Multiple sequence alignment - TraesCS4D01G179900

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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 TraesCS4D01G179900 chr4D 100.000 3500 0 0 1 3500 312946906 312943407 0.000000e+00 6464
1 TraesCS4D01G179900 chr4A 91.815 2871 121 44 510 3323 163345299 163348112 0.000000e+00 3895
2 TraesCS4D01G179900 chr4A 94.581 406 12 6 1 400 163344881 163345282 1.380000e-173 619
3 TraesCS4D01G179900 chr4A 95.652 46 2 0 3395 3440 163350392 163350437 1.350000e-09 75
4 TraesCS4D01G179900 chr4B 93.889 2062 78 10 510 2541 390405199 390403156 0.000000e+00 3066
5 TraesCS4D01G179900 chr4B 87.818 550 22 24 2540 3049 390403108 390402564 1.390000e-168 603
6 TraesCS4D01G179900 chr4B 89.453 256 12 8 149 400 390405460 390405216 3.390000e-80 309
7 TraesCS4D01G179900 chr4B 93.750 80 4 1 33 112 390405536 390405458 6.140000e-23 119
8 TraesCS4D01G179900 chr7D 93.620 768 44 3 1456 2222 444073657 444072894 0.000000e+00 1142
9 TraesCS4D01G179900 chr7D 87.356 435 32 9 2066 2500 444073660 444074071 8.790000e-131 477
10 TraesCS4D01G179900 chr7D 91.241 274 24 0 1074 1347 444072622 444072895 1.190000e-99 374
11 TraesCS4D01G179900 chr7D 89.726 146 14 1 907 1051 444070882 444071027 5.970000e-43 185
12 TraesCS4D01G179900 chr5D 95.763 118 5 0 395 512 89377404 89377287 1.280000e-44 191
13 TraesCS4D01G179900 chr5D 96.460 113 4 0 395 507 139129535 139129647 1.660000e-43 187
14 TraesCS4D01G179900 chr2D 92.537 134 7 2 395 525 458715862 458715995 4.610000e-44 189
15 TraesCS4D01G179900 chr2D 96.460 113 4 0 395 507 20189375 20189487 1.660000e-43 187
16 TraesCS4D01G179900 chr2D 94.167 120 6 1 397 516 389280298 389280416 7.720000e-42 182
17 TraesCS4D01G179900 chr2D 95.495 111 5 0 395 505 249399322 249399432 9.980000e-41 178
18 TraesCS4D01G179900 chr6D 94.915 118 6 0 395 512 201987321 201987438 5.970000e-43 185
19 TraesCS4D01G179900 chr6D 92.913 127 6 3 395 519 394929882 394929757 7.720000e-42 182
20 TraesCS4D01G179900 chr6D 98.276 58 1 0 3443 3500 420569441 420569498 6.180000e-18 102
21 TraesCS4D01G179900 chr1D 94.262 122 6 1 395 516 326157629 326157749 5.970000e-43 185


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 TraesCS4D01G179900 chr4D 312943407 312946906 3499 True 6464.000000 6464 100.0000 1 3500 1 chr4D.!!$R1 3499
1 TraesCS4D01G179900 chr4A 163344881 163350437 5556 False 1529.666667 3895 94.0160 1 3440 3 chr4A.!!$F1 3439
2 TraesCS4D01G179900 chr4B 390402564 390405536 2972 True 1024.250000 3066 91.2275 33 3049 4 chr4B.!!$R1 3016
3 TraesCS4D01G179900 chr7D 444072894 444073657 763 True 1142.000000 1142 93.6200 1456 2222 1 chr7D.!!$R1 766
4 TraesCS4D01G179900 chr7D 444070882 444074071 3189 False 345.333333 477 89.4410 907 2500 3 chr7D.!!$F1 1593

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
36 37 0.856641 TGAAGTCGTTTACAGCGCAC 59.143 50.000 11.47 0.0 0.00 5.34 F
268 272 1.880027 ACTTGAAGCTAAAGCAACGGG 59.120 47.619 4.54 0.0 45.16 5.28 F
1744 3893 0.461870 GCCGTCTCCATGCACACATA 60.462 55.000 0.00 0.0 33.67 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1726 3875 2.138320 GATATGTGTGCATGGAGACGG 58.862 52.381 9.92 0.0 36.58 4.79 R
2008 4160 4.169508 CGACAGAAGATAGTGACAACTGG 58.830 47.826 0.00 0.0 37.19 4.00 R
3456 7937 0.031721 CTCCCCGTATTAGTCGGTGC 59.968 60.000 3.78 0.0 45.63 5.01 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
36 37 0.856641 TGAAGTCGTTTACAGCGCAC 59.143 50.000 11.47 0.00 0.00 5.34
