Multiple sequence alignment - TraesCS1D01G313100

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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 TraesCS1D01G313100 chr1D 100.000 1846 0 0 1 1846 408612142 408613987 0.000000e+00 3410.0
1 TraesCS1D01G313100 chr1D 90.351 912 35 13 938 1818 408745085 408745974 0.000000e+00 1147.0
2 TraesCS1D01G313100 chr1D 100.000 504 0 0 2096 2599 408614237 408614740 0.000000e+00 931.0
3 TraesCS1D01G313100 chr1D 91.344 439 23 4 508 944 408743803 408744228 1.040000e-163 586.0
4 TraesCS1D01G313100 chr1D 79.139 302 33 17 138 417 199608203 199607910 5.710000e-42 182.0
5 TraesCS1D01G313100 chr1A 89.681 1880 90 27 1 1818 504701526 504703363 0.000000e+00 2302.0
6 TraesCS1D01G313100 chr1A 84.694 98 11 3 420 516 62976992 62976898 7.660000e-16 95.3
7 TraesCS1D01G313100 chr1B 92.454 1365 74 12 508 1845 550035058 550036420 0.000000e+00 1923.0
8 TraesCS1D01G313100 chr1B 90.586 478 30 5 1355 1818 550038877 550039353 1.020000e-173 619.0
9 TraesCS1D01G313100 chr1B 92.857 308 15 6 2096 2402 550038369 550038670 8.540000e-120 440.0
10 TraesCS1D01G313100 chr1B 81.979 283 32 12 127 400 280172642 280172370 3.370000e-54 222.0
11 TraesCS1D01G313100 chr5B 84.640 625 69 13 1002 1602 606829229 606829850 4.790000e-167 597.0
12 TraesCS1D01G313100 chr5B 85.689 566 64 11 1050 1601 605627212 605626650 4.820000e-162 580.0
13 TraesCS1D01G313100 chr5B 83.404 470 70 6 1050 1512 606751984 606752452 1.850000e-116 429.0
14 TraesCS1D01G313100 chr5B 76.245 522 83 18 22 514 278248457 278247948 3.340000e-59 239.0
15 TraesCS1D01G313100 chr5B 76.289 485 49 34 520 990 606828745 606829177 5.670000e-47 198.0
16 TraesCS1D01G313100 chr5B 88.272 162 18 1 634 795 606821594 606821754 2.640000e-45 193.0
17 TraesCS1D01G313100 chr5B 78.947 190 19 13 809 990 605627500 605627324 2.730000e-20 110.0
18 TraesCS1D01G313100 chr5D 85.714 553 71 6 1055 1600 490982110 490981559 6.240000e-161 577.0
19 TraesCS1D01G313100 chr5D 84.926 471 62 6 1050 1512 491682629 491683098 3.920000e-128 468.0
20 TraesCS1D01G313100 chr5D 88.482 191 18 3 2412 2599 451480703 451480514 7.240000e-56 228.0
21 TraesCS1D01G313100 chr5D 76.531 490 45 33 520 990 491727087 491727525 1.220000e-48 204.0
22 TraesCS1D01G313100 chr5D 77.562 361 49 22 643 990 490977721 490977380 3.410000e-44 189.0
23 TraesCS1D01G313100 chr5D 87.037 162 20 1 634 795 491682214 491682374 5.710000e-42 182.0
24 TraesCS1D01G313100 chr5D 75.309 324 36 20 669 975 490982543 490982247 5.880000e-22 115.0
25 TraesCS1D01G313100 chr5A 85.776 464 58 6 1056 1512 614255551 614256013 3.890000e-133 484.0
26 TraesCS1D01G313100 chr5A 83.235 507 31 14 721 1184 614355029 614355524 1.440000e-112 416.0
27 TraesCS1D01G313100 chr5A 92.857 196 12 2 2405 2599 600896670 600896864 1.520000e-72 283.0
28 TraesCS1D01G313100 chr5A 91.414 198 13 3 2405 2599 595860159 595860355 4.260000e-68 268.0
29 TraesCS1D01G313100 chr5A 88.068 176 19 2 622 797 614255121 614255294 9.430000e-50 207.0
30 TraesCS1D01G313100 chr5A 79.532 171 23 7 98 265 44090344 44090505 7.600000e-21 111.0
31 TraesCS1D01G313100 chr7B 80.549 437 62 12 1 417 184350311 184350744 5.400000e-82 315.0
32 TraesCS1D01G313100 chr2D 90.722 194 15 3 2407 2599 200368338 200368147 3.320000e-64 255.0
33 TraesCS1D01G313100 chrUn 88.000 200 20 3 2402 2598 49688489 49688291 1.560000e-57 233.0
34 TraesCS1D01G313100 chr6B 86.036 222 23 6 2381 2599 168406277 168406061 5.590000e-57 231.0
35 TraesCS1D01G313100 chr6B 83.721 172 13 7 354 512 585817003 585817172 5.790000e-32 148.0
36 TraesCS1D01G313100 chr3D 89.005 191 15 4 2410 2599 551893714 551893899 5.590000e-57 231.0
