Multiple sequence alignment - TraesCS2A01G322500

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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 TraesCS2A01G322500 chr2A 100.000 3820 0 0 1 3820 551720520 551724339 0.000000e+00 7055.0
1 TraesCS2A01G322500 chr2A 97.167 706 19 1 3115 3820 407427275 407426571 0.000000e+00 1192.0
2 TraesCS2A01G322500 chr2A 97.163 705 20 0 3114 3818 512119094 512118390 0.000000e+00 1192.0
3 TraesCS2A01G322500 chr2A 80.844 924 159 13 994 1911 12702349 12701438 0.000000e+00 710.0
4 TraesCS2A01G322500 chr2A 84.908 709 98 4 2183 2882 12701013 12700305 0.000000e+00 708.0
5 TraesCS2A01G322500 chr2A 82.252 755 119 11 2154 2894 12577660 12576907 4.160000e-179 638.0
6 TraesCS2A01G322500 chr2A 79.968 624 121 4 2188 2809 772219429 772218808 1.250000e-124 457.0
7 TraesCS2A01G322500 chr2A 95.122 41 2 0 448 488 214902112 214902152 8.860000e-07 65.8
8 TraesCS2A01G322500 chr2D 93.423 1338 65 14 669 1994 435072940 435071614 0.000000e+00 1962.0
9 TraesCS2A01G322500 chr2D 94.901 961 37 4 2114 3063 435071152 435070193 0.000000e+00 1493.0
10 TraesCS2A01G322500 chr2D 79.550 1022 182 17 994 2001 11964719 11963711 0.000000e+00 704.0
11 TraesCS2A01G322500 chr2D 83.929 728 105 6 2183 2898 11963385 11962658 0.000000e+00 686.0
12 TraesCS2A01G322500 chr2D 78.509 912 170 17 1001 1905 650656232 650655340 3.310000e-160 575.0
13 TraesCS2A01G322500 chr2D 78.098 936 165 28 994 1906 4029546 4028628 1.200000e-154 556.0
14 TraesCS2A01G322500 chr2D 77.671 936 169 27 994 1906 3971951 3971033 5.620000e-148 534.0
15 TraesCS2A01G322500 chr2D 93.294 343 12 7 1 340 435074382 435074048 2.650000e-136 496.0
16 TraesCS2A01G322500 chr2D 80.609 624 117 4 2188 2809 650654781 650654160 2.670000e-131 479.0
17 TraesCS2A01G322500 chr2D 90.028 351 18 10 341 677 435073772 435073425 4.530000e-119 438.0
18 TraesCS2A01G322500 chr2D 88.095 126 11 2 1974 2096 435071599 435071475 3.080000e-31 147.0
19 TraesCS2A01G322500 chr2D 90.196 51 4 1 441 491 579191490 579191539 8.860000e-07 65.8
20 TraesCS2A01G322500 chr2B 95.794 1070 37 5 994 2062 513481223 513480161 0.000000e+00 1720.0
21 TraesCS2A01G322500 chr2B 93.139 962 53 11 2108 3063 513480158 513479204 0.000000e+00 1399.0
22 TraesCS2A01G322500 chr2B 80.831 626 112 8 2188 2809 787819015 787818394 5.740000e-133 484.0
23 TraesCS2A01G322500 chr2B 96.400 250 3 3 1 244 513496898 513496649 1.280000e-109 407.0
24 TraesCS2A01G322500 chr2B 88.235 204 13 2 695 888 513481595 513481393 2.290000e-57 233.0
25 TraesCS2A01G322500 chr5A 97.592 706 16 1 3115 3820 595444242 595444946 0.000000e+00 1208.0
26 TraesCS2A01G322500 chr5A 97.309 706 19 0 3115 3820 26007147 26006442 0.000000e+00 1199.0
27 TraesCS2A01G322500 chr5A 97.167 706 19 1 3115 3820 534426660 534427364 0.000000e+00 1192.0
28 TraesCS2A01G322500 chr5A 89.041 73 4 4 3046 3114 569658293 569658365 1.890000e-13 87.9
29 TraesCS2A01G322500 chr3A 97.328 711 18 1 3110 3820 733145226 733144517 0.000000e+00 1206.0
30 TraesCS2A01G322500 chr7A 97.309 706 19 0 3115 3820 234272770 234273475 0.000000e+00 1199.0
31 TraesCS2A01G322500 chr1A 97.309 706 18 1 3115 3820 440252430 440251726 0.000000e+00 1197.0
32 TraesCS2A01G322500 chr1A 97.030 707 20 1 3114 3820 275004477 275003772 0.000000e+00 1188.0
33 TraesCS2A01G322500 chr1A 96.078 51 2 0 3062 3112 442631644 442631594 2.450000e-12 84.2
34 TraesCS2A01G322500 chr5D 84.679 966 132 8 1000 1960 522761631 522760677 0.000000e+00 950.0
