Multiple sequence alignment - TraesCS2B01G323200

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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 TraesCS2B01G323200 chr2B 100.000 4619 0 0 1 4619 461982381 461977763 0.000000e+00 8530
1 TraesCS2B01G323200 chr2B 92.322 521 29 7 4110 4619 526409925 526409405 0.000000e+00 730
2 TraesCS2B01G323200 chr2B 92.131 521 30 2 4110 4619 779269635 779269115 0.000000e+00 725
3 TraesCS2B01G323200 chr2B 90.613 522 37 4 4110 4619 443225186 443225707 0.000000e+00 682
4 TraesCS2B01G323200 chr2D 96.419 2318 67 6 1367 3671 390732749 390730435 0.000000e+00 3807
5 TraesCS2B01G323200 chr2D 97.849 1348 27 2 1 1347 390734079 390732733 0.000000e+00 2327
6 TraesCS2B01G323200 chr2A 93.170 1713 78 14 2365 4059 527459277 527457586 0.000000e+00 2479
7 TraesCS2B01G323200 chr2A 97.923 1348 25 3 1 1347 527462356 527461011 0.000000e+00 2331
8 TraesCS2B01G323200 chr2A 97.168 1024 19 3 1367 2383 527461027 527460007 0.000000e+00 1722
9 TraesCS2B01G323200 chr2A 90.548 529 37 4 4103 4619 161927015 161926488 0.000000e+00 688
10 TraesCS2B01G323200 chr7A 93.295 522 23 5 4110 4619 460754503 460753982 0.000000e+00 760
11 TraesCS2B01G323200 chr7A 92.337 522 28 5 4110 4619 201995937 201995416 0.000000e+00 732
12 TraesCS2B01G323200 chr7B 92.514 521 28 7 4110 4619 504236927 504236407 0.000000e+00 736
13 TraesCS2B01G323200 chr3A 92.514 521 28 2 4110 4619 24795152 24794632 0.000000e+00 736
14 TraesCS2B01G323200 chr3A 91.954 522 30 5 4110 4619 655513899 655513378 0.000000e+00 721
15 TraesCS2B01G323200 chr3A 90.975 277 15 1 4110 4376 142038142 142038418 9.440000e-97 364
16 TraesCS2B01G323200 chr5A 91.954 522 30 5 4110 4619 407776485 407777006 0.000000e+00 721
17 TraesCS2B01G323200 chr5A 91.684 481 28 5 4151 4619 480383263 480383743 0.000000e+00 656
18 TraesCS2B01G323200 chr5B 91.188 522 34 4 4110 4619 82155633 82155112 0.000000e+00 699
19 TraesCS2B01G323200 chr3B 89.372 207 12 4 4110 4306 182291337 182291543 7.670000e-63 252
20 TraesCS2B01G323200 chr1D 88.889 207 13 2 4110 4306 106844996 106845202 3.570000e-61 246
21 TraesCS2B01G323200 chr3D 95.652 115 5 0 4110 4224 175660704 175660818 7.890000e-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 TraesCS2B01G323200 chr2B 461977763 461982381 4618 True 8530.000000 8530 100.000 1 4619 1 chr2B.!!$R1 4618
1 TraesCS2B01G323200 chr2B 526409405 526409925 520 True 730.000000 730 92.322 4110 4619 1 chr2B.!!$R2 509
2 TraesCS2B01G323200 chr2B 779269115 779269635 520 True 725.000000 725 92.131 4110 4619 1 chr2B.!!$R3 509
3 TraesCS2B01G323200 chr2B 443225186 443225707 521 False 682.000000 682 90.613 4110 4619 1 chr2B.!!$F1 509
4 TraesCS2B01G323200 chr2D 390730435 390734079 3644 True 3067.000000 3807 97.134 1 3671 2 chr2D.!!$R1 3670
5 TraesCS2B01G323200 chr2A 527457586 527462356 4770 True 2177.333333 2479 96.087 1 4059 3 chr2A.!!$R2 4058
6 TraesCS2B01G323200 chr2A 161926488 161927015 527 True 688.000000 688 90.548 4103 4619 1 chr2A.!!$R1 516
7 TraesCS2B01G323200 chr7A 460753982 460754503 521 True 760.000000 760 93.295 4110 4619 1 chr7A.!!$R2 509
8 TraesCS2B01G323200 chr7A 201995416 201995937 521 True 732.000000 732 92.337 4110 4619 1 chr7A.!!$R1 509
9 TraesCS2B01G323200 chr7B 504236407 504236927 520 True 736.000000 736 92.514 4110 4619 1 chr7B.!!$R1 509
10 TraesCS2B01G323200 chr3A 24794632 24795152 520 True 736.000000 736 92.514 4110 4619 1 chr3A.!!$R1 509
11 TraesCS2B01G323200 chr3A 655513378 655513899 521 True 721.000000 721 91.954 4110 4619 1 chr3A.!!$R2 509
