Multiple sequence alignment - TraesCS5D01G475400

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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 TraesCS5D01G475400 chr5D 100.000 2711 0 0 1 2711 515040753 515038043 0.000000e+00 5007.0
1 TraesCS5D01G475400 chr5D 94.009 701 34 6 933 1628 515094462 515093765 0.000000e+00 1055.0
2 TraesCS5D01G475400 chr5B 91.249 1417 79 22 826 2219 647879722 647878328 0.000000e+00 1888.0
3 TraesCS5D01G475400 chr5B 90.964 332 22 4 333 659 647880413 647880085 8.910000e-120 440.0
4 TraesCS5D01G475400 chr5B 84.034 357 27 14 1 328 647880900 647880545 1.570000e-82 316.0
5 TraesCS5D01G475400 chr5B 94.118 170 6 4 2211 2378 647878306 647878139 3.460000e-64 255.0
6 TraesCS5D01G475400 chr5B 93.496 123 7 1 2375 2496 647877820 647877698 5.960000e-42 182.0
7 TraesCS5D01G475400 chr5B 82.166 157 27 1 4 160 79810836 79810681 1.690000e-27 134.0
8 TraesCS5D01G475400 chr5B 97.222 36 0 1 333 368 647880462 647880428 2.920000e-05 60.2
9 TraesCS5D01G475400 chr5A 89.160 1310 82 29 794 2056 643312357 643311061 0.000000e+00 1578.0
10 TraesCS5D01G475400 chr5A 93.135 874 51 7 1511 2380 643310498 643309630 0.000000e+00 1273.0
11 TraesCS5D01G475400 chr5A 81.541 623 27 34 90 663 643313090 643312507 1.490000e-117 433.0
12 TraesCS5D01G475400 chr5A 92.683 123 8 1 2375 2496 643308592 643308470 2.770000e-40 176.0
13 TraesCS5D01G475400 chr5A 92.453 106 8 0 2500 2605 643308431 643308326 4.680000e-33 152.0
14 TraesCS5D01G475400 chr5A 90.179 112 11 0 2600 2711 643302283 643302172 2.180000e-31 147.0
15 TraesCS5D01G475400 chr5A 91.589 107 7 2 1 105 643313210 643313104 2.180000e-31 147.0
16 TraesCS5D01G475400 chr5A 82.166 157 24 3 4 160 67518676 67518524 6.090000e-27 132.0
17 TraesCS5D01G475400 chr2D 87.847 1226 86 26 774 1953 534129064 534130272 0.000000e+00 1380.0
18 TraesCS5D01G475400 chr2D 88.757 925 82 12 1024 1931 534122862 534123781 0.000000e+00 1112.0
19 TraesCS5D01G475400 chr2D 88.669 556 39 10 1336 1880 633286251 633285709 0.000000e+00 656.0
20 TraesCS5D01G475400 chr2D 88.193 559 44 9 1336 1885 633237061 633236516 0.000000e+00 647.0
21 TraesCS5D01G475400 chr2D 79.954 878 85 49 453 1293 633297178 633298001 1.820000e-156 562.0
22 TraesCS5D01G475400 chr2D 82.301 452 33 19 5 430 633296762 633297192 5.560000e-92 348.0
23 TraesCS5D01G475400 chr2D 89.941 169 16 1 1 168 534127222 534127390 1.630000e-52 217.0
24 TraesCS5D01G475400 chr2D 87.611 113 13 1 168 279 534127417 534127529 2.190000e-26 130.0
25 TraesCS5D01G475400 chr6D 86.158 1192 90 40 770 1937 20475455 20474315 0.000000e+00 1218.0
26 TraesCS5D01G475400 chr2B 87.117 1110 97 24 913 1984 776645958 776644857 0.000000e+00 1216.0
27 TraesCS5D01G475400 chr2B 83.759 862 69 36 1 818 776647080 776646246 0.000000e+00 750.0
28 TraesCS5D01G475400 chr2B 84.841 409 27 16 1 377 634629572 634629977 1.970000e-101 379.0
29 TraesCS5D01G475400 chr2B 87.063 286 17 12 390 663 634631383 634631660 3.390000e-79 305.0
30 TraesCS5D01G475400 chr2B 89.051 137 11 3 2201 2334 634627032 634627167 1.670000e-37 167.0
