Multiple sequence alignment - TraesCS4A01G090300

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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 TraesCS4A01G090300 chr4A 100.000 6801 0 0 1 6801 96488934 96482134 0.000000e+00 12560
1 TraesCS4A01G090300 chr4A 93.730 5439 260 33 861 6250 96433308 96427902 0.000000e+00 8080
2 TraesCS4A01G090300 chr4A 92.821 794 51 5 1 790 332676392 332675601 0.000000e+00 1146
3 TraesCS4A01G090300 chr4A 92.677 792 51 7 1 788 384251137 384251925 0.000000e+00 1134
4 TraesCS4A01G090300 chr4A 92.569 794 52 7 1 788 500706017 500705225 0.000000e+00 1133
5 TraesCS4A01G090300 chr4A 93.172 454 29 2 6286 6737 96550530 96550077 0.000000e+00 665
6 TraesCS4A01G090300 chr3B 94.011 5059 244 31 955 5975 784490170 784485133 0.000000e+00 7609
7 TraesCS4A01G090300 chr3B 93.850 5057 255 30 955 5975 784556390 784551354 0.000000e+00 7564
8 TraesCS4A01G090300 chr3B 95.238 105 5 0 868 972 784490316 784490212 4.220000e-37 167
9 TraesCS4A01G090300 chr3B 95.238 105 5 0 868 972 784556532 784556428 4.220000e-37 167
10 TraesCS4A01G090300 chr5D 95.031 4448 174 24 1044 5456 285457363 285461798 0.000000e+00 6946
11 TraesCS4A01G090300 chr5D 96.173 784 29 1 5508 6290 285461798 285462581 0.000000e+00 1280
12 TraesCS4A01G090300 chr5D 83.757 511 65 10 6294 6792 480484845 480485349 1.030000e-127 468
13 TraesCS4A01G090300 chr5D 86.824 296 9 12 862 1127 285457031 285457326 3.080000e-78 303
14 TraesCS4A01G090300 chr1A 93.291 790 50 3 1 788 503104467 503105255 0.000000e+00 1162
15 TraesCS4A01G090300 chr7A 92.920 791 50 6 1 788 341823036 341823823 0.000000e+00 1146
16 TraesCS4A01G090300 chr6A 92.803 792 52 5 1 788 501747727 501748517 0.000000e+00 1142
17 TraesCS4A01G090300 chr6A 92.794 791 52 5 1 788 358774537 358773749 0.000000e+00 1140
18 TraesCS4A01G090300 chr5A 92.658 790 54 4 1 788 117339093 117338306 0.000000e+00 1134
19 TraesCS4A01G090300 chr2A 92.757 787 54 3 1 786 379144394 379145178 0.000000e+00 1134
20 TraesCS4A01G090300 chr1D 84.149 511 63 8 6294 6792 95929549 95929045 4.770000e-131 479
21 TraesCS4A01G090300 chr1D 83.170 511 68 10 6294 6792 359668474 359668978 1.040000e-122 451
22 TraesCS4A01G090300 chr7D 83.953 511 63 11 6294 6792 416019579 416019076 7.980000e-129 472
23 TraesCS4A01G090300 chr7B 83.622 519 65 11 6294 6799 88240678 88240167 2.870000e-128 470
24 TraesCS4A01G090300 chr7B 81.923 520 76 12 6292 6799 485413281 485412768 2.270000e-114 424
25 TraesCS4A01G090300 chr2D 83.757 511 65 10 6294 6792 126963812 126963308 1.030000e-127 468
26 TraesCS4A01G090300 chr2D 83.562 511 66 10 6294 6792 586115373 586115877 4.810000e-126 462
27 TraesCS4A01G090300 chr6B 82.276 457 71 4 6338 6792 582885678 582886126 2.970000e-103 387
28 TraesCS4A01G090300 chr4B 80.792 505 79 12 6292 6784 570829674 570829176 4.980000e-101 379
29 TraesCS4A01G090300 chr1B 81.757 444 69 9 6292 6723 211321903 211321460 1.800000e-95 361
30 TraesCS4A01G090300 chr1B 77.843 510 95 9 6292 6789 620907242 620906739 3.990000e-77 300
31 TraesCS4A01G090300 chr1B 89.535 86 7 2 6210 6294 1659456 1659540 2.590000e-19 108
32 TraesCS4A01G090300 chr1B 89.535 86 7 2 6210 6294 1661809 1661893 2.590000e-19 108
33 TraesCS4A01G090300 chr2B 79.688 512 89 11 6292 6799 97102244 97101744 8.390000e-94 355
34 TraesCS4A01G090300 chr2B 82.014 278 38 8 6286 6551 685939412 685939689 6.860000e-55 226
35 TraesCS4A01G090300 chr6D 82.723 191 21 9 6286 6464 31842837 31842647 7.060000e-35 159
36 TraesCS4A01G090300 chrUn 94.737 76 3 1 6215 6289 224580494 224580569 4.310000e-22 117
37 TraesCS4A01G090300 chrUn 94.667 75 3 1 6216 6289 261348507 261348433 1.550000e-21 115
