Multiple sequence alignment - TraesCS6D01G097800

Loading Multiple Alignment...

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 TraesCS6D01G097800 chr6D 100.000 2505 0 0 1 2505 61410887 61413391 0.000000e+00 4626.0
1 TraesCS6D01G097800 chr6D 86.082 776 100 8 1586 2356 466998385 466997613 0.000000e+00 828.0
2 TraesCS6D01G097800 chr6D 82.817 774 119 14 1586 2350 122970831 122971599 0.000000e+00 680.0
3 TraesCS6D01G097800 chr6D 81.712 514 65 17 280 787 61191412 61191902 3.880000e-108 401.0
4 TraesCS6D01G097800 chr6D 87.603 242 27 3 1 242 61174023 61174261 6.820000e-71 278.0
5 TraesCS6D01G097800 chr6B 94.561 717 29 6 798 1509 135359920 135360631 0.000000e+00 1099.0
6 TraesCS6D01G097800 chr6B 89.757 371 31 4 1 370 135357071 135357435 3.770000e-128 468.0
7 TraesCS6D01G097800 chr6B 86.850 327 32 10 800 1120 135139147 135139468 3.060000e-94 355.0
8 TraesCS6D01G097800 chr6B 82.110 218 18 9 600 811 135139030 135139232 1.540000e-37 167.0
9 TraesCS6D01G097800 chr6B 96.000 75 3 0 2353 2427 124990680 124990606 3.380000e-24 122.0
10 TraesCS6D01G097800 chr2D 89.844 768 72 5 1586 2351 639214139 639213376 0.000000e+00 981.0
11 TraesCS6D01G097800 chr2D 82.772 772 120 12 1589 2353 131074454 131073689 0.000000e+00 676.0
12 TraesCS6D01G097800 chr6A 88.767 819 45 20 733 1509 78567106 78567919 0.000000e+00 959.0
13 TraesCS6D01G097800 chr6A 84.970 825 76 22 1 811 78566468 78567258 0.000000e+00 793.0
14 TraesCS6D01G097800 chr6A 87.007 431 42 10 800 1225 77962911 77963332 8.110000e-130 473.0
15 TraesCS6D01G097800 chr6A 87.500 416 42 6 800 1212 78002377 78002785 2.920000e-129 472.0
16 TraesCS6D01G097800 chr6A 86.811 417 44 7 800 1213 78127446 78127854 2.940000e-124 455.0
17 TraesCS6D01G097800 chr6A 85.817 416 47 8 800 1212 77912353 77912759 4.950000e-117 431.0
18 TraesCS6D01G097800 chr6A 87.356 348 32 8 800 1142 78155121 78155461 3.020000e-104 388.0
19 TraesCS6D01G097800 chr6A 86.802 197 14 4 599 794 78002256 78002441 2.520000e-50 209.0
20 TraesCS6D01G097800 chr6A 86.070 201 14 6 596 794 78154997 78155185 1.170000e-48 204.0
21 TraesCS6D01G097800 chr6A 85.075 201 17 5 596 794 77962786 77962975 2.540000e-45 193.0
22 TraesCS6D01G097800 chr6A 84.653 202 17 5 596 794 78127320 78127510 3.290000e-44 189.0
23 TraesCS6D01G097800 chr6A 84.080 201 19 5 596 794 77912228 77912417 5.500000e-42 182.0
24 TraesCS6D01G097800 chr6A 83.085 201 21 5 596 794 78064614 78064803 1.190000e-38 171.0
25 TraesCS6D01G097800 chr6A 90.000 110 10 1 169 278 77941875 77941983 9.340000e-30 141.0
26 TraesCS6D01G097800 chr6A 89.091 110 11 1 169 278 78097800 78097908 4.350000e-28 135.0
27 TraesCS6D01G097800 chr6A 88.182 110 12 1 169 278 77901783 77901891 2.020000e-26 130.0
28 TraesCS6D01G097800 chr6A 87.273 110 13 1 169 278 77996886 77996994 9.410000e-25 124.0
29 TraesCS6D01G097800 chr6A 86.250 80 10 1 199 278 78036073 78036151 4.440000e-13 86.1
30 TraesCS6D01G097800 chr3D 87.871 775 88 6 1586 2356 18699532 18698760 0.000000e+00 905.0
31 TraesCS6D01G097800 chr5D 87.653 737 83 8 1620 2353 513395728 513396459 0.000000e+00 850.0
32 TraesCS6D01G097800 chr2A 85.947 797 104 8 1563 2356 768190927 768190136 0.000000e+00 845.0
33 TraesCS6D01G097800 chr2A 96.429 84 3 0 1502 1585 566449521 566449604 3.360000e-29 139.0
34 TraesCS6D01G097800 chr2A 97.436 78 2 0 1508 1585 566441297 566441374 1.560000e-27 134.0
35 TraesCS6D01G097800 chrUn 88.640 669 71 5 1692 2356 101079093 101078426 0.000000e+00 809.0
36 TraesCS6D01G097800 chrUn 91.241 137 10 2 2345 2480 101093532 101093397 4.250000e-43 185.0
37 TraesCS6D01G097800 chr4B 81.019 785 123 25 1586 2356 625959368 625958596 3.570000e-168 601.0
38 TraesCS6D01G097800 chr4B 94.872 78 4 0 1508 1585 571339323 571339246 3.380000e-24 122.0
39 TraesCS6D01G097800 chr1B 85.714 147 20 1 2353 2498 401554004 401554150 1.200000e-33 154.0
40 TraesCS6D01G097800 chr1B 95.000 80 4 0 1506 1585 642936079 642936000 2.620000e-25 126.0
41 TraesCS6D01G097800 chr1B 92.941 85 6 0 1501 1585 642931175 642931091 9.410000e-25 124.0
42 TraesCS6D01G097800 chr7A 94.872 78 4 0 1508 1585 726494816 726494893 3.380000e-24 122.0
43 TraesCS6D01G097800 chr5A 94.872 78 4 0 1508 1585 6157784 6157861 3.380000e-24 122.0
44 TraesCS6D01G097800 chr5A 92.857 84 6 0 1502 1585 6162683 6162766 3.380000e-24 122.0
45 TraesCS6D01G097800 chr3B 94.872 78 4 0 1508 1585 682169379 682169302 3.380000e-24 122.0
46 TraesCS6D01G097800 chr3B 91.304 46 4 0 1138 1183 651268787 651268832 2.080000e-06 63.9
47 TraesCS6D01G097800 chr1A 82.500 80 12 2 1138 1215 547391232 547391153 4.470000e-08 69.4
48 TraesCS6D01G097800 chr7B 84.127 63 9 1 1138 1199 522815518 522815456 2.690000e-05 60.2


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 TraesCS6D01G097800 chr6D 61410887 61413391 2504 False 4626.0 4626 100.0000 1 2505 1 chr6D.!!$F3 2504
1 TraesCS6D01G097800 chr6D 466997613 466998385 772 True 828.0 828 86.0820 1586 2356 1 chr6D.!!$R1 770
2 TraesCS6D01G097800 chr6D 122970831 122971599 768 False 680.0 680 82.8170 1586 2350 1 chr6D.!!$F4 764
3 TraesCS6D01G097800 chr6B 135357071 135360631 3560 False 783.5 1099 92.1590 1 1509 2 chr6B.!!$F2 1508
4 TraesCS6D01G097800 chr2D 639213376 639214139 763 True 981.0 981 89.8440 1586 2351 1 chr2D.!!$R2 765
