Multiple sequence alignment - TraesCS5B01G126300

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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 TraesCS5B01G126300 chr5B 100.000 8832 0 0 1 8832 230434371 230425540 0.000000e+00 16310.0
1 TraesCS5B01G126300 chr5B 82.461 707 92 15 8043 8725 427287124 427287822 2.750000e-164 590.0
2 TraesCS5B01G126300 chr1B 98.635 5348 66 4 1132 6478 60535447 60540788 0.000000e+00 9465.0
3 TraesCS5B01G126300 chr1B 97.386 5356 124 5 1136 6478 94557348 94551996 0.000000e+00 9101.0
4 TraesCS5B01G126300 chr1B 98.791 4879 52 2 1600 6477 654788924 654793796 0.000000e+00 8676.0
5 TraesCS5B01G126300 chr1B 81.189 824 87 30 8075 8831 253005351 253004529 1.270000e-167 601.0
6 TraesCS5B01G126300 chr1B 80.633 821 111 25 8043 8831 322490834 322491638 7.640000e-165 592.0
7 TraesCS5B01G126300 chr6A 98.652 5343 65 3 1136 6477 573434299 573428963 0.000000e+00 9461.0
8 TraesCS5B01G126300 chr6A 98.222 5344 69 5 1136 6477 584715497 584710178 0.000000e+00 9319.0
9 TraesCS5B01G126300 chr6A 78.952 1240 169 61 7658 8830 503730390 503731604 0.000000e+00 760.0
10 TraesCS5B01G126300 chr4B 98.541 5345 72 2 1136 6479 573087859 573082520 0.000000e+00 9433.0
11 TraesCS5B01G126300 chr1A 98.540 5343 76 2 1136 6477 578030283 578035624 0.000000e+00 9433.0
12 TraesCS5B01G126300 chr2B 98.540 5343 70 2 1136 6477 571535338 571540673 0.000000e+00 9428.0
13 TraesCS5B01G126300 chr2B 97.137 5344 119 6 1136 6478 753659566 753664876 0.000000e+00 8990.0
14 TraesCS5B01G126300 chr6B 97.136 5343 116 5 1136 6477 707836521 707831215 0.000000e+00 8985.0
15 TraesCS5B01G126300 chr6B 77.994 1236 198 46 7652 8832 549190941 549189725 0.000000e+00 708.0
16 TraesCS5B01G126300 chr7B 98.652 4970 63 2 1509 6477 68204324 68209290 0.000000e+00 8804.0
17 TraesCS5B01G126300 chr7B 83.635 996 118 24 7756 8724 527984367 527985344 0.000000e+00 894.0
18 TraesCS5B01G126300 chr3A 97.166 4552 110 4 1135 5673 708238024 708242569 0.000000e+00 7673.0
19 TraesCS5B01G126300 chr3A 80.895 827 116 19 8042 8831 277440145 277440966 1.630000e-171 614.0
20 TraesCS5B01G126300 chr4A 98.811 2943 34 1 3537 6478 583940500 583943442 0.000000e+00 5240.0
21 TraesCS5B01G126300 chr5A 92.893 1182 47 11 6478 7649 283014241 283013087 0.000000e+00 1683.0
22 TraesCS5B01G126300 chr5A 91.142 1016 36 17 127 1135 283015205 283014237 0.000000e+00 1328.0
23 TraesCS5B01G126300 chr5A 89.041 584 48 6 8260 8831 283004632 283004053 0.000000e+00 710.0
24 TraesCS5B01G126300 chr5A 81.034 812 116 16 8058 8831 592202401 592203212 5.860000e-171 612.0
25 TraesCS5B01G126300 chr5A 85.988 521 64 3 7742 8259 283013035 283012521 4.660000e-152 549.0
26 TraesCS5B01G126300 chr5A 87.313 134 17 0 1 134 283015365 283015232 4.270000e-33 154.0
27 TraesCS5B01G126300 chr5D 92.406 1172 38 18 6478 7644 215244742 215243617 0.000000e+00 1624.0
28 TraesCS5B01G126300 chr5D 95.388 1019 35 10 127 1135 215245754 215244738 0.000000e+00 1611.0
29 TraesCS5B01G126300 chr5D 89.844 128 13 0 1 128 215245914 215245787 1.970000e-36 165.0
30 TraesCS5B01G126300 chr7A 80.454 1233 150 44 7648 8831 589266619 589267809 0.000000e+00 857.0
31 TraesCS5B01G126300 chr7A 80.581 1205 146 44 7674 8831 589269342 589270505 0.000000e+00 848.0
32 TraesCS5B01G126300 chr7A 76.737 1238 180 69 7654 8831 134009721 134008532 7.640000e-165 592.0
33 TraesCS5B01G126300 chr7A 74.595 370 58 19 8448 8806 535456133 535455789 7.200000e-26 130.0
34 TraesCS5B01G126300 chr7A 96.774 31 1 0 7738 7768 128901722 128901752 1.600000e-02 52.8
35 TraesCS5B01G126300 chr1D 79.316 1286 151 47 7652 8831 182046579 182045303 0.000000e+00 795.0