31 TraesCS5D01G475400 chr2B 85.849 106 12 2 287 389 797201692 797201797 2.850000e-20 110.0
32 TraesCS5D01G475400 chr6B 84.579 1070 76 28 853 1899 33037778 33038781 0.000000e+00 979.0
33 TraesCS5D01G475400 chr7B 90.086 696 59 8 933 1624 113445700 113445011 0.000000e+00 894.0
34 TraesCS5D01G475400 chr7A 87.256 769 75 19 933 1692 151328258 151327504 0.000000e+00 856.0
35 TraesCS5D01G475400 chr7D 87.063 773 77 18 933 1697 151542749 151541992 0.000000e+00 852.0
36 TraesCS5D01G475400 chr1B 89.840 187 14 4 2027 2209 196877483 196877668 4.510000e-58 235.0
37 TraesCS5D01G475400 chr4A 89.516 124 12 1 2211 2334 639978946 639979068 3.610000e-34 156.0
38 TraesCS5D01G475400 chr3D 100.000 29 0 0 2599 2627 579315275 579315303 1.000000e-03 54.7


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 TraesCS5D01G475400 chr5D 515038043 515040753 2710 True 5007.000000 5007 100.000000 1 2711 1 chr5D.!!$R1 2710
1 TraesCS5D01G475400 chr5D 515093765 515094462 697 True 1055.000000 1055 94.009000 933 1628 1 chr5D.!!$R2 695
2 TraesCS5D01G475400 chr5B 647877698 647880900 3202 True 523.533333 1888 91.847167 1 2496 6 chr5B.!!$R2 2495
3 TraesCS5D01G475400 chr5A 643308326 643313210 4884 True 626.500000 1578 90.093500 1 2605 6 chr5A.!!$R3 2604
4 TraesCS5D01G475400 chr2D 534122862 534130272 7410 False 709.750000 1380 88.539000 1 1953 4 chr2D.!!$F1 1952
5 TraesCS5D01G475400 chr2D 633285709 633286251 542 True 656.000000 656 88.669000 1336 1880 1 chr2D.!!$R2 544
6 TraesCS5D01G475400 chr2D 633236516 633237061 545 True 647.000000 647 88.193000 1336 1885 1 chr2D.!!$R1 549
7 TraesCS5D01G475400 chr2D 633296762 633298001 1239 False 455.000000 562 81.127500 5 1293 2 chr2D.!!$F2 1288
8 TraesCS5D01G475400 chr6D 20474315 20475455 1140 True 1218.000000 1218 86.158000 770 1937 1 chr6D.!!$R1 1167
9 TraesCS5D01G475400 chr2B 776644857 776647080 2223 True 983.000000 1216 85.438000 1 1984 2 chr2B.!!$R1 1983
10 TraesCS5D01G475400 chr2B 634627032 634631660 4628 False 283.666667 379 86.985000 1 2334 3 chr2B.!!$F2 2333
11 TraesCS5D01G475400 chr6B 33037778 33038781 1003 False 979.000000 979 84.579000 853 1899 1 chr6B.!!$F1 1046
12 TraesCS5D01G475400 chr7B 113445011 113445700 689 True 894.000000 894 90.086000 933 1624 1 chr7B.!!$R1 691
13 TraesCS5D01G475400 chr7A 151327504 151328258 754 True 856.000000 856 87.256000 933 1692 1 chr7A.!!$R1 759
14 TraesCS5D01G475400 chr7D 151541992 151542749 757 True 852.000000 852 87.063000 933 1697 1 chr7D.!!$R1 764

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
659 8088 1.583194 GTCTAGCCGAGCGAACGTC 60.583 63.158 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1967 11261 0.720173 GTCAACTAAAACGCGTGCCG 60.72 55.0 14.98 4.36 44.21 5.69 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
20 4621 1.962807 TGGGAGTGTGGCAAAAAGATG 59.037 47.619 0.00 0.00 0.00 2.90
28 4629 7.226523 GGAGTGTGGCAAAAAGATGTAAATTTT 59.773 33.333 0.00 0.00 0.00 1.82
35 4638 8.016801 GGCAAAAAGATGTAAATTTTCCATGTG 58.983 33.333 0.00 0.00 0.00 3.21
136 4768 7.279536 ACATGATTATAATGATCTCCGCACATC 59.720 37.037 1.78 0.00 0.00 3.06
186 4846 4.803613 GTGAAACATGACAACTTTGGGAAC 59.196 41.667 0.00 0.00 36.32 3.62
