Multiple sequence alignment - TraesCS2B01G078100

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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 TraesCS2B01G078100 chr2B 100.000 3535 0 0 1 3535 43457343 43453809 0.000000e+00 6529
1 TraesCS2B01G078100 chr2B 95.309 3368 145 9 3 3365 24650826 24654185 0.000000e+00 5332
2 TraesCS2B01G078100 chr2B 99.412 170 1 0 3366 3535 43440513 43440344 3.430000e-80 309
3 TraesCS2B01G078100 chr7B 95.552 3372 133 14 3 3365 412115066 412111703 0.000000e+00 5380
4 TraesCS2B01G078100 chr7B 99.412 170 1 0 3366 3535 443097293 443097462 3.430000e-80 309
5 TraesCS2B01G078100 chr7B 98.830 171 1 1 3366 3535 386325811 386325981 1.590000e-78 303
6 TraesCS2B01G078100 chr5B 95.434 3373 136 16 1 3365 529120774 529124136 0.000000e+00 5360
7 TraesCS2B01G078100 chr5B 94.002 3368 178 21 2 3365 105177528 105180875 0.000000e+00 5079
8 TraesCS2B01G078100 chr5B 92.643 3371 212 28 2 3365 180047116 180050457 0.000000e+00 4819
9 TraesCS2B01G078100 chr4B 95.430 3370 140 11 3 3365 27781405 27778043 0.000000e+00 5358
10 TraesCS2B01G078100 chr4B 94.906 3357 147 18 2 3350 139104311 139100971 0.000000e+00 5230
11 TraesCS2B01G078100 chr4B 99.412 170 0 1 3366 3535 102559171 102559003 1.230000e-79 307
12 TraesCS2B01G078100 chr4B 99.408 169 1 0 3366 3534 102572664 102572496 1.230000e-79 307
13 TraesCS2B01G078100 chr1B 93.620 3370 193 19 2 3365 67113710 67110357 0.000000e+00 5012
14 TraesCS2B01G078100 chr1B 92.194 3369 226 31 2 3365 171621478 171624814 0.000000e+00 4730
15 TraesCS2B01G078100 chr1B 99.412 170 1 0 3366 3535 496272716 496272547 3.430000e-80 309
16 TraesCS2B01G078100 chr6B 99.412 170 1 0 3366 3535 260596736 260596567 3.430000e-80 309
17 TraesCS2B01G078100 chr6B 99.415 171 0 1 3365 3535 471355640 471355471 3.430000e-80 309
18 TraesCS2B01G078100 chr3B 99.412 170 0 1 3366 3535 224577715 224577883 1.230000e-79 307


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 TraesCS2B01G078100 chr2B 43453809 43457343 3534 True 6529 6529 100.000 1 3535 1 chr2B.!!$R2 3534
1 TraesCS2B01G078100 chr2B 24650826 24654185 3359 False 5332 5332 95.309 3 3365 1 chr2B.!!$F1 3362
2 TraesCS2B01G078100 chr7B 412111703 412115066 3363 True 5380 5380 95.552 3 3365 1 chr7B.!!$R1 3362
3 TraesCS2B01G078100 chr5B 529120774 529124136 3362 False 5360 5360 95.434 1 3365 1 chr5B.!!$F3 3364
4 TraesCS2B01G078100 chr5B 105177528 105180875 3347 False 5079 5079 94.002 2 3365 1 chr5B.!!$F1 3363
5 TraesCS2B01G078100 chr5B 180047116 180050457 3341 False 4819 4819 92.643 2 3365 1 chr5B.!!$F2 3363
6 TraesCS2B01G078100 chr4B 27778043 27781405 3362 True 5358 5358 95.430 3 3365 1 chr4B.!!$R1 3362
7 TraesCS2B01G078100 chr4B 139100971 139104311 3340 True 5230 5230 94.906 2 3350 1 chr4B.!!$R4 3348
8 TraesCS2B01G078100 chr1B 67110357 67113710 3353 True 5012 5012 93.620 2 3365 1 chr1B.!!$R1 3363
9 TraesCS2B01G078100 chr1B 171621478 171624814 3336 False 4730 4730 92.194 2 3365 1 chr1B.!!$F1 3363

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
661 671 1.069049 GCTGAACAGGTGGCATTTTGT 59.931 47.619 3.99 0.00 0.00 2.83 F
1363 1388 0.179037 CTGATGGATGTCCGGTGCAT 60.179 55.000 12.66 12.66 39.43 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 1591 1.818674 GTTCGGCATGGATTCCAAACT 59.181 47.619 9.98 0.00 36.95 2.66 R
