Multiple sequence alignment - TraesCS1A01G174700

Loading Multiple Alignment...

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 TraesCS1A01G174700 chr1A 100.000 3028 0 0 1 3028 312162238 312159211 0.000000e+00 5592.0
1 TraesCS1A01G174700 chr1A 93.431 137 8 1 2331 2466 47210027 47209891 5.120000e-48 202.0
2 TraesCS1A01G174700 chr1D 94.253 1479 45 18 866 2332 235159429 235160879 0.000000e+00 2224.0
3 TraesCS1A01G174700 chr1D 91.076 874 30 5 1 868 235158542 235159373 0.000000e+00 1138.0
4 TraesCS1A01G174700 chr1D 89.044 429 35 4 2457 2883 235163186 235163604 3.460000e-144 521.0
5 TraesCS1A01G174700 chr1D 94.118 136 7 1 2331 2465 406733791 406733926 3.960000e-49 206.0
6 TraesCS1A01G174700 chr1B 93.941 1469 45 13 868 2333 340610485 340611912 0.000000e+00 2180.0
7 TraesCS1A01G174700 chr1B 91.619 871 40 6 1 868 340609606 340610446 0.000000e+00 1173.0
8 TraesCS1A01G174700 chr1B 90.541 148 14 0 2319 2466 5000880 5000733 2.380000e-46 196.0
9 TraesCS1A01G174700 chr6A 94.891 137 6 1 2329 2464 423274415 423274279 2.360000e-51 213.0
10 TraesCS1A01G174700 chr7D 95.455 132 6 0 2332 2463 6484596 6484465 8.510000e-51 211.0
11 TraesCS1A01G174700 chr7D 93.478 138 8 1 2325 2461 134010316 134010179 1.420000e-48 204.0
12 TraesCS1A01G174700 chr7D 83.117 77 8 4 2595 2670 486578370 486578442 7.010000e-07 65.8
13 TraesCS1A01G174700 chr7A 93.431 137 9 0 2332 2468 442265881 442265745 1.420000e-48 204.0
14 TraesCS1A01G174700 chr7A 75.000 204 33 10 2595 2782 555503469 555503670 9.000000e-11 78.7
15 TraesCS1A01G174700 chr7A 97.297 37 1 0 2594 2630 555484313 555484349 2.520000e-06 63.9
16 TraesCS1A01G174700 chr5A 91.837 147 9 3 2324 2469 131187488 131187632 5.120000e-48 202.0
17 TraesCS1A01G174700 chr5A 92.308 78 6 0 2516 2593 592689483 592689406 8.870000e-21 111.0
18 TraesCS1A01G174700 chr2B 92.806 139 8 2 2321 2458 394938646 394938783 1.840000e-47 200.0
19 TraesCS1A01G174700 chr2B 96.774 31 1 0 2594 2624 30443642 30443612 5.000000e-03 52.8
20 TraesCS1A01G174700 chr4A 91.111 90 8 0 2504 2593 117703386 117703297 4.100000e-24 122.0
21 TraesCS1A01G174700 chr4A 88.043 92 11 0 2499 2590 181621412 181621321 3.190000e-20 110.0
22 TraesCS1A01G174700 chr4B 75.427 293 48 20 2499 2783 374729719 374729995 1.470000e-23 121.0
23 TraesCS1A01G174700 chr4D 89.362 94 10 0 2499 2592 301021925 301022018 5.300000e-23 119.0
24 TraesCS1A01G174700 chr2A 91.026 78 7 0 2516 2593 637674041 637673964 4.130000e-19 106.0
25 TraesCS1A01G174700 chr2A 88.462 78 8 1 2594 2670 19481717 19481640 3.210000e-15 93.5
26 TraesCS1A01G174700 chr5D 86.170 94 13 0 2500 2593 59247556 59247463 5.340000e-18 102.0
27 TraesCS1A01G174700 chr6B 89.744 78 8 0 2516 2593 465696290 465696367 1.920000e-17 100.0
28 TraesCS1A01G174700 chr7B 89.706 68 6 1 2595 2661 516319430 516319497 5.380000e-13 86.1


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 TraesCS1A01G174700 chr1A 312159211 312162238 3027 True 5592.000000 5592 100.000000 1 3028 1 chr1A.!!$R2 3027
1 TraesCS1A01G174700 chr1D 235158542 235163604 5062 False 1294.333333 2224 91.457667 1 2883 3 chr1D.!!$F2 2882
2 TraesCS1A01G174700 chr1B 340609606 340611912 2306 False 1676.500000 2180 92.780000 1 2333 2 chr1B.!!$F1 2332

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
