTTC 59.133 50.000 0.00 0.00 0.00 2.78
2728 10427 2.501723 AGGGCAGACATCTATCACGTTT 59.498 45.455 0.00 0.00 0.00 3.60
2729 10428 2.111384 AGGGCAGACATCTATCACGTT 58.889 47.619 0.00 0.00 0.00 3.99
2730 10429 1.781786 AGGGCAGACATCTATCACGT 58.218 50.000 0.00 0.00 0.00 4.49
2731 10430 2.898729 AAGGGCAGACATCTATCACG 57.101 50.000 0.00 0.00 0.00 4.35
2732 10431 3.553096 CGGTAAGGGCAGACATCTATCAC 60.553 52.174 0.00 0.00 0.00 3.06
2733 10432 2.628178 CGGTAAGGGCAGACATCTATCA 59.372 50.000 0.00 0.00 0.00 2.15
2734 10433 2.628657 ACGGTAAGGGCAGACATCTATC 59.371 50.000 0.00 0.00 0.00 2.08
2735 10434 2.628657 GACGGTAAGGGCAGACATCTAT 59.371 50.000 0.00 0.00 0.00 1.98
2736 10435 2.029623 GACGGTAAGGGCAGACATCTA 58.970 52.381 0.00 0.00 0.00 1.98
2737 10436 0.824759 GACGGTAAGGGCAGACATCT 59.175 55.000 0.00 0.00 0.00 2.90
2738 10437 0.527817 CGACGGTAAGGGCAGACATC 60.528 60.000 0.00 0.00 0.00 3.06
2739 10438 1.515954 CGACGGTAAGGGCAGACAT 59.484 57.895 0.00 0.00 0.00 3.06
2740 10439 2.642254 CCGACGGTAAGGGCAGACA 61.642 63.158 5.48 0.00 0.00 3.41
2741 10440 2.183555 CCGACGGTAAGGGCAGAC 59.816 66.667 5.48 0.00 0.00 3.51
2742 10441 3.072468 CCCGACGGTAAGGGCAGA 61.072 66.667 13.94 0.00 41.34 4.26
2747 10446 3.846430 GCCCTCCCGACGGTAAGG 61.846 72.222 20.51 20.51 0.00 2.69
2748 10447 2.294132 GAAGCCCTCCCGACGGTAAG 62.294 65.000 13.94 9.72 0.00 2.34
2749 10448 2.284112 AAGCCCTCCCGACGGTAA 60.284 61.111 13.94 0.00 0.00 2.85
2750 10449 2.757099 GAAGCCCTCCCGACGGTA 60.757 66.667 13.94 0.00 0.00 4.02
2753 10452 2.012902 ATAACGAAGCCCTCCCGACG 62.013 60.000 0.00 0.00 0.00 5.12
2754 10453 0.177373 AATAACGAAGCCCTCCCGAC 59.823 55.000 0.00 0.00 0.00 4.79
2755 10454 0.906775 AAATAACGAAGCCCTCCCGA 59.093 50.000 0.00 0.00 0.00 5.14
2756 10455 1.296727 GAAATAACGAAGCCCTCCCG 58.703 55.000 0.00 0.00 0.00 5.14
2757 10456 2.413310 TGAAATAACGAAGCCCTCCC 57.587 50.000 0.00 0.00 0.00 4.30
2758 10457 6.635030 AAATATGAAATAACGAAGCCCTCC 57.365 37.500 0.00 0.00 29.06 4.30
2781 10480 6.166982 CACAAACCCTAACCAAACTCAAAAA 58.833 36.000 0.00 0.00 0.00 1.94
2782 10481 5.246429 ACACAAACCCTAACCAAACTCAAAA 59.754 36.000 0.00 0.00 0.00 2.44
2783 10482 4.773149 ACACAAACCCTAACCAAACTCAAA 59.227 37.500 0.00 0.00 0.00 2.69
2784 10483 4.345854 ACACAAACCCTAACCAAACTCAA 58.654 39.130 0.00 0.00 0.00 3.02