5 TraesCS6D01G097800 chr2D 131073689 131074454 765 True 676.0 676 82.7720 1589 2353 1 chr2D.!!$R1 764
6 TraesCS6D01G097800 chr6A 78566468 78567919 1451 False 876.0 959 86.8685 1 1509 2 chr6A.!!$F12 1508
7 TraesCS6D01G097800 chr6A 78002256 78002785 529 False 340.5 472 87.1510 599 1212 2 chr6A.!!$F9 613
8 TraesCS6D01G097800 chr6A 77962786 77963332 546 False 333.0 473 86.0410 596 1225 2 chr6A.!!$F8 629
9 TraesCS6D01G097800 chr6A 78127320 78127854 534 False 322.0 455 85.7320 596 1213 2 chr6A.!!$F10 617
10 TraesCS6D01G097800 chr6A 77912228 77912759 531 False 306.5 431 84.9485 596 1212 2 chr6A.!!$F7 616
11 TraesCS6D01G097800 chr3D 18698760 18699532 772 True 905.0 905 87.8710 1586 2356 1 chr3D.!!$R1 770
12 TraesCS6D01G097800 chr5D 513395728 513396459 731 False 850.0 850 87.6530 1620 2353 1 chr5D.!!$F1 733
13 TraesCS6D01G097800 chr2A 768190136 768190927 791 True 845.0 845 85.9470 1563 2356 1 chr2A.!!$R1 793
14 TraesCS6D01G097800 chrUn 101078426 101079093 667 True 809.0 809 88.6400 1692 2356 1 chrUn.!!$R1 664
15 TraesCS6D01G097800 chr4B 625958596 625959368 772 True 601.0 601 81.0190 1586 2356 1 chr4B.!!$R2 770

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
181 183 0.391597 GAACACTGTCAGTTCCCCGA 59.608 55.0 1.67 0.0 39.48 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1755 3960 0.105593 GCTCAATGATCTGGCCTCGA 59.894 55.0 3.32 0.03 0.0 4.04 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
26 27 3.379445 CTGGTAGTCCGCACCCGT 61.379 66.667 0.00 0.00 34.99 5.28
50 51 2.301870 TGTGATCCTCTTGTAAAGGCGT 59.698 45.455 0.00 0.00 46.24 5.68
56 57 2.670251 TTGTAAAGGCGTGGGGCG 60.670 61.111 0.00 0.00 44.92 6.13
66 67 2.440247 GTGGGGCGAATTCCTGGG 60.440 66.667 0.00 0.00 0.00 4.45
69 70 2.680370 GGGGCGAATTCCTGGGTCT 61.680 63.158 0.00 0.00 0.00 3.85
77 78 2.717639 ATTCCTGGGTCTGAAATCCG 57.282 50.000 0.00 0.00 0.00 4.18
97 98 2.604174 GCAACCACGTGTCTTCCCG 61.604 63.158 15.65 0.00 0.00 5.14
99 100 0.531090 CAACCACGTGTCTTCCCGAA 60.531 55.000 15.65 0.00 0.00 4.30
111 113 2.165845 TCTTCCCGAAAGAACGAGGATC 59.834 50.000 0.00 0.00 41.10 3.36
131 133 1.341913 TACCATCCCCCACATCCACG 61.342 60.000 0.00 0.00 0.00 4.94
162 164 1.041437 GAGATACTCCCCCAAGGTCG 58.959 60.000 0.00 0.00 36.75 4.79
181 183 0.391597 GAACACTGTCAGTTCCCCGA 59.608 55.000 1.67 0.00 39.48 5.14
208 210 1.681264 AGCTAACACACACCAAAAGCC 59.319 47.619 0.00 0.00 0.00 4.35
233 235 5.640147 TGTTCAACCATCTGAAATTAGGGT 58.360 37.500 0.00 0.00 37.08 4.34
248 250 4.740822 GGTGTCCAAGCCCGCCAT 62.741 66.667 0.00 0.00 0.00 4.40
284 286 6.419413 GCAATTTTTCAACCATCTACGAAACA 59.581 34.615 0.00 0.00 0.00 2.83
323 325 9.466497 AAATCTTCATGATTCTAAACAAGCCTA 57.534 29.630 0.00 0.00 43.99 3.93
342 344 7.961326 AGCCTATAATGGACAAAATTTCTGT 57.039 32.000 5.92 5.92 0.00 3.41
450 2145 7.203218 TCATCGGACTTAGAGATACATTGTTG 58.797 38.462 0.00 0.00 0.00 3.33
459 2154 4.220821 AGAGATACATTGTTGACGGTCACT 59.779 41.667 10.97 0.93 0.00 3.41
460 2155 5.417894 AGAGATACATTGTTGACGGTCACTA 59.582 40.000 10.97 4.09 0.00 2.74
461 2156 5.408356 AGATACATTGTTGACGGTCACTAC 58.592 41.667 10.97 8.15 0.00 2.73
462 2157 3.746045 ACATTGTTGACGGTCACTACT 57.254 42.857 10.97 0.00 0.00 2.57
463 2158 3.650139 ACATTGTTGACGGTCACTACTC 58.350 45.455 10.97 0.58 0.00 2.59
464 2159 3.069016 ACATTGTTGACGGTCACTACTCA 59.931 43.478 10.97 3.11 0.00 3.41
465 2160 2.787601 TGTTGACGGTCACTACTCAC 57.212 50.000 10.97 5.90 0.00 3.51
504 2199 9.665719 ATTGAACAGAACTTGGTATTTTTGTTT 57.334 25.926 0.00 0.00 0.00 2.83
505 2200 8.472683 TGAACAGAACTTGGTATTTTTGTTTG 57.527 30.769 0.00 0.00 0.00 2.93
524 2219 3.855255 TGAAGATGAACTCCACCAACA 57.145 42.857 0.00 0.00 0.00 3.33
547 2245 8.461249 ACAACTATTATATGGTAGACACGACT 57.539 34.615 0.00 0.00 0.00 4.18
548 2246 8.566260 ACAACTATTATATGGTAGACACGACTC 58.434 37.037 0.00 0.00 0.00 3.36
550 2248 4.478843 TTATATGGTAGACACGACTCGC 57.521 45.455 0.00 0.00 0.00 5.03
565 2263 3.665409 CGACTCGCGTTGAACTACTAAAA 59.335 43.478 5.77 0.00 34.64 1.52
576 2274 9.117145 CGTTGAACTACTAAAATAAGTACGTCA 57.883 33.333 0.00 0.00 0.00 4.35
590 2288 1.098869 ACGTCATTTGGTGCAACACA 58.901 45.000 2.40 0.00 39.98 3.72
602 2300 3.564511 GTGCAACACACGAGCAATTAAT 58.435 40.909 0.00 0.00 40.07 1.40
727 2881 8.628882 ATTAATTCTAAAACATTTACCAGCGC 57.371 30.769 0.00 0.00 0.00 5.92
728 2882 5.637006 ATTCTAAAACATTTACCAGCGCA 57.363 34.783 11.47 0.00 0.00 6.09
729 2883 5.637006 TTCTAAAACATTTACCAGCGCAT 57.363 34.783 11.47 0.00 0.00 4.73
730 2884 5.229921 TCTAAAACATTTACCAGCGCATC 57.770 39.130 11.47 0.00 0.00 3.91
731 2885 2.542766 AAACATTTACCAGCGCATCG 57.457 45.000 11.47 0.00 0.00 3.84
732 2886 1.732941 AACATTTACCAGCGCATCGA 58.267 45.000 11.47 0.00 0.00 3.59
733 2887 1.953559 ACATTTACCAGCGCATCGAT 58.046 45.000 11.47 0.00 0.00 3.59
734 2888 3.106242 ACATTTACCAGCGCATCGATA 57.894 42.857 11.47 0.00 0.00 2.92
735 2889 3.462982 ACATTTACCAGCGCATCGATAA 58.537 40.909 11.47 0.00 0.00 1.75
736 2890 3.494626 ACATTTACCAGCGCATCGATAAG 59.505 43.478 11.47 0.00 0.00 1.73
737 2891 2.148916 TTACCAGCGCATCGATAAGG 57.851 50.000 11.47 0.19 0.00 2.69
738 2892 1.324383 TACCAGCGCATCGATAAGGA 58.676 50.000 11.47 0.00 0.00 3.36
739 2893 0.464036 ACCAGCGCATCGATAAGGAA 59.536 50.000 11.47 0.00 0.00 3.36
740 2894 1.134521 ACCAGCGCATCGATAAGGAAA 60.135 47.619 11.47 0.00 0.00 3.13
