Multiple sequence alignment - TraesCS6B01G267800

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6B01G267800 chr6B 100.000 5108 0 0 1 5108 481405132 481400025 0.000000e+00 9433.0
1 TraesCS6B01G267800 chr6B 83.750 80 10 3 5031 5108 486379516 486379594 7.090000e-09 73.1
2 TraesCS6B01G267800 chr6A 92.091 4767 230 55 405 5108 479620678 479625360 0.000000e+00 6578.0
3 TraesCS6B01G267800 chr6A 89.037 301 28 3 67 363 479620388 479620687 8.080000e-98 368.0
4 TraesCS6B01G267800 chr6A 97.222 72 2 0 1 72 479620297 479620368 6.950000e-24 122.0
5 TraesCS6B01G267800 chr6D 94.977 3922 143 24 405 4290 338897436 338901339 0.000000e+00 6102.0
6 TraesCS6B01G267800 chr6D 93.603 297 18 1 67 363 338897150 338897445 4.690000e-120 442.0
7 TraesCS6B01G267800 chr6D 89.610 231 14 5 4275 4500 338901358 338901583 8.370000e-73 285.0
8 TraesCS6B01G267800 chr6D 95.161 62 3 0 11 72 338897069 338897130 1.170000e-16 99.0
9 TraesCS6B01G267800 chr2B 84.000 275 40 3 2668 2940 596654641 596654369 1.410000e-65 261.0
10 TraesCS6B01G267800 chr2B 92.857 42 3 0 362 403 405890517 405890558 1.540000e-05 62.1
11 TraesCS6B01G267800 chr4A 84.343 198 27 4 3866 4061 697388941 697389136 1.880000e-44 191.0
12 TraesCS6B01G267800 chr7D 82.439 205 30 6 3859 4061 31434863 31435063 1.890000e-39 174.0
13 TraesCS6B01G267800 chr7D 100.000 29 0 0 4750 4778 418074867 418074895 3.000000e-03 54.7
14 TraesCS6B01G267800 chr7B 85.227 88 12 1 4969 5055 94581874 94581961 7.040000e-14 89.8
15 TraesCS6B01G267800 chr7B 92.857 42 3 0 362 403 421168183 421168142 1.540000e-05 62.1
16 TraesCS6B01G267800 chr5D 92.857 42 3 0 362 403 300829248 300829207 1.540000e-05 62.1
17 TraesCS6B01G267800 chr5B 92.857 42 3 0 362 403 509725912 509725871 1.540000e-05 62.1
18 TraesCS6B01G267800 chr3B 92.857 42 3 0 362 403 520044717 520044676 1.540000e-05 62.1
19 TraesCS6B01G267800 chr3B 92.857 42 3 0 362 403 675703299 675703258 1.540000e-05 62.1
20 TraesCS6B01G267800 chr2D 92.857 42 3 0 362 403 519543331 519543290 1.540000e-05 62.1
21 TraesCS6B01G267800 chr1B 92.857 42 3 0 362 403 535299954 535299995 1.540000e-05 62.1
22 TraesCS6B01G267800 chr1D 90.476 42 4 0 362 403 168013892 168013933 7.140000e-04 56.5


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 TraesCS6B01G267800 chr6B 481400025 481405132 5107 True 9433 9433 100.000000 1 5108 1 chr6B.!!$R1 5107
1 TraesCS6B01G267800 chr6A 479620297 479625360 5063 False 2356 6578 92.783333 1 5108 3 chr6A.!!$F1 5107
2 TraesCS6B01G267800 chr6D 338897069 338901583 4514 False 1732 6102 93.337750 11 4500 4 chr6D.!!$F1 4489

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
751 785 0.037697 TGGTCCATGTACGCACTGAC 60.038 55.0 0.00 0.00 0.00 3.51 F
1300 1377 0.035630 AGCAGACTCAAGATGGTGGC 60.036 55.0 0.00 0.00 0.00 5.01 F
1883 1961 0.114954 TGGCTGCCCTTGATTCCTTT 59.885 50.0 17.53 0.00 0.00 3.11 F
3086 3164 0.319040 CGTCATAGGCCATGGACGAG 60.319 60.0 28.28 8.41 38.94 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2715 2793 1.982073 GCCGGATTTTGAGAGGCACG 61.982 60.000 5.05 0.00 46.48 5.34 R