2785 10484 3.949113 GACACAAACCCTAACCAAACTCA 59.051 43.478 0.00 0.00 0.00 3.41
2786 10485 3.317149 GGACACAAACCCTAACCAAACTC 59.683 47.826 0.00 0.00 0.00 3.01
2787 10486 3.053170 AGGACACAAACCCTAACCAAACT 60.053 43.478 0.00 0.00 0.00 2.66
2788 10487 3.067601 CAGGACACAAACCCTAACCAAAC 59.932 47.826 0.00 0.00 0.00 2.93
2789 10488 3.292460 CAGGACACAAACCCTAACCAAA 58.708 45.455 0.00 0.00 0.00 3.28
2790 10489 2.242708 ACAGGACACAAACCCTAACCAA 59.757 45.455 0.00 0.00 0.00 3.67
2791 10490 1.847737 ACAGGACACAAACCCTAACCA 59.152 47.619 0.00 0.00 0.00 3.67
2792 10491 2.651382 ACAGGACACAAACCCTAACC 57.349 50.000 0.00 0.00 0.00 2.85
2793 10492 3.547746 TGAACAGGACACAAACCCTAAC 58.452 45.455 0.00 0.00 0.00 2.34
2794 10493 3.456644 TCTGAACAGGACACAAACCCTAA 59.543 43.478 1.93 0.00 0.00 2.69
2795 10494 3.042682 TCTGAACAGGACACAAACCCTA 58.957 45.455 1.93 0.00 0.00 3.53
2796 10495 1.843851 TCTGAACAGGACACAAACCCT 59.156 47.619 1.93 0.00 0.00 4.34
2797 10496 2.158813 TCTCTGAACAGGACACAAACCC 60.159 50.000 1.93 0.00 0.00 4.11
2798 10497 3.134458 CTCTCTGAACAGGACACAAACC 58.866 50.000 1.93 0.00 0.00 3.27
2799 10498 3.804873 GTCTCTCTGAACAGGACACAAAC 59.195 47.826 1.93 0.00 0.00 2.93
2800 10499 3.490933 CGTCTCTCTGAACAGGACACAAA 60.491 47.826 1.93 0.00 0.00 2.83
2801 10500 2.034685 CGTCTCTCTGAACAGGACACAA 59.965 50.000 1.93 0.00 0.00 3.33
2802 10501 1.609072 CGTCTCTCTGAACAGGACACA 59.391 52.381 1.93 0.00 0.00 3.72
2803 10502 1.880675 TCGTCTCTCTGAACAGGACAC 59.119 52.381 1.93 0.00 0.00 3.67
2804 10503 2.155279 CTCGTCTCTCTGAACAGGACA 58.845 52.381 1.93 0.00 0.00 4.02
2805 10504 1.470890 CCTCGTCTCTCTGAACAGGAC 59.529 57.143 1.93 1.71 30.77 3.85
2806 10505 1.827681 CCTCGTCTCTCTGAACAGGA 58.172 55.000 1.93 0.00 30.77 3.86
2807 10506 0.172352 GCCTCGTCTCTCTGAACAGG 59.828 60.000 1.93 0.00 0.00 4.00
2808 10507 0.179176 CGCCTCGTCTCTCTGAACAG 60.179 60.000 0.00 0.00 0.00 3.16
2809 10508 1.587043 CCGCCTCGTCTCTCTGAACA 61.587 60.000 0.00 0.00 0.00 3.18
2810 10509 1.137825 CCGCCTCGTCTCTCTGAAC 59.862 63.158 0.00 0.00 0.00 3.18
2811 10510 2.701780 GCCGCCTCGTCTCTCTGAA 61.702 63.158 0.00 0.00 0.00 3.02
2812 10511 3.134792 GCCGCCTCGTCTCTCTGA 61.135 66.667 0.00 0.00 0.00 3.27
2813 10512 4.544689 CGCCGCCTCGTCTCTCTG 62.545 72.222 0.00 0.00 0.00 3.35