38 TraesCS4A01G090300 chrUn 92.405 79 5 1 6213 6290 425967498 425967420 2.010000e-20 111
39 TraesCS4A01G090300 chr5B 92.593 81 5 1 6210 6289 3044613 3044693 1.550000e-21 115
40 TraesCS4A01G090300 chr5B 92.593 81 5 1 6210 6289 3062536 3062616 1.550000e-21 115
41 TraesCS4A01G090300 chr5B 91.463 82 5 2 6210 6289 3095397 3095478 2.010000e-20 111


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 TraesCS4A01G090300 chr4A 96482134 96488934 6800 True 12560.0 12560 100.0000 1 6801 1 chr4A.!!$R2 6800
1 TraesCS4A01G090300 chr4A 96427902 96433308 5406 True 8080.0 8080 93.7300 861 6250 1 chr4A.!!$R1 5389
2 TraesCS4A01G090300 chr4A 332675601 332676392 791 True 1146.0 1146 92.8210 1 790 1 chr4A.!!$R4 789
3 TraesCS4A01G090300 chr4A 384251137 384251925 788 False 1134.0 1134 92.6770 1 788 1 chr4A.!!$F1 787
4 TraesCS4A01G090300 chr4A 500705225 500706017 792 True 1133.0 1133 92.5690 1 788 1 chr4A.!!$R5 787
5 TraesCS4A01G090300 chr3B 784485133 784490316 5183 True 3888.0 7609 94.6245 868 5975 2 chr3B.!!$R1 5107
6 TraesCS4A01G090300 chr3B 784551354 784556532 5178 True 3865.5 7564 94.5440 868 5975 2 chr3B.!!$R2 5107
7 TraesCS4A01G090300 chr5D 285457031 285462581 5550 False 2843.0 6946 92.6760 862 6290 3 chr5D.!!$F2 5428
8 TraesCS4A01G090300 chr5D 480484845 480485349 504 False 468.0 468 83.7570 6294 6792 1 chr5D.!!$F1 498
9 TraesCS4A01G090300 chr1A 503104467 503105255 788 False 1162.0 1162 93.2910 1 788 1 chr1A.!!$F1 787
10 TraesCS4A01G090300 chr7A 341823036 341823823 787 False 1146.0 1146 92.9200 1 788 1 chr7A.!!$F1 787
11 TraesCS4A01G090300 chr6A 501747727 501748517 790 False 1142.0 1142 92.8030 1 788 1 chr6A.!!$F1 787
12 TraesCS4A01G090300 chr6A 358773749 358774537 788 True 1140.0 1140 92.7940 1 788 1 chr6A.!!$R1 787
13 TraesCS4A01G090300 chr5A 117338306 117339093 787 True 1134.0 1134 92.6580 1 788 1 chr5A.!!$R1 787
14 TraesCS4A01G090300 chr2A 379144394 379145178 784 False 1134.0 1134 92.7570 1 786 1 chr2A.!!$F1 785
15 TraesCS4A01G090300 chr1D 95929045 95929549 504 True 479.0 479 84.1490 6294 6792 1 chr1D.!!$R1 498
16 TraesCS4A01G090300 chr1D 359668474 359668978 504 False 451.0 451 83.1700 6294 6792 1 chr1D.!!$F1 498
17 TraesCS4A01G090300 chr7D 416019076 416019579 503 True 472.0 472 83.9530 6294 6792 1 chr7D.!!$R1 498
18 TraesCS4A01G090300 chr7B 88240167 88240678 511 True 470.0 470 83.6220 6294 6799 1 chr7B.!!$R1 505
19 TraesCS4A01G090300 chr7B 485412768 485413281 513 True 424.0 424 81.9230 6292 6799 1 chr7B.!!$R2 507
20 TraesCS4A01G090300 chr2D 126963308 126963812 504 True 468.0 468 83.7570 6294 6792 1 chr2D.!!$R1 498
21 TraesCS4A01G090300 chr2D 586115373 586115877 504 False 462.0 462 83.5620 6294 6792 1 chr2D.!!$F1 498
22 TraesCS4A01G090300 chr1B 620906739 620907242 503 True 300.0 300 77.8430 6292 6789 1 chr1B.!!$R2 497
23 TraesCS4A01G090300 chr2B 97101744 97102244 500 True 355.0 355 79.6880 6292 6799 1 chr2B.!!$R1 507

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
774 789 0.388649 CGTGGGAGATATAGCCGCAC 60.389 60.000 13.12 13.12 39.43 5.34 F
2462 2682 0.331954 TAAATTGGGCAGGCGGGTTA 59.668 50.000 0.00 0.00 0.00 2.85 F
3260 3491 0.618107 AACGGTTGGGTTGGGGTTTT 60.618 50.000 0.00 0.00 0.00 2.43 F
3633 3865 1.080569 GCACGCAAATTGGTGAGGG 60.081 57.895 15.39 0.00 36.25 4.30 F
4424 4674 1.638529 AGGGGGAAGATCAGCTATCG 58.361 55.000 0.00 0.00 39.79 2.92 F
4575 4825 2.044946 CCCACCTTGCTGCCCTAC 60.045 66.667 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2646 2874 0.739813 GACCTGAACCAATCCGACCG 60.740 60.000 0.00 0.00 0.00 4.79 R
3605 3837 0.320073 ATTTGCGTGCATTGCAGCTT 60.320 45.000 23.81 12.52 44.28 3.74 R
