Multiple sequence alignment - TraesCS7B01G293400

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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 TraesCS7B01G293400 chr7B 100.000 5315 0 0 1 5315 530371979 530377293 0.000000e+00 9816.0
1 TraesCS7B01G293400 chr7B 94.465 795 38 2 1 794 162021079 162021868 0.000000e+00 1219.0
2 TraesCS7B01G293400 chr7B 93.688 301 14 1 494 794 162016424 162016719 3.780000e-121 446.0
3 TraesCS7B01G293400 chr7B 93.667 300 14 1 495 794 530367318 530367612 1.360000e-120 444.0
4 TraesCS7B01G293400 chr7D 93.263 4097 196 33 807 4857 501088409 501092471 0.000000e+00 5963.0
5 TraesCS7B01G293400 chr7D 83.128 812 101 29 3 797 540007721 540006929 0.000000e+00 708.0
6 TraesCS7B01G293400 chr7D 92.826 460 27 3 4856 5310 501092633 501093091 0.000000e+00 662.0
7 TraesCS7B01G293400 chr7D 82.134 806 111 29 6 794 125449855 125450644 0.000000e+00 660.0
8 TraesCS7B01G293400 chr7D 75.399 313 54 18 495 794 125430081 125430383 4.320000e-26 130.0
9 TraesCS7B01G293400 chr7A 92.642 3819 199 40 807 4566 567576374 567580169 0.000000e+00 5421.0
10 TraesCS7B01G293400 chr7A 92.041 490 26 7 4832 5315 567580799 567581281 0.000000e+00 676.0
11 TraesCS7B01G293400 chr7A 82.857 210 28 6 4503 4704 435285064 435285273 1.180000e-41 182.0
12 TraesCS7B01G293400 chrUn 89.043 794 58 13 3 794 35714802 35714036 0.000000e+00 957.0
13 TraesCS7B01G293400 chrUn 88.742 302 27 4 494 794 34811262 34810967 3.910000e-96 363.0
14 TraesCS7B01G293400 chr1A 84.799 796 92 23 15 794 97813509 97812727 0.000000e+00 773.0
15 TraesCS7B01G293400 chr1A 83.560 809 99 29 3 791 111786366 111787160 0.000000e+00 726.0
16 TraesCS7B01G293400 chr1A 85.955 178 22 3 4503 4678 417384986 417385162 2.530000e-43 187.0
17 TraesCS7B01G293400 chr1A 84.211 190 25 5 4503 4688 47902036 47902224 4.230000e-41 180.0
18 TraesCS7B01G293400 chr1A 91.176 68 5 1 728 794 111781969 111782036 2.040000e-14 91.6
19 TraesCS7B01G293400 chr3D 84.321 810 92 30 6 797 237811517 237810725 0.000000e+00 760.0
20 TraesCS7B01G293400 chr5A 83.229 799 100 31 15 794 649842113 649842896 0.000000e+00 702.0
21 TraesCS7B01G293400 chr5A 86.441 413 46 7 2366 2770 592296283 592295873 1.360000e-120 444.0
22 TraesCS7B01G293400 chr5A 87.647 170 16 2 3611 3775 592294778 592294609 5.430000e-45 193.0
23 TraesCS7B01G293400 chr2A 87.214 524 60 5 18 536 34353018 34352497 1.650000e-164 590.0
24 TraesCS7B01G293400 chr5B 78.195 931 124 38 2894 3775 580105721 580104821 6.100000e-144 521.0
25 TraesCS7B01G293400 chr5B 84.703 438 55 6 2344 2770 580106543 580106107 1.370000e-115 427.0
26 TraesCS7B01G293400 chr5B 88.889 126 12 2 2160 2284 580106665 580106541 2.560000e-33 154.0
27 TraesCS7B01G293400 chr5D 83.252 412 49 12 2366 2770 472740965 472740567 1.410000e-95 361.0
28 TraesCS7B01G293400 chr5D 88.889 171 14 2 3611 3776 472739275 472739105 6.980000e-49 206.0
29 TraesCS7B01G293400 chr5D 77.044 318 41 23 495 794 251952950 251952647 2.560000e-33 154.0
30 TraesCS7B01G293400 chr5D 100.000 32 0 0 4942 4973 55802898 55802867 5.750000e-05 60.2