37 TraesCS1D01G313100 chr7A 88.947 190 15 4 2411 2599 632629557 632629373 2.010000e-56 230.0
38 TraesCS1D01G313100 chr7A 78.571 168 20 7 354 519 57698352 57698505 2.130000e-16 97.1
39 TraesCS1D01G313100 chr4B 77.039 466 58 28 103 521 652249498 652249035 3.370000e-54 222.0
40 TraesCS1D01G313100 chr4A 87.310 197 21 3 2406 2599 603830940 603831135 3.370000e-54 222.0
41 TraesCS1D01G313100 chr2B 80.753 239 32 3 292 518 792465825 792466061 9.560000e-40 174.0
42 TraesCS1D01G313100 chr2B 80.513 195 23 6 290 471 731214738 731214930 4.510000e-28 135.0
43 TraesCS1D01G313100 chr6D 82.184 174 24 6 350 522 392508407 392508574 2.700000e-30 143.0
44 TraesCS1D01G313100 chr6D 83.333 144 12 3 349 480 457479964 457479821 3.510000e-24 122.0
45 TraesCS1D01G313100 chr2A 88.288 111 13 0 306 416 63612396 63612286 1.620000e-27 134.0


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 TraesCS1D01G313100 chr1D 408612142 408614740 2598 False 2170.500000 3410 100.000000 1 2599 2 chr1D.!!$F1 2598
1 TraesCS1D01G313100 chr1D 408743803 408745974 2171 False 866.500000 1147 90.847500 508 1818 2 chr1D.!!$F2 1310
2 TraesCS1D01G313100 chr1A 504701526 504703363 1837 False 2302.000000 2302 89.681000 1 1818 1 chr1A.!!$F1 1817
3 TraesCS1D01G313100 chr1B 550035058 550039353 4295 False 994.000000 1923 91.965667 508 2402 3 chr1B.!!$F1 1894
4 TraesCS1D01G313100 chr5B 606828745 606829850 1105 False 397.500000 597 80.464500 520 1602 2 chr5B.!!$F3 1082
5 TraesCS1D01G313100 chr5B 605626650 605627500 850 True 345.000000 580 82.318000 809 1601 2 chr5B.!!$R2 792
6 TraesCS1D01G313100 chr5B 278247948 278248457 509 True 239.000000 239 76.245000 22 514 1 chr5B.!!$R1 492
7 TraesCS1D01G313100 chr5D 491682214 491683098 884 False 325.000000 468 85.981500 634 1512 2 chr5D.!!$F2 878
8 TraesCS1D01G313100 chr5D 490977380 490982543 5163 True 293.666667 577 79.528333 643 1600 3 chr5D.!!$R2 957
9 TraesCS1D01G313100 chr5A 614255121 614256013 892 False 345.500000 484 86.922000 622 1512 2 chr5A.!!$F5 890

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
177 178 0.319555 CCAAACTCGACCTTCTCGCA 60.320 55.0 0.00 0.0 42.62 5.10 F
1000 2017 0.607217 CATCACAGGCCACAAGCAGA 60.607 55.0 5.01 0.0 46.50 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1216 2297 1.135315 AGAGAAAATGGCGTACGCGTA 60.135 47.619 31.78 23.78 43.06 4.42 R
2569 9004 0.032615 TGGCTTTGTTGGGTTGGAGT 60.033 50.000 0.00 0.00 0.00 3.85 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
18 19 2.436824 GGTTCTGCCGCTTCTCCC 60.437 66.667 0.00 0.00 0.00 4.30
19 20 2.436824 GTTCTGCCGCTTCTCCCC 60.437 66.667 0.00 0.00 0.00 4.81
40 41 2.749839 TGCCCGCCTTCAAATCGG 60.750 61.111 0.00 0.00 42.58 4.18
52 53 0.808125 CAAATCGGTCGAATTGGCCA 59.192 50.000 0.00 0.00 32.93 5.36
95 96 2.643551 CCGTATCATTTGAGTTGCCCT 58.356 47.619 0.00 0.00 0.00 5.19
96 97 3.804036 CCGTATCATTTGAGTTGCCCTA 58.196 45.455 0.00 0.00 0.00 3.53
97 98 4.389374 CCGTATCATTTGAGTTGCCCTAT 58.611 43.478 0.00 0.00 0.00 2.57
99 100 5.300752 CGTATCATTTGAGTTGCCCTATCT 58.699 41.667 0.00 0.00 0.00 1.98
107 108 4.490606 TGCCCTATCTCCCCGCCA 62.491 66.667 0.00 0.00 0.00 5.69
165 166 1.081442 CTTTTCCGCCGCCAAACTC 60.081 57.895 0.00 0.00 0.00 3.01
175 176 1.344942 CGCCAAACTCGACCTTCTCG 61.345 60.000 0.00 0.00 44.44 4.04
177 178 0.319555 CCAAACTCGACCTTCTCGCA 60.320 55.000 0.00 0.00 42.62 5.10
183 184 3.112709 GACCTTCTCGCACCGCAC 61.113 66.667 0.00 0.00 0.00 5.34
241 242 4.499023 CGATTCACAACCGCGCCG 62.499 66.667 0.00 0.00 0.00 6.46
272 273 3.854669 CTCCCGCCGCCTCATTCT 61.855 66.667 0.00 0.00 0.00 2.40