4553 4803 1.378762 GGCAGCAAGGTGGGTTCTA 59.621 57.895 0.00 0.00 0.00 2.10 R
4558 4808 2.044946 GTAGGGCAGCAAGGTGGG 60.045 66.667 0.00 0.00 0.00 4.61 R
5389 5642 2.549754 AGCCACATTCTCAGTTGTTTCG 59.450 45.455 0.00 0.00 0.00 3.46 R
6479 6757 2.092158 TGATGGTGGTGTTGTTTCCTGA 60.092 45.455 0.00 0.00 0.00 3.86 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
20 21 0.550914 AAGTTGGGACACCTCTGCAA 59.449 50.000 0.00 0.00 39.29 4.08
43 44 2.113910 TTTGAACTTTCGAAAGCCGC 57.886 45.000 32.49 22.73 39.63 6.53
65 66 1.227527 CGCGGTTATGGGCAGATGA 60.228 57.895 0.00 0.00 0.00 2.92
223 225 7.235430 CGTAAGTAGTTTCAGGATCATTTCC 57.765 40.000 0.00 0.00 45.85 3.13
248 253 6.798482 TGATCTTTATAGCTTTTCGACCGTA 58.202 36.000 0.00 0.00 0.00 4.02
296 301 4.624015 TGCGTAAGTTAGCCACCATATAC 58.376 43.478 3.04 0.00 41.68 1.47
422 433 2.949447 ACTTCCAAACAGATGCAGGTT 58.051 42.857 0.00 0.00 0.00 3.50
424 435 2.957402 TCCAAACAGATGCAGGTTCT 57.043 45.000 0.00 0.00 0.00 3.01
524 535 3.139957 TCCAGATGATCAGTAGAGGAGCT 59.860 47.826 0.09 0.00 0.00 4.09
574 588 9.267084 GCATTTGGGTTGTCTTTCTTTATTTTA 57.733 29.630 0.00 0.00 0.00 1.52
605 619 3.309954 GTCGGACCTTGATTGTATTCTGC 59.690 47.826 0.00 0.00 0.00 4.26
653 668 2.076863 GTGAAGTGGCGATTGTAAGCT 58.923 47.619 0.00 0.00 0.00 3.74
701 716 8.768397 TCAGTACAAGGGATGTGTAAAGATTAT 58.232 33.333 0.00 0.00 43.77 1.28
774 789 0.388649 CGTGGGAGATATAGCCGCAC 60.389 60.000 13.12 13.12 39.43 5.34
942 957 5.931146 TGCCGCATTTTAATTGTTTGATCTT 59.069 32.000 0.00 0.00 0.00 2.40
1023 1097 8.088463 TGATGCACCATTTAATTAGGGAAATT 57.912 30.769 0.00 0.00 40.87 1.82
1184 1378 6.875195 TGCTTGTGTACCACCTTATTAACTAC 59.125 38.462 0.00 0.00 32.73 2.73
1358 1552 0.611618 TCTACCTAAACACCCGCCGA 60.612 55.000 0.00 0.00 0.00 5.54
1387 1581 4.935808 CCTCGAAAAATACAACCTGCTAGT 59.064 41.667 0.00 0.00 0.00 2.57
1410 1604 1.067295 TGGGAGTTCTCATGGTGCTT 58.933 50.000 0.00 0.00 0.00 3.91
1667 1861 7.392494 AGCTAAGCACTTATTTCCCTTTTAC 57.608 36.000 0.00 0.00 0.00 2.01
1684 1878 8.635328 TCCCTTTTACTTTGGTAATTCTTGTTC 58.365 33.333 0.00 0.00 37.69 3.18
1685 1879 8.638873 CCCTTTTACTTTGGTAATTCTTGTTCT 58.361 33.333 0.00 0.00 37.69 3.01
1731 1925 7.588497 TTAGATGTGCTCTTCTTATCTGCTA 57.412 36.000 9.17 0.00 35.28 3.49
1920 2114 5.801350 TTGACACTTTGACTTCAAGACTG 57.199 39.130 0.00 0.00 37.15 3.51
1987 2181 8.023128 TCTGCAAGCTTCAAATAAGTAAATGAC 58.977 33.333 0.00 0.00 0.00 3.06
1990 2184 7.274250 GCAAGCTTCAAATAAGTAAATGACTGG 59.726 37.037 0.00 0.00 38.87 4.00
2194 2411 2.502142 TCAATGCAGTTGATGAGCCT 57.498 45.000 7.27 0.00 41.79 4.58
2210 2429 3.245229 TGAGCCTATCCATTTGTTGTGGT 60.245 43.478 0.00 0.00 37.96 4.16
2213 2432 3.701040 GCCTATCCATTTGTTGTGGTGAT 59.299 43.478 0.00 0.00 37.96 3.06
2255 2474 2.536761 TACAAGGACACAGGGAAACG 57.463 50.000 0.00 0.00 0.00 3.60
2273 2492 6.047231 GGAAACGGTTCAATATACTAGCAGT 58.953 40.000 16.38 0.00 35.25 4.40
2303 2522 6.156083 TGGATACAGTTCATGGTTCATGACTA 59.844 38.462 9.77 0.00 46.14 2.59
2317 2536 7.455638 TGGTTCATGACTAGATGGATCATATGA 59.544 37.037 8.10 8.10 31.83 2.15
2331 2550 7.758609 TGGATCATATGAAGGATACCAAACAT 58.241 34.615 9.99 0.00 37.17 2.71
2453 2673 4.411927 AGTTACATGTGGTAAATTGGGCA 58.588 39.130 9.11 0.00 43.30 5.36
2462 2682 0.331954 TAAATTGGGCAGGCGGGTTA 59.668 50.000 0.00 0.00 0.00 2.85
2475 2701 1.876497 CGGGTTAGGTTCGGGTTCGA 61.876 60.000 0.00 0.00 44.44 3.71
2480 2706 1.619654 TAGGTTCGGGTTCGAGTTGA 58.380 50.000 0.00 0.00 46.75 3.18
2504 2730 1.133730 TGTCGGGTTAGTTTGGCCTTT 60.134 47.619 3.32 0.00 0.00 3.11
2531 2757 2.993264 TCGGGTCGAGTTGGGTCC 60.993 66.667 0.00 0.00 0.00 4.46
2551 2777 1.074248 GTTGGGTGATGGACGGGTT 59.926 57.895 0.00 0.00 0.00 4.11