741 2895 1.528586 CCAGCGCATCGATAAGGAAAG 59.471 52.381 11.47 0.00 0.00 2.62
742 2896 1.528586 CAGCGCATCGATAAGGAAAGG 59.471 52.381 11.47 0.00 0.00 3.11
743 2897 1.412710 AGCGCATCGATAAGGAAAGGA 59.587 47.619 11.47 0.00 0.00 3.36
744 2898 2.037772 AGCGCATCGATAAGGAAAGGAT 59.962 45.455 11.47 0.00 0.00 3.24
745 2899 3.258372 AGCGCATCGATAAGGAAAGGATA 59.742 43.478 11.47 0.00 0.00 2.59
746 2900 3.994392 GCGCATCGATAAGGAAAGGATAA 59.006 43.478 0.30 0.00 0.00 1.75
747 2901 4.451096 GCGCATCGATAAGGAAAGGATAAA 59.549 41.667 0.30 0.00 0.00 1.40
748 2902 5.122396 GCGCATCGATAAGGAAAGGATAAAT 59.878 40.000 0.30 0.00 0.00 1.40
749 2903 6.312918 GCGCATCGATAAGGAAAGGATAAATA 59.687 38.462 0.30 0.00 0.00 1.40
750 2904 7.674240 GCGCATCGATAAGGAAAGGATAAATAC 60.674 40.741 0.30 0.00 0.00 1.89
751 2905 7.462856 CGCATCGATAAGGAAAGGATAAATACG 60.463 40.741 0.00 0.00 0.00 3.06
752 2906 7.331193 GCATCGATAAGGAAAGGATAAATACGT 59.669 37.037 0.00 0.00 0.00 3.57
753 2907 8.648097 CATCGATAAGGAAAGGATAAATACGTG 58.352 37.037 0.00 0.00 0.00 4.49
754 2908 7.944061 TCGATAAGGAAAGGATAAATACGTGA 58.056 34.615 0.00 0.00 0.00 4.35
755 2909 8.415553 TCGATAAGGAAAGGATAAATACGTGAA 58.584 33.333 0.00 0.00 0.00 3.18
756 2910 8.700644 CGATAAGGAAAGGATAAATACGTGAAG 58.299 37.037 0.00 0.00 0.00 3.02
757 2911 9.760077 GATAAGGAAAGGATAAATACGTGAAGA 57.240 33.333 0.00 0.00 0.00 2.87
767 2921 8.827677 GGATAAATACGTGAAGATATAATGGGC 58.172 37.037 0.00 0.00 0.00 5.36
768 2922 9.378551 GATAAATACGTGAAGATATAATGGGCA 57.621 33.333 0.00 0.00 0.00 5.36
769 2923 9.733556 ATAAATACGTGAAGATATAATGGGCAA 57.266 29.630 0.00 0.00 0.00 4.52
770 2924 8.458573 AAATACGTGAAGATATAATGGGCAAA 57.541 30.769 0.00 0.00 0.00 3.68
771 2925 8.458573 AATACGTGAAGATATAATGGGCAAAA 57.541 30.769 0.00 0.00 0.00 2.44
772 2926 6.767524 ACGTGAAGATATAATGGGCAAAAA 57.232 33.333 0.00 0.00 0.00 1.94
773 2927 7.346751 ACGTGAAGATATAATGGGCAAAAAT 57.653 32.000 0.00 0.00 0.00 1.82
774 2928 7.781056 ACGTGAAGATATAATGGGCAAAAATT 58.219 30.769 0.00 0.00 0.00 1.82
775 2929 7.706179 ACGTGAAGATATAATGGGCAAAAATTG 59.294 33.333 0.00 0.00 0.00 2.32
776 2930 7.920151 CGTGAAGATATAATGGGCAAAAATTGA 59.080 33.333 0.00 0.00 0.00 2.57
777 2931 9.768662 GTGAAGATATAATGGGCAAAAATTGAT 57.231 29.630 0.00 0.00 0.00 2.57
796 2950 5.484173 TGATTCTAAAGTATTTGCCAGCG 57.516 39.130 0.00 0.00 39.63 5.18
799 2953 1.396996 CTAAAGTATTTGCCAGCGCGT 59.603 47.619 8.43 0.00 39.63 6.01
817 2971 4.318831 GCGCGTTGATAAGGAAAGGATAAG 60.319 45.833 8.43 0.00 0.00 1.73
940 3123 2.024176 ATAAACACTAGCACGCCCTG 57.976 50.000 0.00 0.00 0.00 4.45
1120 3305 8.522830 ACTCCCTATTTTCACAAATGTAACATG 58.477 33.333 0.00 0.00 34.29 3.21
1121 3306 7.319646 TCCCTATTTTCACAAATGTAACATGC 58.680 34.615 0.00 0.00 34.29 4.06
1188 3379 9.730420 GAGTGAACAAACACAGTAAAATACATT 57.270 29.630 0.00 0.00 42.45 2.71
1279 3470 0.779997 ATTCAGGCAAAGTCCCCAGT 59.220 50.000 0.00 0.00 0.00 4.00
1294 3485 3.829601 TCCCCAGTTGATTTATTTTGCGT 59.170 39.130 0.00 0.00 0.00 5.24
1505 3700 1.202076 GCTGCTGCGTGAGGAAATAAC 60.202 52.381 0.00 0.00 0.00 1.89
1507 3702 2.744202 CTGCTGCGTGAGGAAATAACTT 59.256 45.455 0.00 0.00 0.00 2.66
1508 3703 2.483877 TGCTGCGTGAGGAAATAACTTG 59.516 45.455 0.00 0.00 0.00 3.16
1509 3704 2.484264 GCTGCGTGAGGAAATAACTTGT 59.516 45.455 0.00 0.00 0.00 3.16
1510 3705 3.058224 GCTGCGTGAGGAAATAACTTGTT 60.058 43.478 0.00 0.00 0.00 2.83
1511 3706 4.466828 CTGCGTGAGGAAATAACTTGTTG 58.533 43.478 0.00 0.00 0.00 3.33
1512 3707 4.130857 TGCGTGAGGAAATAACTTGTTGA 58.869 39.130 0.00 0.00 0.00 3.18
1513 3708 4.213270 TGCGTGAGGAAATAACTTGTTGAG 59.787 41.667 0.00 0.00 0.00 3.02
1514 3709 4.451096 GCGTGAGGAAATAACTTGTTGAGA 59.549 41.667 0.00 0.00 0.00 3.27
1515 3710 5.049680 GCGTGAGGAAATAACTTGTTGAGAA 60.050 40.000 0.00 0.00 0.00 2.87
1516 3711 6.348540 GCGTGAGGAAATAACTTGTTGAGAAT 60.349 38.462 0.00 0.00 0.00 2.40
1517 3712 7.584987 CGTGAGGAAATAACTTGTTGAGAATT 58.415 34.615 0.00 0.00 0.00 2.17
1518 3713 7.535258 CGTGAGGAAATAACTTGTTGAGAATTG 59.465 37.037 0.00 0.00 0.00 2.32
1519 3714 8.567948 GTGAGGAAATAACTTGTTGAGAATTGA 58.432 33.333 0.00 0.00 0.00 2.57
1520 3715 8.786898 TGAGGAAATAACTTGTTGAGAATTGAG 58.213 33.333 0.00 0.00 0.00 3.02
1521 3716 8.924511 AGGAAATAACTTGTTGAGAATTGAGA 57.075 30.769 0.00 0.00 0.00 3.27
1522 3717 9.525826 AGGAAATAACTTGTTGAGAATTGAGAT 57.474 29.630 0.00 0.00 0.00 2.75
1523 3718 9.565213 GGAAATAACTTGTTGAGAATTGAGATG 57.435 33.333 0.00 0.00 0.00 2.90
1526 3721 6.814506 AACTTGTTGAGAATTGAGATGAGG 57.185 37.500 0.00 0.00 0.00 3.86
1527 3722 5.874093 ACTTGTTGAGAATTGAGATGAGGT 58.126 37.500 0.00 0.00 0.00 3.85
1528 3723 6.302269 ACTTGTTGAGAATTGAGATGAGGTT 58.698 36.000 0.00 0.00 0.00 3.50
1529 3724 6.206243 ACTTGTTGAGAATTGAGATGAGGTTG 59.794 38.462 0.00 0.00 0.00 3.77
1530 3725 5.005740 TGTTGAGAATTGAGATGAGGTTGG 58.994 41.667 0.00 0.00 0.00 3.77
1531 3726 4.226427 TGAGAATTGAGATGAGGTTGGG 57.774 45.455 0.00 0.00 0.00 4.12
1532 3727 3.845992 TGAGAATTGAGATGAGGTTGGGA 59.154 43.478 0.00 0.00 0.00 4.37
1533 3728 4.476113 TGAGAATTGAGATGAGGTTGGGAT 59.524 41.667 0.00 0.00 0.00 3.85
1534 3729 4.789807 AGAATTGAGATGAGGTTGGGATG 58.210 43.478 0.00 0.00 0.00 3.51
1535 3730 2.425143 TTGAGATGAGGTTGGGATGC 57.575 50.000 0.00 0.00 0.00 3.91
1536 3731 1.288188 TGAGATGAGGTTGGGATGCA 58.712 50.000 0.00 0.00 0.00 3.96
