Multiple sequence alignment - TraesCS2B01G500300

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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 TraesCS2B01G500300 chr2B 100.000 2782 0 0 1 2782 695731288 695734069 0.000000e+00 5138.0
1 TraesCS2B01G500300 chr2B 93.117 1482 51 19 553 2003 695688186 695689647 0.000000e+00 2124.0
2 TraesCS2B01G500300 chr2B 94.488 1288 62 8 703 1983 695692643 695693928 0.000000e+00 1977.0
3 TraesCS2B01G500300 chr2B 93.700 1238 69 6 718 1946 695683961 695685198 0.000000e+00 1845.0
4 TraesCS2B01G500300 chr2B 89.728 847 66 10 1841 2677 695691808 695692643 0.000000e+00 1062.0
5 TraesCS2B01G500300 chr2B 96.117 103 4 0 630 732 695682087 695682189 4.770000e-38 169.0
6 TraesCS2B01G500300 chr2B 89.583 96 7 2 1977 2069 695721568 695721663 4.870000e-23 119.0
7 TraesCS2B01G500300 chr2A 90.056 1438 101 21 542 1946 716424287 716425715 0.000000e+00 1825.0
8 TraesCS2B01G500300 chr2A 89.917 1438 103 21 542 1946 716300988 716302416 0.000000e+00 1814.0
9 TraesCS2B01G500300 chr2A 89.847 1438 104 21 542 1946 716340756 716342184 0.000000e+00 1808.0
10 TraesCS2B01G500300 chr2A 89.646 1439 105 23 542 1946 716393238 716394666 0.000000e+00 1792.0
11 TraesCS2B01G500300 chr2A 90.365 1204 77 18 542 1714 716252445 716253640 0.000000e+00 1544.0
12 TraesCS2B01G500300 chr2A 86.719 1152 89 25 831 1946 716247793 716248916 0.000000e+00 1221.0
13 TraesCS2B01G500300 chr2A 88.929 560 52 1 1 550 716370182 716370741 0.000000e+00 682.0
14 TraesCS2B01G500300 chr2A 88.750 560 52 2 1 550 716282109 716282667 0.000000e+00 675.0
15 TraesCS2B01G500300 chr2A 88.393 560 54 2 1 550 716330404 716330962 0.000000e+00 664.0
16 TraesCS2B01G500300 chr2A 88.214 560 56 1 1 550 716423093 716423652 0.000000e+00 660.0
17 TraesCS2B01G500300 chr2A 82.124 386 39 19 400 766 716247409 716247783 1.250000e-78 303.0
18 TraesCS2B01G500300 chr2A 89.041 73 8 0 1956 2028 716248997 716249069 1.060000e-14 91.6
19 TraesCS2B01G500300 chr2A 87.324 71 9 0 1958 2028 716425798 716425868 6.390000e-12 82.4
20 TraesCS2B01G500300 chr2D 91.886 875 45 9 633 1488 578875148 578876015 0.000000e+00 1199.0
21 TraesCS2B01G500300 chr2D 90.987 821 53 10 1492 2297 578876215 578877029 0.000000e+00 1086.0
22 TraesCS2B01G500300 chr2D 86.299 978 83 15 746 1714 578888175 578889110 0.000000e+00 1016.0
23 TraesCS2B01G500300 chr2D 87.437 398 33 9 2363 2756 578877366 578877750 2.540000e-120 442.0
24 TraesCS2B01G500300 chr2D 86.585 164 17 4 2597 2756 578877791 578877953 2.850000e-40 176.0
25 TraesCS2B01G500300 chr7A 84.170 259 39 2 1 259 628510984 628510728 1.650000e-62 250.0
26 TraesCS2B01G500300 chr1B 84.231 260 38 3 1 259 398897893 398898150 1.650000e-62 250.0
27 TraesCS2B01G500300 chr7B 83.658 257 40 2 1 257 589729811 589730065 9.960000e-60 241.0
28 TraesCS2B01G500300 chr1A 83.142 261 36 8 1 259 393952542 393952796 5.990000e-57 231.0
29 TraesCS2B01G500300 chr5B 81.992 261 40 7 1 259 421690804 421691059 6.030000e-52 215.0
30 TraesCS2B01G500300 chrUn 90.769 65 6 0 2596 2660 95257366 95257430 1.370000e-13 87.9
31 TraesCS2B01G500300 chr6B 93.220 59 4 0 2602 2660 574971800 574971858 1.370000e-13 87.9
32 TraesCS2B01G500300 chr4B 89.394 66 6 1 2596 2660 648196753 648196688 6.390000e-12 82.4
33 TraesCS2B01G500300 chr4B 89.394 66 6 1 2596 2660 648222010 648221945 6.390000e-12 82.4
34 TraesCS2B01G500300 chr4B 89.394 66 6 1 2596 2660 648246021 648245956 6.390000e-12 82.4
35 TraesCS2B01G500300 chr4B 89.394 66 6 1 2596 2660 648271914 648271849 6.390000e-12 82.4