312 342 4.459089 GTCTGCCGGTGCTCCTCC 62.459 72.222 1.90 0.00 38.71 4.30
321 351 2.757508 TGCTCCTCCCAGCTCTCG 60.758 66.667 0.00 0.00 40.39 4.04
489 519 9.533831 ACATCTCCTATTTTACACCTTCAAATT 57.466 29.630 0.00 0.00 0.00 1.82
492 522 8.303876 TCTCCTATTTTACACCTTCAAATTTGC 58.696 33.333 13.54 0.00 0.00 3.68
493 523 7.957002 TCCTATTTTACACCTTCAAATTTGCA 58.043 30.769 13.54 1.37 0.00 4.08
494 524 8.592809 TCCTATTTTACACCTTCAAATTTGCAT 58.407 29.630 13.54 0.00 0.00 3.96
495 525 9.218440 CCTATTTTACACCTTCAAATTTGCATT 57.782 29.630 13.54 0.00 0.00 3.56
605 641 2.487086 CCAAGTGTCCATGTCCAACTGA 60.487 50.000 0.00 0.00 0.00 3.41
999 2016 1.592400 CCATCACAGGCCACAAGCAG 61.592 60.000 5.01 0.00 46.50 4.24
1000 2017 0.607217 CATCACAGGCCACAAGCAGA 60.607 55.000 5.01 0.00 46.50 4.26
1216 2297 2.615493 CCATTAATCTATTCCGGCGGCT 60.615 50.000 23.83 13.77 0.00 5.52
1298 2390 1.122632 TGTTCAAGTACGGGAGCCCA 61.123 55.000 6.34 0.00 35.37 5.36
1603 2699 0.754957 ATGCTCGTGCTCTAGGCTCT 60.755 55.000 11.19 0.00 42.39 4.09
1777 7491 9.567776 TTGGTGAAGTGATAGAAAACAGAATTA 57.432 29.630 0.00 0.00 0.00 1.40
1819 7534 9.169592 CTGAAATTATTTGGGCTTCATTCAAAT 57.830 29.630 0.00 0.00 41.89 2.32
1824 7539 8.915057 TTATTTGGGCTTCATTCAAATTTTCA 57.085 26.923 5.95 0.00 40.33 2.69
1825 7540 9.517868 TTATTTGGGCTTCATTCAAATTTTCAT 57.482 25.926 5.95 0.00 40.33 2.57
1826 7541 7.820578 TTTGGGCTTCATTCAAATTTTCATT 57.179 28.000 0.00 0.00 0.00 2.57
1827 7542 7.437793 TTGGGCTTCATTCAAATTTTCATTC 57.562 32.000 0.00 0.00 0.00 2.67
1828 7543 5.638657 TGGGCTTCATTCAAATTTTCATTCG 59.361 36.000 0.00 0.00 0.00 3.34
1829 7544 5.639082 GGGCTTCATTCAAATTTTCATTCGT 59.361 36.000 0.00 0.00 0.00 3.85
1840 7555 8.371787 TCAAATTTTCATTCGTTTGATATTGCG 58.628 29.630 0.00 0.00 36.11 4.85
1841 7556 5.678910 TTTTCATTCGTTTGATATTGCGC 57.321 34.783 0.00 0.00 0.00 6.09
1842 7557 4.614555 TTCATTCGTTTGATATTGCGCT 57.385 36.364 9.73 0.00 0.00 5.92
1843 7558 3.939088 TCATTCGTTTGATATTGCGCTG 58.061 40.909 9.73 0.00 0.00 5.18
1844 7559 3.620821 TCATTCGTTTGATATTGCGCTGA 59.379 39.130 9.73 0.00 0.00 4.26
1845 7560 3.656651 TTCGTTTGATATTGCGCTGAG 57.343 42.857 9.73 0.00 0.00 3.35
2133 7848 9.528018 TCTGAACATTTTCTAAAATTTGTGGAC 57.472 29.630 0.00 0.00 36.52 4.02
2134 7849 9.533253 CTGAACATTTTCTAAAATTTGTGGACT 57.467 29.630 0.00 0.00 36.52 3.85
2135 7850 9.883142 TGAACATTTTCTAAAATTTGTGGACTT 57.117 25.926 0.00 0.00 36.52 3.01
2163 7878 9.928236 TTTTTACAAGCATTAGCATTTCAAAAC 57.072 25.926 0.00 0.00 45.49 2.43
2164 7879 8.654230 TTTACAAGCATTAGCATTTCAAAACA 57.346 26.923 0.00 0.00 45.49 2.83
2165 7880 8.654230 TTACAAGCATTAGCATTTCAAAACAA 57.346 26.923 0.00 0.00 45.49 2.83
2166 7881 6.947258 ACAAGCATTAGCATTTCAAAACAAC 58.053 32.000 0.00 0.00 45.49 3.32
2167 7882 5.827568 AGCATTAGCATTTCAAAACAACG 57.172 34.783 0.00 0.00 45.49 4.10
2168 7883 5.288804 AGCATTAGCATTTCAAAACAACGT 58.711 33.333 0.00 0.00 45.49 3.99
2169 7884 5.175491 AGCATTAGCATTTCAAAACAACGTG 59.825 36.000 0.00 0.00 45.49 4.49
2170 7885 5.174761 GCATTAGCATTTCAAAACAACGTGA 59.825 36.000 0.00 0.00 41.58 4.35
2171 7886 6.128849 GCATTAGCATTTCAAAACAACGTGAT 60.129 34.615 0.00 0.00 41.58 3.06
2172 7887 7.569226 GCATTAGCATTTCAAAACAACGTGATT 60.569 33.333 0.00 0.00 41.58 2.57
2173 7888 7.763172 TTAGCATTTCAAAACAACGTGATTT 57.237 28.000 0.00 0.00 0.00 2.17
2174 7889 6.660887 AGCATTTCAAAACAACGTGATTTT 57.339 29.167 4.60 4.60 0.00 1.82
2175 7890 7.071014 AGCATTTCAAAACAACGTGATTTTT 57.929 28.000 7.17 2.57 0.00 1.94
2262 7977 7.481275 AACCATGCTTTTTAAAATGACTGTG 57.519 32.000 15.85 8.65 0.00 3.66
2263 7978 6.815089 ACCATGCTTTTTAAAATGACTGTGA 58.185 32.000 15.85 0.00 0.00 3.58