585 597 1.080501 CTGTCGCGTGTCCATCTGT 60.081 57.895 5.77 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2072 2154 0.868406 GCAACGGTCAAACAGAGAGG 59.132 55.0 0.0 0.0 0.0 3.69 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
30 31 7.268199 TGATGAAGGCATGATTATCTTTGTC 57.732 36.000 0.00 0.00 34.11 3.18
45 46 2.985957 TTGTCGATGGATGATGAGCA 57.014 45.000 0.00 0.00 0.00 4.26
247 253 7.786030 AGATTCATCGTCCATAAAGAAGAAGA 58.214 34.615 0.00 0.00 29.04 2.87
248 254 8.260818 AGATTCATCGTCCATAAAGAAGAAGAA 58.739 33.333 0.00 0.00 36.75 2.52
249 255 7.834068 TTCATCGTCCATAAAGAAGAAGAAG 57.166 36.000 0.00 0.00 30.64 2.85
250 256 6.341316 TCATCGTCCATAAAGAAGAAGAAGG 58.659 40.000 0.00 0.00 0.00 3.46
251 257 5.086104 TCGTCCATAAAGAAGAAGAAGGG 57.914 43.478 0.00 0.00 0.00 3.95
282 288 2.505498 CGACGCACGAAGGAATCCG 61.505 63.158 0.00 0.00 45.77 4.18
339 351 5.354513 TCTCTCGCCGGATAAACATATCTAG 59.645 44.000 5.05 0.00 0.00 2.43
340 352 4.106029 TCGCCGGATAAACATATCTAGC 57.894 45.455 5.05 0.00 0.00 3.42
341 353 3.762288 TCGCCGGATAAACATATCTAGCT 59.238 43.478 5.05 0.00 0.00 3.32
342 354 4.945543 TCGCCGGATAAACATATCTAGCTA 59.054 41.667 5.05 0.00 0.00 3.32
343 355 5.066117 TCGCCGGATAAACATATCTAGCTAG 59.934 44.000 15.01 15.01 0.00 3.42
351 363 9.243637 GATAAACATATCTAGCTAGCTATGCAC 57.756 37.037 30.95 19.24 36.41 4.57
362 374 1.626356 GCTATGCACCTCACCTCCCA 61.626 60.000 0.00 0.00 0.00 4.37
378 390 2.746375 CCATCCGGGCAGCTAGGTT 61.746 63.158 0.00 0.00 0.00 3.50
585 597 1.080501 CTGTCGCGTGTCCATCTGT 60.081 57.895 5.77 0.00 0.00 3.41
599 611 5.756347 TGTCCATCTGTACTTGTGTTTGTAC 59.244 40.000 0.00 0.00 39.37 2.90
745 757 3.414700 CGGGCAAGTGACGTCTGC 61.415 66.667 17.92 17.61 0.00 4.26
770 782 2.902423 AAAACACAGCAGCCGGGACA 62.902 55.000 2.18 0.00 0.00 4.02
782 794 1.810412 GCCGGGACATAAAAGAGCGAT 60.810 52.381 2.18 0.00 0.00 4.58
1285 1358 3.467803 GGTCTTAATCATCCAAGTCGGG 58.532 50.000 0.00 0.00 34.36 5.14
1375 1455 1.548357 ATGCTCTGCTCACGAGGGTT 61.548 55.000 0.00 0.00 0.00 4.11
1420 1500 1.600058 TCAAGGCATGGGAGGAGAAT 58.400 50.000 0.00 0.00 0.00 2.40
1462 1544 1.828979 AGTGAGTCTCCCGTTCTCTC 58.171 55.000 0.00 0.00 0.00 3.20
1463 1545 1.353022 AGTGAGTCTCCCGTTCTCTCT 59.647 52.381 0.00 0.00 0.00 3.10
1464 1546 1.741145 GTGAGTCTCCCGTTCTCTCTC 59.259 57.143 0.00 0.00 0.00 3.20
1468 1550 3.020984 AGTCTCCCGTTCTCTCTCAATC 58.979 50.000 0.00 0.00 0.00 2.67
1516 1598 1.134401 TCACCGAGATGGCTCCATTTC 60.134 52.381 8.85 8.85 43.94 2.17
1539 1621 7.715265 TCTATCCGCATTCAGATTTTAACTC 57.285 36.000 0.00 0.00 0.00 3.01
1600 1682 2.854777 CTCGTGTCTCTCATTTAAGCCG 59.145 50.000 0.00 0.00 0.00 5.52
1602 1684 3.441222 TCGTGTCTCTCATTTAAGCCGTA 59.559 43.478 0.00 0.00 0.00 4.02
1603 1685 4.097437 TCGTGTCTCTCATTTAAGCCGTAT 59.903 41.667 0.00 0.00 0.00 3.06
1604 1686 4.804139 CGTGTCTCTCATTTAAGCCGTATT 59.196 41.667 0.00 0.00 0.00 1.89
1605 1687 5.291128 CGTGTCTCTCATTTAAGCCGTATTT 59.709 40.000 0.00 0.00 0.00 1.40
1606 1688 6.183360 CGTGTCTCTCATTTAAGCCGTATTTT 60.183 38.462 0.00 0.00 0.00 1.82
1607 1689 7.527457 GTGTCTCTCATTTAAGCCGTATTTTT 58.473 34.615 0.00 0.00 0.00 1.94
1769 1851 1.777461 GCGACGCCATTTAGTACTACG 59.223 52.381 9.14 5.23 0.00 3.51
1770 1852 2.792542 GCGACGCCATTTAGTACTACGT 60.793 50.000 9.14 13.43 34.58 3.57
1771 1853 3.546020 GCGACGCCATTTAGTACTACGTA 60.546 47.826 9.14 0.00 31.63 3.57