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 TraesCS2B01G500300 chr2B 695731288 695734069 2781 False 5138.00 5138 100.000000 1 2782 1 chr2B.!!$F2 2781
1 TraesCS2B01G500300 chr2B 695682087 695693928 11841 False 1435.40 2124 93.430000 553 2677 5 chr2B.!!$F3 2124
2 TraesCS2B01G500300 chr2A 716300988 716302416 1428 False 1814.00 1814 89.917000 542 1946 1 chr2A.!!$F2 1404
3 TraesCS2B01G500300 chr2A 716340756 716342184 1428 False 1808.00 1808 89.847000 542 1946 1 chr2A.!!$F4 1404
4 TraesCS2B01G500300 chr2A 716393238 716394666 1428 False 1792.00 1792 89.646000 542 1946 1 chr2A.!!$F6 1404
5 TraesCS2B01G500300 chr2A 716423093 716425868 2775 False 855.80 1825 88.531333 1 2028 3 chr2A.!!$F8 2027
6 TraesCS2B01G500300 chr2A 716247409 716253640 6231 False 789.90 1544 87.062250 400 2028 4 chr2A.!!$F7 1628
7 TraesCS2B01G500300 chr2A 716370182 716370741 559 False 682.00 682 88.929000 1 550 1 chr2A.!!$F5 549
8 TraesCS2B01G500300 chr2A 716282109 716282667 558 False 675.00 675 88.750000 1 550 1 chr2A.!!$F1 549
9 TraesCS2B01G500300 chr2A 716330404 716330962 558 False 664.00 664 88.393000 1 550 1 chr2A.!!$F3 549
10 TraesCS2B01G500300 chr2D 578888175 578889110 935 False 1016.00 1016 86.299000 746 1714 1 chr2D.!!$F1 968
11 TraesCS2B01G500300 chr2D 578875148 578877953 2805 False 725.75 1199 89.223750 633 2756 4 chr2D.!!$F2 2123

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
891 6479 0.107456 GAGTGCCATCCATCATCCGT 59.893 55.0 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2335 12636 0.106419 AAGGCGACTAGAGAGGGAGG 60.106 60.0 0.0 0.0 42.68 4.3 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
82 83 4.574013 GCTAGTGCTAACGGTAAGACTAGA 59.426 45.833 21.64 0.00 36.53 2.43
85 86 6.527057 AGTGCTAACGGTAAGACTAGAAAT 57.473 37.500 0.00 0.00 0.00 2.17
124 125 1.720805 ATCTTACACGTGCATGCGAA 58.279 45.000 17.22 0.00 35.59 4.70
151 152 7.478520 TTTTCTCTGAACCTCTTAGTTTTCG 57.521 36.000 0.00 0.00 0.00 3.46
158 159 6.801575 TGAACCTCTTAGTTTTCGCAAATTT 58.198 32.000 0.00 0.00 0.00 1.82
161 162 6.801575 ACCTCTTAGTTTTCGCAAATTTGAA 58.198 32.000 22.31 5.30 0.00 2.69
259 260 4.137543 CCTCTAGGGCATATTTCCAACAC 58.862 47.826 0.00 0.00 0.00 3.32
264 265 2.418609 GGGCATATTTCCAACACTTGCC 60.419 50.000 2.48 2.48 45.73 4.52
287 288 1.744320 AAGAAAGCCAACAACCGCCC 61.744 55.000 0.00 0.00 0.00 6.13
301 302 3.877450 GCCCTGATCCCCGCATCA 61.877 66.667 0.00 0.00 0.00 3.07
303 304 2.446848 CCCTGATCCCCGCATCACT 61.447 63.158 0.00 0.00 0.00 3.41
308 309 2.037641 CTGATCCCCGCATCACTGATAA 59.962 50.000 0.00 0.00 0.00 1.75
314 315 3.016736 CCCGCATCACTGATAAAAACCT 58.983 45.455 0.00 0.00 0.00 3.50
372 373 7.254590 GGTTTCTCCGTGAATAATCAATCTGAG 60.255 40.741 0.00 0.00 37.30 3.35
383 384 9.213799 GAATAATCAATCTGAGTAAGGGATGTC 57.786 37.037 0.00 0.00 30.37 3.06
384 385 4.655762 TCAATCTGAGTAAGGGATGTCG 57.344 45.455 0.00 0.00 0.00 4.35
388 389 2.832129 TCTGAGTAAGGGATGTCGCTTT 59.168 45.455 16.02 1.33 45.22 3.51
393 394 4.024670 AGTAAGGGATGTCGCTTTAGAGT 58.975 43.478 16.02 1.20 45.22 3.24
420 421 4.164221 AGTGGGATAATTCGAGTGGACAAT 59.836 41.667 0.00 0.00 0.00 2.71
442 443 5.215239 TGCATGTACACATTTATCACACG 57.785 39.130 0.00 0.00 33.61 4.49
457 458 1.522258 CACACGCACAAAATTTGGAGC 59.478 47.619 10.71 12.07 34.12 4.70
464 465 3.372822 GCACAAAATTTGGAGCCATGATG 59.627 43.478 10.71 0.00 34.12 3.07
472 473 3.046283 TGGAGCCATGATGTAGGTACT 57.954 47.619 0.00 0.00 46.37 2.73
525 536 5.675575 GCACATTAGGATTCAGCAAGTTCAG 60.676 44.000 0.00 0.00 0.00 3.02
538 549 3.311871 GCAAGTTCAGTCTGCTGGATATG 59.688 47.826 0.00 0.00 42.78 1.78
557 6105 9.914131 TGGATATGTAGAAAGATAGTCGATTTG 57.086 33.333 0.00 0.00 0.00 2.32