1537 3732 1.848388 TGAGATGAGGTTGGGATGCAT 59.152 47.619 0.00 0.00 0.00 3.96
1538 3733 2.158711 TGAGATGAGGTTGGGATGCATC 60.159 50.000 18.81 18.81 36.49 3.91
1539 3734 1.848388 AGATGAGGTTGGGATGCATCA 59.152 47.619 27.25 6.50 38.19 3.07
1540 3735 1.952296 GATGAGGTTGGGATGCATCAC 59.048 52.381 27.25 25.01 36.32 3.06
1541 3736 0.697658 TGAGGTTGGGATGCATCACA 59.302 50.000 27.72 27.72 38.71 3.58
1542 3737 1.098050 GAGGTTGGGATGCATCACAC 58.902 55.000 31.00 23.28 40.51 3.82
1543 3738 0.700564 AGGTTGGGATGCATCACACT 59.299 50.000 31.00 22.09 40.51 3.55
1544 3739 1.076024 AGGTTGGGATGCATCACACTT 59.924 47.619 31.00 18.54 40.51 3.16
1545 3740 1.203052 GGTTGGGATGCATCACACTTG 59.797 52.381 31.00 0.00 40.51 3.16
1546 3741 1.888512 GTTGGGATGCATCACACTTGT 59.111 47.619 31.00 0.00 40.51 3.16
1547 3742 3.081061 GTTGGGATGCATCACACTTGTA 58.919 45.455 31.00 13.74 40.51 2.41
1548 3743 3.650281 TGGGATGCATCACACTTGTAT 57.350 42.857 27.72 0.00 34.77 2.29
1549 3744 3.966979 TGGGATGCATCACACTTGTATT 58.033 40.909 27.72 0.00 34.77 1.89
1550 3745 3.947196 TGGGATGCATCACACTTGTATTC 59.053 43.478 27.72 5.13 34.77 1.75
1551 3746 3.947196 GGGATGCATCACACTTGTATTCA 59.053 43.478 27.25 0.00 0.00 2.57
1552 3747 4.581824 GGGATGCATCACACTTGTATTCAT 59.418 41.667 27.25 0.00 0.00 2.57
1553 3748 5.278169 GGGATGCATCACACTTGTATTCATC 60.278 44.000 27.25 4.63 0.00 2.92
1554 3749 5.278169 GGATGCATCACACTTGTATTCATCC 60.278 44.000 27.25 2.06 40.13 3.51
1555 3750 4.587891 TGCATCACACTTGTATTCATCCA 58.412 39.130 0.00 0.00 0.00 3.41
1556 3751 4.395854 TGCATCACACTTGTATTCATCCAC 59.604 41.667 0.00 0.00 0.00 4.02
1557 3752 4.395854 GCATCACACTTGTATTCATCCACA 59.604 41.667 0.00 0.00 0.00 4.17
1558 3753 5.106197 GCATCACACTTGTATTCATCCACAA 60.106 40.000 0.00 0.00 33.76 3.33
1559 3754 6.570186 GCATCACACTTGTATTCATCCACAAA 60.570 38.462 0.00 0.00 34.43 2.83
1560 3755 6.558771 TCACACTTGTATTCATCCACAAAG 57.441 37.500 0.00 0.00 34.43 2.77
1561 3756 5.473162 TCACACTTGTATTCATCCACAAAGG 59.527 40.000 0.00 0.00 34.43 3.11
1659 3856 0.524862 CGTAGACAGCGTACCAACCT 59.475 55.000 0.00 0.00 0.00 3.50
1660 3857 1.068055 CGTAGACAGCGTACCAACCTT 60.068 52.381 0.00 0.00 0.00 3.50
1718 3920 4.271661 TGACACGGAAAGTTTAGGGTTTT 58.728 39.130 0.72 0.00 0.00 2.43
1721 3923 5.439721 ACACGGAAAGTTTAGGGTTTTAGT 58.560 37.500 0.00 0.00 0.00 2.24
1739 3942 1.148273 TGGCCAAAAGAGTGCGAGT 59.852 52.632 0.61 0.00 0.00 4.18
1755 3960 2.939103 GCGAGTGAAGAATTACATGGCT 59.061 45.455 0.00 0.00 0.00 4.75
1778 3985 0.745845 GGCCAGATCATTGAGCACGT 60.746 55.000 4.52 0.00 0.00 4.49
1863 4071 0.253044 AACATACACCTGGCGCAGAT 59.747 50.000 10.83 0.00 32.44 2.90
1997 4208 3.055385 TCCCCTCAATCCTAGTTTGTTCG 60.055 47.826 3.42 0.00 0.00 3.95
2062 4274 2.203153 ACGCGTTTGTTGCTCCCT 60.203 55.556 5.58 0.00 0.00 4.20
2067 4279 0.821711 CGTTTGTTGCTCCCTTGGGA 60.822 55.000 8.28 8.28 0.00 4.37
2107 4319 0.179084 GATCATTGGAAGACCGCGGA 60.179 55.000 35.90 7.74 39.42 5.54
2113 4325 2.582436 GAAGACCGCGGATCCCAA 59.418 61.111 35.90 0.00 0.00 4.12
2120 4332 2.461110 CGCGGATCCCAAGAAACGG 61.461 63.158 6.06 0.00 0.00 4.44
2153 4365 3.669344 CCGCGCTCCAGGCAAAAA 61.669 61.111 5.56 0.00 41.91 1.94
2238 4450 4.966787 GGTTGCCGGACCTTGCCA 62.967 66.667 5.05 0.00 36.73 4.92
2335 4547 2.349755 GCGTTCCACAGCCCCTTA 59.650 61.111 0.00 0.00 0.00 2.69
2353 4565 2.577020 TAGGCATCGGAAGGGACGGA 62.577 60.000 0.00 0.00 0.00 4.69
2356 4568 3.145551 ATCGGAAGGGACGGACCG 61.146 66.667 13.61 13.61 45.61 4.79
2358 4570 3.823330 CGGAAGGGACGGACCGAG 61.823 72.222 23.38 0.00 46.94 4.63
2359 4571 2.362120 GGAAGGGACGGACCGAGA 60.362 66.667 23.38 0.00 40.11 4.04
2360 4572 1.980772 GGAAGGGACGGACCGAGAA 60.981 63.158 23.38 0.00 40.11 2.87
2361 4573 1.214853 GAAGGGACGGACCGAGAAC 59.785 63.158 23.38 7.69 40.11 3.01
2362 4574 1.228800 AAGGGACGGACCGAGAACT 60.229 57.895 23.38 9.98 40.11 3.01
2363 4575 0.830866 AAGGGACGGACCGAGAACTT 60.831 55.000 23.38 15.30 40.11 2.66
2364 4576 1.080025 GGGACGGACCGAGAACTTG 60.080 63.158 23.38 0.00 40.11 3.16
2365 4577 1.737008 GGACGGACCGAGAACTTGC 60.737 63.158 23.38 0.00 0.00 4.01
2366 4578 1.737008 GACGGACCGAGAACTTGCC 60.737 63.158 23.38 0.00 0.00 4.52
2367 4579 2.809601 CGGACCGAGAACTTGCCG 60.810 66.667 8.64 0.00 0.00 5.69
2369 4581 2.654877 GACCGAGAACTTGCCGGA 59.345 61.111 5.05 0.00 45.58 5.14
2370 4582 1.737008 GACCGAGAACTTGCCGGAC 60.737 63.158 5.05 0.00 45.58 4.79
2371 4583 2.809601 CCGAGAACTTGCCGGACG 60.810 66.667 5.05 0.00 45.58 4.79
2372 4584 2.049433 CGAGAACTTGCCGGACGT 60.049 61.111 5.05 0.00 0.00 4.34
2373 4585 2.372690 CGAGAACTTGCCGGACGTG 61.373 63.158 5.05 0.00 0.00 4.49
2374 4586 2.027625 GAGAACTTGCCGGACGTGG 61.028 63.158 5.05 0.00 0.00 4.94
2375 4587 2.280592 GAACTTGCCGGACGTGGT 60.281 61.111 5.05 0.00 0.00 4.16
2376 4588 2.590575 AACTTGCCGGACGTGGTG 60.591 61.111 5.05 0.00 0.00 4.17
2377 4589 2.981977 GAACTTGCCGGACGTGGTGA 62.982 60.000 5.05 0.00 0.00 4.02
2378 4590 3.041940 CTTGCCGGACGTGGTGAC 61.042 66.667 5.05 0.00 0.00 3.67
2379 4591 3.800685 CTTGCCGGACGTGGTGACA 62.801 63.158 5.05 0.00 38.70 3.58
2380 4592 3.800685 TTGCCGGACGTGGTGACAG 62.801 63.158 5.05 0.00 44.46 3.51
2384 4596 3.936203 GGACGTGGTGACAGCCCA 61.936 66.667 0.00 0.00 44.46 5.36
2385 4597 2.110213 GACGTGGTGACAGCCCAA 59.890 61.111 0.00 0.00 44.46 4.12