36 TraesCS5B01G126300 chr1D 82.506 806 101 13 8058 8829 223470390 223471189 0.000000e+00 671.0
37 TraesCS5B01G126300 chr4D 82.609 805 103 16 8061 8830 51607380 51606578 0.000000e+00 676.0
38 TraesCS5B01G126300 chr4D 83.108 592 79 10 8260 8830 499747860 499747269 3.650000e-143 520.0
39 TraesCS5B01G126300 chrUn 80.750 800 116 19 8067 8831 366934344 366933548 2.750000e-164 590.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G126300 chr5B 230425540 230434371 8831 True 16310.000000 16310 100.0000 1 8832 1 chr5B.!!$R1 8831
1 TraesCS5B01G126300 chr5B 427287124 427287822 698 False 590.000000 590 82.4610 8043 8725 1 chr5B.!!$F1 682
2 TraesCS5B01G126300 chr1B 60535447 60540788 5341 False 9465.000000 9465 98.6350 1132 6478 1 chr1B.!!$F1 5346
3 TraesCS5B01G126300 chr1B 94551996 94557348 5352 True 9101.000000 9101 97.3860 1136 6478 1 chr1B.!!$R1 5342
4 TraesCS5B01G126300 chr1B 654788924 654793796 4872 False 8676.000000 8676 98.7910 1600 6477 1 chr1B.!!$F3 4877
5 TraesCS5B01G126300 chr1B 253004529 253005351 822 True 601.000000 601 81.1890 8075 8831 1 chr1B.!!$R2 756
6 TraesCS5B01G126300 chr1B 322490834 322491638 804 False 592.000000 592 80.6330 8043 8831 1 chr1B.!!$F2 788
7 TraesCS5B01G126300 chr6A 573428963 573434299 5336 True 9461.000000 9461 98.6520 1136 6477 1 chr6A.!!$R1 5341
8 TraesCS5B01G126300 chr6A 584710178 584715497 5319 True 9319.000000 9319 98.2220 1136 6477 1 chr6A.!!$R2 5341
9 TraesCS5B01G126300 chr6A 503730390 503731604 1214 False 760.000000 760 78.9520 7658 8830 1 chr6A.!!$F1 1172
10 TraesCS5B01G126300 chr4B 573082520 573087859 5339 True 9433.000000 9433 98.5410 1136 6479 1 chr4B.!!$R1 5343
11 TraesCS5B01G126300 chr1A 578030283 578035624 5341 False 9433.000000 9433 98.5400 1136 6477 1 chr1A.!!$F1 5341
12 TraesCS5B01G126300 chr2B 571535338 571540673 5335 False 9428.000000 9428 98.5400 1136 6477 1 chr2B.!!$F1 5341
13 TraesCS5B01G126300 chr2B 753659566 753664876 5310 False 8990.000000 8990 97.1370 1136 6478 1 chr2B.!!$F2 5342
14 TraesCS5B01G126300 chr6B 707831215 707836521 5306 True 8985.000000 8985 97.1360 1136 6477 1 chr6B.!!$R2 5341
15 TraesCS5B01G126300 chr6B 549189725 549190941 1216 True 708.000000 708 77.9940 7652 8832 1 chr6B.!!$R1 1180
16 TraesCS5B01G126300 chr7B 68204324 68209290 4966 False 8804.000000 8804 98.6520 1509 6477 1 chr7B.!!$F1 4968
17 TraesCS5B01G126300 chr7B 527984367 527985344 977 False 894.000000 894 83.6350 7756 8724 1 chr7B.!!$F2 968
18 TraesCS5B01G126300 chr3A 708238024 708242569 4545 False 7673.000000 7673 97.1660 1135 5673 1 chr3A.!!$F2 4538
19 TraesCS5B01G126300 chr3A 277440145 277440966 821 False 614.000000 614 80.8950 8042 8831 1 chr3A.!!$F1 789
20 TraesCS5B01G126300 chr4A 583940500 583943442 2942 False 5240.000000 5240 98.8110 3537 6478 1 chr4A.!!$F1 2941
21 TraesCS5B01G126300 chr5A 283012521 283015365 2844 True 928.500000 1683 89.3340 1 8259 4 chr5A.!!$R2 8258
22 TraesCS5B01G126300 chr5A 283004053 283004632 579 True 710.000000 710 89.0410 8260 8831 1 chr5A.!!$R1 571
23 TraesCS5B01G126300 chr5A 592202401 592203212 811 False 612.000000 612 81.0340 8058 8831 1 chr5A.!!$F1 773
24 TraesCS5B01G126300 chr5D 215243617 215245914 2297 True 1133.333333 1624 92.5460 1 7644 3 chr5D.!!$R1 7643
25 TraesCS5B01G126300 chr7A 589266619 589270505 3886 False 852.500000 857 80.5175 7648 8831 2 chr7A.!!$F2 1183
26 TraesCS5B01G126300 chr7A 134008532 134009721 1189 True 592.000000 592 76.7370 7654 8831 1 chr7A.!!$R1 1177
27 TraesCS5B01G126300 chr1D 182045303 182046579 1276 True 795.000000 795 79.3160 7652 8831 1 chr1D.!!$R1 1179
28 TraesCS5B01G126300 chr1D 223470390 223471189 799 False 671.000000 671 82.5060 8058 8829 1 chr1D.!!$F1 771