2069 2151 3.589988 GTCCTCTTCGCTTCATCTTCAA 58.410 45.455 0.00 0.00 0.00 2.69
2072 2154 3.616379 CCTCTTCGCTTCATCTTCAACTC 59.384 47.826 0.00 0.00 0.00 3.01
2174 2256 2.032894 GGTATCATCAATTGCGTCGTGG 60.033 50.000 0.00 0.00 0.00 4.94
2189 2271 4.148166 CGTCGTGGTGTAATTTGTGATTG 58.852 43.478 0.00 0.00 0.00 2.67
2197 2279 7.276658 GTGGTGTAATTTGTGATTGTTTTGTGA 59.723 33.333 0.00 0.00 0.00 3.58
2289 2373 5.606348 ACTTGTTGAAAGCAATTAACCCA 57.394 34.783 0.00 0.00 36.22 4.51
2333 2417 9.712359 GTGTGTTAAGGGATTCGAAAATAATAC 57.288 33.333 0.00 6.79 0.00 1.89
2336 2420 9.333724 TGTTAAGGGATTCGAAAATAATACTCC 57.666 33.333 0.00 1.35 0.00 3.85
2337 2421 8.781196 GTTAAGGGATTCGAAAATAATACTCCC 58.219 37.037 17.71 17.71 0.00 4.30
2340 2424 5.938710 GGGATTCGAAAATAATACTCCCTCC 59.061 44.000 17.99 8.92 0.00 4.30
2342 2426 5.603170 TTCGAAAATAATACTCCCTCCGT 57.397 39.130 0.00 0.00 0.00 4.69
2343 2427 5.192327 TCGAAAATAATACTCCCTCCGTC 57.808 43.478 0.00 0.00 0.00 4.79
2344 2428 4.038402 TCGAAAATAATACTCCCTCCGTCC 59.962 45.833 0.00 0.00 0.00 4.79
2345 2429 4.639334 GAAAATAATACTCCCTCCGTCCC 58.361 47.826 0.00 0.00 0.00 4.46
2347 2431 2.852714 TAATACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
2348 2432 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
2349 2433 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
2352 2436 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2353 2437 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2354 2438 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2355 2439 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2356 2440 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2358 2442 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2362 2446 6.713276 TCCGTCCCAAAATTCTTGTCTTATA 58.287 36.000 0.00 0.00 0.00 0.98
2365 2449 9.116067 CCGTCCCAAAATTCTTGTCTTATATTA 57.884 33.333 0.00 0.00 0.00 0.98
2412 2496 9.871238 AATACTTAAACGTGACTTGATACATCT 57.129 29.630 0.00 0.00 0.00 2.90
2413 2497 7.582435 ACTTAAACGTGACTTGATACATCTG 57.418 36.000 0.00 0.00 0.00 2.90
2414 2498 7.152645 ACTTAAACGTGACTTGATACATCTGT 58.847 34.615 0.00 0.00 0.00 3.41
2415 2499 8.301720 ACTTAAACGTGACTTGATACATCTGTA 58.698 33.333 0.00 0.00 34.67 2.74
2416 2500 9.302345 CTTAAACGTGACTTGATACATCTGTAT 57.698 33.333 2.53 2.53 43.38 2.29
2417 2501 9.647797 TTAAACGTGACTTGATACATCTGTATT 57.352 29.630 4.44 0.00 40.99 1.89
2418 2502 8.547967 AAACGTGACTTGATACATCTGTATTT 57.452 30.769 4.44 0.00 40.99 1.40
2420 2504 8.858003 ACGTGACTTGATACATCTGTATTTAG 57.142 34.615 4.44 7.42 40.99 1.85
2421 2505 8.683615 ACGTGACTTGATACATCTGTATTTAGA 58.316 33.333 14.44 0.00 40.99 2.10
2422 2506 8.959058 CGTGACTTGATACATCTGTATTTAGAC 58.041 37.037 14.44 10.85 40.99 2.59
2423 2507 9.803315 GTGACTTGATACATCTGTATTTAGACA 57.197 33.333 14.44 12.43 40.99 3.41
2449 2533 7.602517 ATCTAAGACAAGAATTTTGAGACGG 57.397 36.000 7.18 0.00 0.00 4.79
2450 2534 6.755206 TCTAAGACAAGAATTTTGAGACGGA 58.245 36.000 7.18 0.00 0.00 4.69
2451 2535 5.931441 AAGACAAGAATTTTGAGACGGAG 57.069 39.130 7.18 0.00 0.00 4.63
2453 2537 3.412386 ACAAGAATTTTGAGACGGAGGG 58.588 45.455 7.18 0.00 0.00 4.30
2454 2538 3.072476 ACAAGAATTTTGAGACGGAGGGA 59.928 43.478 7.18 0.00 0.00 4.20
2455 2539 3.618690 AGAATTTTGAGACGGAGGGAG 57.381 47.619 0.00 0.00 0.00 4.30