31 TraesCS7B01G293400 chr5D 88.235 51 4 2 4942 4991 233966506 233966555 5.750000e-05 60.2
32 TraesCS7B01G293400 chr6A 85.340 191 24 4 4502 4688 539714707 539714897 1.510000e-45 195.0
33 TraesCS7B01G293400 chr6A 82.857 210 28 6 4503 4704 126295092 126295301 1.180000e-41 182.0
34 TraesCS7B01G293400 chr6A 82.692 208 30 4 4503 4704 504476031 504476238 4.230000e-41 180.0
35 TraesCS7B01G293400 chr6A 81.696 224 32 7 4503 4717 131197119 131197342 1.520000e-40 178.0
36 TraesCS7B01G293400 chr4A 81.696 224 32 7 4503 4717 518619471 518619694 1.520000e-40 178.0
37 TraesCS7B01G293400 chr2D 100.000 30 0 0 1139 1168 55059626 55059597 7.440000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G293400 chr7B 530371979 530377293 5314 False 9816.000000 9816 100.0000 1 5315 1 chr7B.!!$F4 5314
1 TraesCS7B01G293400 chr7B 162021079 162021868 789 False 1219.000000 1219 94.4650 1 794 1 chr7B.!!$F2 793
2 TraesCS7B01G293400 chr7D 501088409 501093091 4682 False 3312.500000 5963 93.0445 807 5310 2 chr7D.!!$F3 4503
3 TraesCS7B01G293400 chr7D 540006929 540007721 792 True 708.000000 708 83.1280 3 797 1 chr7D.!!$R1 794
4 TraesCS7B01G293400 chr7D 125449855 125450644 789 False 660.000000 660 82.1340 6 794 1 chr7D.!!$F2 788
5 TraesCS7B01G293400 chr7A 567576374 567581281 4907 False 3048.500000 5421 92.3415 807 5315 2 chr7A.!!$F2 4508
6 TraesCS7B01G293400 chrUn 35714036 35714802 766 True 957.000000 957 89.0430 3 794 1 chrUn.!!$R2 791
7 TraesCS7B01G293400 chr1A 97812727 97813509 782 True 773.000000 773 84.7990 15 794 1 chr1A.!!$R1 779
8 TraesCS7B01G293400 chr1A 111786366 111787160 794 False 726.000000 726 83.5600 3 791 1 chr1A.!!$F3 788
9 TraesCS7B01G293400 chr3D 237810725 237811517 792 True 760.000000 760 84.3210 6 797 1 chr3D.!!$R1 791
10 TraesCS7B01G293400 chr5A 649842113 649842896 783 False 702.000000 702 83.2290 15 794 1 chr5A.!!$F1 779
11 TraesCS7B01G293400 chr5A 592294609 592296283 1674 True 318.500000 444 87.0440 2366 3775 2 chr5A.!!$R1 1409
12 TraesCS7B01G293400 chr2A 34352497 34353018 521 True 590.000000 590 87.2140 18 536 1 chr2A.!!$R1 518
13 TraesCS7B01G293400 chr5B 580104821 580106665 1844 True 367.333333 521 83.9290 2160 3775 3 chr5B.!!$R1 1615
14 TraesCS7B01G293400 chr5D 472739105 472740965 1860 True 283.500000 361 86.0705 2366 3776 2 chr5D.!!$R3 1410

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
933 980 0.035152 TCCCACATCGCTTCATTGCT 60.035 50.0 0.00 0.0 0.0 3.91 F
1869 1922 0.323360 GCAATAGGGCCAGTCACCAA 60.323 55.0 6.18 0.0 0.0 3.67 F
2285 2338 0.033699 AAGGAAGGGCAAGGATGAGC 60.034 55.0 0.00 0.0 0.0 4.26 F
3829 4447 0.990374 AGAAGCTCAGCCAATCCAGT 59.010 50.0 0.00 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2268 2321 0.106318 ATGCTCATCCTTGCCCTTCC 60.106 55.000 0.00 0.0 0.0 3.46 R
3242 3786 0.606401 GCTGGAAGGCAAGTGTAGCA 60.606 55.000 0.00 0.0 0.0 3.49 R
3997 4615 0.251832 TCAGCCCTCGGTTCTTCTCT 60.252 55.000 0.00 0.0 0.0 3.10 R
4910 6125 1.006281 ACAATGTCCATGCCTCCATGT 59.994 47.619 3.34 0.0 45.9 3.21 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