29 TraesCS5B01G126300 chr4D 51606578 51607380 802 True 676.000000 676 82.6090 8061 8830 1 chr4D.!!$R1 769
30 TraesCS5B01G126300 chr4D 499747269 499747860 591 True 520.000000 520 83.1080 8260 8830 1 chr4D.!!$R2 570
31 TraesCS5B01G126300 chrUn 366933548 366934344 796 True 590.000000 590 80.7500 8067 8831 1 chrUn.!!$R1 764

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
272 310 1.074566 AGGGGCTTTTCCTGTCAGAAG 59.925 52.381 0.00 0.00 32.53 2.85 F
809 852 1.968493 ACGTATGGACACAAGACCACT 59.032 47.619 0.00 0.00 42.22 4.00 F
2036 2084 1.003442 CTCCTCCATCCAGGGGTCA 59.997 63.158 0.00 0.00 35.37 4.02 F
2766 2816 1.078823 ACTGGTACATGGACTCTGGGA 59.921 52.381 8.27 0.00 38.20 4.37 F
3532 3583 0.464373 CATGTCCAGTCGGATTGGGG 60.464 60.000 18.18 3.94 45.33 4.96 F
4383 4437 4.695231 CCGTCACGCCGTCTTCGT 62.695 66.667 0.00 0.00 41.28 3.85 F
4809 4875 1.415659 CGGATCCATCTTCTGAGCCTT 59.584 52.381 13.41 0.00 34.90 4.35 F
5597 5663 0.032403 GCATGCTGAAGTGCAAACCA 59.968 50.000 11.37 0.00 46.61 3.67 F
6310 6377 0.396811 AGTTTGAGGCTTGTAGGCGT 59.603 50.000 0.00 0.00 46.58 5.68 F
6695 6762 0.108804 AGTCGCCTGACCATACAACG 60.109 55.000 0.00 0.00 46.74 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1209 1257 1.729586 ACCAGCACAACCCTCTAAGA 58.270 50.000 0.00 0.00 0.00 2.10 R
2766 2816 0.529833 CTGGTCAGATGCTCTGTCGT 59.470 55.000 11.37 0.00 44.58 4.34 R
3040 3091 1.201429 AAGAATGTCCCTCGTGCCCT 61.201 55.000 0.00 0.00 0.00 5.19 R
4131 4185 1.006102 CCAAACGAGCTCCACGTCT 60.006 57.895 8.47 0.00 43.16 4.18 R
4809 4875 1.058428 AGGGCAGCCTGATATGAGCA 61.058 55.000 12.43 0.00 0.00 4.26 R
5597 5663 1.228124 CGACATGGGTGTGGTGGTT 60.228 57.895 0.00 0.00 39.09 3.67 R
6479 6546 0.179026 CTCATCCTCCGTCGGGTAGA 60.179 60.000 12.29 6.35 33.83 2.59 R
6677 6744 0.389426 ACGTTGTATGGTCAGGCGAC 60.389 55.000 0.00 0.00 41.80 5.19 R
7782 7882 0.042708 CTTCGATTTCGGCAGATGCG 60.043 55.000 0.00 0.00 43.26 4.73 R
8351 8537 0.883833 CACTTGTGCAAGGTCATCCC 59.116 55.000 15.31 0.00 42.53 3.85 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
110 111 2.592308 CCAAGGTGGCTAGCTCCC 59.408 66.667 15.72 14.35 32.44 4.30
201 237 2.750237 GCGGGTCCCACATCCAAC 60.750 66.667 9.12 0.00 0.00 3.77
213 249 4.711355 CCCACATCCAACTTAATGGTCAAT 59.289 41.667 0.00 0.00 41.46 2.57
252 288 1.522806 GTGCCACGTGGACTTGACA 60.523 57.895 38.30 21.61 37.39 3.58
253 289 1.227527 TGCCACGTGGACTTGACAG 60.228 57.895 38.30 8.59 37.39 3.51
269 307 2.952714 CAGGGGCTTTTCCTGTCAG 58.047 57.895 2.21 0.00 44.97 3.51
272 310 1.074566 AGGGGCTTTTCCTGTCAGAAG 59.925 52.381 0.00 0.00 32.53 2.85
334 372 8.897872 ATTGAGAAAGTTAGTAAGAAAACCGA 57.102 30.769 0.00 0.00 0.00 4.69
348 386 9.362539 GTAAGAAAACCGATAGATTGTTGTAGA 57.637 33.333 0.00 0.00 39.76 2.59
565 605 9.872721 AAATATGTCATGTCATTTGCATTTGTA 57.127 25.926 10.71 0.00 0.00 2.41
658 699 2.548480 TGCGTCGATCGATGTAGAGATT 59.452 45.455 31.77 0.00 42.86 2.40
809 852 1.968493 ACGTATGGACACAAGACCACT 59.032 47.619 0.00 0.00 42.22 4.00
876 923 4.626081 AGCCAGCCACGTGTCACC 62.626 66.667 15.65 0.00 0.00 4.02
906 953 2.289444 ACGTGATGGGTTTAGTGGACTG 60.289 50.000 0.00 0.00 0.00 3.51
1024 1072 4.704833 TCAACCGGCCTCTGCTGC 62.705 66.667 0.00 0.00 42.87 5.25
1032 1080 2.005451 CGGCCTCTGCTGCATATATTC 58.995 52.381 1.31 0.00 36.98 1.75
1033 1081 2.354503 CGGCCTCTGCTGCATATATTCT 60.355 50.000 1.31 0.00 36.98 2.40
1501 1549 1.153549 GCATCGGCTCCGTCTTCTT 60.154 57.895 8.28 0.00 40.74 2.52
1988 2036 1.046472 TCTACAATCCGGCCCATCGT 61.046 55.000 0.00 0.00 0.00 3.73
2036 2084 1.003442 CTCCTCCATCCAGGGGTCA 59.997 63.158 0.00 0.00 35.37 4.02
2130 2178 3.474486 TTTGCAGCGCAGTCCCAGA 62.474 57.895 11.47 0.00 40.61 3.86
2766 2816 1.078823 ACTGGTACATGGACTCTGGGA 59.921 52.381 8.27 0.00 38.20 4.37
