Multiple sequence alignment - TraesCS2D01G074400

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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 TraesCS2D01G074400 chr2D 100.000 5054 0 0 1 5054 31890757 31885704 0.000000e+00 9334.0
1 TraesCS2D01G074400 chr2D 90.647 1561 105 21 2550 4072 32029805 32028248 0.000000e+00 2036.0
2 TraesCS2D01G074400 chr2D 94.521 803 43 1 3219 4021 31948898 31948097 0.000000e+00 1238.0
3 TraesCS2D01G074400 chr2D 95.944 715 24 3 4345 5054 53240346 53239632 0.000000e+00 1155.0
4 TraesCS2D01G074400 chr2D 95.480 708 28 2 4351 5054 33601299 33602006 0.000000e+00 1127.0
5 TraesCS2D01G074400 chr2D 95.339 708 29 2 4351 5054 536146207 536145500 0.000000e+00 1122.0
6 TraesCS2D01G074400 chr2D 87.815 993 55 33 2125 3072 31949869 31948898 0.000000e+00 1103.0
7 TraesCS2D01G074400 chr2D 84.003 1169 77 36 851 1930 32031610 32030463 0.000000e+00 1022.0
8 TraesCS2D01G074400 chr2D 88.152 709 55 12 861 1555 31951157 31950464 0.000000e+00 817.0
9 TraesCS2D01G074400 chr2D 90.710 366 15 5 2148 2513 32030228 32029882 2.130000e-128 470.0
10 TraesCS2D01G074400 chr2D 86.280 328 19 8 1615 1930 31950451 31950138 2.920000e-87 333.0
11 TraesCS2D01G074400 chr2D 89.796 196 10 3 1931 2126 31950085 31949900 5.060000e-60 243.0
12 TraesCS2D01G074400 chr2D 92.593 162 11 1 2129 2289 32030389 32030228 1.090000e-56 231.0
13 TraesCS2D01G074400 chr2D 86.525 141 17 1 4095 4235 31978030 31977892 2.440000e-33 154.0
14 TraesCS2D01G074400 chr2A 96.981 2186 61 5 2125 4308 34092023 34089841 0.000000e+00 3666.0
15 TraesCS2D01G074400 chr2A 84.310 1160 82 36 851 1930 34093434 34092295 0.000000e+00 1042.0
16 TraesCS2D01G074400 chr2A 77.233 347 37 20 2125 2468 34092384 34092077 1.130000e-36 165.0
17 TraesCS2D01G074400 chr2B 90.206 2236 149 38 2125 4306 52600043 52597824 0.000000e+00 2852.0
18 TraesCS2D01G074400 chr2B 94.679 1090 39 9 854 1930 52348011 52349094 0.000000e+00 1674.0
19 TraesCS2D01G074400 chr2B 89.430 1334 95 23 2788 4094 52350205 52351519 0.000000e+00 1640.0
20 TraesCS2D01G074400 chr2B 92.364 1100 57 13 850 1929 52601405 52600313 0.000000e+00 1541.0
21 TraesCS2D01G074400 chr2B 91.215 683 40 7 2122 2795 52349359 52350030 0.000000e+00 911.0
22 TraesCS2D01G074400 chr2B 88.500 200 10 5 1931 2128 52600259 52600071 3.940000e-56 230.0
23 TraesCS2D01G074400 chr2B 87.940 199 12 3 1931 2128 52349147 52349334 1.830000e-54 224.0
24 TraesCS2D01G074400 chr4D 96.643 715 11 4 4351 5054 479565625 479566337 0.000000e+00 1175.0
25 TraesCS2D01G074400 chr1D 96.620 710 17 5 4351 5054 86316750 86316042 0.000000e+00 1171.0
26 TraesCS2D01G074400 chr1D 95.098 714 25 4 4351 5054 414331583 414330870 0.000000e+00 1116.0
27 TraesCS2D01G074400 chr3D 96.192 709 22 3 4351 5054 392044447 392045155 0.000000e+00 1155.0
28 TraesCS2D01G074400 chr3D 95.211 710 28 3 4351 5054 85258950 85259659 0.000000e+00 1118.0
29 TraesCS2D01G074400 chr3D 97.727 44 1 0 4307 4350 47238263 47238306 5.430000e-10 76.8
30 TraesCS2D01G074400 chr3D 97.561 41 1 0 4307 4347 85397420 85397380 2.520000e-08 71.3
31 TraesCS2D01G074400 chr5D 95.628 709 26 3 4351 5054 27103327 27104035 0.000000e+00 1133.0
32 TraesCS2D01G074400 chr5D 83.133 249 35 5 1108 1354 539075109 539075352 2.370000e-53 220.0
33 TraesCS2D01G074400 chr5D 87.121 132 17 0 2562 2693 286928993 286928862 3.150000e-32 150.0
34 TraesCS2D01G074400 chr5D 97.619 42 1 0 4307 4348 396439192 396439233 7.020000e-09 73.1
35 TraesCS2D01G074400 chr5B 82.727 770 86 26 1 740 690863299 690864051 4.270000e-180 641.0
36 TraesCS2D01G074400 chr5B 83.607 244 40 0 1108 1351 680752102 680752345 3.940000e-56 230.0
37 TraesCS2D01G074400 chr5B 86.567 134 14 4 2562 2693 325934833 325934702 1.470000e-30 145.0
38 TraesCS2D01G074400 chr7D 82.799 686 80 20 1 682 58070840 58070189 3.390000e-161 579.0
39 TraesCS2D01G074400 chr7D 83.755 474 55 12 1 467 454144293 454143835 3.620000e-116 429.0
40 TraesCS2D01G074400 chr7D 92.857 42 2 1 4307 4348 17698757 17698797 5.460000e-05 60.2
41 TraesCS2D01G074400 chr7B 83.564 578 64 16 176 740 672487183 672486624 3.490000e-141 512.0
42 TraesCS2D01G074400 chr7A 83.216 566 73 14 12 569 41723277 41722726 2.720000e-137 499.0
43 TraesCS2D01G074400 chr7A 82.540 567 75 15 12 569 41752680 41752129 1.270000e-130 477.0