2264 7979 7.271511 ACCATGCTTTTTAAAATGACTGTGAA 58.728 30.769 15.85 0.00 0.00 3.18
2266 7981 7.652909 CCATGCTTTTTAAAATGACTGTGAAGA 59.347 33.333 15.85 0.00 0.00 2.87
2267 7982 9.199982 CATGCTTTTTAAAATGACTGTGAAGAT 57.800 29.630 15.85 0.00 0.00 2.40
2269 7984 9.598517 TGCTTTTTAAAATGACTGTGAAGATTT 57.401 25.926 15.85 0.00 0.00 2.17
2294 8009 8.485578 TTTTAGAAGTGGGTGGATATTTTTGT 57.514 30.769 0.00 0.00 0.00 2.83
2296 8011 9.762381 TTTAGAAGTGGGTGGATATTTTTGTAT 57.238 29.630 0.00 0.00 0.00 2.29
2298 8013 8.980481 AGAAGTGGGTGGATATTTTTGTATAG 57.020 34.615 0.00 0.00 0.00 1.31
2299 8014 8.778059 AGAAGTGGGTGGATATTTTTGTATAGA 58.222 33.333 0.00 0.00 0.00 1.98
2300 8015 9.403583 GAAGTGGGTGGATATTTTTGTATAGAA 57.596 33.333 0.00 0.00 0.00 2.10
2301 8016 9.762381 AAGTGGGTGGATATTTTTGTATAGAAA 57.238 29.630 0.00 0.00 0.00 2.52
2302 8017 9.936329 AGTGGGTGGATATTTTTGTATAGAAAT 57.064 29.630 0.00 0.00 0.00 2.17
2304 8019 9.928618 TGGGTGGATATTTTTGTATAGAAATGA 57.071 29.630 0.00 0.00 0.00 2.57
2399 8481 9.952030 AAAAACAGAATCCAAAAGTAAAGGAAA 57.048 25.926 0.00 0.00 34.62 3.13
2401 8483 9.952030 AAACAGAATCCAAAAGTAAAGGAAAAA 57.048 25.926 0.00 0.00 34.62 1.94
2437 8783 9.075678 TCTATACCTACTAATAAAGTGAGGTGC 57.924 37.037 1.63 0.00 39.98 5.01
2438 8784 5.007385 ACCTACTAATAAAGTGAGGTGCG 57.993 43.478 0.00 0.00 39.11 5.34
2444 8790 2.228138 TAAAGTGAGGTGCGTTTCGT 57.772 45.000 0.00 0.00 0.00 3.85
2449 8795 1.263217 GTGAGGTGCGTTTCGTCAAAT 59.737 47.619 0.00 0.00 32.80 2.32
2450 8796 2.477375 GTGAGGTGCGTTTCGTCAAATA 59.523 45.455 0.00 0.00 32.80 1.40
2451 8797 3.059461 GTGAGGTGCGTTTCGTCAAATAA 60.059 43.478 0.00 0.00 32.80 1.40
2455 8801 5.151389 AGGTGCGTTTCGTCAAATAATTTC 58.849 37.500 0.00 0.00 0.00 2.17
2456 8802 4.912766 GGTGCGTTTCGTCAAATAATTTCA 59.087 37.500 0.00 0.00 0.00 2.69
2457 8803 5.571357 GGTGCGTTTCGTCAAATAATTTCAT 59.429 36.000 0.00 0.00 0.00 2.57
2458 8804 6.237201 GGTGCGTTTCGTCAAATAATTTCATC 60.237 38.462 0.00 0.00 0.00 2.92
2459 8805 5.797934 TGCGTTTCGTCAAATAATTTCATCC 59.202 36.000 0.00 0.00 0.00 3.51
2460 8806 5.053286 GCGTTTCGTCAAATAATTTCATCCG 60.053 40.000 0.00 0.00 0.00 4.18
2461 8807 6.019152 CGTTTCGTCAAATAATTTCATCCGT 58.981 36.000 0.00 0.00 0.00 4.69
2462 8808 6.521821 CGTTTCGTCAAATAATTTCATCCGTT 59.478 34.615 0.00 0.00 0.00 4.44
2463 8809 7.252865 CGTTTCGTCAAATAATTTCATCCGTTC 60.253 37.037 0.00 0.00 0.00 3.95
2464 8810 6.729391 TCGTCAAATAATTTCATCCGTTCA 57.271 33.333 0.00 0.00 0.00 3.18
2466 8812 7.406553 TCGTCAAATAATTTCATCCGTTCATC 58.593 34.615 0.00 0.00 0.00 2.92
2467 8813 7.065204 TCGTCAAATAATTTCATCCGTTCATCA 59.935 33.333 0.00 0.00 0.00 3.07
2468 8814 7.857389 CGTCAAATAATTTCATCCGTTCATCAT 59.143 33.333 0.00 0.00 0.00 2.45
2469 8815 9.520204 GTCAAATAATTTCATCCGTTCATCATT 57.480 29.630 0.00 0.00 0.00 2.57
2470 8816 9.518906 TCAAATAATTTCATCCGTTCATCATTG 57.481 29.630 0.00 0.00 0.00 2.82
2471 8817 9.518906 CAAATAATTTCATCCGTTCATCATTGA 57.481 29.630 0.00 0.00 0.00 2.57
2475 8821 8.470040 AATTTCATCCGTTCATCATTGAAAAG 57.530 30.769 0.00 0.00 43.29 2.27
2476 8822 6.816134 TTCATCCGTTCATCATTGAAAAGA 57.184 33.333 0.00 0.00 43.29 2.52
2477 8823 6.182039 TCATCCGTTCATCATTGAAAAGAC 57.818 37.500 0.00 0.00 43.29 3.01
2479 8825 6.430925 TCATCCGTTCATCATTGAAAAGACTT 59.569 34.615 0.00 0.00 43.29 3.01
2480 8826 6.633500 TCCGTTCATCATTGAAAAGACTTT 57.367 33.333 0.00 0.00 43.29 2.66
2482 8828 7.488322 TCCGTTCATCATTGAAAAGACTTTTT 58.512 30.769 14.23 0.00 43.29 1.94
2504 8850 8.866970 TTTTTATCCGAGGTGGTACTAAATTT 57.133 30.769 0.00 0.00 39.52 1.82
2505 8851 8.866970 TTTTATCCGAGGTGGTACTAAATTTT 57.133 30.769 0.00 0.00 39.52 1.82
