Multiple sequence alignment - TraesCS2D01G474200

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 TraesCS2D01G474200 chr2D 100.000 4988 0 0 1 4988 577439631 577444618 0.000000e+00 9212.0
1 TraesCS2D01G474200 chr2D 93.007 1287 66 12 2520 3790 577580507 577579229 0.000000e+00 1857.0
2 TraesCS2D01G474200 chr2D 90.145 1238 104 9 1212 2442 577581729 577580503 0.000000e+00 1594.0
3 TraesCS2D01G474200 chr2D 87.031 1172 116 16 1212 2362 577802661 577801505 0.000000e+00 1290.0
4 TraesCS2D01G474200 chr2D 85.875 1246 112 30 2496 3707 577801375 577800160 0.000000e+00 1267.0
5 TraesCS2D01G474200 chr2D 85.497 1186 129 18 1186 2347 577536378 577537544 0.000000e+00 1197.0
6 TraesCS2D01G474200 chr2D 87.790 647 66 10 3129 3770 577537967 577538605 0.000000e+00 745.0
7 TraesCS2D01G474200 chr2D 79.903 826 137 18 65 865 43976896 43977717 3.350000e-161 579.0
8 TraesCS2D01G474200 chr2D 80.664 693 83 30 3114 3787 578325205 578325865 1.610000e-134 490.0
9 TraesCS2D01G474200 chr2D 79.341 668 89 24 4341 4988 577799322 577798684 1.660000e-114 424.0
10 TraesCS2D01G474200 chr2D 83.797 395 31 17 3707 4093 577800048 577799679 1.330000e-90 344.0
11 TraesCS2D01G474200 chr2D 83.083 266 32 7 4096 4348 577799621 577799356 3.880000e-56 230.0
12 TraesCS2D01G474200 chr2D 86.124 209 7 14 1025 1225 577581967 577581773 6.550000e-49 206.0
13 TraesCS2D01G474200 chr2D 86.905 168 10 4 1064 1228 577802859 577802701 1.430000e-40 178.0
14 TraesCS2D01G474200 chr2D 90.476 126 9 3 1106 1228 578040837 578040962 4.000000e-36 163.0
15 TraesCS2D01G474200 chr2D 87.903 124 14 1 1103 1226 578307448 578307570 1.450000e-30 145.0
16 TraesCS2D01G474200 chr2D 87.200 125 13 3 1107 1228 577536242 577536366 6.730000e-29 139.0
17 TraesCS2D01G474200 chr2A 87.891 3865 290 63 1212 4988 715951039 715947265 0.000000e+00 4381.0
18 TraesCS2D01G474200 chr2A 94.268 785 33 6 3013 3790 715890393 715891172 0.000000e+00 1190.0
19 TraesCS2D01G474200 chr2A 85.677 1159 127 16 1212 2347 715917786 715916644 0.000000e+00 1184.0
20 TraesCS2D01G474200 chr2A 87.730 978 62 29 2078 3011 715887428 715888391 0.000000e+00 1088.0
21 TraesCS2D01G474200 chr2A 88.621 870 91 5 1186 2051 715880785 715881650 0.000000e+00 1051.0
22 TraesCS2D01G474200 chr2A 79.224 1237 204 31 1212 2409 715967017 715965795 0.000000e+00 811.0
23 TraesCS2D01G474200 chr2A 87.558 651 67 11 3129 3770 715916251 715915606 0.000000e+00 741.0
24 TraesCS2D01G474200 chr2A 84.971 692 51 26 2078 2730 715881650 715882327 0.000000e+00 652.0
25 TraesCS2D01G474200 chr2A 80.975 636 111 8 92 720 62471959 62472591 3.470000e-136 496.0
26 TraesCS2D01G474200 chr2A 79.006 362 35 15 883 1228 715951415 715951079 5.060000e-50 209.0
27 TraesCS2D01G474200 chr2A 91.803 122 8 2 1106 1225 715880648 715880769 8.590000e-38 169.0
28 TraesCS2D01G474200 chr2A 90.000 60 6 0 4534 4593 715962708 715962649 1.490000e-10 78.7
29 TraesCS2D01G474200 chr2B 89.805 2668 177 53 1186 3790 695107013 695109648 0.000000e+00 3332.0
30 TraesCS2D01G474200 chr2B 91.035 1372 99 14 1212 2577 695379797 695378444 0.000000e+00 1831.0
31 TraesCS2D01G474200 chr2B 87.910 1158 88 28 3863 4982 695377369 695376226 0.000000e+00 1315.0
32 TraesCS2D01G474200 chr2B 85.370 1162 127 20 1212 2347 695171932 695170788 0.000000e+00 1164.0
33 TraesCS2D01G474200 chr2B 81.655 1172 174 24 1217 2354 695508336 695509500 0.000000e+00 935.0
34 TraesCS2D01G474200 chr2B 79.260 1244 197 43 1212 2411 695439725 695438499 0.000000e+00 811.0
35 TraesCS2D01G474200 chr2B 88.080 646 66 9 3129 3770 695170363 695169725 0.000000e+00 756.0
36 TraesCS2D01G474200 chr2B 88.511 618 49 12 2573 3170 695378393 695377778 0.000000e+00 728.0
37 TraesCS2D01G474200 chr2B 83.141 694 77 21 3069 3730 695410486 695409801 9.240000e-167 597.0
38 TraesCS2D01G474200 chr2B 81.923 697 82 22 3069 3749 695437173 695436505 2.620000e-152 549.0
39 TraesCS2D01G474200 chr2B 90.769 390 30 3 3169 3558 695377748 695377365 2.660000e-142 516.0
40 TraesCS2D01G474200 chr2B 80.075 532 75 22 1900 2411 695412333 695411813 2.840000e-97 366.0
41 TraesCS2D01G474200 chr2B 85.922 206 10 10 1025 1225 695106806 695106997 8.470000e-48 202.0
42 TraesCS2D01G474200 chr2B 85.030 167 11 3 1064 1229 695379996 695379843 1.860000e-34 158.0
43 TraesCS2D01G474200 chr2B 87.705 122 12 3 1110 1228 695172093 695171972 6.730000e-29 139.0
44 TraesCS2D01G474200 chr2B 89.362 94 9 1 4364 4457 695435522 695435430 3.150000e-22 117.0
45 TraesCS2D01G474200 chr6D 79.719 853 142 21 32 865 410410366 410409526 5.560000e-164 588.0
