Multiple sequence alignment - TraesCS5D01G237400

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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 TraesCS5D01G237400 chr5D 100.000 3201 0 0 1 3201 345928883 345925683 0.000000e+00 5912.0
1 TraesCS5D01G237400 chr5D 77.945 730 129 18 1 706 389128160 389127439 8.210000e-116 427.0
2 TraesCS5D01G237400 chr5A 90.828 2464 162 33 776 3193 445286391 445288836 0.000000e+00 3240.0
3 TraesCS5D01G237400 chr5B 94.090 1049 30 16 776 1808 405724407 405725439 0.000000e+00 1565.0
4 TraesCS5D01G237400 chr5B 88.635 1311 107 23 1913 3193 405725535 405726833 0.000000e+00 1557.0
5 TraesCS5D01G237400 chr3A 76.690 725 139 18 4 706 579647661 579648377 3.010000e-100 375.0
6 TraesCS5D01G237400 chr1A 76.860 726 124 29 4 705 579767159 579766454 1.400000e-98 370.0
7 TraesCS5D01G237400 chr1A 74.691 727 150 23 2 707 584532232 584532945 3.120000e-75 292.0
8 TraesCS5D01G237400 chr1A 75.926 540 109 17 204 727 445653243 445653777 1.140000e-64 257.0
9 TraesCS5D01G237400 chr1A 75.485 567 113 17 167 721 494312903 494313455 1.470000e-63 254.0
10 TraesCS5D01G237400 chr2B 76.267 750 132 30 2 727 159585594 159584867 1.090000e-94 357.0
11 TraesCS5D01G237400 chr2B 77.331 547 105 12 204 732 66562259 66561714 4.010000e-79 305.0
12 TraesCS5D01G237400 chr2B 97.222 36 1 0 1838 1873 789268454 789268489 9.590000e-06 62.1
13 TraesCS5D01G237400 chr1D 76.066 727 143 20 2 706 487027461 487028178 1.830000e-92 350.0
14 TraesCS5D01G237400 chr1D 97.297 37 1 0 1838 1874 307667063 307667027 2.670000e-06 63.9
15 TraesCS5D01G237400 chr1B 76.066 727 142 18 2 706 678209709 678210425 1.830000e-92 350.0
16 TraesCS5D01G237400 chr1B 100.000 35 0 0 1838 1872 593826976 593826942 7.410000e-07 65.8
17 TraesCS5D01G237400 chr7A 76.294 734 119 37 1 705 250521934 250522641 1.100000e-89 340.0
18 TraesCS5D01G237400 chr7A 94.737 38 2 0 1836 1873 139470446 139470483 3.450000e-05 60.2
19 TraesCS5D01G237400 chr7A 97.143 35 1 0 1839 1873 734297322 734297356 3.450000e-05 60.2
20 TraesCS5D01G237400 chr6D 75.934 723 126 36 3 706 80033046 80033739 8.560000e-86 327.0
21 TraesCS5D01G237400 chr6D 77.039 466 85 14 253 705 179844625 179844169 6.860000e-62 248.0
22 TraesCS5D01G237400 chr3D 75.070 714 119 37 1 706 591108228 591107566 8.750000e-71 278.0
23 TraesCS5D01G237400 chr3D 77.087 515 82 24 227 729 62791907 62792397 6.810000e-67 265.0
24 TraesCS5D01G237400 chr7D 76.550 516 102 15 204 706 37650920 37650411 6.810000e-67 265.0
25 TraesCS5D01G237400 chr7D 75.313 559 98 22 166 706 636529305 636529841 6.910000e-57 231.0
26 TraesCS5D01G237400 chr2A 76.255 518 94 15 225 727 604923973 604924476 6.860000e-62 248.0
27 TraesCS5D01G237400 chr2A 76.141 482 94 14 255 721 1261521 1261046 1.920000e-57 233.0
28 TraesCS5D01G237400 chr2A 74.494 494 98 23 227 710 42711665 42711190 4.220000e-44 189.0
29 TraesCS5D01G237400 chr4A 73.311 607 110 23 59 644 682152303 682151728 3.280000e-40 176.0
30 TraesCS5D01G237400 chrUn 75.698 358 71 14 378 727 102394632 102394283 7.100000e-37 165.0
31 TraesCS5D01G237400 chr7B 97.368 38 1 0 1838 1875 482681781 482681818 7.410000e-07 65.8
32 TraesCS5D01G237400 chr2D 97.143 35 1 0 1839 1873 30666185 30666151 3.450000e-05 60.2
33 TraesCS5D01G237400 chr2D 92.308 39 3 0 1837 1875 151436192 151436230 4.460000e-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 TraesCS5D01G237400 chr5D 345925683 345928883 3200 True 5912 5912 100.0000 1 3201 1 chr5D.!!$R1 3200
1 TraesCS5D01G237400 chr5D 389127439 389128160 721 True 427 427 77.9450 1 706 1 chr5D.!!$R2 705
2 TraesCS5D01G237400 chr5A 445286391 445288836 2445 False 3240 3240 90.8280 776 3193 1 chr5A.!!$F1 2417
