Multiple sequence alignment - TraesCS7B01G082400

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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 TraesCS7B01G082400 chr7B 100.000 3416 0 0 1 3416 93068981 93065566 0.000000e+00 6309
1 TraesCS7B01G082400 chr7D 94.503 2856 109 13 579 3416 131652709 131649884 0.000000e+00 4361
2 TraesCS7B01G082400 chr7D 83.290 389 36 10 203 588 131653642 131653280 7.070000e-87 331
3 TraesCS7B01G082400 chr7A 89.553 2575 137 49 114 2670 130401531 130399071 0.000000e+00 3144
4 TraesCS7B01G082400 chr7A 93.419 775 46 1 2647 3416 130399028 130398254 0.000000e+00 1144
5 TraesCS7B01G082400 chr1B 87.370 1536 159 24 922 2446 537771425 537772936 0.000000e+00 1729
6 TraesCS7B01G082400 chr1B 86.676 1486 156 21 1008 2468 60109111 60107643 0.000000e+00 1609
7 TraesCS7B01G082400 chr1B 86.583 954 113 7 1515 2460 60473811 60474757 0.000000e+00 1038
8 TraesCS7B01G082400 chr1B 90.795 239 17 1 1192 1425 60473260 60473498 7.120000e-82 315
9 TraesCS7B01G082400 chr1B 97.391 115 3 0 1026 1140 60456829 60456943 2.690000e-46 196
10 TraesCS7B01G082400 chr1B 97.345 113 3 0 1 113 144884102 144883990 3.480000e-45 193
11 TraesCS7B01G082400 chr1A 87.759 1495 147 23 951 2432 497083254 497084725 0.000000e+00 1714
12 TraesCS7B01G082400 chr1A 85.364 1551 151 38 956 2468 39872189 39870677 0.000000e+00 1537
13 TraesCS7B01G082400 chr1A 82.353 136 23 1 358 492 448636268 448636133 2.150000e-22 117
14 TraesCS7B01G082400 chr1D 87.583 1498 144 22 951 2432 400792400 400793871 0.000000e+00 1698
15 TraesCS7B01G082400 chr1D 88.772 953 94 5 1515 2460 40598009 40598955 0.000000e+00 1155
16 TraesCS7B01G082400 chr1D 88.753 409 35 5 1026 1429 40597393 40597795 1.100000e-134 490
17 TraesCS7B01G082400 chr2A 74.170 271 60 10 2658 2924 543312948 543313212 1.680000e-18 104


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 TraesCS7B01G082400 chr7B 93065566 93068981 3415 True 6309.0 6309 100.0000 1 3416 1 chr7B.!!$R1 3415
1 TraesCS7B01G082400 chr7D 131649884 131653642 3758 True 2346.0 4361 88.8965 203 3416 2 chr7D.!!$R1 3213
2 TraesCS7B01G082400 chr7A 130398254 130401531 3277 True 2144.0 3144 91.4860 114 3416 2 chr7A.!!$R1 3302
3 TraesCS7B01G082400 chr1B 537771425 537772936 1511 False 1729.0 1729 87.3700 922 2446 1 chr1B.!!$F2 1524
4 TraesCS7B01G082400 chr1B 60107643 60109111 1468 True 1609.0 1609 86.6760 1008 2468 1 chr1B.!!$R1 1460
5 TraesCS7B01G082400 chr1B 60473260 60474757 1497 False 676.5 1038 88.6890 1192 2460 2 chr1B.!!$F3 1268
6 TraesCS7B01G082400 chr1A 497083254 497084725 1471 False 1714.0 1714 87.7590 951 2432 1 chr1A.!!$F1 1481
7 TraesCS7B01G082400 chr1A 39870677 39872189 1512 True 1537.0 1537 85.3640 956 2468 1 chr1A.!!$R1 1512
8 TraesCS7B01G082400 chr1D 400792400 400793871 1471 False 1698.0 1698 87.5830 951 2432 1 chr1D.!!$F1 1481
9 TraesCS7B01G082400 chr1D 40597393 40598955 1562 False 822.5 1155 88.7625 1026 2460 2 chr1D.!!$F2 1434

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
31 32 0.043053 CCGCAGACATGTAAATCGCG 60.043 55.0 15.67 15.67 37.50 5.87 F
43 44 0.251916 AAATCGCGAACCAGATCCCA 59.748 50.0 15.24 0.00 0.00 4.37 F
105 106 0.316841 GACGGGAGGAGATCAGCATC 59.683 60.0 0.00 0.00 0.00 3.91 F
479 481 0.333993 AGGAATTGCCATGCTCCTGT 59.666 50.0 0.00 0.00 36.92 4.00 F
2241 3159 0.249447 CGAACATGGAGGCGCTCATA 60.249 55.0 7.64 0.00 31.08 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1551 2469 0.316204 CGTACTTGGGACCGTTCACT 59.684 55.000 0.0 0.0 0.00 3.41 R