74 75 2.722487 CCGATAGAGACGCGCCTT 59.278 61.111 5.73 0.00 39.76 4.35
326 328 2.202570 GACGCGGCGTGTCTATGT 60.203 61.111 37.76 12.42 41.37 2.29
475 482 2.029380 CGGTGGTGGGGAGAAAAATTTC 60.029 50.000 0.00 0.00 37.45 2.17
478 485 3.895041 GTGGTGGGGAGAAAAATTTCTGA 59.105 43.478 12.85 0.00 46.84 3.27
505 512 0.981183 TACCAGATTGTCACGCCCTT 59.019 50.000 0.00 0.00 0.00 3.95
522 530 3.372025 GCCCTTATCTGTGAGATTTGGGT 60.372 47.826 17.57 0.00 42.69 4.51
589 607 1.000270 AGAGCGAGAGGAGCAAGGA 60.000 57.895 0.00 0.00 37.01 3.36
630 648 6.316390 CGCAATACTTTTCTTCATACCCTCTT 59.684 38.462 0.00 0.00 0.00 2.85
646 664 1.208052 CTCTTCAGCCAATCCTTCGGA 59.792 52.381 0.00 0.00 35.55 4.55
739 771 1.845809 GCTGGAACGCTGACTTGGTG 61.846 60.000 0.00 0.00 0.00 4.17
794 835 1.523258 GCTGATCTGCAGGCGTGAT 60.523 57.895 18.67 0.00 45.03 3.06
797 838 0.390492 TGATCTGCAGGCGTGATAGG 59.610 55.000 15.13 0.00 0.00 2.57
798 839 0.676184 GATCTGCAGGCGTGATAGGA 59.324 55.000 15.13 2.34 0.00 2.94
799 840 1.069204 GATCTGCAGGCGTGATAGGAA 59.931 52.381 15.13 0.00 0.00 3.36
800 841 0.175760 TCTGCAGGCGTGATAGGAAC 59.824 55.000 15.13 0.00 0.00 3.62
801 842 0.811616 CTGCAGGCGTGATAGGAACC 60.812 60.000 11.29 0.00 0.00 3.62
802 843 1.264749 TGCAGGCGTGATAGGAACCT 61.265 55.000 11.29 0.00 0.00 3.50
803 844 3.369381 CAGGCGTGATAGGAACCTG 57.631 57.895 0.00 0.00 41.78 4.00
804 845 0.537188 CAGGCGTGATAGGAACCTGT 59.463 55.000 0.00 0.00 42.42 4.00
805 846 0.824759 AGGCGTGATAGGAACCTGTC 59.175 55.000 10.05 10.05 35.21 3.51
860 901 6.363896 CGCTAACCAAAAACCGAAATATGTTT 59.636 34.615 0.00 0.00 36.29 2.83
861 902 7.506474 GCTAACCAAAAACCGAAATATGTTTG 58.494 34.615 0.00 0.00 35.03 2.93
862 903 7.382759 GCTAACCAAAAACCGAAATATGTTTGA 59.617 33.333 0.00 0.00 35.03 2.69
865 906 8.669946 ACCAAAAACCGAAATATGTTTGATTT 57.330 26.923 0.00 0.00 35.03 2.17
931 978 2.223641 CCAATCCCACATCGCTTCATTG 60.224 50.000 0.00 0.00 0.00 2.82
933 980 0.035152 TCCCACATCGCTTCATTGCT 60.035 50.000 0.00 0.00 0.00 3.91
1093 1143 2.282958 AAGAGGCCGAGGTCGACA 60.283 61.111 18.91 0.00 43.02 4.35
1267 1320 0.333993 AGGATGCTTTGGTGATGCCT 59.666 50.000 0.00 0.00 38.35 4.75
1361 1414 4.845580 ATGGCAGCGAAGGAGGCG 62.846 66.667 0.00 0.00 35.00 5.52
1448 1501 3.741476 CGCAGAGGGCAGCCAAAC 61.741 66.667 15.19 3.58 45.17 2.93
1477 1530 3.344215 GATGATGGCAGCGCGGAG 61.344 66.667 13.03 1.90 0.00 4.63
1489 1542 2.127869 CGCGGAGGAGGATGAGGAA 61.128 63.158 0.00 0.00 0.00 3.36
1516 1569 2.024941 GGATGATCCAAAGAACTGGGGT 60.025 50.000 6.60 0.00 36.28 4.95
1589 1642 3.202097 GAGTTTGATGAGCTAAGGAGGC 58.798 50.000 0.00 0.00 0.00 4.70
1612 1665 2.679059 GCAGGCAGAGAATAAGCTGTCA 60.679 50.000 0.00 0.00 39.14 3.58
1765 1818 5.537674 AGATTTTGCTGTCCTGTCAAAAGAT 59.462 36.000 0.00 0.00 41.23 2.40
1810 1863 0.397941 CAGCTCCTGAACTGGTTGGA 59.602 55.000 0.00 0.00 32.44 3.53
1828 1881 5.127682 GGTTGGATTACTGGCTGATTTGAAT 59.872 40.000 0.00 0.00 0.00 2.57
1837 1890 2.482490 GGCTGATTTGAATGATGCCCAC 60.482 50.000 0.00 0.00 33.45 4.61
1858 1911 2.019984 GAACAGCTGAAGGCAATAGGG 58.980 52.381 23.35 0.00 44.79 3.53
