Multiple sequence alignment - TraesCS3B01G230900

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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 TraesCS3B01G230900 chr3B 100.000 5580 0 0 1 5580 348492081 348486502 0.000000e+00 10305.0
1 TraesCS3B01G230900 chr3B 87.006 177 21 2 5327 5501 648741459 648741283 1.230000e-46 198.0
2 TraesCS3B01G230900 chr3B 84.118 170 20 6 5331 5495 292163576 292163409 2.080000e-34 158.0
3 TraesCS3B01G230900 chr3A 96.525 3712 90 11 1858 5562 307916722 307913043 0.000000e+00 6104.0
4 TraesCS3B01G230900 chr3A 94.658 1142 22 10 612 1735 307917840 307916720 0.000000e+00 1735.0
5 TraesCS3B01G230900 chr3A 84.150 612 80 16 1 599 293928326 293928933 1.350000e-160 577.0
6 TraesCS3B01G230900 chr3A 83.987 612 84 12 1 599 293810896 293810286 4.850000e-160 575.0
7 TraesCS3B01G230900 chr3A 87.500 144 16 2 5354 5495 11684400 11684257 1.240000e-36 165.0
8 TraesCS3B01G230900 chr3A 86.806 144 17 2 5354 5495 686550031 686549888 5.790000e-35 159.0
9 TraesCS3B01G230900 chr3D 97.938 1843 26 3 1858 3699 248812062 248810231 0.000000e+00 3182.0
10 TraesCS3B01G230900 chr3D 96.486 1878 54 5 3694 5562 248807970 248806096 0.000000e+00 3092.0
11 TraesCS3B01G230900 chr3D 94.133 1142 26 14 612 1735 248813178 248812060 0.000000e+00 1700.0
12 TraesCS3B01G230900 chr3D 80.453 353 52 15 5142 5490 315762444 315762105 2.580000e-63 254.0
13 TraesCS3B01G230900 chr7B 96.235 664 23 2 4918 5580 357528900 357528238 0.000000e+00 1086.0
14 TraesCS3B01G230900 chr7B 96.875 128 4 0 1733 1860 332242761 332242888 1.220000e-51 215.0
15 TraesCS3B01G230900 chr1A 84.804 612 79 11 1 599 244608563 244609173 2.220000e-168 603.0
16 TraesCS3B01G230900 chr1D 84.565 609 82 10 1 599 166902048 166902654 1.340000e-165 593.0
17 TraesCS3B01G230900 chr1D 84.452 611 81 12 1 599 208808854 208809462 1.730000e-164 590.0
18 TraesCS3B01G230900 chr1D 87.500 56 3 4 1916 1968 416034134 416034188 1.680000e-05 62.1
19 TraesCS3B01G230900 chr5D 84.565 609 80 12 1 597 157126545 157127151 4.810000e-165 592.0
20 TraesCS3B01G230900 chr5D 96.094 128 5 0 1733 1860 179325941 179325814 5.660000e-50 209.0
21 TraesCS3B01G230900 chr5D 75.904 166 33 5 5328 5490 527578776 527578937 1.670000e-10 78.7
22 TraesCS3B01G230900 chr5D 75.904 166 33 5 5328 5490 527608381 527608542 1.670000e-10 78.7
23 TraesCS3B01G230900 chr6A 84.314 612 81 13 1 599 272892406 272893015 8.060000e-163 584.0
24 TraesCS3B01G230900 chr6A 86.806 144 17 2 5354 5495 29294189 29294046 5.790000e-35 159.0
25 TraesCS3B01G230900 chr2D 84.288 611 83 11 1 599 278268067 278267458 8.060000e-163 584.0
26 TraesCS3B01G230900 chr7D 84.211 608 79 14 1 597 342377459 342376858 4.850000e-160 575.0
27 TraesCS3B01G230900 chr7D 84.722 144 19 3 5357 5498 406898134 406897992 2.100000e-29 141.0
28 TraesCS3B01G230900 chr4A 85.092 436 44 14 5055 5482 700562456 700562878 5.170000e-115 425.0
29 TraesCS3B01G230900 chr4A 83.293 413 55 9 5085 5490 700731579 700731984 8.830000e-98 368.0
30 TraesCS3B01G230900 chr4A 94.928 138 7 0 1732 1869 477881884 477881747 3.390000e-52 217.0
31 TraesCS3B01G230900 chr4A 94.815 135 7 0 1726 1860 530174013 530173879 1.570000e-50 211.0
32 TraesCS3B01G230900 chr4A 90.728 151 13 1 1710 1860 95379658 95379509 3.410000e-47 200.0
33 TraesCS3B01G230900 chr4A 87.379 103 12 1 1046 1148 309074236 309074135 3.530000e-22 117.0
34 TraesCS3B01G230900 chr4B 83.014 365 42 14 5142 5498 251669088 251669440 4.200000e-81 313.0