241 4902 5.995565 TTTTCGAAGGATCTAGTTCTCCA 57.004 39.130 0.00 0.00 33.75 3.86
251 4912 5.940470 GGATCTAGTTCTCCAAAACACATGT 59.060 40.000 0.00 0.00 0.00 3.21
257 4918 6.507023 AGTTCTCCAAAACACATGTTGAATC 58.493 36.000 0.00 0.00 38.44 2.52
263 4924 7.424803 TCCAAAACACATGTTGAATCTAGTTG 58.575 34.615 0.00 0.00 38.44 3.16
288 4950 4.388577 AGGCAAATTTAGGTGAGAAGGT 57.611 40.909 0.00 0.00 0.00 3.50
335 6251 6.038825 TGCCAAATTAGGAAATGTATGTACCG 59.961 38.462 0.00 0.00 0.00 4.02
388 6316 2.684374 TGATTGATTGGCCGACTGATTG 59.316 45.455 0.00 0.00 0.00 2.67
462 7785 7.092716 CGAAATTCTGGTGAGATGGAAAATTT 58.907 34.615 0.00 0.00 0.00 1.82
474 7797 9.224267 TGAGATGGAAAATTTAGTTCTCTGAAG 57.776 33.333 15.52 0.00 31.61 3.02
481 7804 3.634397 TTAGTTCTCTGAAGCCATGGG 57.366 47.619 15.13 0.00 0.00 4.00
484 7807 2.376518 AGTTCTCTGAAGCCATGGGAAA 59.623 45.455 15.13 0.00 0.00 3.13
485 7808 3.157087 GTTCTCTGAAGCCATGGGAAAA 58.843 45.455 15.13 0.00 0.00 2.29
487 7810 3.624777 TCTCTGAAGCCATGGGAAAATC 58.375 45.455 15.13 0.00 0.00 2.17
488 7811 3.267812 TCTCTGAAGCCATGGGAAAATCT 59.732 43.478 15.13 0.00 0.00 2.40
490 7813 3.094572 CTGAAGCCATGGGAAAATCTGT 58.905 45.455 15.13 0.00 0.00 3.41
526 7858 8.359642 CCCTGAAGAAGACACAAATCAAAATTA 58.640 33.333 0.00 0.00 0.00 1.40
538 7870 8.834465 CACAAATCAAAATTAATTGGTTGACCA 58.166 29.630 14.56 0.00 45.94 4.02
592 7934 3.612479 GCCAGCAACACTAAATTGACCTG 60.612 47.826 0.00 0.00 0.00 4.00
593 7935 3.820467 CCAGCAACACTAAATTGACCTGA 59.180 43.478 0.00 0.00 0.00 3.86
659 8088 1.583194 GTCTAGCCGAGCGAACGTC 60.583 63.158 0.00 0.00 0.00 4.34
661 8090 3.047718 CTAGCCGAGCGAACGTCCA 62.048 63.158 0.00 0.00 0.00 4.02
662 8091 2.337749 CTAGCCGAGCGAACGTCCAT 62.338 60.000 0.00 0.00 0.00 3.41
663 8092 2.607668 TAGCCGAGCGAACGTCCATG 62.608 60.000 0.00 0.00 0.00 3.66
664 8093 3.554692 CCGAGCGAACGTCCATGC 61.555 66.667 0.00 0.00 0.00 4.06
665 8094 2.809174 CGAGCGAACGTCCATGCA 60.809 61.111 0.00 0.00 0.00 3.96
666 8095 2.778679 GAGCGAACGTCCATGCAC 59.221 61.111 0.00 0.00 0.00 4.57
667 8096 3.071459 GAGCGAACGTCCATGCACG 62.071 63.158 7.83 7.83 45.65 5.34
668 8097 4.147322 GCGAACGTCCATGCACGG 62.147 66.667 14.71 0.00 44.41 4.94
669 8098 2.431771 CGAACGTCCATGCACGGA 60.432 61.111 14.71 0.00 44.41 4.69
683 8112 2.430921 CGGACACCGCAGACACTC 60.431 66.667 0.00 0.00 41.17 3.51
684 8113 2.048127 GGACACCGCAGACACTCC 60.048 66.667 0.00 0.00 0.00 3.85
685 8114 2.048127 GACACCGCAGACACTCCC 60.048 66.667 0.00 0.00 0.00 4.30
686 8115 3.916392 GACACCGCAGACACTCCCG 62.916 68.421 0.00 0.00 0.00 5.14
687 8116 3.991051 CACCGCAGACACTCCCGT 61.991 66.667 0.00 0.00 0.00 5.28
688 8117 3.991051 ACCGCAGACACTCCCGTG 61.991 66.667 0.00 0.00 46.63 4.94
689 8118 4.742201 CCGCAGACACTCCCGTGG 62.742 72.222 0.00 0.00 45.50 4.94
696 8125 2.283966 CACTCCCGTGGTCCTCCT 60.284 66.667 0.00 0.00 37.50 3.69
699 8128 3.940506 CTCCCGTGGTCCTCCTCGT 62.941 68.421 7.69 0.00 45.58 4.18
700 8129 3.760035 CCCGTGGTCCTCCTCGTG 61.760 72.222 7.69 0.00 45.58 4.35
734 8163 2.348998 CCTGTGCTCCTCCACACC 59.651 66.667 0.00 0.00 40.55 4.16