46 TraesCS2D01G474200 chr5B 85.152 559 77 6 1 555 256050792 256051348 7.250000e-158 568.0
47 TraesCS2D01G474200 chr5A 83.273 556 91 2 1 555 309959747 309960301 1.240000e-140 510.0
48 TraesCS2D01G474200 chr5A 82.554 556 87 7 8 560 664886418 664886966 9.710000e-132 481.0
49 TraesCS2D01G474200 chr5A 82.194 556 89 7 8 560 666135448 666134900 2.100000e-128 470.0
50 TraesCS2D01G474200 chr5A 80.817 563 98 7 1 560 496332213 496332768 2.760000e-117 433.0
51 TraesCS2D01G474200 chr5A 87.500 328 35 5 542 865 496332786 496333111 1.700000e-99 374.0
52 TraesCS2D01G474200 chr5A 93.023 43 2 1 2421 2463 46587508 46587467 1.500000e-05 62.1
53 TraesCS2D01G474200 chr3A 82.734 556 86 7 8 560 80079999 80080547 2.090000e-133 486.0
54 TraesCS2D01G474200 chr3A 87.500 328 35 5 542 865 80080565 80080890 1.700000e-99 374.0
55 TraesCS2D01G474200 chr3B 81.800 511 90 3 341 848 523274470 523274980 4.620000e-115 425.0
56 TraesCS2D01G474200 chr3B 97.436 39 1 0 2425 2463 637088535 637088497 3.220000e-07 67.6
57 TraesCS2D01G474200 chr3D 76.359 791 144 24 91 848 572184452 572183672 7.830000e-103 385.0
58 TraesCS2D01G474200 chr5D 87.937 315 32 5 555 865 218563048 218562736 2.840000e-97 366.0
59 TraesCS2D01G474200 chr5D 95.122 41 2 0 2425 2465 497870715 497870755 1.160000e-06 65.8
60 TraesCS2D01G474200 chr7A 86.687 323 35 7 548 865 653010386 653010705 7.940000e-93 351.0
61 TraesCS2D01G474200 chr1D 87.025 316 33 5 555 866 7401557 7401868 2.860000e-92 350.0
62 TraesCS2D01G474200 chr4B 97.297 37 1 0 2425 2461 525844418 525844454 4.170000e-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 TraesCS2D01G474200 chr2D 577439631 577444618 4987 False 9212.000000 9212 100.000000 1 4988 1 chr2D.!!$F2 4987
1 TraesCS2D01G474200 chr2D 577579229 577581967 2738 True 1219.000000 1857 89.758667 1025 3790 3 chr2D.!!$R1 2765
2 TraesCS2D01G474200 chr2D 577536242 577538605 2363 False 693.666667 1197 86.829000 1107 3770 3 chr2D.!!$F6 2663
3 TraesCS2D01G474200 chr2D 577798684 577802859 4175 True 622.166667 1290 84.338667 1064 4988 6 chr2D.!!$R2 3924
4 TraesCS2D01G474200 chr2D 43976896 43977717 821 False 579.000000 579 79.903000 65 865 1 chr2D.!!$F1 800
5 TraesCS2D01G474200 chr2D 578325205 578325865 660 False 490.000000 490 80.664000 3114 3787 1 chr2D.!!$F5 673
6 TraesCS2D01G474200 chr2A 715947265 715951415 4150 True 2295.000000 4381 83.448500 883 4988 2 chr2A.!!$R2 4105
7 TraesCS2D01G474200 chr2A 715887428 715891172 3744 False 1139.000000 1190 90.999000 2078 3790 2 chr2A.!!$F3 1712
8 TraesCS2D01G474200 chr2A 715915606 715917786 2180 True 962.500000 1184 86.617500 1212 3770 2 chr2A.!!$R1 2558
9 TraesCS2D01G474200 chr2A 715880648 715882327 1679 False 624.000000 1051 88.465000 1106 2730 3 chr2A.!!$F2 1624
10 TraesCS2D01G474200 chr2A 62471959 62472591 632 False 496.000000 496 80.975000 92 720 1 chr2A.!!$F1 628
11 TraesCS2D01G474200 chr2A 715962649 715967017 4368 True 444.850000 811 84.612000 1212 4593 2 chr2A.!!$R3 3381
12 TraesCS2D01G474200 chr2B 695106806 695109648 2842 False 1767.000000 3332 87.863500 1025 3790 2 chr2B.!!$F2 2765
13 TraesCS2D01G474200 chr2B 695508336 695509500 1164 False 935.000000 935 81.655000 1217 2354 1 chr2B.!!$F1 1137
14 TraesCS2D01G474200 chr2B 695376226 695379996 3770 True 909.600000 1831 88.651000 1064 4982 5 chr2B.!!$R2 3918
15 TraesCS2D01G474200 chr2B 695169725 695172093 2368 True 686.333333 1164 87.051667 1110 3770 3 chr2B.!!$R1 2660
16 TraesCS2D01G474200 chr2B 695435430 695439725 4295 True 492.333333 811 83.515000 1212 4457 3 chr2B.!!$R4 3245
17 TraesCS2D01G474200 chr2B 695409801 695412333 2532 True 481.500000 597 81.608000 1900 3730 2 chr2B.!!$R3 1830
18 TraesCS2D01G474200 chr6D 410409526 410410366 840 True 588.000000 588 79.719000 32 865 1 chr6D.!!$R1 833
19 TraesCS2D01G474200 chr5B 256050792 256051348 556 False 568.000000 568 85.152000 1 555 1 chr5B.!!$F1 554
20 TraesCS2D01G474200 chr5A 309959747 309960301 554 False 510.000000 510 83.273000 1 555 1 chr5A.!!$F1 554
21 TraesCS2D01G474200 chr5A 664886418 664886966 548 False 481.000000 481 82.554000 8 560 1 chr5A.!!$F2 552
22 TraesCS2D01G474200 chr5A 666134900 666135448 548 True 470.000000 470 82.194000 8 560 1 chr5A.!!$R2 552
23 TraesCS2D01G474200 chr5A 496332213 496333111 898 False 403.500000 433 84.158500 1 865 2 chr5A.!!$F3 864
24 TraesCS2D01G474200 chr3A 80079999 80080890 891 False 430.000000 486 85.117000 8 865 2 chr3A.!!$F1 857
25 TraesCS2D01G474200 chr3B 523274470 523274980 510 False 425.000000 425 81.800000 341 848 1 chr3B.!!$F1 507