2988 3043 0.108138 CCGAGAAAGCCGGTCATTCT 60.108 55.000 15.41 15.41 41.91 2.40 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
661 671 1.069049 GCTGAACAGGTGGCATTTTGT 59.931 47.619 3.99 0.00 0.00 2.83
703 713 2.857186 TGTGAGCTGCCACATCTTAA 57.143 45.000 16.47 0.00 41.63 1.85
706 716 3.441222 TGTGAGCTGCCACATCTTAATTG 59.559 43.478 16.47 0.00 41.63 2.32
760 770 4.891168 TCGTACTATCTTGGGCTAACATGA 59.109 41.667 0.00 0.00 0.00 3.07
865 877 6.914259 TGCCATGTTTATGTTTTCGACAATA 58.086 32.000 0.00 0.00 42.62 1.90
946 960 3.244735 TGTTAGATGGCAACTGCTTACCA 60.245 43.478 7.62 0.00 41.70 3.25
969 984 5.177327 CACTTGCATTTTACATTTCCACCAC 59.823 40.000 0.00 0.00 0.00 4.16
1007 1022 2.367894 CCTATCTCAGCAGAATGGCTCA 59.632 50.000 0.00 0.00 43.68 4.26
1302 1326 4.013050 TGTGTTGACTGACAAATTCACCA 58.987 39.130 8.65 0.00 40.36 4.17
1363 1388 0.179037 CTGATGGATGTCCGGTGCAT 60.179 55.000 12.66 12.66 39.43 3.96
1464 1489 2.227388 GGAAGACTACCGTTGAACGAGA 59.773 50.000 20.47 5.32 46.05 4.04
1521 1546 2.857592 TATCAAAGTCCCGTACGAGC 57.142 50.000 18.76 6.21 0.00 5.03
1566 1591 3.955524 TGTTCCCCTGTTTGTTTCCTA 57.044 42.857 0.00 0.00 0.00 2.94
1589 1614 0.037447 TGGAATCCATGCCGAACACA 59.963 50.000 0.00 0.00 0.00 3.72
1659 1684 5.808042 TTTCAAGATGAAGCTACTCATGC 57.192 39.130 5.62 0.00 37.70 4.06
1742 1767 4.466827 CCATCTTGGTGAATGATCCATCA 58.533 43.478 0.00 0.00 35.36 3.07
1802 1832 5.576774 CGATGTCATGTGTAAAGCTAGTGAA 59.423 40.000 0.00 0.00 0.00 3.18
1806 1836 5.122239 GTCATGTGTAAAGCTAGTGAATGCA 59.878 40.000 0.00 0.00 0.00 3.96
1922 1956 8.134895 TGAAGAACATGAATTGGTGTAAGTTTC 58.865 33.333 0.00 0.00 0.00 2.78
1940 1974 1.597854 CTTGCCGACTTCCTGCACA 60.598 57.895 0.00 0.00 34.16 4.57
2800 2853 2.371841 GGGGCCTCAAAACTTTGGAAAT 59.628 45.455 0.84 0.00 38.66 2.17
2829 2882 1.221414 GTGCACTCAGCTTCGTCTTT 58.779 50.000 10.32 0.00 45.94 2.52
2976 3030 3.010584 ACCTGTTGAGCATCTAATTGGGT 59.989 43.478 0.00 0.00 34.92 4.51
2988 3043 5.186256 TCTAATTGGGTAGTTTGCATCCA 57.814 39.130 0.00 0.00 0.00 3.41
3002 3057 1.755179 CATCCAGAATGACCGGCTTT 58.245 50.000 0.00 0.00 39.69 3.51
3102 3158 0.245539 CCCAGAACGTACACATCGGT 59.754 55.000 0.00 0.00 0.00 4.69
3189 3245 3.781770 GATGGAGACGCTGGCCTCG 62.782 68.421 14.81 14.81 0.00 4.63
3206 3262 3.782042 GGCAAGGATGACGACGAC 58.218 61.111 0.00 0.00 0.00 4.34
3365 3422 1.384191 GTTGCCATCAAGGAGGGGT 59.616 57.895 0.00 0.00 41.22 4.95
3366 3423 0.967380 GTTGCCATCAAGGAGGGGTG 60.967 60.000 0.00 0.00 41.22 4.61
3367 3424 1.139498 TTGCCATCAAGGAGGGGTGA 61.139 55.000 0.00 0.00 41.22 4.02
3368 3425 1.139498 TGCCATCAAGGAGGGGTGAA 61.139 55.000 0.00 0.00 41.22 3.18
3369 3426 0.039618 GCCATCAAGGAGGGGTGAAA 59.960 55.000 0.00 0.00 41.22 2.69
3370 3427 1.957113 GCCATCAAGGAGGGGTGAAAG 60.957 57.143 0.00 0.00 41.22 2.62
3371 3428 1.355720 CCATCAAGGAGGGGTGAAAGT 59.644 52.381 0.00 0.00 41.22 2.66
3372 3429 2.440409 CATCAAGGAGGGGTGAAAGTG 58.560 52.381 0.00 0.00 0.00 3.16
3373 3430 0.110486 TCAAGGAGGGGTGAAAGTGC 59.890 55.000 0.00 0.00 0.00 4.40
3374 3431 0.111253 CAAGGAGGGGTGAAAGTGCT 59.889 55.000 0.00 0.00 0.00 4.40
3375 3432 1.351017 CAAGGAGGGGTGAAAGTGCTA 59.649 52.381 0.00 0.00 0.00 3.49
3376 3433 1.280457 AGGAGGGGTGAAAGTGCTAG 58.720 55.000 0.00 0.00 0.00 3.42
3377 3434 0.984995 GGAGGGGTGAAAGTGCTAGT 59.015 55.000 0.00 0.00 0.00 2.57
3378 3435 2.185387 GGAGGGGTGAAAGTGCTAGTA 58.815 52.381 0.00 0.00 0.00 1.82
