Multiple sequence alignment - TraesCS5B01G383100

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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 TraesCS5B01G383100 chr5B 100.000 4495 0 0 1 4495 562045476 562049970 0.000000e+00 8301
1 TraesCS5B01G383100 chr5B 90.156 640 35 11 1392 2031 530921489 530922100 0.000000e+00 808
2 TraesCS5B01G383100 chr5B 91.223 376 27 1 3020 3389 530922093 530922468 1.440000e-139 507
3 TraesCS5B01G383100 chr5D 92.681 3375 146 39 923 4247 458630725 458634048 0.000000e+00 4771
4 TraesCS5B01G383100 chr5D 88.350 515 33 6 1 494 458629482 458629990 1.080000e-165 593
5 TraesCS5B01G383100 chr5D 91.572 439 11 10 499 931 458630027 458630445 2.330000e-162 582
6 TraesCS5B01G383100 chr5D 85.795 176 23 2 2844 3018 476462519 476462693 7.680000e-43 185
7 TraesCS5B01G383100 chr5A 91.716 2728 110 50 915 3609 576582552 576585196 0.000000e+00 3679
8 TraesCS5B01G383100 chr5A 86.091 949 62 33 1 930 576581632 576582529 0.000000e+00 957
9 TraesCS5B01G383100 chr5A 84.211 817 64 34 3636 4436 576585195 576585962 0.000000e+00 734
10 TraesCS5B01G383100 chr2D 94.346 2034 74 20 1392 3420 601057676 601055679 0.000000e+00 3081
11 TraesCS5B01G383100 chr2D 87.692 195 14 5 3444 3633 601055685 601055496 7.570000e-53 219
12 TraesCS5B01G383100 chr4A 92.573 2033 100 19 1394 3420 532160580 532162567 0.000000e+00 2870
13 TraesCS5B01G383100 chr4A 90.116 172 11 4 3444 3610 532162561 532162731 7.570000e-53 219
14 TraesCS5B01G383100 chr7D 95.885 1604 55 5 1823 3420 332691734 332693332 0.000000e+00 2586
15 TraesCS5B01G383100 chr7D 84.478 335 25 7 1392 1726 332691059 332691366 5.650000e-79 305
16 TraesCS5B01G383100 chr2A 91.612 1371 70 19 1392 2762 461411841 461413166 0.000000e+00 1853
17 TraesCS5B01G383100 chr2A 91.248 617 43 5 2787 3397 461413372 461413983 0.000000e+00 830
18 TraesCS5B01G383100 chr1B 91.612 1371 70 19 1392 2762 520243732 520245057 0.000000e+00 1853
19 TraesCS5B01G383100 chr1B 90.924 617 45 5 2787 3397 520245263 520245874 0.000000e+00 819
20 TraesCS5B01G383100 chr1A 91.247 1371 75 18 1392 2762 64843087 64844412 0.000000e+00 1825
21 TraesCS5B01G383100 chr1A 91.248 617 43 5 2787 3397 64844618 64845229 0.000000e+00 830
22 TraesCS5B01G383100 chr3B 90.335 1014 53 19 1392 2405 568297089 568296121 0.000000e+00 1288
23 TraesCS5B01G383100 chr1D 89.535 516 27 10 1392 1907 476219179 476218691 2.950000e-176 628
24 TraesCS5B01G383100 chr1D 89.341 516 28 10 1392 1907 467357272 467357760 1.370000e-174 623


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 TraesCS5B01G383100 chr5B 562045476 562049970 4494 False 8301.0 8301 100.000000 1 4495 1 chr5B.!!$F1 4494
1 TraesCS5B01G383100 chr5B 530921489 530922468 979 False 657.5 808 90.689500 1392 3389 2 chr5B.!!$F2 1997
2 TraesCS5B01G383100 chr5D 458629482 458634048 4566 False 1982.0 4771 90.867667 1 4247 3 chr5D.!!$F2 4246
3 TraesCS5B01G383100 chr5A 576581632 576585962 4330 False 1790.0 3679 87.339333 1 4436 3 chr5A.!!$F1 4435
4 TraesCS5B01G383100 chr2D 601055496 601057676 2180 True 1650.0 3081 91.019000 1392 3633 2 chr2D.!!$R1 2241
5 TraesCS5B01G383100 chr4A 532160580 532162731 2151 False 1544.5 2870 91.344500 1394 3610 2 chr4A.!!$F1 2216
6 TraesCS5B01G383100 chr7D 332691059 332693332 2273 False 1445.5 2586 90.181500 1392 3420 2 chr7D.!!$F1 2028