26 TraesCS2D01G474200 chr3D 572183672 572184452 780 True 385.000000 385 76.359000 91 848 1 chr3D.!!$R1 757

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
482 486 0.106819 GTACCCGGAGCTAGTGGAGA 60.107 60.0 0.73 0.00 0.00 3.71 F
1342 1532 0.387367 CCTCCAAGACGACGACACTG 60.387 60.0 0.00 0.00 0.00 3.66 F
1656 1861 0.526310 CAGAGATTGCGACGCTGCTA 60.526 55.0 22.08 4.22 35.36 3.49 F
3033 6058 0.108329 AGCCATCCGTTAAGTCCGTG 60.108 55.0 0.00 0.00 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1378 1574 0.394216 ATGCAGCCGCCATTGTAGAA 60.394 50.0 0.0 0.0 37.32 2.10 R
2362 2611 0.876399 GCTAGCTCCTCTACTACGGC 59.124 60.0 7.7 0.0 0.00 5.68 R
3508 6712 2.165234 TCTTCTCATCCTCAGCGTCAAG 59.835 50.0 0.0 0.0 0.00 3.02 R
4168 8003 0.378610 TGACGCACATTTTGTCGCAA 59.621 45.0 0.0 0.0 35.40 4.85 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
30 32 4.394712 GCTGCCGCCACACCTACT 62.395 66.667 0.00 0.00 0.00 2.57
38 40 1.812686 GCCACACCTACTGGTCGTCA 61.813 60.000 0.00 0.00 46.60 4.35
44 46 1.663379 CCTACTGGTCGTCATCCGCA 61.663 60.000 0.00 0.00 36.19 5.69
45 47 0.172578 CTACTGGTCGTCATCCGCAA 59.827 55.000 0.00 0.00 36.19 4.85
135 137 4.824515 CGGACCTCTCTCCGCCCT 62.825 72.222 0.00 0.00 46.47 5.19
171 173 0.321671 CTACATGGGTATCCGGCAGG 59.678 60.000 0.00 0.00 39.46 4.85
184 186 3.672503 GCAGGGGTTGTGGGGGAT 61.673 66.667 0.00 0.00 0.00 3.85
209 211 2.433664 GCCGAAATCACCGACCGT 60.434 61.111 0.00 0.00 0.00 4.83
238 240 1.153823 CGTAGAAGTGGGTCGGCTG 60.154 63.158 0.00 0.00 0.00 4.85
273 275 1.222115 GCTCGCGACCATGGAATACC 61.222 60.000 21.47 0.63 0.00 2.73
324 326 1.429423 GCGAGGCTCAATTTTCCCG 59.571 57.895 15.95 0.00 0.00 5.14
332 334 0.250553 TCAATTTTCCCGTCGGCACT 60.251 50.000 5.50 0.00 0.00 4.40
334 336 0.250553 AATTTTCCCGTCGGCACTCA 60.251 50.000 5.50 0.00 0.00 3.41
339 341 2.501128 CCGTCGGCACTCATCCAT 59.499 61.111 0.00 0.00 0.00 3.41
352 355 0.249489 CATCCATTCGACCTCGTCCC 60.249 60.000 0.00 0.00 40.80 4.46
388 391 3.469970 TCCGCTCGGATGGCATGT 61.470 61.111 3.81 0.00 39.76 3.21
395 398 0.977627 TCGGATGGCATGTGAGGACT 60.978 55.000 3.81 0.00 0.00 3.85
482 486 0.106819 GTACCCGGAGCTAGTGGAGA 60.107 60.000 0.73 0.00 0.00 3.71
487 492 1.030488 CGGAGCTAGTGGAGACGGAA 61.030 60.000 0.00 0.00 0.00 4.30
562 576 3.944233 AACAACGACGGCGGCAAC 61.944 61.111 18.49 0.52 43.17 4.17
608 664 4.373116 GCGTCTTCCCCAGCGACA 62.373 66.667 0.00 0.00 0.00 4.35
611 667 1.070786 GTCTTCCCCAGCGACAACA 59.929 57.895 0.00 0.00 0.00 3.33
682 738 1.479709 AGGATTGACTCGACCTCCAG 58.520 55.000 0.00 0.00 0.00 3.86
701 768 2.157085 CAGTTCGGCCGAAAGTAGTTTC 59.843 50.000 40.13 24.89 39.04 2.78
764 845 5.986741 TGCGAGAACTTTATGTGTTGAACTA 59.013 36.000 0.00 0.00 0.00 2.24
813 895 7.474398 TTCAAATTTGATTGAATTCGTGCAA 57.526 28.000 21.10 2.09 42.68 4.08
814 896 7.474398 TCAAATTTGATTGAATTCGTGCAAA 57.526 28.000 16.91 16.51 36.42 3.68
815 897 8.085720 TCAAATTTGATTGAATTCGTGCAAAT 57.914 26.923 16.91 18.55 36.42 2.32
816 898 8.557864 TCAAATTTGATTGAATTCGTGCAAATT 58.442 25.926 24.19 24.19 43.61 1.82
817 899 9.808808 CAAATTTGATTGAATTCGTGCAAATTA 57.191 25.926 26.98 9.29 42.00 1.40
821 903 9.808808 TTTGATTGAATTCGTGCAAATTATTTG 57.191 25.926 12.84 12.84 43.44 2.32
822 904 8.531622 TGATTGAATTCGTGCAAATTATTTGT 57.468 26.923 17.51 0.00 42.56 2.83
823 905 9.631452 TGATTGAATTCGTGCAAATTATTTGTA 57.369 25.926 17.51 11.45 42.56 2.41
834 916 8.335532 TGCAAATTATTTGTACTCAGCTAACT 57.664 30.769 17.51 0.00 42.56 2.24
835 917 8.792633 TGCAAATTATTTGTACTCAGCTAACTT 58.207 29.630 17.51 0.00 42.56 2.66
836 918 9.626045 GCAAATTATTTGTACTCAGCTAACTTT 57.374 29.630 17.51 0.00 42.56 2.66
840 922 9.614792 ATTATTTGTACTCAGCTAACTTTAGGG 57.385 33.333 0.00 0.00 0.00 3.53
841 923 5.416271 TTGTACTCAGCTAACTTTAGGGG 57.584 43.478 0.00 0.00 0.00 4.79
842 924 4.680407 TGTACTCAGCTAACTTTAGGGGA 58.320 43.478 0.00 0.00 0.00 4.81
843 925 5.278061 TGTACTCAGCTAACTTTAGGGGAT 58.722 41.667 0.00 0.00 0.00 3.85
844 926 5.363005 TGTACTCAGCTAACTTTAGGGGATC 59.637 44.000 0.00 0.00 0.00 3.36
845 927 3.385111 ACTCAGCTAACTTTAGGGGATCG 59.615 47.826 0.00 0.00 0.00 3.69
846 928 2.698797 TCAGCTAACTTTAGGGGATCGG 59.301 50.000 0.00 0.00 0.00 4.18
847 929 1.416772 AGCTAACTTTAGGGGATCGGC 59.583 52.381 0.00 0.00 0.00 5.54
848 930 1.872653 GCTAACTTTAGGGGATCGGCG 60.873 57.143 0.00 0.00 0.00 6.46
849 931 0.754472 TAACTTTAGGGGATCGGCGG 59.246 55.000 7.21 0.00 0.00 6.13
850 932 1.269703 AACTTTAGGGGATCGGCGGT 61.270 55.000 7.21 0.00 0.00 5.68
851 933 1.227556 CTTTAGGGGATCGGCGGTG 60.228 63.158 7.21 0.00 0.00 4.94
852 934 3.394635 TTTAGGGGATCGGCGGTGC 62.395 63.158 7.21 4.55 0.00 5.01