35 TraesCS2A01G322500 chr5D 86.838 623 82 0 2181 2803 522759645 522759023 0.000000e+00 697.0
36 TraesCS2A01G322500 chr7D 79.878 820 139 23 1097 1906 591207002 591207805 9.200000e-161 577.0
37 TraesCS2A01G322500 chr7D 78.132 942 173 20 994 1915 263889984 263890912 5.540000e-158 568.0
38 TraesCS2A01G322500 chr7D 96.226 53 1 1 3063 3114 47186525 47186473 6.800000e-13 86.1
39 TraesCS2A01G322500 chr7D 92.857 42 1 2 450 491 439236350 439236311 4.120000e-05 60.2
40 TraesCS2A01G322500 chr6B 96.154 52 2 0 3063 3114 416909775 416909826 6.800000e-13 86.1
41 TraesCS2A01G322500 chr6B 94.231 52 3 0 3063 3114 506544220 506544169 3.160000e-11 80.5
42 TraesCS2A01G322500 chr6B 94.231 52 3 0 3063 3114 518592872 518592923 3.160000e-11 80.5
43 TraesCS2A01G322500 chr6B 94.231 52 3 0 3063 3114 626216567 626216516 3.160000e-11 80.5
44 TraesCS2A01G322500 chr4B 89.706 68 6 1 3059 3125 311202838 311202771 6.800000e-13 86.1
45 TraesCS2A01G322500 chr3B 91.228 57 3 2 3056 3112 463487605 463487659 4.090000e-10 76.8
46 TraesCS2A01G322500 chr4D 90.196 51 3 2 442 491 416070623 416070672 8.860000e-07 65.8
47 TraesCS2A01G322500 chr4D 93.182 44 2 1 448 491 218516286 218516244 3.190000e-06 63.9
48 TraesCS2A01G322500 chr6A 95.122 41 1 1 451 491 39864174 39864213 3.190000e-06 63.9
49 TraesCS2A01G322500 chr1D 91.304 46 2 2 447 491 366474150 366474106 1.150000e-05 62.1


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 TraesCS2A01G322500 chr2A 551720520 551724339 3819 False 7055.000000 7055 100.000000 1 3820 1 chr2A.!!$F2 3819
1 TraesCS2A01G322500 chr2A 407426571 407427275 704 True 1192.000000 1192 97.167000 3115 3820 1 chr2A.!!$R2 705
2 TraesCS2A01G322500 chr2A 512118390 512119094 704 True 1192.000000 1192 97.163000 3114 3818 1 chr2A.!!$R3 704
3 TraesCS2A01G322500 chr2A 12700305 12702349 2044 True 709.000000 710 82.876000 994 2882 2 chr2A.!!$R5 1888
4 TraesCS2A01G322500 chr2A 12576907 12577660 753 True 638.000000 638 82.252000 2154 2894 1 chr2A.!!$R1 740
5 TraesCS2A01G322500 chr2A 772218808 772219429 621 True 457.000000 457 79.968000 2188 2809 1 chr2A.!!$R4 621
6 TraesCS2A01G322500 chr2D 435070193 435074382 4189 True 907.200000 1962 91.948200 1 3063 5 chr2D.!!$R4 3062
7 TraesCS2A01G322500 chr2D 11962658 11964719 2061 True 695.000000 704 81.739500 994 2898 2 chr2D.!!$R3 1904
8 TraesCS2A01G322500 chr2D 4028628 4029546 918 True 556.000000 556 78.098000 994 1906 1 chr2D.!!$R2 912
9 TraesCS2A01G322500 chr2D 3971033 3971951 918 True 534.000000 534 77.671000 994 1906 1 chr2D.!!$R1 912
10 TraesCS2A01G322500 chr2D 650654160 650656232 2072 True 527.000000 575 79.559000 1001 2809 2 chr2D.!!$R5 1808
11 TraesCS2A01G322500 chr2B 513479204 513481595 2391 True 1117.333333 1720 92.389333 695 3063 3 chr2B.!!$R3 2368
12 TraesCS2A01G322500 chr2B 787818394 787819015 621 True 484.000000 484 80.831000 2188 2809 1 chr2B.!!$R2 621
13 TraesCS2A01G322500 chr5A 595444242 595444946 704 False 1208.000000 1208 97.592000 3115 3820 1 chr5A.!!$F3 705
14 TraesCS2A01G322500 chr5A 26006442 26007147 705 True 1199.000000 1199 97.309000 3115 3820 1 chr5A.!!$R1 705
15 TraesCS2A01G322500 chr5A 534426660 534427364 704 False 1192.000000 1192 97.167000 3115 3820 1 chr5A.!!$F1 705
16 TraesCS2A01G322500 chr3A 733144517 733145226 709 True 1206.000000 1206 97.328000 3110 3820 1 chr3A.!!$R1 710