585 6134 8.414778 ACGAAATTGGGTGTAAAGAAAATACAA 58.585 29.630 0.00 0.00 35.21 2.41
586 6135 8.696175 CGAAATTGGGTGTAAAGAAAATACAAC 58.304 33.333 0.00 0.00 39.67 3.32
587 6136 9.758651 GAAATTGGGTGTAAAGAAAATACAACT 57.241 29.630 2.20 0.00 40.15 3.16
625 6176 3.569194 TGGTCAAAAGAACAGCTGGTA 57.431 42.857 19.93 0.00 0.00 3.25
699 6252 4.337763 ACACGCGAGAATAGTTTACGTAG 58.662 43.478 15.93 0.00 0.00 3.51
885 6473 0.531532 CACGAGGAGTGCCATCCATC 60.532 60.000 7.03 1.74 44.72 3.51
886 6474 0.977627 ACGAGGAGTGCCATCCATCA 60.978 55.000 7.03 0.00 42.26 3.07
887 6475 0.395686 CGAGGAGTGCCATCCATCAT 59.604 55.000 7.03 0.00 42.26 2.45
888 6476 1.607509 CGAGGAGTGCCATCCATCATC 60.608 57.143 7.03 0.00 42.26 2.92
889 6477 0.769873 AGGAGTGCCATCCATCATCC 59.230 55.000 7.03 0.00 42.26 3.51
890 6478 0.604780 GGAGTGCCATCCATCATCCG 60.605 60.000 0.00 0.00 39.34 4.18
891 6479 0.107456 GAGTGCCATCCATCATCCGT 59.893 55.000 0.00 0.00 0.00 4.69
911 6499 1.257055 GCCAACCCTGCCTGCATAAA 61.257 55.000 0.00 0.00 0.00 1.40
1019 6615 3.057456 CACCTATTTATAGCTCTCGCCGT 60.057 47.826 0.00 0.00 36.60 5.68
1166 6768 2.270986 GCCTCCACAAACAGCTGGG 61.271 63.158 19.93 9.23 0.00 4.45
1233 6835 1.746615 GCGTCATGGACTGGCACAT 60.747 57.895 0.00 0.00 38.20 3.21
1529 7367 1.522355 CGGCCATCGAGACTGCAAT 60.522 57.895 2.24 0.00 42.43 3.56
1554 8234 3.329889 ATCAAGGTGGAGCCGGCA 61.330 61.111 31.54 4.59 43.70 5.69
1572 8252 1.035932 CAGCCAATGGAGGGAGCTTG 61.036 60.000 2.05 0.00 0.00 4.01
1602 11737 1.129998 GACTCGACGTACAAGCTGCTA 59.870 52.381 0.90 0.00 0.00 3.49
1671 11806 4.242602 GCCATCTTTAAGGCCGCT 57.757 55.556 0.00 0.00 45.18 5.52
1698 11833 2.505982 CTCATCGCCAACCCCGAT 59.494 61.111 0.00 0.00 45.41 4.18
1716 11851 3.430790 CCGATGCCTACAACTGAATCAGA 60.431 47.826 18.20 0.00 35.18 3.27
1748 11883 8.663167 GGGATCATATATGATTATGATGTCCCA 58.337 37.037 27.36 3.59 46.22 4.37
1775 11910 7.382218 AGTTTGATTTTTATGTGCTTTCTTCCG 59.618 33.333 0.00 0.00 0.00 4.30
1863 11999 3.978687 AGTGTGGACGTGAGAAGTTTAG 58.021 45.455 0.00 0.00 0.00 1.85
1866 12003 4.444720 GTGTGGACGTGAGAAGTTTAGAAG 59.555 45.833 0.00 0.00 0.00 2.85
1883 12021 8.975439 AGTTTAGAAGTTAGTATTTGTGACACG 58.025 33.333 0.22 0.00 0.00 4.49
1986 12284 5.621197 TTGGAAAATTATGTGTCGACCTG 57.379 39.130 14.12 0.00 0.00 4.00
1992 12290 7.148306 GGAAAATTATGTGTCGACCTGTTACAT 60.148 37.037 18.77 18.77 36.15 2.29
1994 12292 8.958119 AAATTATGTGTCGACCTGTTACATAT 57.042 30.769 20.08 8.90 35.07 1.78
1995 12293 7.946655 ATTATGTGTCGACCTGTTACATATG 57.053 36.000 20.08 0.00 35.07 1.78
1998 12296 4.461431 TGTGTCGACCTGTTACATATGTCT 59.539 41.667 12.68 0.00 0.00 3.41
2028 12326 9.959721 ATGTATGTGAAATACCTAAACACTCTT 57.040 29.630 0.00 0.00 33.41 2.85
2032 12330 8.263940 TGTGAAATACCTAAACACTCTTATGC 57.736 34.615 0.00 0.00 33.41 3.14
2033 12331 7.064134 TGTGAAATACCTAAACACTCTTATGCG 59.936 37.037 0.00 0.00 33.41 4.73
2034 12332 5.986004 AATACCTAAACACTCTTATGCGC 57.014 39.130 0.00 0.00 0.00 6.09
2035 12333 3.328382 ACCTAAACACTCTTATGCGCA 57.672 42.857 14.96 14.96 0.00 6.09
2036 12334 3.670625 ACCTAAACACTCTTATGCGCAA 58.329 40.909 17.11 0.00 0.00 4.85
2037 12335 4.069304 ACCTAAACACTCTTATGCGCAAA 58.931 39.130 17.11 9.55 0.00 3.68
2038 12336 4.517453 ACCTAAACACTCTTATGCGCAAAA 59.483 37.500 17.11 2.00 0.00 2.44
2039 12337 5.009210 ACCTAAACACTCTTATGCGCAAAAA 59.991 36.000 17.11 11.54 0.00 1.94
2068 12366 8.608844 AAGTTCATATGTCGAGAAAGACTTTT 57.391 30.769 1.12 0.00 41.47 2.27
2134 12432 0.464452 AGTAGGGCATTACACCTCGC 59.536 55.000 0.00 0.00 38.30 5.03
2143 12441 0.172578 TTACACCTCGCGATGACCTG 59.827 55.000 18.54 8.50 0.00 4.00