2461 4727 6.749036 ATTTTGAGACGGAGGGAGTAATAT 57.251 37.500 0.00 0.00 0.00 1.28
2549 4815 3.168292 TCTCTCAACATGAAGCTCTCCA 58.832 45.455 0.00 0.00 0.00 3.86
2583 4849 1.933853 GCCACGTCATCATCCACTAAC 59.066 52.381 0.00 0.00 0.00 2.34
2585 4851 3.797039 CCACGTCATCATCCACTAACAT 58.203 45.455 0.00 0.00 0.00 2.71
2593 4859 7.857389 CGTCATCATCCACTAACATTATTTTGG 59.143 37.037 0.00 0.00 0.00 3.28
2620 4886 9.599866 TCATCATCCACTAACACTATTTTGTAG 57.400 33.333 0.00 0.00 0.00 2.74
2633 4899 6.038603 CACTATTTTGTAGCACATGCATACCT 59.961 38.462 6.64 0.00 45.16 3.08
2665 4932 3.694043 TGCAACTACAATGGTCTAGCA 57.306 42.857 0.00 0.00 0.00 3.49
2675 4942 2.647529 TGGTCTAGCATACACACACG 57.352 50.000 0.00 0.00 0.00 4.49
2683 4950 1.725931 GCATACACACACGCTTGCTTC 60.726 52.381 0.00 0.00 0.00 3.86
2695 4962 5.065988 ACACGCTTGCTTCGGAAAATAATAT 59.934 36.000 0.00 0.00 0.00 1.28
2703 4970 9.868277 TTGCTTCGGAAAATAATATGTTTTGAT 57.132 25.926 4.36 0.00 0.00 2.57
2719 4986 7.045126 TGTTTTGATTTAGGTCATTCGGTTT 57.955 32.000 0.00 0.00 0.00 3.27
2766 5033 8.153724 ACTTTTAAATTTACGCATAAACTCGC 57.846 30.769 0.00 0.00 33.09 5.03
2794 5061 3.788227 TCACCTAGTTGACCAAATGCT 57.212 42.857 0.00 0.00 0.00 3.79
2795 5062 4.901197 TCACCTAGTTGACCAAATGCTA 57.099 40.909 0.00 0.00 0.00 3.49
2840 5107 5.106515 GCCCTCTTGTAAATCACAACTCTTC 60.107 44.000 0.00 0.00 42.29 2.87
2845 5112 9.698309 CTCTTGTAAATCACAACTCTTCTTCTA 57.302 33.333 0.00 0.00 42.29 2.10
2865 5132 9.338622 TCTTCTATTTTAACTAGCTTAATGCCC 57.661 33.333 0.00 0.00 44.23 5.36
2870 5137 0.810031 ACTAGCTTAATGCCCGTGCG 60.810 55.000 0.00 0.00 44.23 5.34
2873 5140 1.514014 GCTTAATGCCCGTGCGTTG 60.514 57.895 7.64 0.00 46.06 4.10
2874 5141 1.873165 CTTAATGCCCGTGCGTTGT 59.127 52.632 7.64 0.00 46.06 3.32
2875 5142 0.179200 CTTAATGCCCGTGCGTTGTC 60.179 55.000 7.64 0.00 46.06 3.18
2876 5143 0.885150 TTAATGCCCGTGCGTTGTCA 60.885 50.000 7.64 0.00 46.06 3.58
2877 5144 0.675208 TAATGCCCGTGCGTTGTCAT 60.675 50.000 7.64 0.00 46.06 3.06
2881 5148 2.358125 CCGTGCGTTGTCATGGGA 60.358 61.111 0.00 0.00 39.02 4.37
2882 5149 1.745115 CCGTGCGTTGTCATGGGAT 60.745 57.895 0.00 0.00 39.02 3.85
2883 5150 0.461163 CCGTGCGTTGTCATGGGATA 60.461 55.000 0.00 0.00 39.02 2.59
2884 5151 1.364721 CGTGCGTTGTCATGGGATAA 58.635 50.000 0.00 0.00 0.00 1.75
2885 5152 1.939934 CGTGCGTTGTCATGGGATAAT 59.060 47.619 0.00 0.00 0.00 1.28
2886 5153 3.127589 CGTGCGTTGTCATGGGATAATA 58.872 45.455 0.00 0.00 0.00 0.98
2887 5154 3.558006 CGTGCGTTGTCATGGGATAATAA 59.442 43.478 0.00 0.00 0.00 1.40
2888 5155 4.213270 CGTGCGTTGTCATGGGATAATAAT 59.787 41.667 0.00 0.00 0.00 1.28
2889 5156 5.407084 CGTGCGTTGTCATGGGATAATAATA 59.593 40.000 0.00 0.00 0.00 0.98
2890 5157 6.073494 CGTGCGTTGTCATGGGATAATAATAA 60.073 38.462 0.00 0.00 0.00 1.40
2891 5158 7.519168 CGTGCGTTGTCATGGGATAATAATAAA 60.519 37.037 0.00 0.00 0.00 1.40
2892 5159 8.132362 GTGCGTTGTCATGGGATAATAATAAAA 58.868 33.333 0.00 0.00 0.00 1.52
2893 5160 8.687242 TGCGTTGTCATGGGATAATAATAAAAA 58.313 29.630 0.00 0.00 0.00 1.94
2922 5189 7.160547 AGACATACAAATGTTGCATTCATCA 57.839 32.000 5.57 0.00 46.49 3.07
2923 5190 7.778083 AGACATACAAATGTTGCATTCATCAT 58.222 30.769 5.57 0.00 46.49 2.45
2924 5191 8.255206 AGACATACAAATGTTGCATTCATCATT 58.745 29.630 5.57 0.00 46.49 2.57
2925 5192 9.518906 GACATACAAATGTTGCATTCATCATTA 57.481 29.630 2.67 0.00 46.49 1.90