2920 2970 4.384056 AGACATGCCAATAGGAATCTTCG 58.616 43.478 0.00 0.00 36.89 3.79
3141 3192 0.969894 CAGTGGAGTTCGGGTCTCTT 59.030 55.000 0.00 0.00 33.06 2.85
3224 3275 4.438336 CGTCGTCATGAGCTTCCTAGTTTA 60.438 45.833 0.00 0.00 0.00 2.01
3532 3583 0.464373 CATGTCCAGTCGGATTGGGG 60.464 60.000 18.18 3.94 45.33 4.96
3807 3861 6.271391 TGAGGTTCTCCTTAATGAACAACCTA 59.729 38.462 17.15 8.58 45.24 3.08
4383 4437 4.695231 CCGTCACGCCGTCTTCGT 62.695 66.667 0.00 0.00 41.28 3.85
4809 4875 1.415659 CGGATCCATCTTCTGAGCCTT 59.584 52.381 13.41 0.00 34.90 4.35
5597 5663 0.032403 GCATGCTGAAGTGCAAACCA 59.968 50.000 11.37 0.00 46.61 3.67
5708 5774 4.067972 TGTTGGTGGACTTCAGTACTTC 57.932 45.455 0.00 0.00 0.00 3.01
5713 5779 3.566523 GTGGACTTCAGTACTTCACGAG 58.433 50.000 0.00 0.00 0.00 4.18
5714 5780 3.004524 GTGGACTTCAGTACTTCACGAGT 59.995 47.826 0.00 0.00 42.55 4.18
5799 5865 3.434309 ACTCATTGGGCTGCTGTTAAAT 58.566 40.909 0.00 0.00 0.00 1.40
6225 6291 2.611518 GTGTATCGCAGAAGCAACTCT 58.388 47.619 0.00 0.00 43.58 3.24
6310 6377 0.396811 AGTTTGAGGCTTGTAGGCGT 59.603 50.000 0.00 0.00 46.58 5.68
6479 6546 7.064229 TCCCCAAAACTTATTGTCTTACAGTT 58.936 34.615 0.00 0.00 0.00 3.16
6480 6547 7.229907 TCCCCAAAACTTATTGTCTTACAGTTC 59.770 37.037 0.00 0.00 0.00 3.01
6481 6548 7.230712 CCCCAAAACTTATTGTCTTACAGTTCT 59.769 37.037 0.00 0.00 0.00 3.01
6606 6673 2.928396 CACCCTTCCCACCTCCGT 60.928 66.667 0.00 0.00 0.00 4.69
6643 6710 4.343814 TGTCAGTGTCAGTCCAGTGAATAA 59.656 41.667 0.59 0.00 44.20 1.40
6654 6721 4.823442 GTCCAGTGAATAATGATGGCATGA 59.177 41.667 3.81 0.00 34.26 3.07
6677 6744 0.886490 ACGCTCTTTGTGGCCTGAAG 60.886 55.000 3.32 5.63 0.00 3.02
6695 6762 0.108804 AGTCGCCTGACCATACAACG 60.109 55.000 0.00 0.00 46.74 4.10
6763 6830 2.231478 CGGAGCAGTGGTTCTTCTTCTA 59.769 50.000 0.00 0.00 0.00 2.10
6986 7056 4.202223 TGGAAGATGAACGAGTATAAGGCC 60.202 45.833 0.00 0.00 0.00 5.19
7024 7094 2.697761 CGACGACCGGACACCAGAT 61.698 63.158 9.46 0.00 33.91 2.90
7066 7141 3.238438 CCAGCTAGCTCTGGCCAT 58.762 61.111 16.15 0.00 46.11 4.40
7069 7144 1.022735 CAGCTAGCTCTGGCCATTTG 58.977 55.000 16.15 0.00 37.85 2.32
7076 7151 1.811558 GCTCTGGCCATTTGATCGCTA 60.812 52.381 5.51 0.00 0.00 4.26
7086 7161 4.682860 CCATTTGATCGCTAATTTGATGCC 59.317 41.667 0.00 0.00 0.00 4.40
7387 7462 1.218316 CTTGGAGCACGACCTACCC 59.782 63.158 0.00 0.00 0.00 3.69
7469 7568 6.455246 GCCGTAATCTAGAACAGTTTTGCTAC 60.455 42.308 0.00 0.00 0.00 3.58
7470 7569 6.035758 CCGTAATCTAGAACAGTTTTGCTACC 59.964 42.308 0.00 0.00 0.00 3.18
7471 7570 6.035758 CGTAATCTAGAACAGTTTTGCTACCC 59.964 42.308 0.00 0.00 0.00 3.69
7472 7571 5.763876 ATCTAGAACAGTTTTGCTACCCT 57.236 39.130 0.00 0.00 0.00 4.34
7473 7572 6.869206 ATCTAGAACAGTTTTGCTACCCTA 57.131 37.500 0.00 0.00 0.00 3.53
7474 7573 6.675413 TCTAGAACAGTTTTGCTACCCTAA 57.325 37.500 0.00 0.00 0.00 2.69
7475 7574 7.069877 TCTAGAACAGTTTTGCTACCCTAAA 57.930 36.000 0.00 0.00 0.00 1.85
7476 7575 7.511268 TCTAGAACAGTTTTGCTACCCTAAAA 58.489 34.615 0.00 0.00 0.00 1.52
7477 7576 7.994334 TCTAGAACAGTTTTGCTACCCTAAAAA 59.006 33.333 0.00 0.00 0.00 1.94
7595 7694 4.354071 TGTGTCAGATTTTGTGTGTGTG 57.646 40.909 0.00 0.00 0.00 3.82
7618 7717 2.769663 TGCGTGATTGTAAGGGTCCTAT 59.230 45.455 0.00 0.00 0.00 2.57
7625 7724 4.689612 TTGTAAGGGTCCTATCTGCATC 57.310 45.455 0.00 0.00 0.00 3.91
7626 7725 2.972713 TGTAAGGGTCCTATCTGCATCC 59.027 50.000 0.00 0.00 0.00 3.51
7629 7728 1.373497 GGTCCTATCTGCATCCGCG 60.373 63.158 0.00 0.00 42.97 6.46
7635 7734 2.363711 TATCTGCATCCGCGGGTGTC 62.364 60.000 36.95 28.41 45.28 3.67
7644 7743 3.335534 GCGGGTGTCGTGTGTGAC 61.336 66.667 0.00 0.00 41.72 3.67