17 TraesCS2A01G322500 chr7A 234272770 234273475 705 False 1199.000000 1199 97.309000 3115 3820 1 chr7A.!!$F1 705
18 TraesCS2A01G322500 chr1A 440251726 440252430 704 True 1197.000000 1197 97.309000 3115 3820 1 chr1A.!!$R2 705
19 TraesCS2A01G322500 chr1A 275003772 275004477 705 True 1188.000000 1188 97.030000 3114 3820 1 chr1A.!!$R1 706
20 TraesCS2A01G322500 chr5D 522759023 522761631 2608 True 823.500000 950 85.758500 1000 2803 2 chr5D.!!$R1 1803
21 TraesCS2A01G322500 chr7D 591207002 591207805 803 False 577.000000 577 79.878000 1097 1906 1 chr7D.!!$F2 809
22 TraesCS2A01G322500 chr7D 263889984 263890912 928 False 568.000000 568 78.132000 994 1915 1 chr7D.!!$F1 921

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
822 1617 0.392863 CGTGATCCATCAGGCAACCA 60.393 55.000 0.0 0.0 37.51 3.67 F
944 1765 0.541863 CATGTTCTTCTACCCCGGCT 59.458 55.000 0.0 0.0 0.00 5.52 F
959 1780 1.202417 CCGGCTGGCTATATATCCGTG 60.202 57.143 0.0 0.0 35.52 4.94 F
1286 2163 1.676014 GGAGGTGATGAAGACCAACGG 60.676 57.143 0.0 0.0 35.76 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1702 2588 1.143183 GGATCCTCTTTACGCGGCA 59.857 57.895 12.47 0.0 0.00 5.69 R
2414 4579 1.270826 CAGTCTTCTCTGGTCTTGCGA 59.729 52.381 0.00 0.0 0.00 5.10 R
2723 4889 3.684788 ACCCGAATTTCTCAGACAAATCG 59.315 43.478 0.00 0.0 0.00 3.34 R
3072 5258 0.403271 AGCCAGCTGTGTTGGATCTT 59.597 50.000 13.81 0.0 35.94 2.40 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
55 56 3.262420 CCACCATACCGAACTTCTTCTG 58.738 50.000 0.00 0.00 0.00 3.02
56 57 3.306780 CCACCATACCGAACTTCTTCTGT 60.307 47.826 0.00 0.00 0.00 3.41
58 59 4.389077 CACCATACCGAACTTCTTCTGTTC 59.611 45.833 0.00 0.00 40.05 3.18
68 71 6.702282 CGAACTTCTTCTGTTCCTAGTCTTTT 59.298 38.462 0.00 0.00 40.26 2.27
77 80 1.825474 TCCTAGTCTTTTCTGAGCCGG 59.175 52.381 0.00 0.00 0.00 6.13
202 205 5.923204 TGTTTTTAAATTGCTGTCCATGGT 58.077 33.333 12.58 0.00 0.00 3.55
217 220 4.746611 GTCCATGGTTTTCTGCTTTTGAAG 59.253 41.667 12.58 0.00 0.00 3.02
220 223 6.097554 TCCATGGTTTTCTGCTTTTGAAGTTA 59.902 34.615 12.58 0.00 0.00 2.24
221 224 6.200854 CCATGGTTTTCTGCTTTTGAAGTTAC 59.799 38.462 2.57 0.00 0.00 2.50
226 229 7.330946 GGTTTTCTGCTTTTGAAGTTACTTGTT 59.669 33.333 0.93 0.00 0.00 2.83
227 230 7.810766 TTTCTGCTTTTGAAGTTACTTGTTG 57.189 32.000 0.93 0.00 0.00 3.33
228 231 6.509418 TCTGCTTTTGAAGTTACTTGTTGT 57.491 33.333 0.93 0.00 0.00 3.32
229 232 6.321717 TCTGCTTTTGAAGTTACTTGTTGTG 58.678 36.000 0.93 0.00 0.00 3.33
230 233 5.406649 TGCTTTTGAAGTTACTTGTTGTGG 58.593 37.500 0.93 0.00 0.00 4.17
231 234 5.184096 TGCTTTTGAAGTTACTTGTTGTGGA 59.816 36.000 0.93 0.00 0.00 4.02
232 235 5.515270 GCTTTTGAAGTTACTTGTTGTGGAC 59.485 40.000 0.93 0.00 0.00 4.02
233 236 4.868450 TTGAAGTTACTTGTTGTGGACG 57.132 40.909 0.93 0.00 0.00 4.79
261 264 1.540267 TATGTTTTCGTGGCCTTGGG 58.460 50.000 3.32 0.00 0.00 4.12
300 303 4.697352 GTGAGATGGCAGAACACAAATAGT 59.303 41.667 13.15 0.00 0.00 2.12
301 304 5.874810 GTGAGATGGCAGAACACAAATAGTA 59.125 40.000 13.15 0.00 0.00 1.82
302 305 6.036517 GTGAGATGGCAGAACACAAATAGTAG 59.963 42.308 13.15 0.00 0.00 2.57
324 327 3.130693 GGAGTAGCTCACAATACGGAAGT 59.869 47.826 0.00 0.00 39.26 3.01
337 340 2.104859 GGAAGTTACCGCGGAAGGC 61.105 63.158 35.90 18.22 38.69 4.35
340 343 1.823169 AAGTTACCGCGGAAGGCTCA 61.823 55.000 35.90 3.68 40.44 4.26
342 345 2.575893 TTACCGCGGAAGGCTCACA 61.576 57.895 35.90 0.72 40.44 3.58
343 346 2.102109 TTACCGCGGAAGGCTCACAA 62.102 55.000 35.90 7.88 40.44 3.33