862 944 4.413800 GGCGGTGCGGCGAAATTT 62.414 61.111 12.98 0.00 43.33 1.82
863 945 2.430075 GCGGTGCGGCGAAATTTT 60.430 55.556 12.98 0.00 0.00 1.82
864 946 1.154188 GCGGTGCGGCGAAATTTTA 60.154 52.632 12.98 0.00 0.00 1.52
865 947 0.729816 GCGGTGCGGCGAAATTTTAA 60.730 50.000 12.98 0.00 0.00 1.52
866 948 1.687628 CGGTGCGGCGAAATTTTAAA 58.312 45.000 12.98 0.00 0.00 1.52
867 949 1.646726 CGGTGCGGCGAAATTTTAAAG 59.353 47.619 12.98 0.00 0.00 1.85
868 950 1.989864 GGTGCGGCGAAATTTTAAAGG 59.010 47.619 12.98 0.00 0.00 3.11
869 951 1.989864 GTGCGGCGAAATTTTAAAGGG 59.010 47.619 12.98 0.00 0.00 3.95
870 952 1.887198 TGCGGCGAAATTTTAAAGGGA 59.113 42.857 12.98 0.00 0.00 4.20
871 953 2.494073 TGCGGCGAAATTTTAAAGGGAT 59.506 40.909 12.98 0.00 0.00 3.85
872 954 3.056465 TGCGGCGAAATTTTAAAGGGATT 60.056 39.130 12.98 0.00 0.00 3.01
873 955 3.305897 GCGGCGAAATTTTAAAGGGATTG 59.694 43.478 12.98 0.00 0.00 2.67
874 956 3.862845 CGGCGAAATTTTAAAGGGATTGG 59.137 43.478 0.00 0.00 0.00 3.16
875 957 4.619628 CGGCGAAATTTTAAAGGGATTGGT 60.620 41.667 0.00 0.00 0.00 3.67
876 958 5.242434 GGCGAAATTTTAAAGGGATTGGTT 58.758 37.500 0.00 0.00 0.00 3.67
877 959 6.399743 GGCGAAATTTTAAAGGGATTGGTTA 58.600 36.000 0.00 0.00 0.00 2.85
878 960 6.533723 GGCGAAATTTTAAAGGGATTGGTTAG 59.466 38.462 0.00 0.00 0.00 2.34
879 961 7.317390 GCGAAATTTTAAAGGGATTGGTTAGA 58.683 34.615 0.00 0.00 0.00 2.10
880 962 7.488150 GCGAAATTTTAAAGGGATTGGTTAGAG 59.512 37.037 0.00 0.00 0.00 2.43
881 963 8.520351 CGAAATTTTAAAGGGATTGGTTAGAGT 58.480 33.333 0.00 0.00 0.00 3.24
885 967 2.808906 AGGGATTGGTTAGAGTTGCC 57.191 50.000 0.00 0.00 0.00 4.52
895 977 4.141344 TGGTTAGAGTTGCCCTAACAAACT 60.141 41.667 13.04 1.55 44.63 2.66
898 980 4.164843 AGAGTTGCCCTAACAAACTGAA 57.835 40.909 0.00 0.00 41.88 3.02
904 986 5.957842 TGCCCTAACAAACTGAACTATTG 57.042 39.130 0.00 0.00 0.00 1.90
905 987 5.381757 TGCCCTAACAAACTGAACTATTGT 58.618 37.500 0.00 0.00 38.85 2.71
906 988 6.535540 TGCCCTAACAAACTGAACTATTGTA 58.464 36.000 0.00 0.00 36.33 2.41
907 989 7.172342 TGCCCTAACAAACTGAACTATTGTAT 58.828 34.615 0.00 0.00 36.33 2.29
908 990 7.335924 TGCCCTAACAAACTGAACTATTGTATC 59.664 37.037 0.00 0.00 36.33 2.24
909 991 7.335924 GCCCTAACAAACTGAACTATTGTATCA 59.664 37.037 0.00 0.00 36.33 2.15
916 998 9.814899 CAAACTGAACTATTGTATCAGAGAGAT 57.185 33.333 18.51 0.00 42.48 2.75
928 1010 9.914131 TTGTATCAGAGAGATAATTTACATCGG 57.086 33.333 0.00 0.00 40.76 4.18
940 1022 8.707796 ATAATTTACATCGGTAGAGAAGAGGA 57.292 34.615 0.00 0.00 0.00 3.71
948 1030 2.624557 GGTAGAGAAGAGGAAGGAGGCA 60.625 54.545 0.00 0.00 0.00 4.75
966 1054 2.329379 GCAGTTAGACGTGGAAGTCAG 58.671 52.381 0.00 0.00 43.24 3.51
980 1068 4.844085 TGGAAGTCAGAACTTATCCTTCCA 59.156 41.667 13.38 13.38 45.80 3.53
994 1082 7.617723 ACTTATCCTTCCATCTATCTCGCTAAT 59.382 37.037 0.00 0.00 0.00 1.73
997 1092 6.486056 TCCTTCCATCTATCTCGCTAATAGT 58.514 40.000 0.00 0.00 0.00 2.12
1000 1095 6.761099 TCCATCTATCTCGCTAATAGTTCC 57.239 41.667 0.00 0.00 0.00 3.62
1002 1097 5.163499 CCATCTATCTCGCTAATAGTTCCCC 60.163 48.000 0.00 0.00 0.00 4.81
1004 1099 5.642165 TCTATCTCGCTAATAGTTCCCCTT 58.358 41.667 0.00 0.00 0.00 3.95
1012 1107 6.015350 TCGCTAATAGTTCCCCTTATCTCTTG 60.015 42.308 0.00 0.00 0.00 3.02
1020 1115 5.319043 TCCCCTTATCTCTTGTGTTGTTT 57.681 39.130 0.00 0.00 0.00 2.83
1022 1117 5.070001 CCCCTTATCTCTTGTGTTGTTTGA 58.930 41.667 0.00 0.00 0.00 2.69
1031 1126 4.816385 TCTTGTGTTGTTTGACTCCTCATC 59.184 41.667 0.00 0.00 0.00 2.92
1062 1157 1.841450 CGCGGATAGGTCTCTGTTTC 58.159 55.000 0.00 0.00 0.00 2.78
1200 1299 1.458588 GATCTTCCTCCGCCTCCCT 60.459 63.158 0.00 0.00 0.00 4.20
1214 1313 2.042930 CCCTAACCTCCCCAGCCT 59.957 66.667 0.00 0.00 0.00 4.58
1215 1314 2.073101 CCCTAACCTCCCCAGCCTC 61.073 68.421 0.00 0.00 0.00 4.70
1218 1381 3.248248 TAACCTCCCCAGCCTCCGT 62.248 63.158 0.00 0.00 0.00 4.69
1342 1532 0.387367 CCTCCAAGACGACGACACTG 60.387 60.000 0.00 0.00 0.00 3.66
1412 1614 2.409055 GCATCGCCATCAAGCACCA 61.409 57.895 0.00 0.00 0.00 4.17
1602 1807 0.527600 CTTGGCTACGCATCGCTGTA 60.528 55.000 0.00 0.00 0.00 2.74
1638 1843 2.673775 TGGAGTGGCAGATTTTTCCA 57.326 45.000 0.00 0.00 32.62 3.53
1656 1861 0.526310 CAGAGATTGCGACGCTGCTA 60.526 55.000 22.08 4.22 35.36 3.49
1737 1942 0.907704 AGTCCATGAGCGGGGTACAA 60.908 55.000 0.00 0.00 0.00 2.41
1739 1944 1.819632 CCATGAGCGGGGTACAAGC 60.820 63.158 0.00 0.00 0.00 4.01
1774 1979 4.990543 TTCGTGCTCAAAACAGATACAG 57.009 40.909 0.00 0.00 0.00 2.74
1846 2051 6.586082 CCAAAAATTTAAGATTGGTCAGACCG 59.414 38.462 15.24 0.00 42.58 4.79