12 TraesCS2B01G323200 chr5A 407776485 407777006 521 False 721.000000 721 91.954 4110 4619 1 chr5A.!!$F1 509
13 TraesCS2B01G323200 chr5B 82155112 82155633 521 True 699.000000 699 91.188 4110 4619 1 chr5B.!!$R1 509

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
307 308 3.133542 CAGATGCAGATGAGTAGGGTGAA 59.866 47.826 0.0 0.0 0.0 3.18 F
1055 1057 0.389166 GTCGTGGTCCTTCTGCTCTG 60.389 60.000 0.0 0.0 0.0 3.35 F
1723 1731 0.670546 ACGCTCCATCGGTGACAAAG 60.671 55.000 0.0 0.0 0.0 2.77 F
2099 2107 0.798776 CATTCTCGTGGGTGTGCTTC 59.201 55.000 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2081 2089 0.687354 AGAAGCACACCCACGAGAAT 59.313 50.0 0.0 0.0 0.00 2.40 R
2207 2215 1.195442 TATGGTTGGTCGGGTCTGCA 61.195 55.0 0.0 0.0 0.00 4.41 R
3310 4068 0.038251 TGCTCTACCACAGAAGTGCG 60.038 55.0 0.0 0.0 44.53 5.34 R
3661 4423 0.248866 GGCACCAGAACAAAACACGG 60.249 55.0 0.0 0.0 0.00 4.94 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
307 308 3.133542 CAGATGCAGATGAGTAGGGTGAA 59.866 47.826 0.00 0.00 0.00 3.18
421 422 3.394940 AGATCATGGATGATGCAGAACCT 59.605 43.478 6.85 0.00 46.84 3.50
464 465 6.127647 TGGCAAAATGATTCTAAGTGATCCAC 60.128 38.462 0.00 0.00 34.10 4.02
622 624 6.370442 TGATTACTTATTTTGGACTCGGTGTG 59.630 38.462 0.00 0.00 0.00 3.82
820 822 3.405831 CAAAGTTCAGGAGCATGAGTCA 58.594 45.455 0.00 0.00 0.00 3.41
1055 1057 0.389166 GTCGTGGTCCTTCTGCTCTG 60.389 60.000 0.00 0.00 0.00 3.35
1344 1346 5.069318 TGTCTTACCATGAAAGATGCAACA 58.931 37.500 11.98 5.07 35.53 3.33
1345 1347 5.048782 TGTCTTACCATGAAAGATGCAACAC 60.049 40.000 11.98 2.00 35.53 3.32
1346 1348 5.182001 GTCTTACCATGAAAGATGCAACACT 59.818 40.000 11.98 0.00 35.53 3.55
1347 1349 5.412594 TCTTACCATGAAAGATGCAACACTC 59.587 40.000 0.00 0.00 0.00 3.51
1348 1350 3.759581 ACCATGAAAGATGCAACACTCT 58.240 40.909 0.00 0.00 0.00 3.24
1349 1351 3.755378 ACCATGAAAGATGCAACACTCTC 59.245 43.478 0.00 0.00 0.00 3.20
1350 1352 4.008330 CCATGAAAGATGCAACACTCTCT 58.992 43.478 0.00 0.00 0.00 3.10
1351 1353 4.458295 CCATGAAAGATGCAACACTCTCTT 59.542 41.667 0.00 0.00 0.00 2.85
1352 1354 5.048224 CCATGAAAGATGCAACACTCTCTTT 60.048 40.000 9.83 9.83 39.86 2.52
1354 1356 5.679734 GAAAGATGCAACACTCTCTTTCA 57.320 39.130 23.70 0.00 46.57 2.69
1355 1357 6.064846 GAAAGATGCAACACTCTCTTTCAA 57.935 37.500 23.70 0.00 46.57 2.69
1356 1358 6.455360 AAAGATGCAACACTCTCTTTCAAA 57.545 33.333 5.15 0.00 33.79 2.69
1357 1359 6.455360 AAGATGCAACACTCTCTTTCAAAA 57.545 33.333 0.00 0.00 0.00 2.44
1358 1360 6.455360 AGATGCAACACTCTCTTTCAAAAA 57.545 33.333 0.00 0.00 0.00 1.94
1359 1361 7.047460 AGATGCAACACTCTCTTTCAAAAAT 57.953 32.000 0.00 0.00 0.00 1.82
1360 1362 8.169977 AGATGCAACACTCTCTTTCAAAAATA 57.830 30.769 0.00 0.00 0.00 1.40
1361 1363 8.632679 AGATGCAACACTCTCTTTCAAAAATAA 58.367 29.630 0.00 0.00 0.00 1.40
1362 1364 9.248291 GATGCAACACTCTCTTTCAAAAATAAA 57.752 29.630 0.00 0.00 0.00 1.40
1363 1365 9.768662 ATGCAACACTCTCTTTCAAAAATAAAT 57.231 25.926 0.00 0.00 0.00 1.40
1407 1415 1.707117 CACTGAGACGTACGTTTGTCG 59.293 52.381 23.70 16.08 46.00 4.35
1419 1427 5.051574 CGTACGTTTGTCGATGCCATTTATA 60.052 40.000 7.22 0.00 42.86 0.98
1600 1608 1.079438 AGGAAAGGAGGGAGCGACT 59.921 57.895 0.00 0.00 0.00 4.18
1716 1724 4.148825 GCCTCACGCTCCATCGGT 62.149 66.667 0.00 0.00 0.00 4.69
1723 1731 0.670546 ACGCTCCATCGGTGACAAAG 60.671 55.000 0.00 0.00 0.00 2.77
1724 1732 1.361668 CGCTCCATCGGTGACAAAGG 61.362 60.000 0.00 0.00 0.00 3.11