1868 1921 1.302949 GCAATAGGGCCAGTCACCA 59.697 57.895 6.18 0.00 0.00 4.17
1869 1922 0.323360 GCAATAGGGCCAGTCACCAA 60.323 55.000 6.18 0.00 0.00 3.67
1955 2008 3.489355 TGTCTGTTGGCTCATTGTCAAT 58.511 40.909 0.00 0.00 42.69 2.57
2268 2321 4.149910 GGCACCATGAAATTGCAAAAAG 57.850 40.909 1.71 0.00 38.04 2.27
2273 2326 5.049267 CACCATGAAATTGCAAAAAGGAAGG 60.049 40.000 1.71 3.38 0.00 3.46
2285 2338 0.033699 AAGGAAGGGCAAGGATGAGC 60.034 55.000 0.00 0.00 0.00 4.26
2361 2414 2.473816 GTTGAAGCAAAAAGGGCTGTC 58.526 47.619 0.00 0.00 41.66 3.51
2390 2445 4.020662 TGAAGCCAAAGTTGTCAAAAACCT 60.021 37.500 0.00 0.00 0.00 3.50
2706 2775 8.263940 ACACCAACAAATATACATACTGTCAC 57.736 34.615 0.00 0.00 0.00 3.67
2722 2791 5.613329 ACTGTCACGTAGGACCAAAATTTA 58.387 37.500 3.81 0.00 36.97 1.40
2723 2792 5.699458 ACTGTCACGTAGGACCAAAATTTAG 59.301 40.000 3.81 0.00 36.97 1.85
2785 2870 4.211584 CAGCTGAATCATCCTGATTTCGAG 59.788 45.833 8.42 3.13 46.20 4.04
2799 2884 5.478407 TGATTTCGAGCAAGTTGACATCTA 58.522 37.500 7.16 0.00 29.83 1.98
2806 2891 6.476706 TCGAGCAAGTTGACATCTATTACATG 59.523 38.462 7.16 0.00 0.00 3.21
2853 2946 5.988287 ACATTCCACATTCCTTTTGTTGTT 58.012 33.333 0.00 0.00 0.00 2.83
2856 2949 5.195001 TCCACATTCCTTTTGTTGTTAGC 57.805 39.130 0.00 0.00 0.00 3.09
2860 2953 5.984926 CACATTCCTTTTGTTGTTAGCATGT 59.015 36.000 0.00 0.00 0.00 3.21
2861 2954 5.984926 ACATTCCTTTTGTTGTTAGCATGTG 59.015 36.000 0.00 0.00 0.00 3.21
2930 3394 2.507484 TGGACTGAAACTGCATCCTTG 58.493 47.619 2.18 0.00 0.00 3.61
2951 3415 2.048444 ACCCAGCTATGTTGCAGATG 57.952 50.000 0.00 0.00 34.99 2.90
2965 3429 2.228059 GCAGATGTTATCAGCCAGCAT 58.772 47.619 0.00 0.00 35.98 3.79
3072 3615 7.498900 TGTCATGGTTTACATATTGATCCTGAC 59.501 37.037 0.00 0.00 37.84 3.51
3077 3621 7.065324 TGGTTTACATATTGATCCTGACGTTTC 59.935 37.037 0.00 0.00 0.00 2.78
3082 3626 2.631418 TGATCCTGACGTTTCTCGAC 57.369 50.000 0.00 0.00 42.86 4.20
3112 3656 5.185249 TCGAGTTCAGTAGGACTTTGCTTAT 59.815 40.000 0.00 0.00 0.00 1.73
3113 3657 5.289675 CGAGTTCAGTAGGACTTTGCTTATG 59.710 44.000 0.00 0.00 0.00 1.90
3129 3673 5.299148 TGCTTATGCTGCAAAAGTGAATTT 58.701 33.333 6.36 0.00 40.48 1.82
3178 3722 5.287035 GCATTTTGTTGCTAGCTGTGAATAC 59.713 40.000 17.23 3.54 39.57 1.89
3195 3739 9.529325 CTGTGAATACGAGAAGAAATACCATTA 57.471 33.333 0.00 0.00 0.00 1.90
3242 3786 1.344763 GTGCTACACTCAGGGACACTT 59.655 52.381 0.00 0.00 0.00 3.16
3345 3890 2.070783 GCCAACAATGCTGGTCAATTG 58.929 47.619 4.47 0.00 36.24 2.32
3379 3925 5.456548 AATGTTGTGTCATGCTTGAATCA 57.543 34.783 3.51 4.18 32.48 2.57
3381 3927 5.456548 TGTTGTGTCATGCTTGAATCATT 57.543 34.783 3.51 0.00 32.48 2.57
3387 3933 4.095932 TGTCATGCTTGAATCATTCTGCTC 59.904 41.667 3.51 6.10 32.48 4.26
3487 4059 3.949113 TGTTTTTCTTAGGGACGCAAACT 59.051 39.130 0.00 0.00 0.00 2.66
3515 4087 9.367444 CGTTACTCTTGTCTTACCAAAGATATT 57.633 33.333 0.00 0.00 43.50 1.28
3541 4113 9.214957 TGTCTGAAATACTTGATGAATTTACGT 57.785 29.630 0.00 0.00 0.00 3.57
3583 4155 7.519032 TCTACAAAACTAAATCCACCCTTTG 57.481 36.000 0.00 0.00 0.00 2.77