7645 7744 2.415843 CGGGTGTCGTGTGTGACT 59.584 61.111 0.00 0.00 39.64 3.41
7646 7745 1.227147 CGGGTGTCGTGTGTGACTT 60.227 57.895 0.00 0.00 39.64 3.01
7647 7746 0.808453 CGGGTGTCGTGTGTGACTTT 60.808 55.000 0.00 0.00 39.64 2.66
7648 7747 1.375551 GGGTGTCGTGTGTGACTTTT 58.624 50.000 0.00 0.00 39.64 2.27
7649 7748 1.063469 GGGTGTCGTGTGTGACTTTTG 59.937 52.381 0.00 0.00 39.64 2.44
7650 7749 1.531058 GGTGTCGTGTGTGACTTTTGC 60.531 52.381 0.00 0.00 39.64 3.68
7665 7764 3.181480 ACTTTTGCATGCGTTTGGTTACT 60.181 39.130 14.09 0.00 0.00 2.24
7668 7767 1.678627 TGCATGCGTTTGGTTACTTGT 59.321 42.857 14.09 0.00 0.00 3.16
7671 7770 4.022762 TGCATGCGTTTGGTTACTTGTATT 60.023 37.500 14.09 0.00 0.00 1.89
7696 7796 5.552870 TTTTTGCCCCTTTGCATACTTTA 57.447 34.783 0.00 0.00 41.70 1.85
7699 7799 5.753721 TTGCCCCTTTGCATACTTTATTT 57.246 34.783 0.00 0.00 41.70 1.40
7722 7822 0.323360 TTGGGCCTGGTTGAGCATAC 60.323 55.000 4.53 0.00 0.00 2.39
7734 7834 7.148018 CCTGGTTGAGCATACATAGACAAAAAT 60.148 37.037 0.00 0.00 0.00 1.82
7735 7835 7.537715 TGGTTGAGCATACATAGACAAAAATG 58.462 34.615 0.00 0.00 0.00 2.32
7769 7869 1.069049 GTTGTTTGGTTGCCTGCATCT 59.931 47.619 0.00 0.00 0.00 2.90
7776 7876 1.474143 GGTTGCCTGCATCTCCTCTAC 60.474 57.143 0.00 0.00 0.00 2.59
7779 7879 2.591923 TGCCTGCATCTCCTCTACTAG 58.408 52.381 0.00 0.00 0.00 2.57
7782 7882 3.005367 GCCTGCATCTCCTCTACTAGTTC 59.995 52.174 0.00 0.00 0.00 3.01
7796 7896 2.205074 CTAGTTCGCATCTGCCGAAAT 58.795 47.619 11.88 11.88 36.16 2.17
7797 7897 1.009829 AGTTCGCATCTGCCGAAATC 58.990 50.000 9.75 2.21 36.16 2.17
7848 7949 1.487142 TCAGGGAAAACACAAGTCCGA 59.513 47.619 0.00 0.00 31.73 4.55
7862 7963 6.038825 ACACAAGTCCGATTGTTTGATTACAA 59.961 34.615 0.00 0.00 41.41 2.41
7892 7996 4.081862 CAGTTATGTGGTAACCTCCTCGAA 60.082 45.833 0.00 0.00 43.02 3.71
7913 8017 1.204146 TGATGAGGTTACCAGAGGCC 58.796 55.000 3.51 0.00 0.00 5.19
7925 8029 1.272092 CCAGAGGCCCACATTGAAAGA 60.272 52.381 0.00 0.00 0.00 2.52
7942 8066 8.509690 CATTGAAAGATAAGAACAAGAGCAAGA 58.490 33.333 0.00 0.00 0.00 3.02
7948 8072 2.565841 AGAACAAGAGCAAGACACACC 58.434 47.619 0.00 0.00 0.00 4.16
7980 8112 8.947115 GTCTTAACCATGCATAGAAGTTTAACT 58.053 33.333 0.00 0.00 0.00 2.24
8070 8229 1.518572 CATTTAGTCGGTCGCGGCT 60.519 57.895 11.94 1.99 0.00 5.52
8128 8288 3.479269 CGCCCTCGTCGCTCAAAC 61.479 66.667 0.00 0.00 0.00 2.93
8181 8341 6.294508 GCAACTTGAATGTTACCATGTACCTT 60.295 38.462 0.00 0.00 0.00 3.50
8201 8361 5.133322 ACCTTATCATGATCTGGTGAATGGT 59.867 40.000 23.60 14.56 0.00 3.55
8228 8388 1.001020 TGGCGCAACCCTGATCAAT 60.001 52.632 10.83 0.00 37.83 2.57
8341 8527 2.043852 ATCGGCAGACTCTCCGGT 60.044 61.111 0.00 3.21 45.31 5.28
8380 8567 0.840617 TGCACAAGTGGTTGGTCCTA 59.159 50.000 2.00 0.00 38.07 2.94
8559 8797 5.627182 AAGGTCAGCACTCATTCATATCT 57.373 39.130 0.00 0.00 0.00 1.98
8602 8843 3.008594 CCCACACTACTTACCCAACATCA 59.991 47.826 0.00 0.00 0.00 3.07
8605 8846 5.245531 CACACTACTTACCCAACATCACAT 58.754 41.667 0.00 0.00 0.00 3.21
8688 8970 2.008242 CCATGAACTCCAACCCCAAA 57.992 50.000 0.00 0.00 0.00 3.28
8691 8973 0.631753 TGAACTCCAACCCCAAACCA 59.368 50.000 0.00 0.00 0.00 3.67
8729 9011 0.045469 ATGGAGGGCCTTCTTCCTCT 59.955 55.000 14.33 0.00 46.51 3.69
8748 9031 1.374252 GGTGTTGCTCGATGACCGT 60.374 57.895 0.00 0.00 39.75 4.83
8787 9080 1.538512 GCTTGAACTTCAGCAGCATCA 59.461 47.619 9.65 0.00 32.14 3.07
8796 9089 2.089201 TCAGCAGCATCAAAGACATGG 58.911 47.619 0.00 0.00 0.00 3.66
8809 11797 0.393537 GACATGGACAAGGAGGCTGG 60.394 60.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.502237 CGTACCCGCTGTTGTAGTT 57.498 52.632 0.00 0.00 0.00 2.24
22 23 1.630244 CTCTGGCGCTCTTTCGTTGG 61.630 60.000 7.64 0.00 0.00 3.77