1632 2550 1.338674 GGGACGATGATGTTGGTGACA 60.339 52.381 0.0 0.0 43.71 3.58 R
2056 2974 1.282157 GATAAGTGGGGTGAAGCCACT 59.718 52.381 0.0 0.0 45.22 4.00 R
2388 3306 0.261696 AGTTGAGGGTGGTTTGGCTT 59.738 50.000 0.0 0.0 0.00 4.35 R
3346 4372 2.143122 TCAGCTTGTAAGGCGTTTCTG 58.857 47.619 0.0 0.0 34.52 3.02 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
19 20 4.899239 CCTCATCCGGCCGCAGAC 62.899 72.222 22.85 0.00 0.00 3.51
20 21 4.147449 CTCATCCGGCCGCAGACA 62.147 66.667 22.85 2.10 0.00 3.41
21 22 3.451556 CTCATCCGGCCGCAGACAT 62.452 63.158 22.85 2.53 0.00 3.06
22 23 3.274586 CATCCGGCCGCAGACATG 61.275 66.667 22.85 11.90 0.00 3.21
23 24 3.785859 ATCCGGCCGCAGACATGT 61.786 61.111 22.85 0.00 0.00 3.21
24 25 2.431454 ATCCGGCCGCAGACATGTA 61.431 57.895 22.85 0.00 0.00 2.29
25 26 1.966901 ATCCGGCCGCAGACATGTAA 61.967 55.000 22.85 0.00 0.00 2.41
26 27 1.743623 CCGGCCGCAGACATGTAAA 60.744 57.895 22.85 0.00 0.00 2.01
27 28 1.095228 CCGGCCGCAGACATGTAAAT 61.095 55.000 22.85 0.00 0.00 1.40
28 29 0.304705 CGGCCGCAGACATGTAAATC 59.695 55.000 14.67 0.00 0.00 2.17
29 30 0.304705 GGCCGCAGACATGTAAATCG 59.695 55.000 0.00 0.11 0.00 3.34
30 31 0.316196 GCCGCAGACATGTAAATCGC 60.316 55.000 0.00 0.00 0.00 4.58
31 32 0.043053 CCGCAGACATGTAAATCGCG 60.043 55.000 15.67 15.67 37.50 5.87
32 33 0.920664 CGCAGACATGTAAATCGCGA 59.079 50.000 13.09 13.09 38.91 5.87
33 34 1.323235 CGCAGACATGTAAATCGCGAA 59.677 47.619 15.24 0.00 38.91 4.70
34 35 2.694043 GCAGACATGTAAATCGCGAAC 58.306 47.619 15.24 7.85 0.00 3.95
35 36 2.536928 GCAGACATGTAAATCGCGAACC 60.537 50.000 15.24 1.38 0.00 3.62
36 37 2.670905 CAGACATGTAAATCGCGAACCA 59.329 45.455 15.24 7.92 0.00 3.67
37 38 2.930040 AGACATGTAAATCGCGAACCAG 59.070 45.455 15.24 4.79 0.00 4.00
38 39 2.927477 GACATGTAAATCGCGAACCAGA 59.073 45.455 15.24 0.00 0.00 3.86
39 40 3.531538 ACATGTAAATCGCGAACCAGAT 58.468 40.909 15.24 1.61 0.00 2.90
40 41 3.555956 ACATGTAAATCGCGAACCAGATC 59.444 43.478 15.24 0.88 0.00 2.75
41 42 2.546778 TGTAAATCGCGAACCAGATCC 58.453 47.619 15.24 0.00 0.00 3.36
42 43 1.865340 GTAAATCGCGAACCAGATCCC 59.135 52.381 15.24 0.00 0.00 3.85
43 44 0.251916 AAATCGCGAACCAGATCCCA 59.748 50.000 15.24 0.00 0.00 4.37
44 45 0.462047 AATCGCGAACCAGATCCCAC 60.462 55.000 15.24 0.00 0.00 4.61
45 46 2.311688 ATCGCGAACCAGATCCCACC 62.312 60.000 15.24 0.00 0.00 4.61
46 47 2.511600 GCGAACCAGATCCCACCG 60.512 66.667 0.00 0.00 0.00 4.94
47 48 2.511600 CGAACCAGATCCCACCGC 60.512 66.667 0.00 0.00 0.00 5.68
48 49 2.124695 GAACCAGATCCCACCGCC 60.125 66.667 0.00 0.00 0.00 6.13
49 50 4.096003 AACCAGATCCCACCGCCG 62.096 66.667 0.00 0.00 0.00 6.46
67 68 4.838152 CCGATGCAGACCACCCCG 62.838 72.222 0.00 0.00 0.00 5.73
68 69 4.838152 CGATGCAGACCACCCCGG 62.838 72.222 0.00 0.00 42.50 5.73
87 88 4.770874 GCCAAGGTAAGCCGCCGA 62.771 66.667 0.00 0.00 40.50 5.54
88 89 2.818274 CCAAGGTAAGCCGCCGAC 60.818 66.667 0.00 0.00 40.50 4.79
89 90 3.186047 CAAGGTAAGCCGCCGACG 61.186 66.667 0.00 0.00 40.50 5.12
99 100 3.967335 CGCCGACGGGAGGAGATC 61.967 72.222 17.22 0.00 34.06 2.75
100 101 2.833582 GCCGACGGGAGGAGATCA 60.834 66.667 17.22 0.00 34.06 2.92
101 102 2.851071 GCCGACGGGAGGAGATCAG 61.851 68.421 17.22 0.00 34.06 2.90
102 103 2.725008 CGACGGGAGGAGATCAGC 59.275 66.667 0.00 0.00 0.00 4.26
103 104 2.121538 CGACGGGAGGAGATCAGCA 61.122 63.158 0.00 0.00 0.00 4.41
104 105 1.459455 CGACGGGAGGAGATCAGCAT 61.459 60.000 0.00 0.00 0.00 3.79
105 106 0.316841 GACGGGAGGAGATCAGCATC 59.683 60.000 0.00 0.00 0.00 3.91