876 8875 3.166560 ACGGAAACTACTAGAGGTGGT 57.833 47.619 0.00 0.00 41.44 4.16
880 8879 2.895242 AACTACTAGAGGTGGTCGGT 57.105 50.000 0.00 0.00 38.71 4.69
1072 9151 3.314080 TCTTGTTGCTAGGGTTTCGTTTG 59.686 43.478 0.00 0.00 0.00 2.93
1239 9324 2.114670 CGACAATGGCATCCCGCTT 61.115 57.895 0.00 0.00 41.91 4.68
1323 9408 2.115266 CCCAAACCGGCCAACTCT 59.885 61.111 0.00 0.00 0.00 3.24
1364 9449 0.409876 TCCTCCACCTCTACTGCAGT 59.590 55.000 25.12 25.12 0.00 4.40
1506 9597 1.202855 ACTTGCCAGACTGTTGCAGAT 60.203 47.619 0.93 0.00 36.21 2.90
1739 10435 5.587043 TCGTGGTACTTGTGAAACTGAATTT 59.413 36.000 0.00 0.00 38.04 1.82
1964 11258 0.876777 TCATTTGTTCGTCGTGCGGT 60.877 50.000 0.00 0.00 41.72 5.68
1991 11285 3.120786 GCACGCGTTTTAGTTGACACTAT 60.121 43.478 10.22 0.00 35.32 2.12
1997 11291 4.142902 CGTTTTAGTTGACACTATGCCCAG 60.143 45.833 0.00 0.00 35.32 4.45
2038 11332 3.003275 TGTGCGCTTTCTTTGTCTTTAGG 59.997 43.478 9.73 0.00 0.00 2.69
2053 11347 5.949354 TGTCTTTAGGGGTTGTTTGGATATG 59.051 40.000 0.00 0.00 0.00 1.78
2238 11564 0.033504 GGCAACGAGAGAGTGGTTGA 59.966 55.000 7.27 0.00 45.25 3.18
2263 11590 3.441572 GTGATTTGGAGGAGTGATTGGTG 59.558 47.826 0.00 0.00 0.00 4.17
2310 11638 7.852945 CGATTTTCTAGATACATGCTTGTTTCC 59.147 37.037 10.85 1.22 35.22 3.13
2320 11648 2.436417 TGCTTGTTTCCCATCAGTAGC 58.564 47.619 0.00 0.00 0.00 3.58
2326 11654 1.965414 TTCCCATCAGTAGCCCTTCA 58.035 50.000 0.00 0.00 0.00 3.02
2357 11685 4.679373 CCCTCGATGGATAATCATAGGG 57.321 50.000 0.00 7.86 45.30 3.53
2465 12833 8.398665 GTCCATACACATTAAGAAAAGGTCATC 58.601 37.037 0.00 0.00 0.00 2.92
2466 12834 8.106462 TCCATACACATTAAGAAAAGGTCATCA 58.894 33.333 0.00 0.00 0.00 3.07
2498 12866 8.117988 TCATTTAAGTGTTTGTTTACTGACGAC 58.882 33.333 0.00 0.00 0.00 4.34
2519 12922 3.869246 ACGGAACTAAACAGAACACACTG 59.131 43.478 0.00 0.00 42.78 3.66
2542 12945 4.555747 GTCTTCGCGTGAACAAAAGAAAAA 59.444 37.500 7.45 0.00 0.00 1.94
2576 12979 9.958234 CACCATGTTCTATCTATATATTCCTCG 57.042 37.037 0.00 0.00 0.00 4.63
2591 12994 5.828299 ATTCCTCGAACACAAGAAAACAA 57.172 34.783 0.00 0.00 0.00 2.83
2597 13000 6.197096 CCTCGAACACAAGAAAACAAAAGATG 59.803 38.462 0.00 0.00 0.00 2.90
2605 13008 6.127196 ACAAGAAAACAAAAGATGTAAGGGCA 60.127 34.615 0.00 0.00 42.99 5.36
2606 13009 6.670695 AGAAAACAAAAGATGTAAGGGCAT 57.329 33.333 0.00 0.00 42.99 4.40
2607 13010 6.691508 AGAAAACAAAAGATGTAAGGGCATC 58.308 36.000 0.00 0.00 42.99 3.91
2616 13019 5.240713 GATGTAAGGGCATCTTCAAAGTG 57.759 43.478 0.00 0.00 41.35 3.16
2617 13020 3.420893 TGTAAGGGCATCTTCAAAGTGG 58.579 45.455 0.00 0.00 36.93 4.00
2618 13021 2.978156 AAGGGCATCTTCAAAGTGGA 57.022 45.000 0.00 0.00 0.00 4.02
2619 13022 2.206576 AGGGCATCTTCAAAGTGGAC 57.793 50.000 0.00 0.00 0.00 4.02
2620 13023 1.177401 GGGCATCTTCAAAGTGGACC 58.823 55.000 0.00 0.00 0.00 4.46
2621 13024 1.177401 GGCATCTTCAAAGTGGACCC 58.823 55.000 0.00 0.00 0.00 4.46
2622 13025 1.272147 GGCATCTTCAAAGTGGACCCT 60.272 52.381 0.00 0.00 0.00 4.34
2623 13026 2.519013 GCATCTTCAAAGTGGACCCTT 58.481 47.619 0.00 0.00 0.00 3.95
2624 13027 3.561313 GGCATCTTCAAAGTGGACCCTTA 60.561 47.826 0.00 0.00 0.00 2.69