411 689 2.877168 AGCGCCATCATCTCTCAATTTC 59.123 45.455 2.29 0.00 0.00 2.17
418 696 4.515028 TCATCTCTCAATTTCAGCCCAT 57.485 40.909 0.00 0.00 0.00 4.00
427 705 7.549839 TCTCAATTTCAGCCCATTAATCTTTG 58.450 34.615 0.00 0.00 0.00 2.77
436 714 0.738389 ATTAATCTTTGGCGGCACCG 59.262 50.000 12.92 4.30 43.94 4.94
437 715 0.606944 TTAATCTTTGGCGGCACCGT 60.607 50.000 12.92 0.00 43.94 4.83
458 736 3.577415 GTGCGGGTATAATCTACTCCCTT 59.423 47.826 0.00 0.00 36.30 3.95
463 741 4.462132 GGGTATAATCTACTCCCTTCGTCC 59.538 50.000 0.00 0.00 35.63 4.79
471 759 5.900437 TCTACTCCCTTCGTCCCATAATAT 58.100 41.667 0.00 0.00 0.00 1.28
472 760 7.036154 TCTACTCCCTTCGTCCCATAATATA 57.964 40.000 0.00 0.00 0.00 0.86
474 762 6.607004 ACTCCCTTCGTCCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
475 763 6.320518 ACTCCCTTCGTCCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
478 766 6.210784 TCCCTTCGTCCCATAATATAAGAGTG 59.789 42.308 0.00 0.00 0.00 3.51
482 770 8.657074 TTCGTCCCATAATATAAGAGTGTTTG 57.343 34.615 0.00 0.00 0.00 2.93
483 771 7.788026 TCGTCCCATAATATAAGAGTGTTTGT 58.212 34.615 0.00 0.00 0.00 2.83
484 772 8.262227 TCGTCCCATAATATAAGAGTGTTTGTT 58.738 33.333 0.00 0.00 0.00 2.83
510 799 3.385115 CTCAGGTGGAGGGGTAGTTAAT 58.615 50.000 0.00 0.00 40.13 1.40
516 805 5.427806 AGGTGGAGGGGTAGTTAATTAGAAC 59.572 44.000 0.00 0.00 0.00 3.01
517 806 5.427806 GGTGGAGGGGTAGTTAATTAGAACT 59.572 44.000 0.00 0.00 42.35 3.01
518 807 6.069789 GGTGGAGGGGTAGTTAATTAGAACTT 60.070 42.308 0.00 0.00 40.22 2.66
524 813 9.059023 AGGGGTAGTTAATTAGAACTTTCATCT 57.941 33.333 0.00 0.00 40.22 2.90
606 896 3.940209 CAGACCTGCTCATCCTATCTC 57.060 52.381 0.00 0.00 0.00 2.75
607 897 3.499338 CAGACCTGCTCATCCTATCTCT 58.501 50.000 0.00 0.00 0.00 3.10
608 898 3.507233 CAGACCTGCTCATCCTATCTCTC 59.493 52.174 0.00 0.00 0.00 3.20
791 1586 1.808945 CTGTTCTCCTGTGATGCCAAC 59.191 52.381 0.00 0.00 0.00 3.77
800 1595 2.221169 TGTGATGCCAACTTCTGTGAC 58.779 47.619 0.00 0.00 0.00 3.67
822 1617 0.392863 CGTGATCCATCAGGCAACCA 60.393 55.000 0.00 0.00 37.51 3.67
845 1640 1.734465 GATTTCTGACCAAGTGAGGCG 59.266 52.381 0.00 0.00 0.00 5.52
932 1746 1.448540 CGGCTTCCGCTCATGTTCT 60.449 57.895 0.00 0.00 41.17 3.01
944 1765 0.541863 CATGTTCTTCTACCCCGGCT 59.458 55.000 0.00 0.00 0.00 5.52
959 1780 1.202417 CCGGCTGGCTATATATCCGTG 60.202 57.143 0.00 0.00 35.52 4.94
973 1794 2.535012 TCCGTGTGTATGCTTGTCAA 57.465 45.000 0.00 0.00 0.00 3.18
980 1801 5.610124 CGTGTGTATGCTTGTCAAATTTTGC 60.610 40.000 4.19 1.16 0.00 3.68
982 1803 5.990386 TGTGTATGCTTGTCAAATTTTGCAT 59.010 32.000 12.30 12.30 42.64 3.96
983 1804 6.145858 TGTGTATGCTTGTCAAATTTTGCATC 59.854 34.615 11.31 6.11 40.82 3.91
985 1806 5.600908 ATGCTTGTCAAATTTTGCATCAC 57.399 34.783 4.19 0.00 36.57 3.06
986 1807 3.490155 TGCTTGTCAAATTTTGCATCACG 59.510 39.130 4.19 3.54 0.00 4.35
987 1808 3.662454 GCTTGTCAAATTTTGCATCACGC 60.662 43.478 4.19 8.66 42.89 5.34
1179 2056 2.436646 CCTCACCGCACCATCACC 60.437 66.667 0.00 0.00 0.00 4.02
1286 2163 1.676014 GGAGGTGATGAAGACCAACGG 60.676 57.143 0.00 0.00 35.76 4.44
2059 3183 2.404215 GCTTTGACTCGCTGACAGTTA 58.596 47.619 3.99 0.00 0.00 2.24
2069 3193 7.602644 TGACTCGCTGACAGTTAATCTTTTATT 59.397 33.333 3.99 0.00 0.00 1.40
2075 3203 9.556030 GCTGACAGTTAATCTTTTATTAACACC 57.444 33.333 18.01 9.82 43.33 4.16
2137 4195 5.486526 ACTTCATGCCAAGTTTGTTTTGAA 58.513 33.333 0.00 0.00 32.34 2.69