2573 2799 6.320418 GGTTAGGTCGGACCAATTTCAATATT 59.680 38.462 27.87 6.20 41.95 1.28
2625 2853 8.000709 AGTTGGATTGGATGCTATTTGATCTTA 58.999 33.333 0.00 0.00 0.00 2.10
2646 2874 2.092914 AGATCGGGTCAGTTTTGGATCC 60.093 50.000 4.20 4.20 32.69 3.36
2680 2911 2.103094 TCAGGTCAGGTCAGTTTGACTG 59.897 50.000 8.89 1.71 46.19 3.51
2741 2972 2.406002 TTTCTCGGGTTGGGTCAGGC 62.406 60.000 0.00 0.00 0.00 4.85
2806 3037 7.601705 TCTTGGTTTCTTCCAGATTGAAATT 57.398 32.000 0.00 0.00 38.80 1.82
2807 3038 7.436118 TCTTGGTTTCTTCCAGATTGAAATTG 58.564 34.615 0.00 0.00 38.80 2.32
2842 3073 2.689691 GGCCAATGAGTGCCCCCTA 61.690 63.158 0.00 0.00 41.97 3.53
2848 3079 3.364549 CAATGAGTGCCCCCTAAAATCA 58.635 45.455 0.00 0.00 0.00 2.57
2873 3104 4.819630 TCAAGTTCTACGCCACAAAAGAAT 59.180 37.500 0.00 0.00 31.16 2.40
3099 3330 7.468441 TGCAATTTCTATGTTTGTATGTACCG 58.532 34.615 0.00 0.00 0.00 4.02
3100 3331 7.119992 TGCAATTTCTATGTTTGTATGTACCGT 59.880 33.333 0.00 0.00 0.00 4.83
3106 3337 5.617528 ATGTTTGTATGTACCGTGGGATA 57.382 39.130 0.00 0.00 0.00 2.59
3170 3401 9.566432 AAAGATTAGGACTTATGATGATGGAAC 57.434 33.333 0.00 0.00 0.00 3.62
3189 3420 4.946157 GGAACACTTGTGATTGGAGATGAT 59.054 41.667 7.83 0.00 0.00 2.45
3260 3491 0.618107 AACGGTTGGGTTGGGGTTTT 60.618 50.000 0.00 0.00 0.00 2.43
3267 3498 2.324541 TGGGTTGGGGTTTTGATCTTG 58.675 47.619 0.00 0.00 0.00 3.02
3270 3501 2.302733 GGTTGGGGTTTTGATCTTGCAT 59.697 45.455 0.00 0.00 0.00 3.96
3417 3649 7.117454 CGATAAAGCTGTTATTTACCAAGACG 58.883 38.462 0.00 0.00 0.00 4.18
3539 3771 3.056891 CGGTATGCCAAATTGGTCACTTT 60.057 43.478 14.17 0.92 40.46 2.66
3599 3831 5.784177 TGTCGAGCTTCTCAAGACTAAAAT 58.216 37.500 0.00 0.00 33.40 1.82
3605 3837 7.063898 CGAGCTTCTCAAGACTAAAATCATGAA 59.936 37.037 0.00 0.00 0.00 2.57
3617 3849 3.603158 AATCATGAAAGCTGCAATGCA 57.397 38.095 7.99 7.99 36.92 3.96
3633 3865 1.080569 GCACGCAAATTGGTGAGGG 60.081 57.895 15.39 0.00 36.25 4.30
3799 4043 8.112822 TCTTTTGTGAAGGTATGGATTATTGGA 58.887 33.333 0.00 0.00 0.00 3.53
3839 4083 4.263462 ACATTTGCTCACATAGGAGGAACA 60.263 41.667 0.00 0.00 43.60 3.18
3849 4093 4.475016 ACATAGGAGGAACAGCATTAGGTT 59.525 41.667 0.00 0.00 0.00 3.50
3876 4121 2.216898 GGGATTGAAGAAGCCGATCAG 58.783 52.381 0.00 0.00 38.66 2.90
3914 4159 8.617290 TTATTCTTTGACTGAAGAGTTTACCC 57.383 34.615 0.00 0.00 37.01 3.69
3969 4214 2.438763 CTCTCAAGCTCAGGGATCCAAT 59.561 50.000 15.23 0.00 0.00 3.16
4004 4249 3.634448 TGCAAATAATTCCCCACCATACG 59.366 43.478 0.00 0.00 0.00 3.06
4095 4342 9.630098 ATGCAAACTAACAACTTTCATTAGATG 57.370 29.630 0.00 0.00 31.61 2.90
4213 4461 4.955811 ACCTGACATTAGACACTGAACA 57.044 40.909 0.00 0.00 0.00 3.18
4308 4558 6.321181 TCTTGGTCACAATAAGTTTTCTGCTT 59.679 34.615 0.00 0.00 35.73 3.91
4424 4674 1.638529 AGGGGGAAGATCAGCTATCG 58.361 55.000 0.00 0.00 39.79 2.92
4553 4803 3.903714 TGGATGGTACCAATCGATCTGAT 59.096 43.478 20.76 0.00 39.67 2.90
4558 4808 6.085555 TGGTACCAATCGATCTGATAGAAC 57.914 41.667 13.60 0.00 35.84 3.01
4560 4810 4.608948 ACCAATCGATCTGATAGAACCC 57.391 45.455 0.00 0.00 35.84 4.11
4575 4825 2.044946 CCCACCTTGCTGCCCTAC 60.045 66.667 0.00 0.00 0.00 3.18
4607 4857 7.846066 TGAAATTTGGACCCAATTTATACCAG 58.154 34.615 14.54 0.00 35.70 4.00
4647 4897 5.366460 TGATTTTGCACCATGTCAAATTGT 58.634 33.333 0.00 0.00 32.92 2.71
4897 5147 4.404073 ACCTTAGCACCACTCTCTAATCAG 59.596 45.833 0.00 0.00 0.00 2.90
4913 5163 8.035394 TCTCTAATCAGTCACAACTACCATTTC 58.965 37.037 0.00 0.00 33.25 2.17
4920 5170 9.179909 TCAGTCACAACTACCATTTCTTTAAAA 57.820 29.630 0.00 0.00 33.25 1.52
5123 5373 4.142049 GGTACAATGAGTTCAGGAGGAGAG 60.142 50.000 0.00 0.00 0.00 3.20