267 271 3.626028 AACTTGAAGCTAAAGCAACGG 57.374 42.857 4.54 0.00 45.16 4.44
268 272 1.880027 ACTTGAAGCTAAAGCAACGGG 59.120 47.619 4.54 0.00 45.16 5.28
346 354 3.763360 CTCCCTTTTTACCATGTGATGCA 59.237 43.478 0.00 0.00 0.00 3.96
400 408 2.547007 CCCCAAAATTCACCGACCAAAC 60.547 50.000 0.00 0.00 0.00 2.93
401 409 2.389998 CCAAAATTCACCGACCAAACG 58.610 47.619 0.00 0.00 0.00 3.60
410 418 3.834732 CGACCAAACGGGAGAGATT 57.165 52.632 0.00 0.00 41.15 2.40
411 419 2.094762 CGACCAAACGGGAGAGATTT 57.905 50.000 0.00 0.00 41.15 2.17
412 420 2.423577 CGACCAAACGGGAGAGATTTT 58.576 47.619 0.00 0.00 41.15 1.82
413 421 2.812011 CGACCAAACGGGAGAGATTTTT 59.188 45.455 0.00 0.00 41.15 1.94
435 443 8.672823 TTTTTCTACAGGGACTAGAAAAAGAC 57.327 34.615 16.61 0.00 46.05 3.01
436 444 7.613551 TTTCTACAGGGACTAGAAAAAGACT 57.386 36.000 0.00 0.00 37.31 3.24
437 445 6.837471 TCTACAGGGACTAGAAAAAGACTC 57.163 41.667 0.00 0.00 36.02 3.36
438 446 6.553857 TCTACAGGGACTAGAAAAAGACTCT 58.446 40.000 0.00 0.00 36.02 3.24
439 447 7.696981 TCTACAGGGACTAGAAAAAGACTCTA 58.303 38.462 0.00 0.00 36.02 2.43
440 448 6.593268 ACAGGGACTAGAAAAAGACTCTAC 57.407 41.667 0.00 0.00 36.02 2.59
441 449 6.316513 ACAGGGACTAGAAAAAGACTCTACT 58.683 40.000 0.00 0.00 36.02 2.57
442 450 7.468496 ACAGGGACTAGAAAAAGACTCTACTA 58.532 38.462 0.00 0.00 36.02 1.82
443 451 7.612633 ACAGGGACTAGAAAAAGACTCTACTAG 59.387 40.741 0.00 0.00 36.02 2.57
444 452 7.830201 CAGGGACTAGAAAAAGACTCTACTAGA 59.170 40.741 0.00 0.00 36.02 2.43
445 453 8.050930 AGGGACTAGAAAAAGACTCTACTAGAG 58.949 40.741 11.06 11.06 42.94 2.43
446 454 8.048514 GGGACTAGAAAAAGACTCTACTAGAGA 58.951 40.741 18.41 0.00 45.07 3.10
447 455 9.452287 GGACTAGAAAAAGACTCTACTAGAGAA 57.548 37.037 18.41 0.00 45.07 2.87
483 491 4.316645 GTCCCTGTGACTAGAAAAAGTCC 58.683 47.826 0.00 0.00 44.40 3.85
484 492 4.040584 GTCCCTGTGACTAGAAAAAGTCCT 59.959 45.833 0.00 0.00 44.40 3.85
485 493 5.245526 GTCCCTGTGACTAGAAAAAGTCCTA 59.754 44.000 0.00 0.00 44.40 2.94
486 494 5.480772 TCCCTGTGACTAGAAAAAGTCCTAG 59.519 44.000 0.00 0.00 44.40 3.02
487 495 5.337652 CCCTGTGACTAGAAAAAGTCCTAGG 60.338 48.000 0.82 0.82 44.40 3.02
488 496 5.480772 CCTGTGACTAGAAAAAGTCCTAGGA 59.519 44.000 7.62 7.62 43.92 2.94
489 497 6.342338 TGTGACTAGAAAAAGTCCTAGGAC 57.658 41.667 31.29 31.29 44.40 3.85
503 511 5.794894 GTCCTAGGACTTCTGAATCAAACA 58.205 41.667 31.12 0.00 41.57 2.83
504 512 5.639931 GTCCTAGGACTTCTGAATCAAACAC 59.360 44.000 31.12 2.21 41.57 3.32
505 513 4.938226 CCTAGGACTTCTGAATCAAACACC 59.062 45.833 1.05 0.00 0.00 4.16
506 514 3.756117 AGGACTTCTGAATCAAACACCC 58.244 45.455 0.00 0.00 0.00 4.61
507 515 3.395941 AGGACTTCTGAATCAAACACCCT 59.604 43.478 0.00 0.00 0.00 4.34
508 516 3.753797 GGACTTCTGAATCAAACACCCTC 59.246 47.826 0.00 0.00 0.00 4.30
532 540 1.962807 CATTGCCAAGTTCCTGTTCCA 59.037 47.619 0.00 0.00 0.00 3.53
567 575 7.094933 TGCATGCATGATCATTCAGACTATTAC 60.095 37.037 30.64 6.12 34.73 1.89
584 592 4.684484 ATTACTCGTTAATCCCCACTCC 57.316 45.455 0.00 0.00 0.00 3.85
585 593 1.946984 ACTCGTTAATCCCCACTCCA 58.053 50.000 0.00 0.00 0.00 3.86
610 639 2.541556 GCTTTGGCTAGTTCTACTCCG 58.458 52.381 0.00 0.00 35.22 4.63
675 704 3.684788 AGGTTAATTACTCACTGCTTGCG 59.315 43.478 0.00 0.00 0.00 4.85
781 818 2.555757 AGTTTAGCTCGTGTACGTCCTT 59.444 45.455 4.20 0.00 40.80 3.36
920 958 3.191371 CCTCTTCGCCAATTATAATGCCC 59.809 47.826 0.00 0.00 0.00 5.36
950 988 2.261671 CAGCACGCGGGTCTAGTT 59.738 61.111 11.45 0.00 0.00 2.24