1725 1733 1.026718 GCTCCATCGGTGACAAAGGG 61.027 60.000 0.00 0.00 0.00 3.95
1772 1780 1.401409 CCTACCGCATTTGTGCAGTTG 60.401 52.381 1.08 0.00 34.41 3.16
2081 2089 3.318839 CCTTTTCATTGCTGGTCACTTCA 59.681 43.478 0.00 0.00 0.00 3.02
2099 2107 0.798776 CATTCTCGTGGGTGTGCTTC 59.201 55.000 0.00 0.00 0.00 3.86
2122 2130 3.314080 TGCTTGTACACTAAAACACCAGC 59.686 43.478 0.00 0.00 32.54 4.85
2134 2142 8.686334 CACTAAAACACCAGCCATCTATAATTT 58.314 33.333 0.00 0.00 0.00 1.82
2207 2215 5.121380 TCCCTACTGTAGTTACCTTCGAT 57.879 43.478 13.42 0.00 0.00 3.59
2390 3147 9.905713 TTAGCTCAATTCTTTACCTACATCATT 57.094 29.630 0.00 0.00 0.00 2.57
2433 3190 1.332686 TGAGATTGCATGAGCGCATTC 59.667 47.619 11.47 0.00 46.23 2.67
2436 3193 1.065102 GATTGCATGAGCGCATTCACT 59.935 47.619 11.47 0.00 46.23 3.41
2449 3206 4.601019 CGCATTCACTCTTTTCAGTTGTT 58.399 39.130 0.00 0.00 0.00 2.83
2852 3609 3.595190 TGAGGCCTAGTCTACTATGCA 57.405 47.619 4.42 0.00 40.41 3.96
3041 3799 3.915437 AAATGGTTCGTTCATGTCACC 57.085 42.857 0.00 0.00 0.00 4.02
3122 3880 3.327757 TCCTGTGGTGAAGCTTGTCTAAT 59.672 43.478 2.10 0.00 0.00 1.73
3123 3881 3.438087 CCTGTGGTGAAGCTTGTCTAATG 59.562 47.826 2.10 0.00 0.00 1.90
3131 3889 6.317857 GTGAAGCTTGTCTAATGAATTCACC 58.682 40.000 11.07 0.00 39.39 4.02
3221 3979 2.168521 CCGATTCTGGAGGAAGTTGCTA 59.831 50.000 0.00 0.00 37.36 3.49
3293 4051 8.359642 TCCACTTTTCAGTTGATTATTCCAAAG 58.640 33.333 0.00 0.00 0.00 2.77
3310 4068 5.540911 TCCAAAGAAATTGCAACTGATTCC 58.459 37.500 0.00 0.00 37.73 3.01
3391 4153 1.202417 AGGATGGTACTGCGAACGATG 60.202 52.381 0.00 0.00 0.00 3.84
3405 4167 0.966920 ACGATGTCCCGACAGACTTT 59.033 50.000 3.61 0.00 45.48 2.66
3474 4236 3.322254 GGGATCTCTTGATGTATGACGGT 59.678 47.826 0.00 0.00 32.19 4.83
3476 4238 4.551388 GATCTCTTGATGTATGACGGTCC 58.449 47.826 5.55 0.00 32.19 4.46
3477 4239 3.361786 TCTCTTGATGTATGACGGTCCA 58.638 45.455 5.55 0.00 0.00 4.02
3483 4245 1.634960 TGTATGACGGTCCAAGGACA 58.365 50.000 20.03 0.71 46.20 4.02
3489 4251 2.990479 GGTCCAAGGACAGCCGAT 59.010 61.111 20.03 0.00 46.20 4.18
3554 4316 3.118592 GCTGCAGTAGAAGTAACCCAGAT 60.119 47.826 16.64 0.00 0.00 2.90
3583 4345 5.680151 GCTGTAGAAGAGGAGGTAACATCAC 60.680 48.000 0.00 0.00 41.41 3.06
3618 4380 6.034683 CGGAGTCCGTTAAAGATGAACTTTAG 59.965 42.308 23.83 0.00 43.07 1.85
3650 4412 2.161410 TGCATCGTATGTGTCCTTTTGC 59.839 45.455 0.00 0.00 0.00 3.68
3656 4418 0.779997 ATGTGTCCTTTTGCTCCCCT 59.220 50.000 0.00 0.00 0.00 4.79
3657 4419 1.440618 TGTGTCCTTTTGCTCCCCTA 58.559 50.000 0.00 0.00 0.00 3.53
3659 4421 2.160205 GTGTCCTTTTGCTCCCCTAAC 58.840 52.381 0.00 0.00 0.00 2.34
3660 4422 2.062636 TGTCCTTTTGCTCCCCTAACT 58.937 47.619 0.00 0.00 0.00 2.24
3661 4423 2.039879 TGTCCTTTTGCTCCCCTAACTC 59.960 50.000 0.00 0.00 0.00 3.01
3665 4429 0.323629 TTTGCTCCCCTAACTCCGTG 59.676 55.000 0.00 0.00 0.00 4.94
3687 4451 0.396974 TTGTTCTGGTGCCCTTGCTT 60.397 50.000 0.00 0.00 38.71 3.91
3688 4452 1.108727 TGTTCTGGTGCCCTTGCTTG 61.109 55.000 0.00 0.00 38.71 4.01
3698 4462 1.928868 CCCTTGCTTGGTGAAATCCT 58.071 50.000 0.00 0.00 0.00 3.24
3702 4466 1.448985 TGCTTGGTGAAATCCTACGC 58.551 50.000 0.00 0.00 0.00 4.42
3711 4475 4.694037 GGTGAAATCCTACGCTTACAAGTT 59.306 41.667 0.00 0.00 0.00 2.66
3725 4489 5.276584 GCTTACAAGTTCATCTATCACGCAG 60.277 44.000 0.00 0.00 0.00 5.18
3749 4513 2.704596 AGCTGAGGATATCACACTGCAT 59.295 45.455 18.66 8.18 33.22 3.96
3756 4520 6.042638 AGGATATCACACTGCATGGTATAC 57.957 41.667 4.83 0.00 0.00 1.47
3761 4525 3.513515 TCACACTGCATGGTATACAGACA 59.486 43.478 5.01 0.00 35.38 3.41