106 107 1.118356 ACGGGAGGAGATCAGCATCC 61.118 60.000 9.91 9.91 35.71 3.51
107 108 1.670590 GGGAGGAGATCAGCATCCG 59.329 63.158 11.53 0.00 40.73 4.18
108 109 1.670590 GGAGGAGATCAGCATCCGG 59.329 63.158 0.00 0.00 40.73 5.14
109 110 1.005156 GAGGAGATCAGCATCCGGC 60.005 63.158 0.00 0.00 40.73 6.13
125 126 2.014128 CCGGCGGAGAAATTGTGTAAT 58.986 47.619 24.41 0.00 0.00 1.89
129 130 4.272504 CGGCGGAGAAATTGTGTAATATGT 59.727 41.667 0.00 0.00 0.00 2.29
133 134 6.687105 GCGGAGAAATTGTGTAATATGTCAAC 59.313 38.462 0.00 0.00 0.00 3.18
171 172 9.582431 TTAGTAATTTCATTCGACGAAGAATCT 57.418 29.630 16.40 11.47 38.66 2.40
235 236 6.773638 AGTCAAACTGATAACAGAAGACCAT 58.226 36.000 7.05 0.00 46.03 3.55
238 239 4.558226 ACTGATAACAGAAGACCATGCA 57.442 40.909 7.05 0.00 46.03 3.96
243 244 2.479566 ACAGAAGACCATGCACGAAT 57.520 45.000 0.00 0.00 0.00 3.34
245 246 3.937814 ACAGAAGACCATGCACGAATAA 58.062 40.909 0.00 0.00 0.00 1.40
247 248 4.393062 ACAGAAGACCATGCACGAATAAAG 59.607 41.667 0.00 0.00 0.00 1.85
248 249 4.393062 CAGAAGACCATGCACGAATAAAGT 59.607 41.667 0.00 0.00 0.00 2.66
249 250 5.580691 CAGAAGACCATGCACGAATAAAGTA 59.419 40.000 0.00 0.00 0.00 2.24
250 251 6.258727 CAGAAGACCATGCACGAATAAAGTAT 59.741 38.462 0.00 0.00 0.00 2.12
254 255 6.482308 AGACCATGCACGAATAAAGTATTACC 59.518 38.462 0.00 0.00 0.00 2.85
274 275 3.119316 ACCGATATGAATCATCCGAGAGC 60.119 47.826 15.94 0.00 31.93 4.09
279 280 3.893326 TGAATCATCCGAGAGCTTCAA 57.107 42.857 0.00 0.00 0.00 2.69
282 283 4.100653 TGAATCATCCGAGAGCTTCAAGAT 59.899 41.667 0.00 0.00 0.00 2.40
299 300 4.748102 TCAAGATAGGTGTGTGTTCGTTTC 59.252 41.667 0.00 0.00 0.00 2.78
316 317 6.236017 TCGTTTCAACTTGGATCACAATAC 57.764 37.500 0.00 0.00 38.65 1.89
317 318 5.760743 TCGTTTCAACTTGGATCACAATACA 59.239 36.000 0.00 0.00 38.65 2.29
319 320 6.512578 CGTTTCAACTTGGATCACAATACACA 60.513 38.462 0.00 0.00 38.65 3.72
320 321 6.558771 TTCAACTTGGATCACAATACACAG 57.441 37.500 0.00 0.00 38.65 3.66
321 322 4.455533 TCAACTTGGATCACAATACACAGC 59.544 41.667 0.00 0.00 38.65 4.40
322 323 3.002791 ACTTGGATCACAATACACAGCG 58.997 45.455 0.00 0.00 38.65 5.18
323 324 3.261580 CTTGGATCACAATACACAGCGA 58.738 45.455 0.00 0.00 38.65 4.93
324 325 3.326836 TGGATCACAATACACAGCGAA 57.673 42.857 0.00 0.00 0.00 4.70
325 326 3.669536 TGGATCACAATACACAGCGAAA 58.330 40.909 0.00 0.00 0.00 3.46
326 327 3.684305 TGGATCACAATACACAGCGAAAG 59.316 43.478 0.00 0.00 0.00 2.62
329 330 5.334879 GGATCACAATACACAGCGAAAGTTT 60.335 40.000 0.00 0.00 0.00 2.66
350 351 6.040166 AGTTTCTTGAGAAGCATGACATTTGT 59.960 34.615 9.71 0.00 37.66 2.83
382 384 3.883830 ATGCCAAGTTGTTCAAACACA 57.116 38.095 1.45 0.00 38.92 3.72
389 391 2.159114 AGTTGTTCAAACACACATGGCC 60.159 45.455 0.00 0.00 38.92 5.36
398 400 1.895131 ACACACATGGCCATTTCTTCC 59.105 47.619 17.92 0.00 0.00 3.46
446 448 7.452562 ACAAGGGATTTTGCTATGAAATTTGT 58.547 30.769 0.00 0.00 0.00 2.83
454 456 5.940192 TGCTATGAAATTTGTCGTGTTCT 57.060 34.783 0.00 0.00 0.00 3.01
458 460 7.386573 TGCTATGAAATTTGTCGTGTTCTCTTA 59.613 33.333 0.00 0.00 0.00 2.10
473 475 4.989279 TCTCTTAAAGGAATTGCCATGC 57.011 40.909 0.00 0.00 40.02 4.06
476 478 3.701040 TCTTAAAGGAATTGCCATGCTCC 59.299 43.478 0.00 0.00 40.02 4.70
477 479 2.242882 AAAGGAATTGCCATGCTCCT 57.757 45.000 0.00 0.00 40.10 3.69
478 480 1.481871 AAGGAATTGCCATGCTCCTG 58.518 50.000 0.00 0.00 38.34 3.86
479 481 0.333993 AGGAATTGCCATGCTCCTGT 59.666 50.000 0.00 0.00 36.92 4.00
480 482 1.565759 AGGAATTGCCATGCTCCTGTA 59.434 47.619 0.00 0.00 36.92 2.74