2386 4598 1.961277 GACGTGGTGACAGCCCAAG 60.961 63.158 0.00 0.00 44.46 3.61
2387 4599 2.111043 CGTGGTGACAGCCCAAGT 59.889 61.111 1.47 0.00 44.46 3.16
2388 4600 1.961277 CGTGGTGACAGCCCAAGTC 60.961 63.158 1.47 0.00 44.46 3.01
2389 4601 1.148273 GTGGTGACAGCCCAAGTCA 59.852 57.895 1.47 0.00 44.46 3.41
2392 4604 2.425592 TGACAGCCCAAGTCACCG 59.574 61.111 0.00 0.00 40.80 4.94
2393 4605 2.137528 TGACAGCCCAAGTCACCGA 61.138 57.895 0.00 0.00 40.80 4.69
2394 4606 1.374758 GACAGCCCAAGTCACCGAG 60.375 63.158 0.00 0.00 36.06 4.63
2395 4607 2.100879 GACAGCCCAAGTCACCGAGT 62.101 60.000 0.00 0.00 36.06 4.18
2396 4608 1.374758 CAGCCCAAGTCACCGAGTC 60.375 63.158 0.00 0.00 0.00 3.36
2397 4609 2.047179 GCCCAAGTCACCGAGTCC 60.047 66.667 0.00 0.00 0.00 3.85
2398 4610 2.261671 CCCAAGTCACCGAGTCCG 59.738 66.667 0.00 0.00 0.00 4.79
2399 4611 2.432628 CCAAGTCACCGAGTCCGC 60.433 66.667 0.00 0.00 0.00 5.54
2400 4612 2.805353 CAAGTCACCGAGTCCGCG 60.805 66.667 0.00 0.00 0.00 6.46
2416 4628 3.680786 CGGACGTGGACAGCTCCA 61.681 66.667 0.00 0.00 45.11 3.86
2427 4639 2.041922 AGCTCCACCGGGCTGATA 60.042 61.111 6.32 0.00 37.41 2.15
2428 4640 1.689233 AGCTCCACCGGGCTGATAA 60.689 57.895 6.32 0.00 37.41 1.75
2429 4641 1.227674 GCTCCACCGGGCTGATAAG 60.228 63.158 6.32 0.00 0.00 1.73
2430 4642 1.227674 CTCCACCGGGCTGATAAGC 60.228 63.158 6.32 0.00 0.00 3.09
2431 4643 1.971505 CTCCACCGGGCTGATAAGCA 61.972 60.000 6.32 0.00 36.33 3.91
2432 4644 1.819632 CCACCGGGCTGATAAGCAC 60.820 63.158 6.32 0.00 36.33 4.40
2436 4648 3.724494 GGGCTGATAAGCACGAGC 58.276 61.111 3.95 0.00 42.56 5.03
2437 4649 1.153369 GGGCTGATAAGCACGAGCA 60.153 57.895 7.77 0.00 45.49 4.26
2438 4650 1.156645 GGGCTGATAAGCACGAGCAG 61.157 60.000 7.77 0.00 45.49 4.24
2439 4651 1.640604 GCTGATAAGCACGAGCAGC 59.359 57.895 7.77 6.95 45.49 5.25
2440 4652 1.922903 CTGATAAGCACGAGCAGCG 59.077 57.895 7.77 0.00 45.49 5.18
2452 4664 2.778679 GCAGCGTTGCTAGGTTCG 59.221 61.111 17.71 0.00 46.95 3.95
2453 4665 3.368455 GCAGCGTTGCTAGGTTCGC 62.368 63.158 17.71 0.00 46.95 4.70
2455 4667 3.562635 GCGTTGCTAGGTTCGCTT 58.437 55.556 0.00 0.00 44.28 4.68
2456 4668 1.132640 GCGTTGCTAGGTTCGCTTG 59.867 57.895 0.00 0.00 44.28 4.01
2457 4669 1.566018 GCGTTGCTAGGTTCGCTTGT 61.566 55.000 0.00 0.00 44.28 3.16
2458 4670 0.865769 CGTTGCTAGGTTCGCTTGTT 59.134 50.000 0.00 0.00 0.00 2.83
2459 4671 1.136336 CGTTGCTAGGTTCGCTTGTTC 60.136 52.381 0.00 0.00 0.00 3.18
2460 4672 2.143925 GTTGCTAGGTTCGCTTGTTCT 58.856 47.619 0.00 0.00 0.00 3.01
2461 4673 2.543777 TGCTAGGTTCGCTTGTTCTT 57.456 45.000 0.00 0.00 0.00 2.52
2462 4674 2.143122 TGCTAGGTTCGCTTGTTCTTG 58.857 47.619 0.00 0.00 0.00 3.02
2463 4675 1.135944 GCTAGGTTCGCTTGTTCTTGC 60.136 52.381 0.00 0.00 0.00 4.01
2464 4676 1.464997 CTAGGTTCGCTTGTTCTTGCC 59.535 52.381 0.00 0.00 0.00 4.52
2465 4677 1.172812 AGGTTCGCTTGTTCTTGCCC 61.173 55.000 0.00 0.00 0.00 5.36
2466 4678 1.452145 GGTTCGCTTGTTCTTGCCCA 61.452 55.000 0.00 0.00 0.00 5.36
2467 4679 0.598065 GTTCGCTTGTTCTTGCCCAT 59.402 50.000 0.00 0.00 0.00 4.00
2468 4680 1.000274 GTTCGCTTGTTCTTGCCCATT 60.000 47.619 0.00 0.00 0.00 3.16
2469 4681 0.597568 TCGCTTGTTCTTGCCCATTG 59.402 50.000 0.00 0.00 0.00 2.82
2470 4682 0.597568 CGCTTGTTCTTGCCCATTGA 59.402 50.000 0.00 0.00 0.00 2.57
2471 4683 1.401931 CGCTTGTTCTTGCCCATTGAG 60.402 52.381 0.00 0.00 0.00 3.02
2472 4684 1.067354 GCTTGTTCTTGCCCATTGAGG 60.067 52.381 0.00 0.00 37.03 3.86
2473 4685 2.242043 CTTGTTCTTGCCCATTGAGGT 58.758 47.619 0.00 0.00 34.66 3.85
2474 4686 1.909700 TGTTCTTGCCCATTGAGGTC 58.090 50.000 0.00 0.00 34.66 3.85
2475 4687 1.177401 GTTCTTGCCCATTGAGGTCC 58.823 55.000 0.00 0.00 34.66 4.46
2476 4688 0.039618 TTCTTGCCCATTGAGGTCCC 59.960 55.000 0.00 0.00 34.66 4.46
2477 4689 1.750399 CTTGCCCATTGAGGTCCCG 60.750 63.158 0.00 0.00 34.66 5.14
2478 4690 2.196997 CTTGCCCATTGAGGTCCCGA 62.197 60.000 0.00 0.00 34.66 5.14
2479 4691 2.124695 GCCCATTGAGGTCCCGAC 60.125 66.667 0.00 0.00 34.66 4.79
2480 4692 2.186903 CCCATTGAGGTCCCGACG 59.813 66.667 0.00 0.00 34.66 5.12
2481 4693 2.355986 CCCATTGAGGTCCCGACGA 61.356 63.158 0.00 0.00 34.66 4.20
2482 4694 1.594833 CCATTGAGGTCCCGACGAA 59.405 57.895 0.00 0.00 0.00 3.85
2483 4695 0.036765 CCATTGAGGTCCCGACGAAA 60.037 55.000 0.00 0.00 0.00 3.46
2484 4696 1.359848 CATTGAGGTCCCGACGAAAG 58.640 55.000 0.00 0.00 0.00 2.62
2497 4709 2.466867 CGAAAGTGGATCGTTGGGG 58.533 57.895 0.00 0.00 35.64 4.96
2498 4710 1.024579 CGAAAGTGGATCGTTGGGGG 61.025 60.000 0.00 0.00 35.64 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 3.559171 GCCTTTACAAGAGGATCACACCA 60.559 47.826 0.00 0.00 37.82 4.17
30 31 2.673368 CACGCCTTTACAAGAGGATCAC 59.327 50.000 0.00 0.00 37.82 3.06
50 51 2.938798 ACCCAGGAATTCGCCCCA 60.939 61.111 0.00 0.00 0.00 4.96
56 57 2.945668 CGGATTTCAGACCCAGGAATTC 59.054 50.000 0.00 0.00 0.00 2.17
66 67 1.069227 GTGGTTGCACGGATTTCAGAC 60.069 52.381 0.00 0.00 0.00 3.51
69 70 1.945522 CGTGGTTGCACGGATTTCA 59.054 52.632 0.00 0.00 44.01 2.69
77 78 1.647084 GGAAGACACGTGGTTGCAC 59.353 57.895 21.57 5.90 0.00 4.57
97 98 4.501743 GGGATGGTAGATCCTCGTTCTTTC 60.502 50.000 0.00 0.00 38.26 2.62
99 100 2.966516 GGGATGGTAGATCCTCGTTCTT 59.033 50.000 0.00 0.00 38.26 2.52
111 113 0.474184 GTGGATGTGGGGGATGGTAG 59.526 60.000 0.00 0.00 0.00 3.18