2149 12447 0.738975 CTCGCGATGACCTGAACCTA 59.261 55.000 10.36 0.00 0.00 3.08
2163 12461 5.119694 CCTGAACCTAGGTAATTCTCTTGC 58.880 45.833 16.67 0.00 32.99 4.01
2165 12463 4.534500 TGAACCTAGGTAATTCTCTTGCCA 59.466 41.667 16.67 0.00 0.00 4.92
2166 12464 4.489306 ACCTAGGTAATTCTCTTGCCAC 57.511 45.455 14.41 0.00 0.00 5.01
2168 12466 3.118738 CCTAGGTAATTCTCTTGCCACGT 60.119 47.826 0.00 0.00 0.00 4.49
2172 12470 1.967319 AATTCTCTTGCCACGTGTGT 58.033 45.000 15.65 0.00 0.00 3.72
2195 12495 1.479757 GGAGTGTTTTAACCCTGGCCA 60.480 52.381 4.71 4.71 0.00 5.36
2206 12506 1.106285 CCCTGGCCAAACAATCTAGC 58.894 55.000 7.01 0.00 0.00 3.42
2230 12530 1.756538 TGCATCGTAGCTCCAATCTCA 59.243 47.619 0.00 0.00 34.99 3.27
2232 12532 2.541762 GCATCGTAGCTCCAATCTCAAC 59.458 50.000 0.00 0.00 0.00 3.18
2235 12535 2.688446 TCGTAGCTCCAATCTCAACGAT 59.312 45.455 0.00 0.00 33.44 3.73
2240 12540 2.555199 CTCCAATCTCAACGATCACCC 58.445 52.381 0.00 0.00 0.00 4.61
2241 12541 1.134818 TCCAATCTCAACGATCACCCG 60.135 52.381 0.00 0.00 0.00 5.28
2290 12591 2.752903 ACTTTATCCGCATTGACCCAAC 59.247 45.455 0.00 0.00 0.00 3.77
2310 12611 6.998258 CAACAATTTGGAAGTGAAGCTAAG 57.002 37.500 0.78 0.00 0.00 2.18
2311 12612 6.738114 CAACAATTTGGAAGTGAAGCTAAGA 58.262 36.000 0.78 0.00 0.00 2.10
2312 12613 7.373493 CAACAATTTGGAAGTGAAGCTAAGAT 58.627 34.615 0.78 0.00 0.00 2.40
2313 12614 7.530426 ACAATTTGGAAGTGAAGCTAAGATT 57.470 32.000 0.78 0.00 0.00 2.40
2314 12615 7.955918 ACAATTTGGAAGTGAAGCTAAGATTT 58.044 30.769 0.78 0.00 0.00 2.17
2315 12616 8.424133 ACAATTTGGAAGTGAAGCTAAGATTTT 58.576 29.630 0.78 0.00 0.00 1.82
2316 12617 9.912634 CAATTTGGAAGTGAAGCTAAGATTTTA 57.087 29.630 0.00 0.00 0.00 1.52
2320 12621 9.959721 TTGGAAGTGAAGCTAAGATTTTATAGT 57.040 29.630 0.00 0.00 0.00 2.12
2321 12622 9.601217 TGGAAGTGAAGCTAAGATTTTATAGTC 57.399 33.333 0.00 0.00 0.00 2.59
2322 12623 9.825109 GGAAGTGAAGCTAAGATTTTATAGTCT 57.175 33.333 0.00 0.00 0.00 3.24
2324 12625 9.825109 AAGTGAAGCTAAGATTTTATAGTCTCC 57.175 33.333 0.00 0.00 0.00 3.71
2325 12626 9.207868 AGTGAAGCTAAGATTTTATAGTCTCCT 57.792 33.333 0.00 0.00 0.00 3.69
2334 12635 8.798975 AGATTTTATAGTCTCCTATTCACCCA 57.201 34.615 0.00 0.00 35.49 4.51
2335 12636 8.652290 AGATTTTATAGTCTCCTATTCACCCAC 58.348 37.037 0.00 0.00 35.49 4.61
2336 12637 6.742559 TTTATAGTCTCCTATTCACCCACC 57.257 41.667 0.00 0.00 35.49 4.61
2337 12638 2.950990 AGTCTCCTATTCACCCACCT 57.049 50.000 0.00 0.00 0.00 4.00
2338 12639 2.753247 AGTCTCCTATTCACCCACCTC 58.247 52.381 0.00 0.00 0.00 3.85
2339 12640 1.763545 GTCTCCTATTCACCCACCTCC 59.236 57.143 0.00 0.00 0.00 4.30
2340 12641 1.132500 CTCCTATTCACCCACCTCCC 58.868 60.000 0.00 0.00 0.00 4.30
2341 12642 0.722676 TCCTATTCACCCACCTCCCT 59.277 55.000 0.00 0.00 0.00 4.20
2342 12643 1.132500 CCTATTCACCCACCTCCCTC 58.868 60.000 0.00 0.00 0.00 4.30
2343 12644 1.344496 CCTATTCACCCACCTCCCTCT 60.344 57.143 0.00 0.00 0.00 3.69
2344 12645 2.043227 CTATTCACCCACCTCCCTCTC 58.957 57.143 0.00 0.00 0.00 3.20
2345 12646 0.419459 ATTCACCCACCTCCCTCTCT 59.581 55.000 0.00 0.00 0.00 3.10
2346 12647 1.089978 TTCACCCACCTCCCTCTCTA 58.910 55.000 0.00 0.00 0.00 2.43
2347 12648 0.631753 TCACCCACCTCCCTCTCTAG 59.368 60.000 0.00 0.00 0.00 2.43
2348 12649 0.336737 CACCCACCTCCCTCTCTAGT 59.663 60.000 0.00 0.00 0.00 2.57
2349 12650 0.632294 ACCCACCTCCCTCTCTAGTC 59.368 60.000 0.00 0.00 0.00 2.59
2350 12651 0.466555 CCCACCTCCCTCTCTAGTCG 60.467 65.000 0.00 0.00 0.00 4.18
2351 12652 1.104577 CCACCTCCCTCTCTAGTCGC 61.105 65.000 0.00 0.00 0.00 5.19
2352 12653 1.104577 CACCTCCCTCTCTAGTCGCC 61.105 65.000 0.00 0.00 0.00 5.54