481 483 2.025037 AGGAATTGCCATGCTCCTGTAA 60.025 45.455 0.00 0.00 36.92 2.41
482 484 2.099756 GGAATTGCCATGCTCCTGTAAC 59.900 50.000 0.00 0.00 36.34 2.50
483 485 2.512692 ATTGCCATGCTCCTGTAACA 57.487 45.000 0.00 0.00 0.00 2.41
484 486 2.512692 TTGCCATGCTCCTGTAACAT 57.487 45.000 0.00 0.00 0.00 2.71
485 487 3.643199 TTGCCATGCTCCTGTAACATA 57.357 42.857 0.00 0.00 0.00 2.29
486 488 3.643199 TGCCATGCTCCTGTAACATAA 57.357 42.857 0.00 0.00 0.00 1.90
487 489 3.961849 TGCCATGCTCCTGTAACATAAA 58.038 40.909 0.00 0.00 0.00 1.40
488 490 4.339748 TGCCATGCTCCTGTAACATAAAA 58.660 39.130 0.00 0.00 0.00 1.52
489 491 4.157656 TGCCATGCTCCTGTAACATAAAAC 59.842 41.667 0.00 0.00 0.00 2.43
490 492 4.730613 GCCATGCTCCTGTAACATAAAACG 60.731 45.833 0.00 0.00 0.00 3.60
491 493 4.342772 CATGCTCCTGTAACATAAAACGC 58.657 43.478 0.00 0.00 0.00 4.84
492 494 2.413796 TGCTCCTGTAACATAAAACGCG 59.586 45.455 3.53 3.53 0.00 6.01
525 527 1.766143 GCGAATGTCATCCCAGCGAC 61.766 60.000 0.00 0.00 0.00 5.19
556 558 6.183359 GCTGCATCATTACCGTTTAACTTTTG 60.183 38.462 0.00 0.00 0.00 2.44
652 1235 5.490472 TTTGAAGAAAATCTCGTACGACG 57.510 39.130 15.28 10.88 44.19 5.12
742 1325 2.028476 CAGAAGTTGGTCATCGGTACCA 60.028 50.000 13.54 0.00 45.26 3.25
786 1369 6.687105 GCGCCATAAAATAAGTGTGAAGTAAG 59.313 38.462 0.00 0.00 0.00 2.34
817 1400 2.235155 TCTTAGCCACTGACGCCAAATA 59.765 45.455 0.00 0.00 0.00 1.40
878 1461 2.097466 CGGAAAGCACAAGAACACAAGT 59.903 45.455 0.00 0.00 0.00 3.16
886 1469 5.582439 CACAAGAACACAAGTGCTACTAG 57.418 43.478 0.00 0.00 30.07 2.57
897 1480 3.912907 CTACTAGCACGCCCGGGG 61.913 72.222 25.28 15.33 0.00 5.73
1366 1992 2.238521 GAGGCCAAGGACATCAACAAA 58.761 47.619 5.01 0.00 0.00 2.83
1381 2007 7.106239 ACATCAACAAATTCTACCTCGAGAAT 58.894 34.615 15.71 2.59 46.02 2.40
1461 2087 1.358103 TCCCTTCTCTTCTCCTTCCGA 59.642 52.381 0.00 0.00 0.00 4.55
1557 2475 2.551270 CTGTTCGGCGCAGTGAAC 59.449 61.111 24.01 24.01 42.39 3.18
1581 2499 1.223187 CCAAGTACGACGGCAAGTTT 58.777 50.000 0.00 0.00 0.00 2.66
1632 2550 4.338539 GTGACCGTCGCCGACACT 62.339 66.667 18.40 0.10 37.79 3.55
1695 2613 0.396435 AGCCGGTCATCTTCAACACA 59.604 50.000 1.90 0.00 0.00 3.72
1737 2655 2.430921 AAGAACGCGCACCTCTCG 60.431 61.111 5.73 0.00 0.00 4.04
2056 2974 1.395045 CCTCCGCTGGCTCTATGACA 61.395 60.000 0.00 0.00 0.00 3.58
2241 3159 0.249447 CGAACATGGAGGCGCTCATA 60.249 55.000 7.64 0.00 31.08 2.15
2380 3298 3.329688 CTCTCCGACGAGCGCAAGT 62.330 63.158 11.47 9.19 39.11 3.16
2435 3358 3.839293 AGACAAGAGACGATTCGAAAGG 58.161 45.455 13.95 0.00 0.00 3.11
2496 3420 8.249327 TCGACCGATCTAGAGTTGTAATATAC 57.751 38.462 0.00 0.00 0.00 1.47
2498 3422 8.719648 CGACCGATCTAGAGTTGTAATATACTT 58.280 37.037 0.00 0.00 0.00 2.24
2622 3547 5.895636 TGCAAGTCGGATCAAACAATATT 57.104 34.783 0.00 0.00 0.00 1.28
2715 3713 4.267536 CATGAGGTCCATGTCACTCAAAT 58.732 43.478 12.52 0.00 45.83 2.32
2745 3743 5.750067 GCATGCAAGGACAAAATATACTTGG 59.250 40.000 14.21 0.00 39.04 3.61
2754 3752 7.037153 AGGACAAAATATACTTGGTAGGGTTGA 60.037 37.037 3.30 0.00 0.00 3.18
2758 3756 8.966868 CAAAATATACTTGGTAGGGTTGATGTT 58.033 33.333 0.00 0.00 0.00 2.71
2789 3787 8.044060 TGAAACTATAAATGAGCTTCACCAAG 57.956 34.615 0.00 0.00 0.00 3.61
2801 3799 3.669023 GCTTCACCAAGAAAAGATGAGCG 60.669 47.826 0.00 0.00 35.40 5.03
2885 3883 1.739067 AAACTCTTCGCATGTAGGGC 58.261 50.000 0.00 0.00 0.00 5.19
2913 3911 4.158209 CACTAAAATGATGCACATGGGTCA 59.842 41.667 0.00 0.00 39.39 4.02
2945 3943 2.979814 TTGGGATAGTGTCACCATCG 57.020 50.000 5.47 0.00 32.18 3.84