3762 4526 4.162131 TCACACTGCATGGTATACAGACAT 59.838 41.667 5.01 0.00 35.38 3.06
3775 4539 1.627329 ACAGACATGAGTGCAGGATGT 59.373 47.619 0.00 5.13 39.31 3.06
3776 4540 2.039480 ACAGACATGAGTGCAGGATGTT 59.961 45.455 0.00 0.00 39.31 2.71
3785 4556 3.755378 GAGTGCAGGATGTTTGTTCAGAT 59.245 43.478 0.00 0.00 39.31 2.90
3793 4564 5.704515 AGGATGTTTGTTCAGATCAGTCTTG 59.295 40.000 0.00 0.00 30.42 3.02
3805 4576 3.667497 TCAGTCTTGGCTTAGTGACAG 57.333 47.619 0.00 0.00 33.66 3.51
3817 4588 5.302059 GGCTTAGTGACAGACCATACAGATA 59.698 44.000 0.00 0.00 0.00 1.98
3819 4590 6.183360 GCTTAGTGACAGACCATACAGATACA 60.183 42.308 0.00 0.00 0.00 2.29
3820 4591 5.843673 AGTGACAGACCATACAGATACAG 57.156 43.478 0.00 0.00 0.00 2.74
3821 4592 5.510430 AGTGACAGACCATACAGATACAGA 58.490 41.667 0.00 0.00 0.00 3.41
3822 4593 6.132658 AGTGACAGACCATACAGATACAGAT 58.867 40.000 0.00 0.00 0.00 2.90
3823 4594 6.609212 AGTGACAGACCATACAGATACAGATT 59.391 38.462 0.00 0.00 0.00 2.40
3824 4595 6.920758 GTGACAGACCATACAGATACAGATTC 59.079 42.308 0.00 0.00 0.00 2.52
3825 4596 6.836007 TGACAGACCATACAGATACAGATTCT 59.164 38.462 0.00 0.00 0.00 2.40
3826 4597 7.343057 TGACAGACCATACAGATACAGATTCTT 59.657 37.037 0.00 0.00 0.00 2.52
3827 4598 8.768501 ACAGACCATACAGATACAGATTCTTA 57.231 34.615 0.00 0.00 0.00 2.10
3828 4599 8.634444 ACAGACCATACAGATACAGATTCTTAC 58.366 37.037 0.00 0.00 0.00 2.34
3829 4600 8.085296 CAGACCATACAGATACAGATTCTTACC 58.915 40.741 0.00 0.00 0.00 2.85
3830 4601 7.785028 AGACCATACAGATACAGATTCTTACCA 59.215 37.037 0.00 0.00 0.00 3.25
3831 4602 7.957002 ACCATACAGATACAGATTCTTACCAG 58.043 38.462 0.00 0.00 0.00 4.00
3832 4603 7.565398 ACCATACAGATACAGATTCTTACCAGT 59.435 37.037 0.00 0.00 0.00 4.00
3840 4611 3.123621 CAGATTCTTACCAGTCGTTGCAC 59.876 47.826 0.00 0.00 0.00 4.57
3850 4621 1.603802 AGTCGTTGCACTGTGGATTTG 59.396 47.619 10.21 0.04 0.00 2.32
3872 4643 4.646945 TGTGATGCCTAAACACCTTTGAAA 59.353 37.500 0.00 0.00 34.18 2.69
3895 4666 2.959465 ATAAGCTTCATGTAGCCCCC 57.041 50.000 19.45 0.00 42.20 5.40
3897 4668 1.002857 AAGCTTCATGTAGCCCCCTT 58.997 50.000 19.45 5.80 42.20 3.95
3899 4670 1.359130 AGCTTCATGTAGCCCCCTTTT 59.641 47.619 19.45 0.00 42.20 2.27
3900 4671 2.580783 AGCTTCATGTAGCCCCCTTTTA 59.419 45.455 19.45 0.00 42.20 1.52
3902 4673 3.960755 GCTTCATGTAGCCCCCTTTTATT 59.039 43.478 12.98 0.00 35.06 1.40
3904 4675 5.451937 GCTTCATGTAGCCCCCTTTTATTTC 60.452 44.000 12.98 0.00 35.06 2.17
3907 4678 4.618378 TGTAGCCCCCTTTTATTTCCAT 57.382 40.909 0.00 0.00 0.00 3.41
3924 4695 5.643379 TTCCATCTCCTATTTTGTGCAAC 57.357 39.130 0.00 0.00 37.35 4.17
3931 4702 2.610232 CCTATTTTGTGCAACCAGGTGC 60.610 50.000 0.00 0.00 45.15 5.01
3938 4709 1.202348 GTGCAACCAGGTGCCTTATTC 59.798 52.381 5.00 0.00 44.26 1.75
3947 4722 5.132502 CCAGGTGCCTTATTCATGAATGTA 58.867 41.667 27.59 15.69 32.50 2.29
3954 4729 9.585099 GTGCCTTATTCATGAATGTATTTTCAA 57.415 29.630 27.59 12.26 38.98 2.69
3981 4756 6.353323 TGAGGAATTCAACAAAGTAGACACA 58.647 36.000 7.93 0.00 31.34 3.72
3983 4758 7.502226 TGAGGAATTCAACAAAGTAGACACAAT 59.498 33.333 7.93 0.00 31.34 2.71
3984 4759 8.918202 AGGAATTCAACAAAGTAGACACAATA 57.082 30.769 7.93 0.00 0.00 1.90
4035 4810 1.756538 CTTATGAATTGTGCCCACCCC 59.243 52.381 0.00 0.00 0.00 4.95
4036 4811 0.395036 TATGAATTGTGCCCACCCCG 60.395 55.000 0.00 0.00 0.00 5.73
4043 4818 2.529643 TGCCCACCCCGAACCTTA 60.530 61.111 0.00 0.00 0.00 2.69
4046 4821 2.271173 CCACCCCGAACCTTAGCC 59.729 66.667 0.00 0.00 0.00 3.93
4050 4825 2.125269 CCCGAACCTTAGCCACGG 60.125 66.667 0.00 0.00 42.67 4.94