3070 3148 1.620323 TCATCTCGTCCATGGCCTATG 59.380 52.381 6.96 6.24 36.50 2.23 R
3852 3952 0.321564 CCCCTGCGATGTTCAGACAA 60.322 55.000 0.00 0.00 39.66 3.18 R
4320 4460 0.108207 GATCTGGAGCACTGGATGGG 59.892 60.000 0.00 0.00 0.00 4.00 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
26 27 4.976224 AAATTTCGGAATACCTTTCCCG 57.024 40.909 0.00 0.00 43.02 5.14
92 118 3.428589 GGAGAAGAACCATCTGCATTTGC 60.429 47.826 0.00 0.00 42.50 3.68
97 123 0.533491 ACCATCTGCATTTGCGCAAT 59.467 45.000 25.64 11.40 45.83 3.56
143 172 2.032681 GCGGTGATAGGCCATCCC 59.967 66.667 5.01 8.68 32.09 3.85
147 176 1.763770 GTGATAGGCCATCCCCCTG 59.236 63.158 5.01 0.00 33.88 4.45
150 179 0.474660 GATAGGCCATCCCCCTGAGT 60.475 60.000 5.01 0.00 33.88 3.41
205 234 3.449018 GGATACTGACAGGAGAAGCAGAA 59.551 47.826 7.51 0.00 32.86 3.02
219 248 3.542676 AGAACACCACGGTCGCCA 61.543 61.111 0.00 0.00 0.00 5.69
326 355 5.012148 ACTTTCCTGTAGCACACTGACTATT 59.988 40.000 0.00 0.00 0.00 1.73
331 360 1.826385 AGCACACTGACTATTTGGCC 58.174 50.000 0.00 0.00 0.00 5.36
332 361 0.447801 GCACACTGACTATTTGGCCG 59.552 55.000 0.00 0.00 0.00 6.13
340 369 2.563620 TGACTATTTGGCCGACTGTACA 59.436 45.455 0.00 0.00 0.00 2.90
344 373 5.357257 ACTATTTGGCCGACTGTACAATAG 58.643 41.667 0.00 1.03 0.00 1.73
353 382 4.919168 CCGACTGTACAATAGAAACAACGA 59.081 41.667 0.00 0.00 0.00 3.85
354 383 5.060569 CCGACTGTACAATAGAAACAACGAG 59.939 44.000 0.00 0.00 0.00 4.18
355 384 5.854866 CGACTGTACAATAGAAACAACGAGA 59.145 40.000 0.00 0.00 0.00 4.04
356 385 6.361481 CGACTGTACAATAGAAACAACGAGAA 59.639 38.462 0.00 0.00 0.00 2.87
357 386 7.096353 CGACTGTACAATAGAAACAACGAGAAA 60.096 37.037 0.00 0.00 0.00 2.52
358 387 8.428186 ACTGTACAATAGAAACAACGAGAAAA 57.572 30.769 0.00 0.00 0.00 2.29
359 388 8.885722 ACTGTACAATAGAAACAACGAGAAAAA 58.114 29.630 0.00 0.00 0.00 1.94
360 389 9.155053 CTGTACAATAGAAACAACGAGAAAAAC 57.845 33.333 0.00 0.00 0.00 2.43
361 390 8.885722 TGTACAATAGAAACAACGAGAAAAACT 58.114 29.630 0.00 0.00 0.00 2.66
362 391 9.155053 GTACAATAGAAACAACGAGAAAAACTG 57.845 33.333 0.00 0.00 0.00 3.16
363 392 7.193595 ACAATAGAAACAACGAGAAAAACTGG 58.806 34.615 0.00 0.00 0.00 4.00
364 393 7.066525 ACAATAGAAACAACGAGAAAAACTGGA 59.933 33.333 0.00 0.00 0.00 3.86
365 394 5.231265 AGAAACAACGAGAAAAACTGGAC 57.769 39.130 0.00 0.00 0.00 4.02
366 395 3.668596 AACAACGAGAAAAACTGGACG 57.331 42.857 0.00 0.00 0.00 4.79
367 396 2.896168 ACAACGAGAAAAACTGGACGA 58.104 42.857 0.00 0.00 0.00 4.20
368 397 3.463944 ACAACGAGAAAAACTGGACGAT 58.536 40.909 0.00 0.00 0.00 3.73
369 398 3.247648 ACAACGAGAAAAACTGGACGATG 59.752 43.478 0.00 0.00 0.00 3.84
370 399 1.798813 ACGAGAAAAACTGGACGATGC 59.201 47.619 0.00 0.00 0.00 3.91
371 400 2.069273 CGAGAAAAACTGGACGATGCT 58.931 47.619 0.00 0.00 0.00 3.79
372 401 2.480419 CGAGAAAAACTGGACGATGCTT 59.520 45.455 0.00 0.00 0.00 3.91
373 402 3.423645 CGAGAAAAACTGGACGATGCTTC 60.424 47.826 0.00 0.00 0.00 3.86
382 411 4.513519 CGATGCTTCGGTGCCTTA 57.486 55.556 13.82 0.00 41.74 2.69
383 412 2.762360 CGATGCTTCGGTGCCTTAA 58.238 52.632 13.82 0.00 41.74 1.85