3099 4097 7.878127 ACATATTAGTGGGGTAATTTCTCATCG 59.122 37.037 0.00 0.00 0.00 3.84
3118 4143 6.485171 TCATCGGTAGAAGATGATCTATCCA 58.515 40.000 0.00 0.00 46.52 3.41
3119 4144 7.122048 TCATCGGTAGAAGATGATCTATCCAT 58.878 38.462 0.00 0.00 46.52 3.41
3120 4145 7.617329 TCATCGGTAGAAGATGATCTATCCATT 59.383 37.037 0.00 0.00 46.52 3.16
3121 4146 7.397892 TCGGTAGAAGATGATCTATCCATTC 57.602 40.000 0.00 0.00 36.40 2.67
3122 4147 7.178573 TCGGTAGAAGATGATCTATCCATTCT 58.821 38.462 0.00 0.00 35.60 2.40
3123 4148 8.329502 TCGGTAGAAGATGATCTATCCATTCTA 58.670 37.037 0.00 0.00 34.21 2.10
3124 4149 9.130661 CGGTAGAAGATGATCTATCCATTCTAT 57.869 37.037 0.00 0.00 36.13 1.98
3241 4267 8.703604 TCATTAGAGTAAATTTGTCTCCTTCG 57.296 34.615 16.29 7.93 0.00 3.79
3312 4338 6.374417 ACATTGGTACTCAAATCCACTACT 57.626 37.500 0.00 0.00 39.05 2.57
3331 4357 7.375834 CACTACTACAGACTTGGAAATGTACA 58.624 38.462 0.00 0.00 0.00 2.90
3360 4386 3.462483 TGACTTCAGAAACGCCTTACA 57.538 42.857 0.00 0.00 0.00 2.41
3371 4397 2.846193 ACGCCTTACAAGCTGAAAGAA 58.154 42.857 0.00 0.00 34.07 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.899239 GTCTGCGGCCGGATGAGG 62.899 72.222 29.38 12.79 0.00 3.86
4 5 3.469970 ATGTCTGCGGCCGGATGA 61.470 61.111 29.38 20.06 0.00 2.92
5 6 2.642996 TACATGTCTGCGGCCGGATG 62.643 60.000 29.38 21.63 0.00 3.51
6 7 1.966901 TTACATGTCTGCGGCCGGAT 61.967 55.000 29.38 10.75 0.00 4.18
7 8 2.173758 TTTACATGTCTGCGGCCGGA 62.174 55.000 29.38 25.47 0.00 5.14
8 9 1.095228 ATTTACATGTCTGCGGCCGG 61.095 55.000 29.38 11.74 0.00 6.13
9 10 0.304705 GATTTACATGTCTGCGGCCG 59.695 55.000 24.05 24.05 0.00 6.13
10 11 0.304705 CGATTTACATGTCTGCGGCC 59.695 55.000 0.00 0.00 0.00 6.13
11 12 0.316196 GCGATTTACATGTCTGCGGC 60.316 55.000 0.00 0.00 0.00 6.53
12 13 0.043053 CGCGATTTACATGTCTGCGG 60.043 55.000 17.08 0.00 40.36 5.69
13 14 0.920664 TCGCGATTTACATGTCTGCG 59.079 50.000 3.71 18.14 44.90 5.18
14 15 2.536928 GGTTCGCGATTTACATGTCTGC 60.537 50.000 10.88 0.00 0.00 4.26
15 16 2.670905 TGGTTCGCGATTTACATGTCTG 59.329 45.455 10.88 0.00 0.00 3.51
16 17 2.930040 CTGGTTCGCGATTTACATGTCT 59.070 45.455 10.88 0.00 0.00 3.41
17 18 2.927477 TCTGGTTCGCGATTTACATGTC 59.073 45.455 10.88 0.00 0.00 3.06
18 19 2.967362 TCTGGTTCGCGATTTACATGT 58.033 42.857 10.88 2.69 0.00 3.21
19 20 3.059597 GGATCTGGTTCGCGATTTACATG 60.060 47.826 10.88 2.13 0.00 3.21
20 21 3.131396 GGATCTGGTTCGCGATTTACAT 58.869 45.455 10.88 0.00 0.00 2.29
21 22 2.546778 GGATCTGGTTCGCGATTTACA 58.453 47.619 10.88 6.00 0.00 2.41
22 23 1.865340 GGGATCTGGTTCGCGATTTAC 59.135 52.381 10.88 5.00 0.00 2.01
23 24 1.483004 TGGGATCTGGTTCGCGATTTA 59.517 47.619 10.88 0.00 0.00 1.40
24 25 0.251916 TGGGATCTGGTTCGCGATTT 59.748 50.000 10.88 0.00 0.00 2.17
25 26 0.462047 GTGGGATCTGGTTCGCGATT 60.462 55.000 10.88 0.00 0.00 3.34
26 27 1.144057 GTGGGATCTGGTTCGCGAT 59.856 57.895 10.88 0.00 0.00 4.58
27 28 2.577059 GTGGGATCTGGTTCGCGA 59.423 61.111 3.71 3.71 0.00 5.87
28 29 2.511600 GGTGGGATCTGGTTCGCG 60.512 66.667 0.00 0.00 0.00 5.87
29 30 2.511600 CGGTGGGATCTGGTTCGC 60.512 66.667 0.00 0.00 0.00 4.70
30 31 2.511600 GCGGTGGGATCTGGTTCG 60.512 66.667 0.00 0.00 0.00 3.95
31 32 2.124695 GGCGGTGGGATCTGGTTC 60.125 66.667 0.00 0.00 0.00 3.62
32 33 4.096003 CGGCGGTGGGATCTGGTT 62.096 66.667 0.00 0.00 0.00 3.67
50 51 4.838152 CGGGGTGGTCTGCATCGG 62.838 72.222 0.00 0.00 0.00 4.18
51 52 4.838152 CCGGGGTGGTCTGCATCG 62.838 72.222 0.00 0.00 0.00 3.84
70 71 4.770874 TCGGCGGCTTACCTTGGC 62.771 66.667 7.21 0.00 0.00 4.52