7 TraesCS5B01G383100 chr2A 461411841 461413983 2142 False 1341.5 1853 91.430000 1392 3397 2 chr2A.!!$F1 2005
8 TraesCS5B01G383100 chr1B 520243732 520245874 2142 False 1336.0 1853 91.268000 1392 3397 2 chr1B.!!$F1 2005
9 TraesCS5B01G383100 chr1A 64843087 64845229 2142 False 1327.5 1825 91.247500 1392 3397 2 chr1A.!!$F1 2005
10 TraesCS5B01G383100 chr3B 568296121 568297089 968 True 1288.0 1288 90.335000 1392 2405 1 chr3B.!!$R1 1013

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
249 254 0.178068 GAAGATCCAGCCAGCGGTAA 59.822 55.0 0.00 0.0 0.0 2.85 F
251 256 0.179000 AGATCCAGCCAGCGGTAAAG 59.821 55.0 0.00 0.0 0.0 1.85 F
662 730 0.250727 CAGCCCTCCCGTGAAGAAAA 60.251 55.0 0.00 0.0 0.0 2.29 F
783 852 0.479815 GCCTCATCCATCCATCCCAA 59.520 55.0 0.00 0.0 0.0 4.12 F
2648 3313 0.604578 GAAGCCAGCCAAATTCTGCA 59.395 50.0 2.46 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1383 1746 0.033504 GTCGAGCACAGAAGGGACAA 59.966 55.000 0.00 0.00 0.00 3.18 R
1596 1964 0.325110 CTCCTCCTCCTCTGCTTCCA 60.325 60.000 0.00 0.00 0.00 3.53 R
1634 2011 0.908198 CTAACCTGCTCCTGCTCCTT 59.092 55.000 0.00 0.00 40.48 3.36 R
2776 3441 1.126113 CTACTCGACAAACGCGCATTT 59.874 47.619 5.73 0.08 42.26 2.32 R
3586 4458 0.117140 AGATGACAGGGGGTGAGACA 59.883 55.000 0.00 0.00 0.00 3.41 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
22 23 1.658717 GTGATCTCATCCGTCCGCG 60.659 63.158 0.00 0.00 37.95 6.46
23 24 2.731348 GATCTCATCCGTCCGCGC 60.731 66.667 0.00 0.00 36.67 6.86
28 29 4.794439 CATCCGTCCGCGCAGTGA 62.794 66.667 8.75 0.00 43.07 3.41
188 193 8.150945 TGTAGACAGATGAATAAAAGGATAGCC 58.849 37.037 0.00 0.00 0.00 3.93
194 199 8.405531 CAGATGAATAAAAGGATAGCCGAAAAA 58.594 33.333 0.00 0.00 39.96 1.94
247 252 1.965754 GAGAAGATCCAGCCAGCGGT 61.966 60.000 0.00 0.00 0.00 5.68
248 253 0.687757 AGAAGATCCAGCCAGCGGTA 60.688 55.000 0.00 0.00 0.00 4.02
249 254 0.178068 GAAGATCCAGCCAGCGGTAA 59.822 55.000 0.00 0.00 0.00 2.85
250 255 0.618458 AAGATCCAGCCAGCGGTAAA 59.382 50.000 0.00 0.00 0.00 2.01
251 256 0.179000 AGATCCAGCCAGCGGTAAAG 59.821 55.000 0.00 0.00 0.00 1.85
252 257 1.440145 GATCCAGCCAGCGGTAAAGC 61.440 60.000 0.00 0.00 37.41 3.51
322 327 5.181245 CCGAAAGCAAACAATTAGAGAAGGA 59.819 40.000 0.00 0.00 0.00 3.36
323 328 6.127897 CCGAAAGCAAACAATTAGAGAAGGAT 60.128 38.462 0.00 0.00 0.00 3.24
328 333 5.803967 GCAAACAATTAGAGAAGGATGCAAG 59.196 40.000 0.00 0.00 0.00 4.01
329 334 5.573337 AACAATTAGAGAAGGATGCAAGC 57.427 39.130 0.00 0.00 0.00 4.01
357 379 1.332997 CGGTGACTACGATGAGTACCC 59.667 57.143 0.00 0.00 0.00 3.69
423 445 2.094803 TGCCTATTGTCGTGCCAAAATG 60.095 45.455 0.00 0.00 0.00 2.32
494 516 3.983344 CCCATTGCACGAAGAAAAGAAAG 59.017 43.478 0.00 0.00 0.00 2.62
521 581 3.313249 CCTTTGCTTTTGCCCTTTTCTTG 59.687 43.478 0.00 0.00 46.87 3.02
661 729 1.374947 CAGCCCTCCCGTGAAGAAA 59.625 57.895 0.00 0.00 0.00 2.52
662 730 0.250727 CAGCCCTCCCGTGAAGAAAA 60.251 55.000 0.00 0.00 0.00 2.29
664 732 0.596577 GCCCTCCCGTGAAGAAAAAC 59.403 55.000 0.00 0.00 0.00 2.43
666 734 1.477923 CCCTCCCGTGAAGAAAAACCA 60.478 52.381 0.00 0.00 0.00 3.67
667 735 2.303175 CCTCCCGTGAAGAAAAACCAA 58.697 47.619 0.00 0.00 0.00 3.67
668 736 2.293399 CCTCCCGTGAAGAAAAACCAAG 59.707 50.000 0.00 0.00 0.00 3.61
669 737 2.293399 CTCCCGTGAAGAAAAACCAAGG 59.707 50.000 0.00 0.00 0.00 3.61