970 1008 4.021544 AGTTCAGCTACCTCTCTCAACTTG 60.022 45.833 0.00 0.00 0.00 3.16
1464 3612 3.723235 GATGGCTGCGGAGAAGCGA 62.723 63.158 8.65 0.00 41.78 4.93
1744 3893 0.461870 GCCGTCTCCATGCACACATA 60.462 55.000 0.00 0.00 33.67 2.29
1874 4023 2.100584 GGCATCTCTGATTCTCTGTCGT 59.899 50.000 0.00 0.00 0.00 4.34
2008 4160 1.782044 ACGTGCCACATCAAATTTGC 58.218 45.000 13.54 1.12 0.00 3.68
2142 4298 3.896133 CTGCACGCCATGGCCATC 61.896 66.667 30.79 18.85 37.98 3.51
2509 4668 2.337583 TCTGTTTCTGAGCGATTTCGG 58.662 47.619 1.75 0.00 40.23 4.30
2521 4680 1.087501 GATTTCGGGTGCTCTGTTCC 58.912 55.000 0.00 0.00 0.00 3.62
2534 4693 0.739462 CTGTTCCGGCTTCATGCGTA 60.739 55.000 0.00 0.00 44.05 4.42
2600 4820 0.537188 ATGGATGTCGGTGACTGACC 59.463 55.000 20.86 7.30 42.07 4.02
2620 4843 1.176527 CCATGATGTTGGTGGTGGTC 58.823 55.000 0.00 0.00 31.74 4.02
2694 4917 0.989890 ACGCGTCGCTTTAGAATGTC 59.010 50.000 16.36 0.00 0.00 3.06
2700 4923 0.931005 CGCTTTAGAATGTCGGAGGC 59.069 55.000 0.00 0.00 0.00 4.70
2821 5052 4.032900 CGTTGAGTTAAGCTTGCATACGAT 59.967 41.667 9.86 0.00 0.00 3.73
2838 5069 6.556212 CATACGATATAGAGAAGGATGCGTT 58.444 40.000 0.00 0.00 0.00 4.84
2844 5075 1.625818 AGAGAAGGATGCGTTTCCAGT 59.374 47.619 8.25 0.00 38.32 4.00
2862 5118 4.971282 TCCAGTTCCATGGATCATCTAGTT 59.029 41.667 22.09 0.00 44.56 2.24
2870 5126 8.127150 TCCATGGATCATCTAGTTGTATAGTG 57.873 38.462 11.44 0.00 0.00 2.74
3050 5322 0.031917 TTGTATCCCGCCTAGGTCCA 60.032 55.000 11.31 0.00 38.74 4.02
3112 5385 0.747255 ACGAGGTCGAGGATTGATGG 59.253 55.000 6.35 0.00 43.02 3.51
3121 5394 5.453339 GGTCGAGGATTGATGGTTCATAGAA 60.453 44.000 0.00 0.00 0.00 2.10
3122 5395 5.463724 GTCGAGGATTGATGGTTCATAGAAC 59.536 44.000 1.37 1.37 0.00 3.01
3126 5399 6.962182 AGGATTGATGGTTCATAGAACTTGA 58.038 36.000 9.46 0.00 0.00 3.02
3133 5406 8.733458 TGATGGTTCATAGAACTTGAAAATCAG 58.267 33.333 9.46 0.00 35.57 2.90
3135 5408 8.690203 TGGTTCATAGAACTTGAAAATCAGAA 57.310 30.769 9.46 0.00 35.03 3.02
3136 5409 9.130661 TGGTTCATAGAACTTGAAAATCAGAAA 57.869 29.630 9.46 0.00 35.03 2.52
3137 5410 9.965824 GGTTCATAGAACTTGAAAATCAGAAAA 57.034 29.630 9.46 0.00 35.03 2.29
3179 5452 0.179000 ATGATGAACCTCTCCACCGC 59.821 55.000 0.00 0.00 0.00 5.68
3185 5458 2.289444 TGAACCTCTCCACCGCTAAAAG 60.289 50.000 0.00 0.00 0.00 2.27
3186 5459 1.640917 ACCTCTCCACCGCTAAAAGA 58.359 50.000 0.00 0.00 0.00 2.52
3187 5460 1.975680 ACCTCTCCACCGCTAAAAGAA 59.024 47.619 0.00 0.00 0.00 2.52
3188 5461 2.370849 ACCTCTCCACCGCTAAAAGAAA 59.629 45.455 0.00 0.00 0.00 2.52
3199 5472 7.083858 CACCGCTAAAAGAAAATCATTGAAGA 58.916 34.615 0.00 0.00 0.00 2.87
3208 5481 7.219484 AGAAAATCATTGAAGAAACCGTCAT 57.781 32.000 0.00 0.00 0.00 3.06
3217 5490 5.175859 TGAAGAAACCGTCATAGGATCAAC 58.824 41.667 0.00 0.00 34.73 3.18
3221 5494 2.888594 ACCGTCATAGGATCAACAACG 58.111 47.619 0.00 0.00 34.73 4.10
3225 5498 7.298323 ACCGTCATAGGATCAACAACGAAGT 62.298 44.000 0.00 0.00 37.40 3.01
3291 5564 3.815401 CCGAAATTATGGGTAGGAAGCAG 59.185 47.826 0.00 0.00 0.00 4.24
3357 7838 1.748879 GGCGAGCCCAACAATGCTA 60.749 57.895 1.97 0.00 38.11 3.49
3359 7840 1.305219 GCGAGCCCAACAATGCTACA 61.305 55.000 0.00 0.00 38.11 2.74
3361 7842 1.745087 CGAGCCCAACAATGCTACATT 59.255 47.619 0.00 0.00 38.11 2.71
3362 7843 2.223340 CGAGCCCAACAATGCTACATTC 60.223 50.000 0.00 0.00 38.11 2.67
3363 7844 2.754552 GAGCCCAACAATGCTACATTCA 59.245 45.455 0.00 0.00 38.11 2.57
3366 7847 2.159393 CCCAACAATGCTACATTCACGG 60.159 50.000 0.00 0.00 0.00 4.94