3 TraesCS5D01G237400 chr5B 405724407 405726833 2426 False 1561 1565 91.3625 776 3193 2 chr5B.!!$F1 2417
4 TraesCS5D01G237400 chr3A 579647661 579648377 716 False 375 375 76.6900 4 706 1 chr3A.!!$F1 702
5 TraesCS5D01G237400 chr1A 579766454 579767159 705 True 370 370 76.8600 4 705 1 chr1A.!!$R1 701
6 TraesCS5D01G237400 chr1A 584532232 584532945 713 False 292 292 74.6910 2 707 1 chr1A.!!$F3 705
7 TraesCS5D01G237400 chr1A 445653243 445653777 534 False 257 257 75.9260 204 727 1 chr1A.!!$F1 523
8 TraesCS5D01G237400 chr1A 494312903 494313455 552 False 254 254 75.4850 167 721 1 chr1A.!!$F2 554
9 TraesCS5D01G237400 chr2B 159584867 159585594 727 True 357 357 76.2670 2 727 1 chr2B.!!$R2 725
10 TraesCS5D01G237400 chr2B 66561714 66562259 545 True 305 305 77.3310 204 732 1 chr2B.!!$R1 528
11 TraesCS5D01G237400 chr1D 487027461 487028178 717 False 350 350 76.0660 2 706 1 chr1D.!!$F1 704
12 TraesCS5D01G237400 chr1B 678209709 678210425 716 False 350 350 76.0660 2 706 1 chr1B.!!$F1 704
13 TraesCS5D01G237400 chr7A 250521934 250522641 707 False 340 340 76.2940 1 705 1 chr7A.!!$F2 704
14 TraesCS5D01G237400 chr6D 80033046 80033739 693 False 327 327 75.9340 3 706 1 chr6D.!!$F1 703
15 TraesCS5D01G237400 chr3D 591107566 591108228 662 True 278 278 75.0700 1 706 1 chr3D.!!$R1 705
16 TraesCS5D01G237400 chr7D 37650411 37650920 509 True 265 265 76.5500 204 706 1 chr7D.!!$R1 502
17 TraesCS5D01G237400 chr7D 636529305 636529841 536 False 231 231 75.3130 166 706 1 chr7D.!!$F1 540
18 TraesCS5D01G237400 chr2A 604923973 604924476 503 False 248 248 76.2550 225 727 1 chr2A.!!$F1 502

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
737 809 0.109039 TGCGACGCATGTGCTAGTTA 60.109 50.0 20.50 0.00 39.32 2.24 F
1947 2051 0.239082 CTGGTGCGACAGTACGTACA 59.761 55.0 26.55 2.77 46.96 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2047 2162 0.038892 CCCACAGCATCAAACTGCAC 60.039 55.0 0.0 0.0 44.77 4.57 R
2780 2914 0.255318 AAGAGAAGAGCAGGCATGGG 59.745 55.0 0.0 0.0 0.00 4.00 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
38 39 1.748879 GCGCTGGCCATTGGTTAGA 60.749 57.895 5.51 0.00 0.00 2.10
45 46 3.565307 TGGCCATTGGTTAGAATGATCC 58.435 45.455 0.00 0.00 35.65 3.36
60 61 2.828877 TGATCCGTTTGTTCGAGTGTT 58.171 42.857 0.00 0.00 0.00 3.32
114 115 5.123027 GTGAGTTTGATCCTTCAACTCATCC 59.877 44.000 20.76 11.40 43.57 3.51
137 143 1.803334 TGTGGATTTTTACTCGCGCT 58.197 45.000 5.56 0.00 0.00 5.92
140 146 2.908626 GTGGATTTTTACTCGCGCTTTG 59.091 45.455 5.56 0.00 0.00 2.77
143 151 2.031037 TTTTTACTCGCGCTTTGCAG 57.969 45.000 5.56 0.00 46.97 4.41
145 153 1.438651 TTTACTCGCGCTTTGCAGAT 58.561 45.000 5.56 0.00 46.97 2.90
201 226 1.651987 CGTCCCACACGCTATTTGAT 58.348 50.000 0.00 0.00 42.87 2.57
215 240 9.378597 CACGCTATTTGATGATAAAAGAGAATG 57.621 33.333 1.13 0.00 29.32 2.67
216 241 8.072567 ACGCTATTTGATGATAAAAGAGAATGC 58.927 33.333 1.13 0.00 29.32 3.56
222 247 4.818534 TGATAAAAGAGAATGCGATGGC 57.181 40.909 0.00 0.00 40.52 4.40
223 248 3.565482 TGATAAAAGAGAATGCGATGGCC 59.435 43.478 0.00 0.00 38.85 5.36
233 258 2.033194 GCGATGGCCGGCTATAACC 61.033 63.158 26.69 12.55 39.04 2.85
286 318 5.923204 AGAGAATATGCTGGTTTGGTCTAG 58.077 41.667 0.00 0.00 0.00 2.43
307 344 4.278310 AGTTAAGAAAAACTGTGGGCACT 58.722 39.130 0.00 0.00 38.28 4.40
319 357 1.290009 GGGCACTTGAGCGCAAAAT 59.710 52.632 11.47 0.00 45.67 1.82
332 370 8.673626 TTGAGCGCAAAATTAATTAAAGAGAG 57.326 30.769 11.47 0.00 0.00 3.20
366 411 6.127140 GGTAAAGAAGAGACTGCCTGGTTATA 60.127 42.308 0.00 0.00 0.00 0.98
370 415 0.464452 AGACTGCCTGGTTATACGCC 59.536 55.000 0.00 0.00 0.00 5.68