35 TraesCS3B01G230900 chr4B 96.154 130 5 0 1734 1863 55926031 55925902 4.380000e-51 213.0
36 TraesCS3B01G230900 chr4B 84.615 91 7 1 1065 1148 259782513 259782603 3.580000e-12 84.2
37 TraesCS3B01G230900 chr4B 97.561 41 1 0 1935 1975 457413388 457413348 2.790000e-08 71.3
38 TraesCS3B01G230900 chr4B 90.385 52 5 0 1097 1148 330774471 330774420 1.000000e-07 69.4
39 TraesCS3B01G230900 chr5B 82.597 362 43 14 5142 5495 208440721 208440372 9.080000e-78 302.0
40 TraesCS3B01G230900 chr1B 86.341 205 25 3 908 1111 672333080 672333282 2.620000e-53 220.0
41 TraesCS3B01G230900 chr1B 90.426 94 9 0 5402 5495 654250414 654250507 2.110000e-24 124.0
42 TraesCS3B01G230900 chr5A 92.667 150 8 2 1712 1860 156158010 156158157 4.380000e-51 213.0
43 TraesCS3B01G230900 chr6B 92.958 142 8 2 1724 1864 214087134 214087274 7.330000e-49 206.0
44 TraesCS3B01G230900 chr6B 92.361 144 9 2 1718 1860 341467158 341467300 2.640000e-48 204.0
45 TraesCS3B01G230900 chr6B 97.674 43 1 0 1935 1977 156067355 156067397 2.160000e-09 75.0
46 TraesCS3B01G230900 chr6B 90.385 52 2 3 1936 1986 123500545 123500496 1.300000e-06 65.8
47 TraesCS3B01G230900 chr6D 92.157 51 3 1 1933 1983 410110865 410110914 2.790000e-08 71.3
48 TraesCS3B01G230900 chr6D 90.566 53 3 1 1927 1977 51141485 51141537 1.000000e-07 69.4
49 TraesCS3B01G230900 chr4D 97.561 41 1 0 1935 1975 372361557 372361517 2.790000e-08 71.3


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 TraesCS3B01G230900 chr3B 348486502 348492081 5579 True 10305.0 10305 100.000000 1 5580 1 chr3B.!!$R2 5579
1 TraesCS3B01G230900 chr3A 307913043 307917840 4797 True 3919.5 6104 95.591500 612 5562 2 chr3A.!!$R4 4950
2 TraesCS3B01G230900 chr3A 293928326 293928933 607 False 577.0 577 84.150000 1 599 1 chr3A.!!$F1 598
3 TraesCS3B01G230900 chr3A 293810286 293810896 610 True 575.0 575 83.987000 1 599 1 chr3A.!!$R2 598
4 TraesCS3B01G230900 chr3D 248806096 248813178 7082 True 2658.0 3182 96.185667 612 5562 3 chr3D.!!$R2 4950
5 TraesCS3B01G230900 chr7B 357528238 357528900 662 True 1086.0 1086 96.235000 4918 5580 1 chr7B.!!$R1 662
6 TraesCS3B01G230900 chr1A 244608563 244609173 610 False 603.0 603 84.804000 1 599 1 chr1A.!!$F1 598
7 TraesCS3B01G230900 chr1D 166902048 166902654 606 False 593.0 593 84.565000 1 599 1 chr1D.!!$F1 598
8 TraesCS3B01G230900 chr1D 208808854 208809462 608 False 590.0 590 84.452000 1 599 1 chr1D.!!$F2 598
9 TraesCS3B01G230900 chr5D 157126545 157127151 606 False 592.0 592 84.565000 1 597 1 chr5D.!!$F1 596
10 TraesCS3B01G230900 chr6A 272892406 272893015 609 False 584.0 584 84.314000 1 599 1 chr6A.!!$F1 598
11 TraesCS3B01G230900 chr2D 278267458 278268067 609 True 584.0 584 84.288000 1 599 1 chr2D.!!$R1 598
12 TraesCS3B01G230900 chr7D 342376858 342377459 601 True 575.0 575 84.211000 1 597 1 chr7D.!!$R1 596

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
950 985 1.078918 TCACCGGCAGCAGATCAAG 60.079 57.895 0.00 0.0 0.00 3.02 F
1748 1783 0.032130 CATGTACTCCATCCGTCCGG 59.968 60.000 0.00 0.0 0.00 5.14 F
2341 2376 1.398390 CCCTTTCTCGCAATCTTTCGG 59.602 52.381 0.00 0.0 0.00 4.30 F
2845 2880 1.899814 TGCACAAGGATTCTACCTCGT 59.100 47.619 0.00 0.0 39.62 4.18 F
3782 6085 2.615912 GCAGCCTGCTTAGAACTATTGG 59.384 50.000 10.04 0.0 40.96 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1845 1880 0.604578 TGTTTTACTCCCTCCGTCCG 59.395 55.000 0.00 0.00 0.00 4.79 R