670 738 2.092321 TCCCGTGAAGAAAAACCAAGGA 60.092 45.455 0.00 0.00 32.39 3.36
671 739 2.890945 CCCGTGAAGAAAAACCAAGGAT 59.109 45.455 0.00 0.00 32.39 3.24
672 740 3.305335 CCCGTGAAGAAAAACCAAGGATG 60.305 47.826 0.00 0.00 32.39 3.51
781 850 1.002868 CGCCTCATCCATCCATCCC 60.003 63.158 0.00 0.00 0.00 3.85
783 852 0.479815 GCCTCATCCATCCATCCCAA 59.520 55.000 0.00 0.00 0.00 4.12
784 853 1.820877 GCCTCATCCATCCATCCCAAC 60.821 57.143 0.00 0.00 0.00 3.77
787 856 3.220110 CTCATCCATCCATCCCAACAAG 58.780 50.000 0.00 0.00 0.00 3.16
789 858 2.512692 TCCATCCATCCCAACAAGTG 57.487 50.000 0.00 0.00 0.00 3.16
790 859 1.710244 TCCATCCATCCCAACAAGTGT 59.290 47.619 0.00 0.00 0.00 3.55
792 861 3.054434 TCCATCCATCCCAACAAGTGTAG 60.054 47.826 0.00 0.00 0.00 2.74
795 864 1.812571 CCATCCCAACAAGTGTAGCAC 59.187 52.381 0.00 0.00 34.10 4.40
796 865 2.503331 CATCCCAACAAGTGTAGCACA 58.497 47.619 2.01 0.00 36.74 4.57
797 866 2.254546 TCCCAACAAGTGTAGCACAG 57.745 50.000 2.01 0.00 36.74 3.66
798 867 1.488812 TCCCAACAAGTGTAGCACAGT 59.511 47.619 2.01 0.00 36.74 3.55
799 868 2.701423 TCCCAACAAGTGTAGCACAGTA 59.299 45.455 2.01 0.00 36.74 2.74
800 869 2.806244 CCCAACAAGTGTAGCACAGTAC 59.194 50.000 2.01 0.00 36.74 2.73
801 870 3.494398 CCCAACAAGTGTAGCACAGTACT 60.494 47.826 2.01 0.00 36.74 2.73
817 887 8.454106 AGCACAGTACTTAATAAGCAGAAAATG 58.546 33.333 0.00 0.00 0.00 2.32
1002 1360 1.809684 GCCTCCCTCAATTATACGGC 58.190 55.000 0.00 0.00 0.00 5.68
1003 1361 1.610886 GCCTCCCTCAATTATACGGCC 60.611 57.143 0.00 0.00 0.00 6.13
1004 1362 1.003233 CCTCCCTCAATTATACGGCCC 59.997 57.143 0.00 0.00 0.00 5.80
1008 1366 0.953960 CTCAATTATACGGCCCGGCC 60.954 60.000 19.64 19.64 46.75 6.13
1066 1426 1.339055 CCTTCCAAATCACAGCTCGGA 60.339 52.381 0.00 0.00 0.00 4.55
1085 1448 2.177594 AACAGCTTGGAGGAGGAGCG 62.178 60.000 0.00 0.00 41.19 5.03
1248 1611 2.433664 GTCGGTTTGTCGGCGGAT 60.434 61.111 7.21 0.00 0.00 4.18
1249 1612 2.030958 GTCGGTTTGTCGGCGGATT 61.031 57.895 7.21 0.00 0.00 3.01
1250 1613 1.301874 TCGGTTTGTCGGCGGATTT 60.302 52.632 7.21 0.00 0.00 2.17
1376 1739 3.441500 AAGGTGGGTTCTCCTTGATTC 57.558 47.619 0.00 0.00 43.08 2.52
1378 1741 2.989571 AGGTGGGTTCTCCTTGATTCTT 59.010 45.455 0.00 0.00 33.44 2.52
1380 1743 4.226168 AGGTGGGTTCTCCTTGATTCTTAG 59.774 45.833 0.00 0.00 33.44 2.18
1383 1746 5.046231 GTGGGTTCTCCTTGATTCTTAGTCT 60.046 44.000 0.00 0.00 36.20 3.24
1389 1757 5.187967 TCTCCTTGATTCTTAGTCTTGTCCC 59.812 44.000 0.00 0.00 0.00 4.46
1421 1789 2.338500 ACGAAATTCCGCTGAGAAGTC 58.662 47.619 0.00 0.00 0.00 3.01
1566 1934 3.709633 TGCCGAGGAGCATGCTGT 61.710 61.111 28.27 12.48 36.27 4.40
1568 1936 2.758089 GCCGAGGAGCATGCTGTTG 61.758 63.158 28.27 15.46 36.27 3.33
1576 1944 2.126071 CATGCTGTTGCTGCTGCC 60.126 61.111 13.47 0.00 40.48 4.85
1596 1964 1.298859 GCGGCGGAAACAGAGATTGT 61.299 55.000 9.78 0.00 43.45 2.71
1624 2001 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1630 2007 2.835895 GAGGAGGAGGAGGACGGC 60.836 72.222 0.00 0.00 0.00 5.68
1634 2011 4.361971 AGGAGGAGGACGGCGACA 62.362 66.667 16.62 0.00 0.00 4.35
1643 2023 4.379243 ACGGCGACAAGGAGCAGG 62.379 66.667 16.62 0.00 32.98 4.85
2134 2799 3.976701 CTACGCCAAGGCCACCCTG 62.977 68.421 5.01 0.00 41.90 4.45
2386 3051 2.737376 GCAACGGTGGAGGACGTC 60.737 66.667 7.13 7.13 43.31 4.34
2648 3313 0.604578 GAAGCCAGCCAAATTCTGCA 59.395 50.000 2.46 0.00 0.00 4.41