375 420 1.145803 GCCTGGTTATACGCCGATTC 58.854 55.000 0.00 0.00 0.00 2.52
376 421 1.415374 CCTGGTTATACGCCGATTCG 58.585 55.000 0.00 0.00 0.00 3.34
395 440 6.142798 CGATTCGGCTAATGAAATTGGATTTG 59.857 38.462 0.00 0.00 36.87 2.32
401 446 2.077413 TGAAATTGGATTTGTGCGCC 57.923 45.000 4.18 0.00 31.47 6.53
406 451 2.504681 GGATTTGTGCGCCGCAAG 60.505 61.111 15.84 0.00 41.47 4.01
424 469 3.769300 GCAAGGAGTAACCCATCCAATTT 59.231 43.478 0.00 0.00 38.12 1.82
449 500 2.222774 CGTCGTAGGAGAGAGTTCGAAC 60.223 54.545 20.71 20.71 0.00 3.95
501 553 1.030457 CAAATGAGGAGGCAGCCATC 58.970 55.000 15.80 9.29 0.00 3.51
536 595 2.287608 GCGAACCTGGAGAAAACAAAGG 60.288 50.000 0.00 0.00 0.00 3.11
537 596 2.949644 CGAACCTGGAGAAAACAAAGGT 59.050 45.455 0.00 0.00 43.10 3.50
538 597 4.131596 CGAACCTGGAGAAAACAAAGGTA 58.868 43.478 0.00 0.00 40.37 3.08
542 601 3.746492 CCTGGAGAAAACAAAGGTACGAG 59.254 47.826 0.00 0.00 0.00 4.18
544 603 4.773013 TGGAGAAAACAAAGGTACGAGTT 58.227 39.130 0.00 0.00 0.00 3.01
592 652 4.704540 CCCTATCACTATCAAGATCTCGCT 59.295 45.833 0.00 0.00 0.00 4.93
603 663 4.081697 TCAAGATCTCGCTGGTCAAACATA 60.082 41.667 0.00 0.00 0.00 2.29
607 667 3.734463 TCTCGCTGGTCAAACATAACAA 58.266 40.909 0.00 0.00 0.00 2.83
647 708 2.490217 CTCTGTCGCCCCACTACG 59.510 66.667 0.00 0.00 0.00 3.51
729 801 0.670239 TCTCATGTTGCGACGCATGT 60.670 50.000 25.09 9.81 42.09 3.21
732 804 2.327343 ATGTTGCGACGCATGTGCT 61.327 52.632 25.09 4.24 38.76 4.40
733 805 1.018752 ATGTTGCGACGCATGTGCTA 61.019 50.000 25.09 4.13 38.76 3.49
734 806 1.059369 GTTGCGACGCATGTGCTAG 59.941 57.895 25.09 0.00 38.76 3.42
735 807 1.374125 TTGCGACGCATGTGCTAGT 60.374 52.632 25.09 0.00 38.76 2.57
736 808 0.948623 TTGCGACGCATGTGCTAGTT 60.949 50.000 25.09 0.00 38.76 2.24
737 809 0.109039 TGCGACGCATGTGCTAGTTA 60.109 50.000 20.50 0.00 39.32 2.24
738 810 1.209128 GCGACGCATGTGCTAGTTAT 58.791 50.000 16.42 0.00 39.32 1.89
739 811 1.593006 GCGACGCATGTGCTAGTTATT 59.407 47.619 16.42 0.00 39.32 1.40
740 812 2.792674 GCGACGCATGTGCTAGTTATTA 59.207 45.455 16.42 0.00 39.32 0.98
741 813 3.361724 GCGACGCATGTGCTAGTTATTAC 60.362 47.826 16.42 0.00 39.32 1.89
742 814 4.042398 CGACGCATGTGCTAGTTATTACT 58.958 43.478 6.08 0.00 39.32 2.24
743 815 5.209977 CGACGCATGTGCTAGTTATTACTA 58.790 41.667 6.08 0.00 39.32 1.82
744 816 5.856986 CGACGCATGTGCTAGTTATTACTAT 59.143 40.000 6.08 0.00 36.32 2.12
745 817 7.019418 CGACGCATGTGCTAGTTATTACTATA 58.981 38.462 6.08 0.00 36.32 1.31
746 818 7.216505 CGACGCATGTGCTAGTTATTACTATAG 59.783 40.741 6.08 0.00 36.32 1.31
747 819 7.313646 ACGCATGTGCTAGTTATTACTATAGG 58.686 38.462 6.08 0.00 36.32 2.57
748 820 7.039923 ACGCATGTGCTAGTTATTACTATAGGT 60.040 37.037 6.08 0.00 36.32 3.08
749 821 8.456471 CGCATGTGCTAGTTATTACTATAGGTA 58.544 37.037 4.43 0.00 36.32 3.08
771 843 8.478877 AGGTAAACAATAGACAGTCATAGAAGG 58.521 37.037 2.66 0.00 0.00 3.46
772 844 7.711339 GGTAAACAATAGACAGTCATAGAAGGG 59.289 40.741 2.66 0.00 0.00 3.95
773 845 5.283457 ACAATAGACAGTCATAGAAGGGC 57.717 43.478 2.66 0.00 0.00 5.19
774 846 4.202161 ACAATAGACAGTCATAGAAGGGCG 60.202 45.833 2.66 0.00 0.00 6.13
793 865 2.034053 GCGACAGGACACAAATTCCAAA 59.966 45.455 0.00 0.00 35.33 3.28
810 882 4.222336 TCCAAAGATTGTCCCAATGTTGT 58.778 39.130 0.79 0.00 0.00 3.32
814 886 6.018016 CCAAAGATTGTCCCAATGTTGTTTTC 60.018 38.462 0.79 0.00 0.00 2.29
815 887 5.213891 AGATTGTCCCAATGTTGTTTTCC 57.786 39.130 0.00 0.00 0.00 3.13
816 888 4.653341 AGATTGTCCCAATGTTGTTTTCCA 59.347 37.500 0.00 0.00 0.00 3.53
817 889 4.826274 TTGTCCCAATGTTGTTTTCCAA 57.174 36.364 0.00 0.00 0.00 3.53
818 890 4.826274 TGTCCCAATGTTGTTTTCCAAA 57.174 36.364 0.00 0.00 34.07 3.28