2814 10513 4.779966 TCGCCGCCTCGTCTCTCT 62.780 66.667 0.00 0.00 0.00 3.10
2815 10514 3.587933 ATCGCCGCCTCGTCTCTC 61.588 66.667 0.00 0.00 0.00 3.20
2816 10515 3.893763 CATCGCCGCCTCGTCTCT 61.894 66.667 0.00 0.00 0.00 3.10
2817 10516 4.933064 CCATCGCCGCCTCGTCTC 62.933 72.222 0.00 0.00 0.00 3.36
2822 10521 2.644555 TAAAGAGCCATCGCCGCCTC 62.645 60.000 0.00 0.00 34.57 4.70
2823 10522 2.252072 TTAAAGAGCCATCGCCGCCT 62.252 55.000 0.00 0.00 34.57 5.52
2824 10523 1.373590 TTTAAAGAGCCATCGCCGCC 61.374 55.000 0.00 0.00 34.57 6.13
2825 10524 0.028110 CTTTAAAGAGCCATCGCCGC 59.972 55.000 9.77 0.00 34.57 6.53
2826 10525 1.651987 TCTTTAAAGAGCCATCGCCG 58.348 50.000 13.99 0.00 34.57 6.46
2827 10526 2.291741 CCATCTTTAAAGAGCCATCGCC 59.708 50.000 21.75 0.00 38.66 5.54
2828 10527 3.206150 TCCATCTTTAAAGAGCCATCGC 58.794 45.455 21.75 0.00 38.66 4.58
2829 10528 7.308229 CCTTATTCCATCTTTAAAGAGCCATCG 60.308 40.741 21.75 7.15 38.66 3.84
2830 10529 7.503902 ACCTTATTCCATCTTTAAAGAGCCATC 59.496 37.037 21.75 0.00 38.66 3.51
2831 10530 7.357471 ACCTTATTCCATCTTTAAAGAGCCAT 58.643 34.615 21.75 13.35 38.66 4.40
2832 10531 6.731467 ACCTTATTCCATCTTTAAAGAGCCA 58.269 36.000 21.75 7.64 38.66 4.75
2833 10532 7.558081 AGAACCTTATTCCATCTTTAAAGAGCC 59.442 37.037 21.75 3.17 38.66 4.70
2834 10533 8.512966 AGAACCTTATTCCATCTTTAAAGAGC 57.487 34.615 21.75 0.78 38.66 4.09
2835 10534 9.114952 GGAGAACCTTATTCCATCTTTAAAGAG 57.885 37.037 21.75 13.77 38.66 2.85
2836 10535 8.053355 GGGAGAACCTTATTCCATCTTTAAAGA 58.947 37.037 19.83 19.83 36.37 2.52
2837 10536 8.226819 GGGAGAACCTTATTCCATCTTTAAAG 57.773 38.462 9.04 9.04 35.85 1.85
2854 10553 1.290130 TGGGACTAGGTAGGGAGAACC 59.710 57.143 0.00 0.00 40.67 3.62
2855 10554 2.024177 ACTGGGACTAGGTAGGGAGAAC 60.024 54.545 0.00 0.00 0.00 3.01
2856 10555 2.244252 GACTGGGACTAGGTAGGGAGAA 59.756 54.545 0.00 0.00 0.00 2.87
2857 10556 1.851653 GACTGGGACTAGGTAGGGAGA 59.148 57.143 0.00 0.00 0.00 3.71
2858 10557 1.133419 GGACTGGGACTAGGTAGGGAG 60.133 61.905 0.00 0.00 0.00 4.30
2859 10558 0.932211 GGACTGGGACTAGGTAGGGA 59.068 60.000 0.00 0.00 0.00 4.20
2860 10559 0.105607 GGGACTGGGACTAGGTAGGG 60.106 65.000 0.00 0.00 0.00 3.53
2861 10560 0.467659 CGGGACTGGGACTAGGTAGG 60.468 65.000 0.00 0.00 0.00 3.18
2862 10561 0.549950 TCGGGACTGGGACTAGGTAG 59.450 60.000 0.00 0.00 0.00 3.18