2930 2965 2.513317 TCCAAATGCCTATGACATCCCA 59.487 45.455 0.00 0.00 0.00 4.37 R
4112 6417 0.538977 AGCACACAAGGCATTGCTCT 60.539 50.000 11.69 0.18 41.53 4.09 R
4139 6444 2.180017 GCAGCACAAGGAATGCCG 59.820 61.111 0.00 0.00 44.53 5.69 R
5031 7343 4.016444 TGGCTTGTTTCACCTCATTATCC 58.984 43.478 0.00 0.00 0.00 2.59 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
24 25 1.687563 TCTGTGACGTCTTGGTCTGA 58.312 50.000 17.92 8.47 37.81 3.27
43 44 4.330347 TCTGATCGTTGAACACAAACGAAA 59.670 37.500 14.41 6.43 34.13 3.46
105 112 5.058490 CCAAAGTCTAAACGACACCCTAAA 58.942 41.667 0.00 0.00 45.32 1.85
106 113 5.528320 CCAAAGTCTAAACGACACCCTAAAA 59.472 40.000 0.00 0.00 45.32 1.52
148 157 1.146152 TGGGGAATTTCGTGACCCTTT 59.854 47.619 9.14 0.00 42.00 3.11
150 159 2.510613 GGGAATTTCGTGACCCTTTGA 58.489 47.619 0.00 0.00 39.28 2.69
201 211 3.143728 GTTTCCCCACACATACGAACTT 58.856 45.455 0.00 0.00 0.00 2.66
202 212 2.754946 TCCCCACACATACGAACTTC 57.245 50.000 0.00 0.00 0.00 3.01
242 252 9.020731 ACTAAAGTATTTCGAAATTTCATGGGT 57.979 29.630 27.10 15.11 40.09 4.51
246 256 6.884295 AGTATTTCGAAATTTCATGGGTCTGA 59.116 34.615 27.10 3.03 0.00 3.27
249 259 3.081061 CGAAATTTCATGGGTCTGACCA 58.919 45.455 26.94 14.17 46.24 4.02
256 266 6.528537 TTTCATGGGTCTGACCAAATAATG 57.471 37.500 26.94 19.47 45.13 1.90
287 297 3.193691 CGACACCTATTATAGCCTCTGGG 59.806 52.174 0.00 0.00 0.00 4.45
311 321 6.426937 GGCGAAATTTATGGAGTAGCATCTTA 59.573 38.462 0.00 0.00 0.00 2.10
395 407 4.410883 TGAAACTCTGTTCTTGTTCCCCTA 59.589 41.667 0.00 0.00 0.00 3.53
396 408 5.104277 TGAAACTCTGTTCTTGTTCCCCTAA 60.104 40.000 0.00 0.00 0.00 2.69
412 424 3.470709 CCCTAACGCATGTCATCATCTT 58.529 45.455 0.00 0.00 31.15 2.40
477 491 6.089249 AGACCCTTCATTTGTAAGCAAAAG 57.911 37.500 0.00 0.00 46.23 2.27
480 494 6.280643 ACCCTTCATTTGTAAGCAAAAGAAC 58.719 36.000 6.63 0.00 46.23 3.01
505 519 6.741109 TGTATCCAATTTAAGCAGCATCATG 58.259 36.000 0.00 0.00 0.00 3.07
511 526 5.752892 ATTTAAGCAGCATCATGTCTCAG 57.247 39.130 0.00 0.00 0.00 3.35
515 530 2.026542 AGCAGCATCATGTCTCAGGAAA 60.027 45.455 0.00 0.00 0.00 3.13
525 540 7.364522 TCATGTCTCAGGAAAATTAGAAACG 57.635 36.000 0.00 0.00 0.00 3.60
526 541 6.934645 TCATGTCTCAGGAAAATTAGAAACGT 59.065 34.615 0.00 0.00 0.00 3.99
528 543 8.717821 CATGTCTCAGGAAAATTAGAAACGTTA 58.282 33.333 0.00 0.00 0.00 3.18
571 588 6.597672 TGATAATTTAATTGACCTGCGTGAGT 59.402 34.615 0.00 0.00 0.00 3.41
573 590 5.705609 ATTTAATTGACCTGCGTGAGTTT 57.294 34.783 0.00 0.00 0.00 2.66
582 599 5.407387 TGACCTGCGTGAGTTTTAGTAATTC 59.593 40.000 0.00 0.00 0.00 2.17
585 602 5.107220 CCTGCGTGAGTTTTAGTAATTCGTT 60.107 40.000 0.00 0.00 0.00 3.85
599 616 9.603298 TTAGTAATTCGTTCAGTATATGTAGCG 57.397 33.333 0.00 0.00 0.00 4.26
600 617 7.646314 AGTAATTCGTTCAGTATATGTAGCGT 58.354 34.615 0.00 0.00 0.00 5.07
601 618 6.749216 AATTCGTTCAGTATATGTAGCGTG 57.251 37.500 0.00 0.00 0.00 5.34
602 619 5.488645 TTCGTTCAGTATATGTAGCGTGA 57.511 39.130 0.00 0.00 0.00 4.35
603 620 5.684550 TCGTTCAGTATATGTAGCGTGAT 57.315 39.130 0.00 0.00 0.00 3.06
604 621 5.686834 TCGTTCAGTATATGTAGCGTGATC 58.313 41.667 0.00 0.00 0.00 2.92
605 622 4.549980 CGTTCAGTATATGTAGCGTGATCG 59.450 45.833 0.00 0.00 40.37 3.69
606 623 5.450171 GTTCAGTATATGTAGCGTGATCGT 58.550 41.667 0.00 0.00 39.49 3.73
607 624 5.030874 TCAGTATATGTAGCGTGATCGTG 57.969 43.478 0.00 0.00 39.49 4.35
608 625 4.083484 TCAGTATATGTAGCGTGATCGTGG 60.083 45.833 0.00 0.00 39.49 4.94
609 626 4.070009 AGTATATGTAGCGTGATCGTGGA 58.930 43.478 0.00 0.00 39.49 4.02