819 891 4.764172 TGTCCCAATGTTGTTTTCCAAAG 58.236 39.130 0.00 0.00 34.07 2.77
820 892 4.223923 TGTCCCAATGTTGTTTTCCAAAGT 59.776 37.500 0.00 0.00 34.07 2.66
883 965 3.697439 ATCCCCATCCAACGGTGCG 62.697 63.158 0.00 0.00 0.00 5.34
1185 1273 6.094048 ACCACAGCTTCACACATATGTATTTC 59.906 38.462 8.32 0.00 36.72 2.17
1362 1466 4.934602 TCTTGAACGAATCACATACATGCA 59.065 37.500 0.00 0.00 37.92 3.96
1363 1467 5.585844 TCTTGAACGAATCACATACATGCAT 59.414 36.000 0.00 0.00 37.92 3.96
1547 1651 1.445582 GTTGCTCCCGTACGTGAGG 60.446 63.158 25.65 15.10 0.00 3.86
1554 1658 1.064296 CCGTACGTGAGGCTAGCTG 59.936 63.158 15.72 2.48 0.00 4.24
1769 1873 0.316196 GCTGCGGCTTAATTAGTGCG 60.316 55.000 11.21 0.00 35.22 5.34
1833 1937 5.942236 ACTACTGTCGAGGTAATCACACTTA 59.058 40.000 0.00 0.00 0.00 2.24
1834 1938 5.056894 ACTGTCGAGGTAATCACACTTAC 57.943 43.478 0.00 0.00 0.00 2.34
1836 1940 5.942236 ACTGTCGAGGTAATCACACTTACTA 59.058 40.000 0.00 0.00 33.13 1.82
1875 1979 1.679153 GGGACGAAAGCCTGTTTCAAA 59.321 47.619 0.00 0.00 0.00 2.69
1877 1981 3.429684 GGGACGAAAGCCTGTTTCAAAAA 60.430 43.478 0.00 0.00 0.00 1.94
1885 1989 4.546570 AGCCTGTTTCAAAAAGTAATCGC 58.453 39.130 0.00 0.00 0.00 4.58
1897 2001 3.344904 AGTAATCGCGCGTACAGTATT 57.655 42.857 30.98 21.88 0.00 1.89
1901 2005 1.401530 TCGCGCGTACAGTATTATGC 58.598 50.000 30.98 0.00 0.00 3.14
1946 2050 0.518636 TCTGGTGCGACAGTACGTAC 59.481 55.000 18.10 18.10 45.13 3.67
1947 2051 0.239082 CTGGTGCGACAGTACGTACA 59.761 55.000 26.55 2.77 46.96 2.90
1949 2053 0.730494 GGTGCGACAGTACGTACACC 60.730 60.000 26.55 19.32 46.96 4.16
1951 2055 1.464608 GTGCGACAGTACGTACACCTA 59.535 52.381 26.55 5.98 45.18 3.08
1955 2070 4.394610 TGCGACAGTACGTACACCTATTTA 59.605 41.667 26.55 4.28 35.59 1.40
1956 2071 5.066375 TGCGACAGTACGTACACCTATTTAT 59.934 40.000 26.55 0.40 35.59 1.40
1985 2100 9.760077 TTCTTTCGAAAGGGAAGTATATATCAC 57.240 33.333 31.82 0.00 36.67 3.06
2014 2129 9.896263 GAAATTAAGTAGTCTTCTATACCCTCG 57.104 37.037 0.00 0.00 35.36 4.63
2017 2132 8.618702 TTAAGTAGTCTTCTATACCCTCGATG 57.381 38.462 0.00 0.00 35.36 3.84
2053 2170 2.967599 TCAGCATCTATTCGTGCAGT 57.032 45.000 0.00 0.00 43.63 4.40
2262 2383 4.151867 GGAGCGACGTTTCTTTTACAGATT 59.848 41.667 0.00 0.00 0.00 2.40
2265 2386 4.839174 GCGACGTTTCTTTTACAGATTGAC 59.161 41.667 0.00 0.00 0.00 3.18
2278 2399 3.055819 ACAGATTGACGTGCCTCTGTAAT 60.056 43.478 17.30 0.00 44.80 1.89
2374 2495 7.594849 AATCTAGGGGAATGGTCATAATCAT 57.405 36.000 0.00 0.00 0.00 2.45
2376 2497 6.090870 TCTAGGGGAATGGTCATAATCATCA 58.909 40.000 0.00 0.00 0.00 3.07
2471 2593 0.244721 GCTCTGGGTCATGTTTTGCC 59.755 55.000 0.00 0.00 0.00 4.52
2489 2611 4.582701 TGCCACTTGTTTTGTTATCCAG 57.417 40.909 0.00 0.00 0.00 3.86
2494 2616 6.705825 GCCACTTGTTTTGTTATCCAGAAATT 59.294 34.615 0.00 0.00 0.00 1.82
2512 2637 1.491274 TTCCAGTCTGCATGAGGGCA 61.491 55.000 0.00 0.00 42.53 5.36
2541 2666 2.027460 CAGTGTTTGGTTGCCCGC 59.973 61.111 0.00 0.00 0.00 6.13
2573 2704 1.527844 GGCCTGGGTGATGCAGATC 60.528 63.158 0.00 0.00 0.00 2.75
2574 2705 1.890979 GCCTGGGTGATGCAGATCG 60.891 63.158 0.00 0.00 0.00 3.69
2580 2711 0.729116 GGTGATGCAGATCGTTGTGG 59.271 55.000 0.00 0.00 0.00 4.17
2643 2774 2.235402 CCTATGTGGTGAGTTTACCGGT 59.765 50.000 13.98 13.98 43.87 5.28
2654 2785 4.343526 TGAGTTTACCGGTTACCACTGTTA 59.656 41.667 15.04 0.00 0.00 2.41
2684 2815 7.708752 TCGCATTGTACTTATGATCATACACAA 59.291 33.333 24.70 24.70 30.79 3.33
2713 2847 8.514594 AGGATAACAAACATACAACAATGACAG 58.485 33.333 0.00 0.00 0.00 3.51
2719 2853 5.902613 ACATACAACAATGACAGATTGGG 57.097 39.130 0.00 0.00 33.56 4.12
2752 2886 6.152932 TGAAGTCGTTCAACCTACTTAACT 57.847 37.500 3.48 0.00 39.85 2.24