2506 8852 8.866970 TTTATCCGAGGTGGTACTAAATTTTT 57.133 30.769 0.00 0.00 39.52 1.94
2507 8853 6.753107 ATCCGAGGTGGTACTAAATTTTTG 57.247 37.500 0.00 0.00 39.52 2.44
2508 8854 5.623169 TCCGAGGTGGTACTAAATTTTTGT 58.377 37.500 0.00 2.00 39.52 2.83
2509 8855 5.470777 TCCGAGGTGGTACTAAATTTTTGTG 59.529 40.000 0.00 0.00 39.52 3.33
2510 8856 5.151389 CGAGGTGGTACTAAATTTTTGTGC 58.849 41.667 0.00 5.15 0.00 4.57
2511 8857 5.116069 AGGTGGTACTAAATTTTTGTGCG 57.884 39.130 0.00 0.00 0.00 5.34
2512 8858 4.581409 AGGTGGTACTAAATTTTTGTGCGT 59.419 37.500 0.00 0.00 0.00 5.24
2513 8859 4.913345 GGTGGTACTAAATTTTTGTGCGTC 59.087 41.667 0.00 2.80 0.00 5.19
2515 8861 5.849604 GTGGTACTAAATTTTTGTGCGTCTC 59.150 40.000 0.00 0.00 0.00 3.36
2517 8863 6.073440 TGGTACTAAATTTTTGTGCGTCTCTC 60.073 38.462 0.00 0.00 0.00 3.20
2518 8864 5.358298 ACTAAATTTTTGTGCGTCTCTCC 57.642 39.130 0.00 0.00 0.00 3.71
2519 8865 4.819630 ACTAAATTTTTGTGCGTCTCTCCA 59.180 37.500 0.00 0.00 0.00 3.86
2520 8866 3.626028 AATTTTTGTGCGTCTCTCCAC 57.374 42.857 0.00 0.00 0.00 4.02
2521 8867 2.325583 TTTTTGTGCGTCTCTCCACT 57.674 45.000 0.00 0.00 33.26 4.00
2523 8869 2.724977 TTTGTGCGTCTCTCCACTAG 57.275 50.000 0.00 0.00 33.26 2.57
2524 8870 1.905637 TTGTGCGTCTCTCCACTAGA 58.094 50.000 0.00 0.00 33.26 2.43
2525 8871 1.905637 TGTGCGTCTCTCCACTAGAA 58.094 50.000 0.00 0.00 32.46 2.10
2527 8873 2.626266 TGTGCGTCTCTCCACTAGAAAA 59.374 45.455 0.00 0.00 32.46 2.29
2528 8874 3.246619 GTGCGTCTCTCCACTAGAAAAG 58.753 50.000 0.00 0.00 32.46 2.27
2530 8876 3.057456 TGCGTCTCTCCACTAGAAAAGAC 60.057 47.826 0.00 1.51 32.46 3.01
2532 8878 4.558898 GCGTCTCTCCACTAGAAAAGACAA 60.559 45.833 0.00 0.00 32.46 3.18
2533 8879 5.529791 CGTCTCTCCACTAGAAAAGACAAA 58.470 41.667 0.00 0.00 32.46 2.83
2534 8880 6.159988 CGTCTCTCCACTAGAAAAGACAAAT 58.840 40.000 0.00 0.00 32.46 2.32
2535 8881 7.313646 CGTCTCTCCACTAGAAAAGACAAATA 58.686 38.462 0.00 0.00 32.46 1.40
2539 8885 9.495572 CTCTCCACTAGAAAAGACAAATAGTTT 57.504 33.333 0.00 0.00 32.46 2.66
2554 8989 6.607689 CAAATAGTTTGTACAGAATTCCGCA 58.392 36.000 0.65 0.00 35.94 5.69
2557 8992 5.705609 AGTTTGTACAGAATTCCGCAATT 57.294 34.783 0.65 0.00 34.70 2.32
2563 8998 0.614415 AGAATTCCGCAATTGGGCCA 60.614 50.000 16.63 0.00 31.94 5.36
2583 9018 2.485795 GCGCACTCCAACCCAACAA 61.486 57.895 0.30 0.00 0.00 2.83
2584 9019 2.010582 GCGCACTCCAACCCAACAAA 62.011 55.000 0.30 0.00 0.00 2.83
2585 9020 0.030638 CGCACTCCAACCCAACAAAG 59.969 55.000 0.00 0.00 0.00 2.77
2586 9021 0.249447 GCACTCCAACCCAACAAAGC 60.249 55.000 0.00 0.00 0.00 3.51
2587 9022 0.389025 CACTCCAACCCAACAAAGCC 59.611 55.000 0.00 0.00 0.00 4.35
2591 9026 0.179059 CCAACCCAACAAAGCCAACC 60.179 55.000 0.00 0.00 0.00 3.77
2592 9027 0.179059 CAACCCAACAAAGCCAACCC 60.179 55.000 0.00 0.00 0.00 4.11
2595 9030 1.048160 CCCAACAAAGCCAACCCAGT 61.048 55.000 0.00 0.00 0.00 4.00
2596 9031 1.698506 CCAACAAAGCCAACCCAGTA 58.301 50.000 0.00 0.00 0.00 2.74
2597 9032 2.035632 CCAACAAAGCCAACCCAGTAA 58.964 47.619 0.00 0.00 0.00 2.24
2598 9033 2.632512 CCAACAAAGCCAACCCAGTAAT 59.367 45.455 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 1.091537 GGCCAATTCGACCGATTTGA 58.908 50.000 21.31 0.00 37.56 2.69
40 41 1.087501 GGAGAAGTGGCCAATTCGAC 58.912 55.000 33.32 29.19 40.03 4.20
52 53 3.718210 GATTCGGCGGCGGAGAAGT 62.718 63.158 31.73 7.51 0.00 3.01
64 65 3.103911 GATACGGCGGCGATTCGG 61.104 66.667 38.93 8.23 0.00 4.30
113 114 3.723348 GGTGTGCGGCTCGAAACC 61.723 66.667 0.00 0.00 0.00 3.27
134 135 1.444895 GAAAAGTGGCAGCGGCATG 60.445 57.895 11.88 0.00 43.71 4.06
135 136 2.639327 GGAAAAGTGGCAGCGGCAT 61.639 57.895 11.88 0.00 43.71 4.40