2367 4532 3.771479 AGAACTCCACTACATGCAGATGA 59.229 43.478 0.00 0.00 33.36 2.92
2390 4555 8.553085 TGATCATCAAGGAGGTTCTTAGATTA 57.447 34.615 0.00 0.00 0.00 1.75
2414 4579 3.782443 CCCGCCGCTTTACTCCCT 61.782 66.667 0.00 0.00 0.00 4.20
2423 4588 2.007547 GCTTTACTCCCTCGCAAGACC 61.008 57.143 0.00 0.00 45.01 3.85
2450 4615 7.337942 AGAGAAGACTGCAAAATTATGGGTTAG 59.662 37.037 0.00 0.00 0.00 2.34
2723 4889 2.072298 GATGCCAACTCAGTGTCACTC 58.928 52.381 1.37 0.00 0.00 3.51
2727 4893 2.868044 GCCAACTCAGTGTCACTCGATT 60.868 50.000 1.37 0.00 0.00 3.34
2803 4969 3.750130 GCTATTCCACATGTATGCTCCAG 59.250 47.826 0.00 0.00 0.00 3.86
2863 5038 9.620259 TCATATGTGTTGCATTGTACCTTTATA 57.380 29.630 1.90 0.00 38.94 0.98
2906 5081 4.022416 TCATGGAATAACTTGTTGTGCCAC 60.022 41.667 11.39 0.00 0.00 5.01
2987 5162 1.135721 GGGAAAGCATGCCAACATCTC 59.864 52.381 15.66 1.88 39.85 2.75
2988 5163 1.202222 GGAAAGCATGCCAACATCTCG 60.202 52.381 15.66 0.00 32.87 4.04
3087 5273 5.596836 TTTTTGAAAGATCCAACACAGCT 57.403 34.783 0.00 0.00 0.00 4.24
3088 5274 4.572985 TTTGAAAGATCCAACACAGCTG 57.427 40.909 13.48 13.48 0.00 4.24
3089 5275 2.507484 TGAAAGATCCAACACAGCTGG 58.493 47.619 19.93 9.66 35.05 4.85
3090 5276 1.200948 GAAAGATCCAACACAGCTGGC 59.799 52.381 19.93 0.00 33.63 4.85
3091 5277 0.403271 AAGATCCAACACAGCTGGCT 59.597 50.000 19.93 0.00 33.63 4.75
3092 5278 0.403271 AGATCCAACACAGCTGGCTT 59.597 50.000 19.93 5.44 33.63 4.35
3093 5279 1.202976 AGATCCAACACAGCTGGCTTT 60.203 47.619 19.93 4.73 33.63 3.51
3094 5280 1.615392 GATCCAACACAGCTGGCTTTT 59.385 47.619 19.93 2.01 33.63 2.27
3095 5281 1.032014 TCCAACACAGCTGGCTTTTC 58.968 50.000 19.93 0.00 33.63 2.29
3096 5282 0.746063 CCAACACAGCTGGCTTTTCA 59.254 50.000 19.93 0.00 0.00 2.69
3097 5283 1.342174 CCAACACAGCTGGCTTTTCAT 59.658 47.619 19.93 0.00 0.00 2.57
3098 5284 2.400399 CAACACAGCTGGCTTTTCATG 58.600 47.619 19.93 6.91 0.00 3.07
3099 5285 1.696063 ACACAGCTGGCTTTTCATGT 58.304 45.000 19.93 7.61 0.00 3.21
3100 5286 2.034124 ACACAGCTGGCTTTTCATGTT 58.966 42.857 19.93 0.00 0.00 2.71
3101 5287 2.223876 ACACAGCTGGCTTTTCATGTTG 60.224 45.455 19.93 4.82 0.00 3.33
3102 5288 2.034939 CACAGCTGGCTTTTCATGTTGA 59.965 45.455 19.93 0.00 0.00 3.18
3103 5289 2.895404 ACAGCTGGCTTTTCATGTTGAT 59.105 40.909 19.93 0.00 0.00 2.57
3104 5290 3.057033 ACAGCTGGCTTTTCATGTTGATC 60.057 43.478 19.93 0.00 0.00 2.92
3105 5291 3.057104 CAGCTGGCTTTTCATGTTGATCA 60.057 43.478 5.57 0.00 0.00 2.92
3106 5292 3.767673 AGCTGGCTTTTCATGTTGATCAT 59.232 39.130 0.00 0.00 37.22 2.45
3107 5293 4.951715 AGCTGGCTTTTCATGTTGATCATA 59.048 37.500 0.00 0.00 34.67 2.15
3108 5294 5.067413 AGCTGGCTTTTCATGTTGATCATAG 59.933 40.000 0.00 0.00 34.67 2.23
3109 5295 5.252969 TGGCTTTTCATGTTGATCATAGC 57.747 39.130 0.00 0.00 35.10 2.97
3110 5296 4.705991 TGGCTTTTCATGTTGATCATAGCA 59.294 37.500 0.00 0.00 36.61 3.49
3111 5297 5.163591 TGGCTTTTCATGTTGATCATAGCAG 60.164 40.000 0.00 0.00 36.61 4.24
3112 5298 5.066893 GGCTTTTCATGTTGATCATAGCAGA 59.933 40.000 0.00 0.00 36.61 4.26
3327 5513 1.137086 ACACATCTATGAGCCGGTGTC 59.863 52.381 1.90 0.33 34.68 3.67
3420 5606 3.827302 AGACAACAACTCGAGACATAGGT 59.173 43.478 21.68 9.62 0.00 3.08
3594 5780 3.306156 GCTCCACGACTAAGTCCTTTCTT 60.306 47.826 0.00 0.00 0.00 2.52
3720 5906 0.315568 GCTGTAGGCCGGATGACTAG 59.684 60.000 5.05 0.00 34.27 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.073209 TGGTAAAGACAGCATGGGTGTAA 59.927 43.478 0.54 0.00 44.55 2.41