2353 12654 1.283381 ACCTCCCTCTCTAGTCGCCT 61.283 60.000 0.00 0.00 0.00 5.52
2354 12655 0.106419 CCTCCCTCTCTAGTCGCCTT 60.106 60.000 0.00 0.00 0.00 4.35
2355 12656 1.314730 CTCCCTCTCTAGTCGCCTTC 58.685 60.000 0.00 0.00 0.00 3.46
2356 12657 0.920438 TCCCTCTCTAGTCGCCTTCT 59.080 55.000 0.00 0.00 0.00 2.85
2357 12658 1.134037 TCCCTCTCTAGTCGCCTTCTC 60.134 57.143 0.00 0.00 0.00 2.87
2358 12659 1.408961 CCCTCTCTAGTCGCCTTCTCA 60.409 57.143 0.00 0.00 0.00 3.27
2359 12660 2.370349 CCTCTCTAGTCGCCTTCTCAA 58.630 52.381 0.00 0.00 0.00 3.02
2360 12661 2.955660 CCTCTCTAGTCGCCTTCTCAAT 59.044 50.000 0.00 0.00 0.00 2.57
2361 12662 3.004315 CCTCTCTAGTCGCCTTCTCAATC 59.996 52.174 0.00 0.00 0.00 2.67
2379 12951 4.946772 TCAATCTGTTTGACACACTGGAAA 59.053 37.500 0.00 0.00 39.44 3.13
2380 12952 4.900635 ATCTGTTTGACACACTGGAAAC 57.099 40.909 0.00 0.00 0.00 2.78
2381 12953 3.680490 TCTGTTTGACACACTGGAAACA 58.320 40.909 0.00 0.00 34.67 2.83
2382 12954 3.438781 TCTGTTTGACACACTGGAAACAC 59.561 43.478 0.00 0.00 33.33 3.32
2384 12956 3.570125 TGTTTGACACACTGGAAACACAA 59.430 39.130 0.00 0.00 32.49 3.33
2385 12957 4.038042 TGTTTGACACACTGGAAACACAAA 59.962 37.500 0.00 0.00 32.49 2.83
2386 12958 3.840890 TGACACACTGGAAACACAAAC 57.159 42.857 0.00 0.00 35.60 2.93
2387 12959 3.417101 TGACACACTGGAAACACAAACT 58.583 40.909 0.00 0.00 35.60 2.66
2388 12960 3.190327 TGACACACTGGAAACACAAACTG 59.810 43.478 0.00 0.00 35.60 3.16
2389 12961 3.153919 ACACACTGGAAACACAAACTGT 58.846 40.909 0.00 0.00 35.60 3.55
2390 12962 3.572255 ACACACTGGAAACACAAACTGTT 59.428 39.130 0.00 0.00 45.68 3.16
2435 13007 4.694037 GGTCTCAACCAACCATAAGTACAC 59.306 45.833 0.00 0.00 45.68 2.90
2436 13008 4.387862 GTCTCAACCAACCATAAGTACACG 59.612 45.833 0.00 0.00 0.00 4.49
2437 13009 4.039488 TCTCAACCAACCATAAGTACACGT 59.961 41.667 0.00 0.00 0.00 4.49
2438 13010 4.059511 TCAACCAACCATAAGTACACGTG 58.940 43.478 15.48 15.48 0.00 4.49
2439 13011 2.419667 ACCAACCATAAGTACACGTGC 58.580 47.619 17.22 0.00 0.00 5.34
2455 13027 1.466167 CGTGCACAATGAAAGAGGAGG 59.534 52.381 18.64 0.00 0.00 4.30
2462 13034 4.400567 CACAATGAAAGAGGAGGGGAAATC 59.599 45.833 0.00 0.00 0.00 2.17
2509 13081 8.570068 TGGTACAATTAGTCCAAAATAAGGAC 57.430 34.615 4.23 4.23 46.34 3.85
2522 13094 8.390921 TCCAAAATAAGGACTGTTAAGAGGAAT 58.609 33.333 4.45 0.00 0.00 3.01
2560 13132 6.613699 TGAGCCCAACAGATCCATAAAATAT 58.386 36.000 0.00 0.00 0.00 1.28
2562 13134 5.244626 AGCCCAACAGATCCATAAAATATGC 59.755 40.000 0.00 0.00 0.00 3.14
2593 13165 4.445453 CATTGTGAGTGCCAGCTTATCTA 58.555 43.478 0.00 0.00 0.00 1.98
2625 13197 2.773993 ATTTACTACCCACGGTGGTG 57.226 50.000 24.70 17.98 46.61 4.17
2660 13232 8.231007 TGGCCCCAATTTTTATCTCTGATTATA 58.769 33.333 0.00 0.00 0.00 0.98
2661 13233 9.088987 GGCCCCAATTTTTATCTCTGATTATAA 57.911 33.333 0.00 0.00 0.00 0.98
2694 13270 7.818930 CCATTTCTATACAACCAAAATGCACTT 59.181 33.333 0.00 0.00 36.47 3.16
2697 13273 2.618442 ACAACCAAAATGCACTTGGG 57.382 45.000 25.68 15.88 46.48 4.12
2704 13280 1.058284 AAATGCACTTGGGCCAATGT 58.942 45.000 21.25 16.56 0.00 2.71
2717 13293 2.430694 GGCCAATGTCATAAGAAACCCC 59.569 50.000 0.00 0.00 0.00 4.95
2719 13295 3.706086 GCCAATGTCATAAGAAACCCCAT 59.294 43.478 0.00 0.00 0.00 4.00
2721 13297 5.539955 GCCAATGTCATAAGAAACCCCATAT 59.460 40.000 0.00 0.00 0.00 1.78
2725 13301 6.823286 TGTCATAAGAAACCCCATATCTCA 57.177 37.500 0.00 0.00 0.00 3.27
2779 13361 1.135315 GTGTAGTTGCCACCATGCATG 60.135 52.381 20.19 20.19 41.70 4.06
2780 13362 1.176527 GTAGTTGCCACCATGCATGT 58.823 50.000 24.58 10.59 41.70 3.21