24 25 2.029844 GCTCTGGCGCTCTTTCGTT 61.030 57.895 7.64 0.00 0.00 3.85
81 82 2.113139 CCTTGGCCACCAACGAGT 59.887 61.111 3.88 0.00 38.75 4.18
110 111 4.337060 CATCATGCCATGGCGCCG 62.337 66.667 30.87 21.07 45.51 6.46
122 123 1.134007 TGGCATTTCCTCGAGCATCAT 60.134 47.619 6.99 0.00 35.26 2.45
125 126 0.035152 TGTGGCATTTCCTCGAGCAT 60.035 50.000 6.99 0.00 35.26 3.79
177 212 2.063015 ATGTGGGACCCGCTTGACAA 62.063 55.000 24.48 3.72 34.70 3.18
213 249 6.016610 GGCACTAAAAGTCAAGACAAATGGTA 60.017 38.462 2.72 0.00 0.00 3.25
252 288 1.074566 CTTCTGACAGGAAAAGCCCCT 59.925 52.381 1.81 0.00 37.37 4.79
253 289 1.202940 ACTTCTGACAGGAAAAGCCCC 60.203 52.381 1.81 0.00 37.37 5.80
269 307 5.659440 TTGGAGCCAATTATTCCAACTTC 57.341 39.130 11.42 0.00 43.94 3.01
334 372 9.388506 CATTCTTTGGACTCTACAACAATCTAT 57.611 33.333 0.00 0.00 0.00 1.98
341 379 5.063880 ACCACATTCTTTGGACTCTACAAC 58.936 41.667 0.00 0.00 37.58 3.32
348 386 3.788227 TGCTACCACATTCTTTGGACT 57.212 42.857 0.00 0.00 37.58 3.85
543 583 6.927416 AGTACAAATGCAAATGACATGACAT 58.073 32.000 4.76 4.76 0.00 3.06
613 654 3.608073 GCAATCGTTTGTATTGTGAAGGC 59.392 43.478 7.97 0.00 36.82 4.35
629 670 2.239847 GATCGACGCACGCAATCG 59.760 61.111 6.39 6.39 42.26 3.34
658 699 4.771590 TTCTTTTCTAAGCGTAGTCCGA 57.228 40.909 6.57 0.00 39.56 4.55
770 813 3.949113 ACGTGTGGTTTGGTTTGTCTTAT 59.051 39.130 0.00 0.00 0.00 1.73
809 852 2.167161 CGTGGTACGTACGGTGGTA 58.833 57.895 21.06 0.00 36.74 3.25
876 923 0.036388 ACCCATCACGTAGGCAACAG 60.036 55.000 0.00 0.00 41.41 3.16
1024 1072 4.559251 GCAACCTAGCGACGAGAATATATG 59.441 45.833 0.00 0.00 0.00 1.78
1032 1080 2.161486 GCTGCAACCTAGCGACGAG 61.161 63.158 0.00 0.00 37.31 4.18
1033 1081 2.126071 GCTGCAACCTAGCGACGA 60.126 61.111 0.00 0.00 37.31 4.20
1205 1253 2.300152 CAGCACAACCCTCTAAGAGTGA 59.700 50.000 0.00 0.00 0.00 3.41
1209 1257 1.729586 ACCAGCACAACCCTCTAAGA 58.270 50.000 0.00 0.00 0.00 2.10
1988 2036 4.631740 TCCTGCCCCGTCCAGACA 62.632 66.667 0.00 0.00 32.03 3.41
2130 2178 1.857318 CGGAGTGCAGAGACACGAGT 61.857 60.000 0.00 0.00 45.45 4.18
2766 2816 0.529833 CTGGTCAGATGCTCTGTCGT 59.470 55.000 11.37 0.00 44.58 4.34
3040 3091 1.201429 AAGAATGTCCCTCGTGCCCT 61.201 55.000 0.00 0.00 0.00 5.19
3141 3192 1.374631 GAGCATGCCACTGTGACGA 60.375 57.895 15.66 0.00 0.00 4.20
3224 3275 9.973450 CACACTGCTACATCTTTATTACTAGAT 57.027 33.333 0.00 0.00 0.00 1.98
3637 3691 6.484643 AGCTTCAACAATATGACGATGCTTAT 59.515 34.615 0.00 0.00 32.98 1.73
3877 3931 5.519206 ACACACTTCTTAGAACGAAACTCAC 59.481 40.000 0.00 0.00 0.00 3.51
4131 4185 1.006102 CCAAACGAGCTCCACGTCT 60.006 57.895 8.47 0.00 43.16 4.18
4809 4875 1.058428 AGGGCAGCCTGATATGAGCA 61.058 55.000 12.43 0.00 0.00 4.26
5597 5663 1.228124 CGACATGGGTGTGGTGGTT 60.228 57.895 0.00 0.00 39.09 3.67
5708 5774 5.870433 AGAGATATCTGGTATCGTACTCGTG 59.130 44.000 10.74 0.00 43.30 4.35
5713 5779 8.126074 CAGCATAAGAGATATCTGGTATCGTAC 58.874 40.741 10.74 0.00 43.30 3.67
5714 5780 7.829706 ACAGCATAAGAGATATCTGGTATCGTA 59.170 37.037 10.74 0.00 43.30 3.43
5719 5785 9.143155 TGTTAACAGCATAAGAGATATCTGGTA 57.857 33.333 10.74 2.18 0.00 3.25
5799 5865 5.468409 TGAACTGAACATAACGAAGAATGCA 59.532 36.000 0.00 0.00 0.00 3.96
6310 6377 9.543231 TCTAAAGAACTGAGAAGGGTAAGATTA 57.457 33.333 0.00 0.00 0.00 1.75
6479 6546 0.179026 CTCATCCTCCGTCGGGTAGA 60.179 60.000 12.29 6.35 33.83 2.59
6480 6547 1.797211 GCTCATCCTCCGTCGGGTAG 61.797 65.000 12.29 1.80 33.83 3.18
6481 6548 1.826921 GCTCATCCTCCGTCGGGTA 60.827 63.158 12.29 0.00 33.83 3.69
6606 6673 4.689071 ACACTGACACGATGAACTTACAA 58.311 39.130 0.00 0.00 0.00 2.41
6643 6710 2.191513 GCGTGCCTCATGCCATCAT 61.192 57.895 0.00 0.00 40.14 2.45
6654 6721 2.980233 GCCACAAAGAGCGTGCCT 60.980 61.111 0.00 0.00 32.85 4.75