2763 2897 6.604396 TCAACCTACTTAACTCGATATGACCA 59.396 38.462 0.00 0.00 0.00 4.02
2764 2898 6.636562 ACCTACTTAACTCGATATGACCAG 57.363 41.667 0.00 0.00 0.00 4.00
2765 2899 5.009811 ACCTACTTAACTCGATATGACCAGC 59.990 44.000 0.00 0.00 0.00 4.85
2768 2902 0.249489 AACTCGATATGACCAGCGCC 60.249 55.000 2.29 0.00 0.00 6.53
2780 2914 3.400054 AGCGCCCCCTTGTCTACC 61.400 66.667 2.29 0.00 0.00 3.18
2788 2922 1.281925 CCCTTGTCTACCCCATGCCT 61.282 60.000 0.00 0.00 0.00 4.75
2806 2940 3.517100 TGCCTGCTCTTCTCTTTGACTAT 59.483 43.478 0.00 0.00 0.00 2.12
2868 3002 7.180229 TCTCAAACCCTCTATGACAACTATTCA 59.820 37.037 0.00 0.00 0.00 2.57
2875 3009 7.382488 CCCTCTATGACAACTATTCATGTAACG 59.618 40.741 0.00 0.00 35.31 3.18
2884 3018 7.874016 ACAACTATTCATGTAACGGTTCACTTA 59.126 33.333 0.00 0.00 0.00 2.24
2909 3043 2.497138 TGGCAAGTCTGTCATGAACTG 58.503 47.619 0.00 0.00 30.26 3.16
2928 3062 2.498078 CTGTAGACTCCTGAAACCCTCC 59.502 54.545 0.00 0.00 0.00 4.30
2929 3063 2.111972 TGTAGACTCCTGAAACCCTCCT 59.888 50.000 0.00 0.00 0.00 3.69
2943 3077 1.002087 CCCTCCTTGAGTACACCACAC 59.998 57.143 0.00 0.00 0.00 3.82
2946 3080 2.365617 CTCCTTGAGTACACCACACACT 59.634 50.000 0.00 0.00 0.00 3.55
2951 3085 5.010314 CCTTGAGTACACCACACACTACTTA 59.990 44.000 0.00 0.00 0.00 2.24
2955 3089 6.265876 TGAGTACACCACACACTACTTAATCA 59.734 38.462 0.00 0.00 0.00 2.57
2958 3092 5.676552 ACACCACACACTACTTAATCAACA 58.323 37.500 0.00 0.00 0.00 3.33
3004 3138 6.387041 ACATGGAGAACAAGCAATCATATG 57.613 37.500 0.00 0.00 0.00 1.78
3005 3139 5.301045 ACATGGAGAACAAGCAATCATATGG 59.699 40.000 2.13 0.00 0.00 2.74
3006 3140 3.633525 TGGAGAACAAGCAATCATATGGC 59.366 43.478 2.13 0.00 0.00 4.40
3007 3141 3.633525 GGAGAACAAGCAATCATATGGCA 59.366 43.478 2.13 0.00 0.00 4.92
3018 3154 5.250982 CAATCATATGGCAGATAAGGCTGA 58.749 41.667 2.13 0.00 38.14 4.26
3024 3160 2.573462 TGGCAGATAAGGCTGAGTTTCT 59.427 45.455 0.00 0.00 38.14 2.52
3048 3184 7.615365 TCTGACAAAATTAGGGCATGACTAAAT 59.385 33.333 12.44 4.24 34.42 1.40
3062 3198 6.521133 GCATGACTAAATTCAACGTCTTTCAG 59.479 38.462 0.00 0.00 0.00 3.02
3084 3220 3.694072 GTGCCTACAATGGTTAGCATCAA 59.306 43.478 0.00 0.00 36.58 2.57
3089 3225 7.287466 TGCCTACAATGGTTAGCATCAATAATT 59.713 33.333 0.00 0.00 31.35 1.40
3096 3232 5.754406 TGGTTAGCATCAATAATTGCAATGC 59.246 36.000 13.82 11.75 41.35 3.56
3098 3234 3.386486 AGCATCAATAATTGCAATGCGG 58.614 40.909 13.82 3.59 42.44 5.69
3118 3254 3.668757 CGGACAAGAACAATGCATCACTG 60.669 47.826 0.00 0.00 0.00 3.66
3160 3296 1.197055 CAATGTTGAGCATGCATCGC 58.803 50.000 21.98 11.67 37.96 4.58
3165 3301 3.962421 GAGCATGCATCGCTGGGC 61.962 66.667 21.98 11.49 40.63 5.36
3169 3305 2.116533 CATGCATCGCTGGGCAAGA 61.117 57.895 0.00 0.00 44.20 3.02
3194 3330 4.329392 TGAATGATCTTCACTGCATGTGT 58.671 39.130 13.59 0.00 46.27 3.72
3195 3331 4.763279 TGAATGATCTTCACTGCATGTGTT 59.237 37.500 13.59 2.49 46.27 3.32
3196 3332 5.242171 TGAATGATCTTCACTGCATGTGTTT 59.758 36.000 13.59 1.63 46.27 2.83
3197 3333 5.717078 ATGATCTTCACTGCATGTGTTTT 57.283 34.783 13.59 1.89 46.27 2.43
3198 3334 5.518848 TGATCTTCACTGCATGTGTTTTT 57.481 34.783 13.59 2.16 46.27 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.064060 GCCAGCGCGAATGTTTAAGAT 59.936 47.619 12.10 0.00 0.00 2.40
38 39 3.399330 ACACTCGAACAAACGGATCATT 58.601 40.909 0.00 0.00 0.00 2.57
45 46 3.579147 TGCTAAACACTCGAACAAACG 57.421 42.857 0.00 0.00 0.00 3.60
114 115 3.360758 GCGCGAGTAAAAATCCACAAAAG 59.639 43.478 12.10 0.00 0.00 2.27
137 143 3.252215 CCAAAACGACCTGTATCTGCAAA 59.748 43.478 0.00 0.00 0.00 3.68
140 146 2.159627 CACCAAAACGACCTGTATCTGC 59.840 50.000 0.00 0.00 0.00 4.26