2772 3437 3.872696 TGACTGCTTCTGACAAGTCAAA 58.127 40.909 11.68 1.98 39.39 2.69
2820 3666 2.045926 GTTGCCGGCTCCATGACT 60.046 61.111 29.70 0.00 0.00 3.41
2821 3667 2.109126 GTTGCCGGCTCCATGACTC 61.109 63.158 29.70 3.49 0.00 3.36
2822 3668 3.664025 TTGCCGGCTCCATGACTCG 62.664 63.158 29.70 0.00 0.00 4.18
2823 3669 4.148825 GCCGGCTCCATGACTCGT 62.149 66.667 22.15 0.00 0.00 4.18
2824 3670 2.202797 CCGGCTCCATGACTCGTG 60.203 66.667 0.00 0.00 0.00 4.35
3429 4290 2.393557 CCATGATGGTGTACGGTGC 58.606 57.895 2.54 0.00 31.35 5.01
3430 4291 0.392327 CCATGATGGTGTACGGTGCA 60.392 55.000 2.54 0.00 31.35 4.57
3431 4292 1.009078 CATGATGGTGTACGGTGCAG 58.991 55.000 0.00 0.00 0.00 4.41
3432 4293 0.744414 ATGATGGTGTACGGTGCAGC 60.744 55.000 19.37 19.37 35.19 5.25
3470 4333 1.439353 CGCCATCTCCCATTCCGTTG 61.439 60.000 0.00 0.00 0.00 4.10
3535 4405 4.886579 AGATGAAAATGGTTCCAAGTTGC 58.113 39.130 0.00 0.00 0.00 4.17
3544 4414 0.179015 TTCCAAGTTGCCACGGCTAA 60.179 50.000 9.92 0.00 42.51 3.09
3586 4458 1.766143 GAGATCGAGCGCGGCAAAAT 61.766 55.000 10.69 0.00 38.28 1.82
3587 4459 1.652329 GATCGAGCGCGGCAAAATG 60.652 57.895 10.69 0.00 38.28 2.32
3597 4470 1.595093 CGGCAAAATGTCTCACCCCC 61.595 60.000 0.00 0.00 0.00 5.40
3610 4483 2.052690 ACCCCCTGTCATCTCGTCG 61.053 63.158 0.00 0.00 0.00 5.12
3611 4484 2.786495 CCCCCTGTCATCTCGTCGG 61.786 68.421 0.00 0.00 0.00 4.79
3612 4485 2.105128 CCCTGTCATCTCGTCGGC 59.895 66.667 0.00 0.00 0.00 5.54
3613 4486 2.710902 CCCTGTCATCTCGTCGGCA 61.711 63.158 0.00 0.00 0.00 5.69
3649 4522 1.092921 TTCGTGTGACCACTGCCAAC 61.093 55.000 1.62 0.00 39.55 3.77
3685 4558 1.172180 ACAGGGGTTGTTCATGTGCG 61.172 55.000 0.00 0.00 36.31 5.34
3733 4606 0.308993 GCGCTGTGATTATGGCCTTC 59.691 55.000 3.32 0.00 0.00 3.46
3842 4721 5.359009 CCATCATTGGCTGTTAGAATTGAGT 59.641 40.000 0.00 0.00 35.85 3.41
3843 4722 6.127535 CCATCATTGGCTGTTAGAATTGAGTT 60.128 38.462 0.00 0.00 35.85 3.01
3872 4751 1.329292 CGTGTTGTTTCGAAAGCCTCA 59.671 47.619 11.66 2.60 0.00 3.86
3874 4753 1.329292 TGTTGTTTCGAAAGCCTCACG 59.671 47.619 11.66 0.00 0.00 4.35
3911 4790 4.189639 GAAGAATGTCTTCCGGTACTGT 57.810 45.455 0.00 0.00 45.34 3.55
3924 4803 3.072211 CGGTACTGTCTGTCTGTCACTA 58.928 50.000 0.00 0.00 0.00 2.74
3929 4808 3.259374 ACTGTCTGTCTGTCACTATTGGG 59.741 47.826 0.00 0.00 0.00 4.12
3946 4825 2.607499 TGGGTTGCAAGTTGAATGGAT 58.393 42.857 7.16 0.00 0.00 3.41
3949 4828 4.402155 TGGGTTGCAAGTTGAATGGATATC 59.598 41.667 7.16 0.00 0.00 1.63
3950 4829 4.646492 GGGTTGCAAGTTGAATGGATATCT 59.354 41.667 7.16 0.00 0.00 1.98
3996 4878 4.385825 TGTCCGCTCACTTTGTTTCTATT 58.614 39.130 0.00 0.00 0.00 1.73
4029 4911 3.328382 TGCATTGCGTAGAAAGTAGGT 57.672 42.857 3.84 0.00 0.00 3.08
4057 4939 0.888736 ATGCCTGTGCTGCGTACAAA 60.889 50.000 0.00 0.00 38.71 2.83
4058 4940 1.207593 GCCTGTGCTGCGTACAAAG 59.792 57.895 0.00 0.00 33.53 2.77
4059 4941 1.507141 GCCTGTGCTGCGTACAAAGT 61.507 55.000 0.00 0.00 33.53 2.66
4106 4988 7.600065 TCTACAGTAATATTGTATTCTCGCCC 58.400 38.462 0.00 0.00 31.17 6.13
4107 4989 5.227908 ACAGTAATATTGTATTCTCGCCCG 58.772 41.667 0.00 0.00 0.00 6.13
4192 5082 2.176045 TCACATCTCGAGTGCCCTTAA 58.824 47.619 13.13 0.00 36.93 1.85
4241 5136 3.725490 GGCGGTATTTTAGTACTCCCAG 58.275 50.000 0.00 0.00 0.00 4.45
4243 5138 4.383444 GGCGGTATTTTAGTACTCCCAGTT 60.383 45.833 0.00 0.00 0.00 3.16