131 133 4.361420 GGGAGTATCTCGCAGTAGTTTTC 58.639 47.826 8.55 0.00 42.00 2.29
162 164 0.391597 TCGGGGAACTGACAGTGTTC 59.608 55.000 9.33 3.69 42.04 3.18
208 210 6.153340 ACCCTAATTTCAGATGGTTGAACATG 59.847 38.462 0.00 0.00 36.84 3.21
233 235 3.918253 GACATGGCGGGCTTGGACA 62.918 63.158 19.21 0.00 0.00 4.02
248 250 4.428294 TGAAAAATTGCCCAAATGGACA 57.572 36.364 0.00 0.00 37.39 4.02
284 286 6.051074 TCATGAAGATTTCGTAGATGCACAT 58.949 36.000 0.00 0.00 35.04 3.21
318 320 7.961326 ACAGAAATTTTGTCCATTATAGGCT 57.039 32.000 0.00 0.00 0.00 4.58
370 372 6.957631 AGTGAACACCCATGTAAGATTATCA 58.042 36.000 1.11 0.00 38.45 2.15
371 373 7.047891 TGAGTGAACACCCATGTAAGATTATC 58.952 38.462 1.11 0.00 38.45 1.75
372 374 6.957631 TGAGTGAACACCCATGTAAGATTAT 58.042 36.000 1.11 0.00 38.45 1.28
373 375 6.367374 TGAGTGAACACCCATGTAAGATTA 57.633 37.500 1.11 0.00 38.45 1.75
376 378 4.102524 AGTTGAGTGAACACCCATGTAAGA 59.897 41.667 1.11 0.00 38.45 2.10
377 379 4.389374 AGTTGAGTGAACACCCATGTAAG 58.611 43.478 1.11 0.00 38.45 2.34
378 380 4.431416 AGTTGAGTGAACACCCATGTAA 57.569 40.909 1.11 0.00 38.45 2.41
415 2107 6.207614 TCTCTAAGTCCGATGATCGATCAAAT 59.792 38.462 30.41 16.43 43.74 2.32
419 2111 5.811399 ATCTCTAAGTCCGATGATCGATC 57.189 43.478 17.52 18.72 43.74 3.69
420 2112 6.174049 TGTATCTCTAAGTCCGATGATCGAT 58.826 40.000 17.52 0.00 43.74 3.59
421 2113 5.548406 TGTATCTCTAAGTCCGATGATCGA 58.452 41.667 17.52 0.00 43.74 3.59
422 2114 5.864628 TGTATCTCTAAGTCCGATGATCG 57.135 43.478 8.05 8.05 40.07 3.69
428 2120 6.561614 GTCAACAATGTATCTCTAAGTCCGA 58.438 40.000 0.00 0.00 0.00 4.55
450 2145 3.080319 ACCTTAGTGAGTAGTGACCGTC 58.920 50.000 0.00 0.00 0.00 4.79
463 2158 7.504924 TCTGTTCAATAAAACCACCTTAGTG 57.495 36.000 0.00 0.00 44.12 2.74
464 2159 7.778382 AGTTCTGTTCAATAAAACCACCTTAGT 59.222 33.333 0.00 0.00 0.00 2.24
465 2160 8.166422 AGTTCTGTTCAATAAAACCACCTTAG 57.834 34.615 0.00 0.00 0.00 2.18
504 2199 3.855255 TGTTGGTGGAGTTCATCTTCA 57.145 42.857 0.00 0.00 0.00 3.02
505 2200 4.137543 AGTTGTTGGTGGAGTTCATCTTC 58.862 43.478 0.00 0.00 0.00 2.87
524 2219 7.572724 GCGAGTCGTGTCTACCATATAATAGTT 60.573 40.741 15.08 0.00 0.00 2.24
547 2245 7.007367 CGTACTTATTTTAGTAGTTCAACGCGA 59.993 37.037 15.93 0.00 31.56 5.87
548 2246 7.100544 CGTACTTATTTTAGTAGTTCAACGCG 58.899 38.462 3.53 3.53 31.56 6.01
550 2248 9.117145 TGACGTACTTATTTTAGTAGTTCAACG 57.883 33.333 0.00 0.00 31.56 4.10
565 2263 4.757657 TGTTGCACCAAATGACGTACTTAT 59.242 37.500 0.00 0.00 0.00 1.73
576 2274 0.030638 GCTCGTGTGTTGCACCAAAT 59.969 50.000 0.00 0.00 44.97 2.32
579 2277 1.100463 ATTGCTCGTGTGTTGCACCA 61.100 50.000 0.00 0.00 44.97 4.17
581 2279 2.679355 TAATTGCTCGTGTGTTGCAC 57.321 45.000 0.00 0.00 44.36 4.57
720 2874 0.464036 TTCCTTATCGATGCGCTGGT 59.536 50.000 9.73 0.00 0.00 4.00
721 2875 1.528586 CTTTCCTTATCGATGCGCTGG 59.471 52.381 9.73 3.13 0.00 4.85
722 2876 1.528586 CCTTTCCTTATCGATGCGCTG 59.471 52.381 9.73 0.00 0.00 5.18
723 2877 1.412710 TCCTTTCCTTATCGATGCGCT 59.587 47.619 9.73 0.00 0.00 5.92
724 2878 1.865865 TCCTTTCCTTATCGATGCGC 58.134 50.000 8.54 0.00 0.00 6.09
725 2879 6.727824 ATTTATCCTTTCCTTATCGATGCG 57.272 37.500 8.54 0.00 0.00 4.73
726 2880 7.331193 ACGTATTTATCCTTTCCTTATCGATGC 59.669 37.037 8.54 0.00 0.00 3.91
727 2881 8.648097 CACGTATTTATCCTTTCCTTATCGATG 58.352 37.037 8.54 0.00 0.00 3.84
728 2882 8.582437 TCACGTATTTATCCTTTCCTTATCGAT 58.418 33.333 2.16 2.16 0.00 3.59
729 2883 7.944061 TCACGTATTTATCCTTTCCTTATCGA 58.056 34.615 0.00 0.00 0.00 3.59
730 2884 8.583810 TTCACGTATTTATCCTTTCCTTATCG 57.416 34.615 0.00 0.00 0.00 2.92
731 2885 9.760077 TCTTCACGTATTTATCCTTTCCTTATC 57.240 33.333 0.00 0.00 0.00 1.75
741 2895 8.827677 GCCCATTATATCTTCACGTATTTATCC 58.172 37.037 0.00 0.00 0.00 2.59
742 2896 9.378551 TGCCCATTATATCTTCACGTATTTATC 57.621 33.333 0.00 0.00 0.00 1.75
743 2897 9.733556 TTGCCCATTATATCTTCACGTATTTAT 57.266 29.630 0.00 0.00 0.00 1.40
744 2898 9.562408 TTTGCCCATTATATCTTCACGTATTTA 57.438 29.630 0.00 0.00 0.00 1.40
745 2899 8.458573 TTTGCCCATTATATCTTCACGTATTT 57.541 30.769 0.00 0.00 0.00 1.40
746 2900 8.458573 TTTTGCCCATTATATCTTCACGTATT 57.541 30.769 0.00 0.00 0.00 1.89
747 2901 8.458573 TTTTTGCCCATTATATCTTCACGTAT 57.541 30.769 0.00 0.00 0.00 3.06
748 2902 7.867305 TTTTTGCCCATTATATCTTCACGTA 57.133 32.000 0.00 0.00 0.00 3.57
749 2903 6.767524 TTTTTGCCCATTATATCTTCACGT 57.232 33.333 0.00 0.00 0.00 4.49
750 2904 7.920151 TCAATTTTTGCCCATTATATCTTCACG 59.080 33.333 0.00 0.00 0.00 4.35
751 2905 9.768662 ATCAATTTTTGCCCATTATATCTTCAC 57.231 29.630 0.00 0.00 0.00 3.18
765 2919 9.759259 GCAAATACTTTAGAATCAATTTTTGCC 57.241 29.630 0.00 0.00 39.29 4.52
766 2920 9.759259 GGCAAATACTTTAGAATCAATTTTTGC 57.241 29.630 0.00 0.00 42.53 3.68
769 2923 9.154847 GCTGGCAAATACTTTAGAATCAATTTT 57.845 29.630 0.00 0.00 0.00 1.82
770 2924 7.489113 CGCTGGCAAATACTTTAGAATCAATTT 59.511 33.333 0.00 0.00 0.00 1.82
771 2925 6.974622 CGCTGGCAAATACTTTAGAATCAATT 59.025 34.615 0.00 0.00 0.00 2.32
772 2926 6.498304 CGCTGGCAAATACTTTAGAATCAAT 58.502 36.000 0.00 0.00 0.00 2.57
773 2927 5.676079 GCGCTGGCAAATACTTTAGAATCAA 60.676 40.000 0.00 0.00 39.62 2.57
774 2928 4.201910 GCGCTGGCAAATACTTTAGAATCA 60.202 41.667 0.00 0.00 39.62 2.57
775 2929 4.282873 GCGCTGGCAAATACTTTAGAATC 58.717 43.478 0.00 0.00 39.62 2.52