143 151 1.467342 GGCACCAAAACGACCTGTATC 59.533 52.381 0.00 0.00 0.00 2.24
145 153 0.470766 AGGCACCAAAACGACCTGTA 59.529 50.000 0.00 0.00 0.00 2.74
201 226 3.565482 GGCCATCGCATTCTCTTTTATCA 59.435 43.478 0.00 0.00 36.38 2.15
215 240 2.033194 GGTTATAGCCGGCCATCGC 61.033 63.158 26.15 11.38 37.59 4.58
216 241 4.278956 GGTTATAGCCGGCCATCG 57.721 61.111 26.15 0.00 38.88 3.84
233 258 3.676091 GTGCCCACGATTTCTTTCG 57.324 52.632 0.00 0.00 44.56 3.46
286 318 4.649088 AGTGCCCACAGTTTTTCTTAAC 57.351 40.909 0.82 0.00 0.00 2.01
307 344 8.296713 ACTCTCTTTAATTAATTTTGCGCTCAA 58.703 29.630 9.73 0.80 0.00 3.02
332 370 6.366604 GCAGTCTCTTCTTTACCAGAGTTTAC 59.633 42.308 0.00 0.00 38.20 2.01
370 415 4.811555 TCCAATTTCATTAGCCGAATCG 57.188 40.909 0.00 0.00 0.00 3.34
375 420 4.268405 GCACAAATCCAATTTCATTAGCCG 59.732 41.667 0.00 0.00 0.00 5.52
376 421 4.268405 CGCACAAATCCAATTTCATTAGCC 59.732 41.667 0.00 0.00 0.00 3.93
395 440 2.740826 TTACTCCTTGCGGCGCAC 60.741 61.111 36.57 5.66 38.71 5.34
401 446 0.251916 TGGATGGGTTACTCCTTGCG 59.748 55.000 0.00 0.00 36.25 4.85
406 451 2.357952 GCGAAATTGGATGGGTTACTCC 59.642 50.000 0.00 0.00 0.00 3.85
407 452 2.357952 GGCGAAATTGGATGGGTTACTC 59.642 50.000 0.00 0.00 0.00 2.59
413 458 1.727467 GACGGCGAAATTGGATGGG 59.273 57.895 16.62 0.00 0.00 4.00
424 469 1.521010 CTCTCTCCTACGACGGCGA 60.521 63.158 22.49 0.00 41.64 5.54
449 500 2.733227 GCGATCTTTGAAGCATGGTTGG 60.733 50.000 16.18 2.82 0.00 3.77
485 537 2.459086 GGGATGGCTGCCTCCTCAT 61.459 63.158 25.91 11.53 0.00 2.90
501 553 3.234630 TTCGCCTCCGTGTCAAGGG 62.235 63.158 4.87 0.00 35.54 3.95
531 588 2.140717 GACCACCAACTCGTACCTTTG 58.859 52.381 0.00 0.00 0.00 2.77
536 595 1.735559 GGCGACCACCAACTCGTAC 60.736 63.158 0.00 0.00 32.30 3.67
537 596 2.652530 GGCGACCACCAACTCGTA 59.347 61.111 0.00 0.00 32.30 3.43
538 597 4.657824 CGGCGACCACCAACTCGT 62.658 66.667 0.00 0.00 32.30 4.18
592 652 3.734463 TCTCGCTTGTTATGTTTGACCA 58.266 40.909 0.00 0.00 0.00 4.02
647 708 3.004315 TGTTCATCAAAAAGGTCTTCGCC 59.996 43.478 0.00 0.00 0.00 5.54
721 793 7.485277 CCTATAGTAATAACTAGCACATGCGTC 59.515 40.741 0.00 0.00 41.46 5.19
745 817 8.478877 CCTTCTATGACTGTCTATTGTTTACCT 58.521 37.037 9.51 0.00 0.00 3.08
746 818 7.711339 CCCTTCTATGACTGTCTATTGTTTACC 59.289 40.741 9.51 0.00 0.00 2.85
747 819 7.224949 GCCCTTCTATGACTGTCTATTGTTTAC 59.775 40.741 9.51 0.00 0.00 2.01
748 820 7.272978 GCCCTTCTATGACTGTCTATTGTTTA 58.727 38.462 9.51 0.00 0.00 2.01
749 821 6.116126 GCCCTTCTATGACTGTCTATTGTTT 58.884 40.000 9.51 0.00 0.00 2.83
750 822 5.675538 GCCCTTCTATGACTGTCTATTGTT 58.324 41.667 9.51 0.00 0.00 2.83
751 823 4.202161 CGCCCTTCTATGACTGTCTATTGT 60.202 45.833 9.51 0.00 0.00 2.71
752 824 4.038042 TCGCCCTTCTATGACTGTCTATTG 59.962 45.833 9.51 3.03 0.00 1.90
753 825 4.038162 GTCGCCCTTCTATGACTGTCTATT 59.962 45.833 9.51 0.00 0.00 1.73
754 826 3.570550 GTCGCCCTTCTATGACTGTCTAT 59.429 47.826 9.51 3.99 0.00 1.98
755 827 2.950309 GTCGCCCTTCTATGACTGTCTA 59.050 50.000 9.51 0.00 0.00 2.59
756 828 1.751924 GTCGCCCTTCTATGACTGTCT 59.248 52.381 9.51 0.00 0.00 3.41
757 829 1.476891 TGTCGCCCTTCTATGACTGTC 59.523 52.381 0.00 0.00 32.64 3.51
758 830 1.478510 CTGTCGCCCTTCTATGACTGT 59.521 52.381 0.00 0.00 32.64 3.55
759 831 1.202463 CCTGTCGCCCTTCTATGACTG 60.202 57.143 0.00 0.00 32.64 3.51
760 832 1.115467 CCTGTCGCCCTTCTATGACT 58.885 55.000 0.00 0.00 32.64 3.41
761 833 1.112113 TCCTGTCGCCCTTCTATGAC 58.888 55.000 0.00 0.00 0.00 3.06
762 834 1.112113 GTCCTGTCGCCCTTCTATGA 58.888 55.000 0.00 0.00 0.00 2.15
763 835 0.824109 TGTCCTGTCGCCCTTCTATG 59.176 55.000 0.00 0.00 0.00 2.23
764 836 0.824759 GTGTCCTGTCGCCCTTCTAT 59.175 55.000 0.00 0.00 0.00 1.98