3379 3436 2.772515 GGAGGGGTGAAAGTGCTAGTAT 59.227 50.000 0.00 0.00 0.00 2.12
3380 3437 3.181464 GGAGGGGTGAAAGTGCTAGTATC 60.181 52.174 0.00 0.00 0.00 2.24
3381 3438 2.431057 AGGGGTGAAAGTGCTAGTATCG 59.569 50.000 0.00 0.00 0.00 2.92
3382 3439 2.429610 GGGGTGAAAGTGCTAGTATCGA 59.570 50.000 0.00 0.00 0.00 3.59
3383 3440 3.445857 GGGTGAAAGTGCTAGTATCGAC 58.554 50.000 0.00 0.00 0.00 4.20
3384 3441 3.130693 GGGTGAAAGTGCTAGTATCGACT 59.869 47.826 0.00 0.00 39.92 4.18
3385 3442 4.337555 GGGTGAAAGTGCTAGTATCGACTA 59.662 45.833 0.00 0.00 37.10 2.59
3408 3465 3.821306 GGGGGTGAATAGGCGATTT 57.179 52.632 0.00 0.00 0.00 2.17
3409 3466 2.067365 GGGGGTGAATAGGCGATTTT 57.933 50.000 0.00 0.00 0.00 1.82
3410 3467 2.384828 GGGGGTGAATAGGCGATTTTT 58.615 47.619 0.00 0.00 0.00 1.94
3411 3468 2.100749 GGGGGTGAATAGGCGATTTTTG 59.899 50.000 0.00 0.00 0.00 2.44
3412 3469 2.758423 GGGGTGAATAGGCGATTTTTGT 59.242 45.455 0.00 0.00 0.00 2.83
3413 3470 3.428862 GGGGTGAATAGGCGATTTTTGTG 60.429 47.826 0.00 0.00 0.00 3.33
3414 3471 3.442273 GGGTGAATAGGCGATTTTTGTGA 59.558 43.478 0.00 0.00 0.00 3.58
3415 3472 4.082463 GGGTGAATAGGCGATTTTTGTGAA 60.082 41.667 0.00 0.00 0.00 3.18
3416 3473 5.465935 GGTGAATAGGCGATTTTTGTGAAA 58.534 37.500 0.00 0.00 0.00 2.69
3417 3474 5.572896 GGTGAATAGGCGATTTTTGTGAAAG 59.427 40.000 0.00 0.00 0.00 2.62
3418 3475 6.149633 GTGAATAGGCGATTTTTGTGAAAGT 58.850 36.000 0.00 0.00 0.00 2.66
3419 3476 6.305638 GTGAATAGGCGATTTTTGTGAAAGTC 59.694 38.462 0.00 0.00 0.00 3.01
3420 3477 6.206634 TGAATAGGCGATTTTTGTGAAAGTCT 59.793 34.615 0.00 0.00 31.44 3.24
3421 3478 4.918810 AGGCGATTTTTGTGAAAGTCTT 57.081 36.364 0.00 0.00 31.44 3.01
3422 3479 4.860072 AGGCGATTTTTGTGAAAGTCTTC 58.140 39.130 0.00 0.00 31.44 2.87
3423 3480 4.338118 AGGCGATTTTTGTGAAAGTCTTCA 59.662 37.500 0.00 0.00 39.30 3.02
3424 3481 5.040635 GGCGATTTTTGTGAAAGTCTTCAA 58.959 37.500 0.00 0.00 43.18 2.69
3425 3482 5.518487 GGCGATTTTTGTGAAAGTCTTCAAA 59.482 36.000 0.00 0.00 43.18 2.69
3426 3483 6.035542 GGCGATTTTTGTGAAAGTCTTCAAAA 59.964 34.615 6.58 6.58 43.18 2.44
3427 3484 6.894517 GCGATTTTTGTGAAAGTCTTCAAAAC 59.105 34.615 9.16 1.70 43.18 2.43
3428 3485 7.201435 GCGATTTTTGTGAAAGTCTTCAAAACT 60.201 33.333 9.16 5.73 43.18 2.66
3429 3486 8.647226 CGATTTTTGTGAAAGTCTTCAAAACTT 58.353 29.630 9.16 2.98 43.18 2.66
3430 3487 9.745323 GATTTTTGTGAAAGTCTTCAAAACTTG 57.255 29.630 9.16 0.00 43.18 3.16
3431 3488 7.650834 TTTTGTGAAAGTCTTCAAAACTTGG 57.349 32.000 6.58 0.00 43.18 3.61
3432 3489 6.582677 TTGTGAAAGTCTTCAAAACTTGGA 57.417 33.333 0.00 0.00 43.18 3.53
3433 3490 6.582677 TGTGAAAGTCTTCAAAACTTGGAA 57.417 33.333 0.00 0.00 43.18 3.53
3434 3491 6.620678 TGTGAAAGTCTTCAAAACTTGGAAG 58.379 36.000 0.73 0.73 43.18 3.46
3435 3492 6.208599 TGTGAAAGTCTTCAAAACTTGGAAGT 59.791 34.615 6.50 0.00 43.18 3.01
3436 3493 7.090808 GTGAAAGTCTTCAAAACTTGGAAGTT 58.909 34.615 6.50 0.00 43.18 2.66
3449 3506 7.696992 AACTTGGAAGTTTAGAAGACAAACA 57.303 32.000 0.00 0.00 46.52 2.83
3450 3507 7.696992 ACTTGGAAGTTTAGAAGACAAACAA 57.303 32.000 0.00 0.00 38.16 2.83
3451 3508 7.535997 ACTTGGAAGTTTAGAAGACAAACAAC 58.464 34.615 0.00 0.00 38.16 3.32
3452 3509 7.175990 ACTTGGAAGTTTAGAAGACAAACAACA 59.824 33.333 0.00 0.00 38.16 3.33
3453 3510 7.083875 TGGAAGTTTAGAAGACAAACAACAG 57.916 36.000 0.00 0.00 38.16 3.16
3454 3511 6.882140 TGGAAGTTTAGAAGACAAACAACAGA 59.118 34.615 0.00 0.00 38.16 3.41