3367 7848 2.746904 CCAACAATGCTACATTCACGGA 59.253 45.455 0.00 0.00 0.00 4.69
3369 7850 3.334583 ACAATGCTACATTCACGGACT 57.665 42.857 0.00 0.00 0.00 3.85
3370 7851 4.465632 ACAATGCTACATTCACGGACTA 57.534 40.909 0.00 0.00 0.00 2.59
3372 7853 4.630069 ACAATGCTACATTCACGGACTAAC 59.370 41.667 0.00 0.00 0.00 2.34
3373 7854 3.945981 TGCTACATTCACGGACTAACA 57.054 42.857 0.00 0.00 0.00 2.41
3375 7856 3.006003 TGCTACATTCACGGACTAACACA 59.994 43.478 0.00 0.00 0.00 3.72
3376 7857 3.612860 GCTACATTCACGGACTAACACAG 59.387 47.826 0.00 0.00 0.00 3.66
3378 7859 2.289444 ACATTCACGGACTAACACAGGG 60.289 50.000 0.00 0.00 0.00 4.45
3379 7860 0.682852 TTCACGGACTAACACAGGGG 59.317 55.000 0.00 0.00 0.00 4.79
3380 7861 1.375523 CACGGACTAACACAGGGGC 60.376 63.158 0.00 0.00 0.00 5.80
3381 7862 2.125673 CGGACTAACACAGGGGCG 60.126 66.667 0.00 0.00 0.00 6.13
3382 7863 2.267961 GGACTAACACAGGGGCGG 59.732 66.667 0.00 0.00 0.00 6.13
3383 7864 2.267961 GACTAACACAGGGGCGGG 59.732 66.667 0.00 0.00 0.00 6.13
3384 7865 3.971109 GACTAACACAGGGGCGGGC 62.971 68.421 0.00 0.00 0.00 6.13
3385 7866 4.796495 CTAACACAGGGGCGGGCC 62.796 72.222 13.01 13.01 0.00 5.80
3428 7909 4.666237 GCTGATTGAAAATCCTACAGCAC 58.334 43.478 0.00 0.00 45.33 4.40
3440 7921 2.751259 CCTACAGCACGTAGTACTTGGA 59.249 50.000 0.00 0.00 45.40 3.53
3441 7922 3.181499 CCTACAGCACGTAGTACTTGGAG 60.181 52.174 0.00 0.00 45.40 3.86
3442 7923 1.067776 ACAGCACGTAGTACTTGGAGC 60.068 52.381 0.00 3.94 41.61 4.70
3443 7924 0.170561 AGCACGTAGTACTTGGAGCG 59.829 55.000 0.00 1.50 41.61 5.03
3444 7925 0.169672 GCACGTAGTACTTGGAGCGA 59.830 55.000 0.00 0.00 41.61 4.93
3445 7926 1.401931 GCACGTAGTACTTGGAGCGAA 60.402 52.381 0.00 0.00 41.61 4.70
3446 7927 2.923605 GCACGTAGTACTTGGAGCGAAA 60.924 50.000 0.00 0.00 41.61 3.46
3447 7928 3.311106 CACGTAGTACTTGGAGCGAAAA 58.689 45.455 0.00 0.00 41.61 2.29
3448 7929 3.924686 CACGTAGTACTTGGAGCGAAAAT 59.075 43.478 0.00 0.00 41.61 1.82
3449 7930 4.387862 CACGTAGTACTTGGAGCGAAAATT 59.612 41.667 0.00 0.00 41.61 1.82
3450 7931 4.624452 ACGTAGTACTTGGAGCGAAAATTC 59.376 41.667 0.00 0.00 41.94 2.17
3451 7932 4.863131 CGTAGTACTTGGAGCGAAAATTCT 59.137 41.667 0.00 0.00 0.00 2.40
3452 7933 6.032094 CGTAGTACTTGGAGCGAAAATTCTA 58.968 40.000 0.00 0.00 0.00 2.10
3453 7934 6.529125 CGTAGTACTTGGAGCGAAAATTCTAA 59.471 38.462 0.00 0.00 0.00 2.10
3454 7935 7.062605 CGTAGTACTTGGAGCGAAAATTCTAAA 59.937 37.037 0.00 0.00 0.00 1.85
3455 7936 7.130303 AGTACTTGGAGCGAAAATTCTAAAC 57.870 36.000 0.00 0.00 0.00 2.01
3456 7937 5.030874 ACTTGGAGCGAAAATTCTAAACG 57.969 39.130 0.00 0.00 0.00 3.60
3461 7942 1.902504 GCGAAAATTCTAAACGCACCG 59.097 47.619 0.00 0.00 46.75 4.94
3462 7943 2.411806 GCGAAAATTCTAAACGCACCGA 60.412 45.455 0.00 0.00 46.75 4.69
3463 7944 3.150731 CGAAAATTCTAAACGCACCGAC 58.849 45.455 0.00 0.00 0.00 4.79
3464 7945 3.120786 CGAAAATTCTAAACGCACCGACT 60.121 43.478 0.00 0.00 0.00 4.18
3465 7946 4.090354 CGAAAATTCTAAACGCACCGACTA 59.910 41.667 0.00 0.00 0.00 2.59
3466 7947 5.388682 CGAAAATTCTAAACGCACCGACTAA 60.389 40.000 0.00 0.00 0.00 2.24
3467 7948 6.490566 AAAATTCTAAACGCACCGACTAAT 57.509 33.333 0.00 0.00 0.00 1.73
3468 7949 7.463119 CGAAAATTCTAAACGCACCGACTAATA 60.463 37.037 0.00 0.00 0.00 0.98
3469 7950 6.579491 AATTCTAAACGCACCGACTAATAC 57.421 37.500 0.00 0.00 0.00 1.89
3470 7951 3.683989 TCTAAACGCACCGACTAATACG 58.316 45.455 0.00 0.00 0.00 3.06
3480 7961 3.969899 CCGACTAATACGGGGAGTTTAC 58.030 50.000 0.00 0.00 45.65 2.01