6677 6744 0.389426 ACGTTGTATGGTCAGGCGAC 60.389 55.000 0.00 0.00 41.80 5.19
6722 6789 3.989787 TCTTGCACGCTCGCCTCA 61.990 61.111 0.00 0.00 0.00 3.86
6849 6916 0.458260 GAAGAGGAGGAGAAGACGCC 59.542 60.000 0.00 0.00 36.22 5.68
6999 7069 3.279116 TCCGGTCGTCGTGTCGTT 61.279 61.111 0.00 0.00 37.11 3.85
7024 7094 2.435120 TACCCTGAGAGGTGCCGTCA 62.435 60.000 3.30 0.00 41.42 4.35
7066 7141 3.953612 AGGGCATCAAATTAGCGATCAAA 59.046 39.130 0.00 0.00 0.00 2.69
7069 7144 4.065088 TGTAGGGCATCAAATTAGCGATC 58.935 43.478 0.00 0.00 0.00 3.69
7076 7151 2.749600 TGGCATGTAGGGCATCAAATT 58.250 42.857 0.00 0.00 38.55 1.82
7086 7161 7.458409 AGAGCAAATTATTATGGCATGTAGG 57.542 36.000 10.98 0.00 0.00 3.18
7116 7191 3.738982 TGAATTCGTTCCTCAGCTGAAA 58.261 40.909 18.85 7.35 0.00 2.69
7237 7312 3.617735 TGTTGGCTGCCGACGGTA 61.618 61.111 28.96 10.62 40.66 4.02
7387 7462 4.399004 AATCTAAGCTACTGCACCAGAG 57.601 45.455 0.00 0.00 42.74 3.35
7475 7574 7.807907 CGACTTCCATATAGCAAAACTGTTTTT 59.192 33.333 15.41 5.70 35.15 1.94
7476 7575 7.305474 CGACTTCCATATAGCAAAACTGTTTT 58.695 34.615 12.50 12.50 0.00 2.43
7477 7576 6.622896 GCGACTTCCATATAGCAAAACTGTTT 60.623 38.462 0.00 0.00 0.00 2.83
7478 7577 5.163754 GCGACTTCCATATAGCAAAACTGTT 60.164 40.000 0.00 0.00 0.00 3.16
7479 7578 4.332819 GCGACTTCCATATAGCAAAACTGT 59.667 41.667 0.00 0.00 0.00 3.55
7480 7579 4.260784 GGCGACTTCCATATAGCAAAACTG 60.261 45.833 0.00 0.00 0.00 3.16
7481 7580 3.877508 GGCGACTTCCATATAGCAAAACT 59.122 43.478 0.00 0.00 0.00 2.66
7482 7581 3.877508 AGGCGACTTCCATATAGCAAAAC 59.122 43.478 0.00 0.00 37.44 2.43
7483 7582 4.150897 AGGCGACTTCCATATAGCAAAA 57.849 40.909 0.00 0.00 37.44 2.44
7484 7583 3.838244 AGGCGACTTCCATATAGCAAA 57.162 42.857 0.00 0.00 37.44 3.68
7485 7584 4.948341 TTAGGCGACTTCCATATAGCAA 57.052 40.909 0.00 0.00 43.67 3.91
7486 7585 4.948341 TTTAGGCGACTTCCATATAGCA 57.052 40.909 0.00 0.00 43.67 3.49
7487 7586 6.803154 AATTTTAGGCGACTTCCATATAGC 57.197 37.500 0.00 0.00 43.67 2.97
7488 7587 9.490379 AGTAAATTTTAGGCGACTTCCATATAG 57.510 33.333 0.00 0.00 43.67 1.31
7489 7588 9.841295 AAGTAAATTTTAGGCGACTTCCATATA 57.159 29.630 0.00 0.00 43.67 0.86
7490 7589 8.747538 AAGTAAATTTTAGGCGACTTCCATAT 57.252 30.769 0.00 0.00 43.67 1.78
7569 7668 8.453320 CACACACACAAAATCTGACACATATAT 58.547 33.333 0.00 0.00 0.00 0.86
7570 7669 7.443879 ACACACACACAAAATCTGACACATATA 59.556 33.333 0.00 0.00 0.00 0.86
7571 7670 6.262944 ACACACACACAAAATCTGACACATAT 59.737 34.615 0.00 0.00 0.00 1.78
7572 7671 5.588246 ACACACACACAAAATCTGACACATA 59.412 36.000 0.00 0.00 0.00 2.29
7595 7694 1.467342 GGACCCTTACAATCACGCAAC 59.533 52.381 0.00 0.00 0.00 4.17
7618 7717 4.451150 GACACCCGCGGATGCAGA 62.451 66.667 30.73 0.00 42.97 4.26
7626 7725 4.934942 TCACACACGACACCCGCG 62.935 66.667 0.00 0.00 43.32 6.46
7629 7728 1.063469 CAAAAGTCACACACGACACCC 59.937 52.381 0.00 0.00 38.43 4.61
7635 7734 1.122849 GCATGCAAAAGTCACACACG 58.877 50.000 14.21 0.00 0.00 4.49
7644 7743 3.380142 AGTAACCAAACGCATGCAAAAG 58.620 40.909 19.57 3.36 0.00 2.27
7645 7744 3.444703 AGTAACCAAACGCATGCAAAA 57.555 38.095 19.57 0.00 0.00 2.44
7646 7745 3.119291 CAAGTAACCAAACGCATGCAAA 58.881 40.909 19.57 0.00 0.00 3.68
7647 7746 2.099921 ACAAGTAACCAAACGCATGCAA 59.900 40.909 19.57 0.00 0.00 4.08
7648 7747 1.678627 ACAAGTAACCAAACGCATGCA 59.321 42.857 19.57 0.00 0.00 3.96
7649 7748 2.415697 ACAAGTAACCAAACGCATGC 57.584 45.000 7.91 7.91 0.00 4.06
7650 7749 5.457140 ACAATACAAGTAACCAAACGCATG 58.543 37.500 0.00 0.00 0.00 4.06
7696 7796 1.133199 TCAACCAGGCCCAACTGAAAT 60.133 47.619 0.00 0.00 40.97 2.17
7699 7799 1.455849 CTCAACCAGGCCCAACTGA 59.544 57.895 0.00 0.00 40.97 3.41