3455 3512 7.392113 TGGAAGTTTAGAAGACAAACAACAGAA 59.608 33.333 0.00 0.00 38.16 3.02
3456 3513 8.241367 GGAAGTTTAGAAGACAAACAACAGAAA 58.759 33.333 0.00 0.00 38.16 2.52
3457 3514 9.788960 GAAGTTTAGAAGACAAACAACAGAAAT 57.211 29.630 0.00 0.00 38.16 2.17
3462 3519 7.881775 AGAAGACAAACAACAGAAATAACCT 57.118 32.000 0.00 0.00 0.00 3.50
3463 3520 8.974060 AGAAGACAAACAACAGAAATAACCTA 57.026 30.769 0.00 0.00 0.00 3.08
3464 3521 9.057089 AGAAGACAAACAACAGAAATAACCTAG 57.943 33.333 0.00 0.00 0.00 3.02
3465 3522 8.747538 AAGACAAACAACAGAAATAACCTAGT 57.252 30.769 0.00 0.00 0.00 2.57
3466 3523 8.747538 AGACAAACAACAGAAATAACCTAGTT 57.252 30.769 0.00 0.00 0.00 2.24
3467 3524 8.621286 AGACAAACAACAGAAATAACCTAGTTG 58.379 33.333 0.00 0.00 41.37 3.16
3468 3525 8.514330 ACAAACAACAGAAATAACCTAGTTGA 57.486 30.769 9.73 0.00 38.80 3.18
3469 3526 9.131791 ACAAACAACAGAAATAACCTAGTTGAT 57.868 29.630 9.73 0.00 38.80 2.57
3473 3530 8.893727 ACAACAGAAATAACCTAGTTGATATGC 58.106 33.333 9.73 0.00 38.80 3.14
3474 3531 8.892723 CAACAGAAATAACCTAGTTGATATGCA 58.107 33.333 0.00 0.00 38.80 3.96
3475 3532 8.668510 ACAGAAATAACCTAGTTGATATGCAG 57.331 34.615 0.00 0.00 0.00 4.41
3476 3533 7.227512 ACAGAAATAACCTAGTTGATATGCAGC 59.772 37.037 0.00 0.00 0.00 5.25
3477 3534 6.425114 AGAAATAACCTAGTTGATATGCAGCG 59.575 38.462 0.00 0.00 32.34 5.18
3478 3535 2.533266 ACCTAGTTGATATGCAGCGG 57.467 50.000 0.00 0.00 32.34 5.52
3479 3536 2.039418 ACCTAGTTGATATGCAGCGGA 58.961 47.619 0.00 0.00 32.34 5.54
3480 3537 2.434336 ACCTAGTTGATATGCAGCGGAA 59.566 45.455 0.00 0.00 32.34 4.30
3481 3538 3.062763 CCTAGTTGATATGCAGCGGAAG 58.937 50.000 0.00 0.00 32.34 3.46
3482 3539 2.988010 AGTTGATATGCAGCGGAAGA 57.012 45.000 0.00 0.00 32.34 2.87
3483 3540 3.482156 AGTTGATATGCAGCGGAAGAT 57.518 42.857 0.00 0.00 32.34 2.40
3484 3541 4.607293 AGTTGATATGCAGCGGAAGATA 57.393 40.909 0.00 0.00 32.34 1.98
3485 3542 4.960938 AGTTGATATGCAGCGGAAGATAA 58.039 39.130 0.00 0.00 32.34 1.75
3486 3543 5.368145 AGTTGATATGCAGCGGAAGATAAA 58.632 37.500 0.00 0.00 32.34 1.40
3487 3544 5.237344 AGTTGATATGCAGCGGAAGATAAAC 59.763 40.000 0.00 0.00 32.34 2.01
3488 3545 4.960938 TGATATGCAGCGGAAGATAAACT 58.039 39.130 0.00 0.00 0.00 2.66
3489 3546 6.096673 TGATATGCAGCGGAAGATAAACTA 57.903 37.500 0.00 0.00 0.00 2.24
3490 3547 5.926542 TGATATGCAGCGGAAGATAAACTAC 59.073 40.000 0.00 0.00 0.00 2.73
3491 3548 2.901249 TGCAGCGGAAGATAAACTACC 58.099 47.619 0.00 0.00 0.00 3.18
3492 3549 2.500098 TGCAGCGGAAGATAAACTACCT 59.500 45.455 0.00 0.00 0.00 3.08
3493 3550 3.055385 TGCAGCGGAAGATAAACTACCTT 60.055 43.478 0.00 0.00 0.00 3.50
3494 3551 4.160814 TGCAGCGGAAGATAAACTACCTTA 59.839 41.667 0.00 0.00 0.00 2.69
3495 3552 5.114081 GCAGCGGAAGATAAACTACCTTAA 58.886 41.667 0.00 0.00 0.00 1.85
3496 3553 5.234543 GCAGCGGAAGATAAACTACCTTAAG 59.765 44.000 0.00 0.00 0.00 1.85
3497 3554 5.234543 CAGCGGAAGATAAACTACCTTAAGC 59.765 44.000 0.00 0.00 0.00 3.09
3498 3555 4.208666 GCGGAAGATAAACTACCTTAAGCG 59.791 45.833 0.00 0.00 0.00 4.68
3499 3556 5.585390 CGGAAGATAAACTACCTTAAGCGA 58.415 41.667 0.00 0.00 0.00 4.93
3500 3557 5.686397 CGGAAGATAAACTACCTTAAGCGAG 59.314 44.000 0.00 0.00 0.00 5.03
3501 3558 5.462729 GGAAGATAAACTACCTTAAGCGAGC 59.537 44.000 0.00 0.00 0.00 5.03
3502 3559 4.946445 AGATAAACTACCTTAAGCGAGCC 58.054 43.478 0.00 0.00 0.00 4.70
3503 3560 4.404715 AGATAAACTACCTTAAGCGAGCCA 59.595 41.667 0.00 0.00 0.00 4.75