1878 2083 6.541641 GGAAGCTCTGTATTGTGAATGAGAAT 59.458 38.462 0.00 0.00 0.00 2.40
1984 2189 2.803492 GCTAGCTTTATGGAGGTCACCG 60.803 54.545 7.70 0.00 0.00 4.94
2235 2468 3.449377 TCTCGGTAAGCAATGTGACCATA 59.551 43.478 0.00 0.00 31.89 2.74
2288 2528 9.964303 GTCCATAAATTGTATGCAATGATGTTA 57.036 29.630 20.54 12.66 43.89 2.41
2382 2653 1.543871 GCCGTAGTAGAGGAGCTAGCT 60.544 57.143 19.45 19.45 0.00 3.32
2525 2852 8.213489 TGAGGGTTTATGCAGGTTATATGATA 57.787 34.615 0.00 0.00 0.00 2.15
2601 3024 8.000709 ACATGAATGGCCTAGATTTATCAGAAA 58.999 33.333 3.32 0.00 0.00 2.52
2606 3029 9.866655 AATGGCCTAGATTTATCAGAAATGTTA 57.133 29.630 3.32 0.00 0.00 2.41
2635 3058 6.704289 TTTGGAGGATTTCTGCAGATTATG 57.296 37.500 19.04 0.00 44.58 1.90
2780 3710 8.774586 TCTTTCTCCTAAATTTTTCGTCTTCTG 58.225 33.333 0.00 0.00 0.00 3.02
2783 3713 3.846335 CCTAAATTTTTCGTCTTCTGCGC 59.154 43.478 0.00 0.00 0.00 6.09
2973 3914 2.635443 ATGTTTTTGGAGGCGGGCG 61.635 57.895 0.00 0.00 0.00 6.13
2976 3917 3.776347 TTTTTGGAGGCGGGCGACA 62.776 57.895 0.00 0.00 0.00 4.35
2977 3918 3.561120 TTTTGGAGGCGGGCGACAT 62.561 57.895 0.00 0.00 0.00 3.06
3011 3958 6.312426 GCTTTCTAGCTATAGGTGCATACATG 59.688 42.308 14.72 0.00 44.27 3.21
3033 6058 0.108329 AGCCATCCGTTAAGTCCGTG 60.108 55.000 0.00 0.00 0.00 4.94
3508 6712 2.849294 AGAGGCCTTCTCACTTTGTC 57.151 50.000 6.77 0.00 44.81 3.18
3771 7440 5.759273 TGCGTTGGTACTTTAGCTTTTAGAA 59.241 36.000 0.00 0.00 0.00 2.10
3772 7441 6.073440 TGCGTTGGTACTTTAGCTTTTAGAAG 60.073 38.462 0.00 0.00 35.92 2.85
3773 7442 6.146673 GCGTTGGTACTTTAGCTTTTAGAAGA 59.853 38.462 0.00 0.00 34.71 2.87
3774 7443 7.621633 GCGTTGGTACTTTAGCTTTTAGAAGAG 60.622 40.741 0.00 0.00 34.71 2.85
3844 7549 1.478916 GTTGGCAGGAGTCCTAGTCTC 59.521 57.143 12.53 0.00 29.64 3.36
3888 7593 6.154445 GTCGTTTTAGAGATGACTTGTACCA 58.846 40.000 0.00 0.00 31.79 3.25
3894 7599 8.918202 TTTAGAGATGACTTGTACCAACAAAT 57.082 30.769 0.00 0.00 44.79 2.32
3937 7642 9.605275 TGTGATTCTTTATCTCTGTTCCTAATG 57.395 33.333 0.00 0.00 34.17 1.90
3980 7685 7.994425 TGTCAGCTTGGTATTAAATCTTTCA 57.006 32.000 0.00 0.00 0.00 2.69
4019 7724 3.848019 GCATTTAATGTGTGAGCGAGTTG 59.152 43.478 6.81 0.00 0.00 3.16
4020 7725 4.378356 GCATTTAATGTGTGAGCGAGTTGA 60.378 41.667 6.81 0.00 0.00 3.18
4022 7727 4.990543 TTAATGTGTGAGCGAGTTGAAG 57.009 40.909 0.00 0.00 0.00 3.02
4029 7738 4.266502 GTGTGAGCGAGTTGAAGATCATAC 59.733 45.833 0.00 0.00 37.62 2.39
4049 7758 6.429692 TCATACAAATAAAGGTGTGTGGTCAG 59.570 38.462 0.00 0.00 37.43 3.51
4064 7775 3.868077 GTGGTCAGTCTCTGTTGCATATC 59.132 47.826 0.00 0.00 32.61 1.63
4137 7966 4.328169 GGTTTATTCAGATTGCAGCAAAGC 59.672 41.667 12.97 7.59 0.00 3.51
4138 7967 5.166398 GTTTATTCAGATTGCAGCAAAGCT 58.834 37.500 12.97 9.92 40.77 3.74
4139 7968 6.324819 GTTTATTCAGATTGCAGCAAAGCTA 58.675 36.000 12.97 0.00 36.40 3.32
4172 8007 8.607459 AGTAATCATTTTTCTCTGTATCTTGCG 58.393 33.333 0.00 0.00 0.00 4.85
4205 8046 7.551262 TGTGCGTCATTTACTTTTAGATGGTAT 59.449 33.333 0.00 0.00 0.00 2.73
4206 8047 9.037737 GTGCGTCATTTACTTTTAGATGGTATA 57.962 33.333 0.00 0.00 0.00 1.47
4255 8103 7.333423 GCCCACTTTATTTTTCCATTTTAGGAC 59.667 37.037 0.00 0.00 37.42 3.85
4262 8127 5.705609 TTTTCCATTTTAGGACTGCTCAC 57.294 39.130 0.00 0.00 37.42 3.51
4286 8151 5.157067 GTGAGCAAGCCATTCTTAACTTTC 58.843 41.667 0.00 0.00 32.74 2.62
4290 8155 4.089361 CAAGCCATTCTTAACTTTCCCCT 58.911 43.478 0.00 0.00 32.74 4.79
4397 8303 2.646175 GGGAGCGCAGACTACACCA 61.646 63.158 11.47 0.00 0.00 4.17
4416 8323 7.326968 ACACCAAATTTTGTTAACAAATGGG 57.673 32.000 34.22 29.26 43.00 4.00
4467 8374 0.707616 AGGAGACAGGGCAGTAGACT 59.292 55.000 0.00 0.00 0.00 3.24
4614 8583 0.707616 AGTCTACTCTGGGGAGCACT 59.292 55.000 0.00 0.00 42.98 4.40
4713 8682 1.134037 TGTTGCGAAAGGTAACACCCT 60.134 47.619 0.00 0.00 44.74 4.34
4782 8753 0.528684 CGCTTGCCTGCTAGTAGGTC 60.529 60.000 25.59 18.37 40.11 3.85
4811 8789 1.935300 GCGCAACCGACATCCCTATAG 60.935 57.143 0.30 0.00 36.29 1.31
4814 8792 3.192844 CGCAACCGACATCCCTATAGTAT 59.807 47.826 0.00 0.00 36.29 2.12
4816 8794 4.463186 GCAACCGACATCCCTATAGTATCT 59.537 45.833 0.00 0.00 0.00 1.98
4853 8834 3.289834 CCACAGCCACCACACTGC 61.290 66.667 0.00 0.00 37.42 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 17 4.015406 CCAGTAGGTGTGGCGGCA 62.015 66.667 7.97 7.97 0.00 5.69
44 46 3.311110 TGGCTCGAGGAAGCGGTT 61.311 61.111 15.58 0.00 43.45 4.44
45 47 4.070552 GTGGCTCGAGGAAGCGGT 62.071 66.667 15.58 0.00 43.45 5.68
171 173 2.037208 CCACATCCCCCACAACCC 59.963 66.667 0.00 0.00 0.00 4.11
184 186 1.602323 GTGATTTCGGCCACCCACA 60.602 57.895 2.24 0.00 0.00 4.17