3481 7962 3.548818 CCGACTAATACGGGGAGTTTACG 60.549 52.174 0.00 0.00 45.65 3.18
3482 7963 3.548818 CGACTAATACGGGGAGTTTACGG 60.549 52.174 0.00 0.00 0.00 4.02
3483 7964 3.631250 ACTAATACGGGGAGTTTACGGA 58.369 45.455 0.00 0.00 0.00 4.69
3484 7965 2.967599 AATACGGGGAGTTTACGGAC 57.032 50.000 0.00 0.00 0.00 4.79
3485 7966 2.149973 ATACGGGGAGTTTACGGACT 57.850 50.000 0.00 0.00 0.00 3.85
3486 7967 1.463674 TACGGGGAGTTTACGGACTC 58.536 55.000 7.17 7.17 44.20 3.36
3493 7974 3.294816 GAGTTTACGGACTCCTTCGTT 57.705 47.619 4.97 0.00 40.10 3.85
3494 7975 4.425577 GAGTTTACGGACTCCTTCGTTA 57.574 45.455 4.97 0.00 40.10 3.18
3495 7976 4.798574 GAGTTTACGGACTCCTTCGTTAA 58.201 43.478 4.97 0.00 40.10 2.01
3496 7977 4.550422 AGTTTACGGACTCCTTCGTTAAC 58.450 43.478 8.89 8.89 44.13 2.01
3497 7978 4.279420 AGTTTACGGACTCCTTCGTTAACT 59.721 41.667 12.33 12.33 46.82 2.24
3498 7979 5.699839 GTTTACGGACTCCTTCGTTAACTA 58.300 41.667 3.71 0.00 42.09 2.24
3499 7980 5.957842 TTACGGACTCCTTCGTTAACTAA 57.042 39.130 3.71 0.00 40.31 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.802738 TGTAAACGACTTCAATCTTATGTTGG 58.197 34.615 0.00 0.00 0.00 3.77
10 11 5.220416 GCGCTGTAAACGACTTCAATCTTAT 60.220 40.000 0.00 0.00 0.00 1.73
15 16 2.096417 GTGCGCTGTAAACGACTTCAAT 60.096 45.455 9.73 0.00 0.00 2.57
36 37 1.326213 ACTCTCCTCTGGGACATGCG 61.326 60.000 0.00 0.00 38.20 4.73
105 109 3.264947 CATTCTGCTAGTTGCTGCTACA 58.735 45.455 16.07 2.31 43.37 2.74
125 129 4.072131 GTGTACAGCAATTTCCTCTTCCA 58.928 43.478 0.00 0.00 0.00 3.53
126 130 3.125316 CGTGTACAGCAATTTCCTCTTCC 59.875 47.826 0.00 0.00 0.00 3.46
282 290 6.398918 CATCATGATGAGACATGCATCTCTA 58.601 40.000 28.37 5.68 44.71 2.43
287 295 3.503748 CAGCATCATGATGAGACATGCAT 59.496 43.478 34.65 9.84 44.79 3.96
412 420 7.509659 AGAGTCTTTTTCTAGTCCCTGTAGAAA 59.490 37.037 1.96 1.96 42.24 2.52
413 421 7.011382 AGAGTCTTTTTCTAGTCCCTGTAGAA 58.989 38.462 0.00 0.00 35.21 2.10
414 422 6.553857 AGAGTCTTTTTCTAGTCCCTGTAGA 58.446 40.000 0.00 0.00 0.00 2.59
415 423 6.844097 AGAGTCTTTTTCTAGTCCCTGTAG 57.156 41.667 0.00 0.00 0.00 2.74
416 424 7.468496 AGTAGAGTCTTTTTCTAGTCCCTGTA 58.532 38.462 0.00 0.00 0.00 2.74
417 425 6.316513 AGTAGAGTCTTTTTCTAGTCCCTGT 58.683 40.000 0.00 0.00 0.00 4.00
418 426 6.844097 AGTAGAGTCTTTTTCTAGTCCCTG 57.156 41.667 0.00 0.00 0.00 4.45
419 427 7.931046 TCTAGTAGAGTCTTTTTCTAGTCCCT 58.069 38.462 0.00 0.00 33.84 4.20
420 428 8.048514 TCTCTAGTAGAGTCTTTTTCTAGTCCC 58.951 40.741 23.51 0.00 42.83 4.46
421 429 9.452287 TTCTCTAGTAGAGTCTTTTTCTAGTCC 57.548 37.037 23.51 0.00 42.83 3.85
461 469 4.040584 AGGACTTTTTCTAGTCACAGGGAC 59.959 45.833 0.00 0.00 45.07 4.46
462 470 4.232091 AGGACTTTTTCTAGTCACAGGGA 58.768 43.478 6.17 0.00 45.07 4.20
463 471 4.625607 AGGACTTTTTCTAGTCACAGGG 57.374 45.455 6.17 0.00 45.07 4.45
464 472 5.480772 TCCTAGGACTTTTTCTAGTCACAGG 59.519 44.000 7.62 12.89 45.07 4.00
465 473 6.391537 GTCCTAGGACTTTTTCTAGTCACAG 58.608 44.000 31.12 2.61 45.07 3.66
466 474 6.342338 GTCCTAGGACTTTTTCTAGTCACA 57.658 41.667 31.12 0.00 45.07 3.58
480 488 5.639931 GTGTTTGATTCAGAAGTCCTAGGAC 59.360 44.000 31.29 31.29 44.86 3.85
481 489 5.280011 GGTGTTTGATTCAGAAGTCCTAGGA 60.280 44.000 7.62 7.62 0.00 2.94
482 490 4.938226 GGTGTTTGATTCAGAAGTCCTAGG 59.062 45.833 0.82 0.82 0.00 3.02
483 491 4.938226 GGGTGTTTGATTCAGAAGTCCTAG 59.062 45.833 0.00 0.00 0.00 3.02
484 492 4.597507 AGGGTGTTTGATTCAGAAGTCCTA 59.402 41.667 0.00 0.00 0.00 2.94
485 493 3.395941 AGGGTGTTTGATTCAGAAGTCCT 59.604 43.478 0.00 0.00 0.00 3.85