5131 5381 6.019748 TGAGTTCAGGAGGAGAGTATTTCTT 58.980 40.000 0.00 0.00 35.87 2.52
5158 5408 6.187682 TCCAATAAAAAGTTGGGAGGATCTC 58.812 40.000 5.18 0.00 44.92 2.75
5231 5481 8.954950 TGATGTAGAGAAATTGGATCTTCTTC 57.045 34.615 0.00 0.00 32.01 2.87
5252 5502 5.241403 TCTTGGTCTTATGGCAGAGAAAA 57.759 39.130 5.09 3.45 0.00 2.29
5283 5533 4.770010 AGGGATTTTCCATAAGCGAAACAA 59.230 37.500 0.00 0.00 38.64 2.83
5299 5549 6.479660 AGCGAAACAACATTCAACATTTTCAT 59.520 30.769 0.00 0.00 0.00 2.57
5329 5579 6.698008 TGGCATCAAGGTGATATTTAGTTG 57.302 37.500 0.00 0.00 34.28 3.16
5427 5680 7.938140 ATGTGGCTTAAGCTAATTTTCACTA 57.062 32.000 25.88 13.71 41.70 2.74
5460 5713 4.746535 ACCCAAACCGAAGTTCAAAAAT 57.253 36.364 3.32 0.00 34.19 1.82
5479 5732 9.684448 TCAAAAATGCAAGAAAACATAACGATA 57.316 25.926 0.00 0.00 0.00 2.92
5510 5763 8.871125 CATTATGGGTACTTTACTGGTAGATCT 58.129 37.037 0.00 0.00 0.00 2.75
5623 5876 5.426833 ACACATCTCTATAAACAGGAGGCTT 59.573 40.000 0.00 0.00 0.00 4.35
5624 5877 6.611642 ACACATCTCTATAAACAGGAGGCTTA 59.388 38.462 0.00 0.00 0.00 3.09
5630 5883 6.113411 TCTATAAACAGGAGGCTTAAAGCAC 58.887 40.000 0.00 0.00 44.75 4.40
5726 5979 2.159099 GGCCTACGAGATGTGATCAACA 60.159 50.000 0.00 0.00 44.79 3.33
5763 6016 2.664402 ACTGCCAACTGGATGAAGTT 57.336 45.000 0.00 0.00 41.08 2.66
5773 6026 3.196685 ACTGGATGAAGTTCTCTAGTGCC 59.803 47.826 15.47 4.41 32.68 5.01
5780 6033 5.571285 TGAAGTTCTCTAGTGCCTTCTCTA 58.429 41.667 17.40 3.80 34.15 2.43
5792 6045 2.421952 GCCTTCTCTATGTGGGATGCAA 60.422 50.000 0.00 0.00 0.00 4.08
5822 6075 3.262151 GTGCAAAAATAAAAGGCCCCCTA 59.738 43.478 0.00 0.00 31.13 3.53
5834 6087 2.731379 AGGCCCCCTACCATATGTACTA 59.269 50.000 0.00 0.00 28.47 1.82
5984 6237 8.626576 CACAAGTTGTATGCTTATTTGTTTACG 58.373 33.333 8.49 0.00 0.00 3.18
6271 6525 3.915346 ACTTATTGTTTTGGGGTCCCT 57.085 42.857 8.15 0.00 36.94 4.20
6275 6529 0.930726 TTGTTTTGGGGTCCCTGAGT 59.069 50.000 8.15 0.00 36.94 3.41
6309 6563 6.575162 ATTGTATGTTGTCCTTTGAACTCC 57.425 37.500 0.00 0.00 0.00 3.85
6311 6565 5.690865 TGTATGTTGTCCTTTGAACTCCTT 58.309 37.500 0.00 0.00 0.00 3.36
6323 6577 3.565307 TGAACTCCTTGCCTTGACAATT 58.435 40.909 0.00 0.00 0.00 2.32
6360 6614 1.348036 AGTTCATAAGGATAGCCGGGC 59.652 52.381 12.11 12.11 39.96 6.13
6398 6653 5.381174 TGACAAATCCATCAAAAGCTCTG 57.619 39.130 0.00 0.00 0.00 3.35
6423 6679 5.241403 ACCATCCTACTTTGACACATGAA 57.759 39.130 0.00 0.00 0.00 2.57
6424 6680 5.819991 ACCATCCTACTTTGACACATGAAT 58.180 37.500 0.00 0.00 0.00 2.57
6426 6682 7.402054 ACCATCCTACTTTGACACATGAATTA 58.598 34.615 0.00 0.00 0.00 1.40
6439 6717 8.143193 TGACACATGAATTATGAGTTTTGCTTT 58.857 29.630 0.00 0.00 40.11 3.51
6479 6757 3.254166 AGATCGTTTGCATGCAAGACTTT 59.746 39.130 30.25 19.38 37.24 2.66
6544 6822 5.707242 ATGGCTTTCATCTCATTAGCATG 57.293 39.130 0.00 0.00 33.60 4.06
6574 6852 6.364701 TCCAATTTGAATCACTATACCCCTG 58.635 40.000 0.00 0.00 0.00 4.45
6610 6888 6.202188 GGGTACATGGTATAGTGAATTTCGTG 59.798 42.308 0.00 0.00 0.00 4.35
6612 6890 4.574828 ACATGGTATAGTGAATTTCGTGGC 59.425 41.667 0.00 0.00 0.00 5.01
6617 6895 5.050091 GGTATAGTGAATTTCGTGGCTCATG 60.050 44.000 0.00 0.00 0.00 3.07
6638 6916 2.541588 GGTGCCTTACAAATAGCGCATG 60.542 50.000 11.47 5.50 37.47 4.06
6651 6929 2.377004 CGCATGACTCGCTCAACAT 58.623 52.632 0.00 0.00 30.60 2.71
6673 6951 0.328926 TGCCAATGCACATCTCCTGA 59.671 50.000 0.00 0.00 44.23 3.86
6678 6956 3.697542 CCAATGCACATCTCCTGAATTGA 59.302 43.478 0.00 0.00 31.39 2.57
6727 7005 1.251527 AACGAGATGTCAGGCCGAGT 61.252 55.000 0.00 0.00 0.00 4.18
6728 7006 0.393944 ACGAGATGTCAGGCCGAGTA 60.394 55.000 0.00 0.00 0.00 2.59
6729 7007 0.309302 CGAGATGTCAGGCCGAGTAG 59.691 60.000 0.00 0.00 0.00 2.57