765 837 0.541063 TGTGTCCTGTCGCCCTTCTA 60.541 55.000 0.00 0.00 0.00 2.10
766 838 1.407656 TTGTGTCCTGTCGCCCTTCT 61.408 55.000 0.00 0.00 0.00 2.85
767 839 0.534203 TTTGTGTCCTGTCGCCCTTC 60.534 55.000 0.00 0.00 0.00 3.46
768 840 0.110486 ATTTGTGTCCTGTCGCCCTT 59.890 50.000 0.00 0.00 0.00 3.95
769 841 0.110486 AATTTGTGTCCTGTCGCCCT 59.890 50.000 0.00 0.00 0.00 5.19
770 842 0.521735 GAATTTGTGTCCTGTCGCCC 59.478 55.000 0.00 0.00 0.00 6.13
771 843 0.521735 GGAATTTGTGTCCTGTCGCC 59.478 55.000 0.00 0.00 31.94 5.54
772 844 1.234821 TGGAATTTGTGTCCTGTCGC 58.765 50.000 0.00 0.00 36.03 5.19
773 845 3.563808 TCTTTGGAATTTGTGTCCTGTCG 59.436 43.478 0.00 0.00 36.03 4.35
774 846 5.712152 ATCTTTGGAATTTGTGTCCTGTC 57.288 39.130 0.00 0.00 36.03 3.51
793 865 5.130145 TTGGAAAACAACATTGGGACAATCT 59.870 36.000 0.00 0.00 37.65 2.40
810 882 8.140677 TCGTTCGTCTATTTTACTTTGGAAAA 57.859 30.769 0.00 0.00 0.00 2.29
814 886 5.445540 GCCTCGTTCGTCTATTTTACTTTGG 60.446 44.000 0.00 0.00 0.00 3.28
815 887 5.119588 TGCCTCGTTCGTCTATTTTACTTTG 59.880 40.000 0.00 0.00 0.00 2.77
816 888 5.232463 TGCCTCGTTCGTCTATTTTACTTT 58.768 37.500 0.00 0.00 0.00 2.66
817 889 4.813027 TGCCTCGTTCGTCTATTTTACTT 58.187 39.130 0.00 0.00 0.00 2.24
818 890 4.445452 TGCCTCGTTCGTCTATTTTACT 57.555 40.909 0.00 0.00 0.00 2.24
819 891 4.208666 GGATGCCTCGTTCGTCTATTTTAC 59.791 45.833 0.00 0.00 0.00 2.01
820 892 4.365723 GGATGCCTCGTTCGTCTATTTTA 58.634 43.478 0.00 0.00 0.00 1.52
883 965 0.521735 GTGAAGGATTTGACGTGCCC 59.478 55.000 0.00 0.00 0.00 5.36
1185 1273 1.293924 GATCAGATGCCACAACTCGG 58.706 55.000 0.00 0.00 0.00 4.63
1362 1466 6.422100 GCGCGATCACTGATTAATATCCATAT 59.578 38.462 12.10 0.00 0.00 1.78
1363 1467 5.748630 GCGCGATCACTGATTAATATCCATA 59.251 40.000 12.10 0.00 0.00 2.74
1547 1651 1.082690 GGTCAGAACAAGCAGCTAGC 58.917 55.000 6.62 6.62 46.19 3.42
1554 1658 1.200020 CCAAATCGGGTCAGAACAAGC 59.800 52.381 0.00 0.00 0.00 4.01
1585 1689 2.500229 ACACAATCAGTTAACCACCCG 58.500 47.619 0.88 0.00 0.00 5.28
1755 1859 8.898983 TTATTTGTAAACGCACTAATTAAGCC 57.101 30.769 4.51 0.00 0.00 4.35
1836 1940 8.836268 TCGTCCCGTTTTATATATAAAGCAAT 57.164 30.769 23.58 0.00 34.42 3.56
1853 1957 0.883370 GAAACAGGCTTTCGTCCCGT 60.883 55.000 0.00 0.00 0.00 5.28
1875 1979 1.986698 ACTGTACGCGCGATTACTTT 58.013 45.000 39.36 15.18 0.00 2.66
1877 1981 3.344904 AATACTGTACGCGCGATTACT 57.655 42.857 39.36 16.91 0.00 2.24
1885 1989 0.433492 GCCGCATAATACTGTACGCG 59.567 55.000 3.53 3.53 42.21 6.01
1897 2001 1.340248 GAACTAGCTAGGTGCCGCATA 59.660 52.381 24.35 0.00 44.23 3.14
1901 2005 0.818296 ACTGAACTAGCTAGGTGCCG 59.182 55.000 24.35 10.76 44.23 5.69
2047 2162 0.038892 CCCACAGCATCAAACTGCAC 60.039 55.000 0.00 0.00 44.77 4.57
2080 2197 3.963476 TCCCTTGGGAACTTTCTGAAA 57.037 42.857 5.82 2.44 0.00 2.69
2222 2343 3.533547 GCTCCTGATCATCCATATCTGC 58.466 50.000 0.00 0.00 0.00 4.26
2262 2383 9.772973 AAAAATATATATTACAGAGGCACGTCA 57.227 29.630 8.39 0.00 0.00 4.35
2374 2495 1.066303 GCAACCAAACACGTCCAATGA 59.934 47.619 0.00 0.00 0.00 2.57
2376 2497 1.336755 GAGCAACCAAACACGTCCAAT 59.663 47.619 0.00 0.00 0.00 3.16
2471 2593 7.925483 TGGAATTTCTGGATAACAAAACAAGTG 59.075 33.333 0.00 0.00 0.00 3.16
2489 2611 2.686915 CCCTCATGCAGACTGGAATTTC 59.313 50.000 0.00 0.00 0.00 2.17
2494 2616 1.276859 ATGCCCTCATGCAGACTGGA 61.277 55.000 4.26 0.73 45.93 3.86
2512 2637 2.173519 CAAACACTGGGGAGCATTGAT 58.826 47.619 0.00 0.00 0.00 2.57
2541 2666 0.109319 CAGGCCAAAATCCCGAAACG 60.109 55.000 5.01 0.00 0.00 3.60
2573 2704 0.102120 ATGTGCAACCAACCACAACG 59.898 50.000 0.00 0.00 44.22 4.10
2574 2705 2.307934 AATGTGCAACCAACCACAAC 57.692 45.000 0.00 0.00 44.22 3.32