44 TraesCS2D01G074400 chr7A 82.540 567 72 16 12 569 41781206 41780658 1.650000e-129 473.0
45 TraesCS2D01G074400 chr5A 82.699 578 71 17 1 569 380791369 380790812 2.120000e-133 486.0
46 TraesCS2D01G074400 chr5A 84.328 134 17 4 2562 2693 379020369 379020238 1.480000e-25 128.0
47 TraesCS2D01G074400 chrUn 82.272 581 75 20 1 570 83369761 83370324 1.270000e-130 477.0
48 TraesCS2D01G074400 chr4A 84.979 233 33 2 1123 1354 629424352 629424121 8.460000e-58 235.0
49 TraesCS2D01G074400 chr4A 84.979 233 33 2 1123 1354 629436285 629436054 8.460000e-58 235.0
50 TraesCS2D01G074400 chr3B 97.619 42 1 0 4307 4348 41635816 41635775 7.020000e-09 73.1
51 TraesCS2D01G074400 chr1B 97.561 41 1 0 4307 4347 383211577 383211617 2.520000e-08 71.3
52 TraesCS2D01G074400 chr6B 95.238 42 2 0 4307 4348 461962540 461962581 3.270000e-07 67.6
53 TraesCS2D01G074400 chr3A 95.122 41 1 1 4308 4348 19067761 19067722 4.220000e-06 63.9


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 TraesCS2D01G074400 chr2D 31885704 31890757 5053 True 9334.000000 9334 100.000000 1 5054 1 chr2D.!!$R1 5053
1 TraesCS2D01G074400 chr2D 53239632 53240346 714 True 1155.000000 1155 95.944000 4345 5054 1 chr2D.!!$R3 709
2 TraesCS2D01G074400 chr2D 33601299 33602006 707 False 1127.000000 1127 95.480000 4351 5054 1 chr2D.!!$F1 703
3 TraesCS2D01G074400 chr2D 536145500 536146207 707 True 1122.000000 1122 95.339000 4351 5054 1 chr2D.!!$R4 703
4 TraesCS2D01G074400 chr2D 32028248 32031610 3362 True 939.750000 2036 89.488250 851 4072 4 chr2D.!!$R6 3221
5 TraesCS2D01G074400 chr2D 31948097 31951157 3060 True 746.800000 1238 89.312800 861 4021 5 chr2D.!!$R5 3160
6 TraesCS2D01G074400 chr2A 34089841 34093434 3593 True 1624.333333 3666 86.174667 851 4308 3 chr2A.!!$R1 3457
7 TraesCS2D01G074400 chr2B 52597824 52601405 3581 True 1541.000000 2852 90.356667 850 4306 3 chr2B.!!$R1 3456
8 TraesCS2D01G074400 chr2B 52348011 52351519 3508 False 1112.250000 1674 90.816000 854 4094 4 chr2B.!!$F1 3240
9 TraesCS2D01G074400 chr4D 479565625 479566337 712 False 1175.000000 1175 96.643000 4351 5054 1 chr4D.!!$F1 703
10 TraesCS2D01G074400 chr1D 86316042 86316750 708 True 1171.000000 1171 96.620000 4351 5054 1 chr1D.!!$R1 703
11 TraesCS2D01G074400 chr1D 414330870 414331583 713 True 1116.000000 1116 95.098000 4351 5054 1 chr1D.!!$R2 703
12 TraesCS2D01G074400 chr3D 392044447 392045155 708 False 1155.000000 1155 96.192000 4351 5054 1 chr3D.!!$F3 703
13 TraesCS2D01G074400 chr3D 85258950 85259659 709 False 1118.000000 1118 95.211000 4351 5054 1 chr3D.!!$F2 703
14 TraesCS2D01G074400 chr5D 27103327 27104035 708 False 1133.000000 1133 95.628000 4351 5054 1 chr5D.!!$F1 703
15 TraesCS2D01G074400 chr5B 690863299 690864051 752 False 641.000000 641 82.727000 1 740 1 chr5B.!!$F2 739
16 TraesCS2D01G074400 chr7D 58070189 58070840 651 True 579.000000 579 82.799000 1 682 1 chr7D.!!$R1 681
17 TraesCS2D01G074400 chr7B 672486624 672487183 559 True 512.000000 512 83.564000 176 740 1 chr7B.!!$R1 564
18 TraesCS2D01G074400 chr7A 41722726 41723277 551 True 499.000000 499 83.216000 12 569 1 chr7A.!!$R1 557
19 TraesCS2D01G074400 chr7A 41752129 41752680 551 True 477.000000 477 82.540000 12 569 1 chr7A.!!$R2 557
20 TraesCS2D01G074400 chr7A 41780658 41781206 548 True 473.000000 473 82.540000 12 569 1 chr7A.!!$R3 557
21 TraesCS2D01G074400 chr5A 380790812 380791369 557 True 486.000000 486 82.699000 1 569 1 chr5A.!!$R2 568
22 TraesCS2D01G074400 chrUn 83369761 83370324 563 False 477.000000 477 82.272000 1 570 1 chrUn.!!$F1 569

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
832 883 0.039074 CCGCAAAGTCTCAGTCGACT 60.039 55.000 13.58 13.58 45.73 4.18 F
833 884 1.056103 CGCAAAGTCTCAGTCGACTG 58.944 55.000 34.76 34.76 43.14 3.51 F
2027 2257 1.270274 TGCACAACATCAGTCATTGGC 59.730 47.619 0.00 0.00 0.00 4.52 F
3369 4050 0.664761 CAGGCCACCATTAATCTGCG 59.335 55.000 5.01 0.00 0.00 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2299 2685 1.828979 TTTCCAGAATACGGGCCAAC 58.171 50.000 4.39 0.0 0.00 3.77 R
2790 3443 3.554934 TGGACTGACAAAAGAGCATTGT 58.445 40.909 0.00 0.0 43.37 2.71 R
3650 4332 0.103937 GGTCTTCCAGAGAGGCATCG 59.896 60.000 0.00 0.0 34.31 3.84 R