2926 5193 9.872721 ACATACAAATGTTGCATTCATCATTAA 57.127 25.926 2.67 0.00 44.07 1.40
3001 5268 4.935702 CATTGACCAAATGTGACTGTTGT 58.064 39.130 0.00 0.00 40.78 3.32
3002 5269 4.368874 TTGACCAAATGTGACTGTTGTG 57.631 40.909 0.00 0.00 0.00 3.33
3003 5270 2.687425 TGACCAAATGTGACTGTTGTGG 59.313 45.455 0.00 0.00 0.00 4.17
3004 5271 2.687935 GACCAAATGTGACTGTTGTGGT 59.312 45.455 0.00 0.00 40.53 4.16
3005 5272 3.880490 GACCAAATGTGACTGTTGTGGTA 59.120 43.478 0.00 0.00 38.00 3.25
3006 5273 3.882888 ACCAAATGTGACTGTTGTGGTAG 59.117 43.478 0.00 0.00 36.15 3.18
3007 5274 3.882888 CCAAATGTGACTGTTGTGGTAGT 59.117 43.478 0.00 0.00 0.00 2.73
3008 5275 4.024048 CCAAATGTGACTGTTGTGGTAGTC 60.024 45.833 0.00 0.00 42.77 2.59
3009 5276 2.902705 TGTGACTGTTGTGGTAGTCC 57.097 50.000 0.00 0.00 41.99 3.85
3010 5277 2.394632 TGTGACTGTTGTGGTAGTCCT 58.605 47.619 0.00 0.00 41.99 3.85
3011 5278 2.364324 TGTGACTGTTGTGGTAGTCCTC 59.636 50.000 0.00 0.00 41.99 3.71
3012 5279 2.628657 GTGACTGTTGTGGTAGTCCTCT 59.371 50.000 0.00 0.00 41.99 3.69
3013 5280 3.069729 GTGACTGTTGTGGTAGTCCTCTT 59.930 47.826 0.00 0.00 41.99 2.85
3014 5281 3.069586 TGACTGTTGTGGTAGTCCTCTTG 59.930 47.826 0.00 0.00 41.99 3.02
3015 5282 3.039011 ACTGTTGTGGTAGTCCTCTTGT 58.961 45.455 0.00 0.00 34.23 3.16
3016 5283 4.220724 ACTGTTGTGGTAGTCCTCTTGTA 58.779 43.478 0.00 0.00 34.23 2.41
3017 5284 4.652421 ACTGTTGTGGTAGTCCTCTTGTAA 59.348 41.667 0.00 0.00 34.23 2.41
3018 5285 4.952460 TGTTGTGGTAGTCCTCTTGTAAC 58.048 43.478 0.00 0.00 34.23 2.50
3019 5286 4.202284 TGTTGTGGTAGTCCTCTTGTAACC 60.202 45.833 0.00 0.00 34.23 2.85
3020 5287 2.901839 TGTGGTAGTCCTCTTGTAACCC 59.098 50.000 0.00 0.00 34.23 4.11
3021 5288 2.901839 GTGGTAGTCCTCTTGTAACCCA 59.098 50.000 0.00 0.00 34.23 4.51
3022 5289 3.518303 GTGGTAGTCCTCTTGTAACCCAT 59.482 47.826 0.00 0.00 34.23 4.00
3023 5290 4.713321 GTGGTAGTCCTCTTGTAACCCATA 59.287 45.833 0.00 0.00 34.23 2.74
3024 5291 5.188359 GTGGTAGTCCTCTTGTAACCCATAA 59.812 44.000 0.00 0.00 34.23 1.90
3025 5292 5.188359 TGGTAGTCCTCTTGTAACCCATAAC 59.812 44.000 0.00 0.00 34.23 1.89
3026 5293 5.424573 GGTAGTCCTCTTGTAACCCATAACT 59.575 44.000 0.00 0.00 0.00 2.24
3027 5294 5.678955 AGTCCTCTTGTAACCCATAACTC 57.321 43.478 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.246430 ACAAAGATAATCATGCCTTCATCATT 57.754 30.769 0.00 0.00 28.64 2.57
30 31 0.954449 GCCCTGCTCATCATCCATCG 60.954 60.000 0.00 0.00 0.00 3.84
45 46 0.612174 TGTAGTCTTCTCGCTGCCCT 60.612 55.000 0.00 0.00 0.00 5.19
240 246 4.684757 GCCTAATCTGTCCCCTTCTTCTTC 60.685 50.000 0.00 0.00 0.00 2.87
245 251 1.512735 GGCCTAATCTGTCCCCTTCT 58.487 55.000 0.00 0.00 0.00 2.85
247 253 0.326238 TCGGCCTAATCTGTCCCCTT 60.326 55.000 0.00 0.00 0.00 3.95
248 254 1.049289 GTCGGCCTAATCTGTCCCCT 61.049 60.000 0.00 0.00 0.00 4.79
249 255 1.446366 GTCGGCCTAATCTGTCCCC 59.554 63.158 0.00 0.00 0.00 4.81
250 256 1.067582 CGTCGGCCTAATCTGTCCC 59.932 63.158 0.00 0.00 0.00 4.46
251 257 1.591863 GCGTCGGCCTAATCTGTCC 60.592 63.158 0.00 0.00 0.00 4.02
339 351 0.755686 AGGTGAGGTGCATAGCTAGC 59.244 55.000 6.62 6.62 34.13 3.42
340 352 1.342819 GGAGGTGAGGTGCATAGCTAG 59.657 57.143 0.00 0.00 34.13 3.42
341 353 1.414158 GGAGGTGAGGTGCATAGCTA 58.586 55.000 0.00 0.00 34.13 3.32
342 354 1.341156 GGGAGGTGAGGTGCATAGCT 61.341 60.000 0.00 0.00 37.35 3.32