2625 13028 4.079253 GCATCTTCAAAGTGGACCCTTAA 58.921 43.478 0.00 0.00 0.00 1.85
2626 13029 4.522789 GCATCTTCAAAGTGGACCCTTAAA 59.477 41.667 0.00 0.00 0.00 1.52
2627 13030 5.185828 GCATCTTCAAAGTGGACCCTTAAAT 59.814 40.000 0.00 0.00 0.00 1.40
2628 13031 6.625960 GCATCTTCAAAGTGGACCCTTAAATC 60.626 42.308 0.00 0.00 0.00 2.17
2629 13032 6.200878 TCTTCAAAGTGGACCCTTAAATCT 57.799 37.500 0.00 0.00 0.00 2.40
2630 13033 6.610830 TCTTCAAAGTGGACCCTTAAATCTT 58.389 36.000 0.00 0.00 0.00 2.40
2631 13034 7.066781 TCTTCAAAGTGGACCCTTAAATCTTT 58.933 34.615 0.00 0.00 0.00 2.52
2632 13035 8.221944 TCTTCAAAGTGGACCCTTAAATCTTTA 58.778 33.333 0.00 0.00 0.00 1.85
2633 13036 7.754851 TCAAAGTGGACCCTTAAATCTTTAC 57.245 36.000 0.00 0.00 0.00 2.01
2634 13037 7.523415 TCAAAGTGGACCCTTAAATCTTTACT 58.477 34.615 0.00 0.00 0.00 2.24
2635 13038 8.662255 TCAAAGTGGACCCTTAAATCTTTACTA 58.338 33.333 0.00 0.00 0.00 1.82
2636 13039 9.462606 CAAAGTGGACCCTTAAATCTTTACTAT 57.537 33.333 0.00 0.00 0.00 2.12
2664 13067 2.507407 ACAACAGTGTCCAAACCACT 57.493 45.000 0.00 0.00 43.76 4.00
2665 13068 2.802719 ACAACAGTGTCCAAACCACTT 58.197 42.857 0.00 0.00 41.10 3.16
2666 13069 3.161866 ACAACAGTGTCCAAACCACTTT 58.838 40.909 0.00 0.00 41.10 2.66
2667 13070 3.576550 ACAACAGTGTCCAAACCACTTTT 59.423 39.130 0.00 0.00 41.10 2.27
2668 13071 3.866883 ACAGTGTCCAAACCACTTTTG 57.133 42.857 0.00 0.00 41.10 2.44
2669 13072 2.094234 ACAGTGTCCAAACCACTTTTGC 60.094 45.455 0.00 0.00 43.03 3.68
2670 13073 1.480545 AGTGTCCAAACCACTTTTGCC 59.519 47.619 0.00 0.00 43.03 4.52
2671 13074 1.205893 GTGTCCAAACCACTTTTGCCA 59.794 47.619 0.00 0.00 43.03 4.92
2672 13075 2.114616 TGTCCAAACCACTTTTGCCAT 58.885 42.857 0.00 0.00 43.03 4.40
2673 13076 2.102252 TGTCCAAACCACTTTTGCCATC 59.898 45.455 0.00 0.00 43.03 3.51
2674 13077 1.691434 TCCAAACCACTTTTGCCATCC 59.309 47.619 0.00 0.00 43.03 3.51
2675 13078 1.415659 CCAAACCACTTTTGCCATCCA 59.584 47.619 0.00 0.00 43.03 3.41
2676 13079 2.158842 CCAAACCACTTTTGCCATCCAA 60.159 45.455 0.00 0.00 43.03 3.53
2677 13080 3.496515 CCAAACCACTTTTGCCATCCAAT 60.497 43.478 0.00 0.00 43.03 3.16
2678 13081 3.405823 AACCACTTTTGCCATCCAATG 57.594 42.857 0.00 0.00 32.49 2.82
2679 13082 2.607499 ACCACTTTTGCCATCCAATGA 58.393 42.857 0.00 0.00 32.49 2.57
2680 13083 2.564062 ACCACTTTTGCCATCCAATGAG 59.436 45.455 0.00 0.00 32.49 2.90
2681 13084 2.093869 CCACTTTTGCCATCCAATGAGG 60.094 50.000 0.00 0.00 39.47 3.86
2696 13099 7.237209 TCCAATGAGGATCTGTATATGTCTG 57.763 40.000 0.00 0.00 43.07 3.51
2697 13100 5.873712 CCAATGAGGATCTGTATATGTCTGC 59.126 44.000 0.00 0.00 41.22 4.26
2698 13101 6.295745 CCAATGAGGATCTGTATATGTCTGCT 60.296 42.308 0.00 0.00 41.22 4.24
2699 13102 6.931790 ATGAGGATCTGTATATGTCTGCTT 57.068 37.500 0.00 0.00 34.92 3.91
2700 13103 6.737720 TGAGGATCTGTATATGTCTGCTTT 57.262 37.500 0.00 0.00 34.92 3.51
2701 13104 6.519382 TGAGGATCTGTATATGTCTGCTTTG 58.481 40.000 0.00 0.00 34.92 2.77
2702 13105 5.303971 AGGATCTGTATATGTCTGCTTTGC 58.696 41.667 0.00 0.00 0.00 3.68
2703 13106 5.071519 AGGATCTGTATATGTCTGCTTTGCT 59.928 40.000 0.00 0.00 0.00 3.91
2704 13107 6.268617 AGGATCTGTATATGTCTGCTTTGCTA 59.731 38.462 0.00 0.00 0.00 3.49