3590 4162 3.683365 AAATCCACCCTTTGAACATGC 57.317 42.857 0.00 0.00 0.00 4.06
3591 4163 2.307496 ATCCACCCTTTGAACATGCA 57.693 45.000 0.00 0.00 0.00 3.96
3625 4237 1.832883 ATCGGTTGTTGCAATGGCTA 58.167 45.000 0.59 0.00 41.91 3.93
3655 4272 6.509523 TTCCTAACCCTTTTTCTCTTCTGA 57.490 37.500 0.00 0.00 0.00 3.27
3668 4285 5.752036 TCTCTTCTGACCATCATTTCAGT 57.248 39.130 0.00 0.00 40.25 3.41
3829 4447 0.990374 AGAAGCTCAGCCAATCCAGT 59.010 50.000 0.00 0.00 0.00 4.00
3997 4615 1.412710 AGGAAGATTTCGCGGCAGATA 59.587 47.619 6.13 0.00 0.00 1.98
4034 4652 0.235926 GACACGCTCCAGAAACAAGC 59.764 55.000 0.00 0.00 0.00 4.01
4051 4669 2.549754 CAAGCAACTCAAGAATCCACGT 59.450 45.455 0.00 0.00 0.00 4.49
4066 4684 7.210873 AGAATCCACGTAAGAAATACAGGATC 58.789 38.462 8.93 0.00 43.19 3.36
4081 4699 9.911788 AAATACAGGATCAAGAGTGATAAACAT 57.088 29.630 0.00 0.00 44.83 2.71
4105 4723 2.278332 AAAGGAGGCAAGGTCAAGTC 57.722 50.000 0.00 0.00 0.00 3.01
4112 4730 1.597854 CAAGGTCAAGTCCGCAGCA 60.598 57.895 0.00 0.00 0.00 4.41
4253 4872 3.322230 TTGTTTGGTTTAGTTCGCGTC 57.678 42.857 5.77 0.31 0.00 5.19
4320 4939 7.320399 AGTAAACAGTTTTGGTGGAAAGAAAG 58.680 34.615 3.25 0.00 0.00 2.62
4426 5045 7.178983 TGTTTGATGGGAATTAGAAGCAGAAAT 59.821 33.333 0.00 0.00 0.00 2.17
4447 5069 8.772250 AGAAATATGAAGAACCAGTTCCTATCA 58.228 33.333 6.91 9.57 40.33 2.15
4448 5070 9.566432 GAAATATGAAGAACCAGTTCCTATCAT 57.434 33.333 19.35 19.35 40.33 2.45
4454 5076 7.824289 TGAAGAACCAGTTCCTATCATACTTTG 59.176 37.037 6.91 0.00 40.33 2.77
4493 5115 4.598406 TTACATAATGTTGCTGTGCTCG 57.402 40.909 0.00 0.00 0.00 5.03
4505 5127 0.249868 TGTGCTCGAAACAGTCAGGG 60.250 55.000 0.00 0.00 0.00 4.45
4511 5133 1.000955 TCGAAACAGTCAGGGCTCTTC 59.999 52.381 0.00 0.00 0.00 2.87
4527 5154 5.440610 GGCTCTTCTGATTCAAAGGGATTA 58.559 41.667 10.69 0.00 0.00 1.75
4583 5210 1.444836 TTTCCTATGGCGGTCGTTTG 58.555 50.000 0.00 0.00 0.00 2.93
4584 5211 0.609151 TTCCTATGGCGGTCGTTTGA 59.391 50.000 0.00 0.00 0.00 2.69
4585 5212 0.828022 TCCTATGGCGGTCGTTTGAT 59.172 50.000 0.00 0.00 0.00 2.57
4586 5213 1.208535 TCCTATGGCGGTCGTTTGATT 59.791 47.619 0.00 0.00 0.00 2.57
4587 5214 2.014128 CCTATGGCGGTCGTTTGATTT 58.986 47.619 0.00 0.00 0.00 2.17
4723 5775 3.381045 TCGTCCATTCATGTATTCGCTC 58.619 45.455 0.00 0.00 0.00 5.03
4724 5776 3.068165 TCGTCCATTCATGTATTCGCTCT 59.932 43.478 0.00 0.00 0.00 4.09
4735 5787 9.894783 TTCATGTATTCGCTCTAGTAGTAAATC 57.105 33.333 0.00 0.00 0.00 2.17
4785 5837 2.616510 CCTGCGAATCAAAGAGGACCTT 60.617 50.000 0.00 0.00 36.47 3.50
4801 5853 7.331791 AGAGGACCTTGAACTACATAATGTTC 58.668 38.462 0.00 0.00 41.87 3.18
4811 5863 5.200483 ACTACATAATGTTCATTGTGGGGG 58.800 41.667 20.29 13.84 0.00 5.40
4910 6125 3.071457 TCATCTTTGCCACTCAAGACTGA 59.929 43.478 0.00 0.00 35.84 3.41
4933 6148 1.075212 TGGAGGCATGGACATTGTCAA 59.925 47.619 18.09 7.78 33.68 3.18
5014 6230 3.571571 CTGCAGTCAACACATGGAAATG 58.428 45.455 5.25 0.00 0.00 2.32
5032 6248 2.877097 TGCCTTCTCAAGCAATACCA 57.123 45.000 0.00 0.00 35.69 3.25
5037 6253 5.300034 TGCCTTCTCAAGCAATACCATATTG 59.700 40.000 4.51 4.51 35.69 1.90