136 137 3.294493 GGAAAAGTGGCAGCGGCA 61.294 61.111 11.88 5.90 43.71 5.69
241 242 1.372087 CGGGAGCTCAAATGGTCAGC 61.372 60.000 17.19 0.00 36.30 4.26
312 342 4.504916 CCGAGCACCGAGAGCTGG 62.505 72.222 0.00 0.00 43.58 4.85
512 542 3.526931 TCGTCAAGGCCAATCTTAGAG 57.473 47.619 5.01 0.00 0.00 2.43
605 641 4.555348 TCTTTTGCGTTATGTTTCGGTT 57.445 36.364 0.00 0.00 0.00 4.44
694 764 2.614779 CGCATCAGTCACAAGAGATGT 58.385 47.619 0.00 0.00 45.34 3.06
999 2016 2.921634 TCACTGACTGAGTACGCATC 57.078 50.000 0.00 1.37 31.73 3.91
1000 2017 2.159184 CCATCACTGACTGAGTACGCAT 60.159 50.000 0.00 0.00 31.73 4.73
1044 2105 2.594592 AAGGCCACAGCGAACACC 60.595 61.111 5.01 0.00 41.24 4.16
1216 2297 1.135315 AGAGAAAATGGCGTACGCGTA 60.135 47.619 31.78 23.78 43.06 4.42
1580 2676 1.440893 CTAGAGCACGAGCATGGCT 59.559 57.895 7.77 1.46 45.49 4.75
1603 2699 6.071560 ACAATATGTAGAAGGTCGTCTTGTGA 60.072 38.462 0.00 0.00 35.50 3.58
1718 6326 7.570324 GCAAGGAAAGATAGCTTCGCTAATAAG 60.570 40.741 0.00 0.00 44.62 1.73
1819 7534 5.285845 CAGCGCAATATCAAACGAATGAAAA 59.714 36.000 11.47 0.00 32.06 2.29
1821 7536 4.094146 TCAGCGCAATATCAAACGAATGAA 59.906 37.500 11.47 0.00 32.06 2.57
1823 7538 3.939088 TCAGCGCAATATCAAACGAATG 58.061 40.909 11.47 0.00 0.00 2.67
1824 7539 4.201208 CTCAGCGCAATATCAAACGAAT 57.799 40.909 11.47 0.00 0.00 3.34
1825 7540 3.656651 CTCAGCGCAATATCAAACGAA 57.343 42.857 11.47 0.00 0.00 3.85
2107 7822 9.528018 GTCCACAAATTTTAGAAAATGTTCAGA 57.472 29.630 0.00 0.00 38.53 3.27
2108 7823 9.533253 AGTCCACAAATTTTAGAAAATGTTCAG 57.467 29.630 0.00 0.00 38.53 3.02
2109 7824 9.883142 AAGTCCACAAATTTTAGAAAATGTTCA 57.117 25.926 0.00 0.00 38.53 3.18
2137 7852 9.928236 GTTTTGAAATGCTAATGCTTGTAAAAA 57.072 25.926 0.00 0.00 40.48 1.94
2138 7853 9.102757 TGTTTTGAAATGCTAATGCTTGTAAAA 57.897 25.926 0.00 0.00 40.48 1.52
2139 7854 8.654230 TGTTTTGAAATGCTAATGCTTGTAAA 57.346 26.923 0.00 0.00 40.48 2.01
2140 7855 8.547069 GTTGTTTTGAAATGCTAATGCTTGTAA 58.453 29.630 0.00 0.00 40.48 2.41
2141 7856 7.096271 CGTTGTTTTGAAATGCTAATGCTTGTA 60.096 33.333 0.00 0.00 40.48 2.41
2142 7857 6.292274 CGTTGTTTTGAAATGCTAATGCTTGT 60.292 34.615 0.00 0.00 40.48 3.16
2143 7858 6.066410 CGTTGTTTTGAAATGCTAATGCTTG 58.934 36.000 0.00 0.00 40.48 4.01
2144 7859 5.752955 ACGTTGTTTTGAAATGCTAATGCTT 59.247 32.000 0.00 0.00 40.48 3.91
2145 7860 5.175491 CACGTTGTTTTGAAATGCTAATGCT 59.825 36.000 0.00 0.00 40.48 3.79
2146 7861 5.174761 TCACGTTGTTTTGAAATGCTAATGC 59.825 36.000 0.00 0.00 40.20 3.56
2147 7862 6.746104 TCACGTTGTTTTGAAATGCTAATG 57.254 33.333 0.00 0.00 0.00 1.90
2148 7863 7.945033 AATCACGTTGTTTTGAAATGCTAAT 57.055 28.000 0.00 0.00 0.00 1.73
2149 7864 7.763172 AAATCACGTTGTTTTGAAATGCTAA 57.237 28.000 0.00 0.00 0.00 3.09
2150 7865 7.763172 AAAATCACGTTGTTTTGAAATGCTA 57.237 28.000 6.81 0.00 0.00 3.49
2151 7866 6.660887 AAAATCACGTTGTTTTGAAATGCT 57.339 29.167 6.81 0.00 0.00 3.79
2178 7893 9.388506 TGGTTTCAAAACATGTTCATACAATTT 57.611 25.926 12.39 0.00 40.63 1.82
2179 7894 8.954950 TGGTTTCAAAACATGTTCATACAATT 57.045 26.923 12.39 0.00 40.63 2.32
2180 7895 8.991026 CATGGTTTCAAAACATGTTCATACAAT 58.009 29.630 18.64 2.94 40.63 2.71
2181 7896 8.200120 TCATGGTTTCAAAACATGTTCATACAA 58.800 29.630 24.41 3.27 40.63 2.41
2182 7897 7.651304 GTCATGGTTTCAAAACATGTTCATACA 59.349 33.333 24.41 3.96 40.63 2.29
2183 7898 7.867403 AGTCATGGTTTCAAAACATGTTCATAC 59.133 33.333 24.41 15.98 40.63 2.39
2184 7899 7.950512 AGTCATGGTTTCAAAACATGTTCATA 58.049 30.769 24.41 5.34 40.63 2.15
2185 7900 6.819284 AGTCATGGTTTCAAAACATGTTCAT 58.181 32.000 24.41 9.06 40.63 2.57
2186 7901 6.219417 AGTCATGGTTTCAAAACATGTTCA 57.781 33.333 24.41 6.04 40.63 3.18