4244 5139 5.163416 GGCGGTATTTTAGTACTCCCAGTTA 60.163 44.000 0.00 0.00 0.00 2.24
4245 5140 5.750547 GCGGTATTTTAGTACTCCCAGTTAC 59.249 44.000 0.00 0.00 0.00 2.50
4262 5157 0.317799 TACTAGTTTTGCACCGGCGA 59.682 50.000 9.30 0.00 45.35 5.54
4292 5187 3.340928 GCTTTAACGAACACCCCTGTAT 58.659 45.455 0.00 0.00 0.00 2.29
4323 5218 9.357161 ATGTTAACATACAGGTTTGACCTTTAA 57.643 29.630 19.51 0.00 39.91 1.52
4341 5236 5.163834 CCTTTAATGGCATCATTGTTTGCAC 60.164 40.000 0.00 6.39 42.93 4.57
4363 5258 3.181488 CCATTGCTGTCACAAGTTCACAA 60.181 43.478 0.00 0.00 31.96 3.33
4417 5312 7.499321 AAAACACACCTAACATAATTCGTGA 57.501 32.000 0.00 0.00 0.00 4.35
4418 5313 7.499321 AAACACACCTAACATAATTCGTGAA 57.501 32.000 0.00 0.00 0.00 3.18
4419 5314 7.681939 AACACACCTAACATAATTCGTGAAT 57.318 32.000 0.00 0.00 0.00 2.57
4420 5315 8.780846 AACACACCTAACATAATTCGTGAATA 57.219 30.769 0.00 0.00 0.00 1.75
4421 5316 8.780846 ACACACCTAACATAATTCGTGAATAA 57.219 30.769 0.00 0.00 0.00 1.40
4422 5317 9.391006 ACACACCTAACATAATTCGTGAATAAT 57.609 29.630 0.00 0.00 0.00 1.28
4438 5333 9.773328 TCGTGAATAATTTTTGAATCTGTGATC 57.227 29.630 0.00 0.00 0.00 2.92
4439 5334 9.013490 CGTGAATAATTTTTGAATCTGTGATCC 57.987 33.333 0.00 0.00 0.00 3.36
4456 5351 9.519191 TCTGTGATCCTTCTTAAAAATTCATGA 57.481 29.630 0.00 0.00 0.00 3.07
4458 5353 9.912634 TGTGATCCTTCTTAAAAATTCATGAAC 57.087 29.630 11.07 0.00 0.00 3.18
4459 5354 9.912634 GTGATCCTTCTTAAAAATTCATGAACA 57.087 29.630 11.07 0.00 0.00 3.18
4478 5373 7.912949 TGAACATTCTTTTGAATTCGTGAAG 57.087 32.000 0.04 5.14 46.12 3.02
4481 5376 8.925161 AACATTCTTTTGAATTCGTGAAGAAA 57.075 26.923 23.03 8.02 46.12 2.52
4494 5389 7.548196 TTCGTGAAGAAAAATAGTTCAGTGT 57.452 32.000 0.00 0.00 35.61 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.531264 CGCATTCAAGCTGATCACTGC 60.531 52.381 0.00 0.00 40.45 4.40
23 24 1.531264 GCGCATTCAAGCTGATCACTG 60.531 52.381 0.30 0.00 0.00 3.66
28 29 1.308069 AACGGCGCATTCAAGCTGAT 61.308 50.000 10.83 0.00 42.01 2.90
63 64 2.098680 GTCAGACGAGACGAGCGG 59.901 66.667 0.00 0.00 0.00 5.52
91 92 2.040544 GTGCAGGCCATGTAAGCGT 61.041 57.895 5.01 0.00 0.00 5.07
188 193 8.579682 AATCACCATTCTTTCTTTCTTTTTCG 57.420 30.769 0.00 0.00 0.00 3.46
194 199 7.175641 CACCACTAATCACCATTCTTTCTTTCT 59.824 37.037 0.00 0.00 0.00 2.52
247 252 1.134907 CCGTCCTCCGCTTTAGCTTTA 60.135 52.381 0.00 0.00 39.32 1.85
248 253 0.391263 CCGTCCTCCGCTTTAGCTTT 60.391 55.000 0.00 0.00 39.32 3.51
249 254 1.218316 CCGTCCTCCGCTTTAGCTT 59.782 57.895 0.00 0.00 39.32 3.74
250 255 1.043673 ATCCGTCCTCCGCTTTAGCT 61.044 55.000 0.00 0.00 39.32 3.32
251 256 0.179081 AATCCGTCCTCCGCTTTAGC 60.179 55.000 0.00 0.00 34.38 3.09
252 257 1.136305 TGAATCCGTCCTCCGCTTTAG 59.864 52.381 0.00 0.00 34.38 1.85
330 335 4.824166 CGTAGTCACCGTCGCCCG 62.824 72.222 0.00 0.00 0.00 6.13
331 336 2.768492 ATCGTAGTCACCGTCGCCC 61.768 63.158 0.00 0.00 0.00 6.13
337 359 1.332997 GGGTACTCATCGTAGTCACCG 59.667 57.143 0.00 0.00 30.32 4.94
344 366 0.680601 TGCGGTGGGTACTCATCGTA 60.681 55.000 28.06 22.35 42.63 3.43
405 427 3.214697 TGCATTTTGGCACGACAATAG 57.785 42.857 0.00 0.00 39.25 1.73
406 428 3.312828 GTTGCATTTTGGCACGACAATA 58.687 40.909 0.00 0.00 44.86 1.90
451 473 0.321653 AAGGCGCCGAGAAAATGAGT 60.322 50.000 23.20 0.00 0.00 3.41
494 516 0.603707 GGGCAAAAGCAAAGGCCTTC 60.604 55.000 20.79 7.35 45.68 3.46