209 211 1.611977 CACTTCTACGTGTGGGTCTCA 59.388 52.381 0.00 0.00 0.00 3.27
300 302 0.949105 AAATTGAGCCTCGCGTCGTT 60.949 50.000 5.77 0.00 0.00 3.85
301 303 0.949105 AAAATTGAGCCTCGCGTCGT 60.949 50.000 5.77 0.00 0.00 4.34
324 326 0.179111 TCGAATGGATGAGTGCCGAC 60.179 55.000 0.00 0.00 0.00 4.79
332 334 0.744874 GGACGAGGTCGAATGGATGA 59.255 55.000 6.35 0.00 43.02 2.92
334 336 1.400530 GGGGACGAGGTCGAATGGAT 61.401 60.000 6.35 0.00 43.02 3.41
339 341 2.678934 CTGGGGGACGAGGTCGAA 60.679 66.667 6.35 0.00 43.02 3.71
385 388 0.259065 TCGCCTCCTAGTCCTCACAT 59.741 55.000 0.00 0.00 0.00 3.21
386 389 0.394488 CTCGCCTCCTAGTCCTCACA 60.394 60.000 0.00 0.00 0.00 3.58
388 391 1.227664 CCTCGCCTCCTAGTCCTCA 59.772 63.158 0.00 0.00 0.00 3.86
395 398 2.442272 GCACTCCCTCGCCTCCTA 60.442 66.667 0.00 0.00 0.00 2.94
482 486 1.214589 CCAAGATCGTCCGTTCCGT 59.785 57.895 0.00 0.00 0.00 4.69
562 576 4.031089 CACTTCTTGACGTTGATCTCATCG 59.969 45.833 8.65 8.65 42.75 3.84
572 622 1.871080 CTCTGCCACTTCTTGACGTT 58.129 50.000 0.00 0.00 0.00 3.99
581 631 1.004440 GGAAGACGCTCTGCCACTT 60.004 57.895 7.05 0.00 42.14 3.16
659 715 2.531206 GAGGTCGAGTCAATCCTTTCG 58.469 52.381 0.00 0.00 34.56 3.46
661 717 2.234908 CTGGAGGTCGAGTCAATCCTTT 59.765 50.000 0.00 0.00 0.00 3.11
670 726 2.637383 GCCGAACTGGAGGTCGAGT 61.637 63.158 15.64 0.00 42.00 4.18
682 738 2.137523 TGAAACTACTTTCGGCCGAAC 58.862 47.619 38.87 24.42 39.01 3.95
764 845 8.627208 ACCGAGAGATGATGCATTTAAAATAT 57.373 30.769 0.00 0.00 0.00 1.28
784 866 6.582295 ACGAATTCAATCAAATTTGAACCGAG 59.418 34.615 23.91 12.23 45.55 4.63
807 889 5.631026 AGCTGAGTACAAATAATTTGCACG 58.369 37.500 0.00 0.00 44.39 5.34
809 891 8.335532 AGTTAGCTGAGTACAAATAATTTGCA 57.664 30.769 0.00 0.00 44.39 4.08
810 892 9.626045 AAAGTTAGCTGAGTACAAATAATTTGC 57.374 29.630 0.00 0.00 44.39 3.68
814 896 9.614792 CCCTAAAGTTAGCTGAGTACAAATAAT 57.385 33.333 0.00 0.00 0.00 1.28
815 897 8.044908 CCCCTAAAGTTAGCTGAGTACAAATAA 58.955 37.037 0.00 0.00 0.00 1.40
816 898 7.400915 TCCCCTAAAGTTAGCTGAGTACAAATA 59.599 37.037 0.00 0.00 0.00 1.40
817 899 6.214819 TCCCCTAAAGTTAGCTGAGTACAAAT 59.785 38.462 0.00 0.00 0.00 2.32
818 900 5.544948 TCCCCTAAAGTTAGCTGAGTACAAA 59.455 40.000 0.00 0.00 0.00 2.83
819 901 5.088730 TCCCCTAAAGTTAGCTGAGTACAA 58.911 41.667 0.00 0.00 0.00 2.41
820 902 4.680407 TCCCCTAAAGTTAGCTGAGTACA 58.320 43.478 0.00 0.00 0.00 2.90
821 903 5.507650 CGATCCCCTAAAGTTAGCTGAGTAC 60.508 48.000 0.00 0.00 0.00 2.73
822 904 4.583489 CGATCCCCTAAAGTTAGCTGAGTA 59.417 45.833 0.00 0.00 0.00 2.59
823 905 3.385111 CGATCCCCTAAAGTTAGCTGAGT 59.615 47.826 0.00 0.00 0.00 3.41
824 906 3.243907 CCGATCCCCTAAAGTTAGCTGAG 60.244 52.174 0.00 0.00 0.00 3.35
825 907 2.698797 CCGATCCCCTAAAGTTAGCTGA 59.301 50.000 0.00 0.00 0.00 4.26
826 908 2.807108 GCCGATCCCCTAAAGTTAGCTG 60.807 54.545 0.00 0.00 0.00 4.24
827 909 1.416772 GCCGATCCCCTAAAGTTAGCT 59.583 52.381 0.00 0.00 0.00 3.32
828 910 1.872653 CGCCGATCCCCTAAAGTTAGC 60.873 57.143 0.00 0.00 0.00 3.09
829 911 1.270147 CCGCCGATCCCCTAAAGTTAG 60.270 57.143 0.00 0.00 0.00 2.34
830 912 0.754472 CCGCCGATCCCCTAAAGTTA 59.246 55.000 0.00 0.00 0.00 2.24
831 913 1.269703 ACCGCCGATCCCCTAAAGTT 61.270 55.000 0.00 0.00 0.00 2.66
832 914 1.688187 ACCGCCGATCCCCTAAAGT 60.688 57.895 0.00 0.00 0.00 2.66
833 915 1.227556 CACCGCCGATCCCCTAAAG 60.228 63.158 0.00 0.00 0.00 1.85
834 916 2.904905 CACCGCCGATCCCCTAAA 59.095 61.111 0.00 0.00 0.00 1.85
835 917 3.857038 GCACCGCCGATCCCCTAA 61.857 66.667 0.00 0.00 0.00 2.69
845 927 2.530465 TAAAATTTCGCCGCACCGCC 62.530 55.000 0.00 0.00 0.00 6.13
846 928 0.729816 TTAAAATTTCGCCGCACCGC 60.730 50.000 0.00 0.00 0.00 5.68
847 929 1.646726 CTTTAAAATTTCGCCGCACCG 59.353 47.619 0.00 0.00 0.00 4.94
848 930 1.989864 CCTTTAAAATTTCGCCGCACC 59.010 47.619 0.00 0.00 0.00 5.01
849 931 1.989864 CCCTTTAAAATTTCGCCGCAC 59.010 47.619 0.00 0.00 0.00 5.34
850 932 1.887198 TCCCTTTAAAATTTCGCCGCA 59.113 42.857 0.00 0.00 0.00 5.69
851 933 2.640346 TCCCTTTAAAATTTCGCCGC 57.360 45.000 0.00 0.00 0.00 6.53
852 934 3.862845 CCAATCCCTTTAAAATTTCGCCG 59.137 43.478 0.00 0.00 0.00 6.46
853 935 4.827692 ACCAATCCCTTTAAAATTTCGCC 58.172 39.130 0.00 0.00 0.00 5.54
854 936 7.317390 TCTAACCAATCCCTTTAAAATTTCGC 58.683 34.615 0.00 0.00 0.00 4.70
855 937 8.520351 ACTCTAACCAATCCCTTTAAAATTTCG 58.480 33.333 0.00 0.00 0.00 3.46
857 939 9.996554 CAACTCTAACCAATCCCTTTAAAATTT 57.003 29.630 0.00 0.00 0.00 1.82
858 940 8.094548 GCAACTCTAACCAATCCCTTTAAAATT 58.905 33.333 0.00 0.00 0.00 1.82
859 941 7.310423 GGCAACTCTAACCAATCCCTTTAAAAT 60.310 37.037 0.00 0.00 0.00 1.82