610 627 3.560902 ATATGTAGCGTGATCGTGGAG 57.439 47.619 0.00 0.00 39.49 3.86
624 641 2.101249 TCGTGGAGTAAGTCGTTTTGGT 59.899 45.455 0.00 0.00 0.00 3.67
798 821 2.309504 CCCCCTTCCCTTCAGGTCC 61.310 68.421 0.00 0.00 36.75 4.46
844 867 1.602327 GGTCGTTTCCCTAGGTCGCT 61.602 60.000 8.29 0.00 0.00 4.93
938 973 1.730487 CTCAGATCGAGGTCACCGG 59.270 63.158 0.00 0.00 38.18 5.28
939 974 2.105128 CAGATCGAGGTCACCGGC 59.895 66.667 0.00 0.00 0.00 6.13
940 975 2.362503 AGATCGAGGTCACCGGCA 60.363 61.111 0.00 0.00 0.00 5.69
941 976 2.105128 GATCGAGGTCACCGGCAG 59.895 66.667 0.00 0.00 0.00 4.85
942 977 4.148825 ATCGAGGTCACCGGCAGC 62.149 66.667 0.00 0.00 0.00 5.25
945 980 3.695606 GAGGTCACCGGCAGCAGA 61.696 66.667 0.00 0.00 0.00 4.26
946 981 3.005539 AGGTCACCGGCAGCAGAT 61.006 61.111 0.00 0.00 0.00 2.90
947 982 2.512515 GGTCACCGGCAGCAGATC 60.513 66.667 0.00 0.00 0.00 2.75
948 983 2.265739 GTCACCGGCAGCAGATCA 59.734 61.111 0.00 0.00 0.00 2.92
949 984 1.375908 GTCACCGGCAGCAGATCAA 60.376 57.895 0.00 0.00 0.00 2.57
950 985 1.078918 TCACCGGCAGCAGATCAAG 60.079 57.895 0.00 0.00 0.00 3.02
951 986 2.110967 CACCGGCAGCAGATCAAGG 61.111 63.158 0.00 0.00 0.00 3.61
952 987 2.270205 CCGGCAGCAGATCAAGGT 59.730 61.111 0.00 0.00 0.00 3.50
1233 1268 0.953727 TCTGCACAATCACACTTGCC 59.046 50.000 0.00 0.00 33.86 4.52
1339 1374 7.571080 TTTTGGTCACCGTTTATAGAGTTTT 57.429 32.000 0.00 0.00 0.00 2.43
1390 1425 7.044181 GTGATACTCATCCATTTCTCAACTGA 58.956 38.462 0.00 0.00 0.00 3.41
1633 1668 4.158394 GCTCCCTTGCTTGATCAAATTGTA 59.842 41.667 9.88 0.00 0.00 2.41
1652 1687 4.338012 TGTATGTTACTCCTTCCGTCTCA 58.662 43.478 0.00 0.00 0.00 3.27
1743 1778 7.672983 AAATTATTAGCATGTACTCCATCCG 57.327 36.000 0.00 0.00 0.00 4.18
1744 1779 5.801531 TTATTAGCATGTACTCCATCCGT 57.198 39.130 0.00 0.00 0.00 4.69
1745 1780 3.728076 TTAGCATGTACTCCATCCGTC 57.272 47.619 0.00 0.00 0.00 4.79
1746 1781 0.753262 AGCATGTACTCCATCCGTCC 59.247 55.000 0.00 0.00 0.00 4.79
1747 1782 0.597637 GCATGTACTCCATCCGTCCG 60.598 60.000 0.00 0.00 0.00 4.79
1748 1783 0.032130 CATGTACTCCATCCGTCCGG 59.968 60.000 0.00 0.00 0.00 5.14
1759 1794 2.660189 TCCGTCCGGAAATACTTGTC 57.340 50.000 5.23 0.00 42.05 3.18
1760 1795 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
1761 1796 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
1762 1797 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
1763 1798 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
1764 1799 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
1765 1800 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
1766 1801 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
1767 1802 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
1768 1803 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
1769 1804 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
1770 1805 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
1771 1806 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
1779 1814 9.918630 ACTTGTCATCAAAATGAATAAAAGGAG 57.081 29.630 0.00 0.00 43.42 3.69
1835 1870 9.603921 ACATCCATTTTTATCCATTTTGATGAC 57.396 29.630 0.00 0.00 32.39 3.06
1836 1871 9.602568 CATCCATTTTTATCCATTTTGATGACA 57.397 29.630 0.00 0.00 0.00 3.58
1838 1873 9.656040 TCCATTTTTATCCATTTTGATGACAAG 57.344 29.630 0.00 0.00 37.32 3.16
1839 1874 9.439500 CCATTTTTATCCATTTTGATGACAAGT 57.561 29.630 0.00 0.00 37.32 3.16
1846 1881 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