4313 5003 0.121197 TGGGGTCCTCCTCCATTTCT 59.879 55.000 0.00 0.0 32.02 2.52 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
27 28 2.563013 AAAGAGCGGGCCAGATGCAT 62.563 55.000 7.23 0.00 43.89 3.96
80 85 6.071952 GGAAGCAAACTAATTGGACATGAGAA 60.072 38.462 0.00 0.00 39.54 2.87
82 87 7.472334 AGCAAACTAATTGGACATGAGAAAT 57.528 32.000 0.00 0.00 39.54 2.17
85 90 9.076596 GCAAACTAATTGGACATGAGAAATAAC 57.923 33.333 0.00 0.00 39.54 1.89
86 91 9.573133 CAAACTAATTGGACATGAGAAATAACC 57.427 33.333 0.00 0.00 35.27 2.85
152 160 1.002069 ATGGAGTTGCATTCTGGGGA 58.998 50.000 0.00 0.00 0.00 4.81
157 165 2.627699 GAGTTGCATTCTGGGGAAACAA 59.372 45.455 0.00 0.00 34.90 2.83
159 167 3.259123 AGTTGCATTCTGGGGAAACAATC 59.741 43.478 0.00 0.00 35.54 2.67
172 180 2.550830 AACAATCGCAGTTGAGGTCT 57.449 45.000 5.19 0.00 33.37 3.85
295 308 5.165961 AGCTTCTTTTAGACTGGCATACA 57.834 39.130 0.00 0.00 0.00 2.29
317 330 7.061566 ACATAACACAAAGCCAAACCTAAAT 57.938 32.000 0.00 0.00 0.00 1.40
320 333 9.482627 CATAACACAAAGCCAAACCTAAATAAA 57.517 29.630 0.00 0.00 0.00 1.40
323 336 7.561251 ACACAAAGCCAAACCTAAATAAACTT 58.439 30.769 0.00 0.00 0.00 2.66
359 379 6.205853 TGGATGCTTGTTCTATACAAAAACGT 59.794 34.615 0.00 0.00 45.69 3.99
366 386 3.061322 TCTATACAAAAACGTGTGCGCT 58.939 40.909 9.73 0.00 42.83 5.92
443 464 7.764443 TGATGCTACACTAGAAAAACTACATCC 59.236 37.037 0.00 0.00 31.72 3.51
497 519 2.434185 AGCCACACATACGCACGG 60.434 61.111 0.00 0.00 0.00 4.94
506 530 1.758280 ACATACGCACGGGGATTCTAA 59.242 47.619 0.00 0.00 0.00 2.10
507 531 2.168936 ACATACGCACGGGGATTCTAAA 59.831 45.455 0.00 0.00 0.00 1.85
508 532 3.199677 CATACGCACGGGGATTCTAAAA 58.800 45.455 0.00 0.00 0.00 1.52
509 533 1.734163 ACGCACGGGGATTCTAAAAG 58.266 50.000 0.00 0.00 0.00 2.27
510 534 1.276989 ACGCACGGGGATTCTAAAAGA 59.723 47.619 0.00 0.00 0.00 2.52
553 582 9.973450 CTCACAAAAGATGCTACTACAGTATAT 57.027 33.333 0.00 0.00 28.44 0.86
630 679 5.103473 TCCTAGTCAGGGATCACTCTTACAT 60.103 44.000 0.00 0.00 42.87 2.29
651 700 9.566432 TTACATTTTGTAAAATTTGAAGGCCAT 57.434 25.926 5.01 0.00 39.62 4.40
676 727 1.878953 AAGACACACCACCTAAAGCG 58.121 50.000 0.00 0.00 0.00 4.68
684 735 1.298859 CCACCTAAAGCGTGCCACTC 61.299 60.000 0.00 0.00 0.00 3.51
708 759 2.209315 CCCAGCCCAACACCCAAAG 61.209 63.158 0.00 0.00 0.00 2.77
740 791 1.767759 ACAAGACACAAAAGCAGCCT 58.232 45.000 0.00 0.00 0.00 4.58
741 792 2.930950 ACAAGACACAAAAGCAGCCTA 58.069 42.857 0.00 0.00 0.00 3.93
742 793 3.490348 ACAAGACACAAAAGCAGCCTAT 58.510 40.909 0.00 0.00 0.00 2.57
743 794 3.503748 ACAAGACACAAAAGCAGCCTATC 59.496 43.478 0.00 0.00 0.00 2.08
744 795 3.710209 AGACACAAAAGCAGCCTATCT 57.290 42.857 0.00 0.00 0.00 1.98
745 796 3.604582 AGACACAAAAGCAGCCTATCTC 58.395 45.455 0.00 0.00 0.00 2.75
746 797 3.008375 AGACACAAAAGCAGCCTATCTCA 59.992 43.478 0.00 0.00 0.00 3.27
747 798 3.077359 ACACAAAAGCAGCCTATCTCAC 58.923 45.455 0.00 0.00 0.00 3.51
748 799 3.244700 ACACAAAAGCAGCCTATCTCACT 60.245 43.478 0.00 0.00 0.00 3.41
749 800 3.755378 CACAAAAGCAGCCTATCTCACTT 59.245 43.478 0.00 0.00 0.00 3.16
750 801 4.006319 ACAAAAGCAGCCTATCTCACTTC 58.994 43.478 0.00 0.00 0.00 3.01
751 802 2.593346 AAGCAGCCTATCTCACTTCG 57.407 50.000 0.00 0.00 0.00 3.79
752 803 1.479709 AGCAGCCTATCTCACTTCGT 58.520 50.000 0.00 0.00 0.00 3.85
753 804 1.407258 AGCAGCCTATCTCACTTCGTC 59.593 52.381 0.00 0.00 0.00 4.20
754 805 1.537135 GCAGCCTATCTCACTTCGTCC 60.537 57.143 0.00 0.00 0.00 4.79
755 806 1.751351 CAGCCTATCTCACTTCGTCCA 59.249 52.381 0.00 0.00 0.00 4.02
756 807 2.363680 CAGCCTATCTCACTTCGTCCAT 59.636 50.000 0.00 0.00 0.00 3.41
757 808 2.363680 AGCCTATCTCACTTCGTCCATG 59.636 50.000 0.00 0.00 0.00 3.66
758 809 2.101582 GCCTATCTCACTTCGTCCATGT 59.898 50.000 0.00 0.00 0.00 3.21
759 810 3.318275 GCCTATCTCACTTCGTCCATGTA 59.682 47.826 0.00 0.00 0.00 2.29
760 811 4.793353 GCCTATCTCACTTCGTCCATGTAC 60.793 50.000 0.00 0.00 0.00 2.90
761 812 2.913777 TCTCACTTCGTCCATGTACG 57.086 50.000 4.18 4.18 44.19 3.67
762 813 2.156917 TCTCACTTCGTCCATGTACGT 58.843 47.619 10.78 0.00 43.31 3.57
763 814 3.337358 TCTCACTTCGTCCATGTACGTA 58.663 45.455 10.78 0.04 43.31 3.57
764 815 3.373130 TCTCACTTCGTCCATGTACGTAG 59.627 47.826 14.36 14.36 43.38 3.51
765 816 2.421073 TCACTTCGTCCATGTACGTAGG 59.579 50.000 18.82 9.84 42.45 3.18
766 817 2.163010 CACTTCGTCCATGTACGTAGGT 59.837 50.000 18.82 10.14 42.45 3.08