860 942 6.014925 GGCAACTCTAACCAATCCCTTTAAAA 60.015 38.462 0.00 0.00 0.00 1.52
861 943 5.479027 GGCAACTCTAACCAATCCCTTTAAA 59.521 40.000 0.00 0.00 0.00 1.52
862 944 5.014202 GGCAACTCTAACCAATCCCTTTAA 58.986 41.667 0.00 0.00 0.00 1.52
863 945 4.569015 GGGCAACTCTAACCAATCCCTTTA 60.569 45.833 0.00 0.00 0.00 1.85
864 946 3.431415 GGCAACTCTAACCAATCCCTTT 58.569 45.455 0.00 0.00 0.00 3.11
865 947 2.291605 GGGCAACTCTAACCAATCCCTT 60.292 50.000 0.00 0.00 0.00 3.95
866 948 1.285078 GGGCAACTCTAACCAATCCCT 59.715 52.381 0.00 0.00 0.00 4.20
867 949 1.285078 AGGGCAACTCTAACCAATCCC 59.715 52.381 0.00 0.00 0.00 3.85
868 950 2.808906 AGGGCAACTCTAACCAATCC 57.191 50.000 0.00 0.00 0.00 3.01
869 951 4.585879 TGTTAGGGCAACTCTAACCAATC 58.414 43.478 13.39 0.00 43.70 2.67
870 952 4.650972 TGTTAGGGCAACTCTAACCAAT 57.349 40.909 13.39 0.00 43.70 3.16
871 953 4.440826 TTGTTAGGGCAACTCTAACCAA 57.559 40.909 13.39 6.55 43.70 3.67
872 954 4.139038 GTTTGTTAGGGCAACTCTAACCA 58.861 43.478 13.39 1.60 43.70 3.67
873 955 4.215613 CAGTTTGTTAGGGCAACTCTAACC 59.784 45.833 13.39 0.76 43.70 2.85
874 956 5.061179 TCAGTTTGTTAGGGCAACTCTAAC 58.939 41.667 9.89 9.89 44.17 2.34
875 957 5.298989 TCAGTTTGTTAGGGCAACTCTAA 57.701 39.130 0.00 0.00 38.05 2.10
876 958 4.967084 TCAGTTTGTTAGGGCAACTCTA 57.033 40.909 0.00 0.00 38.05 2.43
877 959 3.857157 TCAGTTTGTTAGGGCAACTCT 57.143 42.857 0.00 0.00 38.05 3.24
878 960 3.883489 AGTTCAGTTTGTTAGGGCAACTC 59.117 43.478 0.00 0.00 38.05 3.01
879 961 3.898482 AGTTCAGTTTGTTAGGGCAACT 58.102 40.909 0.00 0.00 38.05 3.16
880 962 5.959618 ATAGTTCAGTTTGTTAGGGCAAC 57.040 39.130 0.00 0.00 37.67 4.17
881 963 5.830991 ACAATAGTTCAGTTTGTTAGGGCAA 59.169 36.000 0.00 0.00 29.60 4.52
885 967 9.653287 TCTGATACAATAGTTCAGTTTGTTAGG 57.347 33.333 0.00 0.00 35.86 2.69
906 988 9.521841 TCTACCGATGTAAATTATCTCTCTGAT 57.478 33.333 0.00 0.00 39.11 2.90
907 989 8.919777 TCTACCGATGTAAATTATCTCTCTGA 57.080 34.615 0.00 0.00 0.00 3.27
908 990 9.004717 TCTCTACCGATGTAAATTATCTCTCTG 57.995 37.037 0.00 0.00 0.00 3.35
909 991 9.575868 TTCTCTACCGATGTAAATTATCTCTCT 57.424 33.333 0.00 0.00 0.00 3.10
916 998 8.529424 TTCCTCTTCTCTACCGATGTAAATTA 57.471 34.615 0.00 0.00 0.00 1.40
917 999 7.418025 CCTTCCTCTTCTCTACCGATGTAAATT 60.418 40.741 0.00 0.00 0.00 1.82
920 1002 4.888239 CCTTCCTCTTCTCTACCGATGTAA 59.112 45.833 0.00 0.00 0.00 2.41
926 1008 2.303175 CCTCCTTCCTCTTCTCTACCG 58.697 57.143 0.00 0.00 0.00 4.02
928 1010 2.693074 CTGCCTCCTTCCTCTTCTCTAC 59.307 54.545 0.00 0.00 0.00 2.59
940 1022 0.608640 CCACGTCTAACTGCCTCCTT 59.391 55.000 0.00 0.00 0.00 3.36
948 1030 3.890147 AGTTCTGACTTCCACGTCTAACT 59.110 43.478 0.00 0.00 36.70 2.24
966 1054 6.071616 AGCGAGATAGATGGAAGGATAAGTTC 60.072 42.308 0.00 0.00 0.00 3.01
980 1068 5.833340 AGGGGAACTATTAGCGAGATAGAT 58.167 41.667 9.90 0.45 32.63 1.98
994 1082 5.546499 ACAACACAAGAGATAAGGGGAACTA 59.454 40.000 0.00 0.00 0.00 2.24
997 1092 4.993705 ACAACACAAGAGATAAGGGGAA 57.006 40.909 0.00 0.00 0.00 3.97
1000 1095 5.765182 AGTCAAACAACACAAGAGATAAGGG 59.235 40.000 0.00 0.00 0.00 3.95
1002 1097 6.708054 AGGAGTCAAACAACACAAGAGATAAG 59.292 38.462 0.00 0.00 0.00 1.73
1004 1099 6.174720 AGGAGTCAAACAACACAAGAGATA 57.825 37.500 0.00 0.00 0.00 1.98
1012 1107 2.814336 GGGATGAGGAGTCAAACAACAC 59.186 50.000 0.00 0.00 35.88 3.32
1020 1115 1.362584 TGGAAGAGGGATGAGGAGTCA 59.637 52.381 0.00 0.00 37.02 3.41
1022 1117 2.476199 CTTGGAAGAGGGATGAGGAGT 58.524 52.381 0.00 0.00 0.00 3.85
1031 1126 2.028125 TATCCGCGCTTGGAAGAGGG 62.028 60.000 8.16 0.00 42.46 4.30
1200 1299 2.365105 CGGAGGCTGGGGAGGTTA 60.365 66.667 0.00 0.00 0.00 2.85
1259 1422 2.688507 CTATTGTGTGTGCGAGGAAGT 58.311 47.619 0.00 0.00 0.00 3.01
1371 1567 1.129811 CCGCCATTGTAGAAAACCGAC 59.870 52.381 0.00 0.00 0.00 4.79
1378 1574 0.394216 ATGCAGCCGCCATTGTAGAA 60.394 50.000 0.00 0.00 37.32 2.10
1412 1614 1.825281 AACTCTCTGCTTGGCGCTCT 61.825 55.000 7.64 0.00 40.11 4.09
1602 1807 2.103771 CTCCATGGTGTCCGATGAGAAT 59.896 50.000 12.58 0.00 0.00 2.40
1638 1843 0.526524 GTAGCAGCGTCGCAATCTCT 60.527 55.000 21.09 10.44 0.00 3.10
1737 1942 1.337823 ACGAAAATGTACTCGCTGGCT 60.338 47.619 2.47 0.00 38.64 4.75
1739 1944 1.201921 GCACGAAAATGTACTCGCTGG 60.202 52.381 2.47 0.00 38.64 4.85
1846 2051 2.877168 CAATACAGAGCTTCCCATCAGC 59.123 50.000 0.00 0.00 37.56 4.26
1878 2083 8.523915 AGATCCAAATACTAAACATGCATTCA 57.476 30.769 0.00 0.00 0.00 2.57
1984 2189 3.334583 TGTATCTTCCACTGAACAGCC 57.665 47.619 1.46 0.00 0.00 4.85
2289 2529 9.534565 CATATATAGCAATACAATCGCCTTAGT 57.465 33.333 0.00 0.00 0.00 2.24