1847 1882 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
1848 1883 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
1849 1884 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
1850 1885 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
1851 1886 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
1852 1887 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
1853 1888 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
1854 1889 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
1855 1890 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
1856 1891 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
1857 1892 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
1858 1893 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
1859 1894 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
1887 1922 9.855021 AACACAAAATTAGTATCACCAAATAGC 57.145 29.630 0.00 0.00 0.00 2.97
1949 1984 9.998106 ATTGTATACTCCAAAACGCTCTTATAT 57.002 29.630 4.17 0.00 0.00 0.86
2023 2058 6.642131 CACATTTTGTACCATTTGACTTGAGG 59.358 38.462 0.00 0.00 0.00 3.86
2145 2180 3.256631 AGGTGGACAACATTGATGAAAGC 59.743 43.478 0.43 0.00 0.00 3.51
2341 2376 1.398390 CCCTTTCTCGCAATCTTTCGG 59.602 52.381 0.00 0.00 0.00 4.30
2845 2880 1.899814 TGCACAAGGATTCTACCTCGT 59.100 47.619 0.00 0.00 39.62 4.18
3006 3041 4.381932 CAAACTATTGGATGGAACAAGCCC 60.382 45.833 0.00 0.00 35.57 5.19
3288 3323 5.163311 GCCTTGGCCTTATTAAATGGATTGT 60.163 40.000 3.32 0.00 0.00 2.71
3699 6002 4.757657 TGGCGTAAAAGATGTACACATGTT 59.242 37.500 0.00 0.00 40.93 2.71
3782 6085 2.615912 GCAGCCTGCTTAGAACTATTGG 59.384 50.000 10.04 0.00 40.96 3.16
3921 6224 8.024865 CGTTTGATATGGATGTTTCATATGCAT 58.975 33.333 3.79 3.79 37.77 3.96
3998 6301 8.770438 AAAAATCGCAAGCCATTAGATAAAAA 57.230 26.923 0.00 0.00 37.18 1.94
4139 6444 0.383231 GCCTTGTGTGCTATGATGCC 59.617 55.000 0.00 0.00 0.00 4.40
4206 6511 5.279960 GCCCTTATTTTTCCATTTCAGGTGT 60.280 40.000 0.00 0.00 0.00 4.16
4260 6565 4.036144 GCAGCCTCATCTTCATTCCTAAAC 59.964 45.833 0.00 0.00 0.00 2.01
4409 6714 2.024176 AATCGTGGCGCTAGAACAAT 57.976 45.000 7.64 0.00 0.00 2.71
4702 7013 4.511454 TCACTGCTGTTTCTGTATGTTGTC 59.489 41.667 0.00 0.00 0.00 3.18
4711 7022 9.398170 CTGTTTCTGTATGTTGTCCAAATTTAG 57.602 33.333 0.00 0.00 0.00 1.85
4744 7055 4.459390 TGCATGGGAAGTTTGATGATTG 57.541 40.909 0.00 0.00 0.00 2.67
4799 7110 7.222999 GGAGACTATAACTTTCAACCTTGATCG 59.777 40.741 0.00 0.00 37.00 3.69
4813 7124 6.155475 ACCTTGATCGGAAAATTTTGAACA 57.845 33.333 8.47 2.85 0.00 3.18
5031 7343 4.319766 GCAAGTTTACAGGGATGATATGCG 60.320 45.833 0.00 0.00 0.00 4.73
5338 7651 1.271102 TGCGGTGCCTTCAATAAAACC 59.729 47.619 0.00 0.00 0.00 3.27
5342 7655 3.375922 CGGTGCCTTCAATAAAACCGTAT 59.624 43.478 3.96 0.00 44.17 3.06
5436 7749 9.486857 GTATCCTAGTTTTTAGAAAATTGTCGC 57.513 33.333 0.00 0.00 0.00 5.19
5441 7754 1.430479 TTAGAAAATTGTCGCGCCGA 58.570 45.000 0.00 0.00 0.00 5.54
5459 7772 2.646719 GCGTATCCCCGTATCGCA 59.353 61.111 0.00 0.00 45.01 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 8.661257 TCATATATTTCGTTTGTGTTCAACGAT 58.339 29.630 8.57 0.00 37.16 3.73
64 65 9.143155 AGACTTTGGGTTTGTTTAGATTAACAT 57.857 29.630 0.00 0.00 37.81 2.71
69 70 8.132995 CGTTTAGACTTTGGGTTTGTTTAGATT 58.867 33.333 0.00 0.00 0.00 2.40
70 71 7.499895 TCGTTTAGACTTTGGGTTTGTTTAGAT 59.500 33.333 0.00 0.00 0.00 1.98
72 73 6.908820 GTCGTTTAGACTTTGGGTTTGTTTAG 59.091 38.462 0.00 0.00 46.13 1.85