71 72 2.818274 GTCGGCGGCTTACCTTGG 60.818 66.667 3.23 0.00 0.00 3.61
72 73 3.186047 CGTCGGCGGCTTACCTTG 61.186 66.667 10.76 0.00 0.00 3.61
82 83 3.967335 GATCTCCTCCCGTCGGCG 61.967 72.222 0.29 0.29 37.95 6.46
83 84 2.833582 TGATCTCCTCCCGTCGGC 60.834 66.667 5.50 0.00 0.00 5.54
84 85 2.851071 GCTGATCTCCTCCCGTCGG 61.851 68.421 3.60 3.60 0.00 4.79
85 86 1.459455 ATGCTGATCTCCTCCCGTCG 61.459 60.000 0.00 0.00 0.00 5.12
86 87 0.316841 GATGCTGATCTCCTCCCGTC 59.683 60.000 0.00 0.00 0.00 4.79
87 88 1.118356 GGATGCTGATCTCCTCCCGT 61.118 60.000 0.00 0.00 0.00 5.28
88 89 1.670590 GGATGCTGATCTCCTCCCG 59.329 63.158 0.00 0.00 0.00 5.14
89 90 1.670590 CGGATGCTGATCTCCTCCC 59.329 63.158 0.00 0.00 0.00 4.30
90 91 1.670590 CCGGATGCTGATCTCCTCC 59.329 63.158 0.00 0.00 0.00 4.30
91 92 1.005156 GCCGGATGCTGATCTCCTC 60.005 63.158 5.05 0.00 36.87 3.71
92 93 2.865598 CGCCGGATGCTGATCTCCT 61.866 63.158 5.05 0.00 38.05 3.69
93 94 2.356793 CGCCGGATGCTGATCTCC 60.357 66.667 5.05 0.00 38.05 3.71
94 95 2.356793 CCGCCGGATGCTGATCTC 60.357 66.667 5.05 0.00 38.05 2.75
95 96 2.839632 TCCGCCGGATGCTGATCT 60.840 61.111 5.05 0.00 38.05 2.75
96 97 2.356793 CTCCGCCGGATGCTGATC 60.357 66.667 6.16 0.00 38.05 2.92
97 98 1.971505 TTTCTCCGCCGGATGCTGAT 61.972 55.000 6.16 0.00 38.05 2.90
98 99 1.971505 ATTTCTCCGCCGGATGCTGA 61.972 55.000 6.16 0.00 38.05 4.26
99 100 1.097547 AATTTCTCCGCCGGATGCTG 61.098 55.000 6.16 0.00 38.05 4.41
100 101 1.097547 CAATTTCTCCGCCGGATGCT 61.098 55.000 6.16 0.00 38.05 3.79
101 102 1.356624 CAATTTCTCCGCCGGATGC 59.643 57.895 6.16 0.00 0.00 3.91
102 103 0.378257 CACAATTTCTCCGCCGGATG 59.622 55.000 6.16 3.85 0.00 3.51
103 104 0.035439 ACACAATTTCTCCGCCGGAT 60.035 50.000 6.16 0.00 0.00 4.18
104 105 0.609151 TACACAATTTCTCCGCCGGA 59.391 50.000 5.05 5.37 0.00 5.14
105 106 1.444836 TTACACAATTTCTCCGCCGG 58.555 50.000 0.00 0.00 0.00 6.13
106 107 4.272504 ACATATTACACAATTTCTCCGCCG 59.727 41.667 0.00 0.00 0.00 6.46
107 108 5.295787 TGACATATTACACAATTTCTCCGCC 59.704 40.000 0.00 0.00 0.00 6.13
108 109 6.358118 TGACATATTACACAATTTCTCCGC 57.642 37.500 0.00 0.00 0.00 5.54
109 110 7.747888 TGTTGACATATTACACAATTTCTCCG 58.252 34.615 0.00 0.00 0.00 4.63
110 111 9.906660 TTTGTTGACATATTACACAATTTCTCC 57.093 29.630 0.00 0.00 0.00 3.71
218 219 3.308053 CGTGCATGGTCTTCTGTTATCAG 59.692 47.826 0.00 0.00 42.54 2.90
235 236 8.083462 TCATATCGGTAATACTTTATTCGTGCA 58.917 33.333 0.00 0.00 0.00 4.57
243 244 9.797556 CGGATGATTCATATCGGTAATACTTTA 57.202 33.333 0.00 0.00 33.23 1.85
245 246 8.063200 TCGGATGATTCATATCGGTAATACTT 57.937 34.615 16.62 0.00 33.23 2.24
247 248 7.704271 TCTCGGATGATTCATATCGGTAATAC 58.296 38.462 16.62 0.00 33.23 1.89
248 249 7.468768 GCTCTCGGATGATTCATATCGGTAATA 60.469 40.741 16.62 2.87 33.23 0.98
249 250 6.681616 GCTCTCGGATGATTCATATCGGTAAT 60.682 42.308 16.62 0.00 33.23 1.89
250 251 5.393135 GCTCTCGGATGATTCATATCGGTAA 60.393 44.000 16.62 6.73 33.23 2.85
254 255 4.368874 AGCTCTCGGATGATTCATATCG 57.631 45.455 12.78 12.78 33.23 2.92
265 266 3.320541 CACCTATCTTGAAGCTCTCGGAT 59.679 47.826 0.00 0.00 0.00 4.18
266 267 2.690497 CACCTATCTTGAAGCTCTCGGA 59.310 50.000 0.00 0.00 0.00 4.55
274 275 4.307432 ACGAACACACACCTATCTTGAAG 58.693 43.478 0.00 0.00 0.00 3.02
279 280 4.330944 TGAAACGAACACACACCTATCT 57.669 40.909 0.00 0.00 0.00 1.98
282 283 3.864243 AGTTGAAACGAACACACACCTA 58.136 40.909 0.00 0.00 0.00 3.08
299 300 4.669965 CGCTGTGTATTGTGATCCAAGTTG 60.670 45.833 0.00 0.00 36.25 3.16
316 317 4.521943 CTTCTCAAGAAACTTTCGCTGTG 58.478 43.478 0.00 0.71 33.07 3.66