776 2930 3.242739 CGCGCTGGCAAATACTTTAGAAT 60.243 43.478 5.56 0.00 39.92 2.40
777 2931 2.095213 CGCGCTGGCAAATACTTTAGAA 59.905 45.455 5.56 0.00 39.92 2.10
778 2932 1.663643 CGCGCTGGCAAATACTTTAGA 59.336 47.619 5.56 0.00 39.92 2.10
796 2950 6.759827 TGTACTTATCCTTTCCTTATCAACGC 59.240 38.462 0.00 0.00 0.00 4.84
817 2971 7.667043 TTTCGCCCATTATATCTTCATGTAC 57.333 36.000 0.00 0.00 0.00 2.90
940 3123 2.442188 GCGACGATGTCACCGGAAC 61.442 63.158 9.46 6.63 32.09 3.62
1085 3268 5.481473 TGTGAAAATAGGGAGTACGTACCTT 59.519 40.000 21.80 7.08 35.84 3.50
1505 3700 6.349115 CCAACCTCATCTCAATTCTCAACAAG 60.349 42.308 0.00 0.00 0.00 3.16
1507 3702 5.005740 CCAACCTCATCTCAATTCTCAACA 58.994 41.667 0.00 0.00 0.00 3.33
1508 3703 4.397417 CCCAACCTCATCTCAATTCTCAAC 59.603 45.833 0.00 0.00 0.00 3.18
1509 3704 4.289410 TCCCAACCTCATCTCAATTCTCAA 59.711 41.667 0.00 0.00 0.00 3.02
1510 3705 3.845992 TCCCAACCTCATCTCAATTCTCA 59.154 43.478 0.00 0.00 0.00 3.27
1511 3706 4.494091 TCCCAACCTCATCTCAATTCTC 57.506 45.455 0.00 0.00 0.00 2.87
1512 3707 4.789807 CATCCCAACCTCATCTCAATTCT 58.210 43.478 0.00 0.00 0.00 2.40
1513 3708 3.317430 GCATCCCAACCTCATCTCAATTC 59.683 47.826 0.00 0.00 0.00 2.17
1514 3709 3.294214 GCATCCCAACCTCATCTCAATT 58.706 45.455 0.00 0.00 0.00 2.32
1515 3710 2.242965 TGCATCCCAACCTCATCTCAAT 59.757 45.455 0.00 0.00 0.00 2.57
1516 3711 1.634973 TGCATCCCAACCTCATCTCAA 59.365 47.619 0.00 0.00 0.00 3.02
1517 3712 1.288188 TGCATCCCAACCTCATCTCA 58.712 50.000 0.00 0.00 0.00 3.27
1518 3713 2.158711 TGATGCATCCCAACCTCATCTC 60.159 50.000 23.67 0.00 35.74 2.75
1519 3714 1.848388 TGATGCATCCCAACCTCATCT 59.152 47.619 23.67 0.00 35.74 2.90
1520 3715 1.952296 GTGATGCATCCCAACCTCATC 59.048 52.381 23.67 0.00 35.40 2.92
1521 3716 1.285667 TGTGATGCATCCCAACCTCAT 59.714 47.619 23.67 0.00 0.00 2.90
1522 3717 0.697658 TGTGATGCATCCCAACCTCA 59.302 50.000 23.67 0.80 0.00 3.86
1523 3718 1.098050 GTGTGATGCATCCCAACCTC 58.902 55.000 23.67 3.08 0.00 3.85
1524 3719 0.700564 AGTGTGATGCATCCCAACCT 59.299 50.000 23.67 10.07 0.00 3.50
1525 3720 1.203052 CAAGTGTGATGCATCCCAACC 59.797 52.381 23.67 7.87 0.00 3.77
1526 3721 1.888512 ACAAGTGTGATGCATCCCAAC 59.111 47.619 23.67 17.58 0.00 3.77
1527 3722 2.291209 ACAAGTGTGATGCATCCCAA 57.709 45.000 23.67 6.60 0.00 4.12
1528 3723 3.650281 ATACAAGTGTGATGCATCCCA 57.350 42.857 23.67 16.21 0.00 4.37
1529 3724 3.947196 TGAATACAAGTGTGATGCATCCC 59.053 43.478 23.67 13.46 0.00 3.85
1530 3725 5.278169 GGATGAATACAAGTGTGATGCATCC 60.278 44.000 23.67 15.02 41.45 3.51
1531 3726 5.297527 TGGATGAATACAAGTGTGATGCATC 59.702 40.000 20.14 20.14 0.00 3.91
1532 3727 5.066893 GTGGATGAATACAAGTGTGATGCAT 59.933 40.000 0.00 0.00 0.00 3.96
1533 3728 4.395854 GTGGATGAATACAAGTGTGATGCA 59.604 41.667 0.00 0.00 0.00 3.96
1534 3729 4.395854 TGTGGATGAATACAAGTGTGATGC 59.604 41.667 0.00 0.00 0.00 3.91
1535 3730 6.499234 TTGTGGATGAATACAAGTGTGATG 57.501 37.500 0.00 0.00 33.29 3.07
1536 3731 6.151648 CCTTTGTGGATGAATACAAGTGTGAT 59.848 38.462 0.00 0.00 37.98 3.06
1537 3732 5.473162 CCTTTGTGGATGAATACAAGTGTGA 59.527 40.000 0.00 0.00 37.98 3.58
1538 3733 5.335897 CCCTTTGTGGATGAATACAAGTGTG 60.336 44.000 0.00 0.00 37.98 3.82
1539 3734 4.766891 CCCTTTGTGGATGAATACAAGTGT 59.233 41.667 0.00 0.00 37.98 3.55
1540 3735 4.766891 ACCCTTTGTGGATGAATACAAGTG 59.233 41.667 0.00 0.00 37.98 3.16
1541 3736 4.998051 ACCCTTTGTGGATGAATACAAGT 58.002 39.130 0.00 0.00 37.98 3.16
1542 3737 7.645058 ATTACCCTTTGTGGATGAATACAAG 57.355 36.000 0.00 0.00 37.98 3.16
1543 3738 9.707957 ATTATTACCCTTTGTGGATGAATACAA 57.292 29.630 0.00 0.00 38.35 2.41
1636 3833 1.237533 TGGTACGCTGTCTACGTTGA 58.762 50.000 0.00 0.00 41.93 3.18
1641 3838 2.288640 ACAAGGTTGGTACGCTGTCTAC 60.289 50.000 0.00 0.00 0.00 2.59
1659 3856 3.322541 TCCGTGGTCTTGTAAGATGACAA 59.677 43.478 0.00 0.00 37.39 3.18
1660 3857 2.894765 TCCGTGGTCTTGTAAGATGACA 59.105 45.455 0.00 0.00 37.39 3.58
1718 3920 0.394938 TCGCACTCTTTTGGCCACTA 59.605 50.000 3.88 0.00 0.00 2.74
1721 3923 1.148273 ACTCGCACTCTTTTGGCCA 59.852 52.632 0.00 0.00 0.00 5.36
1739 3942 3.797039 CCTCGAGCCATGTAATTCTTCA 58.203 45.455 6.99 0.00 0.00 3.02
1755 3960 0.105593 GCTCAATGATCTGGCCTCGA 59.894 55.000 3.32 0.03 0.00 4.04
1778 3985 0.179043 TTGGTTTGTGTGCGAGCCTA 60.179 50.000 0.00 0.00 31.36 3.93
1863 4071 2.039480 AGATGAAGCAAGCTCAAGACCA 59.961 45.455 0.00 0.00 0.00 4.02
1955 4165 3.774959 CTTCCCGACTCATCCGGCG 62.775 68.421 0.00 0.00 45.24 6.46
1989 4200 5.963586 GCATTATGGCTTACTACGAACAAAC 59.036 40.000 0.00 0.00 0.00 2.93
1997 4208 4.351874 TCTGGGCATTATGGCTTACTAC 57.648 45.455 18.01 1.43 43.20 2.73
2062 4274 0.687757 CCATCCTCGACTCCTCCCAA 60.688 60.000 0.00 0.00 0.00 4.12
2067 4279 0.545171 TACGTCCATCCTCGACTCCT 59.455 55.000 0.00 0.00 0.00 3.69
2107 4319 1.678970 GGCTGCCGTTTCTTGGGAT 60.679 57.895 1.35 0.00 0.00 3.85
2238 4450 3.007182 CACCTCTGAAAATGTGGCCAAAT 59.993 43.478 7.24 3.97 0.00 2.32
2335 4547 3.470888 CCGTCCCTTCCGATGCCT 61.471 66.667 0.00 0.00 0.00 4.75
2353 4565 2.342648 GTCCGGCAAGTTCTCGGT 59.657 61.111 0.00 0.00 43.75 4.69
2356 4568 2.027625 CCACGTCCGGCAAGTTCTC 61.028 63.158 0.00 0.00 0.00 2.87
2357 4569 2.030562 CCACGTCCGGCAAGTTCT 59.969 61.111 0.00 0.00 0.00 3.01
2358 4570 2.280592 ACCACGTCCGGCAAGTTC 60.281 61.111 0.00 0.00 0.00 3.01
2359 4571 2.590575 CACCACGTCCGGCAAGTT 60.591 61.111 0.00 0.00 0.00 2.66