384 413 1.083489 CGATGCTTCGGTGCCTTAAA 58.917 50.000 13.82 0.00 41.74 1.52
385 414 1.062587 CGATGCTTCGGTGCCTTAAAG 59.937 52.381 13.82 0.00 41.74 1.85
386 415 1.401905 GATGCTTCGGTGCCTTAAAGG 59.598 52.381 0.00 0.00 38.80 3.11
398 427 3.268023 CCTTAAAGGCACCTACCTCTG 57.732 52.381 0.00 0.00 39.93 3.35
399 428 2.572104 CCTTAAAGGCACCTACCTCTGT 59.428 50.000 0.00 0.00 39.93 3.41
400 429 3.600388 CTTAAAGGCACCTACCTCTGTG 58.400 50.000 0.00 0.00 39.93 3.66
401 430 1.435256 AAAGGCACCTACCTCTGTGT 58.565 50.000 0.00 0.00 39.93 3.72
402 431 0.977395 AAGGCACCTACCTCTGTGTC 59.023 55.000 0.00 0.00 39.93 3.67
403 432 0.905337 AGGCACCTACCTCTGTGTCC 60.905 60.000 0.00 0.00 37.82 4.02
460 494 4.202070 GCTACTGTAGTCTGAAGGTGATCC 60.202 50.000 15.71 0.00 0.00 3.36
473 507 2.019984 GGTGATCCATTGCTCTTGTCC 58.980 52.381 0.00 0.00 0.00 4.02
607 641 4.691216 GGGTTTTGTCTCACTATGTCACTC 59.309 45.833 0.00 0.00 0.00 3.51
747 781 1.803334 TCTTTGGTCCATGTACGCAC 58.197 50.000 0.00 0.00 0.00 5.34
748 782 1.346395 TCTTTGGTCCATGTACGCACT 59.654 47.619 0.00 0.00 0.00 4.40
749 783 1.464608 CTTTGGTCCATGTACGCACTG 59.535 52.381 0.00 0.00 0.00 3.66
750 784 0.682292 TTGGTCCATGTACGCACTGA 59.318 50.000 0.00 0.00 0.00 3.41
751 785 0.037697 TGGTCCATGTACGCACTGAC 60.038 55.000 0.00 0.00 0.00 3.51
752 786 0.037697 GGTCCATGTACGCACTGACA 60.038 55.000 0.00 0.00 32.97 3.58
753 787 1.405526 GGTCCATGTACGCACTGACAT 60.406 52.381 0.00 0.00 36.73 3.06
755 789 3.883779 CATGTACGCACTGACATGC 57.116 52.632 2.35 0.00 44.59 4.06
756 790 0.374758 CATGTACGCACTGACATGCC 59.625 55.000 2.35 0.00 44.59 4.40
757 791 0.250234 ATGTACGCACTGACATGCCT 59.750 50.000 0.00 0.00 42.99 4.75
758 792 0.670239 TGTACGCACTGACATGCCTG 60.670 55.000 0.00 0.00 42.99 4.85
759 793 1.079197 TACGCACTGACATGCCTGG 60.079 57.895 0.00 0.00 42.99 4.45
1036 1103 0.804933 GGTACTGGCGTCGGATCAAC 60.805 60.000 0.98 0.00 0.00 3.18
1041 1108 1.519455 GGCGTCGGATCAACTGGAG 60.519 63.158 0.00 0.00 0.00 3.86
1124 1192 6.791887 ATGACTGAATTGGTTAGATATGCG 57.208 37.500 0.00 0.00 0.00 4.73
1146 1214 7.197017 TGCGTAAATTATGTGTCACTGTTTTT 58.803 30.769 4.27 2.84 0.00 1.94
1198 1275 8.984891 TTATAAGCTTGTTCAATGACCATTTG 57.015 30.769 9.86 0.00 0.00 2.32
1300 1377 0.035630 AGCAGACTCAAGATGGTGGC 60.036 55.000 0.00 0.00 0.00 5.01
1359 1436 3.271729 TGCTTGACGAACAGGTAAAACA 58.728 40.909 0.00 0.00 0.00 2.83
1382 1459 4.650588 AGAGCTGAGTTGCTGATAGATTCT 59.349 41.667 0.00 0.00 44.17 2.40
1388 1465 8.619546 GCTGAGTTGCTGATAGATTCTTATTTT 58.380 33.333 0.00 0.00 0.00 1.82
1422 1499 6.086765 GGCTTTATTATTGATGCATTCGTTCG 59.913 38.462 0.00 0.00 0.00 3.95
1433 1510 2.708514 CATTCGTTCGACCATCAATGC 58.291 47.619 0.00 0.00 0.00 3.56
1436 1513 1.731709 TCGTTCGACCATCAATGCTTG 59.268 47.619 0.00 0.00 0.00 4.01
1469 1546 1.001860 TCACGCCATCTGTGTTCATGA 59.998 47.619 0.00 0.00 38.48 3.07
1470 1547 1.129251 CACGCCATCTGTGTTCATGAC 59.871 52.381 0.00 0.00 34.84 3.06
1474 1551 2.816087 GCCATCTGTGTTCATGACAGTT 59.184 45.455 11.56 2.74 41.43 3.16
1475 1552 3.254166 GCCATCTGTGTTCATGACAGTTT 59.746 43.478 11.56 0.95 41.43 2.66