343 355 1.147153 GGGAGGTGAGGTGCATAGC 59.853 63.158 0.00 0.00 0.00 2.97
362 374 2.444256 GGAACCTAGCTGCCCGGAT 61.444 63.158 0.73 0.00 0.00 4.18
376 388 0.670854 GACAGCGACTTGGAGGGAAC 60.671 60.000 0.00 0.00 0.00 3.62
378 390 2.283529 GGACAGCGACTTGGAGGGA 61.284 63.158 0.00 0.00 0.00 4.20
585 597 5.464057 CCATTCAGACGTACAAACACAAGTA 59.536 40.000 0.00 0.00 0.00 2.24
770 782 3.060602 GCGCCTTCTATCGCTCTTTTAT 58.939 45.455 0.00 0.00 46.92 1.40
782 794 1.682451 ATTAGGTGGCGCGCCTTCTA 61.682 55.000 45.79 38.39 42.24 2.10
1095 1167 1.384191 GACAACCAGGGCCTTGGAT 59.616 57.895 38.54 26.02 40.87 3.41
1098 1170 3.365265 GCGACAACCAGGGCCTTG 61.365 66.667 8.15 8.15 0.00 3.61
1270 1343 3.931907 TGATTCCCGACTTGGATGATT 57.068 42.857 0.00 0.00 42.00 2.57
1271 1344 3.545703 GTTGATTCCCGACTTGGATGAT 58.454 45.455 0.00 0.00 42.00 2.45
1375 1455 0.895530 AAATCCTCTTCTCGGTCGCA 59.104 50.000 0.00 0.00 0.00 5.10
1462 1544 3.927142 GGTGGTTACTCGTGAAGATTGAG 59.073 47.826 0.00 0.00 35.85 3.02
1463 1545 3.322541 TGGTGGTTACTCGTGAAGATTGA 59.677 43.478 0.00 0.00 0.00 2.57
1464 1546 3.432252 GTGGTGGTTACTCGTGAAGATTG 59.568 47.826 0.00 0.00 0.00 2.67
1468 1550 1.069513 TGGTGGTGGTTACTCGTGAAG 59.930 52.381 0.00 0.00 0.00 3.02
1516 1598 6.073003 GGGAGTTAAAATCTGAATGCGGATAG 60.073 42.308 0.00 0.00 39.20 2.08
1539 1621 1.466167 CTGAATTCTGAGTGCAACGGG 59.534 52.381 7.05 0.00 45.86 5.28
1617 1699 1.069906 GCGTGACACGAGAAAGCAAAT 60.070 47.619 31.08 0.00 46.05 2.32
1621 1703 1.488957 CTGCGTGACACGAGAAAGC 59.511 57.895 31.08 12.66 46.05 3.51
1769 1851 6.144080 CCAATCAGTAATAGCTTACGTGCTAC 59.856 42.308 9.54 1.12 46.60 3.58
1771 1853 5.050490 CCAATCAGTAATAGCTTACGTGCT 58.950 41.667 5.65 5.65 46.11 4.40
1812 1894 1.153901 CCTGCACGTACGTAGGTGG 60.154 63.158 35.90 25.09 41.10 4.61
1963 2045 4.382320 GGTACTTGGCGGCGGTCA 62.382 66.667 9.78 0.00 0.00 4.02
2047 2129 2.093973 TGAAGATGAAGCGAAGAGGACC 60.094 50.000 0.00 0.00 0.00 4.46
2069 2151 1.705873 ACGGTCAAACAGAGAGGAGT 58.294 50.000 0.00 0.00 0.00 3.85
2072 2154 0.868406 GCAACGGTCAAACAGAGAGG 59.132 55.000 0.00 0.00 0.00 3.69
2103 2185 3.788333 ATACACAAGTGATGCAATGGC 57.212 42.857 7.28 0.00 41.68 4.40
2174 2256 8.627487 TCTCACAAAACAATCACAAATTACAC 57.373 30.769 0.00 0.00 0.00 2.90
2189 2271 5.995897 AGTACACCCAAGTATCTCACAAAAC 59.004 40.000 0.00 0.00 0.00 2.43
2197 2279 8.834004 TCTTTATACAGTACACCCAAGTATCT 57.166 34.615 0.00 0.00 0.00 1.98
2270 2354 5.543507 ATGTGGGTTAATTGCTTTCAACA 57.456 34.783 0.00 0.00 34.60 3.33
2289 2373 9.814899 TTAACACACAAAAATGATTCTGAATGT 57.185 25.926 7.78 0.00 0.00 2.71
2333 2417 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
2335 2419 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2336 2420 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2337 2421 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2386 2470 9.871238 AGATGTATCAAGTCACGTTTAAGTATT 57.129 29.630 0.00 0.00 0.00 1.89
2391 2475 9.647797 AATACAGATGTATCAAGTCACGTTTAA 57.352 29.630 5.97 0.00 40.10 1.52
2392 2476 9.647797 AAATACAGATGTATCAAGTCACGTTTA 57.352 29.630 5.97 0.00 40.10 2.01
2394 2478 9.302345 CTAAATACAGATGTATCAAGTCACGTT 57.698 33.333 5.97 0.00 40.10 3.99
2395 2479 8.683615 TCTAAATACAGATGTATCAAGTCACGT 58.316 33.333 5.97 0.00 40.10 4.49
2397 2481 9.803315 TGTCTAAATACAGATGTATCAAGTCAC 57.197 33.333 5.97 3.82 40.10 3.67