2360 4572 3.542676 TCACCACGTCCGGCAAGT 61.543 61.111 0.00 0.00 0.00 3.16
2361 4573 3.041940 GTCACCACGTCCGGCAAG 61.042 66.667 0.00 0.00 0.00 4.01
2362 4574 3.800685 CTGTCACCACGTCCGGCAA 62.801 63.158 0.00 0.00 0.00 4.52
2363 4575 4.293648 CTGTCACCACGTCCGGCA 62.294 66.667 0.00 0.00 0.00 5.69
2367 4579 3.469863 TTGGGCTGTCACCACGTCC 62.470 63.158 0.00 0.00 37.82 4.79
2368 4580 1.961277 CTTGGGCTGTCACCACGTC 60.961 63.158 0.00 0.00 37.82 4.34
2369 4581 2.111043 CTTGGGCTGTCACCACGT 59.889 61.111 0.00 0.00 37.82 4.49
2370 4582 1.961277 GACTTGGGCTGTCACCACG 60.961 63.158 0.00 0.00 37.82 4.94
2371 4583 1.148273 TGACTTGGGCTGTCACCAC 59.852 57.895 4.89 0.00 39.23 4.16
2372 4584 3.654021 TGACTTGGGCTGTCACCA 58.346 55.556 4.89 0.00 39.23 4.17
2375 4587 2.099652 CTCGGTGACTTGGGCTGTCA 62.100 60.000 4.89 4.89 41.48 3.58
2376 4588 1.374758 CTCGGTGACTTGGGCTGTC 60.375 63.158 0.00 0.00 35.21 3.51
2377 4589 2.100879 GACTCGGTGACTTGGGCTGT 62.101 60.000 0.00 0.00 0.00 4.40
2378 4590 1.374758 GACTCGGTGACTTGGGCTG 60.375 63.158 0.00 0.00 0.00 4.85
2379 4591 2.584391 GGACTCGGTGACTTGGGCT 61.584 63.158 0.00 0.00 0.00 5.19
2380 4592 2.047179 GGACTCGGTGACTTGGGC 60.047 66.667 0.00 0.00 0.00 5.36
2381 4593 2.261671 CGGACTCGGTGACTTGGG 59.738 66.667 0.00 0.00 0.00 4.12
2382 4594 2.432628 GCGGACTCGGTGACTTGG 60.433 66.667 0.00 0.00 36.79 3.61
2383 4595 2.805353 CGCGGACTCGGTGACTTG 60.805 66.667 0.00 0.00 36.79 3.16
2384 4596 4.052229 CCGCGGACTCGGTGACTT 62.052 66.667 24.07 0.00 44.18 3.01
2392 4604 4.773117 GTCCACGTCCGCGGACTC 62.773 72.222 44.83 27.76 46.83 3.36
2399 4611 3.680786 TGGAGCTGTCCACGTCCG 61.681 66.667 0.00 0.00 46.77 4.79
2410 4622 1.689233 TTATCAGCCCGGTGGAGCT 60.689 57.895 0.00 0.00 40.89 4.09
2411 4623 1.227674 CTTATCAGCCCGGTGGAGC 60.228 63.158 0.00 0.00 0.00 4.70
2412 4624 1.227674 GCTTATCAGCCCGGTGGAG 60.228 63.158 0.00 0.00 40.61 3.86
2413 4625 1.992834 TGCTTATCAGCCCGGTGGA 60.993 57.895 0.00 0.00 46.74 4.02
2414 4626 1.819632 GTGCTTATCAGCCCGGTGG 60.820 63.158 0.00 0.00 46.74 4.61
2415 4627 2.173669 CGTGCTTATCAGCCCGGTG 61.174 63.158 0.00 0.00 46.74 4.94
2416 4628 2.186903 CGTGCTTATCAGCCCGGT 59.813 61.111 0.00 0.00 46.74 5.28
2417 4629 1.592669 CTCGTGCTTATCAGCCCGG 60.593 63.158 3.95 0.00 45.95 5.73
2419 4631 1.153369 TGCTCGTGCTTATCAGCCC 60.153 57.895 11.19 0.00 46.74 5.19
2420 4632 1.770085 GCTGCTCGTGCTTATCAGCC 61.770 60.000 11.19 0.00 46.74 4.85
2422 4634 1.922903 CGCTGCTCGTGCTTATCAG 59.077 57.895 11.19 0.27 40.48 2.90
2423 4635 4.093115 CGCTGCTCGTGCTTATCA 57.907 55.556 11.19 0.00 40.48 2.15
2436 4648 2.778679 GCGAACCTAGCAACGCTG 59.221 61.111 14.83 0.00 46.06 5.18
2439 4651 0.865769 AACAAGCGAACCTAGCAACG 59.134 50.000 0.00 0.00 37.01 4.10
2440 4652 2.143925 AGAACAAGCGAACCTAGCAAC 58.856 47.619 0.00 0.00 37.01 4.17
2441 4653 2.543777 AGAACAAGCGAACCTAGCAA 57.456 45.000 0.00 0.00 37.01 3.91
2442 4654 2.143122 CAAGAACAAGCGAACCTAGCA 58.857 47.619 0.00 0.00 37.01 3.49
2443 4655 1.135944 GCAAGAACAAGCGAACCTAGC 60.136 52.381 0.00 0.00 0.00 3.42
2444 4656 1.464997 GGCAAGAACAAGCGAACCTAG 59.535 52.381 0.00 0.00 0.00 3.02
2445 4657 1.519408 GGCAAGAACAAGCGAACCTA 58.481 50.000 0.00 0.00 0.00 3.08
2446 4658 1.172812 GGGCAAGAACAAGCGAACCT 61.173 55.000 0.00 0.00 0.00 3.50
2447 4659 1.285950 GGGCAAGAACAAGCGAACC 59.714 57.895 0.00 0.00 0.00 3.62
2448 4660 0.598065 ATGGGCAAGAACAAGCGAAC 59.402 50.000 0.00 0.00 0.00 3.95
2449 4661 1.000385 CAATGGGCAAGAACAAGCGAA 60.000 47.619 0.00 0.00 0.00 4.70
2450 4662 0.597568 CAATGGGCAAGAACAAGCGA 59.402 50.000 0.00 0.00 0.00 4.93
2451 4663 0.597568 TCAATGGGCAAGAACAAGCG 59.402 50.000 0.00 0.00 0.00 4.68
2452 4664 1.067354 CCTCAATGGGCAAGAACAAGC 60.067 52.381 0.00 0.00 0.00 4.01
2453 4665 2.229784 GACCTCAATGGGCAAGAACAAG 59.770 50.000 0.00 0.00 45.54 3.16
2454 4666 2.238521 GACCTCAATGGGCAAGAACAA 58.761 47.619 0.00 0.00 45.54 2.83
2455 4667 1.909700 GACCTCAATGGGCAAGAACA 58.090 50.000 0.00 0.00 45.54 3.18
2462 4674 2.124695 GTCGGGACCTCAATGGGC 60.125 66.667 0.00 0.00 45.48 5.36
2463 4675 1.895020 TTCGTCGGGACCTCAATGGG 61.895 60.000 0.00 0.00 41.11 4.00
2464 4676 0.036765 TTTCGTCGGGACCTCAATGG 60.037 55.000 0.00 0.00 42.93 3.16
2465 4677 1.337823 ACTTTCGTCGGGACCTCAATG 60.338 52.381 0.00 0.00 0.00 2.82
2466 4678 0.974383 ACTTTCGTCGGGACCTCAAT 59.026 50.000 0.00 0.00 0.00 2.57
2467 4679 0.032952 CACTTTCGTCGGGACCTCAA 59.967 55.000 0.00 0.00 0.00 3.02
2468 4680 1.663739 CACTTTCGTCGGGACCTCA 59.336 57.895 0.00 0.00 0.00 3.86
2469 4681 1.080025 CCACTTTCGTCGGGACCTC 60.080 63.158 0.00 0.00 0.00 3.85
2470 4682 0.903454 ATCCACTTTCGTCGGGACCT 60.903 55.000 0.00 0.00 31.04 3.85
2471 4683 0.459759 GATCCACTTTCGTCGGGACC 60.460 60.000 0.00 0.00 31.04 4.46
2472 4684 0.801067 CGATCCACTTTCGTCGGGAC 60.801 60.000 0.00 0.00 31.04 4.46
2473 4685 1.246056 ACGATCCACTTTCGTCGGGA 61.246 55.000 0.00 0.00 46.13 5.14
2474 4686 1.214589 ACGATCCACTTTCGTCGGG 59.785 57.895 0.00 0.00 46.13 5.14
2475 4687 4.883026 ACGATCCACTTTCGTCGG 57.117 55.556 0.00 0.00 46.13 4.79
2479 4691 1.024579 CCCCCAACGATCCACTTTCG 61.025 60.000 0.00 0.00 42.20 3.46
2480 4692 2.868253 CCCCCAACGATCCACTTTC 58.132 57.895 0.00 0.00 0.00 2.62


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

AutoCloner maintained by Alex Coulton.