2580 2711 3.309410 CAGGTCAAAAATGTGCAACCAAC 59.691 43.478 2.97 0.00 34.36 3.77
2643 2774 5.182487 ACAATGCGATGATAACAGTGGTAA 58.818 37.500 0.00 0.00 33.92 2.85
2654 2785 9.091784 GTATGATCATAAGTACAATGCGATGAT 57.908 33.333 16.97 0.00 36.88 2.45
2698 2832 4.675510 GCCCAATCTGTCATTGTTGTATG 58.324 43.478 0.00 0.00 0.00 2.39
2706 2840 6.942005 TCATAATATTCGCCCAATCTGTCATT 59.058 34.615 0.00 0.00 0.00 2.57
2708 2842 5.863965 TCATAATATTCGCCCAATCTGTCA 58.136 37.500 0.00 0.00 0.00 3.58
2713 2847 5.408604 ACGACTTCATAATATTCGCCCAATC 59.591 40.000 0.00 0.00 32.91 2.67
2719 2853 6.018994 AGGTTGAACGACTTCATAATATTCGC 60.019 38.462 0.00 0.00 36.26 4.70
2752 2886 2.734591 GGGCGCTGGTCATATCGA 59.265 61.111 7.64 0.00 0.00 3.59
2763 2897 3.400054 GGTAGACAAGGGGGCGCT 61.400 66.667 7.64 0.00 0.00 5.92
2764 2898 4.484872 GGGTAGACAAGGGGGCGC 62.485 72.222 0.00 0.00 0.00 6.53
2765 2899 3.793888 GGGGTAGACAAGGGGGCG 61.794 72.222 0.00 0.00 0.00 6.13
2768 2902 1.227383 GCATGGGGTAGACAAGGGG 59.773 63.158 0.00 0.00 0.00 4.79
2775 2909 0.621571 AAGAGCAGGCATGGGGTAGA 60.622 55.000 0.00 0.00 0.00 2.59
2780 2914 0.255318 AAGAGAAGAGCAGGCATGGG 59.745 55.000 0.00 0.00 0.00 4.00
2788 2922 6.352016 AGTTCATAGTCAAAGAGAAGAGCA 57.648 37.500 0.00 0.00 0.00 4.26
2806 2940 9.213777 AGGTAGATGATTATTACTCCAAGTTCA 57.786 33.333 0.00 0.00 0.00 3.18
2821 2955 6.331572 TGAGACTAGAGAGGAGGTAGATGATT 59.668 42.308 0.00 0.00 0.00 2.57
2868 3002 5.175859 CCATGAGTAAGTGAACCGTTACAT 58.824 41.667 0.00 0.00 32.49 2.29
2884 3018 2.303890 TCATGACAGACTTGCCATGAGT 59.696 45.455 2.96 0.00 45.49 3.41
2909 3043 2.822697 AGGAGGGTTTCAGGAGTCTAC 58.177 52.381 0.00 0.00 0.00 2.59
2928 3062 4.585955 AGTAGTGTGTGGTGTACTCAAG 57.414 45.455 0.00 0.00 34.84 3.02
2929 3063 6.468333 TTAAGTAGTGTGTGGTGTACTCAA 57.532 37.500 0.00 0.00 34.84 3.02
2943 3077 6.801539 TCTGCCTTTGTTGATTAAGTAGTG 57.198 37.500 0.00 0.00 0.00 2.74
2946 3080 8.635765 ATTCTTCTGCCTTTGTTGATTAAGTA 57.364 30.769 0.00 0.00 0.00 2.24
2989 3123 6.015688 CCTTATCTGCCATATGATTGCTTGTT 60.016 38.462 3.65 0.00 0.00 2.83
3004 3138 2.941720 CAGAAACTCAGCCTTATCTGCC 59.058 50.000 0.00 0.00 34.19 4.85
3005 3139 3.620821 GTCAGAAACTCAGCCTTATCTGC 59.379 47.826 0.00 0.00 35.44 4.26
3006 3140 4.825422 TGTCAGAAACTCAGCCTTATCTG 58.175 43.478 0.00 0.00 36.50 2.90
3007 3141 5.489792 TTGTCAGAAACTCAGCCTTATCT 57.510 39.130 0.00 0.00 0.00 1.98
3018 3154 5.774690 TCATGCCCTAATTTTGTCAGAAACT 59.225 36.000 0.00 0.00 0.00 2.66
3024 3160 7.716799 ATTTAGTCATGCCCTAATTTTGTCA 57.283 32.000 5.76 0.00 0.00 3.58
3048 3184 2.325583 AGGCACTGAAAGACGTTGAA 57.674 45.000 0.00 0.00 37.18 2.69
3062 3198 3.278574 TGATGCTAACCATTGTAGGCAC 58.721 45.455 0.00 0.00 35.79 5.01
3084 3220 4.082300 TGTTCTTGTCCGCATTGCAATTAT 60.082 37.500 9.83 0.00 0.00 1.28
3089 3225 1.028130 TTGTTCTTGTCCGCATTGCA 58.972 45.000 9.69 0.00 0.00 4.08
3096 3232 2.485426 AGTGATGCATTGTTCTTGTCCG 59.515 45.455 0.00 0.00 0.00 4.79
3098 3234 3.240069 GCAGTGATGCATTGTTCTTGTC 58.760 45.455 0.00 0.00 34.41 3.18
3118 3254 5.362430 TGTTTCCCCTCATATTTACCATTGC 59.638 40.000 0.00 0.00 0.00 3.56
3128 3264 4.646492 GCTCAACATTGTTTCCCCTCATAT 59.354 41.667 0.00 0.00 0.00 1.78
3129 3265 4.016444 GCTCAACATTGTTTCCCCTCATA 58.984 43.478 0.00 0.00 0.00 2.15
3132 3268 2.238521 TGCTCAACATTGTTTCCCCTC 58.761 47.619 0.00 0.00 0.00 4.30
3160 3296 3.618351 AGATCATTCAAGTCTTGCCCAG 58.382 45.455 7.78 0.00 0.00 4.45
3165 3301 5.180680 TGCAGTGAAGATCATTCAAGTCTTG 59.819 40.000 6.21 6.21 32.67 3.02
3169 3305 5.008331 ACATGCAGTGAAGATCATTCAAGT 58.992 37.500 8.55 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.