3504 3561 3.629142 AAACTACCTTAAGCGAGCCAT 57.371 42.857 0.00 0.00 0.00 4.40
3505 3562 4.748277 AAACTACCTTAAGCGAGCCATA 57.252 40.909 0.00 0.00 0.00 2.74
3506 3563 4.323553 AACTACCTTAAGCGAGCCATAG 57.676 45.455 0.00 0.00 0.00 2.23
3507 3564 3.297736 ACTACCTTAAGCGAGCCATAGT 58.702 45.455 0.00 0.00 0.00 2.12
3508 3565 2.892784 ACCTTAAGCGAGCCATAGTC 57.107 50.000 0.00 0.00 0.00 2.59
3509 3566 2.108168 ACCTTAAGCGAGCCATAGTCA 58.892 47.619 0.00 0.00 0.00 3.41
3510 3567 2.500098 ACCTTAAGCGAGCCATAGTCAA 59.500 45.455 0.00 0.00 0.00 3.18
3511 3568 3.126831 CCTTAAGCGAGCCATAGTCAAG 58.873 50.000 0.00 0.00 0.00 3.02
3512 3569 3.430929 CCTTAAGCGAGCCATAGTCAAGT 60.431 47.826 0.00 0.00 0.00 3.16
3513 3570 4.202121 CCTTAAGCGAGCCATAGTCAAGTA 60.202 45.833 0.00 0.00 0.00 2.24
3514 3571 5.509840 CCTTAAGCGAGCCATAGTCAAGTAT 60.510 44.000 0.00 0.00 0.00 2.12
3515 3572 3.377346 AGCGAGCCATAGTCAAGTATG 57.623 47.619 0.00 0.00 0.00 2.39
3516 3573 1.795286 GCGAGCCATAGTCAAGTATGC 59.205 52.381 0.00 0.00 0.00 3.14
3517 3574 2.803133 GCGAGCCATAGTCAAGTATGCA 60.803 50.000 0.00 0.00 0.00 3.96
3518 3575 3.457234 CGAGCCATAGTCAAGTATGCAA 58.543 45.455 0.00 0.00 0.00 4.08
3519 3576 4.060900 CGAGCCATAGTCAAGTATGCAAT 58.939 43.478 0.00 0.00 0.00 3.56
3520 3577 4.084171 CGAGCCATAGTCAAGTATGCAATG 60.084 45.833 0.00 0.00 0.00 2.82
3521 3578 5.039920 AGCCATAGTCAAGTATGCAATGA 57.960 39.130 0.00 0.00 0.00 2.57
3522 3579 5.628130 AGCCATAGTCAAGTATGCAATGAT 58.372 37.500 0.00 0.00 0.00 2.45
3523 3580 5.472478 AGCCATAGTCAAGTATGCAATGATG 59.528 40.000 0.00 0.00 0.00 3.07
3524 3581 5.240183 GCCATAGTCAAGTATGCAATGATGT 59.760 40.000 0.00 0.00 0.00 3.06
3525 3582 6.665465 CCATAGTCAAGTATGCAATGATGTG 58.335 40.000 0.00 0.00 0.00 3.21
3526 3583 6.484308 CCATAGTCAAGTATGCAATGATGTGA 59.516 38.462 0.00 0.00 0.00 3.58
3527 3584 7.012610 CCATAGTCAAGTATGCAATGATGTGAA 59.987 37.037 0.00 0.00 0.00 3.18
3528 3585 6.822667 AGTCAAGTATGCAATGATGTGAAA 57.177 33.333 0.00 0.00 0.00 2.69
3529 3586 6.849502 AGTCAAGTATGCAATGATGTGAAAG 58.150 36.000 0.00 0.00 0.00 2.62
3530 3587 6.432162 AGTCAAGTATGCAATGATGTGAAAGT 59.568 34.615 0.00 0.00 0.00 2.66
3531 3588 7.607607 AGTCAAGTATGCAATGATGTGAAAGTA 59.392 33.333 0.00 0.00 0.00 2.24
3532 3589 7.693951 GTCAAGTATGCAATGATGTGAAAGTAC 59.306 37.037 0.00 0.00 0.00 2.73
3533 3590 7.390162 TCAAGTATGCAATGATGTGAAAGTACA 59.610 33.333 0.00 0.00 34.63 2.90
3534 3591 7.312657 AGTATGCAATGATGTGAAAGTACAG 57.687 36.000 0.00 0.00 33.44 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
661 671 6.603997 ACACACTGTCCTAAAAATACACCAAA 59.396 34.615 0.00 0.00 0.00 3.28
703 713 4.405116 AAAACCTGCACATCACAACAAT 57.595 36.364 0.00 0.00 0.00 2.71
706 716 3.306703 CACAAAAACCTGCACATCACAAC 59.693 43.478 0.00 0.00 0.00 3.32
717 727 6.300354 ACGATAGAAAGTCACAAAAACCTG 57.700 37.500 0.00 0.00 41.38 4.00
760 770 9.218440 ACTTGAAAACAAAAATGTTGAAGATGT 57.782 25.926 11.94 0.00 31.64 3.06
813 823 2.414029 CGCGTTGGTTGCATTATCAAGT 60.414 45.455 0.00 0.00 0.00 3.16
865 877 1.198759 ACACACGCACCCCTCCTATT 61.199 55.000 0.00 0.00 0.00 1.73
946 960 5.296748 GTGGTGGAAATGTAAAATGCAAGT 58.703 37.500 0.00 0.00 0.00 3.16
969 984 5.178797 AGATAGGAACAGACCAAATTGTCG 58.821 41.667 0.00 0.00 40.26 4.35
1042 1060 1.647545 CGATTGCGCTGTGGTGGATT 61.648 55.000 9.73 0.00 0.00 3.01
1302 1326 0.107945 GCAGCTCCCTTCTGATCGTT 60.108 55.000 0.00 0.00 33.54 3.85