55 56 3.254892 CGGCTCAGAAAAGACTAGGAAC 58.745 50.000 0.00 0.00 0.00 3.62
56 57 2.233922 CCGGCTCAGAAAAGACTAGGAA 59.766 50.000 0.00 0.00 0.00 3.36
58 59 1.825474 TCCGGCTCAGAAAAGACTAGG 59.175 52.381 0.00 0.00 0.00 3.02
68 71 0.758734 CCATACCATTCCGGCTCAGA 59.241 55.000 0.00 0.00 39.03 3.27
77 80 4.282703 ACACTCCGGTATACCATACCATTC 59.717 45.833 21.76 0.00 37.44 2.67
202 205 7.870445 ACAACAAGTAACTTCAAAAGCAGAAAA 59.130 29.630 0.00 0.00 0.00 2.29
217 220 4.114794 ACTACACGTCCACAACAAGTAAC 58.885 43.478 0.00 0.00 0.00 2.50
220 223 2.973694 ACTACACGTCCACAACAAGT 57.026 45.000 0.00 0.00 0.00 3.16
221 224 6.588756 ACATATTACTACACGTCCACAACAAG 59.411 38.462 0.00 0.00 0.00 3.16
226 229 6.308524 CGAAAACATATTACTACACGTCCACA 59.691 38.462 0.00 0.00 0.00 4.17
227 230 6.308766 ACGAAAACATATTACTACACGTCCAC 59.691 38.462 0.00 0.00 0.00 4.02
228 231 6.308524 CACGAAAACATATTACTACACGTCCA 59.691 38.462 0.00 0.00 0.00 4.02
229 232 6.237648 CCACGAAAACATATTACTACACGTCC 60.238 42.308 0.00 0.00 0.00 4.79
230 233 6.689547 CCACGAAAACATATTACTACACGTC 58.310 40.000 0.00 0.00 0.00 4.34
231 234 5.062558 GCCACGAAAACATATTACTACACGT 59.937 40.000 0.00 0.00 0.00 4.49
232 235 5.486706 GCCACGAAAACATATTACTACACG 58.513 41.667 0.00 0.00 0.00 4.49
233 236 5.583457 AGGCCACGAAAACATATTACTACAC 59.417 40.000 5.01 0.00 0.00 2.90
261 264 1.139853 CTCACCTTGGACAGCCCTATC 59.860 57.143 0.00 0.00 35.38 2.08
268 271 0.325933 TGCCATCTCACCTTGGACAG 59.674 55.000 0.00 0.00 34.81 3.51
300 303 4.160642 TCCGTATTGTGAGCTACTCCTA 57.839 45.455 0.00 0.00 0.00 2.94
301 304 3.014304 TCCGTATTGTGAGCTACTCCT 57.986 47.619 0.00 0.00 0.00 3.69
302 305 3.130693 ACTTCCGTATTGTGAGCTACTCC 59.869 47.826 0.00 0.00 0.00 3.85
324 327 2.102109 TTGTGAGCCTTCCGCGGTAA 62.102 55.000 27.15 16.74 44.76 2.85
337 340 6.382869 AAAGGAAAACAGATGAGTTGTGAG 57.617 37.500 0.00 0.00 0.00 3.51
340 343 6.378280 ACAGAAAAGGAAAACAGATGAGTTGT 59.622 34.615 0.00 0.00 0.00 3.32
342 345 7.340487 AGAACAGAAAAGGAAAACAGATGAGTT 59.660 33.333 0.00 0.00 0.00 3.01
343 346 6.830838 AGAACAGAAAAGGAAAACAGATGAGT 59.169 34.615 0.00 0.00 0.00 3.41
385 663 1.865970 GAGAGATGATGGCGCTCTTTG 59.134 52.381 7.64 0.00 39.00 2.77
388 666 1.117994 TTGAGAGATGATGGCGCTCT 58.882 50.000 7.64 0.35 41.42 4.09
411 689 1.067516 CCGCCAAAGATTAATGGGCTG 59.932 52.381 12.51 5.32 42.43 4.85
418 696 0.606944 ACGGTGCCGCCAAAGATTAA 60.607 50.000 10.87 0.00 44.19 1.40
436 714 3.163467 AGGGAGTAGATTATACCCGCAC 58.837 50.000 0.00 0.00 44.57 5.34
437 715 3.537795 AGGGAGTAGATTATACCCGCA 57.462 47.619 0.00 0.00 44.57 5.69
458 736 7.788026 ACAAACACTCTTATATTATGGGACGA 58.212 34.615 0.00 0.00 0.00 4.20
471 759 7.431249 CACCTGAGTAGTAACAAACACTCTTA 58.569 38.462 0.00 0.00 37.25 2.10
472 760 6.281405 CACCTGAGTAGTAACAAACACTCTT 58.719 40.000 0.00 0.00 37.25 2.85
474 762 4.989168 CCACCTGAGTAGTAACAAACACTC 59.011 45.833 0.00 0.00 37.06 3.51
475 763 4.652421 TCCACCTGAGTAGTAACAAACACT 59.348 41.667 0.00 0.00 0.00 3.55
478 766 4.562963 CCCTCCACCTGAGTAGTAACAAAC 60.563 50.000 0.00 0.00 39.65 2.93
482 770 2.108970 CCCCTCCACCTGAGTAGTAAC 58.891 57.143 0.00 0.00 39.65 2.50
483 771 1.720533 ACCCCTCCACCTGAGTAGTAA 59.279 52.381 0.00 0.00 39.65 2.24
484 772 1.390287 ACCCCTCCACCTGAGTAGTA 58.610 55.000 0.00 0.00 39.65 1.82
492 780 5.230746 TCTAATTAACTACCCCTCCACCT 57.769 43.478 0.00 0.00 0.00 4.00
494 782 6.556974 AGTTCTAATTAACTACCCCTCCAC 57.443 41.667 0.00 0.00 37.93 4.02