2863 10562 1.133575 CATCGGGACTGGGACTAGGTA 60.134 57.143 0.00 0.00 0.00 3.08
2864 10563 0.397254 CATCGGGACTGGGACTAGGT 60.397 60.000 0.00 0.00 0.00 3.08
2865 10564 0.106167 TCATCGGGACTGGGACTAGG 60.106 60.000 0.00 0.00 0.00 3.02
2866 10565 1.615883 CATCATCGGGACTGGGACTAG 59.384 57.143 0.00 0.00 0.00 2.57
2867 10566 1.063190 ACATCATCGGGACTGGGACTA 60.063 52.381 0.00 0.00 0.00 2.59
2868 10567 0.325671 ACATCATCGGGACTGGGACT 60.326 55.000 0.00 0.00 0.00 3.85
2869 10568 0.541863 AACATCATCGGGACTGGGAC 59.458 55.000 0.00 0.00 0.00 4.46
2870 10569 1.209504 GAAACATCATCGGGACTGGGA 59.790 52.381 0.00 0.00 0.00 4.37
2871 10570 1.210478 AGAAACATCATCGGGACTGGG 59.790 52.381 0.00 0.00 0.00 4.45
2872 10571 2.698855 AGAAACATCATCGGGACTGG 57.301 50.000 0.00 0.00 0.00 4.00
2873 10572 3.126831 GCTAGAAACATCATCGGGACTG 58.873 50.000 0.00 0.00 0.00 3.51
2874 10573 2.766263 TGCTAGAAACATCATCGGGACT 59.234 45.455 0.00 0.00 0.00 3.85
2875 10574 3.179443 TGCTAGAAACATCATCGGGAC 57.821 47.619 0.00 0.00 0.00 4.46
2876 10575 3.995199 GATGCTAGAAACATCATCGGGA 58.005 45.455 0.00 0.00 42.83 5.14
2880 10579 3.426859 CCGACGATGCTAGAAACATCATC 59.573 47.826 0.00 0.00 43.36 2.92
2881 10580 3.068165 TCCGACGATGCTAGAAACATCAT 59.932 43.478 0.00 0.00 43.36 2.45
2882 10581 2.425668 TCCGACGATGCTAGAAACATCA 59.574 45.455 0.00 0.00 43.36 3.07
2883 10582 3.046390 CTCCGACGATGCTAGAAACATC 58.954 50.000 0.00 0.00 40.45 3.06
2884 10583 2.223829 CCTCCGACGATGCTAGAAACAT 60.224 50.000 0.00 0.00 0.00 2.71
2885 10584 1.134367 CCTCCGACGATGCTAGAAACA 59.866 52.381 0.00 0.00 0.00 2.83
2886 10585 1.536284 CCCTCCGACGATGCTAGAAAC 60.536 57.143 0.00 0.00 0.00 2.78
2887 10586 0.744874 CCCTCCGACGATGCTAGAAA 59.255 55.000 0.00 0.00 0.00 2.52
2888 10587 1.735376 GCCCTCCGACGATGCTAGAA 61.735 60.000 0.00 0.00 0.00 2.10
2889 10588 2.194212 GCCCTCCGACGATGCTAGA 61.194 63.158 0.00 0.00 0.00 2.43
2890 10589 2.336809 GCCCTCCGACGATGCTAG 59.663 66.667 0.00 0.00 0.00 3.42
2891 10590 3.592814 CGCCCTCCGACGATGCTA 61.593 66.667 0.00 0.00 40.02 3.49
2894 10593 4.129737 ACACGCCCTCCGACGATG 62.130 66.667 0.00 0.00 41.02 3.84
2895 10594 4.129737 CACACGCCCTCCGACGAT 62.130 66.667 0.00 0.00 41.02 3.73


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

AutoCloner maintained by Alex Coulton.