2781 13363 1.135315 GTAGTTGCCACCATGCATGTG 60.135 52.381 24.58 20.38 41.70 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 6.996509 AGTGTTGCATGATGGTTCTATTTTT 58.003 32.000 0.00 0.00 0.00 1.94
36 37 4.650734 TCAAGTGTTGCATGATGGTTCTA 58.349 39.130 0.00 0.00 0.00 2.10
38 39 3.829948 CTCAAGTGTTGCATGATGGTTC 58.170 45.455 0.00 0.00 0.00 3.62
41 42 1.816835 AGCTCAAGTGTTGCATGATGG 59.183 47.619 0.00 0.00 0.00 3.51
65 66 9.747293 AATAAGATTTCTAGTCTTACCGTTAGC 57.253 33.333 4.01 0.00 40.03 3.09
108 109 2.979401 AAATTCGCATGCACGTGTAA 57.021 40.000 19.57 6.47 0.00 2.41
151 152 7.809665 AGAATTGCTATGGTTTTCAAATTTGC 58.190 30.769 13.54 0.00 0.00 3.68
158 159 8.271458 TCTATGGTAGAATTGCTATGGTTTTCA 58.729 33.333 0.00 0.00 0.00 2.69
259 260 3.040965 TGGCTTTCTTGGAGGCAAG 57.959 52.632 0.00 0.00 45.29 4.01
264 265 1.001378 CGGTTGTTGGCTTTCTTGGAG 60.001 52.381 0.00 0.00 0.00 3.86
274 275 2.676471 ATCAGGGCGGTTGTTGGC 60.676 61.111 0.00 0.00 0.00 4.52
275 276 2.046285 GGATCAGGGCGGTTGTTGG 61.046 63.158 0.00 0.00 0.00 3.77
287 288 0.395686 ATCAGTGATGCGGGGATCAG 59.604 55.000 4.39 0.00 32.92 2.90
301 302 4.891168 ACCCGTCAAAAGGTTTTTATCAGT 59.109 37.500 0.00 0.00 29.94 3.41
303 304 4.038162 CCACCCGTCAAAAGGTTTTTATCA 59.962 41.667 0.00 0.00 32.72 2.15
308 309 1.855295 ACCACCCGTCAAAAGGTTTT 58.145 45.000 0.00 0.00 32.72 2.43
314 315 1.489649 TGGTCTTACCACCCGTCAAAA 59.510 47.619 0.00 0.00 44.79 2.44
372 373 4.388378 ACTCTAAAGCGACATCCCTTAC 57.612 45.455 0.00 0.00 0.00 2.34
383 384 3.040147 TCCCACTGAAACTCTAAAGCG 57.960 47.619 0.00 0.00 0.00 4.68
384 385 7.466050 CGAATTATCCCACTGAAACTCTAAAGC 60.466 40.741 0.00 0.00 0.00 3.51
388 389 6.380274 ACTCGAATTATCCCACTGAAACTCTA 59.620 38.462 0.00 0.00 0.00 2.43
393 394 4.224147 TCCACTCGAATTATCCCACTGAAA 59.776 41.667 0.00 0.00 0.00 2.69
420 421 5.215239 CGTGTGATAAATGTGTACATGCA 57.785 39.130 0.00 0.00 36.56 3.96
442 443 3.042871 TCATGGCTCCAAATTTTGTGC 57.957 42.857 8.26 10.92 0.00 4.57
457 458 2.050144 AGGGCAGTACCTACATCATGG 58.950 52.381 0.00 0.00 39.65 3.66
503 514 5.564550 ACTGAACTTGCTGAATCCTAATGT 58.435 37.500 0.00 0.00 0.00 2.71
525 536 7.891561 ACTATCTTTCTACATATCCAGCAGAC 58.108 38.462 0.00 0.00 0.00 3.51
538 549 7.966157 TCGTTCAAATCGACTATCTTTCTAC 57.034 36.000 0.00 0.00 32.30 2.59
556 5692 6.452494 TTTCTTTACACCCAATTTCGTTCA 57.548 33.333 0.00 0.00 0.00 3.18
557 6105 7.940178 ATTTTCTTTACACCCAATTTCGTTC 57.060 32.000 0.00 0.00 0.00 3.95
585 6134 4.287067 ACCATCCTTGACACTATGTTCAGT 59.713 41.667 0.00 0.00 0.00 3.41
586 6135 4.836825 ACCATCCTTGACACTATGTTCAG 58.163 43.478 0.00 0.00 0.00 3.02
587 6136 4.285775 TGACCATCCTTGACACTATGTTCA 59.714 41.667 0.00 0.00 0.00 3.18
699 6252 3.055819 TCTTTCAGTGGGCTACATGTCTC 60.056 47.826 0.00 0.00 0.00 3.36
885 6473 3.443045 GCAGGGTTGGCACGGATG 61.443 66.667 0.00 0.00 0.00 3.51
911 6499 3.177228 AGGGACAGCAGTTCAGACTTAT 58.823 45.455 0.00 0.00 32.54 1.73
1166 6768 2.024871 CGACTCGATCTCGTGGGC 59.975 66.667 6.61 0.16 40.80 5.36
1233 6835 2.032528 CGAGCTTGGGTGCCAGAA 59.967 61.111 0.00 0.00 33.81 3.02
1529 7367 0.320683 CTCCACCTTGATGTGCGACA 60.321 55.000 0.00 0.00 34.85 4.35
1554 8234 1.305623 CAAGCTCCCTCCATTGGCT 59.694 57.895 0.00 0.00 34.52 4.75
1560 8240 1.492133 CCTTCACCAAGCTCCCTCCA 61.492 60.000 0.00 0.00 0.00 3.86
1572 8252 1.080705 CGTCGAGTCCACCTTCACC 60.081 63.158 0.00 0.00 0.00 4.02
1602 11737 2.224159 ATTCACCTCCACGCCTGGT 61.224 57.895 1.44 0.00 38.90 4.00
1698 11833 4.467438 TCTCATCTGATTCAGTTGTAGGCA 59.533 41.667 19.33 4.52 34.12 4.75
1748 11883 9.045223 GGAAGAAAGCACATAAAAATCAAACTT 57.955 29.630 0.00 0.00 0.00 2.66
1761 11896 4.487714 TTAGATCCGGAAGAAAGCACAT 57.512 40.909 9.01 0.00 0.00 3.21