2362 2611 0.876399 GCTAGCTCCTCTACTACGGC 59.124 60.000 7.70 0.00 0.00 5.68
2363 2612 2.147958 CAGCTAGCTCCTCTACTACGG 58.852 57.143 16.15 0.00 0.00 4.02
2382 2653 4.314522 TTGAAGGAATGGGAATAGCACA 57.685 40.909 0.00 0.00 0.00 4.57
2525 2852 5.065731 GCTTTGTATCTCAATGCTACTGCTT 59.934 40.000 9.91 0.00 46.65 3.91
2601 3024 9.822185 GCAGAAATCCTCCAAATATTTTAACAT 57.178 29.630 0.00 0.00 0.00 2.71
2606 3029 7.722949 TCTGCAGAAATCCTCCAAATATTTT 57.277 32.000 15.67 0.00 0.00 1.82
2635 3058 9.219603 TGTGGAGCTTTATAATAATGCTATCAC 57.780 33.333 18.50 18.50 37.91 3.06
2676 3106 8.150296 TGCAGAAACTAGCTATTCATATGCTAA 58.850 33.333 15.31 0.00 38.59 3.09
2698 3371 8.709386 ATCTGAATACTTAAACACTACTGCAG 57.291 34.615 13.48 13.48 0.00 4.41
2780 3710 2.596862 GACATTAATTTGAAACCGGCGC 59.403 45.455 0.00 0.00 0.00 6.53
3011 3958 2.199236 CGGACTTAACGGATGGCTAAC 58.801 52.381 0.00 0.00 0.00 2.34
3317 6521 7.340122 TGTGACAAAATGGAAATTCAGTGTA 57.660 32.000 0.00 0.00 0.00 2.90
3318 6522 6.219417 TGTGACAAAATGGAAATTCAGTGT 57.781 33.333 0.00 0.00 0.00 3.55
3319 6523 5.693104 CCTGTGACAAAATGGAAATTCAGTG 59.307 40.000 0.00 0.00 0.00 3.66
3320 6524 5.598005 TCCTGTGACAAAATGGAAATTCAGT 59.402 36.000 0.00 0.00 0.00 3.41
3321 6525 6.088016 TCCTGTGACAAAATGGAAATTCAG 57.912 37.500 0.00 0.00 0.00 3.02
3322 6526 5.010922 CCTCCTGTGACAAAATGGAAATTCA 59.989 40.000 0.00 0.00 0.00 2.57
3323 6527 5.243730 TCCTCCTGTGACAAAATGGAAATTC 59.756 40.000 0.00 0.00 0.00 2.17
3324 6528 5.147032 TCCTCCTGTGACAAAATGGAAATT 58.853 37.500 0.00 0.00 0.00 1.82
3325 6529 4.739793 TCCTCCTGTGACAAAATGGAAAT 58.260 39.130 0.00 0.00 0.00 2.17
3326 6530 4.177537 TCCTCCTGTGACAAAATGGAAA 57.822 40.909 0.00 0.00 0.00 3.13
3327 6531 3.874383 TCCTCCTGTGACAAAATGGAA 57.126 42.857 0.00 0.00 0.00 3.53
3453 6657 3.006940 TGCGTCACCATCCTTAATCAAC 58.993 45.455 0.00 0.00 0.00 3.18
3508 6712 2.165234 TCTTCTCATCCTCAGCGTCAAG 59.835 50.000 0.00 0.00 0.00 3.02
3771 7440 1.134965 GCTAACGTCATCACAGCCTCT 60.135 52.381 0.00 0.00 0.00 3.69
3772 7441 1.134965 AGCTAACGTCATCACAGCCTC 60.135 52.381 0.00 0.00 32.58 4.70
3773 7442 0.898320 AGCTAACGTCATCACAGCCT 59.102 50.000 0.00 0.00 32.58 4.58
3774 7443 1.002366 CAGCTAACGTCATCACAGCC 58.998 55.000 0.00 0.00 32.58 4.85
3888 7593 6.538945 AAGTTTGGGACTTGTACATTTGTT 57.461 33.333 0.00 0.00 46.66 2.83
3911 7616 9.605275 CATTAGGAACAGAGATAAAGAATCACA 57.395 33.333 0.00 0.00 37.03 3.58
3937 7642 5.531634 TGACAAAAGCTTGAAACATCATCC 58.468 37.500 0.00 0.00 36.33 3.51
4003 7708 3.111853 TCTTCAACTCGCTCACACATT 57.888 42.857 0.00 0.00 0.00 2.71
4019 7724 8.184192 CCACACACCTTTATTTGTATGATCTTC 58.816 37.037 0.00 0.00 0.00 2.87
4020 7725 7.669722 ACCACACACCTTTATTTGTATGATCTT 59.330 33.333 0.00 0.00 0.00 2.40
4022 7727 7.120579 TGACCACACACCTTTATTTGTATGATC 59.879 37.037 0.00 0.00 0.00 2.92
4029 7738 4.821805 AGACTGACCACACACCTTTATTTG 59.178 41.667 0.00 0.00 0.00 2.32
4106 7935 7.042051 GCTGCAATCTGAATAAACCGAACTATA 60.042 37.037 0.00 0.00 0.00 1.31
4113 7942 3.763097 TGCTGCAATCTGAATAAACCG 57.237 42.857 0.00 0.00 0.00 4.44
4164 7999 7.095446 ATGACGCACATTTTGTCGCAAGATA 62.095 40.000 0.00 0.00 42.55 1.98
4166 8001 5.143363 ATGACGCACATTTTGTCGCAAGA 62.143 43.478 0.00 0.00 39.42 3.02
4168 8003 0.378610 TGACGCACATTTTGTCGCAA 59.621 45.000 0.00 0.00 35.40 4.85
4205 8046 8.792633 GGCAAGTGCAGGAAATAATAATATGTA 58.207 33.333 5.52 0.00 44.36 2.29
4206 8047 7.255942 GGGCAAGTGCAGGAAATAATAATATGT 60.256 37.037 5.52 0.00 44.36 2.29
4262 8127 2.744202 AGTTAAGAATGGCTTGCTCACG 59.256 45.455 0.00 0.00 37.42 4.35
4271 8136 3.969553 AGAGGGGAAAGTTAAGAATGGC 58.030 45.455 0.00 0.00 0.00 4.40
4286 8151 3.195610 GGTAGAAAATGGCAAAAGAGGGG 59.804 47.826 0.00 0.00 0.00 4.79
4290 8155 6.303839 AGTACTGGTAGAAAATGGCAAAAGA 58.696 36.000 0.00 0.00 0.00 2.52
4357 8263 8.146053 TCCCTCAGATACTAGTTTCATTCAAA 57.854 34.615 14.67 0.00 0.00 2.69
4467 8374 5.588648 GGGCACTTGCTATTAACATAGAACA 59.411 40.000 0.38 0.00 41.70 3.18
4589 8558 1.038130 CCCCAGAGTAGACTCCACCG 61.038 65.000 6.05 0.00 43.88 4.94
4675 8644 4.413969 CAACATGCGCAATCAAAGTCATA 58.586 39.130 17.11 0.00 0.00 2.15
4713 8682 4.293648 CGACGGGCAGACCACACA 62.294 66.667 0.00 0.00 40.22 3.72
4811 8789 6.314896 GCCTGGATGCTATAATTGTGAGATAC 59.685 42.308 0.00 0.00 0.00 2.24
4814 8792 4.505566 GGCCTGGATGCTATAATTGTGAGA 60.506 45.833 0.00 0.00 0.00 3.27
4816 8794 3.138098 TGGCCTGGATGCTATAATTGTGA 59.862 43.478 3.32 0.00 0.00 3.58
4853 8834 1.592064 AAAAACAAATTGCCTGGCGG 58.408 45.000 14.98 3.48 0.00 6.13


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

AutoCloner maintained by Alex Coulton.