1363 1388 3.750371 CATACAGGGTTGACAAGGTTCA 58.250 45.455 0.00 0.00 0.00 3.18
1442 1467 2.228343 CTCGTTCAACGGTAGTCTTCCT 59.772 50.000 10.69 0.00 42.81 3.36
1464 1489 3.818773 CCCAAAGTACAGAACACGGATTT 59.181 43.478 0.00 0.00 0.00 2.17
1534 1559 2.658807 GGGGAACAACACTTCCTCTT 57.341 50.000 0.00 0.00 37.76 2.85
1566 1591 1.818674 GTTCGGCATGGATTCCAAACT 59.181 47.619 9.98 0.00 36.95 2.66
1659 1684 2.414481 CGAAAACAGCTGAGATGAGGTG 59.586 50.000 23.35 0.00 45.23 4.00
1940 1974 5.163581 GGTACATCTTGCTTGAGAATGCATT 60.164 40.000 12.83 12.83 39.07 3.56
2002 2037 5.344743 AGAGTGTTCACAGAAAGAACTGA 57.655 39.130 5.74 0.00 44.30 3.41
2205 2240 4.525996 TGTATGTGCTAGTTGCCATCATT 58.474 39.130 4.40 0.00 42.00 2.57
2370 2414 3.066064 AGACAGTCGACATACATGAGCTC 59.934 47.826 19.50 6.82 0.00 4.09
2514 2558 5.914898 ACCTACAGTTTTCCATATTTGGC 57.085 39.130 0.00 0.00 43.29 4.52
2532 2576 8.098912 GTGGATAGAGAAACCAAAACTAACCTA 58.901 37.037 0.00 0.00 35.40 3.08
2540 2584 4.069304 CCGTGTGGATAGAGAAACCAAAA 58.931 43.478 0.00 0.00 37.49 2.44
2592 2638 3.045634 TCATCCCTTATGAACCACGGAT 58.954 45.455 0.00 0.00 41.75 4.18
2800 2853 0.320683 CTGAGTGCACGTCCATCCAA 60.321 55.000 12.01 0.00 0.00 3.53
2863 2916 7.271511 TCAACAAATAATCCACAGCAAAAACT 58.728 30.769 0.00 0.00 0.00 2.66
2872 2926 5.618863 GCGTGACATCAACAAATAATCCACA 60.619 40.000 0.00 0.00 0.00 4.17
2976 3030 3.270027 CGGTCATTCTGGATGCAAACTA 58.730 45.455 0.00 0.00 35.64 2.24
2988 3043 0.108138 CCGAGAAAGCCGGTCATTCT 60.108 55.000 15.41 15.41 41.91 2.40
3002 3057 0.685097 CCTCAACCAACTTCCCGAGA 59.315 55.000 0.00 0.00 0.00 4.04
3053 3108 4.927782 AACTGCCTCGCAACCGCA 62.928 61.111 0.00 0.00 38.41 5.69
3189 3245 2.158959 CGTCGTCGTCATCCTTGCC 61.159 63.158 0.00 0.00 0.00 4.52
3206 3262 1.805943 TGTTGCACATTCTCCATGTCG 59.194 47.619 0.00 0.00 43.17 4.35
3303 3359 5.696724 CCGTATGTTCTTTGACTTTCTCTGT 59.303 40.000 0.00 0.00 0.00 3.41
3390 3447 2.067365 AAAATCGCCTATTCACCCCC 57.933 50.000 0.00 0.00 0.00 5.40
3391 3448 2.758423 ACAAAAATCGCCTATTCACCCC 59.242 45.455 0.00 0.00 0.00 4.95
3392 3449 3.442273 TCACAAAAATCGCCTATTCACCC 59.558 43.478 0.00 0.00 0.00 4.61
3393 3450 4.695217 TCACAAAAATCGCCTATTCACC 57.305 40.909 0.00 0.00 0.00 4.02
3394 3451 6.149633 ACTTTCACAAAAATCGCCTATTCAC 58.850 36.000 0.00 0.00 0.00 3.18
3395 3452 6.206634 AGACTTTCACAAAAATCGCCTATTCA 59.793 34.615 0.00 0.00 0.00 2.57
3396 3453 6.612306 AGACTTTCACAAAAATCGCCTATTC 58.388 36.000 0.00 0.00 0.00 1.75
3397 3454 6.575162 AGACTTTCACAAAAATCGCCTATT 57.425 33.333 0.00 0.00 0.00 1.73
3398 3455 6.206634 TGAAGACTTTCACAAAAATCGCCTAT 59.793 34.615 0.00 0.00 38.37 2.57
3399 3456 5.529430 TGAAGACTTTCACAAAAATCGCCTA 59.471 36.000 0.00 0.00 38.37 3.93
3400 3457 4.338118 TGAAGACTTTCACAAAAATCGCCT 59.662 37.500 0.00 0.00 38.37 5.52
3401 3458 4.606961 TGAAGACTTTCACAAAAATCGCC 58.393 39.130 0.00 0.00 38.37 5.54
3402 3459 6.567769 TTTGAAGACTTTCACAAAAATCGC 57.432 33.333 0.00 0.00 42.79 4.58
3403 3460 8.173321 AGTTTTGAAGACTTTCACAAAAATCG 57.827 30.769 12.37 0.00 42.79 3.34
3404 3461 9.745323 CAAGTTTTGAAGACTTTCACAAAAATC 57.255 29.630 12.37 4.85 42.79 2.17
3405 3462 8.720562 CCAAGTTTTGAAGACTTTCACAAAAAT 58.279 29.630 12.37 9.87 42.79 1.82
3406 3463 7.928706 TCCAAGTTTTGAAGACTTTCACAAAAA 59.071 29.630 12.37 3.57 42.79 1.94
3407 3464 7.437748 TCCAAGTTTTGAAGACTTTCACAAAA 58.562 30.769 0.00 8.46 42.79 2.44