486 494 3.753797 GAGGGTGTTTGATTCAGAAGTCC 59.246 47.826 0.00 0.00 0.00 3.85
487 495 4.646572 AGAGGGTGTTTGATTCAGAAGTC 58.353 43.478 0.00 0.00 0.00 3.01
488 496 4.713792 AGAGGGTGTTTGATTCAGAAGT 57.286 40.909 0.00 0.00 0.00 3.01
489 497 6.409704 TGATAGAGGGTGTTTGATTCAGAAG 58.590 40.000 0.00 0.00 0.00 2.85
490 498 6.373005 TGATAGAGGGTGTTTGATTCAGAA 57.627 37.500 0.00 0.00 0.00 3.02
491 499 6.566079 ATGATAGAGGGTGTTTGATTCAGA 57.434 37.500 0.00 0.00 0.00 3.27
492 500 6.459298 GCAATGATAGAGGGTGTTTGATTCAG 60.459 42.308 0.00 0.00 0.00 3.02
493 501 5.357878 GCAATGATAGAGGGTGTTTGATTCA 59.642 40.000 0.00 0.00 0.00 2.57
494 502 5.221126 GGCAATGATAGAGGGTGTTTGATTC 60.221 44.000 0.00 0.00 0.00 2.52
495 503 4.646492 GGCAATGATAGAGGGTGTTTGATT 59.354 41.667 0.00 0.00 0.00 2.57
496 504 4.210331 GGCAATGATAGAGGGTGTTTGAT 58.790 43.478 0.00 0.00 0.00 2.57
497 505 3.010027 TGGCAATGATAGAGGGTGTTTGA 59.990 43.478 0.00 0.00 0.00 2.69
498 506 3.355378 TGGCAATGATAGAGGGTGTTTG 58.645 45.455 0.00 0.00 0.00 2.93
499 507 3.737559 TGGCAATGATAGAGGGTGTTT 57.262 42.857 0.00 0.00 0.00 2.83
500 508 3.010584 ACTTGGCAATGATAGAGGGTGTT 59.989 43.478 0.00 0.00 0.00 3.32
501 509 2.578021 ACTTGGCAATGATAGAGGGTGT 59.422 45.455 0.00 0.00 0.00 4.16
502 510 3.287867 ACTTGGCAATGATAGAGGGTG 57.712 47.619 0.00 0.00 0.00 4.61
503 511 3.372025 GGAACTTGGCAATGATAGAGGGT 60.372 47.826 0.00 0.00 0.00 4.34
504 512 3.117738 AGGAACTTGGCAATGATAGAGGG 60.118 47.826 0.00 0.00 27.25 4.30
505 513 3.881688 CAGGAACTTGGCAATGATAGAGG 59.118 47.826 0.00 0.00 34.60 3.69
506 514 4.521146 ACAGGAACTTGGCAATGATAGAG 58.479 43.478 0.00 0.00 34.60 2.43
507 515 4.574674 ACAGGAACTTGGCAATGATAGA 57.425 40.909 0.00 0.00 34.60 1.98
508 516 4.096984 GGAACAGGAACTTGGCAATGATAG 59.903 45.833 0.00 0.00 34.60 2.08
532 540 0.466963 TCATGCATGCATCTCGAGGT 59.533 50.000 30.07 5.14 33.90 3.85
567 575 1.134491 GGTGGAGTGGGGATTAACGAG 60.134 57.143 0.00 0.00 0.00 4.18
584 592 1.303317 AACTAGCCAAAGCCGGGTG 60.303 57.895 7.07 0.00 41.25 4.61
585 593 1.002502 GAACTAGCCAAAGCCGGGT 60.003 57.895 0.00 0.00 41.25 5.28
610 639 0.314302 AGTACGGTGTGTCACAGAGC 59.686 55.000 5.74 0.00 35.86 4.09
781 818 1.048601 AGAGACGGGACAAAAGCTGA 58.951 50.000 0.00 0.00 0.00 4.26
822 860 5.604758 ACCGAGGGTAATTTAGGTAACTC 57.395 43.478 0.00 0.00 40.08 3.01
950 988 2.828520 CCAAGTTGAGAGAGGTAGCTGA 59.171 50.000 3.87 0.00 0.00 4.26
970 1008 3.246619 GAGTCTTGACTCGTGAATGTCC 58.753 50.000 14.00 0.00 32.67 4.02
1140 2751 4.862823 GGCGGTAGGGAGGCCTCT 62.863 72.222 31.36 16.10 43.52 3.69
1726 3875 2.138320 GATATGTGTGCATGGAGACGG 58.862 52.381 9.92 0.00 36.58 4.79
2008 4160 4.169508 CGACAGAAGATAGTGACAACTGG 58.830 47.826 0.00 0.00 37.19 4.00
2142 4298 4.446413 GTCGCCGGGTGGTGGTAG 62.446 72.222 2.18 0.00 46.22 3.18
2427 4583 2.593436 CCAAACTGGCCGAACGGT 60.593 61.111 14.63 0.00 37.65 4.83
2509 4668 2.032681 AAGCCGGAACAGAGCACC 59.967 61.111 5.05 0.00 0.00 5.01
2521 4680 1.794455 CGTACGTACGCATGAAGCCG 61.794 60.000 32.36 7.79 43.14 5.52
2534 4693 1.080705 GCTTGCTCCACTCGTACGT 60.081 57.895 16.05 0.00 0.00 3.57
2600 4820 0.251742 ACCACCACCAACATCATGGG 60.252 55.000 0.00 0.00 45.18 4.00
2620 4843 4.088638 CAGCGTATCCGATCTTTCAATACG 59.911 45.833 8.42 8.42 41.69 3.06
2694 4917 1.880340 GCTCACTTCATCGCCTCCG 60.880 63.158 0.00 0.00 0.00 4.63
2700 4923 1.991264 CTCACTGTGCTCACTTCATCG 59.009 52.381 2.12 0.00 0.00 3.84
2821 5052 4.649674 ACTGGAAACGCATCCTTCTCTATA 59.350 41.667 8.39 0.00 40.35 1.31