5060 6276 3.136443 TCCTTGGTCACAGAGTCAAACAT 59.864 43.478 0.00 0.00 0.00 2.71
5173 6395 3.201487 AGAACAGGCATTGGATGATCTCA 59.799 43.478 0.00 0.00 0.00 3.27
5178 6400 6.131264 ACAGGCATTGGATGATCTCATTTTA 58.869 36.000 0.00 0.00 36.57 1.52
5183 6405 8.985805 GGCATTGGATGATCTCATTTTATTTTC 58.014 33.333 0.00 0.00 36.57 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
326 328 2.305607 CCCCCATCCAAACCCTCGA 61.306 63.158 0.00 0.00 0.00 4.04
505 512 4.406972 CCTCTCACCCAAATCTCACAGATA 59.593 45.833 0.00 0.00 32.89 1.98
589 607 1.561643 TGCGTGATTTCCTCTCTCCT 58.438 50.000 0.00 0.00 0.00 3.69
668 688 4.589700 GTGTGGCGTGCGTGTGTG 62.590 66.667 0.00 0.00 0.00 3.82
794 835 0.035739 GCAAACGGGACAGGTTCCTA 59.964 55.000 0.00 0.00 45.09 2.94
797 838 2.265904 GGGCAAACGGGACAGGTTC 61.266 63.158 0.00 0.00 0.00 3.62
798 839 2.203437 GGGCAAACGGGACAGGTT 60.203 61.111 0.00 0.00 0.00 3.50
799 840 3.175710 AGGGCAAACGGGACAGGT 61.176 61.111 0.00 0.00 0.00 4.00
800 841 2.672996 CAGGGCAAACGGGACAGG 60.673 66.667 0.00 0.00 0.00 4.00
801 842 1.672356 CTCAGGGCAAACGGGACAG 60.672 63.158 0.00 0.00 0.00 3.51
802 843 2.429930 CTCAGGGCAAACGGGACA 59.570 61.111 0.00 0.00 0.00 4.02
803 844 3.056328 GCTCAGGGCAAACGGGAC 61.056 66.667 0.00 0.00 41.35 4.46
804 845 3.249189 AGCTCAGGGCAAACGGGA 61.249 61.111 0.00 0.00 44.79 5.14
805 846 2.747855 GAGCTCAGGGCAAACGGG 60.748 66.667 9.40 0.00 44.79 5.28
860 901 4.518970 GCCTTCAGTGGTTAACTCAAATCA 59.481 41.667 5.42 0.00 36.83 2.57
861 902 4.082733 GGCCTTCAGTGGTTAACTCAAATC 60.083 45.833 5.42 0.00 36.83 2.17
862 903 3.826729 GGCCTTCAGTGGTTAACTCAAAT 59.173 43.478 5.42 0.00 36.83 2.32
865 906 1.073284 GGGCCTTCAGTGGTTAACTCA 59.927 52.381 0.84 0.00 36.83 3.41
931 978 3.922893 GTGCGATGCGAGCAGAGC 61.923 66.667 16.71 16.71 46.10 4.09
933 980 2.507769 CTGTGCGATGCGAGCAGA 60.508 61.111 3.58 0.00 46.10 4.26
1267 1320 1.217585 CGCCCTCGACGTCGTAGATA 61.218 60.000 34.40 16.33 36.90 1.98
1405 1458 7.854916 GCTCTCTTGATTTTTGCAGTATATGAC 59.145 37.037 0.00 0.00 0.00 3.06
1448 1501 3.882326 ATCATCCCCGGCAGCCTG 61.882 66.667 10.54 2.04 0.00 4.85
1477 1530 1.403687 CCTCCGGTTCCTCATCCTCC 61.404 65.000 0.00 0.00 0.00 4.30
1480 1533 0.394565 CATCCTCCGGTTCCTCATCC 59.605 60.000 0.00 0.00 0.00 3.51
1489 1542 1.879575 TCTTTGGATCATCCTCCGGT 58.120 50.000 4.96 0.00 38.21 5.28
1516 1569 8.988060 TCATCATAGTATGTTTTCTTCCCTGTA 58.012 33.333 9.94 0.00 0.00 2.74
1589 1642 1.941294 CAGCTTATTCTCTGCCTGCAG 59.059 52.381 12.91 12.91 44.86 4.41
1612 1665 7.340232 TCATCTTCCAATCCGAAATCTTTCATT 59.660 33.333 3.77 0.00 37.01 2.57
1675 1728 0.749454 GCTTCACTTGATGGCCGGAT 60.749 55.000 5.05 0.00 0.00 4.18
1765 1818 5.163509 GCTGTACACTACATCCATCTTCTCA 60.164 44.000 0.00 0.00 38.15 3.27
1810 1863 5.221382 GGCATCATTCAAATCAGCCAGTAAT 60.221 40.000 0.00 0.00 40.29 1.89
1828 1881 1.672030 CAGCTGTTCGTGGGCATCA 60.672 57.895 5.25 0.00 0.00 3.07
1837 1890 1.667724 CCTATTGCCTTCAGCTGTTCG 59.332 52.381 14.67 2.96 44.23 3.95
1868 1921 1.980772 GCCCAGCTGCCAACTCATT 60.981 57.895 8.66 0.00 0.00 2.57