2187 7902 8.816640 AATAGTCATGGTTTCAAAACATGTTC 57.183 30.769 24.41 18.54 40.63 3.18
2188 7903 9.612066 AAAATAGTCATGGTTTCAAAACATGTT 57.388 25.926 24.41 17.09 40.63 2.71
2189 7904 9.612066 AAAAATAGTCATGGTTTCAAAACATGT 57.388 25.926 24.41 11.45 40.63 3.21
2220 7935 9.995003 AGCATGGTTTTTAAAAATATTCACAGA 57.005 25.926 16.02 0.00 0.00 3.41
2236 7951 8.397148 CACAGTCATTTTAAAAAGCATGGTTTT 58.603 29.630 25.81 25.81 33.00 2.43
2237 7952 7.768120 TCACAGTCATTTTAAAAAGCATGGTTT 59.232 29.630 16.92 16.92 0.00 3.27
2238 7953 7.271511 TCACAGTCATTTTAAAAAGCATGGTT 58.728 30.769 3.82 3.82 0.00 3.67
2239 7954 6.815089 TCACAGTCATTTTAAAAAGCATGGT 58.185 32.000 4.44 0.00 0.00 3.55
2240 7955 7.652909 TCTTCACAGTCATTTTAAAAAGCATGG 59.347 33.333 4.44 0.00 0.00 3.66
2241 7956 8.578308 TCTTCACAGTCATTTTAAAAAGCATG 57.422 30.769 4.44 5.51 0.00 4.06
2242 7957 9.768662 AATCTTCACAGTCATTTTAAAAAGCAT 57.231 25.926 4.44 0.00 0.00 3.79
2243 7958 9.598517 AAATCTTCACAGTCATTTTAAAAAGCA 57.401 25.926 4.44 0.00 0.00 3.91
2269 7984 8.485578 ACAAAAATATCCACCCACTTCTAAAA 57.514 30.769 0.00 0.00 0.00 1.52
2273 7988 8.778059 TCTATACAAAAATATCCACCCACTTCT 58.222 33.333 0.00 0.00 0.00 2.85
2275 7990 9.762381 TTTCTATACAAAAATATCCACCCACTT 57.238 29.630 0.00 0.00 0.00 3.16
2276 7991 9.936329 ATTTCTATACAAAAATATCCACCCACT 57.064 29.630 0.00 0.00 0.00 4.00
2277 7992 9.965824 CATTTCTATACAAAAATATCCACCCAC 57.034 33.333 0.00 0.00 0.00 4.61
2373 8455 9.952030 TTTCCTTTACTTTTGGATTCTGTTTTT 57.048 25.926 0.00 0.00 0.00 1.94
2411 8493 9.075678 GCACCTCACTTTATTAGTAGGTATAGA 57.924 37.037 0.00 0.00 38.09 1.98
2412 8494 8.021973 CGCACCTCACTTTATTAGTAGGTATAG 58.978 40.741 0.00 0.00 38.09 1.31
2413 8495 7.503566 ACGCACCTCACTTTATTAGTAGGTATA 59.496 37.037 0.00 0.00 38.09 1.47
2414 8496 6.323225 ACGCACCTCACTTTATTAGTAGGTAT 59.677 38.462 0.00 0.00 38.09 2.73
2416 8498 4.465305 ACGCACCTCACTTTATTAGTAGGT 59.535 41.667 0.00 0.00 39.43 3.08
2417 8499 5.007385 ACGCACCTCACTTTATTAGTAGG 57.993 43.478 0.00 0.00 34.56 3.18
2418 8500 6.237490 CGAAACGCACCTCACTTTATTAGTAG 60.237 42.308 0.00 0.00 34.56 2.57
2423 8769 3.135994 ACGAAACGCACCTCACTTTATT 58.864 40.909 0.00 0.00 0.00 1.40
2430 8776 1.588674 ATTTGACGAAACGCACCTCA 58.411 45.000 0.00 0.00 0.00 3.86
2434 8780 6.237201 GGATGAAATTATTTGACGAAACGCAC 60.237 38.462 0.00 0.00 0.00 5.34
2436 8782 5.053286 CGGATGAAATTATTTGACGAAACGC 60.053 40.000 0.00 0.00 0.00 4.84
2437 8783 6.019152 ACGGATGAAATTATTTGACGAAACG 58.981 36.000 0.00 0.00 0.00 3.60
2438 8784 7.535940 TGAACGGATGAAATTATTTGACGAAAC 59.464 33.333 0.00 0.00 0.00 2.78
2444 8790 9.518906 CAATGATGAACGGATGAAATTATTTGA 57.481 29.630 0.00 0.00 0.00 2.69
2449 8795 9.571810 CTTTTCAATGATGAACGGATGAAATTA 57.428 29.630 0.00 0.00 45.01 1.40
2450 8796 8.306038 TCTTTTCAATGATGAACGGATGAAATT 58.694 29.630 0.00 0.00 45.01 1.82
2451 8797 7.756722 GTCTTTTCAATGATGAACGGATGAAAT 59.243 33.333 0.00 0.00 45.01 2.17
2455 8801 6.187125 AGTCTTTTCAATGATGAACGGATG 57.813 37.500 0.00 0.00 45.01 3.51
2456 8802 6.824305 AAGTCTTTTCAATGATGAACGGAT 57.176 33.333 0.00 0.00 45.01 4.18
2457 8803 6.633500 AAAGTCTTTTCAATGATGAACGGA 57.367 33.333 0.00 0.00 45.01 4.69
2458 8804 7.698836 AAAAAGTCTTTTCAATGATGAACGG 57.301 32.000 10.95 0.00 45.01 4.44
2479 8825 8.866970 AAATTTAGTACCACCTCGGATAAAAA 57.133 30.769 0.00 0.00 38.63 1.94
2480 8826 8.866970 AAAATTTAGTACCACCTCGGATAAAA 57.133 30.769 0.00 0.00 38.63 1.52
2482 8828 7.884354 ACAAAAATTTAGTACCACCTCGGATAA 59.116 33.333 0.00 0.00 38.63 1.75
2484 8830 6.150474 CACAAAAATTTAGTACCACCTCGGAT 59.850 38.462 0.00 0.00 38.63 4.18
2485 8831 5.470777 CACAAAAATTTAGTACCACCTCGGA 59.529 40.000 0.00 0.00 38.63 4.55