3408 3465 6.987386 TCCAAGTTTTGAAGACTTTCACAAA 58.013 32.000 0.00 0.00 42.79 2.83
3409 3466 6.582677 TCCAAGTTTTGAAGACTTTCACAA 57.417 33.333 0.00 0.00 42.79 3.33
3410 3467 6.208599 ACTTCCAAGTTTTGAAGACTTTCACA 59.791 34.615 15.51 0.00 38.36 3.58
3411 3468 6.621613 ACTTCCAAGTTTTGAAGACTTTCAC 58.378 36.000 15.51 0.00 38.36 3.18
3412 3469 6.834168 ACTTCCAAGTTTTGAAGACTTTCA 57.166 33.333 15.51 0.00 37.48 2.69
3426 3483 7.175990 TGTTGTTTGTCTTCTAAACTTCCAAGT 59.824 33.333 0.00 0.00 42.04 3.16
3427 3484 7.535139 TGTTGTTTGTCTTCTAAACTTCCAAG 58.465 34.615 0.00 0.00 38.50 3.61
3428 3485 7.392113 TCTGTTGTTTGTCTTCTAAACTTCCAA 59.608 33.333 0.00 0.00 38.50 3.53
3429 3486 6.882140 TCTGTTGTTTGTCTTCTAAACTTCCA 59.118 34.615 0.00 0.00 38.50 3.53
3430 3487 7.316544 TCTGTTGTTTGTCTTCTAAACTTCC 57.683 36.000 0.00 0.00 38.50 3.46
3431 3488 9.788960 ATTTCTGTTGTTTGTCTTCTAAACTTC 57.211 29.630 0.00 0.00 38.50 3.01
3436 3493 9.403583 AGGTTATTTCTGTTGTTTGTCTTCTAA 57.596 29.630 0.00 0.00 0.00 2.10
3437 3494 8.974060 AGGTTATTTCTGTTGTTTGTCTTCTA 57.026 30.769 0.00 0.00 0.00 2.10
3438 3495 7.881775 AGGTTATTTCTGTTGTTTGTCTTCT 57.118 32.000 0.00 0.00 0.00 2.85
3439 3496 8.837389 ACTAGGTTATTTCTGTTGTTTGTCTTC 58.163 33.333 0.00 0.00 0.00 2.87
3440 3497 8.747538 ACTAGGTTATTTCTGTTGTTTGTCTT 57.252 30.769 0.00 0.00 0.00 3.01
3441 3498 8.621286 CAACTAGGTTATTTCTGTTGTTTGTCT 58.379 33.333 0.00 0.00 32.70 3.41
3442 3499 8.617809 TCAACTAGGTTATTTCTGTTGTTTGTC 58.382 33.333 0.00 0.00 36.93 3.18
3443 3500 8.514330 TCAACTAGGTTATTTCTGTTGTTTGT 57.486 30.769 0.00 0.00 36.93 2.83
3447 3504 8.893727 GCATATCAACTAGGTTATTTCTGTTGT 58.106 33.333 0.00 0.00 36.93 3.32
3448 3505 8.892723 TGCATATCAACTAGGTTATTTCTGTTG 58.107 33.333 0.00 0.00 36.93 3.33
3449 3506 9.113838 CTGCATATCAACTAGGTTATTTCTGTT 57.886 33.333 0.00 0.00 0.00 3.16
3450 3507 7.227512 GCTGCATATCAACTAGGTTATTTCTGT 59.772 37.037 0.00 0.00 0.00 3.41
3451 3508 7.570140 CGCTGCATATCAACTAGGTTATTTCTG 60.570 40.741 0.00 0.00 0.00 3.02
3452 3509 6.425114 CGCTGCATATCAACTAGGTTATTTCT 59.575 38.462 0.00 0.00 0.00 2.52
3453 3510 6.347725 CCGCTGCATATCAACTAGGTTATTTC 60.348 42.308 0.00 0.00 0.00 2.17
3454 3511 5.470098 CCGCTGCATATCAACTAGGTTATTT 59.530 40.000 0.00 0.00 0.00 1.40
3455 3512 4.997395 CCGCTGCATATCAACTAGGTTATT 59.003 41.667 0.00 0.00 0.00 1.40
3456 3513 4.283467 TCCGCTGCATATCAACTAGGTTAT 59.717 41.667 0.00 0.00 0.00 1.89
3457 3514 3.639561 TCCGCTGCATATCAACTAGGTTA 59.360 43.478 0.00 0.00 0.00 2.85
3458 3515 2.434336 TCCGCTGCATATCAACTAGGTT 59.566 45.455 0.00 0.00 0.00 3.50
3459 3516 2.039418 TCCGCTGCATATCAACTAGGT 58.961 47.619 0.00 0.00 0.00 3.08
3460 3517 2.820059 TCCGCTGCATATCAACTAGG 57.180 50.000 0.00 0.00 0.00 3.02
3461 3518 3.982475 TCTTCCGCTGCATATCAACTAG 58.018 45.455 0.00 0.00 0.00 2.57
3462 3519 4.607293 ATCTTCCGCTGCATATCAACTA 57.393 40.909 0.00 0.00 0.00 2.24
3463 3520 2.988010 TCTTCCGCTGCATATCAACT 57.012 45.000 0.00 0.00 0.00 3.16
3464 3521 5.237344 AGTTTATCTTCCGCTGCATATCAAC 59.763 40.000 0.00 0.00 0.00 3.18
3465 3522 5.368145 AGTTTATCTTCCGCTGCATATCAA 58.632 37.500 0.00 0.00 0.00 2.57
3466 3523 4.960938 AGTTTATCTTCCGCTGCATATCA 58.039 39.130 0.00 0.00 0.00 2.15
3467 3524 5.348997 GGTAGTTTATCTTCCGCTGCATATC 59.651 44.000 0.00 0.00 0.00 1.63
3468 3525 5.012148 AGGTAGTTTATCTTCCGCTGCATAT 59.988 40.000 0.00 0.00 38.42 1.78