1869 1922 2.362120 GCCCAGCTGCCAACTCAT 60.362 61.111 8.66 0.00 0.00 2.90
1955 2008 6.689561 TCATAAGGAGGTAGAAGGTAATGGA 58.310 40.000 0.00 0.00 0.00 3.41
2184 2237 5.185056 GCACCCTGTTTTACTTTGTCCATAT 59.815 40.000 0.00 0.00 0.00 1.78
2186 2239 3.320826 GCACCCTGTTTTACTTTGTCCAT 59.679 43.478 0.00 0.00 0.00 3.41
2268 2321 0.106318 ATGCTCATCCTTGCCCTTCC 60.106 55.000 0.00 0.00 0.00 3.46
2273 2326 1.542492 CCCATATGCTCATCCTTGCC 58.458 55.000 0.00 0.00 0.00 4.52
2304 2357 7.439056 GGATTGCTCTTCTTTTCAACATTTCAA 59.561 33.333 0.00 0.00 0.00 2.69
2305 2358 6.925165 GGATTGCTCTTCTTTTCAACATTTCA 59.075 34.615 0.00 0.00 0.00 2.69
2361 2414 5.499139 TGACAACTTTGGCTTCAACTTAG 57.501 39.130 0.00 0.00 37.03 2.18
2630 2696 6.252967 TCACCACATGCATAAAACACTTAG 57.747 37.500 0.00 0.00 0.00 2.18
2631 2697 6.641169 TTCACCACATGCATAAAACACTTA 57.359 33.333 0.00 0.00 0.00 2.24
2706 2775 4.638421 TGGCATCTAAATTTTGGTCCTACG 59.362 41.667 0.00 0.00 0.00 3.51
2722 2791 9.632638 ATTTACAGTAAGAAACATATGGCATCT 57.367 29.630 1.65 4.64 0.00 2.90
2746 2816 9.842775 TGATTCAGCTGAATACTATCAAGAATT 57.157 29.630 35.74 14.60 44.14 2.17
2853 2946 6.340962 ACTCGCCTAATATTACACATGCTA 57.659 37.500 0.00 0.00 0.00 3.49
2856 2949 7.246674 ACAAACTCGCCTAATATTACACATG 57.753 36.000 0.00 0.00 0.00 3.21
2905 3369 5.324409 AGGATGCAGTTTCAGTCCATTTAA 58.676 37.500 3.24 0.00 0.00 1.52
2906 3370 4.922206 AGGATGCAGTTTCAGTCCATTTA 58.078 39.130 3.24 0.00 0.00 1.40
2907 3371 3.771216 AGGATGCAGTTTCAGTCCATTT 58.229 40.909 3.24 0.00 0.00 2.32
2908 3372 3.446442 AGGATGCAGTTTCAGTCCATT 57.554 42.857 3.24 0.00 0.00 3.16
2909 3373 3.087031 CAAGGATGCAGTTTCAGTCCAT 58.913 45.455 3.24 0.00 0.00 3.41
2912 3376 3.437049 GGTACAAGGATGCAGTTTCAGTC 59.563 47.826 0.00 0.00 0.00 3.51
2930 3394 2.691409 TCTGCAACATAGCTGGGTAC 57.309 50.000 0.00 0.00 34.63 3.34
2951 3415 9.254133 CATGTATAGTATATGCTGGCTGATAAC 57.746 37.037 3.24 0.00 0.00 1.89
3018 3559 7.286316 CAGCTCCAAAATCACCTAATAATCCTT 59.714 37.037 0.00 0.00 0.00 3.36
3072 3615 2.242769 TCGAGACATGTCGAGAAACG 57.757 50.000 19.85 17.43 43.91 3.60
3082 3626 3.692101 AGTCCTACTGAACTCGAGACATG 59.308 47.826 21.68 13.61 0.00 3.21
3112 3656 6.680874 AAATTCAAATTCACTTTTGCAGCA 57.319 29.167 0.00 0.00 36.69 4.41
3113 3657 7.188157 TCAAAATTCAAATTCACTTTTGCAGC 58.812 30.769 0.00 0.00 36.96 5.25
3129 3673 9.585099 GCCATGTCAAAGTATTATCAAAATTCA 57.415 29.630 0.00 0.00 0.00 2.57
3242 3786 0.606401 GCTGGAAGGCAAGTGTAGCA 60.606 55.000 0.00 0.00 0.00 3.49
3364 3910 4.014406 AGCAGAATGATTCAAGCATGACA 58.986 39.130 19.70 0.00 39.69 3.58
3379 3925 7.880195 AGATTACAAACACTAACAGAGCAGAAT 59.120 33.333 0.00 0.00 0.00 2.40
3381 3927 6.759272 AGATTACAAACACTAACAGAGCAGA 58.241 36.000 0.00 0.00 0.00 4.26
3487 4059 6.808829 TCTTTGGTAAGACAAGAGTAACGAA 58.191 36.000 0.00 0.00 35.49 3.85
3515 4087 9.214957 ACGTAAATTCATCAAGTATTTCAGACA 57.785 29.630 0.00 0.00 30.96 3.41
3540 4112 7.019774 TGTAGATGAGCAATAATCAGCAAAC 57.980 36.000 0.00 0.00 35.55 2.93
3541 4113 7.628769 TTGTAGATGAGCAATAATCAGCAAA 57.371 32.000 0.00 0.00 35.55 3.68