521 581 1.159285 GGCTTTGGATTTTGGCAAGC 58.841 50.000 0.00 0.00 39.35 4.01
658 726 2.093500 GCCATCCCATCCTTGGTTTTTC 60.093 50.000 0.00 0.00 41.91 2.29
661 729 0.684153 CGCCATCCCATCCTTGGTTT 60.684 55.000 0.00 0.00 41.91 3.27
662 730 1.076777 CGCCATCCCATCCTTGGTT 60.077 57.895 0.00 0.00 41.91 3.67
664 732 1.526917 GTCGCCATCCCATCCTTGG 60.527 63.158 0.00 0.00 43.23 3.61
666 734 2.063979 TCGTCGCCATCCCATCCTT 61.064 57.895 0.00 0.00 0.00 3.36
667 735 2.443952 TCGTCGCCATCCCATCCT 60.444 61.111 0.00 0.00 0.00 3.24
668 736 2.280186 GTCGTCGCCATCCCATCC 60.280 66.667 0.00 0.00 0.00 3.51
669 737 2.658593 CGTCGTCGCCATCCCATC 60.659 66.667 0.00 0.00 0.00 3.51
781 850 6.838198 TTAAGTACTGTGCTACACTTGTTG 57.162 37.500 0.00 0.00 35.11 3.33
783 852 7.331193 GCTTATTAAGTACTGTGCTACACTTGT 59.669 37.037 0.00 1.55 35.11 3.16
784 853 7.330946 TGCTTATTAAGTACTGTGCTACACTTG 59.669 37.037 0.00 0.00 35.11 3.16
787 856 7.033791 TCTGCTTATTAAGTACTGTGCTACAC 58.966 38.462 0.00 0.00 34.56 2.90
789 858 8.475331 TTTCTGCTTATTAAGTACTGTGCTAC 57.525 34.615 0.00 0.00 0.00 3.58
790 859 9.667107 ATTTTCTGCTTATTAAGTACTGTGCTA 57.333 29.630 0.00 0.00 0.00 3.49
792 861 8.450964 TCATTTTCTGCTTATTAAGTACTGTGC 58.549 33.333 0.00 0.00 0.00 4.57
857 927 3.279875 GGAAAGCTATGGCCGCCG 61.280 66.667 4.58 0.00 39.73 6.46
982 1340 1.939838 GCCGTATAATTGAGGGAGGCG 60.940 57.143 5.38 0.00 33.66 5.52
1004 1362 4.598894 CTCTGATGAGCCCGGCCG 62.599 72.222 21.04 21.04 33.12 6.13
1008 1366 0.319728 CATACCCTCTGATGAGCCCG 59.680 60.000 0.00 0.00 38.93 6.13
1010 1368 4.689612 TTTACATACCCTCTGATGAGCC 57.310 45.455 0.00 0.00 38.93 4.70
1011 1369 4.453819 GCATTTACATACCCTCTGATGAGC 59.546 45.833 0.00 0.00 38.93 4.26
1013 1371 4.503123 CCGCATTTACATACCCTCTGATGA 60.503 45.833 0.00 0.00 0.00 2.92
1014 1372 3.748048 CCGCATTTACATACCCTCTGATG 59.252 47.826 0.00 0.00 0.00 3.07
1015 1373 3.391296 ACCGCATTTACATACCCTCTGAT 59.609 43.478 0.00 0.00 0.00 2.90
1046 1406 1.089920 CCGAGCTGTGATTTGGAAGG 58.910 55.000 0.00 0.00 0.00 3.46
1066 1426 1.682257 GCTCCTCCTCCAAGCTGTT 59.318 57.895 0.00 0.00 33.23 3.16
1072 1432 3.393970 CTGCCGCTCCTCCTCCAA 61.394 66.667 0.00 0.00 0.00 3.53
1248 1611 7.254387 CGAAAACAGCAAAATCCATCAGAAAAA 60.254 33.333 0.00 0.00 0.00 1.94
1249 1612 6.200665 CGAAAACAGCAAAATCCATCAGAAAA 59.799 34.615 0.00 0.00 0.00 2.29
1250 1613 5.691305 CGAAAACAGCAAAATCCATCAGAAA 59.309 36.000 0.00 0.00 0.00 2.52
1366 1729 5.188751 AGGGACAAGACTAAGAATCAAGGAG 59.811 44.000 0.00 0.00 0.00 3.69
1368 1731 5.428184 AGGGACAAGACTAAGAATCAAGG 57.572 43.478 0.00 0.00 0.00 3.61
1369 1732 6.593382 CAGAAGGGACAAGACTAAGAATCAAG 59.407 42.308 0.00 0.00 0.00 3.02
1371 1734 5.544176 ACAGAAGGGACAAGACTAAGAATCA 59.456 40.000 0.00 0.00 0.00 2.57
1372 1735 5.872070 CACAGAAGGGACAAGACTAAGAATC 59.128 44.000 0.00 0.00 0.00 2.52
1373 1736 5.799213 CACAGAAGGGACAAGACTAAGAAT 58.201 41.667 0.00 0.00 0.00 2.40
1374 1737 4.503296 GCACAGAAGGGACAAGACTAAGAA 60.503 45.833 0.00 0.00 0.00 2.52
1376 1739 3.007398 AGCACAGAAGGGACAAGACTAAG 59.993 47.826 0.00 0.00 0.00 2.18
1378 1741 2.563179 GAGCACAGAAGGGACAAGACTA 59.437 50.000 0.00 0.00 0.00 2.59
1380 1743 1.802069 GAGCACAGAAGGGACAAGAC 58.198 55.000 0.00 0.00 0.00 3.01
1383 1746 0.033504 GTCGAGCACAGAAGGGACAA 59.966 55.000 0.00 0.00 0.00 3.18
1389 1757 2.092838 GGAATTTCGTCGAGCACAGAAG 59.907 50.000 0.00 0.00 0.00 2.85