2705 13108 7.038445 AGGATCTGTATATGTCTGCTTTGCTAT 60.038 37.037 0.00 0.00 0.00 2.97
2706 13109 7.605691 GGATCTGTATATGTCTGCTTTGCTATT 59.394 37.037 0.00 0.00 0.00 1.73
2707 13110 7.953158 TCTGTATATGTCTGCTTTGCTATTC 57.047 36.000 0.00 0.00 0.00 1.75
2708 13111 6.642540 TCTGTATATGTCTGCTTTGCTATTCG 59.357 38.462 0.00 0.00 0.00 3.34
2709 13112 5.696270 TGTATATGTCTGCTTTGCTATTCGG 59.304 40.000 0.00 0.00 0.00 4.30
2710 13113 2.760634 TGTCTGCTTTGCTATTCGGA 57.239 45.000 0.00 0.00 0.00 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 4609 8.016801 CACATGGAAAATTTACATCTTTTTGCC 58.983 33.333 0.00 0.00 31.93 4.52
224 4884 6.231211 TGTGTTTTGGAGAACTAGATCCTTC 58.769 40.000 0.00 0.00 36.50 3.46
225 4885 6.187727 TGTGTTTTGGAGAACTAGATCCTT 57.812 37.500 0.00 0.00 36.50 3.36
231 4892 6.618287 TCAACATGTGTTTTGGAGAACTAG 57.382 37.500 0.00 0.00 35.83 2.57
241 4902 7.995289 TGTCAACTAGATTCAACATGTGTTTT 58.005 30.769 0.00 0.00 35.83 2.43
251 4912 6.899393 ATTTGCCTTGTCAACTAGATTCAA 57.101 33.333 0.00 0.00 0.00 2.69
257 4918 6.206634 TCACCTAAATTTGCCTTGTCAACTAG 59.793 38.462 0.00 0.00 0.00 2.57
263 4924 5.335976 CCTTCTCACCTAAATTTGCCTTGTC 60.336 44.000 0.00 0.00 0.00 3.18
288 4950 9.823647 TGGCATGTTTTCAAAGAACTAAATTTA 57.176 25.926 0.00 0.00 0.00 1.40
335 6251 3.748048 TGCTATGCTTGTGTCTTCTTCAC 59.252 43.478 0.00 0.00 36.48 3.18
373 6301 1.660560 GCTGCAATCAGTCGGCCAAT 61.661 55.000 2.24 0.00 42.29 3.16
377 6305 2.789917 CTGCTGCAATCAGTCGGC 59.210 61.111 3.02 0.00 42.29 5.54
388 6316 2.138596 TTTAGTTTTGCTGCTGCTGC 57.861 45.000 22.51 22.51 40.48 5.25
462 7785 2.832838 TCCCATGGCTTCAGAGAACTA 58.167 47.619 6.09 0.00 0.00 2.24
474 7797 7.054491 ACATTATTACAGATTTTCCCATGGC 57.946 36.000 6.09 0.00 0.00 4.40
484 7807 9.838339 CTTCTTCAGGGTACATTATTACAGATT 57.162 33.333 0.00 0.00 0.00 2.40
485 7808 9.213777 TCTTCTTCAGGGTACATTATTACAGAT 57.786 33.333 0.00 0.00 0.00 2.90
487 7810 8.258007 TGTCTTCTTCAGGGTACATTATTACAG 58.742 37.037 0.00 0.00 0.00 2.74
488 7811 8.038944 GTGTCTTCTTCAGGGTACATTATTACA 58.961 37.037 0.00 0.00 0.00 2.41
490 7813 8.141298 TGTGTCTTCTTCAGGGTACATTATTA 57.859 34.615 0.00 0.00 0.00 0.98
538 7870 7.173562 TGCTGCTGCTTTAATCAATCAATTTTT 59.826 29.630 17.00 0.00 40.48 1.94
592 7934 0.745128 TCTTCTCGCTCCCGTCTCTC 60.745 60.000 0.00 0.00 35.54 3.20
593 7935 0.746563 CTCTTCTCGCTCCCGTCTCT 60.747 60.000 0.00 0.00 35.54 3.10
634 7989 1.153823 GCTCGGCTAGACGCTTGAA 60.154 57.895 14.83 0.00 39.13 2.69
667 8096 2.048127 GGAGTGTCTGCGGTGTCC 60.048 66.667 0.00 0.00 0.00 4.02
668 8097 2.048127 GGGAGTGTCTGCGGTGTC 60.048 66.667 0.00 0.00 0.00 3.67
669 8098 3.991051 CGGGAGTGTCTGCGGTGT 61.991 66.667 0.00 0.00 0.00 4.16
670 8099 3.991051 ACGGGAGTGTCTGCGGTG 61.991 66.667 0.00 0.00 44.82 4.94
680 8109 3.940506 CGAGGAGGACCACGGGAGT 62.941 68.421 0.00 0.00 44.22 3.85
681 8110 3.141488 CGAGGAGGACCACGGGAG 61.141 72.222 0.00 0.00 44.22 4.30
686 8115 4.436998 CCGCACGAGGAGGACCAC 62.437 72.222 0.00 0.00 39.08 4.16
689 8118 4.803426 CAGCCGCACGAGGAGGAC 62.803 72.222 5.89 0.00 39.08 3.85
876 8875 1.153489 CGACTCGAGTAGGGACCGA 60.153 63.158 20.09 0.00 0.00 4.69