1476 1553 4.455533 GCCATCTGTGTTCATGACAGTTTA 59.544 41.667 11.56 0.00 41.43 2.01
1477 1554 5.048782 GCCATCTGTGTTCATGACAGTTTAA 60.049 40.000 11.56 0.00 41.43 1.52
1589 1666 2.236146 TGCCATACTCACGGAACATTCT 59.764 45.455 0.00 0.00 0.00 2.40
1592 1669 4.503910 CCATACTCACGGAACATTCTGAA 58.496 43.478 7.45 0.00 37.03 3.02
1883 1961 0.114954 TGGCTGCCCTTGATTCCTTT 59.885 50.000 17.53 0.00 0.00 3.11
2074 2152 6.877855 TCAGCTGCTTCCATAATCAGATAATC 59.122 38.462 9.47 0.00 31.77 1.75
2079 2157 8.571461 TGCTTCCATAATCAGATAATCCAATC 57.429 34.615 0.00 0.00 0.00 2.67
2090 2168 8.558713 TCAGATAATCCAATCCTCATATAGGG 57.441 38.462 0.00 0.00 46.55 3.53
2372 2450 1.480954 GACTATTCGGTGAGCCTTGGA 59.519 52.381 0.00 0.00 0.00 3.53
2546 2624 4.274459 GCTTTGGCGTATGATCTGAATTCT 59.726 41.667 7.05 0.00 0.00 2.40
2688 2766 1.973812 GTTGGGTTCTGCCAGAGCC 60.974 63.158 18.47 18.47 43.92 4.70
2989 3067 0.734889 TTCCGGTAATCCTCGTCGTC 59.265 55.000 0.00 0.00 0.00 4.20
3028 3106 4.371624 ACTCTTGTCATGGTCATGGAAA 57.628 40.909 10.61 5.43 39.24 3.13
3049 3127 4.868314 ACTAGGCTCCGGATACATTTAC 57.132 45.455 3.57 0.00 0.00 2.01
3056 3134 4.508124 GCTCCGGATACATTTACTGACTTG 59.492 45.833 3.57 0.00 0.00 3.16
3070 3148 3.251004 ACTGACTTGAATTCTTTGCCGTC 59.749 43.478 7.05 5.06 0.00 4.79
3086 3164 0.319040 CGTCATAGGCCATGGACGAG 60.319 60.000 28.28 8.41 38.94 4.18
3147 3225 1.539869 AGGCAAAGGAGAGGCAGGA 60.540 57.895 0.00 0.00 0.00 3.86
3304 3382 9.781834 TTGTAGTTGTTGAATGTACTCTTTTTG 57.218 29.630 0.00 0.00 0.00 2.44
3306 3384 9.434559 GTAGTTGTTGAATGTACTCTTTTTGAC 57.565 33.333 0.00 0.00 0.00 3.18
3307 3385 7.186804 AGTTGTTGAATGTACTCTTTTTGACG 58.813 34.615 0.00 0.00 0.00 4.35
3308 3386 5.507077 TGTTGAATGTACTCTTTTTGACGC 58.493 37.500 0.00 0.00 0.00 5.19
3309 3387 4.383774 TGAATGTACTCTTTTTGACGCG 57.616 40.909 3.53 3.53 0.00 6.01
3579 3657 1.202818 GCAGTTCCCTTGTCTTGACCT 60.203 52.381 0.00 0.00 0.00 3.85
3580 3658 2.498167 CAGTTCCCTTGTCTTGACCTG 58.502 52.381 0.00 0.00 0.00 4.00
3588 3666 1.667236 TGTCTTGACCTGTGCAGTTG 58.333 50.000 0.00 0.00 0.00 3.16
3591 3669 0.947244 CTTGACCTGTGCAGTTGTCC 59.053 55.000 6.89 0.00 0.00 4.02
3707 3785 2.202810 GGCTCCAGCTACTGCGTC 60.203 66.667 0.00 0.00 45.42 5.19
3710 3788 4.476410 TCCAGCTACTGCGTCGCG 62.476 66.667 13.38 0.00 45.42 5.87
3797 3884 1.225983 CAGTCCACCACCACCAACA 59.774 57.895 0.00 0.00 0.00 3.33
3799 3886 2.184167 GTCCACCACCACCAACACG 61.184 63.158 0.00 0.00 0.00 4.49
3804 3891 1.049855 ACCACCACCAACACGGAGTA 61.050 55.000 0.00 0.00 41.61 2.59
3809 3896 2.289444 ACCACCAACACGGAGTATGAAG 60.289 50.000 0.00 0.00 41.61 3.02
3814 3910 2.673368 CAACACGGAGTATGAAGGAAGC 59.327 50.000 0.00 0.00 41.61 3.86
3838 3934 5.359756 GTTTCCTTTTCTGAACCTTGCATT 58.640 37.500 0.00 0.00 0.00 3.56
3841 3941 2.420628 TTTCTGAACCTTGCATTGCG 57.579 45.000 3.84 0.00 0.00 4.85
3842 3942 1.603456 TTCTGAACCTTGCATTGCGA 58.397 45.000 3.84 0.59 0.00 5.10
3848 3948 1.825090 ACCTTGCATTGCGATTCTCA 58.175 45.000 3.84 0.00 0.00 3.27
3849 3949 1.470098 ACCTTGCATTGCGATTCTCAC 59.530 47.619 3.84 0.00 0.00 3.51