2422 2506 9.322776 CGTCTCAAAATTCTTGTCTTAGATTTG 57.677 33.333 0.00 0.00 30.65 2.32
2423 2507 8.507249 CCGTCTCAAAATTCTTGTCTTAGATTT 58.493 33.333 0.00 0.00 0.00 2.17
2424 2508 7.878127 TCCGTCTCAAAATTCTTGTCTTAGATT 59.122 33.333 0.00 0.00 0.00 2.40
2425 2509 7.386851 TCCGTCTCAAAATTCTTGTCTTAGAT 58.613 34.615 0.00 0.00 0.00 1.98
2426 2510 6.755206 TCCGTCTCAAAATTCTTGTCTTAGA 58.245 36.000 0.00 0.00 0.00 2.10
2427 2511 6.091441 CCTCCGTCTCAAAATTCTTGTCTTAG 59.909 42.308 0.00 0.00 0.00 2.18
2428 2512 5.932303 CCTCCGTCTCAAAATTCTTGTCTTA 59.068 40.000 0.00 0.00 0.00 2.10
2429 2513 4.757149 CCTCCGTCTCAAAATTCTTGTCTT 59.243 41.667 0.00 0.00 0.00 3.01
2430 2514 4.319177 CCTCCGTCTCAAAATTCTTGTCT 58.681 43.478 0.00 0.00 0.00 3.41
2431 2515 3.437049 CCCTCCGTCTCAAAATTCTTGTC 59.563 47.826 0.00 0.00 0.00 3.18
2432 2516 3.072476 TCCCTCCGTCTCAAAATTCTTGT 59.928 43.478 0.00 0.00 0.00 3.16
2433 2517 3.674997 TCCCTCCGTCTCAAAATTCTTG 58.325 45.455 0.00 0.00 0.00 3.02
2434 2518 3.328050 ACTCCCTCCGTCTCAAAATTCTT 59.672 43.478 0.00 0.00 0.00 2.52
2435 2519 2.907042 ACTCCCTCCGTCTCAAAATTCT 59.093 45.455 0.00 0.00 0.00 2.40
2436 2520 3.336138 ACTCCCTCCGTCTCAAAATTC 57.664 47.619 0.00 0.00 0.00 2.17
2437 2521 4.903045 TTACTCCCTCCGTCTCAAAATT 57.097 40.909 0.00 0.00 0.00 1.82
2438 2522 6.749036 ATATTACTCCCTCCGTCTCAAAAT 57.251 37.500 0.00 0.00 0.00 1.82
2439 2523 6.555463 AATATTACTCCCTCCGTCTCAAAA 57.445 37.500 0.00 0.00 0.00 2.44
2440 2524 6.070424 ACAAATATTACTCCCTCCGTCTCAAA 60.070 38.462 0.00 0.00 0.00 2.69
2441 2525 5.424252 ACAAATATTACTCCCTCCGTCTCAA 59.576 40.000 0.00 0.00 0.00 3.02
2446 2530 5.431179 AACACAAATATTACTCCCTCCGT 57.569 39.130 0.00 0.00 0.00 4.69
2447 2531 6.819649 TGTTAACACAAATATTACTCCCTCCG 59.180 38.462 3.59 0.00 0.00 4.63
2583 4849 8.685427 TGTTAGTGGATGATGACCAAAATAATG 58.315 33.333 0.00 0.00 39.22 1.90
2585 4851 7.888021 AGTGTTAGTGGATGATGACCAAAATAA 59.112 33.333 0.00 0.00 39.22 1.40
2593 4859 8.268850 ACAAAATAGTGTTAGTGGATGATGAC 57.731 34.615 0.00 0.00 0.00 3.06
2650 4917 5.520288 GTGTGTGTATGCTAGACCATTGTAG 59.480 44.000 0.00 0.00 0.00 2.74
2652 4919 4.253685 GTGTGTGTATGCTAGACCATTGT 58.746 43.478 0.00 0.00 0.00 2.71
2665 4932 0.790207 CGAAGCAAGCGTGTGTGTAT 59.210 50.000 0.59 0.00 0.00 2.29
2675 4942 7.755582 AAACATATTATTTTCCGAAGCAAGC 57.244 32.000 0.00 0.00 0.00 4.01
2695 4962 6.642707 AACCGAATGACCTAAATCAAAACA 57.357 33.333 0.00 0.00 30.82 2.83
2740 5007 8.632551 GCGAGTTTATGCGTAAATTTAAAAGTT 58.367 29.630 14.00 0.00 32.76 2.66
2741 5008 8.153724 GCGAGTTTATGCGTAAATTTAAAAGT 57.846 30.769 14.00 0.00 32.76 2.66
2755 5022 1.002792 GATTTCCCCGCGAGTTTATGC 60.003 52.381 8.23 0.00 0.00 3.14
2756 5023 2.031683 GTGATTTCCCCGCGAGTTTATG 59.968 50.000 8.23 0.00 0.00 1.90
2757 5024 2.285977 GTGATTTCCCCGCGAGTTTAT 58.714 47.619 8.23 0.00 0.00 1.40
2758 5025 1.676615 GGTGATTTCCCCGCGAGTTTA 60.677 52.381 8.23 0.00 0.00 2.01
2759 5026 0.958876 GGTGATTTCCCCGCGAGTTT 60.959 55.000 8.23 0.00 0.00 2.66
2760 5027 1.376812 GGTGATTTCCCCGCGAGTT 60.377 57.895 8.23 0.00 0.00 3.01
2761 5028 0.974010 TAGGTGATTTCCCCGCGAGT 60.974 55.000 8.23 0.00 0.00 4.18
2762 5029 0.249489 CTAGGTGATTTCCCCGCGAG 60.249 60.000 8.23 0.00 0.00 5.03
2763 5030 0.974010 ACTAGGTGATTTCCCCGCGA 60.974 55.000 8.23 0.00 0.00 5.87
2764 5031 0.107848 AACTAGGTGATTTCCCCGCG 60.108 55.000 0.00 0.00 0.00 6.46