880 8879 0.177604 GGAGACGACTCGAGTAGGGA 59.822 60.000 26.31 0.00 43.44 4.20
1072 9151 2.717139 GATCGGACGATTGGGAGGCC 62.717 65.000 8.75 0.00 34.60 5.19
1239 9324 0.824595 TCTTGGAGTCGACGTTGGGA 60.825 55.000 10.46 4.79 0.00 4.37
1506 9597 2.965831 CGGAGTCTTCCCCTTGATCATA 59.034 50.000 0.00 0.00 40.67 2.15
1539 9630 8.908786 AGTCATTCTTGATGTTGAAAGTCTTA 57.091 30.769 0.00 0.00 37.06 2.10
1693 10370 8.993121 CACGATAGGTTTCTTCTTGCATAATAT 58.007 33.333 0.00 0.00 43.77 1.28
1739 10435 9.829507 AATCAAAACATCCACTTGACAAATAAA 57.170 25.926 0.00 0.00 32.19 1.40
1785 10490 5.874261 TCTCAAATCACACGCATAAATCAGA 59.126 36.000 0.00 0.00 0.00 3.27
1875 11157 5.104374 GCCAAATGAAAATCATGTCGACAT 58.896 37.500 25.18 25.18 37.15 3.06
1914 11199 2.997986 GTGTTAACGATCCAACGGTCAT 59.002 45.455 0.26 0.00 37.61 3.06
1964 11258 3.718097 CTAAAACGCGTGCCGGCA 61.718 61.111 29.03 29.03 42.52 5.69
1967 11261 0.720173 GTCAACTAAAACGCGTGCCG 60.720 55.000 14.98 4.36 44.21 5.69
1971 11265 3.120786 GCATAGTGTCAACTAAAACGCGT 60.121 43.478 5.58 5.58 42.17 6.01
1997 11291 2.952310 ACAAAAACTTCACTCCAGCTCC 59.048 45.455 0.00 0.00 0.00 4.70
2009 11303 3.993736 ACAAAGAAAGCGCACAAAAACTT 59.006 34.783 11.47 2.20 0.00 2.66
2064 11358 9.364989 CACAAACTGGTTTTCTAAAATCTCAAA 57.635 29.630 0.58 0.00 30.42 2.69
2238 11564 4.338879 CAATCACTCCTCCAAATCACCTT 58.661 43.478 0.00 0.00 0.00 3.50
2263 11590 3.058501 CGAACTAAACCAACATGTCCACC 60.059 47.826 0.00 0.00 0.00 4.61
2310 11638 2.947652 CAATGTGAAGGGCTACTGATGG 59.052 50.000 0.00 0.00 0.00 3.51
2320 11648 0.929244 AGGGGATCCAATGTGAAGGG 59.071 55.000 15.23 0.00 34.83 3.95
2326 11654 0.767375 CCATCGAGGGGATCCAATGT 59.233 55.000 15.23 0.00 31.28 2.71
2436 12804 9.391006 GACCTTTTCTTAATGTGTATGGACATA 57.609 33.333 0.00 0.00 38.04 2.29
2489 12857 3.814842 TCTGTTTAGTTCCGTCGTCAGTA 59.185 43.478 0.00 0.00 0.00 2.74
2496 12864 4.025979 CAGTGTGTTCTGTTTAGTTCCGTC 60.026 45.833 0.00 0.00 0.00 4.79
2498 12866 3.869246 ACAGTGTGTTCTGTTTAGTTCCG 59.131 43.478 0.00 0.00 44.92 4.30
2519 12922 3.313274 TTCTTTTGTTCACGCGAAGAC 57.687 42.857 15.93 8.40 0.00 3.01
2542 12945 3.525199 AGATAGAACATGGTGAGCCCTTT 59.475 43.478 0.00 0.00 0.00 3.11
2545 12948 4.899352 ATAGATAGAACATGGTGAGCCC 57.101 45.455 0.00 0.00 0.00 5.19
2576 12979 8.807581 CCTTACATCTTTTGTTTTCTTGTGTTC 58.192 33.333 0.00 0.00 39.87 3.18
2579 12982 6.200854 GCCCTTACATCTTTTGTTTTCTTGTG 59.799 38.462 0.00 0.00 39.87 3.33
2597 13000 3.440522 GTCCACTTTGAAGATGCCCTTAC 59.559 47.826 0.00 0.00 34.68 2.34
2605 13008 6.794534 AGATTTAAGGGTCCACTTTGAAGAT 58.205 36.000 0.00 0.00 32.02 2.40
2606 13009 6.200878 AGATTTAAGGGTCCACTTTGAAGA 57.799 37.500 0.00 0.00 32.02 2.87
2607 13010 6.901081 AAGATTTAAGGGTCCACTTTGAAG 57.099 37.500 0.00 0.00 32.02 3.02
2608 13011 8.002459 AGTAAAGATTTAAGGGTCCACTTTGAA 58.998 33.333 0.00 0.00 32.02 2.69
2609 13012 7.523415 AGTAAAGATTTAAGGGTCCACTTTGA 58.477 34.615 0.00 0.00 32.02 2.69
2610 13013 7.761038 AGTAAAGATTTAAGGGTCCACTTTG 57.239 36.000 0.00 0.00 32.02 2.77
2625 13028 9.823647 CTGTTGTCCAGACATATAGTAAAGATT 57.176 33.333 0.48 0.00 44.49 2.40