1542 1910 2.366393 TGCTCCTCGGCATTGGCTA 61.366 57.895 8.71 0.00 40.87 3.93
1576 1944 2.100631 AATCTCTGTTTCCGCCGCG 61.101 57.895 5.59 5.59 0.00 6.46
1596 1964 0.325110 CTCCTCCTCCTCTGCTTCCA 60.325 60.000 0.00 0.00 0.00 3.53
1624 2001 4.373116 TGCTCCTTGTCGCCGTCC 62.373 66.667 0.00 0.00 0.00 4.79
1630 2007 1.447489 CTGCTCCTGCTCCTTGTCG 60.447 63.158 0.00 0.00 40.48 4.35
1634 2011 0.908198 CTAACCTGCTCCTGCTCCTT 59.092 55.000 0.00 0.00 40.48 3.36
1643 2023 1.414550 GTCCTCCATCCTAACCTGCTC 59.585 57.143 0.00 0.00 0.00 4.26
1676 2056 1.201429 AAGTCCGGGAAGGTGATGCT 61.201 55.000 0.00 0.00 41.99 3.79
2386 3051 1.519751 CGGAGTAGCTCGGGATGAGG 61.520 65.000 0.00 0.00 45.38 3.86
2731 3396 3.443329 TCAATGACAAATCGGGGAATGTG 59.557 43.478 0.00 0.00 0.00 3.21
2776 3441 1.126113 CTACTCGACAAACGCGCATTT 59.874 47.619 5.73 0.08 42.26 2.32
2820 3666 2.027024 GCACCACTCACGACACGA 59.973 61.111 0.00 0.00 0.00 4.35
2821 3667 1.664649 ATGCACCACTCACGACACG 60.665 57.895 0.00 0.00 0.00 4.49
2822 3668 1.862123 CATGCACCACTCACGACAC 59.138 57.895 0.00 0.00 0.00 3.67
2823 3669 1.960763 GCATGCACCACTCACGACA 60.961 57.895 14.21 0.00 0.00 4.35
2824 3670 1.300971 ATGCATGCACCACTCACGAC 61.301 55.000 25.37 0.00 0.00 4.34
3134 3983 2.126307 CTCTCCTGCACCGTCGTG 60.126 66.667 0.00 0.00 43.35 4.35
3191 4040 3.007920 CTCTCCAGGCCCTGCACT 61.008 66.667 4.81 0.00 0.00 4.40
3432 4293 3.333189 CGATCATCCTGCGCACCG 61.333 66.667 5.66 0.00 0.00 4.94
3470 4333 3.641986 TGAAACACGCCGCGTTCC 61.642 61.111 17.45 6.19 38.32 3.62
3480 4343 3.366422 GCTCTTCTCTGATCGTGAAACAC 59.634 47.826 0.00 0.00 35.74 3.32
3535 4405 1.153823 CTCGTCTGGTTAGCCGTGG 60.154 63.158 0.00 0.00 37.67 4.94
3544 4414 2.156098 GTCTTCACTCTCTCGTCTGGT 58.844 52.381 0.00 0.00 0.00 4.00
3586 4458 0.117140 AGATGACAGGGGGTGAGACA 59.883 55.000 0.00 0.00 0.00 3.41
3587 4459 0.827368 GAGATGACAGGGGGTGAGAC 59.173 60.000 0.00 0.00 0.00 3.36
3597 4470 4.079090 GTGCCGACGAGATGACAG 57.921 61.111 0.00 0.00 0.00 3.51
3610 4483 4.322385 GGGTGCGTCAAACGTGCC 62.322 66.667 0.00 4.06 44.73 5.01
3611 4484 4.659874 CGGGTGCGTCAAACGTGC 62.660 66.667 0.00 0.00 44.73 5.34
3612 4485 1.837538 AATCGGGTGCGTCAAACGTG 61.838 55.000 0.00 0.00 44.73 4.49
3613 4486 1.562575 GAATCGGGTGCGTCAAACGT 61.563 55.000 1.14 0.00 44.73 3.99
3617 4490 2.024868 CACGAATCGGGTGCGTCAA 61.025 57.895 7.80 0.00 35.90 3.18
3685 4558 3.982058 GCTAAGCATATCGTACAGACACC 59.018 47.826 0.00 0.00 0.00 4.16
3733 4606 1.208358 CACCACATCACAAGCTGCG 59.792 57.895 0.00 0.00 0.00 5.18
3826 4699 6.546395 CATGTACAACTCAATTCTAACAGCC 58.454 40.000 0.00 0.00 0.00 4.85
3842 4721 2.286477 CGAAACAACACGGCATGTACAA 60.286 45.455 0.00 0.00 42.31 2.41
3843 4722 1.261885 CGAAACAACACGGCATGTACA 59.738 47.619 0.00 0.00 42.31 2.90
3903 4782 1.880675 AGTGACAGACAGACAGTACCG 59.119 52.381 0.00 0.00 0.00 4.02
3911 4790 3.557054 GCAACCCAATAGTGACAGACAGA 60.557 47.826 0.00 0.00 0.00 3.41
3924 4803 2.971330 TCCATTCAACTTGCAACCCAAT 59.029 40.909 0.00 0.00 31.91 3.16
3929 4808 6.441093 TGAGATATCCATTCAACTTGCAAC 57.559 37.500 0.00 0.00 0.00 4.17
3946 4825 5.993055 TCTGCAAAAGATGGACATGAGATA 58.007 37.500 0.00 0.00 0.00 1.98
3949 4828 4.094590 GTCTCTGCAAAAGATGGACATGAG 59.905 45.833 0.00 0.00 32.73 2.90
3950 4829 4.005650 GTCTCTGCAAAAGATGGACATGA 58.994 43.478 0.00 0.00 32.73 3.07