317 318 3.002759 GCTTCTCAAGAAACTTTCGCTGT 59.997 43.478 0.00 0.00 33.07 4.40
319 320 3.206150 TGCTTCTCAAGAAACTTTCGCT 58.794 40.909 0.00 0.00 33.07 4.93
320 321 3.609103 TGCTTCTCAAGAAACTTTCGC 57.391 42.857 0.00 0.00 33.07 4.70
321 322 5.142962 GTCATGCTTCTCAAGAAACTTTCG 58.857 41.667 0.00 0.00 33.07 3.46
322 323 6.064846 TGTCATGCTTCTCAAGAAACTTTC 57.935 37.500 0.00 0.00 33.07 2.62
323 324 6.645790 ATGTCATGCTTCTCAAGAAACTTT 57.354 33.333 0.00 0.00 33.07 2.66
324 325 6.645790 AATGTCATGCTTCTCAAGAAACTT 57.354 33.333 0.00 0.00 33.07 2.66
325 326 6.040166 ACAAATGTCATGCTTCTCAAGAAACT 59.960 34.615 0.00 0.00 33.07 2.66
326 327 6.211515 ACAAATGTCATGCTTCTCAAGAAAC 58.788 36.000 0.00 0.00 33.07 2.78
329 330 5.618056 GACAAATGTCATGCTTCTCAAGA 57.382 39.130 8.63 0.00 44.18 3.02
372 374 2.818130 ATGGCCATGTGTGTTTGAAC 57.182 45.000 20.04 0.00 0.00 3.18
382 384 3.976704 TCGGAAGAAATGGCCATGT 57.023 47.368 21.63 15.42 37.03 3.21
446 448 4.454504 GGCAATTCCTTTAAGAGAACACGA 59.545 41.667 0.00 0.00 0.00 4.35
454 456 3.701040 GGAGCATGGCAATTCCTTTAAGA 59.299 43.478 0.00 0.00 35.26 2.10
458 460 1.829222 CAGGAGCATGGCAATTCCTTT 59.171 47.619 13.23 0.00 37.97 3.11
473 475 2.997986 ACCGCGTTTTATGTTACAGGAG 59.002 45.455 4.92 0.00 0.00 3.69
476 478 4.392619 TTCACCGCGTTTTATGTTACAG 57.607 40.909 4.92 0.00 0.00 2.74
477 479 4.808077 TTTCACCGCGTTTTATGTTACA 57.192 36.364 4.92 0.00 0.00 2.41
478 480 5.385213 CGTTTTTCACCGCGTTTTATGTTAC 60.385 40.000 4.92 0.00 0.00 2.50
479 481 4.669728 CGTTTTTCACCGCGTTTTATGTTA 59.330 37.500 4.92 0.00 0.00 2.41
480 482 3.482833 CGTTTTTCACCGCGTTTTATGTT 59.517 39.130 4.92 0.00 0.00 2.71
481 483 3.037324 CGTTTTTCACCGCGTTTTATGT 58.963 40.909 4.92 0.00 0.00 2.29
482 484 3.037324 ACGTTTTTCACCGCGTTTTATG 58.963 40.909 4.92 0.00 33.54 1.90
483 485 3.337301 ACGTTTTTCACCGCGTTTTAT 57.663 38.095 4.92 0.00 33.54 1.40
484 486 2.821307 ACGTTTTTCACCGCGTTTTA 57.179 40.000 4.92 0.00 33.54 1.52
485 487 1.912756 GAACGTTTTTCACCGCGTTTT 59.087 42.857 4.92 0.00 45.68 2.43
486 488 1.537212 GAACGTTTTTCACCGCGTTT 58.463 45.000 4.92 0.00 45.68 3.60
488 490 1.012014 CGAACGTTTTTCACCGCGT 60.012 52.632 4.92 0.00 39.37 6.01
489 491 2.344237 GCGAACGTTTTTCACCGCG 61.344 57.895 12.93 0.00 33.42 6.46
490 492 2.344237 CGCGAACGTTTTTCACCGC 61.344 57.895 16.88 16.88 39.33 5.68
491 493 0.315220 TTCGCGAACGTTTTTCACCG 60.315 50.000 19.38 0.74 41.18 4.94
492 494 1.706597 CATTCGCGAACGTTTTTCACC 59.293 47.619 26.00 0.00 41.18 4.02
525 527 0.304705 GGTAATGATGCAGCGAACGG 59.695 55.000 0.00 0.00 0.00 4.44
535 537 6.584563 CCCACAAAAGTTAAACGGTAATGATG 59.415 38.462 0.00 0.00 0.00 3.07
585 1168 4.855340 ACAAGACAAAGAAAGTGGAAGGA 58.145 39.130 0.00 0.00 0.00 3.36
652 1235 2.113289 GAAGAGCAGCGACGATACTTC 58.887 52.381 0.00 5.16 0.00 3.01
656 1239 0.450583 AACGAAGAGCAGCGACGATA 59.549 50.000 0.00 0.00 0.00 2.92
817 1400 3.326880 CCTACCGGGCTATTTAACTCCAT 59.673 47.826 6.32 0.00 0.00 3.41
884 1467 3.857038 GATTCCCCGGGCGTGCTA 61.857 66.667 17.73 0.00 0.00 3.49
886 1469 4.796495 AAGATTCCCCGGGCGTGC 62.796 66.667 17.73 3.99 0.00 5.34
897 1480 1.148759 GCTCGCTCCCGTCAAGATTC 61.149 60.000 0.00 0.00 35.54 2.52
1342 1968 0.911769 TGATGTCCTTGGCCTCGAAT 59.088 50.000 3.32 0.00 0.00 3.34
1366 1992 1.694696 GGCCCATTCTCGAGGTAGAAT 59.305 52.381 13.56 1.94 45.07 2.40
1381 2007 1.304879 CGGGAAAATCTTGGGCCCA 60.305 57.895 24.45 24.45 38.75 5.36
1551 2469 0.316204 CGTACTTGGGACCGTTCACT 59.684 55.000 0.00 0.00 0.00 3.41