606 896 1.265635 CGAGTATTCCGCTGGAGAGAG 59.734 57.143 0.00 0.00 31.21 3.20
607 897 1.309950 CGAGTATTCCGCTGGAGAGA 58.690 55.000 0.00 0.00 31.21 3.10
608 898 1.025812 ACGAGTATTCCGCTGGAGAG 58.974 55.000 0.00 0.00 31.21 3.20
671 1456 6.127338 TGGGCAATAACTATCTATCGATCTGG 60.127 42.308 0.00 0.00 0.00 3.86
791 1586 2.754472 TGGATCACGTTGTCACAGAAG 58.246 47.619 0.00 0.00 0.00 2.85
800 1595 1.131126 GTTGCCTGATGGATCACGTTG 59.869 52.381 0.00 0.00 34.57 4.10
822 1617 4.681781 CGCCTCACTTGGTCAGAAATCTAT 60.682 45.833 0.00 0.00 0.00 1.98
845 1640 2.103263 ACGCTCCCTTGGATGACTATTC 59.897 50.000 0.00 0.00 0.00 1.75
944 1765 4.709886 AGCATACACACGGATATATAGCCA 59.290 41.667 16.97 0.00 0.00 4.75
959 1780 5.903764 TGCAAAATTTGACAAGCATACAC 57.096 34.783 10.26 0.00 0.00 2.90
987 1808 4.100084 TCCATGGCAGGCCGAGTG 62.100 66.667 6.96 4.67 39.42 3.51
988 1809 3.790437 CTCCATGGCAGGCCGAGT 61.790 66.667 6.96 0.00 39.42 4.18
989 1810 4.559063 CCTCCATGGCAGGCCGAG 62.559 72.222 6.96 6.30 39.42 4.63
992 1813 4.066139 AACCCTCCATGGCAGGCC 62.066 66.667 19.48 2.62 0.00 5.19
1082 1959 3.368571 GCAGGTGCAGGTGCTTCC 61.369 66.667 12.09 6.14 42.66 3.46
1179 2056 4.794439 TGCCGGCGACACAGATCG 62.794 66.667 23.90 0.00 45.09 3.69
1286 2163 3.119096 GGTTGGAGAAGGCGACGC 61.119 66.667 12.43 12.43 0.00 5.19
1702 2588 1.143183 GGATCCTCTTTACGCGGCA 59.857 57.895 12.47 0.00 0.00 5.69
2025 3149 1.606668 TCAAAGCCCAAAGTTACAGCG 59.393 47.619 0.00 0.00 0.00 5.18
2069 3193 9.845740 AGTATGCAAGTATTTCATATGGTGTTA 57.154 29.630 2.13 0.00 0.00 2.41
2367 4532 8.324191 TGTAATCTAAGAACCTCCTTGATGAT 57.676 34.615 0.00 0.00 0.00 2.45
2390 4555 2.961893 TAAAGCGGCGGGTGGATGT 61.962 57.895 9.78 0.00 0.00 3.06
2414 4579 1.270826 CAGTCTTCTCTGGTCTTGCGA 59.729 52.381 0.00 0.00 0.00 5.10
2423 4588 5.416952 ACCCATAATTTTGCAGTCTTCTCTG 59.583 40.000 0.00 0.00 38.35 3.35
2723 4889 3.684788 ACCCGAATTTCTCAGACAAATCG 59.315 43.478 0.00 0.00 0.00 3.34
2727 4893 3.813166 GTGAACCCGAATTTCTCAGACAA 59.187 43.478 0.00 0.00 0.00 3.18
2803 4969 7.661536 TCTTGGATCTATATATGTGTAGCCC 57.338 40.000 0.00 0.00 0.00 5.19
2863 5038 8.874156 TCCATGAGCTCTTATTCTAATGTATGT 58.126 33.333 16.19 0.00 0.00 2.29
2962 5137 1.070601 GTTGGCATGCTTTCCCAGTTT 59.929 47.619 18.92 0.00 0.00 2.66
2963 5138 0.681175 GTTGGCATGCTTTCCCAGTT 59.319 50.000 18.92 0.00 0.00 3.16
2966 5141 0.896923 GATGTTGGCATGCTTTCCCA 59.103 50.000 18.92 3.25 35.07 4.37
2987 5162 0.597568 TCAAAATTGGCCACAGAGCG 59.402 50.000 3.88 0.00 0.00 5.03
2988 5163 2.297033 TCTTCAAAATTGGCCACAGAGC 59.703 45.455 3.88 0.00 0.00 4.09
3065 5251 5.350633 CAGCTGTGTTGGATCTTTCAAAAA 58.649 37.500 5.25 0.00 0.00 1.94
3066 5252 4.202141 CCAGCTGTGTTGGATCTTTCAAAA 60.202 41.667 13.81 0.00 35.94 2.44
3067 5253 3.318839 CCAGCTGTGTTGGATCTTTCAAA 59.681 43.478 13.81 0.00 35.94 2.69
3068 5254 2.886523 CCAGCTGTGTTGGATCTTTCAA 59.113 45.455 13.81 0.00 35.94 2.69
3069 5255 2.507484 CCAGCTGTGTTGGATCTTTCA 58.493 47.619 13.81 0.00 35.94 2.69
3070 5256 1.200948 GCCAGCTGTGTTGGATCTTTC 59.799 52.381 13.81 0.00 35.94 2.62
3071 5257 1.202976 AGCCAGCTGTGTTGGATCTTT 60.203 47.619 13.81 0.00 35.94 2.52
3072 5258 0.403271 AGCCAGCTGTGTTGGATCTT 59.597 50.000 13.81 0.00 35.94 2.40
3073 5259 0.403271 AAGCCAGCTGTGTTGGATCT 59.597 50.000 13.81 0.00 35.94 2.75
3074 5260 1.251251 AAAGCCAGCTGTGTTGGATC 58.749 50.000 13.81 0.00 35.94 3.36
3075 5261 1.615392 GAAAAGCCAGCTGTGTTGGAT 59.385 47.619 13.81 0.00 35.94 3.41