767 818 2.821969 ACTTCGTCCATGTACGTAGGTT 59.178 45.455 18.82 0.00 42.45 3.50
768 819 2.925578 TCGTCCATGTACGTAGGTTG 57.074 50.000 10.78 0.00 43.31 3.77
769 820 1.135315 TCGTCCATGTACGTAGGTTGC 60.135 52.381 10.78 0.00 43.31 4.17
770 821 1.403116 CGTCCATGTACGTAGGTTGCA 60.403 52.381 2.18 0.00 38.07 4.08
771 822 2.737359 CGTCCATGTACGTAGGTTGCAT 60.737 50.000 2.18 0.00 38.07 3.96
772 823 2.607635 GTCCATGTACGTAGGTTGCATG 59.392 50.000 18.08 18.08 37.71 4.06
773 824 1.330521 CCATGTACGTAGGTTGCATGC 59.669 52.381 11.82 11.82 37.18 4.06
774 825 2.006169 CATGTACGTAGGTTGCATGCA 58.994 47.619 18.46 18.46 34.21 3.96
775 826 2.394930 TGTACGTAGGTTGCATGCAT 57.605 45.000 23.37 9.62 0.00 3.96
776 827 2.276201 TGTACGTAGGTTGCATGCATC 58.724 47.619 23.37 20.66 0.00 3.91
777 828 2.093711 TGTACGTAGGTTGCATGCATCT 60.094 45.455 23.37 22.60 0.00 2.90
778 829 2.979814 ACGTAGGTTGCATGCATCTA 57.020 45.000 23.37 21.59 0.00 1.98
779 830 3.260475 ACGTAGGTTGCATGCATCTAA 57.740 42.857 23.37 10.05 0.00 2.10
780 831 3.605634 ACGTAGGTTGCATGCATCTAAA 58.394 40.909 23.37 2.36 0.00 1.85
781 832 4.006989 ACGTAGGTTGCATGCATCTAAAA 58.993 39.130 23.37 1.46 0.00 1.52
782 833 4.094887 ACGTAGGTTGCATGCATCTAAAAG 59.905 41.667 23.37 19.43 0.00 2.27
783 834 3.515330 AGGTTGCATGCATCTAAAAGC 57.485 42.857 23.37 14.90 0.00 3.51
784 835 2.827322 AGGTTGCATGCATCTAAAAGCA 59.173 40.909 23.37 0.00 45.92 3.91
785 836 3.258872 AGGTTGCATGCATCTAAAAGCAA 59.741 39.130 23.37 13.95 44.88 3.91
787 838 3.938289 TGCATGCATCTAAAAGCAACA 57.062 38.095 18.46 0.00 44.88 3.33
788 839 3.840468 TGCATGCATCTAAAAGCAACAG 58.160 40.909 18.46 0.00 44.88 3.16
789 840 2.601763 GCATGCATCTAAAAGCAACAGC 59.398 45.455 14.21 0.00 44.88 4.40
790 841 3.840468 CATGCATCTAAAAGCAACAGCA 58.160 40.909 0.00 0.00 44.88 4.41
791 842 4.239304 CATGCATCTAAAAGCAACAGCAA 58.761 39.130 0.00 0.00 44.88 3.91
792 843 4.319139 TGCATCTAAAAGCAACAGCAAA 57.681 36.364 0.00 0.00 37.90 3.68
793 844 4.885413 TGCATCTAAAAGCAACAGCAAAT 58.115 34.783 0.00 0.00 37.90 2.32
794 845 4.925054 TGCATCTAAAAGCAACAGCAAATC 59.075 37.500 0.00 0.00 37.90 2.17
795 846 5.166398 GCATCTAAAAGCAACAGCAAATCT 58.834 37.500 0.00 0.00 0.00 2.40
796 847 7.281658 TGCATCTAAAAGCAACAGCAAATCTG 61.282 38.462 0.00 0.00 41.23 2.90
797 848 6.384224 CATCTAAAAGCAACAGCAAATCTGA 58.616 36.000 0.00 0.00 45.72 3.27
798 849 5.762045 TCTAAAAGCAACAGCAAATCTGAC 58.238 37.500 0.00 0.00 45.72 3.51
799 850 2.693797 AAGCAACAGCAAATCTGACG 57.306 45.000 0.00 0.00 45.72 4.35
800 851 0.877071 AGCAACAGCAAATCTGACGG 59.123 50.000 0.00 0.00 45.72 4.79
801 852 0.593128 GCAACAGCAAATCTGACGGT 59.407 50.000 0.00 0.00 45.72 4.83
802 853 1.400242 GCAACAGCAAATCTGACGGTC 60.400 52.381 0.00 0.00 45.72 4.79
803 854 1.136252 CAACAGCAAATCTGACGGTCG 60.136 52.381 3.34 0.00 45.72 4.79
804 855 0.317160 ACAGCAAATCTGACGGTCGA 59.683 50.000 3.34 4.55 45.72 4.20
805 856 0.994995 CAGCAAATCTGACGGTCGAG 59.005 55.000 3.34 2.81 45.72 4.04
806 857 0.108615 AGCAAATCTGACGGTCGAGG 60.109 55.000 3.34 0.00 0.00 4.63
807 858 0.108804 GCAAATCTGACGGTCGAGGA 60.109 55.000 3.34 2.52 0.00 3.71
808 859 1.914634 CAAATCTGACGGTCGAGGAG 58.085 55.000 3.34 0.00 0.00 3.69
809 860 1.202582 CAAATCTGACGGTCGAGGAGT 59.797 52.381 3.34 0.00 0.00 3.85
810 861 1.096416 AATCTGACGGTCGAGGAGTC 58.904 55.000 3.34 7.63 35.61 3.36
812 863 2.745100 TGACGGTCGAGGAGTCGG 60.745 66.667 3.34 0.00 46.80 4.79
819 870 4.735132 CGAGGAGTCGGCCGCAAA 62.735 66.667 23.51 0.00 42.87 3.68
820 871 2.815647 GAGGAGTCGGCCGCAAAG 60.816 66.667 23.51 0.00 0.00 2.77
821 872 3.591254 GAGGAGTCGGCCGCAAAGT 62.591 63.158 23.51 6.26 0.00 2.66
822 873 3.119096 GGAGTCGGCCGCAAAGTC 61.119 66.667 23.51 16.00 0.00 3.01
823 874 2.048127 GAGTCGGCCGCAAAGTCT 60.048 61.111 23.51 11.14 0.00 3.24
824 875 2.048127 AGTCGGCCGCAAAGTCTC 60.048 61.111 23.51 2.93 0.00 3.36
825 876 2.357034 GTCGGCCGCAAAGTCTCA 60.357 61.111 23.51 0.00 0.00 3.27
826 877 2.048222 TCGGCCGCAAAGTCTCAG 60.048 61.111 23.51 0.00 0.00 3.35
827 878 2.357517 CGGCCGCAAAGTCTCAGT 60.358 61.111 14.67 0.00 0.00 3.41
828 879 2.383527 CGGCCGCAAAGTCTCAGTC 61.384 63.158 14.67 0.00 0.00 3.51
829 880 2.383527 GGCCGCAAAGTCTCAGTCG 61.384 63.158 0.00 0.00 0.00 4.18
830 881 1.372997 GCCGCAAAGTCTCAGTCGA 60.373 57.895 0.00 0.00 0.00 4.20