3850 3950 1.202222 CCTTGCATTGCGATTCTCACC 60.202 52.381 3.84 0.00 0.00 4.02
3852 3952 1.825090 TGCATTGCGATTCTCACCTT 58.175 45.000 3.84 0.00 0.00 3.50
4083 4189 4.728102 TCCATCGCCGCGACGTTT 62.728 61.111 19.45 0.00 39.18 3.60
4157 4263 2.728383 GCATGGATCAATGCGCGC 60.728 61.111 27.26 27.26 43.22 6.86
4158 4264 2.426261 CATGGATCAATGCGCGCG 60.426 61.111 28.44 28.44 0.00 6.86
4159 4265 4.318021 ATGGATCAATGCGCGCGC 62.318 61.111 45.02 45.02 42.35 6.86
4214 4320 2.352388 GTCGCTGTAAATGTTAGGCCA 58.648 47.619 5.01 0.00 0.00 5.36
4244 4350 1.207593 GCTAGGTGCTGCGTTTGTG 59.792 57.895 0.00 0.00 38.95 3.33
4245 4351 1.507141 GCTAGGTGCTGCGTTTGTGT 61.507 55.000 0.00 0.00 38.95 3.72
4256 4362 1.857364 GTTTGTGTGGCGTACGGAG 59.143 57.895 18.39 0.00 0.00 4.63
4320 4460 8.219105 CACGGTTCTAAATAAAACTGTACTGAC 58.781 37.037 6.77 0.00 41.78 3.51
4381 4523 4.464112 CAACGCCAAGAGCTAAAAAGTAC 58.536 43.478 0.00 0.00 40.39 2.73
4403 4545 9.106070 AGTACGTAAAGATTTGGATATTTGGAC 57.894 33.333 0.00 0.00 30.02 4.02
4411 4556 3.281727 TGGATATTTGGACAGAGCCAC 57.718 47.619 0.00 0.00 37.75 5.01
4418 4563 1.668151 GGACAGAGCCACACCGTTC 60.668 63.158 0.00 0.00 0.00 3.95
4435 4580 1.958579 GTTCCGGTGGTTAGGCTTTTT 59.041 47.619 0.00 0.00 0.00 1.94
4457 4602 3.158537 TTTCCTCACGCTCGTGGCA 62.159 57.895 20.36 3.44 45.43 4.92
4471 4616 0.733150 GTGGCAGCGGTTCCTATTTC 59.267 55.000 4.63 0.00 0.00 2.17
4485 4630 2.536365 CTATTTCACGCTTAGGTCGCA 58.464 47.619 0.00 0.00 0.00 5.10
4560 4705 6.670077 TTTCTTTTGGTTTTCCCATTTTCG 57.330 33.333 0.00 0.00 44.74 3.46
4629 4776 8.391075 TCTATTTTTCTCATGTTCGTTTTCCT 57.609 30.769 0.00 0.00 0.00 3.36
4712 4863 4.561735 TTTCCGAACATTGTTCCAAGTC 57.438 40.909 20.87 0.00 0.00 3.01
4821 4972 6.660887 TCTTTGAAAATTGTGCACCTTTTC 57.339 33.333 29.59 29.59 38.66 2.29
4957 5112 9.686683 TTTTTGAAATTGGGGAATAGTTTTTGA 57.313 25.926 0.00 0.00 0.00 2.69
4958 5113 9.686683 TTTTGAAATTGGGGAATAGTTTTTGAA 57.313 25.926 0.00 0.00 0.00 2.69
4959 5114 8.900983 TTGAAATTGGGGAATAGTTTTTGAAG 57.099 30.769 0.00 0.00 0.00 3.02
4960 5115 8.028652 TGAAATTGGGGAATAGTTTTTGAAGT 57.971 30.769 0.00 0.00 0.00 3.01
4961 5116 8.490311 TGAAATTGGGGAATAGTTTTTGAAGTT 58.510 29.630 0.00 0.00 0.00 2.66
4962 5117 8.902540 AAATTGGGGAATAGTTTTTGAAGTTC 57.097 30.769 0.00 0.00 0.00 3.01
4963 5118 7.610580 ATTGGGGAATAGTTTTTGAAGTTCA 57.389 32.000 0.08 0.08 0.00 3.18
4964 5119 7.610580 TTGGGGAATAGTTTTTGAAGTTCAT 57.389 32.000 6.36 0.00 0.00 2.57
4965 5120 7.610580 TGGGGAATAGTTTTTGAAGTTCATT 57.389 32.000 6.36 0.00 0.00 2.57
4966 5121 8.713708 TGGGGAATAGTTTTTGAAGTTCATTA 57.286 30.769 6.36 0.00 0.00 1.90
4967 5122 9.320295 TGGGGAATAGTTTTTGAAGTTCATTAT 57.680 29.630 6.36 0.00 0.00 1.28
5037 5192 6.748333 TCATGGACAGCTCTTGAAATTAAG 57.252 37.500 0.00 0.00 0.00 1.85
5105 5260 7.753132 GTGAACAGTTCTCAATGTAAAAACACA 59.247 33.333 14.51 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.421919 AACGGGAAAGGTATTCCGAAA 57.578 42.857 7.63 0.00 44.69 3.46
26 27 2.023673 TGGCATCATCAATCGGGAAAC 58.976 47.619 0.00 0.00 0.00 2.78
143 172 2.046892 CCACCGCTCAACTCAGGG 60.047 66.667 0.00 0.00 0.00 4.45