119 126 5.359860 GTCACGAAATTCCCCATTATTCCTT 59.640 40.000 0.00 0.00 0.00 3.36
127 135 0.999712 AGGGTCACGAAATTCCCCAT 59.000 50.000 7.60 0.00 40.70 4.00
128 136 0.774908 AAGGGTCACGAAATTCCCCA 59.225 50.000 7.60 0.00 40.70 4.96
148 157 1.064825 GGTTTCAGACCCCTCCTTCA 58.935 55.000 0.00 0.00 43.06 3.02
235 245 5.439721 CTCATTATTTGGTCAGACCCATGA 58.560 41.667 17.59 14.02 37.50 3.07
242 252 5.245531 GTGTCACCTCATTATTTGGTCAGA 58.754 41.667 0.00 0.00 30.72 3.27
246 256 4.000988 GTCGTGTCACCTCATTATTTGGT 58.999 43.478 0.00 0.00 33.87 3.67
287 297 5.931441 AGATGCTACTCCATAAATTTCGC 57.069 39.130 0.00 0.00 0.00 4.70
299 309 9.856488 TTGGACGAAATATATAAGATGCTACTC 57.144 33.333 0.00 0.00 0.00 2.59
311 321 5.182001 GCATGAAGGCTTGGACGAAATATAT 59.818 40.000 3.46 0.00 0.00 0.86
359 369 7.500227 AGAACAGAGTTTCAAGTGATGATTCAA 59.500 33.333 0.00 0.00 38.03 2.69
361 371 7.432350 AGAACAGAGTTTCAAGTGATGATTC 57.568 36.000 0.00 0.00 38.03 2.52
395 407 4.547406 CATGAAGATGATGACATGCGTT 57.453 40.909 0.00 0.00 36.82 4.84
412 424 5.970317 ACATTGAACAAGATCAAGCATGA 57.030 34.783 0.00 0.00 42.21 3.07
456 470 6.478512 TTCTTTTGCTTACAAATGAAGGGT 57.521 33.333 12.91 0.00 46.57 4.34
494 508 1.201424 TCCTGAGACATGATGCTGCT 58.799 50.000 0.00 0.00 0.00 4.24
505 519 8.080083 TGTAACGTTTCTAATTTTCCTGAGAC 57.920 34.615 5.91 0.00 0.00 3.36
539 556 8.560374 GCAGGTCAATTAAATTATCAGGTACTC 58.440 37.037 0.00 0.00 34.60 2.59
562 579 5.511088 ACGAATTACTAAAACTCACGCAG 57.489 39.130 0.00 0.00 0.00 5.18
573 590 9.603298 CGCTACATATACTGAACGAATTACTAA 57.397 33.333 0.00 0.00 0.00 2.24
582 599 4.549980 CGATCACGCTACATATACTGAACG 59.450 45.833 0.00 0.00 0.00 3.95
585 602 4.083484 CCACGATCACGCTACATATACTGA 60.083 45.833 0.00 0.00 43.96 3.41
599 616 2.915738 ACGACTTACTCCACGATCAC 57.084 50.000 0.00 0.00 0.00 3.06
600 617 3.928727 AAACGACTTACTCCACGATCA 57.071 42.857 0.00 0.00 0.00 2.92
601 618 3.367025 CCAAAACGACTTACTCCACGATC 59.633 47.826 0.00 0.00 0.00 3.69
602 619 3.243975 ACCAAAACGACTTACTCCACGAT 60.244 43.478 0.00 0.00 0.00 3.73
603 620 2.101249 ACCAAAACGACTTACTCCACGA 59.899 45.455 0.00 0.00 0.00 4.35
604 621 2.476821 ACCAAAACGACTTACTCCACG 58.523 47.619 0.00 0.00 0.00 4.94
605 622 4.888038 AAACCAAAACGACTTACTCCAC 57.112 40.909 0.00 0.00 0.00 4.02
606 623 5.900865 AAAAACCAAAACGACTTACTCCA 57.099 34.783 0.00 0.00 0.00 3.86
921 956 2.415608 GCCGGTGACCTCGATCTGA 61.416 63.158 1.90 0.00 0.00 3.27
933 968 2.110967 CCTTGATCTGCTGCCGGTG 61.111 63.158 1.90 0.00 0.00 4.94
934 969 2.270205 CCTTGATCTGCTGCCGGT 59.730 61.111 1.90 0.00 0.00 5.28
935 970 1.817099 GACCTTGATCTGCTGCCGG 60.817 63.158 0.00 0.00 0.00 6.13
936 971 1.078918 TGACCTTGATCTGCTGCCG 60.079 57.895 0.00 0.00 0.00 5.69
937 972 1.028868 GGTGACCTTGATCTGCTGCC 61.029 60.000 0.00 0.00 0.00 4.85
938 973 1.364626 CGGTGACCTTGATCTGCTGC 61.365 60.000 0.00 0.00 0.00 5.25
939 974 0.742281 CCGGTGACCTTGATCTGCTG 60.742 60.000 0.00 0.00 0.00 4.41
940 975 1.599047 CCGGTGACCTTGATCTGCT 59.401 57.895 0.00 0.00 0.00 4.24
941 976 2.109126 GCCGGTGACCTTGATCTGC 61.109 63.158 1.90 0.00 0.00 4.26
942 977 0.742281 CTGCCGGTGACCTTGATCTG 60.742 60.000 1.90 0.00 0.00 2.90
943 978 1.599047 CTGCCGGTGACCTTGATCT 59.401 57.895 1.90 0.00 0.00 2.75
944 979 2.109126 GCTGCCGGTGACCTTGATC 61.109 63.158 1.90 0.00 0.00 2.92
945 980 1.264749 TAGCTGCCGGTGACCTTGAT 61.265 55.000 1.90 0.00 0.00 2.57
946 981 1.476845 TTAGCTGCCGGTGACCTTGA 61.477 55.000 1.90 0.00 0.00 3.02