831 882 1.618640 GCCGCAAAGTCTCAGTCGAC 61.619 60.000 7.70 7.70 0.00 4.20
832 883 0.039074 CCGCAAAGTCTCAGTCGACT 60.039 55.000 13.58 13.58 45.73 4.18
833 884 1.056103 CGCAAAGTCTCAGTCGACTG 58.944 55.000 34.76 34.76 43.14 3.51
848 899 6.478588 CAGTCGACTGATTTTTAATAGCACC 58.521 40.000 36.73 0.00 46.59 5.01
849 900 5.291128 AGTCGACTGATTTTTAATAGCACCG 59.709 40.000 19.30 0.00 0.00 4.94
850 901 5.063060 GTCGACTGATTTTTAATAGCACCGT 59.937 40.000 8.70 0.00 0.00 4.83
851 902 6.254157 GTCGACTGATTTTTAATAGCACCGTA 59.746 38.462 8.70 0.00 0.00 4.02
852 903 6.812656 TCGACTGATTTTTAATAGCACCGTAA 59.187 34.615 0.00 0.00 0.00 3.18
1131 1217 2.504244 GCACCTCCGTTCGAGTCG 60.504 66.667 6.09 6.09 36.82 4.18
1380 1487 3.667497 ACTCTGCATTTCTCTCGTCAA 57.333 42.857 0.00 0.00 0.00 3.18
1412 1527 6.759497 AACCATTGTTAGGACTGCTTTATC 57.241 37.500 0.00 0.00 31.36 1.75
1432 1549 4.067972 TCTGTTCCTTATATGAACCCGC 57.932 45.455 11.19 0.00 41.08 6.13
1639 1774 7.041721 CAGTGTTGTAGAATCATTAGCTGGTA 58.958 38.462 0.00 0.00 0.00 3.25
1640 1775 7.712639 CAGTGTTGTAGAATCATTAGCTGGTAT 59.287 37.037 0.00 0.00 0.00 2.73
1662 1797 7.870445 GGTATTGCAATTTCTTTTGTCCTTGTA 59.130 33.333 18.75 0.00 0.00 2.41
1835 1992 4.666253 ACCGCAGCAGCCAACCAT 62.666 61.111 0.00 0.00 37.52 3.55
1864 2021 5.703978 TGCCATCACCGATTAATTATTGG 57.296 39.130 0.00 0.00 42.79 3.16
1903 2076 3.911868 TGTTGTGCTGCATTATGAAACC 58.088 40.909 5.27 0.00 0.00 3.27
1904 2077 3.573538 TGTTGTGCTGCATTATGAAACCT 59.426 39.130 5.27 0.00 0.00 3.50
1905 2078 4.764308 TGTTGTGCTGCATTATGAAACCTA 59.236 37.500 5.27 0.00 0.00 3.08
1906 2079 5.106197 TGTTGTGCTGCATTATGAAACCTAG 60.106 40.000 5.27 0.00 0.00 3.02
1907 2080 3.378112 TGTGCTGCATTATGAAACCTAGC 59.622 43.478 5.27 0.00 0.00 3.42
1940 2165 9.793252 CATAGGAAACACAGAAGGAAATTATTG 57.207 33.333 0.00 0.00 0.00 1.90
1946 2171 8.485578 AACACAGAAGGAAATTATTGGGTTAA 57.514 30.769 0.00 0.00 33.01 2.01
1982 2211 9.753674 AACCTACTTGATATGATTTCTTTTGGA 57.246 29.630 0.00 0.00 0.00 3.53
2019 2249 1.391485 GTCGTAGCTGCACAACATCAG 59.609 52.381 1.02 0.00 0.00 2.90
2027 2257 1.270274 TGCACAACATCAGTCATTGGC 59.730 47.619 0.00 0.00 0.00 4.52
2033 2263 3.668141 ACATCAGTCATTGGCCCAATA 57.332 42.857 9.03 0.00 32.35 1.90
2034 2264 3.979911 ACATCAGTCATTGGCCCAATAA 58.020 40.909 9.03 0.00 32.35 1.40
2060 2290 1.339055 ACGGCATGTTCTATGTGCAGT 60.339 47.619 0.00 0.00 41.28 4.40
2096 2327 7.560991 ACAGAATTCAATCAACAATGGCCTATA 59.439 33.333 8.44 0.00 0.00 1.31
2127 2390 5.762045 GAGTAATCAAAACTCTTGCTGCAA 58.238 37.500 15.16 15.16 40.21 4.08
2137 2400 3.118665 ACTCTTGCTGCAACCAAACAAAT 60.119 39.130 11.69 0.00 0.00 2.32
2252 2515 3.126831 GACACAAAGCGGATAGATCAGG 58.873 50.000 0.00 0.00 0.00 3.86
2267 2530 1.951209 TCAGGGCCTACAATGAGACA 58.049 50.000 5.28 0.00 0.00 3.41
2276 2539 4.156008 GCCTACAATGAGACAAAACGGAAT 59.844 41.667 0.00 0.00 0.00 3.01
2277 2540 5.335661 GCCTACAATGAGACAAAACGGAATT 60.336 40.000 0.00 0.00 0.00 2.17
2420 2806 5.734855 ACCAAATACGACATGTTCTATGC 57.265 39.130 0.00 0.00 0.00 3.14
2472 2858 6.540438 ACAAGAACCTAGATTGTATCCGAA 57.460 37.500 0.00 0.00 35.47 4.30
2491 2886 7.624360 TCCGAAAATAATCTTTGCTGTACAT 57.376 32.000 0.00 0.00 0.00 2.29
2545 3007 2.063156 TTTGATTGACAATGGCACGC 57.937 45.000 5.14 0.00 38.36 5.34
2828 3481 7.888021 TGTCAGTCCAGACAATTTTGGTATATT 59.112 33.333 0.00 0.00 44.92 1.28
2894 3547 6.782082 ACTCAGTCAGTTCAGCATATAAGA 57.218 37.500 0.00 0.00 26.56 2.10
3089 3770 3.256879 TCCTCAACGATATCTCTGCCATC 59.743 47.826 0.34 0.00 0.00 3.51
3126 3807 0.911769 CCCACATCTTCCTGTAGGCA 59.088 55.000 0.00 0.00 34.44 4.75
3188 3869 0.949105 GGTTCACCGCAACGATCACT 60.949 55.000 0.00 0.00 0.00 3.41
3307 3988 2.208132 ACAGATCCACTCGAGTCAGT 57.792 50.000 16.96 4.59 0.00 3.41
3369 4050 0.664761 CAGGCCACCATTAATCTGCG 59.335 55.000 5.01 0.00 0.00 5.18
3612 4293 7.020827 TCCTATCTCAAGTTTCCAGTCAATT 57.979 36.000 0.00 0.00 0.00 2.32
3650 4332 2.301870 TGACATGAGGTACTGACAACCC 59.698 50.000 0.00 0.00 41.55 4.11
3927 4609 0.755698 ACGAGACCGCCATGGATAGT 60.756 55.000 18.40 8.86 42.00 2.12
4103 4790 7.504574 TGAAAATCCTCTGATGTCCGTATAGTA 59.495 37.037 0.00 0.00 0.00 1.82
4259 4948 7.436673 CCGTTTGTGATTTTCTACATTTGGAAA 59.563 33.333 0.00 0.00 0.00 3.13