147 176 1.594331 AGAAAACCACCGCTCAACTC 58.406 50.000 0.00 0.00 0.00 3.01
150 179 3.134574 ACATAGAAAACCACCGCTCAA 57.865 42.857 0.00 0.00 0.00 3.02
205 234 2.913578 TAGTGGCGACCGTGGTGT 60.914 61.111 0.00 0.00 0.00 4.16
219 248 5.411361 TCAAGAAACATAAATGTGCGCTAGT 59.589 36.000 9.73 0.00 41.61 2.57
326 355 3.965379 TTCTATTGTACAGTCGGCCAA 57.035 42.857 2.24 0.00 0.00 4.52
331 360 5.854866 TCTCGTTGTTTCTATTGTACAGTCG 59.145 40.000 0.00 0.00 0.00 4.18
332 361 7.633361 TTCTCGTTGTTTCTATTGTACAGTC 57.367 36.000 0.00 0.00 0.00 3.51
340 369 7.415229 GTCCAGTTTTTCTCGTTGTTTCTATT 58.585 34.615 0.00 0.00 0.00 1.73
344 373 4.026407 CGTCCAGTTTTTCTCGTTGTTTC 58.974 43.478 0.00 0.00 0.00 2.78
353 382 2.480419 CGAAGCATCGTCCAGTTTTTCT 59.520 45.455 2.58 0.00 44.06 2.52
354 383 2.839474 CGAAGCATCGTCCAGTTTTTC 58.161 47.619 2.58 0.00 44.06 2.29
355 384 2.969443 CGAAGCATCGTCCAGTTTTT 57.031 45.000 2.58 0.00 44.06 1.94
366 395 1.401905 CCTTTAAGGCACCGAAGCATC 59.598 52.381 0.00 0.00 35.83 3.91
367 396 1.463674 CCTTTAAGGCACCGAAGCAT 58.536 50.000 0.00 0.00 35.83 3.79
368 397 2.941210 CCTTTAAGGCACCGAAGCA 58.059 52.632 0.00 0.00 35.83 3.91
378 407 2.572104 ACAGAGGTAGGTGCCTTTAAGG 59.428 50.000 6.64 6.64 39.34 2.69
379 408 3.008049 ACACAGAGGTAGGTGCCTTTAAG 59.992 47.826 0.00 0.00 39.34 1.85
380 409 2.976882 ACACAGAGGTAGGTGCCTTTAA 59.023 45.455 0.00 0.00 39.34 1.52
381 410 2.565834 GACACAGAGGTAGGTGCCTTTA 59.434 50.000 0.00 0.00 39.34 1.85
382 411 1.348036 GACACAGAGGTAGGTGCCTTT 59.652 52.381 0.00 0.00 39.34 3.11
383 412 0.977395 GACACAGAGGTAGGTGCCTT 59.023 55.000 0.00 0.00 39.34 4.35
384 413 0.905337 GGACACAGAGGTAGGTGCCT 60.905 60.000 0.00 0.00 42.53 4.75
385 414 1.192146 TGGACACAGAGGTAGGTGCC 61.192 60.000 0.00 0.00 38.57 5.01
386 415 2.362242 TGGACACAGAGGTAGGTGC 58.638 57.895 0.00 0.00 38.57 5.01
401 430 1.452145 GCCGGTGCAGTTTTTCTGGA 61.452 55.000 1.90 0.00 43.78 3.86
402 431 1.007387 GCCGGTGCAGTTTTTCTGG 60.007 57.895 1.90 0.00 43.78 3.86
403 432 1.370414 CGCCGGTGCAGTTTTTCTG 60.370 57.895 0.00 0.00 46.12 3.02
460 494 1.068055 GTGCCTTGGACAAGAGCAATG 60.068 52.381 21.34 5.10 42.12 2.82
473 507 3.639162 TTGCAAAGAACGTGCCTTG 57.361 47.368 0.01 0.01 41.49 3.61
518 552 4.449068 GCTAAGCATCTCTATTAAAGCGCA 59.551 41.667 11.47 0.00 0.00 6.09
681 715 9.057089 GGAGAACCTAAGATAATGTTAACATGG 57.943 37.037 21.46 17.29 36.56 3.66
727 761 2.147958 GTGCGTACATGGACCAAAGAA 58.852 47.619 1.43 0.00 0.00 2.52
747 781 1.888018 CCAAAGCCAGGCATGTCAG 59.112 57.895 15.80 0.00 0.00 3.51
748 782 4.100479 CCAAAGCCAGGCATGTCA 57.900 55.556 15.80 0.00 0.00 3.58
755 789 1.675641 ACTAAGCGCCAAAGCCAGG 60.676 57.895 2.29 0.00 38.01 4.45
756 790 1.237285 ACACTAAGCGCCAAAGCCAG 61.237 55.000 2.29 0.00 38.01 4.85
757 791 1.228124 ACACTAAGCGCCAAAGCCA 60.228 52.632 2.29 0.00 38.01 4.75
758 792 1.210155 CACACTAAGCGCCAAAGCC 59.790 57.895 2.29 0.00 38.01 4.35
759 793 1.442688 GCACACTAAGCGCCAAAGC 60.443 57.895 2.29 0.00 37.41 3.51
1036 1103 3.772025 ACATACTCTTTCCACTCCTCCAG 59.228 47.826 0.00 0.00 0.00 3.86