7735 7835 9.072294 GCAACCAAACAACATGTAGATATTAAC 57.928 33.333 0.00 0.00 0.00 2.01
7745 7845 1.473080 GCAGGCAACCAAACAACATGT 60.473 47.619 0.00 0.00 37.17 3.21
7753 7853 0.112995 AGGAGATGCAGGCAACCAAA 59.887 50.000 14.41 0.00 37.17 3.28
7769 7869 2.619177 GCAGATGCGAACTAGTAGAGGA 59.381 50.000 3.59 0.00 0.00 3.71
7776 7876 1.640428 TTTCGGCAGATGCGAACTAG 58.360 50.000 10.22 0.00 43.26 2.57
7779 7879 0.315382 CGATTTCGGCAGATGCGAAC 60.315 55.000 10.22 2.62 43.26 3.95
7782 7882 0.042708 CTTCGATTTCGGCAGATGCG 60.043 55.000 0.00 0.00 43.26 4.73
7796 7896 2.198827 ACCAAACATCATGCCTTCGA 57.801 45.000 0.00 0.00 0.00 3.71
7797 7897 2.030007 ACAACCAAACATCATGCCTTCG 60.030 45.455 0.00 0.00 0.00 3.79
7862 7963 5.339477 AGGTTACCACATAACTGTCCTAGT 58.661 41.667 3.51 0.00 42.58 2.57
7892 7996 2.173569 GGCCTCTGGTAACCTCATCATT 59.826 50.000 0.00 0.00 0.00 2.57
7913 8017 7.025963 GCTCTTGTTCTTATCTTTCAATGTGG 58.974 38.462 0.00 0.00 0.00 4.17
7925 8029 4.757149 GGTGTGTCTTGCTCTTGTTCTTAT 59.243 41.667 0.00 0.00 0.00 1.73
7942 8066 5.734720 CATGGTTAAGACTATGAGGTGTGT 58.265 41.667 0.00 0.00 44.81 3.72
7948 8072 8.147058 ACTTCTATGCATGGTTAAGACTATGAG 58.853 37.037 10.16 0.38 44.81 2.90
7980 8112 5.823570 TGCTGCAGTTTGGTTTAAGTACTTA 59.176 36.000 16.64 11.38 0.00 2.24
8070 8229 1.443194 GAAGCACGACGACGCCTTA 60.443 57.895 7.30 0.00 43.96 2.69
8122 8282 2.679837 CCATGAAGGTGATCGGTTTGAG 59.320 50.000 0.00 0.00 0.00 3.02
8148 8308 1.145738 ACATTCAAGTTGCTGACCCCT 59.854 47.619 10.97 0.00 0.00 4.79
8181 8341 4.747623 GCCACCATTCACCAGATCATGATA 60.748 45.833 8.54 0.00 0.00 2.15
8214 8374 1.474077 GTCACCATTGATCAGGGTTGC 59.526 52.381 16.15 9.72 33.11 4.17
8228 8388 4.289101 TCGACGGGAGGGTCACCA 62.289 66.667 0.00 0.00 40.13 4.17
8254 8420 1.728971 CTCAAGATGAACACCGACAGC 59.271 52.381 0.00 0.00 0.00 4.40
8341 8527 1.075601 AGGTCATCCCTGCTCCAAAA 58.924 50.000 0.00 0.00 44.08 2.44
8351 8537 0.883833 CACTTGTGCAAGGTCATCCC 59.116 55.000 15.31 0.00 42.53 3.85
8380 8567 2.439507 ACGGGCATTATCATGAGGAGTT 59.560 45.455 0.09 0.00 31.07 3.01
8559 8797 8.066867 TGTGGGTAAATATAGGAGTGTTAGGTA 58.933 37.037 0.00 0.00 0.00 3.08
8626 8867 3.103742 GAGAGGTGGAAGAGGAGATGTT 58.896 50.000 0.00 0.00 0.00 2.71
8627 8868 2.314549 AGAGAGGTGGAAGAGGAGATGT 59.685 50.000 0.00 0.00 0.00 3.06
8628 8869 3.030873 AGAGAGGTGGAAGAGGAGATG 57.969 52.381 0.00 0.00 0.00 2.90
8629 8870 5.417170 AATAGAGAGGTGGAAGAGGAGAT 57.583 43.478 0.00 0.00 0.00 2.75
8630 8871 4.890499 AATAGAGAGGTGGAAGAGGAGA 57.110 45.455 0.00 0.00 0.00 3.71
8631 8872 4.959210 TGAAATAGAGAGGTGGAAGAGGAG 59.041 45.833 0.00 0.00 0.00 3.69
8632 8873 4.712337 GTGAAATAGAGAGGTGGAAGAGGA 59.288 45.833 0.00 0.00 0.00 3.71
8633 8874 4.141824 GGTGAAATAGAGAGGTGGAAGAGG 60.142 50.000 0.00 0.00 0.00 3.69
8634 8875 4.467795 TGGTGAAATAGAGAGGTGGAAGAG 59.532 45.833 0.00 0.00 0.00 2.85
8635 8876 4.223032 GTGGTGAAATAGAGAGGTGGAAGA 59.777 45.833 0.00 0.00 0.00 2.87
8636 8877 4.508662 GTGGTGAAATAGAGAGGTGGAAG 58.491 47.826 0.00 0.00 0.00 3.46
8637 8878 3.263425 GGTGGTGAAATAGAGAGGTGGAA 59.737 47.826 0.00 0.00 0.00 3.53
8638 8879 2.838202 GGTGGTGAAATAGAGAGGTGGA 59.162 50.000 0.00 0.00 0.00 4.02
8639 8880 2.840651 AGGTGGTGAAATAGAGAGGTGG 59.159 50.000 0.00 0.00 0.00 4.61
8729 9011 1.374125 CGGTCATCGAGCAACACCA 60.374 57.895 0.00 0.00 42.43 4.17
8748 9031 4.689612 AGCAGGTGTTCTCAAACTTCTA 57.310 40.909 0.00 0.00 36.30 2.10
8787 9080 1.707427 AGCCTCCTTGTCCATGTCTTT 59.293 47.619 0.00 0.00 0.00 2.52
8796 9089 2.317149 ATAGCGCCAGCCTCCTTGTC 62.317 60.000 2.29 0.00 46.67 3.18
8809 11797 4.307432 TGTAGCCTTCTTAATCATAGCGC 58.693 43.478 0.00 0.00 0.00 5.92


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

AutoCloner maintained by Alex Coulton.