4260 4949 8.977505 CGTTTGTGATTTTCTACATTTGGAAAT 58.022 29.630 0.00 0.00 32.54 2.17
4308 4998 4.272504 CCCGCGTGTATATTCATCAAGTTT 59.727 41.667 4.92 0.00 0.00 2.66
4309 4999 5.220777 CCCGCGTGTATATTCATCAAGTTTT 60.221 40.000 4.92 0.00 0.00 2.43
4310 5000 6.255215 CCGCGTGTATATTCATCAAGTTTTT 58.745 36.000 4.92 0.00 0.00 1.94
4330 5020 4.586306 TTTTAGAAATGGAGGAGGACCC 57.414 45.455 0.00 0.00 36.73 4.46
4331 5021 2.191981 TAGAAATGGAGGAGGACCCC 57.808 55.000 0.00 0.00 36.73 4.95
4332 5022 0.121197 AGAAATGGAGGAGGACCCCA 59.879 55.000 2.29 0.00 39.52 4.96
4333 5023 0.548510 GAAATGGAGGAGGACCCCAG 59.451 60.000 2.29 0.00 38.94 4.45
4334 5024 1.575447 AAATGGAGGAGGACCCCAGC 61.575 60.000 2.29 0.00 38.94 4.85
4335 5025 4.741239 TGGAGGAGGACCCCAGCC 62.741 72.222 2.29 3.73 33.66 4.85
4336 5026 4.423209 GGAGGAGGACCCCAGCCT 62.423 72.222 2.29 0.00 38.81 4.58
4340 5030 3.791586 GAGGACCCCAGCCTCTGC 61.792 72.222 0.00 0.00 46.70 4.26
4341 5031 4.664267 AGGACCCCAGCCTCTGCA 62.664 66.667 0.00 0.00 41.13 4.41
4342 5032 3.415087 GGACCCCAGCCTCTGCAT 61.415 66.667 0.00 0.00 41.13 3.96
4343 5033 2.191641 GACCCCAGCCTCTGCATC 59.808 66.667 0.00 0.00 41.13 3.91
4389 5079 3.560453 CCTTTTGTCCCGGTTCATAAGGA 60.560 47.826 25.83 4.54 41.69 3.36
4435 5125 5.091431 CGGGACTAAAGTGTCGTTACTAAG 58.909 45.833 0.00 0.55 37.81 2.18
4579 5270 2.710902 ATCCACGCGTCAGCAGCTA 61.711 57.895 9.86 0.00 45.49 3.32
4878 5579 7.390996 ACAAGTTCTCGTATATCTATCCGACAT 59.609 37.037 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.707989 TGGTGATGGGCTGTTTTAGGA 59.292 47.619 0.00 0.00 0.00 2.94
66 71 5.505780 TCGGGTTATTTCTCATGTCCAATT 58.494 37.500 0.00 0.00 0.00 2.32
121 129 2.294233 GCAACTCCATGTCTTCAAAGCA 59.706 45.455 0.00 0.00 0.00 3.91
152 160 2.549754 CAGACCTCAACTGCGATTGTTT 59.450 45.455 0.00 0.00 0.00 2.83
157 165 2.625737 CAATCAGACCTCAACTGCGAT 58.374 47.619 0.00 0.00 35.61 4.58
159 167 0.445436 GCAATCAGACCTCAACTGCG 59.555 55.000 0.00 0.00 35.61 5.18
172 180 4.337274 TCTTAGTCGATTCGGTAGCAATCA 59.663 41.667 6.18 3.44 31.53 2.57
263 275 8.447053 CCAGTCTAAAAGAAGCTTAGATGAAAC 58.553 37.037 0.00 0.00 37.63 2.78
266 278 6.109359 GCCAGTCTAAAAGAAGCTTAGATGA 58.891 40.000 0.00 0.00 37.63 2.92
273 285 5.165961 TGTATGCCAGTCTAAAAGAAGCT 57.834 39.130 0.00 0.00 0.00 3.74
274 286 7.065803 TGTTATGTATGCCAGTCTAAAAGAAGC 59.934 37.037 0.00 0.00 0.00 3.86
295 308 9.483916 GTTTATTTAGGTTTGGCTTTGTGTTAT 57.516 29.630 0.00 0.00 0.00 1.89
366 386 2.622965 TTTTTGGAGATGCGCGTGA 58.377 47.368 6.97 0.00 0.00 4.35
417 438 7.764443 GGATGTAGTTTTTCTAGTGTAGCATCA 59.236 37.037 0.00 0.00 31.78 3.07
424 445 9.574516 AGATTTTGGATGTAGTTTTTCTAGTGT 57.425 29.630 0.00 0.00 0.00 3.55
518 547 8.317679 AGTAGCATCTTTTGTGAGTATTTCTCT 58.682 33.333 0.00 0.00 43.13 3.10
699 750 0.106918 TTTCTGTCGGCTTTGGGTGT 60.107 50.000 0.00 0.00 0.00 4.16
701 752 1.770294 TTTTTCTGTCGGCTTTGGGT 58.230 45.000 0.00 0.00 0.00 4.51
722 773 3.755378 AGATAGGCTGCTTTTGTGTCTTG 59.245 43.478 0.00 0.00 0.00 3.02
723 774 4.006319 GAGATAGGCTGCTTTTGTGTCTT 58.994 43.478 0.00 0.00 0.00 3.01
729 780 3.063180 CGAAGTGAGATAGGCTGCTTTTG 59.937 47.826 0.00 0.00 0.00 2.44
730 781 3.265791 CGAAGTGAGATAGGCTGCTTTT 58.734 45.455 0.00 0.00 0.00 2.27
747 798 3.176708 CAACCTACGTACATGGACGAAG 58.823 50.000 36.10 23.87 45.82 3.79
748 799 2.671914 GCAACCTACGTACATGGACGAA 60.672 50.000 36.10 0.00 45.82 3.85
749 800 1.135315 GCAACCTACGTACATGGACGA 60.135 52.381 36.10 18.37 45.82 4.20
751 802 2.373540 TGCAACCTACGTACATGGAC 57.626 50.000 6.37 0.00 0.00 4.02
752 803 2.899976 CATGCAACCTACGTACATGGA 58.100 47.619 12.83 5.12 34.95 3.41
753 804 1.330521 GCATGCAACCTACGTACATGG 59.669 52.381 14.21 10.49 37.25 3.66
754 805 2.006169 TGCATGCAACCTACGTACATG 58.994 47.619 20.30 15.23 38.66 3.21
755 806 2.394930 TGCATGCAACCTACGTACAT 57.605 45.000 20.30 0.00 0.00 2.29
756 807 2.093711 AGATGCATGCAACCTACGTACA 60.094 45.455 26.68 0.00 0.00 2.90
757 808 2.550978 AGATGCATGCAACCTACGTAC 58.449 47.619 26.68 7.63 0.00 3.67
758 809 2.979814 AGATGCATGCAACCTACGTA 57.020 45.000 26.68 0.00 0.00 3.57
759 810 2.979814 TAGATGCATGCAACCTACGT 57.020 45.000 26.68 5.83 0.00 3.57
760 811 4.591202 CTTTTAGATGCATGCAACCTACG 58.409 43.478 26.68 14.35 0.00 3.51
761 812 4.142403 TGCTTTTAGATGCATGCAACCTAC 60.142 41.667 26.68 15.60 33.94 3.18