2844 5075 8.588472 CACTATACAACTAGATGATCCATGGAA 58.412 37.037 20.67 2.92 0.00 3.53
2889 5148 7.333423 TCCACATAAACTCGTAAATCCAGAAAG 59.667 37.037 0.00 0.00 0.00 2.62
2973 5239 9.780186 TTGGAAAAGTTTCAAGGTTAAGAAAAA 57.220 25.926 6.15 0.00 38.92 1.94
3007 5273 2.423892 CGAGCAAGAAGGCACTACTCTA 59.576 50.000 0.00 0.00 38.49 2.43
3008 5274 1.203523 CGAGCAAGAAGGCACTACTCT 59.796 52.381 0.00 0.00 38.49 3.24
3009 5275 1.634702 CGAGCAAGAAGGCACTACTC 58.365 55.000 0.00 0.00 38.49 2.59
3062 5335 2.158740 TCCCGCCCATTTCGAATGATAA 60.159 45.455 0.00 0.00 0.00 1.75
3076 5349 4.011517 TTCGAACACCTCCCGCCC 62.012 66.667 0.00 0.00 0.00 6.13
3121 5394 7.169158 TGTCACCTTTTTCTGATTTTCAAGT 57.831 32.000 0.00 0.00 0.00 3.16
3122 5395 8.652810 AATGTCACCTTTTTCTGATTTTCAAG 57.347 30.769 0.00 0.00 0.00 3.02
3126 5399 9.317936 GAGAAAATGTCACCTTTTTCTGATTTT 57.682 29.630 16.35 0.00 46.62 1.82
3130 5403 7.645058 AAGAGAAAATGTCACCTTTTTCTGA 57.355 32.000 16.35 0.00 46.62 3.27
3131 5404 7.975616 TGAAAGAGAAAATGTCACCTTTTTCTG 59.024 33.333 16.35 0.00 46.62 3.02
3133 5406 8.702163 TTGAAAGAGAAAATGTCACCTTTTTC 57.298 30.769 5.35 5.35 41.51 2.29
3135 5408 9.671279 ATTTTGAAAGAGAAAATGTCACCTTTT 57.329 25.926 0.00 0.00 33.93 2.27
3136 5409 9.101655 CATTTTGAAAGAGAAAATGTCACCTTT 57.898 29.630 0.00 0.00 42.23 3.11
3137 5410 8.477256 TCATTTTGAAAGAGAAAATGTCACCTT 58.523 29.630 14.42 0.00 45.19 3.50
3138 5411 8.010733 TCATTTTGAAAGAGAAAATGTCACCT 57.989 30.769 14.42 0.00 45.19 4.00
3139 5412 8.706035 CATCATTTTGAAAGAGAAAATGTCACC 58.294 33.333 14.42 0.00 45.19 4.02
3152 5425 6.385033 GTGGAGAGGTTCATCATTTTGAAAG 58.615 40.000 0.00 0.00 37.36 2.62
3162 5435 1.112113 TAGCGGTGGAGAGGTTCATC 58.888 55.000 0.00 0.00 0.00 2.92
3179 5452 9.463443 ACGGTTTCTTCAATGATTTTCTTTTAG 57.537 29.630 0.00 0.00 0.00 1.85
3185 5458 7.698130 CCTATGACGGTTTCTTCAATGATTTTC 59.302 37.037 0.00 0.00 0.00 2.29
3186 5459 7.393234 TCCTATGACGGTTTCTTCAATGATTTT 59.607 33.333 0.00 0.00 0.00 1.82
3187 5460 6.884295 TCCTATGACGGTTTCTTCAATGATTT 59.116 34.615 0.00 0.00 0.00 2.17
3188 5461 6.414732 TCCTATGACGGTTTCTTCAATGATT 58.585 36.000 0.00 0.00 0.00 2.57
3199 5472 3.682858 CGTTGTTGATCCTATGACGGTTT 59.317 43.478 0.00 0.00 0.00 3.27
3208 5481 2.301870 AGCCACTTCGTTGTTGATCCTA 59.698 45.455 0.00 0.00 0.00 2.94
3242 5515 3.365868 CGAGAATAATCCCAGAGAGCGAG 60.366 52.174 0.00 0.00 0.00 5.03
3245 5518 4.054671 CAACGAGAATAATCCCAGAGAGC 58.945 47.826 0.00 0.00 0.00 4.09
3291 5564 2.271497 AGCATGCTCCACTGCTCC 59.729 61.111 16.30 0.00 45.30 4.70
3348 7829 3.674997 AGTCCGTGAATGTAGCATTGTT 58.325 40.909 0.00 0.00 0.00 2.83
3349 7830 3.334583 AGTCCGTGAATGTAGCATTGT 57.665 42.857 0.00 0.00 0.00 2.71
3350 7831 4.629634 TGTTAGTCCGTGAATGTAGCATTG 59.370 41.667 0.00 0.00 0.00 2.82
3352 7833 4.181578 GTGTTAGTCCGTGAATGTAGCAT 58.818 43.478 0.00 0.00 0.00 3.79
3353 7834 3.006003 TGTGTTAGTCCGTGAATGTAGCA 59.994 43.478 0.00 0.00 0.00 3.49
3354 7835 3.581755 TGTGTTAGTCCGTGAATGTAGC 58.418 45.455 0.00 0.00 0.00 3.58
3355 7836 4.174009 CCTGTGTTAGTCCGTGAATGTAG 58.826 47.826 0.00 0.00 0.00 2.74
3357 7838 2.289444 CCCTGTGTTAGTCCGTGAATGT 60.289 50.000 0.00 0.00 0.00 2.71
3359 7840 1.278127 CCCCTGTGTTAGTCCGTGAAT 59.722 52.381 0.00 0.00 0.00 2.57
3361 7842 1.823169 GCCCCTGTGTTAGTCCGTGA 61.823 60.000 0.00 0.00 0.00 4.35
3362 7843 1.375523 GCCCCTGTGTTAGTCCGTG 60.376 63.158 0.00 0.00 0.00 4.94
3363 7844 2.939261 CGCCCCTGTGTTAGTCCGT 61.939 63.158 0.00 0.00 0.00 4.69