4059 4834 0.108585 CTTAGCCACGGCCACCATAT 59.891 55.000 2.24 0.00 43.17 1.78
4060 4835 0.548989 TTAGCCACGGCCACCATATT 59.451 50.000 2.24 0.00 43.17 1.28
4061 4836 0.179032 TAGCCACGGCCACCATATTG 60.179 55.000 2.24 0.00 43.17 1.90
4062 4837 1.752694 GCCACGGCCACCATATTGT 60.753 57.895 2.24 0.00 34.56 2.71
4063 4838 2.003658 GCCACGGCCACCATATTGTG 62.004 60.000 2.24 0.00 35.98 3.33
4064 4839 0.393673 CCACGGCCACCATATTGTGA 60.394 55.000 8.47 0.00 38.55 3.58
4065 4840 0.732571 CACGGCCACCATATTGTGAC 59.267 55.000 8.47 0.00 38.55 3.67
4066 4841 0.393808 ACGGCCACCATATTGTGACC 60.394 55.000 8.47 5.41 38.55 4.02
4067 4842 0.393673 CGGCCACCATATTGTGACCA 60.394 55.000 11.95 0.00 38.56 4.02
4068 4843 1.750332 CGGCCACCATATTGTGACCAT 60.750 52.381 11.95 0.00 38.56 3.55
4069 4844 1.682854 GGCCACCATATTGTGACCATG 59.317 52.381 8.47 0.00 38.52 3.66
4070 4845 1.067516 GCCACCATATTGTGACCATGC 59.932 52.381 8.47 0.00 38.55 4.06
4071 4846 1.682854 CCACCATATTGTGACCATGCC 59.317 52.381 8.47 0.00 38.55 4.40
4072 4847 2.377073 CACCATATTGTGACCATGCCA 58.623 47.619 0.56 0.00 38.55 4.92
4073 4848 2.960384 CACCATATTGTGACCATGCCAT 59.040 45.455 0.56 0.00 38.55 4.40
4074 4849 3.005050 CACCATATTGTGACCATGCCATC 59.995 47.826 0.56 0.00 38.55 3.51
4075 4850 3.117398 ACCATATTGTGACCATGCCATCT 60.117 43.478 0.00 0.00 0.00 2.90
4076 4851 3.504906 CCATATTGTGACCATGCCATCTC 59.495 47.826 0.00 0.00 0.00 2.75
4077 4852 2.812836 ATTGTGACCATGCCATCTCA 57.187 45.000 0.00 0.00 0.00 3.27
4078 4853 2.583024 TTGTGACCATGCCATCTCAA 57.417 45.000 0.00 0.00 0.00 3.02
4079 4854 2.583024 TGTGACCATGCCATCTCAAA 57.417 45.000 0.00 0.00 0.00 2.69
4080 4855 2.161855 TGTGACCATGCCATCTCAAAC 58.838 47.619 0.00 0.00 0.00 2.93
4081 4856 1.131126 GTGACCATGCCATCTCAAACG 59.869 52.381 0.00 0.00 0.00 3.60
4082 4857 1.003003 TGACCATGCCATCTCAAACGA 59.997 47.619 0.00 0.00 0.00 3.85
4083 4858 1.398390 GACCATGCCATCTCAAACGAC 59.602 52.381 0.00 0.00 0.00 4.34
4084 4859 1.003580 ACCATGCCATCTCAAACGACT 59.996 47.619 0.00 0.00 0.00 4.18
4085 4860 2.086869 CCATGCCATCTCAAACGACTT 58.913 47.619 0.00 0.00 0.00 3.01
4086 4861 2.489329 CCATGCCATCTCAAACGACTTT 59.511 45.455 0.00 0.00 0.00 2.66
4087 4862 3.426695 CCATGCCATCTCAAACGACTTTC 60.427 47.826 0.00 0.00 0.00 2.62
4088 4863 2.844946 TGCCATCTCAAACGACTTTCA 58.155 42.857 0.00 0.00 0.00 2.69
4089 4864 3.411446 TGCCATCTCAAACGACTTTCAT 58.589 40.909 0.00 0.00 0.00 2.57
4090 4865 3.189080 TGCCATCTCAAACGACTTTCATG 59.811 43.478 0.00 0.00 0.00 3.07
4091 4866 3.436704 GCCATCTCAAACGACTTTCATGA 59.563 43.478 0.00 0.00 0.00 3.07
4092 4867 4.083324 GCCATCTCAAACGACTTTCATGAA 60.083 41.667 3.38 3.38 0.00 2.57
4093 4868 5.562696 GCCATCTCAAACGACTTTCATGAAA 60.563 40.000 19.45 19.45 0.00 2.69
4178 4953 9.722184 AAGGAGGAGAGTTTTAAAGTACATAAC 57.278 33.333 0.00 0.00 0.00 1.89
4251 5038 3.041211 TGATAATGCTCAGGTGCCTAGT 58.959 45.455 0.00 0.00 0.00 2.57
4264 5051 0.889306 GCCTAGTTCCTGTCGTGACT 59.111 55.000 1.23 0.00 0.00 3.41
4269 5056 2.822764 AGTTCCTGTCGTGACTCAAAC 58.177 47.619 1.23 3.40 0.00 2.93
4273 5060 3.869065 TCCTGTCGTGACTCAAACTTTT 58.131 40.909 1.23 0.00 0.00 2.27
4396 5183 0.709992 TAAGGGAAGCCATGGCCTTT 59.290 50.000 33.14 21.83 43.17 3.11
4397 5184 0.178894 AAGGGAAGCCATGGCCTTTT 60.179 50.000 33.14 21.04 43.17 2.27
4510 5297 4.082125 CAAGCCACTCCTTTACCAATCTT 58.918 43.478 0.00 0.00 0.00 2.40
4564 5352 3.400590 GCGCGGACGTCTCGTTTT 61.401 61.111 23.68 0.00 41.37 2.43
4590 5378 3.652687 CAGAGGGTGCATAGGCCT 58.347 61.111 11.78 11.78 40.13 5.19