1041 1108 3.944087 AGCAACATACTCTTTCCACTCC 58.056 45.455 0.00 0.00 0.00 3.85
1198 1275 7.938715 AGTGAGCAAATGATTCATAAGATTCC 58.061 34.615 0.00 0.00 0.00 3.01
1300 1377 7.391554 TCCTTAAGAACCTGTTCATGATTTCTG 59.608 37.037 12.21 0.00 41.84 3.02
1359 1436 4.650588 AGAATCTATCAGCAACTCAGCTCT 59.349 41.667 0.00 0.00 44.54 4.09
1393 1470 7.661437 ACGAATGCATCAATAATAAAGCCTCTA 59.339 33.333 0.00 0.00 0.00 2.43
1397 1474 6.086765 CGAACGAATGCATCAATAATAAAGCC 59.913 38.462 0.00 0.00 0.00 4.35
1413 1490 2.352651 AGCATTGATGGTCGAACGAATG 59.647 45.455 12.84 12.84 32.13 2.67
1453 1530 2.430465 ACTGTCATGAACACAGATGGC 58.570 47.619 17.34 0.00 43.54 4.40
1469 1546 8.579006 TCAATCTGCAATGAAGAATTAAACTGT 58.421 29.630 0.00 0.00 0.00 3.55
1470 1547 8.975410 TCAATCTGCAATGAAGAATTAAACTG 57.025 30.769 0.00 0.00 0.00 3.16
1474 1551 9.426837 CCTTTTCAATCTGCAATGAAGAATTAA 57.573 29.630 0.00 0.00 36.93 1.40
1475 1552 8.587608 ACCTTTTCAATCTGCAATGAAGAATTA 58.412 29.630 0.00 0.00 36.93 1.40
1476 1553 7.447594 ACCTTTTCAATCTGCAATGAAGAATT 58.552 30.769 0.00 0.00 36.93 2.17
1477 1554 7.001099 ACCTTTTCAATCTGCAATGAAGAAT 57.999 32.000 0.00 0.00 36.93 2.40
1589 1666 7.362662 GCACTTGAGAAACTTGTGATATTTCA 58.637 34.615 0.00 0.00 35.26 2.69
1592 1669 5.700832 TCGCACTTGAGAAACTTGTGATATT 59.299 36.000 0.00 0.00 0.00 1.28
2372 2450 3.349006 CAAACAGTCGCTGCGGCT 61.349 61.111 25.01 25.01 44.88 5.52
2546 2624 4.381612 CGGCCAAGTATGAGAACAGTTAGA 60.382 45.833 2.24 0.00 0.00 2.10
2658 2736 3.320541 CAGAACCCAACCTGCATACAAAA 59.679 43.478 0.00 0.00 0.00 2.44
2715 2793 1.982073 GCCGGATTTTGAGAGGCACG 61.982 60.000 5.05 0.00 46.48 5.34
3028 3106 4.281182 CAGTAAATGTATCCGGAGCCTAGT 59.719 45.833 11.34 0.00 0.00 2.57
3049 3127 3.250762 TGACGGCAAAGAATTCAAGTCAG 59.749 43.478 8.44 0.00 34.01 3.51
3070 3148 1.620323 TCATCTCGTCCATGGCCTATG 59.380 52.381 6.96 6.24 36.50 2.23
3086 3164 2.863809 ACCGCCCTCCAAATTATCATC 58.136 47.619 0.00 0.00 0.00 2.92
3147 3225 4.566545 TCGTTGTTGTCTGCATTTTCAT 57.433 36.364 0.00 0.00 0.00 2.57
3301 3379 1.931551 GTGAAGAGCACGCGTCAAA 59.068 52.632 9.86 0.00 37.83 2.69
3302 3380 3.625232 GTGAAGAGCACGCGTCAA 58.375 55.556 9.86 0.00 37.83 3.18
3414 3492 2.310233 CGTGCTCGTGGACCAGTTG 61.310 63.158 0.00 0.00 0.00 3.16
3489 3567 4.887748 ACAGATTGGTGATATAGCTTCCG 58.112 43.478 0.00 0.00 0.00 4.30
3566 3644 1.233019 CTGCACAGGTCAAGACAAGG 58.767 55.000 2.29 0.00 0.00 3.61
3570 3648 1.599542 GACAACTGCACAGGTCAAGAC 59.400 52.381 2.21 0.00 0.00 3.01
3588 3666 2.396157 GGATGTGAAACGGCCGGAC 61.396 63.158 31.76 19.71 42.39 4.79
3591 3669 1.241315 AAAGGGATGTGAAACGGCCG 61.241 55.000 26.86 26.86 42.39 6.13
3707 3785 2.312061 GACACGACGTATTGCGCG 59.688 61.111 0.00 0.00 46.11 6.86
3710 3788 1.740043 GAGCCGACACGACGTATTGC 61.740 60.000 0.00 1.35 0.00 3.56
3713 3791 1.022982 TGAGAGCCGACACGACGTAT 61.023 55.000 0.00 0.00 0.00 3.06
3776 3854 1.134037 GTTGGTGGTGGTGGACTGTTA 60.134 52.381 0.00 0.00 0.00 2.41
3782 3860 2.190843 CGTGTTGGTGGTGGTGGA 59.809 61.111 0.00 0.00 0.00 4.02
3797 3884 1.183549 ACGCTTCCTTCATACTCCGT 58.816 50.000 0.00 0.00 0.00 4.69