6730 7008 0.031449 GAGATGTCAGGCCGAGTAGC 59.969 60.000 0.00 0.00 0.00 3.58
6731 7009 0.684479 AGATGTCAGGCCGAGTAGCA 60.684 55.000 0.00 0.00 0.00 3.49
6732 7010 0.528684 GATGTCAGGCCGAGTAGCAC 60.529 60.000 0.00 0.00 0.00 4.40
6761 7039 3.714144 AGCTAGGTACATGAGTGAACCT 58.286 45.455 0.00 6.69 44.47 3.50
6799 7077 8.615211 GTGTCTCATTTAATCTACATTCATGCA 58.385 33.333 0.00 0.00 0.00 3.96
6800 7078 9.346005 TGTCTCATTTAATCTACATTCATGCAT 57.654 29.630 0.00 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.692101 TCGAAAGTTCAAAACCTTGCAGA 59.308 39.130 0.00 0.00 32.14 4.26
20 21 3.488553 CGGCTTTCGAAAGTTCAAAACCT 60.489 43.478 32.32 0.00 42.43 3.50
65 66 9.326413 CTCTACAACCGGATATTAACAAATTCT 57.674 33.333 9.46 0.00 0.00 2.40
180 181 6.259167 ACTTACGTTCAAGCATAACACAAGAA 59.741 34.615 0.00 0.00 0.00 2.52
219 221 7.280205 GGTCGAAAAGCTATAAAGATCAGGAAA 59.720 37.037 0.00 0.00 0.00 3.13
223 225 5.749109 ACGGTCGAAAAGCTATAAAGATCAG 59.251 40.000 0.00 0.00 0.00 2.90
239 244 2.295349 AGAGAAGCAAAGTACGGTCGAA 59.705 45.455 0.00 0.00 0.00 3.71
248 253 2.298729 AGAGCGAGAAGAGAAGCAAAGT 59.701 45.455 0.00 0.00 0.00 2.66
524 535 3.781307 CCCGATCGCCCCAACTGA 61.781 66.667 10.32 0.00 0.00 3.41
653 668 8.826765 ACTGAATAAGAAAGGGATAAAGAGTCA 58.173 33.333 0.00 0.00 0.00 3.41
701 716 1.600511 TACGCATGTCGCAGAAGGGA 61.601 55.000 9.04 0.00 42.60 4.20
706 721 0.805711 CATGGTACGCATGTCGCAGA 60.806 55.000 13.27 0.00 42.60 4.26
707 722 1.637934 CATGGTACGCATGTCGCAG 59.362 57.895 13.27 0.00 42.60 5.18
856 871 9.366216 GTTAGAATTGACACACACAGACATATA 57.634 33.333 0.00 0.00 0.00 0.86
857 872 7.063426 CGTTAGAATTGACACACACAGACATAT 59.937 37.037 0.00 0.00 0.00 1.78
858 873 6.364976 CGTTAGAATTGACACACACAGACATA 59.635 38.462 0.00 0.00 0.00 2.29
859 874 5.177511 CGTTAGAATTGACACACACAGACAT 59.822 40.000 0.00 0.00 0.00 3.06
860 875 4.506288 CGTTAGAATTGACACACACAGACA 59.494 41.667 0.00 0.00 0.00 3.41
863 878 3.247411 TGCGTTAGAATTGACACACACAG 59.753 43.478 0.00 0.00 0.00 3.66
974 1048 5.355467 ACTTAATTTGGCGCAATTTTTGG 57.645 34.783 10.83 2.10 0.00 3.28
1328 1522 6.401394 GGTGTTTAGGTAGAGTAAACCGATT 58.599 40.000 3.87 0.00 42.15 3.34
1358 1552 4.077108 GGTTGTATTTTTCGAGGAGGGTT 58.923 43.478 0.00 0.00 0.00 4.11
1387 1581 2.862541 CACCATGAGAACTCCCAACAA 58.137 47.619 0.00 0.00 0.00 2.83
1410 1604 2.661718 GAACTCCTTGGGGTCAAACAA 58.338 47.619 0.00 0.00 31.77 2.83
1503 1697 2.886523 CAACTGGCTTCATGTTTCTCCA 59.113 45.455 0.00 0.00 0.00 3.86
1645 1839 9.626045 CAAAGTAAAAGGGAAATAAGTGCTTAG 57.374 33.333 0.00 0.00 0.00 2.18
1690 1884 8.982685 GCACATCTAAAGCATGCGTATATATAT 58.017 33.333 13.01 0.00 0.00 0.86
1699 1893 1.938577 AGAGCACATCTAAAGCATGCG 59.061 47.619 13.01 0.00 41.23 4.73
1987 2181 7.979115 TTTTTGAGTTTCAACGTTAATCCAG 57.021 32.000 0.00 0.00 35.89 3.86
2177 2394 3.117776 TGGATAGGCTCATCAACTGCATT 60.118 43.478 0.00 0.00 0.00 3.56
2194 2411 6.663093 AGCTTTATCACCACAACAAATGGATA 59.337 34.615 0.00 0.00 39.87 2.59
2210 2429 3.774766 TCTCCTGGCTAACAGCTTTATCA 59.225 43.478 0.00 0.00 46.14 2.15
2213 2432 3.441101 TCTCTCCTGGCTAACAGCTTTA 58.559 45.455 0.00 0.00 46.14 1.85
2255 2474 6.293626 CCATGCAACTGCTAGTATATTGAACC 60.294 42.308 2.95 0.00 42.66 3.62
2273 2492 3.966979 ACCATGAACTGTATCCATGCAA 58.033 40.909 0.00 0.00 37.07 4.08
2303 2522 7.819521 TTGGTATCCTTCATATGATCCATCT 57.180 36.000 6.17 0.00 0.00 2.90
2317 2536 3.119029 GCATGCACATGTTTGGTATCCTT 60.119 43.478 14.21 0.00 40.80 3.36
2331 2550 5.664294 AGGAATTAAATCAAGCATGCACA 57.336 34.783 21.98 2.71 0.00 4.57
2363 2583 9.877178 TTTTTAAGACTTCAACAAATTAAGGCA 57.123 25.926 0.00 0.00 30.22 4.75
2453 2673 3.396570 CCCGAACCTAACCCGCCT 61.397 66.667 0.00 0.00 0.00 5.52