4614 5402 0.251832 TCTCCCAACCTCGCTTCTCT 60.252 55.000 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
307 308 5.009710 CCATCAGCATTTTCAGCATCTACAT 59.990 40.000 0.00 0.00 0.00 2.29
421 422 5.287674 TGCCATTTTTCTTTTCATCACCA 57.712 34.783 0.00 0.00 0.00 4.17
475 476 0.103572 CCAAGCAAAACTGCTGCACT 59.896 50.000 0.00 0.00 45.54 4.40
820 822 3.254411 GGCTTGTTTGCTAGCTTCTCTTT 59.746 43.478 17.23 0.00 41.90 2.52
1137 1139 3.177884 TGCTTGGCCACCACCTCT 61.178 61.111 3.88 0.00 30.78 3.69
1362 1364 9.399797 TGTCTCAGTATTGCATCTTTCATTTAT 57.600 29.630 0.00 0.00 0.00 1.40
1363 1365 8.668353 GTGTCTCAGTATTGCATCTTTCATTTA 58.332 33.333 0.00 0.00 0.00 1.40
1364 1366 7.392673 AGTGTCTCAGTATTGCATCTTTCATTT 59.607 33.333 0.00 0.00 0.00 2.32
1365 1367 6.883217 AGTGTCTCAGTATTGCATCTTTCATT 59.117 34.615 0.00 0.00 0.00 2.57
1366 1368 6.315642 CAGTGTCTCAGTATTGCATCTTTCAT 59.684 38.462 0.00 0.00 0.00 2.57
1367 1369 5.640783 CAGTGTCTCAGTATTGCATCTTTCA 59.359 40.000 0.00 0.00 0.00 2.69
1368 1370 5.871524 TCAGTGTCTCAGTATTGCATCTTTC 59.128 40.000 0.00 0.00 0.00 2.62
1369 1371 5.798132 TCAGTGTCTCAGTATTGCATCTTT 58.202 37.500 0.00 0.00 0.00 2.52
1370 1372 5.186603 TCTCAGTGTCTCAGTATTGCATCTT 59.813 40.000 0.00 0.00 0.00 2.40
1371 1373 4.708909 TCTCAGTGTCTCAGTATTGCATCT 59.291 41.667 0.00 0.00 0.00 2.90
1372 1374 4.803088 GTCTCAGTGTCTCAGTATTGCATC 59.197 45.833 0.00 0.00 0.00 3.91
1373 1375 4.676459 CGTCTCAGTGTCTCAGTATTGCAT 60.676 45.833 0.00 0.00 0.00 3.96
1374 1376 3.366374 CGTCTCAGTGTCTCAGTATTGCA 60.366 47.826 0.00 0.00 0.00 4.08
1375 1377 3.175152 CGTCTCAGTGTCTCAGTATTGC 58.825 50.000 0.00 0.00 0.00 3.56
1376 1378 4.427096 ACGTCTCAGTGTCTCAGTATTG 57.573 45.455 0.00 0.00 0.00 1.90
1377 1379 4.093115 CGTACGTCTCAGTGTCTCAGTATT 59.907 45.833 7.22 0.00 0.00 1.89
1378 1380 3.617706 CGTACGTCTCAGTGTCTCAGTAT 59.382 47.826 7.22 0.00 0.00 2.12
1379 1381 2.991866 CGTACGTCTCAGTGTCTCAGTA 59.008 50.000 7.22 0.00 0.00 2.74
1407 1415 6.201997 TCACACGTACACATATAAATGGCATC 59.798 38.462 0.00 0.00 37.43 3.91
1419 1427 4.692228 TGCATCATATCACACGTACACAT 58.308 39.130 0.00 0.00 0.00 3.21
1600 1608 2.124736 GCCACCATAGGCGCTCAA 60.125 61.111 7.64 0.00 46.12 3.02
1725 1733 0.775542 AACTTACAAGGACCACCCCC 59.224 55.000 0.00 0.00 36.73 5.40
1772 1780 7.176589 TCAAGAGATTAAGGAAAGAGAGGTC 57.823 40.000 0.00 0.00 0.00 3.85
2081 2089 0.687354 AGAAGCACACCCACGAGAAT 59.313 50.000 0.00 0.00 0.00 2.40
2099 2107 4.554723 GCTGGTGTTTTAGTGTACAAGCAG 60.555 45.833 13.66 13.66 31.58 4.24
2134 2142 6.532988 TTGCATCATCATCAAAATCCTGAA 57.467 33.333 0.00 0.00 0.00 3.02
2150 2158 7.177216 ACCTCAATAAACTTCTTGATTGCATCA 59.823 33.333 0.00 0.00 37.55 3.07
2207 2215 1.195442 TATGGTTGGTCGGGTCTGCA 61.195 55.000 0.00 0.00 0.00 4.41
2383 3140 9.507329 GTTGGTCCTATGTTGATATAATGATGT 57.493 33.333 0.00 0.00 0.00 3.06
2390 3147 9.559732 CTCAAATGTTGGTCCTATGTTGATATA 57.440 33.333 0.00 0.00 0.00 0.86
2590 3347 2.030363 TGCGGTTGAAACATCACCAATC 60.030 45.455 0.00 0.00 0.00 2.67
3122 3880 0.608856 AGTGCCATGCGGTGAATTCA 60.609 50.000 3.38 3.38 33.28 2.57
3123 3881 0.527565 AAGTGCCATGCGGTGAATTC 59.472 50.000 0.00 0.00 33.28 2.17
3131 3889 1.442769 ACTACAAGAAGTGCCATGCG 58.557 50.000 0.00 0.00 0.00 4.73
3293 4051 2.663119 GTGCGGAATCAGTTGCAATTTC 59.337 45.455 0.59 4.27 39.34 2.17
3310 4068 0.038251 TGCTCTACCACAGAAGTGCG 60.038 55.000 0.00 0.00 44.53 5.34
3391 4153 2.027625 CCGCAAAGTCTGTCGGGAC 61.028 63.158 0.00 0.00 39.55 4.46