3996 4878 0.173029 CAATGCATGCCGCCTTTACA 59.827 50.000 16.68 0.00 41.33 2.41
4029 4911 2.858622 GCACAGGCATGCTTGAGTA 58.141 52.632 33.61 0.00 42.62 2.59
4085 4967 5.227908 ACGGGCGAGAATACAATATTACTG 58.772 41.667 0.00 0.00 0.00 2.74
4086 4968 5.464030 ACGGGCGAGAATACAATATTACT 57.536 39.130 0.00 0.00 0.00 2.24
4087 4969 4.624452 GGACGGGCGAGAATACAATATTAC 59.376 45.833 0.00 0.00 0.00 1.89
4088 4970 4.616604 CGGACGGGCGAGAATACAATATTA 60.617 45.833 0.00 0.00 0.00 0.98
4089 4971 3.660865 GGACGGGCGAGAATACAATATT 58.339 45.455 0.00 0.00 0.00 1.28
4090 4972 2.352421 CGGACGGGCGAGAATACAATAT 60.352 50.000 0.00 0.00 0.00 1.28
4091 4973 1.001048 CGGACGGGCGAGAATACAATA 60.001 52.381 0.00 0.00 0.00 1.90
4092 4974 0.249322 CGGACGGGCGAGAATACAAT 60.249 55.000 0.00 0.00 0.00 2.71
4160 5050 4.495422 TCGAGATGTGAAGAAAAGCTACC 58.505 43.478 0.00 0.00 0.00 3.18
4192 5082 8.596781 AGTACTCCAAGTCACTAAACATATCT 57.403 34.615 0.00 0.00 0.00 1.98
4241 5136 1.136169 CGCCGGTGCAAAACTAGTAAC 60.136 52.381 0.00 0.00 37.32 2.50
4243 5138 0.317799 TCGCCGGTGCAAAACTAGTA 59.682 50.000 11.05 0.00 37.32 1.82
4244 5139 0.321298 ATCGCCGGTGCAAAACTAGT 60.321 50.000 11.05 0.00 37.32 2.57
4245 5140 0.373716 GATCGCCGGTGCAAAACTAG 59.626 55.000 11.05 0.00 37.32 2.57
4262 5157 2.546368 TGTTCGTTAAAGCGTTGCTGAT 59.454 40.909 0.00 0.00 39.62 2.90
4277 5172 5.145564 ACATATCTATACAGGGGTGTTCGT 58.854 41.667 0.00 0.00 0.00 3.85
4292 5187 9.826574 GGTCAAACCTGTATGTTAACATATCTA 57.173 33.333 26.70 16.72 36.94 1.98
4314 5209 5.999205 AACAATGATGCCATTAAAGGTCA 57.001 34.783 0.00 0.00 40.81 4.02
4323 5218 1.624312 TGGTGCAAACAATGATGCCAT 59.376 42.857 11.73 0.00 41.87 4.40
4341 5236 2.358582 TGTGAACTTGTGACAGCAATGG 59.641 45.455 0.00 0.00 0.00 3.16
4363 5258 2.923605 TTTTTGCTTGAAACGGACGT 57.076 40.000 0.00 0.00 0.00 4.34
4412 5307 9.773328 GATCACAGATTCAAAAATTATTCACGA 57.227 29.630 0.00 0.00 0.00 4.35
4413 5308 9.013490 GGATCACAGATTCAAAAATTATTCACG 57.987 33.333 0.00 0.00 0.00 4.35
4430 5325 9.519191 TCATGAATTTTTAAGAAGGATCACAGA 57.481 29.630 0.00 0.00 0.00 3.41
4432 5327 9.912634 GTTCATGAATTTTTAAGAAGGATCACA 57.087 29.630 12.12 0.00 0.00 3.58
4433 5328 9.912634 TGTTCATGAATTTTTAAGAAGGATCAC 57.087 29.630 12.12 0.00 0.00 3.06
4448 5343 9.480053 ACGAATTCAAAAGAATGTTCATGAATT 57.520 25.926 21.07 21.07 0.00 2.17
4449 5344 8.918658 CACGAATTCAAAAGAATGTTCATGAAT 58.081 29.630 12.12 11.98 0.00 2.57
4450 5345 8.134261 TCACGAATTCAAAAGAATGTTCATGAA 58.866 29.630 3.38 3.38 0.00 2.57
4451 5346 7.647228 TCACGAATTCAAAAGAATGTTCATGA 58.353 30.769 6.22 0.00 0.00 3.07
4452 5347 7.856492 TCACGAATTCAAAAGAATGTTCATG 57.144 32.000 6.22 0.00 0.00 3.07
4453 5348 8.352201 TCTTCACGAATTCAAAAGAATGTTCAT 58.648 29.630 6.22 0.00 0.00 2.57
4454 5349 7.702386 TCTTCACGAATTCAAAAGAATGTTCA 58.298 30.769 6.22 0.00 0.00 3.18
4455 5350 8.560576 TTCTTCACGAATTCAAAAGAATGTTC 57.439 30.769 16.77 0.00 32.57 3.18
4456 5351 8.925161 TTTCTTCACGAATTCAAAAGAATGTT 57.075 26.923 19.42 0.00 36.25 2.71
4457 5352 8.925161 TTTTCTTCACGAATTCAAAAGAATGT 57.075 26.923 19.42 1.53 36.25 2.71
4465 5360 9.663904 CTGAACTATTTTTCTTCACGAATTCAA 57.336 29.630 6.22 0.00 28.42 2.69
4466 5361 8.836413 ACTGAACTATTTTTCTTCACGAATTCA 58.164 29.630 6.22 0.00 0.00 2.57
4467 5362 9.107367 CACTGAACTATTTTTCTTCACGAATTC 57.893 33.333 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.