2462 2682 0.754472 TTCAACTCGAACCCGAACCT 59.246 50.000 0.00 0.00 45.04 3.50
2475 2701 3.832615 ACTAACCCGACAAGTTCAACT 57.167 42.857 0.00 0.00 0.00 3.16
2480 2706 1.951602 GCCAAACTAACCCGACAAGTT 59.048 47.619 0.00 0.00 35.01 2.66
2487 2713 3.414269 TCTAAAAGGCCAAACTAACCCG 58.586 45.455 5.01 0.00 0.00 5.28
2531 2757 2.435938 CCGTCCATCACCCAACCG 60.436 66.667 0.00 0.00 0.00 4.44
2551 2777 8.269317 AGTTAATATTGAAATTGGTCCGACCTA 58.731 33.333 18.54 11.62 39.58 3.08
2583 2809 8.036575 CCAATCCAACTCAAATCAACATACAAT 58.963 33.333 0.00 0.00 0.00 2.71
2585 2811 6.718912 TCCAATCCAACTCAAATCAACATACA 59.281 34.615 0.00 0.00 0.00 2.29
2625 2853 2.092914 GGATCCAAAACTGACCCGATCT 60.093 50.000 6.95 0.00 0.00 2.75
2646 2874 0.739813 GACCTGAACCAATCCGACCG 60.740 60.000 0.00 0.00 0.00 4.79
2653 2884 2.057922 ACTGACCTGACCTGAACCAAT 58.942 47.619 0.00 0.00 0.00 3.16
2680 2911 1.068816 CCGACCCGACATTTTCCAAAC 60.069 52.381 0.00 0.00 0.00 2.93
2718 2949 1.702957 TGACCCAACCCGAGAAATCTT 59.297 47.619 0.00 0.00 0.00 2.40
2741 2972 5.091261 ACTAACAATTAGAGGTGGCAGAG 57.909 43.478 2.65 0.00 36.73 3.35
2806 3037 1.321474 CCACTTCTTTTGGAGCTGCA 58.679 50.000 2.72 2.72 36.02 4.41
2807 3038 0.038801 GCCACTTCTTTTGGAGCTGC 60.039 55.000 0.00 0.00 36.02 5.25
2842 3073 5.240623 TGTGGCGTAGAACTTGAATGATTTT 59.759 36.000 0.00 0.00 0.00 1.82
2848 3079 4.819630 TCTTTTGTGGCGTAGAACTTGAAT 59.180 37.500 0.00 0.00 0.00 2.57
2873 3104 5.808366 ATTCCATCAGAATTCGTAGGCTA 57.192 39.130 0.00 0.00 42.86 3.93
3099 3330 4.081420 CCATATACTGCACTCCTATCCCAC 60.081 50.000 0.00 0.00 0.00 4.61
3100 3331 4.096681 CCATATACTGCACTCCTATCCCA 58.903 47.826 0.00 0.00 0.00 4.37
3106 3337 8.435931 TCATTATTACCATATACTGCACTCCT 57.564 34.615 0.00 0.00 0.00 3.69
3150 3381 7.092891 ACAAGTGTTCCATCATCATAAGTCCTA 60.093 37.037 0.00 0.00 0.00 2.94
3161 3392 4.665451 TCCAATCACAAGTGTTCCATCAT 58.335 39.130 0.00 0.00 0.00 2.45
3170 3401 4.267536 ACCATCATCTCCAATCACAAGTG 58.732 43.478 0.00 0.00 0.00 3.16
3174 3405 4.472470 AGAAGACCATCATCTCCAATCACA 59.528 41.667 0.00 0.00 0.00 3.58
3180 3411 4.012374 GCAAAAGAAGACCATCATCTCCA 58.988 43.478 0.00 0.00 0.00 3.86
3189 3420 3.072915 TCTCCTCATGCAAAAGAAGACCA 59.927 43.478 0.00 0.00 0.00 4.02
3366 3598 2.297701 GTGGCAAGAAGTCAAGGACAA 58.702 47.619 0.00 0.00 34.60 3.18
3370 3602 0.535102 ACGGTGGCAAGAAGTCAAGG 60.535 55.000 0.00 0.00 30.62 3.61
3599 3831 1.401800 CGTGCATTGCAGCTTTCATGA 60.402 47.619 12.53 0.00 40.08 3.07
3605 3837 0.320073 ATTTGCGTGCATTGCAGCTT 60.320 45.000 23.81 12.52 44.28 3.74
3617 3849 2.507407 ATACCCTCACCAATTTGCGT 57.493 45.000 0.00 0.00 0.00 5.24
3738 3982 7.220740 TCAGGTAAATTGTACACATTCTCACA 58.779 34.615 0.00 0.00 0.00 3.58
3813 4057 6.994421 TCCTCCTATGTGAGCAAATGTATA 57.006 37.500 0.00 0.00 0.00 1.47
3823 4067 3.834489 ATGCTGTTCCTCCTATGTGAG 57.166 47.619 0.00 0.00 0.00 3.51
3849 4093 1.888512 GCTTCTTCAATCCCACAAGCA 59.111 47.619 0.00 0.00 36.94 3.91
3876 4121 2.256117 AGAATAAGGTACGCCATGGC 57.744 50.000 27.67 27.67 37.19 4.40
3914 4159 7.821595 TTATGGACTACATTCTGTAAACACG 57.178 36.000 0.00 0.00 41.03 4.49
3929 4174 5.897250 TGAGAGTGCTTGGTATTATGGACTA 59.103 40.000 0.00 0.00 31.51 2.59
3931 4176 5.023533 TGAGAGTGCTTGGTATTATGGAC 57.976 43.478 0.00 0.00 0.00 4.02
3935 4180 5.104776 TGAGCTTGAGAGTGCTTGGTATTAT 60.105 40.000 0.00 0.00 39.91 1.28
4004 4249 1.953559 TTGTGTGCTCACTCTTCCAC 58.046 50.000 18.85 0.00 44.14 4.02
4031 4276 2.653234 ATGAGAGGAATGGATGCCAC 57.347 50.000 0.00 0.00 35.80 5.01
4168 4416 7.770897 GGTTCAGTAATCCATGATGTAAGAGTT 59.229 37.037 0.00 0.00 0.00 3.01
4308 4558 9.727859 TCAGTTATACTAAAAATGTGCTAACCA 57.272 29.630 0.00 0.00 0.00 3.67