3799 3886 2.937149 GGAAACGCTTCCTTCATACTCC 59.063 50.000 10.41 0.00 46.80 3.85
3814 3910 3.181491 TGCAAGGTTCAGAAAAGGAAACG 60.181 43.478 0.00 0.00 37.06 3.60
3830 3926 2.184385 GTGAGAATCGCAATGCAAGG 57.816 50.000 5.91 0.00 46.97 3.61
3838 3934 7.925392 TGTTCAGACAAAGGTGAGAATCGCA 62.925 44.000 0.00 0.00 39.23 5.10
3841 3941 5.163913 CGATGTTCAGACAAAGGTGAGAATC 60.164 44.000 0.00 0.00 39.66 2.52
3842 3942 4.692625 CGATGTTCAGACAAAGGTGAGAAT 59.307 41.667 0.00 0.00 39.66 2.40
3848 3948 2.146342 CTGCGATGTTCAGACAAAGGT 58.854 47.619 0.00 0.00 39.66 3.50
3849 3949 1.466167 CCTGCGATGTTCAGACAAAGG 59.534 52.381 0.00 0.00 39.66 3.11
3850 3950 1.466167 CCCTGCGATGTTCAGACAAAG 59.534 52.381 0.00 0.00 39.66 2.77
3852 3952 0.321564 CCCCTGCGATGTTCAGACAA 60.322 55.000 0.00 0.00 39.66 3.18
4074 4180 1.154727 GTAAGTGCCAAACGTCGCG 60.155 57.895 0.00 0.00 0.00 5.87
4083 4189 0.548989 ACAGGGTGTTGTAAGTGCCA 59.451 50.000 0.00 0.00 0.00 4.92
4127 4233 4.271661 TGATCCATGCTTAACTTGATGCA 58.728 39.130 0.00 0.00 39.83 3.96
4128 4234 4.906065 TGATCCATGCTTAACTTGATGC 57.094 40.909 0.00 0.00 0.00 3.91
4159 4265 4.711949 AGCAGCTTGGCCTCACCG 62.712 66.667 3.32 0.00 43.94 4.94
4160 4266 3.060615 CAGCAGCTTGGCCTCACC 61.061 66.667 3.32 0.00 39.84 4.02
4161 4267 1.860484 GAACAGCAGCTTGGCCTCAC 61.860 60.000 3.32 0.00 0.00 3.51
4162 4268 1.601759 GAACAGCAGCTTGGCCTCA 60.602 57.895 3.32 0.00 0.00 3.86
4163 4269 2.684843 CGAACAGCAGCTTGGCCTC 61.685 63.158 3.32 0.00 0.00 4.70
4214 4320 2.362369 ACCTAGCACTGGCAGCGAT 61.362 57.895 15.89 6.44 44.61 4.58
4244 4350 2.813908 CAAGCCTCCGTACGCCAC 60.814 66.667 10.49 0.00 0.00 5.01
4245 4351 3.307906 ACAAGCCTCCGTACGCCA 61.308 61.111 10.49 0.00 0.00 5.69
4320 4460 0.108207 GATCTGGAGCACTGGATGGG 59.892 60.000 0.00 0.00 0.00 4.00
4381 4523 8.208718 TCTGTCCAAATATCCAAATCTTTACG 57.791 34.615 0.00 0.00 0.00 3.18
4435 4580 3.980583 ACGAGCGTGAGGAAAGAAA 57.019 47.368 0.00 0.00 0.00 2.52
4452 4597 0.733150 GAAATAGGAACCGCTGCCAC 59.267 55.000 0.00 0.00 0.00 5.01
4457 4602 0.249398 AGCGTGAAATAGGAACCGCT 59.751 50.000 0.00 0.00 45.70 5.52
4471 4616 1.129809 CGTTTGCGACCTAAGCGTG 59.870 57.895 0.00 0.00 41.33 5.34
4485 4630 1.663173 CCGGCCCAAATTCACGTTT 59.337 52.632 0.00 0.00 0.00 3.60
4605 4752 9.463443 AAAGGAAAACGAACATGAGAAAAATAG 57.537 29.630 0.00 0.00 0.00 1.73
4678 4829 9.372369 ACAATGTTCGGAAAATGAAAACTAAAA 57.628 25.926 0.00 0.00 0.00 1.52
4679 4830 8.934507 ACAATGTTCGGAAAATGAAAACTAAA 57.065 26.923 0.00 0.00 0.00 1.85
4680 4831 8.934507 AACAATGTTCGGAAAATGAAAACTAA 57.065 26.923 0.00 0.00 0.00 2.24
4790 4941 5.353400 TGCACAATTTTCAAAGATGTTTGCA 59.647 32.000 10.37 0.00 42.55 4.08
5019 5174 9.521503 AAAAAGTTCTTAATTTCAAGAGCTGTC 57.478 29.630 7.78 0.00 42.97 3.51
5074 5229 8.596271 TTTACATTGAGAACTGTTCACGAATA 57.404 30.769 21.50 9.87 0.00 1.75
5078 5233 6.964370 TGTTTTTACATTGAGAACTGTTCACG 59.036 34.615 21.50 6.56 0.00 4.35
5080 5235 7.821652 TGTGTTTTTACATTGAGAACTGTTCA 58.178 30.769 21.50 0.49 0.00 3.18


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

AutoCloner maintained by Alex Coulton.