2765 5032 1.065709 TCAACTAGGTGATTTCCCCGC 60.066 52.381 6.32 0.00 0.00 6.13
2766 5033 2.629051 GTCAACTAGGTGATTTCCCCG 58.371 52.381 14.87 0.00 0.00 5.73
2794 5061 1.437772 CCACAACGCCACAAACGGTA 61.438 55.000 0.00 0.00 34.00 4.02
2795 5062 2.766400 CCACAACGCCACAAACGGT 61.766 57.895 0.00 0.00 34.00 4.83
2807 5074 2.741486 TACAAGAGGGCCGCCACAAC 62.741 60.000 12.58 0.00 0.00 3.32
2840 5107 8.283291 CGGGCATTAAGCTAGTTAAAATAGAAG 58.717 37.037 0.00 0.00 44.79 2.85
2845 5112 5.449999 GCACGGGCATTAAGCTAGTTAAAAT 60.450 40.000 3.77 0.00 44.79 1.82
2847 5114 3.375922 GCACGGGCATTAAGCTAGTTAAA 59.624 43.478 3.77 0.00 44.79 1.52
2865 5132 1.364721 TTATCCCATGACAACGCACG 58.635 50.000 0.00 0.00 0.00 5.34
2896 5163 8.905850 TGATGAATGCAACATTTGTATGTCTAT 58.094 29.630 10.31 0.00 44.14 1.98
2897 5164 8.278729 TGATGAATGCAACATTTGTATGTCTA 57.721 30.769 10.31 0.00 44.14 2.59
2898 5165 7.160547 TGATGAATGCAACATTTGTATGTCT 57.839 32.000 10.31 0.00 44.14 3.41
2899 5166 7.997107 ATGATGAATGCAACATTTGTATGTC 57.003 32.000 10.31 0.00 44.14 3.06
2900 5167 9.872721 TTAATGATGAATGCAACATTTGTATGT 57.127 25.926 13.89 0.00 42.61 2.29
2965 5232 9.859427 CATTTGGTCAATGTTATGTGATTAAGT 57.141 29.630 0.00 0.00 38.01 2.24
2980 5247 4.202141 CCACAACAGTCACATTTGGTCAAT 60.202 41.667 0.00 0.00 0.00 2.57
2981 5248 3.130164 CCACAACAGTCACATTTGGTCAA 59.870 43.478 0.00 0.00 0.00 3.18
2982 5249 2.687425 CCACAACAGTCACATTTGGTCA 59.313 45.455 0.00 0.00 0.00 4.02
2983 5250 2.687935 ACCACAACAGTCACATTTGGTC 59.312 45.455 0.00 0.00 29.70 4.02
2984 5251 2.733956 ACCACAACAGTCACATTTGGT 58.266 42.857 0.00 0.00 0.00 3.67
2985 5252 3.882888 ACTACCACAACAGTCACATTTGG 59.117 43.478 0.00 0.00 0.00 3.28
2986 5253 4.024048 GGACTACCACAACAGTCACATTTG 60.024 45.833 4.32 0.00 42.45 2.32
2987 5254 4.134563 GGACTACCACAACAGTCACATTT 58.865 43.478 4.32 0.00 42.45 2.32
2988 5255 3.391296 AGGACTACCACAACAGTCACATT 59.609 43.478 4.32 0.00 42.45 2.71
2989 5256 2.972713 AGGACTACCACAACAGTCACAT 59.027 45.455 4.32 0.00 42.45 3.21
2990 5257 2.364324 GAGGACTACCACAACAGTCACA 59.636 50.000 4.32 0.00 42.45 3.58
2991 5258 2.628657 AGAGGACTACCACAACAGTCAC 59.371 50.000 4.32 0.00 42.45 3.67
2992 5259 2.958818 AGAGGACTACCACAACAGTCA 58.041 47.619 4.32 0.00 42.45 3.41
2993 5260 3.069729 ACAAGAGGACTACCACAACAGTC 59.930 47.826 0.00 0.00 40.40 3.51
2994 5261 3.039011 ACAAGAGGACTACCACAACAGT 58.961 45.455 0.00 0.00 38.94 3.55
2995 5262 3.753294 ACAAGAGGACTACCACAACAG 57.247 47.619 0.00 0.00 38.94 3.16
2996 5263 4.202284 GGTTACAAGAGGACTACCACAACA 60.202 45.833 0.00 0.00 38.94 3.33
2997 5264 4.313282 GGTTACAAGAGGACTACCACAAC 58.687 47.826 0.00 0.00 38.94 3.32
2998 5265 3.325716 GGGTTACAAGAGGACTACCACAA 59.674 47.826 0.00 0.00 38.94 3.33
2999 5266 2.901839 GGGTTACAAGAGGACTACCACA 59.098 50.000 0.00 0.00 38.94 4.17
3000 5267 2.901839 TGGGTTACAAGAGGACTACCAC 59.098 50.000 0.00 0.00 38.94 4.16
3001 5268 3.263369 TGGGTTACAAGAGGACTACCA 57.737 47.619 0.00 0.00 38.94 3.25
3002 5269 5.424573 AGTTATGGGTTACAAGAGGACTACC 59.575 44.000 0.00 0.00 0.00 3.18
3003 5270 6.541934 AGTTATGGGTTACAAGAGGACTAC 57.458 41.667 0.00 0.00 0.00 2.73
3004 5271 6.786967 GAGTTATGGGTTACAAGAGGACTA 57.213 41.667 0.00 0.00 0.00 2.59
3005 5272 5.678955 GAGTTATGGGTTACAAGAGGACT 57.321 43.478 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.