1557 2475 2.180017 CCGTCGTACTTGGGACCG 59.820 66.667 0.00 0.00 0.00 4.79
1581 2499 2.928301 GCTCTTGATCTTGTCGTGCAGA 60.928 50.000 0.00 0.00 0.00 4.26
1632 2550 1.338674 GGGACGATGATGTTGGTGACA 60.339 52.381 0.00 0.00 43.71 3.58
1695 2613 1.623542 GGTCCACCTTGGCCTCGTAT 61.624 60.000 3.32 0.00 37.47 3.06
2056 2974 1.282157 GATAAGTGGGGTGAAGCCACT 59.718 52.381 0.00 0.00 45.22 4.00
2241 3159 2.872408 CAACATGTTGCCGATCCCT 58.128 52.632 24.69 0.00 33.45 4.20
2388 3306 0.261696 AGTTGAGGGTGGTTTGGCTT 59.738 50.000 0.00 0.00 0.00 4.35
2435 3358 4.386350 GCTAGTTTTCTTCGTCTCTGTTCC 59.614 45.833 0.00 0.00 0.00 3.62
2622 3547 5.892686 TGATAATCATGAGACAAATTGCCCA 59.107 36.000 0.09 0.00 0.00 5.36
2655 3653 1.287425 CCGATTAGTCGCCAACTTCC 58.713 55.000 1.48 0.00 46.32 3.46
2715 3713 0.605050 TTGTCCTTGCATGCACGCTA 60.605 50.000 22.58 4.47 0.00 4.26
2745 3743 6.879458 AGTTTCATGTAGAACATCAACCCTAC 59.121 38.462 10.39 0.00 36.53 3.18
2885 3883 6.263344 CCATGTGCATCATTTTAGTGAGAAG 58.737 40.000 0.00 0.00 34.09 2.85
2913 3911 5.163088 ACACTATCCCAAAGACAAAACTCCT 60.163 40.000 0.00 0.00 0.00 3.69
2945 3943 9.443283 GTAGTTGCTCATGTCATCATTTATTTC 57.557 33.333 0.00 0.00 31.15 2.17
3112 4137 9.295214 GTGTTCGACATATGATAGAATGGATAG 57.705 37.037 10.38 0.00 0.00 2.08
3113 4138 8.251026 GGTGTTCGACATATGATAGAATGGATA 58.749 37.037 10.38 0.00 0.00 2.59
3114 4139 7.099764 GGTGTTCGACATATGATAGAATGGAT 58.900 38.462 10.38 0.00 0.00 3.41
3115 4140 6.041523 TGGTGTTCGACATATGATAGAATGGA 59.958 38.462 10.38 0.00 0.00 3.41
3116 4141 6.223120 TGGTGTTCGACATATGATAGAATGG 58.777 40.000 10.38 0.00 0.00 3.16
3117 4142 7.895975 ATGGTGTTCGACATATGATAGAATG 57.104 36.000 10.38 0.00 0.00 2.67
3118 4143 8.370940 AGAATGGTGTTCGACATATGATAGAAT 58.629 33.333 10.38 0.00 0.00 2.40
3119 4144 7.726216 AGAATGGTGTTCGACATATGATAGAA 58.274 34.615 10.38 8.69 0.00 2.10
3120 4145 7.231519 AGAGAATGGTGTTCGACATATGATAGA 59.768 37.037 10.38 2.68 0.00 1.98
3121 4146 7.374272 AGAGAATGGTGTTCGACATATGATAG 58.626 38.462 10.38 0.14 0.00 2.08
3122 4147 7.290110 AGAGAATGGTGTTCGACATATGATA 57.710 36.000 10.38 0.00 0.00 2.15
3123 4148 6.166984 AGAGAATGGTGTTCGACATATGAT 57.833 37.500 10.38 0.00 0.00 2.45
3124 4149 5.598416 AGAGAATGGTGTTCGACATATGA 57.402 39.130 10.38 0.00 0.00 2.15
3125 4150 7.095481 CCATAAGAGAATGGTGTTCGACATATG 60.095 40.741 0.00 0.00 41.38 1.78
3126 4151 6.931281 CCATAAGAGAATGGTGTTCGACATAT 59.069 38.462 0.00 0.00 41.38 1.78
3127 4152 6.097696 TCCATAAGAGAATGGTGTTCGACATA 59.902 38.462 2.98 0.00 45.67 2.29
3128 4153 5.104941 TCCATAAGAGAATGGTGTTCGACAT 60.105 40.000 2.98 0.00 45.67 3.06
3129 4154 4.221924 TCCATAAGAGAATGGTGTTCGACA 59.778 41.667 2.98 0.00 45.67 4.35
3130 4155 4.567159 GTCCATAAGAGAATGGTGTTCGAC 59.433 45.833 2.98 0.00 45.67 4.20
3131 4156 4.382685 GGTCCATAAGAGAATGGTGTTCGA 60.383 45.833 2.98 0.00 45.67 3.71
3132 4157 3.871594 GGTCCATAAGAGAATGGTGTTCG 59.128 47.826 2.98 0.00 45.67 3.95
3133 4158 4.843728 TGGTCCATAAGAGAATGGTGTTC 58.156 43.478 2.98 0.00 45.67 3.18
3241 4267 7.255277 GGCAACAACCAAAGATATCTTATCTCC 60.255 40.741 18.23 6.89 34.61 3.71
3247 4273 4.396166 CGAGGCAACAACCAAAGATATCTT 59.604 41.667 12.37 12.37 41.41 2.40
3312 4338 6.367374 TCCATGTACATTTCCAAGTCTGTA 57.633 37.500 5.37 0.00 0.00 2.74
3346 4372 2.143122 TCAGCTTGTAAGGCGTTTCTG 58.857 47.619 0.00 0.00 34.52 3.02
3360 4386 7.807977 TGACAGAAGTTTATTCTTTCAGCTT 57.192 32.000 3.07 0.00 32.27 3.74
3371 4397 6.332635 TCATCCCCCATATGACAGAAGTTTAT 59.667 38.462 3.65 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.