3405 4167 2.836360 GGGTATCCCTCGACCGCA 60.836 66.667 0.00 0.00 41.34 5.69
3474 4236 0.614697 TCTCATCGGCTGTCCTTGGA 60.615 55.000 0.00 0.00 0.00 3.53
3476 4238 1.137675 TGATCTCATCGGCTGTCCTTG 59.862 52.381 0.00 0.00 0.00 3.61
3477 4239 1.489481 TGATCTCATCGGCTGTCCTT 58.511 50.000 0.00 0.00 0.00 3.36
3489 4251 9.948964 TTCTTCTTGATAAAACTGATGATCTCA 57.051 29.630 0.00 0.00 0.00 3.27
3554 4316 2.292521 ACCTCCTCTTCTACAGCATCCA 60.293 50.000 0.00 0.00 0.00 3.41
3596 4358 7.439381 TGACTAAAGTTCATCTTTAACGGACT 58.561 34.615 0.00 0.00 44.68 3.85
3650 4412 2.224450 ACAAAACACGGAGTTAGGGGAG 60.224 50.000 0.00 0.00 41.61 4.30
3656 4418 3.623960 CACCAGAACAAAACACGGAGTTA 59.376 43.478 0.00 0.00 41.61 2.24
3657 4419 2.422127 CACCAGAACAAAACACGGAGTT 59.578 45.455 0.00 0.00 41.61 3.01
3659 4421 1.268539 GCACCAGAACAAAACACGGAG 60.269 52.381 0.00 0.00 0.00 4.63
3660 4422 0.736053 GCACCAGAACAAAACACGGA 59.264 50.000 0.00 0.00 0.00 4.69
3661 4423 0.248866 GGCACCAGAACAAAACACGG 60.249 55.000 0.00 0.00 0.00 4.94
3687 4451 3.965379 TGTAAGCGTAGGATTTCACCA 57.035 42.857 0.00 0.00 0.00 4.17
3688 4452 4.251268 ACTTGTAAGCGTAGGATTTCACC 58.749 43.478 0.00 0.00 0.00 4.02
3698 4462 5.969435 CGTGATAGATGAACTTGTAAGCGTA 59.031 40.000 0.00 0.00 0.00 4.42
3702 4466 5.233050 CCTGCGTGATAGATGAACTTGTAAG 59.767 44.000 0.00 0.00 0.00 2.34
3711 4475 2.515926 GCTTCCTGCGTGATAGATGA 57.484 50.000 0.00 0.00 0.00 2.92
3725 4489 3.726607 CAGTGTGATATCCTCAGCTTCC 58.273 50.000 0.00 0.00 33.51 3.46
3749 4513 3.132824 CCTGCACTCATGTCTGTATACCA 59.867 47.826 0.00 0.00 0.00 3.25
3756 4520 2.398252 ACATCCTGCACTCATGTCTG 57.602 50.000 0.00 0.00 0.00 3.51
3761 4525 3.489355 TGAACAAACATCCTGCACTCAT 58.511 40.909 0.00 0.00 0.00 2.90
3762 4526 2.880268 CTGAACAAACATCCTGCACTCA 59.120 45.455 0.00 0.00 0.00 3.41
3775 4539 4.090761 AGCCAAGACTGATCTGAACAAA 57.909 40.909 6.60 0.00 34.48 2.83
3776 4540 3.777106 AGCCAAGACTGATCTGAACAA 57.223 42.857 6.60 0.00 34.48 2.83
3785 4556 3.005897 GTCTGTCACTAAGCCAAGACTGA 59.994 47.826 0.00 0.00 36.86 3.41
3793 4564 3.447586 TCTGTATGGTCTGTCACTAAGCC 59.552 47.826 0.00 0.00 0.00 4.35
3805 4576 7.952671 TGGTAAGAATCTGTATCTGTATGGTC 58.047 38.462 0.00 0.00 0.00 4.02
3817 4588 3.244078 TGCAACGACTGGTAAGAATCTGT 60.244 43.478 0.00 0.00 0.00 3.41
3819 4590 3.006967 AGTGCAACGACTGGTAAGAATCT 59.993 43.478 0.00 0.00 45.86 2.40
3820 4591 3.123621 CAGTGCAACGACTGGTAAGAATC 59.876 47.826 0.00 0.00 45.86 2.52
3821 4592 3.067106 CAGTGCAACGACTGGTAAGAAT 58.933 45.455 0.00 0.00 45.86 2.40
3822 4593 2.159014 ACAGTGCAACGACTGGTAAGAA 60.159 45.455 6.95 0.00 46.56 2.52
3823 4594 1.411246 ACAGTGCAACGACTGGTAAGA 59.589 47.619 6.95 0.00 46.56 2.10
3824 4595 1.526887 CACAGTGCAACGACTGGTAAG 59.473 52.381 6.95 0.00 46.56 2.34
3825 4596 1.577468 CACAGTGCAACGACTGGTAA 58.423 50.000 6.95 0.00 46.56 2.85
3826 4597 0.249699 CCACAGTGCAACGACTGGTA 60.250 55.000 6.95 0.00 46.56 3.25
3827 4598 1.523711 CCACAGTGCAACGACTGGT 60.524 57.895 6.95 0.00 46.56 4.00
3828 4599 0.603707 ATCCACAGTGCAACGACTGG 60.604 55.000 6.95 0.00 46.56 4.00
3830 4601 1.603802 CAAATCCACAGTGCAACGACT 59.396 47.619 0.00 0.00 45.86 4.18
3831 4602 1.333619 ACAAATCCACAGTGCAACGAC 59.666 47.619 0.00 0.00 45.86 4.34
3832 4603 1.333308 CACAAATCCACAGTGCAACGA 59.667 47.619 0.00 0.00 45.86 3.85
3840 4611 4.218200 TGTTTAGGCATCACAAATCCACAG 59.782 41.667 0.00 0.00 0.00 3.66
3850 4621 4.846779 TTCAAAGGTGTTTAGGCATCAC 57.153 40.909 0.00 0.00 0.00 3.06
3872 4643 4.401925 GGGGCTACATGAAGCTTATTCAT 58.598 43.478 0.00 0.00 42.37 2.57