3076 5262 1.032014 GAAAAGCCAGCTGTGTTGGA 58.968 50.000 13.81 0.00 35.94 3.53
3077 5263 0.746063 TGAAAAGCCAGCTGTGTTGG 59.254 50.000 13.81 0.00 36.98 3.77
3078 5264 2.223876 ACATGAAAAGCCAGCTGTGTTG 60.224 45.455 13.81 0.00 0.00 3.33
3079 5265 2.034124 ACATGAAAAGCCAGCTGTGTT 58.966 42.857 13.81 2.19 0.00 3.32
3080 5266 1.696063 ACATGAAAAGCCAGCTGTGT 58.304 45.000 13.81 4.68 0.00 3.72
3081 5267 2.034939 TCAACATGAAAAGCCAGCTGTG 59.965 45.455 13.81 5.37 0.00 3.66
3082 5268 2.309613 TCAACATGAAAAGCCAGCTGT 58.690 42.857 13.81 0.00 0.00 4.40
3083 5269 3.057104 TGATCAACATGAAAAGCCAGCTG 60.057 43.478 6.78 6.78 0.00 4.24
3084 5270 3.159472 TGATCAACATGAAAAGCCAGCT 58.841 40.909 0.00 0.00 0.00 4.24
3085 5271 3.581024 TGATCAACATGAAAAGCCAGC 57.419 42.857 0.00 0.00 0.00 4.85
3086 5272 5.163591 TGCTATGATCAACATGAAAAGCCAG 60.164 40.000 0.00 0.00 39.77 4.85
3087 5273 4.705991 TGCTATGATCAACATGAAAAGCCA 59.294 37.500 0.00 0.00 39.77 4.75
3088 5274 5.066893 TCTGCTATGATCAACATGAAAAGCC 59.933 40.000 0.00 0.00 39.77 4.35
3089 5275 6.127810 TCTGCTATGATCAACATGAAAAGC 57.872 37.500 0.00 0.13 39.77 3.51
3090 5276 7.148289 ACACTCTGCTATGATCAACATGAAAAG 60.148 37.037 0.00 0.00 39.77 2.27
3091 5277 6.656270 ACACTCTGCTATGATCAACATGAAAA 59.344 34.615 0.00 0.00 39.77 2.29
3092 5278 6.175471 ACACTCTGCTATGATCAACATGAAA 58.825 36.000 0.00 0.00 39.77 2.69
3093 5279 5.737860 ACACTCTGCTATGATCAACATGAA 58.262 37.500 0.00 0.00 39.77 2.57
3094 5280 5.349061 ACACTCTGCTATGATCAACATGA 57.651 39.130 0.00 0.00 39.77 3.07
3095 5281 5.220796 CCAACACTCTGCTATGATCAACATG 60.221 44.000 0.00 0.00 39.77 3.21
3096 5282 4.880120 CCAACACTCTGCTATGATCAACAT 59.120 41.667 0.00 0.00 42.39 2.71
3097 5283 4.256110 CCAACACTCTGCTATGATCAACA 58.744 43.478 0.00 0.00 0.00 3.33
3098 5284 3.624861 CCCAACACTCTGCTATGATCAAC 59.375 47.826 0.00 0.00 0.00 3.18
3099 5285 3.370846 CCCCAACACTCTGCTATGATCAA 60.371 47.826 0.00 0.00 0.00 2.57
3100 5286 2.171237 CCCCAACACTCTGCTATGATCA 59.829 50.000 0.00 0.00 0.00 2.92
3101 5287 2.435805 TCCCCAACACTCTGCTATGATC 59.564 50.000 0.00 0.00 0.00 2.92
3102 5288 2.481441 TCCCCAACACTCTGCTATGAT 58.519 47.619 0.00 0.00 0.00 2.45
3103 5289 1.951209 TCCCCAACACTCTGCTATGA 58.049 50.000 0.00 0.00 0.00 2.15
3104 5290 4.630644 ATATCCCCAACACTCTGCTATG 57.369 45.455 0.00 0.00 0.00 2.23
3105 5291 5.846714 AGTAATATCCCCAACACTCTGCTAT 59.153 40.000 0.00 0.00 0.00 2.97
3106 5292 5.216622 AGTAATATCCCCAACACTCTGCTA 58.783 41.667 0.00 0.00 0.00 3.49
3107 5293 4.040755 AGTAATATCCCCAACACTCTGCT 58.959 43.478 0.00 0.00 0.00 4.24
3108 5294 4.423625 AGTAATATCCCCAACACTCTGC 57.576 45.455 0.00 0.00 0.00 4.26
3109 5295 6.463049 CCAGTAGTAATATCCCCAACACTCTG 60.463 46.154 0.00 0.00 0.00 3.35
3110 5296 5.602978 CCAGTAGTAATATCCCCAACACTCT 59.397 44.000 0.00 0.00 0.00 3.24
3111 5297 5.221661 CCCAGTAGTAATATCCCCAACACTC 60.222 48.000 0.00 0.00 0.00 3.51
3112 5298 4.658901 CCCAGTAGTAATATCCCCAACACT 59.341 45.833 0.00 0.00 0.00 3.55
3192 5378 4.140924 TGAGCCCTCATCTACCTTCATAGA 60.141 45.833 0.00 0.00 35.67 1.98
3194 5380 4.199002 TGAGCCCTCATCTACCTTCATA 57.801 45.455 0.00 0.00 34.14 2.15
3327 5513 0.455633 CGTCGGTTTACAGAGTCCCG 60.456 60.000 0.00 0.00 39.98 5.14
3420 5606 2.106511 ACTAGGGAGCAAACAAGCTTCA 59.893 45.455 0.00 0.00 46.75 3.02
3594 5780 1.262417 TGTCACGGCAGATGTCCTAA 58.738 50.000 0.00 0.00 0.00 2.69
3720 5906 3.567797 GCTTGCCGCGATGACTCC 61.568 66.667 8.23 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.