2486 8832 5.695818 CACAAAAATTTAGTACCACCTCGG 58.304 41.667 0.00 0.00 42.50 4.63
2488 8834 5.151389 CGCACAAAAATTTAGTACCACCTC 58.849 41.667 0.00 0.00 0.00 3.85
2489 8835 4.581409 ACGCACAAAAATTTAGTACCACCT 59.419 37.500 0.00 0.00 0.00 4.00
2490 8836 4.862350 ACGCACAAAAATTTAGTACCACC 58.138 39.130 0.00 0.00 0.00 4.61
2491 8837 5.754778 AGACGCACAAAAATTTAGTACCAC 58.245 37.500 0.00 0.00 0.00 4.16
2492 8838 5.761234 AGAGACGCACAAAAATTTAGTACCA 59.239 36.000 0.00 0.00 0.00 3.25
2493 8839 6.237313 AGAGACGCACAAAAATTTAGTACC 57.763 37.500 0.00 0.00 0.00 3.34
2494 8840 6.073440 TGGAGAGACGCACAAAAATTTAGTAC 60.073 38.462 0.00 0.00 0.00 2.73
2496 8842 4.819630 TGGAGAGACGCACAAAAATTTAGT 59.180 37.500 0.00 0.00 0.00 2.24
2497 8843 5.049405 AGTGGAGAGACGCACAAAAATTTAG 60.049 40.000 0.00 0.00 0.00 1.85
2499 8845 3.632145 AGTGGAGAGACGCACAAAAATTT 59.368 39.130 0.00 0.00 0.00 1.82
2500 8846 3.214328 AGTGGAGAGACGCACAAAAATT 58.786 40.909 0.00 0.00 0.00 1.82
2501 8847 2.851195 AGTGGAGAGACGCACAAAAAT 58.149 42.857 0.00 0.00 0.00 1.82
2502 8848 2.325583 AGTGGAGAGACGCACAAAAA 57.674 45.000 0.00 0.00 0.00 1.94
2503 8849 2.626266 TCTAGTGGAGAGACGCACAAAA 59.374 45.455 0.00 0.00 0.00 2.44
2504 8850 2.235891 TCTAGTGGAGAGACGCACAAA 58.764 47.619 0.00 0.00 0.00 2.83
2505 8851 1.905637 TCTAGTGGAGAGACGCACAA 58.094 50.000 0.00 0.00 0.00 3.33
2506 8852 1.905637 TTCTAGTGGAGAGACGCACA 58.094 50.000 0.00 0.00 34.93 4.57
2507 8853 3.057456 TCTTTTCTAGTGGAGAGACGCAC 60.057 47.826 0.00 0.00 34.93 5.34
2508 8854 3.057456 GTCTTTTCTAGTGGAGAGACGCA 60.057 47.826 6.42 0.00 34.93 5.24
2509 8855 3.057456 TGTCTTTTCTAGTGGAGAGACGC 60.057 47.826 13.58 0.00 39.57 5.19
2510 8856 4.768130 TGTCTTTTCTAGTGGAGAGACG 57.232 45.455 13.58 0.00 39.57 4.18
2511 8857 8.308207 ACTATTTGTCTTTTCTAGTGGAGAGAC 58.692 37.037 12.34 12.34 38.39 3.36
2512 8858 8.423906 ACTATTTGTCTTTTCTAGTGGAGAGA 57.576 34.615 0.00 0.00 34.93 3.10
2513 8859 9.495572 AAACTATTTGTCTTTTCTAGTGGAGAG 57.504 33.333 0.00 0.00 34.93 3.20
2530 8876 6.607689 TGCGGAATTCTGTACAAACTATTTG 58.392 36.000 15.63 0.00 45.95 2.32
2532 8878 6.811253 TTGCGGAATTCTGTACAAACTATT 57.189 33.333 15.63 0.00 0.00 1.73
2533 8879 7.250569 CAATTGCGGAATTCTGTACAAACTAT 58.749 34.615 12.36 0.00 28.65 2.12
2534 8880 6.348950 CCAATTGCGGAATTCTGTACAAACTA 60.349 38.462 12.36 0.00 28.65 2.24
2535 8881 5.460646 CAATTGCGGAATTCTGTACAAACT 58.539 37.500 12.36 2.49 28.65 2.66
2539 8885 2.752354 CCCAATTGCGGAATTCTGTACA 59.248 45.455 12.36 3.49 28.65 2.90
2541 8887 1.748493 GCCCAATTGCGGAATTCTGTA 59.252 47.619 12.36 8.60 28.65 2.74
2542 8888 0.532115 GCCCAATTGCGGAATTCTGT 59.468 50.000 12.36 0.00 28.65 3.41
2543 8889 0.179103 GGCCCAATTGCGGAATTCTG 60.179 55.000 12.36 10.10 28.65 3.02
2544 8890 0.614415 TGGCCCAATTGCGGAATTCT 60.614 50.000 12.36 0.00 28.65 2.40
2547 8893 2.059786 CCTGGCCCAATTGCGGAAT 61.060 57.895 14.92 0.00 0.00 3.01
2548 8894 2.679642 CCTGGCCCAATTGCGGAA 60.680 61.111 14.92 0.00 0.00 4.30
2554 8989 4.684134 AGTGCGCCTGGCCCAATT 62.684 61.111 14.12 0.00 42.61 2.32
2563 8998 3.884774 TTGGGTTGGAGTGCGCCT 61.885 61.111 4.18 0.32 0.00 5.52
2569 9004 0.032615 TGGCTTTGTTGGGTTGGAGT 60.033 50.000 0.00 0.00 0.00 3.85
2570 9005 1.118838 TTGGCTTTGTTGGGTTGGAG 58.881 50.000 0.00 0.00 0.00 3.86
2573 9008 0.179059 GGGTTGGCTTTGTTGGGTTG 60.179 55.000 0.00 0.00 0.00 3.77
2574 9009 0.618968 TGGGTTGGCTTTGTTGGGTT 60.619 50.000 0.00 0.00 0.00 4.11
2576 9011 1.048160 ACTGGGTTGGCTTTGTTGGG 61.048 55.000 0.00 0.00 0.00 4.12
2577 9012 1.698506 TACTGGGTTGGCTTTGTTGG 58.301 50.000 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.