3895 4666 9.305925 GCACAAAATAGGAGATGGAAATAAAAG 57.694 33.333 0.00 0.00 0.00 2.27
3897 4668 8.359875 TGCACAAAATAGGAGATGGAAATAAA 57.640 30.769 0.00 0.00 0.00 1.40
3899 4670 7.147915 GGTTGCACAAAATAGGAGATGGAAATA 60.148 37.037 0.00 0.00 0.00 1.40
3900 4671 6.351286 GGTTGCACAAAATAGGAGATGGAAAT 60.351 38.462 0.00 0.00 0.00 2.17
3902 4673 4.462483 GGTTGCACAAAATAGGAGATGGAA 59.538 41.667 0.00 0.00 0.00 3.53
3904 4675 3.763360 TGGTTGCACAAAATAGGAGATGG 59.237 43.478 0.00 0.00 0.00 3.51
3907 4678 3.181434 ACCTGGTTGCACAAAATAGGAGA 60.181 43.478 12.90 0.00 0.00 3.71
3924 4695 3.956199 ACATTCATGAATAAGGCACCTGG 59.044 43.478 20.32 7.02 0.00 4.45
3954 4729 8.352942 GTGTCTACTTTGTTGAATTCCTCAATT 58.647 33.333 2.27 2.37 45.74 2.32
3981 4756 9.241317 CATTTTGCAGAGAAATAAAGCGATATT 57.759 29.630 0.00 0.00 0.00 1.28
3983 4758 7.148086 ACCATTTTGCAGAGAAATAAAGCGATA 60.148 33.333 0.00 0.00 0.00 2.92
3984 4759 6.038356 CCATTTTGCAGAGAAATAAAGCGAT 58.962 36.000 0.00 0.00 0.00 4.58
4035 4810 2.818274 GGCCGTGGCTAAGGTTCG 60.818 66.667 11.25 0.00 41.60 3.95
4036 4811 2.038837 GTGGCCGTGGCTAAGGTTC 61.039 63.158 11.25 0.00 41.60 3.62
4043 4818 1.453745 CAATATGGTGGCCGTGGCT 60.454 57.895 11.25 0.00 41.60 4.75
4046 4821 0.732571 GTCACAATATGGTGGCCGTG 59.267 55.000 10.43 0.00 37.42 4.94
4050 4825 1.067516 GCATGGTCACAATATGGTGGC 59.932 52.381 10.43 8.42 42.56 5.01
4059 4834 2.557924 GTTTGAGATGGCATGGTCACAA 59.442 45.455 3.81 0.00 0.00 3.33
4060 4835 2.161855 GTTTGAGATGGCATGGTCACA 58.838 47.619 3.81 0.00 0.00 3.58
4061 4836 1.131126 CGTTTGAGATGGCATGGTCAC 59.869 52.381 3.81 0.00 0.00 3.67
4062 4837 1.003003 TCGTTTGAGATGGCATGGTCA 59.997 47.619 3.81 4.72 0.00 4.02
4063 4838 1.398390 GTCGTTTGAGATGGCATGGTC 59.602 52.381 3.81 1.65 0.00 4.02
4064 4839 1.003580 AGTCGTTTGAGATGGCATGGT 59.996 47.619 3.81 0.00 0.00 3.55
4065 4840 1.742761 AGTCGTTTGAGATGGCATGG 58.257 50.000 3.81 0.00 0.00 3.66
4066 4841 3.189080 TGAAAGTCGTTTGAGATGGCATG 59.811 43.478 3.81 0.00 0.00 4.06
4067 4842 3.411446 TGAAAGTCGTTTGAGATGGCAT 58.589 40.909 0.00 0.00 0.00 4.40
4068 4843 2.844946 TGAAAGTCGTTTGAGATGGCA 58.155 42.857 0.00 0.00 0.00 4.92
4069 4844 3.436704 TCATGAAAGTCGTTTGAGATGGC 59.563 43.478 0.00 0.00 0.00 4.40
4070 4845 5.611796 TTCATGAAAGTCGTTTGAGATGG 57.388 39.130 5.45 0.00 0.00 3.51
4071 4846 6.891624 TCTTTCATGAAAGTCGTTTGAGATG 58.108 36.000 35.56 15.60 45.88 2.90
4072 4847 7.496529 TTCTTTCATGAAAGTCGTTTGAGAT 57.503 32.000 35.56 0.00 45.88 2.75
4073 4848 6.918892 TTCTTTCATGAAAGTCGTTTGAGA 57.081 33.333 35.56 18.69 45.88 3.27
4074 4849 7.600467 CTTTCTTTCATGAAAGTCGTTTGAG 57.400 36.000 35.56 22.62 45.88 3.02
4178 4953 1.089920 GCTATGTTGTGGAGCCACTG 58.910 55.000 19.47 5.45 46.30 3.66
4251 5038 3.536956 AAGTTTGAGTCACGACAGGAA 57.463 42.857 0.00 0.00 0.00 3.36
4264 5051 5.850557 TCCAAGATGAAGCAAAAGTTTGA 57.149 34.783 7.96 0.00 40.55 2.69
4269 5056 8.822652 AAAACTAATCCAAGATGAAGCAAAAG 57.177 30.769 0.00 0.00 0.00 2.27
4273 5060 8.862325 TTCTAAAACTAATCCAAGATGAAGCA 57.138 30.769 0.00 0.00 0.00 3.91
4396 5183 2.041686 GCCCAATACGGCGAACCAA 61.042 57.895 16.62 0.00 39.64 3.67
4397 5184 2.437002 GCCCAATACGGCGAACCA 60.437 61.111 16.62 0.00 39.64 3.67
4417 5204 3.295093 ACATTGGTGGACAAACATGTCA 58.705 40.909 0.00 0.00 43.46 3.58
4510 5297 1.017177 GGTTCACCTTGCGCGTATGA 61.017 55.000 8.43 0.51 0.00 2.15
4564 5352 2.596851 GCACCCTCTGCAGAAGGGA 61.597 63.158 37.38 13.75 46.29 4.20
4590 5378 0.984230 AGCGAGGTTGGGAGAATTGA 59.016 50.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.