4447 4697 8.582437 CACAAGCTTGATATCCCATTGATAATT 58.418 33.333 32.50 0.33 39.36 1.40
4553 4803 1.378762 GGCAGCAAGGTGGGTTCTA 59.621 57.895 0.00 0.00 0.00 2.10
4558 4808 2.044946 GTAGGGCAGCAAGGTGGG 60.045 66.667 0.00 0.00 0.00 4.61
4560 4810 2.559785 CTTGTAGGGCAGCAAGGTG 58.440 57.895 0.00 0.00 38.61 4.00
4575 4825 5.736951 TTGGGTCCAAATTTCATACCTTG 57.263 39.130 0.00 0.00 32.44 3.61
4607 4857 7.658982 TGCAAAATCATGATCCTCTACTGATAC 59.341 37.037 9.06 0.00 0.00 2.24
4647 4897 7.060421 GGATTATTCTTGGTGGATCCTTGTAA 58.940 38.462 14.23 2.49 37.07 2.41
5158 5408 3.928727 ATTGCATCCTTGTCACTTGTG 57.071 42.857 0.00 0.00 0.00 3.33
5231 5481 5.964958 TTTTTCTCTGCCATAAGACCAAG 57.035 39.130 0.00 0.00 0.00 3.61
5268 5518 5.009110 TGTTGAATGTTGTTTCGCTTATGGA 59.991 36.000 0.00 0.00 0.00 3.41
5283 5533 9.896263 GCCATTAAAAATGAAAATGTTGAATGT 57.104 25.926 1.23 0.00 0.00 2.71
5329 5579 7.602517 ACTTTGTCTAGCATTCATCAGTTAC 57.397 36.000 0.00 0.00 0.00 2.50
5389 5642 2.549754 AGCCACATTCTCAGTTGTTTCG 59.450 45.455 0.00 0.00 0.00 3.46
5427 5680 7.276658 ACTTCGGTTTGGGTAAATTTTGAATT 58.723 30.769 0.00 0.00 0.00 2.17
5460 5713 6.372937 TGGTCATATCGTTATGTTTTCTTGCA 59.627 34.615 12.12 0.00 37.16 4.08
5479 5732 6.159751 ACCAGTAAAGTACCCATAATGGTCAT 59.840 38.462 13.43 0.00 42.49 3.06
5623 5876 7.980062 TGCTTGTAATAAATCGATGTGCTTTA 58.020 30.769 0.00 0.00 0.00 1.85
5624 5877 6.851609 TGCTTGTAATAAATCGATGTGCTTT 58.148 32.000 0.00 0.00 0.00 3.51
5726 5979 3.622455 GCAGTAATTTCAGGGTAGTGCCT 60.622 47.826 0.00 0.00 37.95 4.75
5763 6016 4.211125 CCACATAGAGAAGGCACTAGAGA 58.789 47.826 0.00 0.00 38.49 3.10
5773 6026 4.521146 AGTTTGCATCCCACATAGAGAAG 58.479 43.478 0.00 0.00 0.00 2.85
5780 6033 4.517285 CACTAGTAGTTTGCATCCCACAT 58.483 43.478 0.00 0.00 0.00 3.21
5792 6045 7.375834 GGCCTTTTATTTTTGCACTAGTAGTT 58.624 34.615 0.00 0.00 0.00 2.24
5822 6075 6.239008 GCCAAATTGCATGTAGTACATATGGT 60.239 38.462 15.38 0.73 36.53 3.55
6115 6368 9.430838 GTAGATGTACAAGTATACACTGTAACG 57.569 37.037 15.55 0.00 37.88 3.18
6164 6417 5.950549 ACAGAAAAAGATGATGATCAAGCCT 59.049 36.000 0.00 0.00 0.00 4.58
6271 6525 5.487433 ACATACAATCGTGGAAATCACTCA 58.513 37.500 0.00 0.00 43.94 3.41
6275 6529 5.123186 GGACAACATACAATCGTGGAAATCA 59.877 40.000 0.00 0.00 0.00 2.57
6290 6544 4.518970 GCAAGGAGTTCAAAGGACAACATA 59.481 41.667 0.00 0.00 0.00 2.29
6360 6614 2.639970 TCATTGGTTGACAAGCCGG 58.360 52.632 14.49 0.00 43.48 6.13
6398 6653 5.705441 TCATGTGTCAAAGTAGGATGGTTTC 59.295 40.000 0.00 0.00 0.00 2.78
6423 6679 8.492673 TCGACTATGAAAGCAAAACTCATAAT 57.507 30.769 0.00 0.00 32.96 1.28
6424 6680 7.899178 TCGACTATGAAAGCAAAACTCATAA 57.101 32.000 0.00 0.00 32.96 1.90
6426 6682 6.820656 AGATCGACTATGAAAGCAAAACTCAT 59.179 34.615 0.00 0.00 34.29 2.90
6468 6746 4.402155 TGTTGTTTCCTGAAAGTCTTGCAT 59.598 37.500 0.00 0.00 0.00 3.96
6479 6757 2.092158 TGATGGTGGTGTTGTTTCCTGA 60.092 45.455 0.00 0.00 0.00 3.86
6517 6795 7.508687 TGCTAATGAGATGAAAGCCATAAGTA 58.491 34.615 0.00 0.00 35.17 2.24
6522 6800 5.382616 TCATGCTAATGAGATGAAAGCCAT 58.617 37.500 0.00 0.00 37.91 4.40
6591 6869 5.036117 AGCCACGAAATTCACTATACCAT 57.964 39.130 0.00 0.00 0.00 3.55
6612 6890 3.002656 CGCTATTTGTAAGGCACCATGAG 59.997 47.826 0.00 0.00 0.00 2.90
6617 6895 1.091537 TGCGCTATTTGTAAGGCACC 58.908 50.000 9.73 0.00 0.00 5.01
6638 6916 0.654683 GGCATGATGTTGAGCGAGTC 59.345 55.000 0.00 0.00 0.00 3.36
6671 6949 3.810310 AGCCGGTTTGTTTTCAATTCA 57.190 38.095 1.90 0.00 39.70 2.57
6673 6951 5.270893 ACTAAGCCGGTTTGTTTTCAATT 57.729 34.783 14.54 0.00 39.70 2.32
6710 6988 0.309302 CTACTCGGCCTGACATCTCG 59.691 60.000 0.00 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.