762 813 4.015764 TGCTTTTAGATGCATGCAACCTA 58.984 39.130 26.68 23.70 33.94 3.08
763 814 2.827322 TGCTTTTAGATGCATGCAACCT 59.173 40.909 26.68 24.72 33.94 3.50
764 815 3.235157 TGCTTTTAGATGCATGCAACC 57.765 42.857 26.68 19.07 33.94 3.77
766 817 4.239304 CTGTTGCTTTTAGATGCATGCAA 58.761 39.130 26.68 13.95 39.07 4.08
767 818 3.840468 CTGTTGCTTTTAGATGCATGCA 58.160 40.909 25.04 25.04 39.07 3.96
768 819 2.601763 GCTGTTGCTTTTAGATGCATGC 59.398 45.455 11.82 11.82 39.07 4.06
769 820 3.840468 TGCTGTTGCTTTTAGATGCATG 58.160 40.909 2.46 0.00 39.07 4.06
770 821 4.524316 TTGCTGTTGCTTTTAGATGCAT 57.476 36.364 0.00 0.00 39.07 3.96
771 822 4.319139 TTTGCTGTTGCTTTTAGATGCA 57.681 36.364 0.00 0.00 40.48 3.96
772 823 5.061808 CAGATTTGCTGTTGCTTTTAGATGC 59.938 40.000 0.00 0.00 39.85 3.91
773 824 6.307318 GTCAGATTTGCTGTTGCTTTTAGATG 59.693 38.462 0.00 0.00 45.14 2.90
774 825 6.385033 GTCAGATTTGCTGTTGCTTTTAGAT 58.615 36.000 0.00 0.00 45.14 1.98
775 826 5.560760 CGTCAGATTTGCTGTTGCTTTTAGA 60.561 40.000 0.00 0.00 45.14 2.10
776 827 4.614284 CGTCAGATTTGCTGTTGCTTTTAG 59.386 41.667 0.00 0.00 45.14 1.85
777 828 4.536065 CGTCAGATTTGCTGTTGCTTTTA 58.464 39.130 0.00 0.00 45.14 1.52
778 829 3.374745 CGTCAGATTTGCTGTTGCTTTT 58.625 40.909 0.00 0.00 45.14 2.27
779 830 2.287788 CCGTCAGATTTGCTGTTGCTTT 60.288 45.455 0.00 0.00 45.14 3.51
780 831 1.267806 CCGTCAGATTTGCTGTTGCTT 59.732 47.619 0.00 0.00 45.14 3.91
781 832 0.877071 CCGTCAGATTTGCTGTTGCT 59.123 50.000 0.00 0.00 45.14 3.91
782 833 0.593128 ACCGTCAGATTTGCTGTTGC 59.407 50.000 0.00 0.00 45.14 4.17
783 834 1.136252 CGACCGTCAGATTTGCTGTTG 60.136 52.381 0.00 0.00 45.14 3.33
784 835 1.148310 CGACCGTCAGATTTGCTGTT 58.852 50.000 0.00 0.00 45.14 3.16
785 836 0.317160 TCGACCGTCAGATTTGCTGT 59.683 50.000 0.00 0.00 45.14 4.40
786 837 0.994995 CTCGACCGTCAGATTTGCTG 59.005 55.000 0.00 0.00 46.31 4.41
787 838 0.108615 CCTCGACCGTCAGATTTGCT 60.109 55.000 0.00 0.00 0.00 3.91
788 839 0.108804 TCCTCGACCGTCAGATTTGC 60.109 55.000 0.00 0.00 0.00 3.68
789 840 1.202582 ACTCCTCGACCGTCAGATTTG 59.797 52.381 0.00 0.00 0.00 2.32
790 841 1.473278 GACTCCTCGACCGTCAGATTT 59.527 52.381 0.00 0.00 0.00 2.17
791 842 1.096416 GACTCCTCGACCGTCAGATT 58.904 55.000 0.00 0.00 0.00 2.40
792 843 1.090625 CGACTCCTCGACCGTCAGAT 61.091 60.000 0.00 0.00 43.06 2.90
793 844 1.740664 CGACTCCTCGACCGTCAGA 60.741 63.158 0.00 0.00 43.06 3.27
794 845 2.751913 CCGACTCCTCGACCGTCAG 61.752 68.421 0.00 0.00 43.06 3.51
795 846 2.745100 CCGACTCCTCGACCGTCA 60.745 66.667 0.00 0.00 43.06 4.35
796 847 4.176851 GCCGACTCCTCGACCGTC 62.177 72.222 0.00 0.00 43.06 4.79
802 853 4.735132 TTTGCGGCCGACTCCTCG 62.735 66.667 33.48 0.00 39.83 4.63
803 854 2.815647 CTTTGCGGCCGACTCCTC 60.816 66.667 33.48 10.79 0.00 3.71
804 855 3.591254 GACTTTGCGGCCGACTCCT 62.591 63.158 33.48 7.12 0.00 3.69
805 856 3.119096 GACTTTGCGGCCGACTCC 61.119 66.667 33.48 12.13 0.00 3.85
806 857 2.048127 AGACTTTGCGGCCGACTC 60.048 61.111 33.48 12.57 0.00 3.36
807 858 2.048127 GAGACTTTGCGGCCGACT 60.048 61.111 33.48 16.55 0.00 4.18
808 859 2.357034 TGAGACTTTGCGGCCGAC 60.357 61.111 33.48 21.14 0.00 4.79
809 860 2.048222 CTGAGACTTTGCGGCCGA 60.048 61.111 33.48 11.82 0.00 5.54
810 861 2.357517 ACTGAGACTTTGCGGCCG 60.358 61.111 24.05 24.05 0.00 6.13
811 862 2.383527 CGACTGAGACTTTGCGGCC 61.384 63.158 0.00 0.00 0.00 6.13
812 863 1.372997 TCGACTGAGACTTTGCGGC 60.373 57.895 0.00 0.00 0.00 6.53
813 864 2.435741 GTCGACTGAGACTTTGCGG 58.564 57.895 8.70 0.00 38.09 5.69
824 875 6.478588 GGTGCTATTAAAAATCAGTCGACTG 58.521 40.000 34.76 34.76 45.08 3.51
825 876 5.291128 CGGTGCTATTAAAAATCAGTCGACT 59.709 40.000 13.58 13.58 0.00 4.18
826 877 5.063060 ACGGTGCTATTAAAAATCAGTCGAC 59.937 40.000 7.70 7.70 0.00 4.20
827 878 5.172934 ACGGTGCTATTAAAAATCAGTCGA 58.827 37.500 0.00 0.00 0.00 4.20
828 879 5.464965 ACGGTGCTATTAAAAATCAGTCG 57.535 39.130 0.00 0.00 0.00 4.18
829 880 9.615295 TTTTTACGGTGCTATTAAAAATCAGTC 57.385 29.630 0.00 0.00 32.40 3.51
1412 1527 3.804036 TGCGGGTTCATATAAGGAACAG 58.196 45.455 17.40 13.03 44.96 3.16
1432 1549 9.880157 AAGAAAAAGAATTATGTTGGGATCATG 57.120 29.630 0.00 0.00 0.00 3.07
1502 1632 9.695526 TCCTGAAAAAGAATTAACATTCACATG 57.304 29.630 0.00 0.00 41.37 3.21
1639 1774 8.907222 ATTACAAGGACAAAAGAAATTGCAAT 57.093 26.923 5.99 5.99 33.52 3.56