3366 7847 2.267961 CCCGCCCCTGTGTTAGTC 59.732 66.667 0.00 0.00 0.00 2.59
3367 7848 4.029809 GCCCGCCCCTGTGTTAGT 62.030 66.667 0.00 0.00 0.00 2.24
3387 7868 0.652592 CAAGCCTACGCACACATAGC 59.347 55.000 0.00 0.00 37.52 2.97
3389 7870 0.249120 AGCAAGCCTACGCACACATA 59.751 50.000 0.00 0.00 37.52 2.29
3390 7871 1.003355 AGCAAGCCTACGCACACAT 60.003 52.632 0.00 0.00 37.52 3.21
3391 7872 1.960763 CAGCAAGCCTACGCACACA 60.961 57.895 0.00 0.00 37.52 3.72
3393 7874 0.321564 AATCAGCAAGCCTACGCACA 60.322 50.000 0.00 0.00 37.52 4.57
3398 7879 4.400567 AGGATTTTCAATCAGCAAGCCTAC 59.599 41.667 0.00 0.00 0.00 3.18
3428 7909 4.863131 AGAATTTTCGCTCCAAGTACTACG 59.137 41.667 0.00 0.00 0.00 3.51
3440 7921 2.412325 CGGTGCGTTTAGAATTTTCGCT 60.412 45.455 9.08 0.00 45.69 4.93
3441 7922 1.902504 CGGTGCGTTTAGAATTTTCGC 59.097 47.619 0.00 0.00 45.70 4.70
3442 7923 3.120786 AGTCGGTGCGTTTAGAATTTTCG 60.121 43.478 0.00 0.00 0.00 3.46
3443 7924 4.400036 AGTCGGTGCGTTTAGAATTTTC 57.600 40.909 0.00 0.00 0.00 2.29
3444 7925 5.927954 TTAGTCGGTGCGTTTAGAATTTT 57.072 34.783 0.00 0.00 0.00 1.82
3445 7926 6.237648 CGTATTAGTCGGTGCGTTTAGAATTT 60.238 38.462 0.00 0.00 0.00 1.82
3446 7927 5.230726 CGTATTAGTCGGTGCGTTTAGAATT 59.769 40.000 0.00 0.00 0.00 2.17
3447 7928 4.736793 CGTATTAGTCGGTGCGTTTAGAAT 59.263 41.667 0.00 0.00 0.00 2.40
3448 7929 4.097714 CGTATTAGTCGGTGCGTTTAGAA 58.902 43.478 0.00 0.00 0.00 2.10
3449 7930 3.487376 CCGTATTAGTCGGTGCGTTTAGA 60.487 47.826 0.00 0.00 42.62 2.10
3450 7931 2.785477 CCGTATTAGTCGGTGCGTTTAG 59.215 50.000 0.00 0.00 42.62 1.85
3451 7932 2.479389 CCCGTATTAGTCGGTGCGTTTA 60.479 50.000 3.78 0.00 45.63 2.01
3452 7933 1.632422 CCGTATTAGTCGGTGCGTTT 58.368 50.000 0.00 0.00 42.62 3.60
3453 7934 0.179129 CCCGTATTAGTCGGTGCGTT 60.179 55.000 3.78 0.00 45.63 4.84
3454 7935 1.434696 CCCGTATTAGTCGGTGCGT 59.565 57.895 3.78 0.00 45.63 5.24
3455 7936 1.299620 CCCCGTATTAGTCGGTGCG 60.300 63.158 3.78 0.00 45.63 5.34
3456 7937 0.031721 CTCCCCGTATTAGTCGGTGC 59.968 60.000 3.78 0.00 45.63 5.01
3457 7938 1.396653 ACTCCCCGTATTAGTCGGTG 58.603 55.000 3.78 0.00 45.63 4.94
3458 7939 2.149973 AACTCCCCGTATTAGTCGGT 57.850 50.000 3.78 0.00 45.63 4.69
3459 7940 3.548818 CGTAAACTCCCCGTATTAGTCGG 60.549 52.174 0.00 0.00 46.49 4.79
3460 7941 3.548818 CCGTAAACTCCCCGTATTAGTCG 60.549 52.174 0.00 0.00 0.00 4.18
3461 7942 3.632145 TCCGTAAACTCCCCGTATTAGTC 59.368 47.826 0.00 0.00 0.00 2.59
3462 7943 3.381590 GTCCGTAAACTCCCCGTATTAGT 59.618 47.826 0.00 0.00 0.00 2.24
3463 7944 3.633986 AGTCCGTAAACTCCCCGTATTAG 59.366 47.826 0.00 0.00 0.00 1.73
3464 7945 3.631250 AGTCCGTAAACTCCCCGTATTA 58.369 45.455 0.00 0.00 0.00 0.98
3465 7946 2.428530 GAGTCCGTAAACTCCCCGTATT 59.571 50.000 0.00 0.00 39.85 1.89
3466 7947 2.027385 GAGTCCGTAAACTCCCCGTAT 58.973 52.381 0.00 0.00 39.85 3.06
3467 7948 1.463674 GAGTCCGTAAACTCCCCGTA 58.536 55.000 0.00 0.00 39.85 4.02
3468 7949 2.270959 GAGTCCGTAAACTCCCCGT 58.729 57.895 0.00 0.00 39.85 5.28
3473 7954 3.294816 AACGAAGGAGTCCGTAAACTC 57.705 47.619 2.76 2.21 44.08 3.01
3474 7955 4.279420 AGTTAACGAAGGAGTCCGTAAACT 59.721 41.667 2.76 6.22 38.13 2.66
3475 7956 4.550422 AGTTAACGAAGGAGTCCGTAAAC 58.450 43.478 2.76 4.11 38.13 2.01
3476 7957 4.853924 AGTTAACGAAGGAGTCCGTAAA 57.146 40.909 2.76 0.00 38.13 2.01
3477 7958 5.957842 TTAGTTAACGAAGGAGTCCGTAA 57.042 39.130 2.76 0.00 38.13 3.18


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

AutoCloner maintained by Alex Coulton.