3469 3526 4.344102 AGGTAGTTTATCTTCCGCTGCATA 59.656 41.667 0.00 0.00 38.42 3.14
3470 3527 3.134804 AGGTAGTTTATCTTCCGCTGCAT 59.865 43.478 0.00 0.00 38.42 3.96
3471 3528 2.500098 AGGTAGTTTATCTTCCGCTGCA 59.500 45.455 0.00 0.00 38.42 4.41
3472 3529 3.180891 AGGTAGTTTATCTTCCGCTGC 57.819 47.619 0.00 0.00 38.42 5.25
3473 3530 5.234543 GCTTAAGGTAGTTTATCTTCCGCTG 59.765 44.000 4.29 0.00 38.42 5.18
3474 3531 5.358090 GCTTAAGGTAGTTTATCTTCCGCT 58.642 41.667 4.29 0.00 38.42 5.52
3475 3532 4.208666 CGCTTAAGGTAGTTTATCTTCCGC 59.791 45.833 4.29 0.00 38.42 5.54
3476 3533 5.585390 TCGCTTAAGGTAGTTTATCTTCCG 58.415 41.667 4.29 0.00 38.42 4.30
3477 3534 5.462729 GCTCGCTTAAGGTAGTTTATCTTCC 59.537 44.000 4.29 0.00 34.39 3.46
3478 3535 5.462729 GGCTCGCTTAAGGTAGTTTATCTTC 59.537 44.000 4.29 0.00 30.42 2.87
3479 3536 5.105064 TGGCTCGCTTAAGGTAGTTTATCTT 60.105 40.000 4.29 0.00 32.93 2.40
3480 3537 4.404715 TGGCTCGCTTAAGGTAGTTTATCT 59.595 41.667 4.29 0.00 0.00 1.98
3481 3538 4.690122 TGGCTCGCTTAAGGTAGTTTATC 58.310 43.478 4.29 0.00 0.00 1.75
3482 3539 4.748277 TGGCTCGCTTAAGGTAGTTTAT 57.252 40.909 4.29 0.00 0.00 1.40
3483 3540 4.748277 ATGGCTCGCTTAAGGTAGTTTA 57.252 40.909 4.29 0.00 0.00 2.01
3484 3541 3.629142 ATGGCTCGCTTAAGGTAGTTT 57.371 42.857 4.29 0.00 0.00 2.66
3485 3542 3.705072 ACTATGGCTCGCTTAAGGTAGTT 59.295 43.478 4.29 0.00 0.00 2.24
3486 3543 3.297736 ACTATGGCTCGCTTAAGGTAGT 58.702 45.455 4.29 0.00 0.00 2.73
3487 3544 3.318275 TGACTATGGCTCGCTTAAGGTAG 59.682 47.826 4.29 0.00 0.00 3.18
3488 3545 3.293337 TGACTATGGCTCGCTTAAGGTA 58.707 45.455 4.29 0.00 0.00 3.08
3489 3546 2.108168 TGACTATGGCTCGCTTAAGGT 58.892 47.619 4.29 0.00 0.00 3.50
3490 3547 2.890808 TGACTATGGCTCGCTTAAGG 57.109 50.000 4.29 0.00 0.00 2.69
3491 3548 3.786635 ACTTGACTATGGCTCGCTTAAG 58.213 45.455 0.00 0.00 0.00 1.85
3492 3549 3.887621 ACTTGACTATGGCTCGCTTAA 57.112 42.857 0.00 0.00 0.00 1.85
3493 3550 4.796290 GCATACTTGACTATGGCTCGCTTA 60.796 45.833 0.00 0.00 0.00 3.09
3494 3551 3.722147 CATACTTGACTATGGCTCGCTT 58.278 45.455 0.00 0.00 0.00 4.68
3495 3552 2.546795 GCATACTTGACTATGGCTCGCT 60.547 50.000 0.00 0.00 0.00 4.93
3496 3553 1.795286 GCATACTTGACTATGGCTCGC 59.205 52.381 0.00 0.00 0.00 5.03
3497 3554 3.097877 TGCATACTTGACTATGGCTCG 57.902 47.619 0.00 0.00 0.00 5.03
3498 3555 5.059161 TCATTGCATACTTGACTATGGCTC 58.941 41.667 0.00 0.00 0.00 4.70
3499 3556 5.039920 TCATTGCATACTTGACTATGGCT 57.960 39.130 0.00 0.00 0.00 4.75
3500 3557 5.240183 ACATCATTGCATACTTGACTATGGC 59.760 40.000 0.00 0.00 0.00 4.40
3501 3558 6.484308 TCACATCATTGCATACTTGACTATGG 59.516 38.462 0.00 0.00 0.00 2.74
3502 3559 7.486802 TCACATCATTGCATACTTGACTATG 57.513 36.000 0.00 0.00 0.00 2.23
3503 3560 8.510243 TTTCACATCATTGCATACTTGACTAT 57.490 30.769 0.00 0.00 0.00 2.12
3504 3561 7.607607 ACTTTCACATCATTGCATACTTGACTA 59.392 33.333 0.00 0.00 0.00 2.59
3505 3562 6.432162 ACTTTCACATCATTGCATACTTGACT 59.568 34.615 0.00 0.00 0.00 3.41
3506 3563 6.615088 ACTTTCACATCATTGCATACTTGAC 58.385 36.000 0.00 0.00 0.00 3.18
3507 3564 6.822667 ACTTTCACATCATTGCATACTTGA 57.177 33.333 0.00 0.00 0.00 3.02
3508 3565 7.529158 TGTACTTTCACATCATTGCATACTTG 58.471 34.615 0.00 0.00 0.00 3.16
3509 3566 7.686438 TGTACTTTCACATCATTGCATACTT 57.314 32.000 0.00 0.00 0.00 2.24
3510 3567 7.312657 CTGTACTTTCACATCATTGCATACT 57.687 36.000 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.