1640 1775 9.255304 GTATTACAAGGACAAAAGAAATTGCAA 57.745 29.630 0.00 0.00 33.52 4.08
1662 1797 5.304686 TCACAAGGTGACCTTTCAGTATT 57.695 39.130 15.48 0.00 41.69 1.89
1835 1992 9.733556 ATAATTAATCGGTGATGGCAATAGTTA 57.266 29.630 0.00 0.00 0.00 2.24
1864 2021 6.290799 GCACAACAAACAAACAAACAAACAAC 60.291 34.615 0.00 0.00 0.00 3.32
1903 2076 5.730550 TGTGTTTCCTATGTGGTTAGCTAG 58.269 41.667 0.00 0.00 37.07 3.42
1904 2077 5.482526 TCTGTGTTTCCTATGTGGTTAGCTA 59.517 40.000 0.00 0.00 37.07 3.32
1905 2078 4.286032 TCTGTGTTTCCTATGTGGTTAGCT 59.714 41.667 0.00 0.00 37.07 3.32
1906 2079 4.575885 TCTGTGTTTCCTATGTGGTTAGC 58.424 43.478 0.00 0.00 37.07 3.09
1907 2080 5.643777 CCTTCTGTGTTTCCTATGTGGTTAG 59.356 44.000 0.00 0.00 37.07 2.34
2034 2264 5.105957 TGCACATAGAACATGCCGTATTTTT 60.106 36.000 0.00 0.00 38.63 1.94
2123 2386 3.132646 AGCAAGAGATTTGTTTGGTTGCA 59.867 39.130 6.89 0.00 40.97 4.08
2127 2390 3.953612 TGACAGCAAGAGATTTGTTTGGT 59.046 39.130 0.00 0.00 33.25 3.67
2137 2400 3.953712 TTAATCGGTGACAGCAAGAGA 57.046 42.857 5.35 0.00 0.00 3.10
2252 2515 2.161609 CCGTTTTGTCTCATTGTAGGCC 59.838 50.000 0.00 0.00 0.00 5.19
2299 2685 1.828979 TTTCCAGAATACGGGCCAAC 58.171 50.000 4.39 0.00 0.00 3.77
2472 2858 7.895759 ACACCAATGTACAGCAAAGATTATTT 58.104 30.769 0.33 0.00 37.26 1.40
2545 3007 4.263572 TGCCCAAGGACCACCGTG 62.264 66.667 0.00 0.00 43.45 4.94
2790 3443 3.554934 TGGACTGACAAAAGAGCATTGT 58.445 40.909 0.00 0.00 43.37 2.71
3089 3770 1.067354 GGGAAGACATGCAAGCCAAAG 60.067 52.381 0.00 0.00 0.00 2.77
3290 3971 2.520069 ACAACTGACTCGAGTGGATCT 58.480 47.619 25.58 0.00 0.00 2.75
3307 3988 8.192110 TGTGCTAGACATATTAATCACGTACAA 58.808 33.333 0.00 0.00 0.00 2.41
3369 4050 2.307686 TCACTTCCCAGGGGTTTCATAC 59.692 50.000 5.33 0.00 36.47 2.39
3498 4179 6.708457 TCATCAGTCATGCTCCGAAAGGTC 62.708 50.000 0.00 0.00 41.77 3.85
3612 4293 3.459145 TGTCAAATGGTCGACGAAAAGA 58.541 40.909 9.92 2.00 34.78 2.52
3650 4332 0.103937 GGTCTTCCAGAGAGGCATCG 59.896 60.000 0.00 0.00 34.31 3.84
3730 4412 2.452505 GGTGGCTGGGTAATGCTTTAA 58.547 47.619 0.00 0.00 0.00 1.52
4208 4895 7.148457 GGCTACACTTAAATTACTGAACTGTCC 60.148 40.741 0.00 0.00 0.00 4.02
4308 4998 4.264217 GGGGTCCTCCTCCATTTCTAAAAA 60.264 45.833 0.00 0.00 35.33 1.94
4309 4999 3.268595 GGGGTCCTCCTCCATTTCTAAAA 59.731 47.826 0.00 0.00 35.33 1.52
4310 5000 2.850568 GGGGTCCTCCTCCATTTCTAAA 59.149 50.000 0.00 0.00 35.33 1.85
4311 5001 2.226039 TGGGGTCCTCCTCCATTTCTAA 60.226 50.000 0.00 0.00 32.02 2.10
4312 5002 1.368203 TGGGGTCCTCCTCCATTTCTA 59.632 52.381 0.00 0.00 32.02 2.10
4313 5003 0.121197 TGGGGTCCTCCTCCATTTCT 59.879 55.000 0.00 0.00 32.02 2.52
4314 5004 0.548510 CTGGGGTCCTCCTCCATTTC 59.451 60.000 0.00 0.00 34.94 2.17
4315 5005 1.575447 GCTGGGGTCCTCCTCCATTT 61.575 60.000 0.00 0.00 34.94 2.32
4316 5006 2.003548 GCTGGGGTCCTCCTCCATT 61.004 63.158 0.00 0.00 34.94 3.16
4317 5007 2.367512 GCTGGGGTCCTCCTCCAT 60.368 66.667 0.00 0.00 34.94 3.41
4318 5008 4.741239 GGCTGGGGTCCTCCTCCA 62.741 72.222 0.00 0.00 34.50 3.86
4319 5009 4.423209 AGGCTGGGGTCCTCCTCC 62.423 72.222 0.00 0.00 32.02 4.30
4320 5010 2.766229 GAGGCTGGGGTCCTCCTC 60.766 72.222 0.00 8.98 43.32 3.71
4324 5014 3.958629 ATGCAGAGGCTGGGGTCCT 62.959 63.158 0.00 0.00 41.91 3.85
4325 5015 3.412624 GATGCAGAGGCTGGGGTCC 62.413 68.421 0.00 0.00 41.91 4.46
4326 5016 2.191641 GATGCAGAGGCTGGGGTC 59.808 66.667 0.00 0.00 41.91 4.46
4327 5017 2.285969 AGATGCAGAGGCTGGGGT 60.286 61.111 0.00 0.00 41.91 4.95
4328 5018 2.192443 CAGATGCAGAGGCTGGGG 59.808 66.667 0.00 0.00 41.91 4.96
4329 5019 2.192443 CCAGATGCAGAGGCTGGG 59.808 66.667 15.93 0.00 44.24 4.45
4331 5021 3.008141 CATCCAGATGCAGAGGCTG 57.992 57.895 0.00 0.00 41.91 4.85
4340 5030 6.259608 CCTTTTTCTACTAGTGCATCCAGATG 59.740 42.308 5.39 3.17 41.60 2.90
4341 5031 6.352516 CCTTTTTCTACTAGTGCATCCAGAT 58.647 40.000 5.39 0.00 0.00 2.90
4342 5032 5.338381 CCCTTTTTCTACTAGTGCATCCAGA 60.338 44.000 5.39 0.00 0.00 3.86
4343 5033 4.878397 CCCTTTTTCTACTAGTGCATCCAG 59.122 45.833 5.39 0.00 0.00 3.86
4348 5038 2.642807 AGGCCCTTTTTCTACTAGTGCA 59.357 45.455 5.39 0.00 0.00 4.57
4389 5079 0.981943 CCAGAACCGGGACTAAAGGT 59.018 55.000 6.32 0.00 40.50 3.50


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

AutoCloner maintained by Alex Coulton.