947 982 0.392998 ATTAGCTGCCGGTGACCTTG 60.393 55.000 1.90 0.00 0.00 3.61
948 983 0.107654 GATTAGCTGCCGGTGACCTT 60.108 55.000 1.90 0.00 0.00 3.50
949 984 1.522569 GATTAGCTGCCGGTGACCT 59.477 57.895 1.90 0.00 0.00 3.85
950 985 1.883084 CGATTAGCTGCCGGTGACC 60.883 63.158 1.90 0.00 0.00 4.02
951 986 2.526120 GCGATTAGCTGCCGGTGAC 61.526 63.158 1.90 0.00 44.04 3.67
952 987 2.202878 GCGATTAGCTGCCGGTGA 60.203 61.111 1.90 0.00 44.04 4.02
1120 1155 4.565564 CCCTCTGTTCCGTTTTATAAGTCG 59.434 45.833 4.97 4.97 0.00 4.18
1233 1268 1.743394 GAAACAACTTGGCCCTATCCG 59.257 52.381 0.00 0.00 0.00 4.18
1303 1338 2.966516 GTGACCAAAAATACCCCCAACA 59.033 45.455 0.00 0.00 0.00 3.33
1390 1425 9.227777 CAAGGTTAACTAAAGCTAGGTGTAATT 57.772 33.333 5.42 0.00 45.11 1.40
1633 1668 4.884668 TTTGAGACGGAAGGAGTAACAT 57.115 40.909 0.00 0.00 0.00 2.71
1666 1701 7.920151 CACCATTTGACTTGAGACAACAATTAA 59.080 33.333 0.00 0.00 30.20 1.40
1735 1770 1.687123 AGTATTTCCGGACGGATGGAG 59.313 52.381 14.89 0.00 44.74 3.86
1736 1771 1.784358 AGTATTTCCGGACGGATGGA 58.216 50.000 14.89 4.49 44.74 3.41
1737 1772 2.210116 CAAGTATTTCCGGACGGATGG 58.790 52.381 14.89 0.00 44.74 3.51
1738 1773 2.864343 GACAAGTATTTCCGGACGGATG 59.136 50.000 14.89 10.86 44.74 3.51
1739 1774 2.498481 TGACAAGTATTTCCGGACGGAT 59.502 45.455 14.89 3.07 44.74 4.18
1740 1775 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
1741 1776 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
1742 1777 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
1743 1778 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
1744 1779 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
1745 1780 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
1746 1781 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
1753 1788 9.918630 CTCCTTTTATTCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16
1809 1844 9.603921 GTCATCAAAATGGATAAAAATGGATGT 57.396 29.630 0.00 0.00 33.42 3.06
1810 1845 9.602568 TGTCATCAAAATGGATAAAAATGGATG 57.397 29.630 0.00 0.00 33.42 3.51
1812 1847 9.656040 CTTGTCATCAAAATGGATAAAAATGGA 57.344 29.630 0.00 0.00 33.42 3.41
1813 1848 9.439500 ACTTGTCATCAAAATGGATAAAAATGG 57.561 29.630 0.00 0.00 33.42 3.16
1821 1856 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
1822 1857 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
1823 1858 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
1824 1859 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
1825 1860 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
1826 1861 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
1827 1862 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
1828 1863 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
1829 1864 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
1830 1865 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
1831 1866 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
1832 1867 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
1833 1868 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
1834 1869 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
1835 1870 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
1836 1871 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
1837 1872 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
1838 1873 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
1839 1874 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