2626 13029 8.982723 ACTGTTGTCCAGACATATAGTAAAGAT 58.017 33.333 0.48 0.00 44.49 2.40
2627 13030 8.251026 CACTGTTGTCCAGACATATAGTAAAGA 58.749 37.037 0.48 0.00 44.49 2.52
2628 13031 8.035394 ACACTGTTGTCCAGACATATAGTAAAG 58.965 37.037 0.48 0.00 44.49 1.85
2629 13032 7.903145 ACACTGTTGTCCAGACATATAGTAAA 58.097 34.615 0.48 0.00 44.49 2.01
2630 13033 7.476540 ACACTGTTGTCCAGACATATAGTAA 57.523 36.000 0.48 0.00 44.49 2.24
2631 13034 7.096884 GACACTGTTGTCCAGACATATAGTA 57.903 40.000 0.48 0.00 45.77 1.82
2632 13035 5.967088 GACACTGTTGTCCAGACATATAGT 58.033 41.667 0.48 4.19 45.77 2.12
2645 13048 2.507407 AGTGGTTTGGACACTGTTGT 57.493 45.000 0.00 0.00 46.67 3.32
2651 13054 1.205893 TGGCAAAAGTGGTTTGGACAC 59.794 47.619 1.38 0.00 45.79 3.67
2652 13055 1.561643 TGGCAAAAGTGGTTTGGACA 58.438 45.000 1.38 0.00 45.79 4.02
2653 13056 2.547855 GGATGGCAAAAGTGGTTTGGAC 60.548 50.000 0.00 0.00 45.79 4.02
2654 13057 1.691434 GGATGGCAAAAGTGGTTTGGA 59.309 47.619 0.00 0.00 45.79 3.53
2655 13058 1.415659 TGGATGGCAAAAGTGGTTTGG 59.584 47.619 0.00 0.00 45.79 3.28
2657 13060 3.390639 TCATTGGATGGCAAAAGTGGTTT 59.609 39.130 0.00 0.00 0.00 3.27
2658 13061 2.971330 TCATTGGATGGCAAAAGTGGTT 59.029 40.909 0.00 0.00 0.00 3.67
2659 13062 2.564062 CTCATTGGATGGCAAAAGTGGT 59.436 45.455 0.00 0.00 0.00 4.16
2660 13063 2.093869 CCTCATTGGATGGCAAAAGTGG 60.094 50.000 0.00 0.00 38.35 4.00
2661 13064 2.827322 TCCTCATTGGATGGCAAAAGTG 59.173 45.455 0.00 0.00 40.56 3.16
2662 13065 3.173953 TCCTCATTGGATGGCAAAAGT 57.826 42.857 0.00 0.00 40.56 2.66
2673 13076 5.873712 GCAGACATATACAGATCCTCATTGG 59.126 44.000 0.00 0.00 37.10 3.16
2674 13077 6.699366 AGCAGACATATACAGATCCTCATTG 58.301 40.000 0.00 0.00 0.00 2.82
2675 13078 6.931790 AGCAGACATATACAGATCCTCATT 57.068 37.500 0.00 0.00 0.00 2.57
2676 13079 6.931790 AAGCAGACATATACAGATCCTCAT 57.068 37.500 0.00 0.00 0.00 2.90
2677 13080 6.519382 CAAAGCAGACATATACAGATCCTCA 58.481 40.000 0.00 0.00 0.00 3.86
2678 13081 5.407995 GCAAAGCAGACATATACAGATCCTC 59.592 44.000 0.00 0.00 0.00 3.71
2679 13082 5.071519 AGCAAAGCAGACATATACAGATCCT 59.928 40.000 0.00 0.00 0.00 3.24
2680 13083 5.303971 AGCAAAGCAGACATATACAGATCC 58.696 41.667 0.00 0.00 0.00 3.36
2681 13084 8.545229 AATAGCAAAGCAGACATATACAGATC 57.455 34.615 0.00 0.00 0.00 2.75
2682 13085 7.330454 CGAATAGCAAAGCAGACATATACAGAT 59.670 37.037 0.00 0.00 0.00 2.90
2683 13086 6.642540 CGAATAGCAAAGCAGACATATACAGA 59.357 38.462 0.00 0.00 0.00 3.41
2684 13087 6.128715 CCGAATAGCAAAGCAGACATATACAG 60.129 42.308 0.00 0.00 0.00 2.74
2685 13088 5.696270 CCGAATAGCAAAGCAGACATATACA 59.304 40.000 0.00 0.00 0.00 2.29
2686 13089 5.926542 TCCGAATAGCAAAGCAGACATATAC 59.073 40.000 0.00 0.00 0.00 1.47
2687 13090 6.096673 TCCGAATAGCAAAGCAGACATATA 57.903 37.500 0.00 0.00 0.00 0.86
2688 13091 4.960938 TCCGAATAGCAAAGCAGACATAT 58.039 39.130 0.00 0.00 0.00 1.78
2689 13092 4.400529 TCCGAATAGCAAAGCAGACATA 57.599 40.909 0.00 0.00 0.00 2.29
2690 13093 3.266510 TCCGAATAGCAAAGCAGACAT 57.733 42.857 0.00 0.00 0.00 3.06
2691 13094 2.760634 TCCGAATAGCAAAGCAGACA 57.239 45.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.