3590 4162 2.548057 ACCGATACACAAAGCACAAGTG 59.452 45.455 0.00 0.00 39.12 3.16
3591 4163 2.846193 ACCGATACACAAAGCACAAGT 58.154 42.857 0.00 0.00 0.00 3.16
3625 4237 8.338418 AGAGAAAAAGGGTTAGGAATAGCTAT 57.662 34.615 0.00 0.00 0.00 2.97
3655 4272 5.363580 ACCAGAAACAAACTGAAATGATGGT 59.636 36.000 0.00 0.00 37.54 3.55
3668 4285 6.294675 GGAATGTCATCATCACCAGAAACAAA 60.295 38.462 0.00 0.00 33.76 2.83
3829 4447 4.657039 TCATGATCATCACCATCTTCCTCA 59.343 41.667 4.86 0.00 0.00 3.86
3841 4459 5.368816 AGACCCTGAAGATTCATGATCATCA 59.631 40.000 4.86 10.08 39.46 3.07
3997 4615 0.251832 TCAGCCCTCGGTTCTTCTCT 60.252 55.000 0.00 0.00 0.00 3.10
4034 4652 6.539649 TTTCTTACGTGGATTCTTGAGTTG 57.460 37.500 0.00 0.00 0.00 3.16
4081 4699 4.349930 ACTTGACCTTGCCTCCTTTTACTA 59.650 41.667 0.00 0.00 0.00 1.82
4105 4723 3.793144 GGCTTCTTCGTGCTGCGG 61.793 66.667 0.00 0.00 41.72 5.69
4112 4730 1.545706 GGACCAGAGGGCTTCTTCGT 61.546 60.000 0.00 0.00 37.90 3.85
4253 4872 3.312828 TCAAACGAAAATTTCATGCCCG 58.687 40.909 6.53 0.00 0.00 6.13
4320 4939 4.448395 TCTTAAACAATGCAAACATGCTGC 59.552 37.500 12.35 12.35 36.36 5.25
4365 4984 1.279496 AGGCAGATAGAGCAACCACA 58.721 50.000 0.00 0.00 0.00 4.17
4426 5045 8.783660 AGTATGATAGGAACTGGTTCTTCATA 57.216 34.615 18.40 18.40 41.52 2.15
4447 5069 9.880157 AATAGAAGCATTTGCAAATCAAAGTAT 57.120 25.926 21.70 12.77 46.68 2.12
4493 5115 2.037772 TCAGAAGAGCCCTGACTGTTTC 59.962 50.000 0.00 0.00 35.89 2.78
4505 5127 5.882557 TGTAATCCCTTTGAATCAGAAGAGC 59.117 40.000 6.71 0.00 0.00 4.09
4527 5154 7.185318 TCCAAATGCTCCAAAAATCATATGT 57.815 32.000 1.90 0.00 0.00 2.29
4583 5210 3.010200 AGGATTCCAGTCCAGCAAATC 57.990 47.619 5.29 0.00 40.90 2.17
4584 5211 3.463048 AAGGATTCCAGTCCAGCAAAT 57.537 42.857 5.29 0.00 40.90 2.32
4585 5212 2.978156 AAGGATTCCAGTCCAGCAAA 57.022 45.000 5.29 0.00 40.90 3.68
4586 5213 2.239654 CCTAAGGATTCCAGTCCAGCAA 59.760 50.000 5.29 0.00 40.90 3.91
4587 5214 1.839994 CCTAAGGATTCCAGTCCAGCA 59.160 52.381 5.29 0.00 40.90 4.41
4694 5746 3.836949 ACATGAATGGACGAATGTTTGC 58.163 40.909 0.00 0.00 28.99 3.68
4701 5753 3.792401 AGCGAATACATGAATGGACGAA 58.208 40.909 0.00 0.00 0.00 3.85
4801 5853 1.756538 GTAATCCTTGCCCCCACAATG 59.243 52.381 0.00 0.00 0.00 2.82
4872 6087 7.307573 GGCAAAGATGATTTCAGGTTTTCTTTG 60.308 37.037 19.63 19.63 43.61 2.77
4874 6089 6.183360 TGGCAAAGATGATTTCAGGTTTTCTT 60.183 34.615 0.00 0.00 0.00 2.52
4910 6125 1.006281 ACAATGTCCATGCCTCCATGT 59.994 47.619 3.34 0.00 45.90 3.21
4933 6148 6.753913 TCCAAATATTCCAGCAGACTAGAT 57.246 37.500 0.00 0.00 0.00 1.98
5014 6230 5.300286 ACAATATGGTATTGCTTGAGAAGGC 59.700 40.000 9.06 0.00 32.55 4.35
5032 6248 4.532126 TGACTCTGTGACCAAGGACAATAT 59.468 41.667 0.00 0.00 0.00 1.28
5037 6253 2.872858 GTTTGACTCTGTGACCAAGGAC 59.127 50.000 0.00 0.00 0.00 3.85
5060 6276 3.582647 TCTCCAAGGTGTCTGCATTCTTA 59.417 43.478 0.00 0.00 0.00 2.10
5178 6400 9.586435 AGAAAAACAAGACGAAGAAATGAAAAT 57.414 25.926 0.00 0.00 0.00 1.82
5183 6405 9.464248 CAAAAAGAAAAACAAGACGAAGAAATG 57.536 29.630 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.