1775 11910 8.093927 AGAGATTGTAGCAGCTTTATTAGATCC 58.906 37.037 0.00 0.00 0.00 3.36
1863 11999 7.288672 CCTTTCGTGTCACAAATACTAACTTC 58.711 38.462 3.42 0.00 0.00 3.01
1866 12003 5.106830 CCCCTTTCGTGTCACAAATACTAAC 60.107 44.000 3.42 0.00 0.00 2.34
1878 12015 1.228154 AACAGGCCCCTTTCGTGTC 60.228 57.895 0.00 0.00 32.19 3.67
1883 12021 1.408969 TCAAACAACAGGCCCCTTTC 58.591 50.000 0.00 0.00 0.00 2.62
1970 12268 7.985184 ACATATGTAACAGGTCGACACATAATT 59.015 33.333 22.10 13.19 36.12 1.40
2037 12335 9.273016 TCTTTCTCGACATATGAACTTCTTTTT 57.727 29.630 10.38 0.00 0.00 1.94
2038 12336 8.713271 GTCTTTCTCGACATATGAACTTCTTTT 58.287 33.333 10.38 0.00 34.11 2.27
2039 12337 8.091449 AGTCTTTCTCGACATATGAACTTCTTT 58.909 33.333 10.38 0.00 36.38 2.52
2105 12403 3.963428 AATGCCCTACTCCGCTTATAG 57.037 47.619 0.00 0.00 0.00 1.31
2134 12432 4.939052 ATTACCTAGGTTCAGGTCATCG 57.061 45.455 22.11 0.00 46.34 3.84
2143 12441 4.876679 GTGGCAAGAGAATTACCTAGGTTC 59.123 45.833 22.11 12.07 0.00 3.62
2149 12447 2.038557 ACACGTGGCAAGAGAATTACCT 59.961 45.455 21.57 0.00 0.00 3.08
2155 12453 2.412870 CATACACACGTGGCAAGAGAA 58.587 47.619 21.57 0.00 34.19 2.87
2163 12461 2.163818 AACACTCCATACACACGTGG 57.836 50.000 21.57 11.39 36.82 4.94
2165 12463 4.512571 GGTTAAAACACTCCATACACACGT 59.487 41.667 0.00 0.00 0.00 4.49
2166 12464 4.083696 GGGTTAAAACACTCCATACACACG 60.084 45.833 0.00 0.00 0.00 4.49
2168 12466 5.067273 CAGGGTTAAAACACTCCATACACA 58.933 41.667 0.00 0.00 41.69 3.72
2172 12470 3.562609 GGCCAGGGTTAAAACACTCCATA 60.563 47.826 0.00 0.00 41.69 2.74
2195 12495 2.679837 CGATGCACCTGCTAGATTGTTT 59.320 45.455 0.00 0.00 42.66 2.83
2206 12506 0.108186 TTGGAGCTACGATGCACCTG 60.108 55.000 17.24 0.00 42.78 4.00
2230 12530 0.245539 ATTGTCGACGGGTGATCGTT 59.754 50.000 11.62 0.00 43.96 3.85
2232 12532 0.645355 CAATTGTCGACGGGTGATCG 59.355 55.000 11.62 0.00 41.00 3.69
2235 12535 0.321210 ATGCAATTGTCGACGGGTGA 60.321 50.000 11.62 0.00 0.00 4.02
2240 12540 6.933130 TCTTTCTAATATGCAATTGTCGACG 58.067 36.000 11.62 0.00 0.00 5.12
2241 12541 8.391106 AGTTCTTTCTAATATGCAATTGTCGAC 58.609 33.333 9.11 9.11 0.00 4.20
2290 12591 8.822652 AAAATCTTAGCTTCACTTCCAAATTG 57.177 30.769 0.00 0.00 0.00 2.32
2298 12599 9.825109 GGAGACTATAAAATCTTAGCTTCACTT 57.175 33.333 0.00 0.00 0.00 3.16
2299 12600 9.207868 AGGAGACTATAAAATCTTAGCTTCACT 57.792 33.333 0.00 0.00 40.61 3.41
2319 12620 1.763545 GGAGGTGGGTGAATAGGAGAC 59.236 57.143 0.00 0.00 0.00 3.36
2320 12621 1.344087 GGGAGGTGGGTGAATAGGAGA 60.344 57.143 0.00 0.00 0.00 3.71
2321 12622 1.132500 GGGAGGTGGGTGAATAGGAG 58.868 60.000 0.00 0.00 0.00 3.69
2322 12623 0.722676 AGGGAGGTGGGTGAATAGGA 59.277 55.000 0.00 0.00 0.00 2.94
2323 12624 1.132500 GAGGGAGGTGGGTGAATAGG 58.868 60.000 0.00 0.00 0.00 2.57
2324 12625 2.043227 GAGAGGGAGGTGGGTGAATAG 58.957 57.143 0.00 0.00 0.00 1.73
2325 12626 1.651770 AGAGAGGGAGGTGGGTGAATA 59.348 52.381 0.00 0.00 0.00 1.75
2326 12627 0.419459 AGAGAGGGAGGTGGGTGAAT 59.581 55.000 0.00 0.00 0.00 2.57
2327 12628 1.007238 CTAGAGAGGGAGGTGGGTGAA 59.993 57.143 0.00 0.00 0.00 3.18
2328 12629 0.631753 CTAGAGAGGGAGGTGGGTGA 59.368 60.000 0.00 0.00 0.00 4.02
2329 12630 0.336737 ACTAGAGAGGGAGGTGGGTG 59.663 60.000 0.00 0.00 0.00 4.61
2330 12631 0.632294 GACTAGAGAGGGAGGTGGGT 59.368 60.000 0.00 0.00 0.00 4.51
2331 12632 0.466555 CGACTAGAGAGGGAGGTGGG 60.467 65.000 0.00 0.00 0.00 4.61
2332 12633 1.104577 GCGACTAGAGAGGGAGGTGG 61.105 65.000 0.00 0.00 0.00 4.61
2333 12634 1.104577 GGCGACTAGAGAGGGAGGTG 61.105 65.000 0.00 0.00 0.00 4.00
2334 12635 1.227946 GGCGACTAGAGAGGGAGGT 59.772 63.158 0.00 0.00 0.00 3.85