1840 1875 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
1841 1876 1.631405 TTACTCCCTCCGTCCGAAAA 58.369 50.000 0.00 0.00 0.00 2.29
1842 1877 1.631405 TTTACTCCCTCCGTCCGAAA 58.369 50.000 0.00 0.00 0.00 3.46
1843 1878 1.273327 GTTTTACTCCCTCCGTCCGAA 59.727 52.381 0.00 0.00 0.00 4.30
1844 1879 0.890683 GTTTTACTCCCTCCGTCCGA 59.109 55.000 0.00 0.00 0.00 4.55
1845 1880 0.604578 TGTTTTACTCCCTCCGTCCG 59.395 55.000 0.00 0.00 0.00 4.79
1846 1881 1.345415 TGTGTTTTACTCCCTCCGTCC 59.655 52.381 0.00 0.00 0.00 4.79
1847 1882 2.825861 TGTGTTTTACTCCCTCCGTC 57.174 50.000 0.00 0.00 0.00 4.79
1848 1883 3.564053 TTTGTGTTTTACTCCCTCCGT 57.436 42.857 0.00 0.00 0.00 4.69
1849 1884 5.447624 AATTTTGTGTTTTACTCCCTCCG 57.552 39.130 0.00 0.00 0.00 4.63
1850 1885 7.520451 ACTAATTTTGTGTTTTACTCCCTCC 57.480 36.000 0.00 0.00 0.00 4.30
1852 1887 9.802039 TGATACTAATTTTGTGTTTTACTCCCT 57.198 29.630 0.00 0.00 0.00 4.20
1853 1888 9.836076 GTGATACTAATTTTGTGTTTTACTCCC 57.164 33.333 0.00 0.00 0.00 4.30
1854 1889 9.836076 GGTGATACTAATTTTGTGTTTTACTCC 57.164 33.333 0.00 0.00 0.00 3.85
1949 1984 0.613853 CTACTCCCTCCGTCCCACAA 60.614 60.000 0.00 0.00 0.00 3.33
2023 2058 5.049474 CCAAAAGAAGGCCAGTAAATTTTGC 60.049 40.000 5.01 0.00 35.74 3.68
2145 2180 9.045223 TCTTGAACCATATCATCAAATAAGTCG 57.955 33.333 0.00 0.00 33.08 4.18
2341 2376 3.506067 ACAACCTCCACCGAATCAATTTC 59.494 43.478 0.00 0.00 0.00 2.17
2398 2433 4.473520 CCCAACCATCCGCTCGCT 62.474 66.667 0.00 0.00 0.00 4.93
2719 2754 4.397417 GCTTTGTTCATAAGCAGATGTCCT 59.603 41.667 0.00 0.00 45.64 3.85
2845 2880 4.406456 ACAAGTGATATTGTCTTGCCCAA 58.594 39.130 12.25 0.00 39.13 4.12
2930 2965 2.513317 TCCAAATGCCTATGACATCCCA 59.487 45.455 0.00 0.00 0.00 4.37
3713 6016 9.289303 GAAATAATGAAGAAATAGCGAGCAAAA 57.711 29.630 0.00 0.00 0.00 2.44
3782 6085 4.538738 ACAGGGTCTCAGTATCCTAACTC 58.461 47.826 0.00 0.00 0.00 3.01
3824 6127 2.363680 CGAGATACTCAGGGATGTTGCT 59.636 50.000 0.00 0.00 0.00 3.91
3921 6224 3.392947 TCAGAACAATAACCACAGGACCA 59.607 43.478 0.00 0.00 0.00 4.02
3979 6282 7.754069 TTCAATTTTTATCTAATGGCTTGCG 57.246 32.000 0.00 0.00 0.00 4.85
3998 6301 9.559958 GAAACACATTGAGATTACGATTTCAAT 57.440 29.630 0.00 0.00 43.83 2.57
4017 6320 5.555966 TGTATCAGTTATGCAGGAAACACA 58.444 37.500 10.80 4.84 0.00 3.72
4112 6417 0.538977 AGCACACAAGGCATTGCTCT 60.539 50.000 11.69 0.18 41.53 4.09
4139 6444 2.180017 GCAGCACAAGGAATGCCG 59.820 61.111 0.00 0.00 44.53 5.69
4229 6534 4.910195 TGAAGATGAGGCTGCTTAGAAAA 58.090 39.130 0.00 0.00 0.00 2.29
4409 6714 6.544928 TGACAGCCTGTTTGATTCTATAGA 57.455 37.500 0.00 0.00 0.00 1.98
4637 6948 6.918892 ATACTGTCGCAGCAAAATATACAA 57.081 33.333 6.74 0.00 34.37 2.41
4744 7055 5.121611 AGCATTTTGTTTAAAAATAGCGGCC 59.878 36.000 0.00 0.00 39.09 6.13
4799 7110 6.295249 TCCCATTCCTTGTTCAAAATTTTCC 58.705 36.000 0.00 0.00 0.00 3.13
4813 7124 5.003096 AGTCAAGTTTCATCCCATTCCTT 57.997 39.130 0.00 0.00 0.00 3.36
4977 7288 7.119262 CGAGTAATAAAGTGTGTTTCCCTCAAT 59.881 37.037 0.00 0.00 0.00 2.57
5031 7343 4.016444 TGGCTTGTTTCACCTCATTATCC 58.984 43.478 0.00 0.00 0.00 2.59
5338 7651 4.693566 TGAGTTTTTGGTAGGAAGCATACG 59.306 41.667 0.00 0.00 32.06 3.06
5342 7655 4.892934 ACAATGAGTTTTTGGTAGGAAGCA 59.107 37.500 0.00 0.00 0.00 3.91
5459 7772 8.515695 TGAATACTTGGATACGTATCGGATAT 57.484 34.615 25.21 17.43 42.51 1.63


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

AutoCloner maintained by Alex Coulton.