2335 12636 0.106419 AAGGCGACTAGAGAGGGAGG 60.106 60.000 0.00 0.00 42.68 4.30
2336 12637 1.133915 AGAAGGCGACTAGAGAGGGAG 60.134 57.143 0.00 0.00 42.68 4.30
2337 12638 0.920438 AGAAGGCGACTAGAGAGGGA 59.080 55.000 0.00 0.00 42.68 4.20
2338 12639 1.314730 GAGAAGGCGACTAGAGAGGG 58.685 60.000 0.00 0.00 42.68 4.30
2339 12640 2.045561 TGAGAAGGCGACTAGAGAGG 57.954 55.000 0.00 0.00 42.68 3.69
2340 12641 3.882888 AGATTGAGAAGGCGACTAGAGAG 59.117 47.826 0.00 0.00 42.68 3.20
2341 12642 3.629855 CAGATTGAGAAGGCGACTAGAGA 59.370 47.826 0.00 0.00 42.68 3.10
2342 12643 3.380004 ACAGATTGAGAAGGCGACTAGAG 59.620 47.826 0.00 0.00 42.68 2.43
2343 12644 3.357203 ACAGATTGAGAAGGCGACTAGA 58.643 45.455 0.00 0.00 42.68 2.43
2344 12645 3.791973 ACAGATTGAGAAGGCGACTAG 57.208 47.619 0.00 0.00 42.68 2.57
2345 12646 4.021456 TCAAACAGATTGAGAAGGCGACTA 60.021 41.667 0.00 0.00 43.08 2.59
2346 12647 3.070018 CAAACAGATTGAGAAGGCGACT 58.930 45.455 0.00 0.00 42.13 4.18
2347 12648 3.067106 TCAAACAGATTGAGAAGGCGAC 58.933 45.455 0.00 0.00 43.08 5.19
2348 12649 3.401033 TCAAACAGATTGAGAAGGCGA 57.599 42.857 0.00 0.00 43.08 5.54
2356 12657 4.149511 TCCAGTGTGTCAAACAGATTGA 57.850 40.909 0.00 0.00 45.71 2.57
2357 12658 4.898829 TTCCAGTGTGTCAAACAGATTG 57.101 40.909 0.00 0.00 40.26 2.67
2358 12659 4.704540 TGTTTCCAGTGTGTCAAACAGATT 59.295 37.500 0.00 0.00 40.26 2.40
2359 12660 4.096382 GTGTTTCCAGTGTGTCAAACAGAT 59.904 41.667 0.00 0.00 40.26 2.90
2360 12661 3.438781 GTGTTTCCAGTGTGTCAAACAGA 59.561 43.478 0.00 0.00 40.26 3.41
2361 12662 3.190327 TGTGTTTCCAGTGTGTCAAACAG 59.810 43.478 0.00 0.00 40.26 3.16
2424 12996 3.682377 TCATTGTGCACGTGTACTTATGG 59.318 43.478 30.92 20.72 30.80 2.74
2431 13003 2.805671 CCTCTTTCATTGTGCACGTGTA 59.194 45.455 18.38 10.46 0.00 2.90
2435 13007 1.466167 CCTCCTCTTTCATTGTGCACG 59.534 52.381 13.13 0.00 0.00 5.34
2436 13008 1.815003 CCCTCCTCTTTCATTGTGCAC 59.185 52.381 10.75 10.75 0.00 4.57
2437 13009 1.272092 CCCCTCCTCTTTCATTGTGCA 60.272 52.381 0.00 0.00 0.00 4.57
2438 13010 1.004745 TCCCCTCCTCTTTCATTGTGC 59.995 52.381 0.00 0.00 0.00 4.57
2439 13011 3.439857 TTCCCCTCCTCTTTCATTGTG 57.560 47.619 0.00 0.00 0.00 3.33
2504 13076 6.681729 TGTGTATTCCTCTTAACAGTCCTT 57.318 37.500 0.00 0.00 0.00 3.36
2509 13081 7.817478 TGTGTACATGTGTATTCCTCTTAACAG 59.183 37.037 9.11 0.00 32.54 3.16
2511 13083 8.604035 CATGTGTACATGTGTATTCCTCTTAAC 58.396 37.037 9.11 0.00 46.40 2.01
2541 13113 7.149973 CCTTGCATATTTTATGGATCTGTTGG 58.850 38.462 0.00 0.00 0.00 3.77
2544 13116 5.834742 TGCCTTGCATATTTTATGGATCTGT 59.165 36.000 0.00 0.00 31.71 3.41
2560 13132 0.315886 CTCACAATGCTTGCCTTGCA 59.684 50.000 9.83 0.00 44.95 4.08
2562 13134 1.933500 GCACTCACAATGCTTGCCTTG 60.934 52.381 8.64 8.64 40.08 3.61
2593 13165 8.872845 CGTGGGTAGTAAATTATTTTCGTAAGT 58.127 33.333 0.00 0.00 39.48 2.24
2618 13190 1.745115 CCATGTGTAGCCACCACCG 60.745 63.158 0.00 0.00 41.09 4.94
2668 13244 7.322664 AGTGCATTTTGGTTGTATAGAAATGG 58.677 34.615 0.00 0.00 37.87 3.16
2669 13245 8.649841 CAAGTGCATTTTGGTTGTATAGAAATG 58.350 33.333 0.00 0.00 39.48 2.32
2694 13270 3.096092 GGTTTCTTATGACATTGGCCCA 58.904 45.455 0.00 0.00 0.00 5.36
2696 13272 2.430694 GGGGTTTCTTATGACATTGGCC 59.569 50.000 0.00 0.00 0.00 5.36
2697 13273 3.096092 TGGGGTTTCTTATGACATTGGC 58.904 45.455 0.00 0.00 0.00 4.52
2735 13311 5.891551 CACCCTTTGGTATAAGTGCCTTTAT 59.108 40.000 0.00 0.00 45.57 1.40
2736 13312 5.222171 ACACCCTTTGGTATAAGTGCCTTTA 60.222 40.000 0.00 0.00 45.57 1.85
2749 13325 4.352651 TGGCAACTACACACCCTTTGGT 62.353 50.000 0.00 0.00 42.16 3.67


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

AutoCloner maintained by Alex Coulton.