Multiple sequence alignment - TraesCS2D01G478900

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 TraesCS2D01G478900 chr2D 100.000 2531 0 0 1 2531 580004889 580002359 0.000000e+00 4674.0
1 TraesCS2D01G478900 chr2D 83.051 590 75 13 989 1562 561937084 561936504 1.740000e-141 512.0
2 TraesCS2D01G478900 chr2D 82.700 526 44 18 1981 2463 559298219 559298740 8.370000e-115 424.0
3 TraesCS2D01G478900 chr2D 78.049 246 50 4 1027 1270 561935308 561935065 4.360000e-33 152.0
4 TraesCS2D01G478900 chr2D 91.346 104 7 1 1819 1922 559294944 559294843 9.440000e-30 141.0
5 TraesCS2D01G478900 chr2D 94.872 78 3 1 2454 2531 559298691 559298767 1.230000e-23 121.0
6 TraesCS2D01G478900 chr2B 92.984 1183 70 5 663 1837 698303320 698302143 0.000000e+00 1712.0
7 TraesCS2D01G478900 chr2B 97.857 280 6 0 1 280 698952236 698951957 3.790000e-133 484.0
8 TraesCS2D01G478900 chr2B 94.286 280 14 1 1 280 698303980 698303703 6.470000e-116 427.0
9 TraesCS2D01G478900 chr2B 82.438 484 48 9 2016 2463 16279258 16279740 3.050000e-104 388.0
10 TraesCS2D01G478900 chr2B 94.783 230 12 0 355 584 698951566 698951337 2.390000e-95 359.0
11 TraesCS2D01G478900 chr2B 85.780 218 11 12 1570 1779 671390712 671390507 1.970000e-51 213.0
12 TraesCS2D01G478900 chr2B 94.697 132 6 1 295 426 698303719 698303589 1.190000e-48 204.0
13 TraesCS2D01G478900 chr2B 96.907 97 3 0 395 491 698303589 698303493 2.010000e-36 163.0
14 TraesCS2D01G478900 chr2B 75.510 245 58 2 1027 1270 671213657 671213414 4.420000e-23 119.0
15 TraesCS2D01G478900 chr2B 95.522 67 3 0 295 361 698951973 698951907 9.570000e-20 108.0
16 TraesCS2D01G478900 chr2A 90.934 1103 76 15 467 1553 717879007 717877913 0.000000e+00 1461.0
17 TraesCS2D01G478900 chr2A 97.119 243 7 0 1 243 717879844 717879602 6.520000e-111 411.0
18 TraesCS2D01G478900 chr2A 95.294 170 7 1 295 463 717879341 717879172 4.150000e-68 268.0
19 TraesCS2D01G478900 chr2A 86.818 220 11 10 1721 1936 717877601 717877396 1.960000e-56 230.0
20 TraesCS2D01G478900 chr2A 91.566 166 11 2 1563 1728 717877808 717877646 2.530000e-55 226.0
21 TraesCS2D01G478900 chr2A 77.823 248 47 5 1027 1270 702194070 702193827 2.030000e-31 147.0
22 TraesCS2D01G478900 chr2A 94.737 57 3 0 1126 1182 702246232 702246176 3.470000e-14 89.8
23 TraesCS2D01G478900 chr4D 85.808 458 51 5 2016 2463 400236438 400236891 8.190000e-130 473.0
24 TraesCS2D01G478900 chr4D 81.443 485 51 18 2016 2463 407119051 407118569 6.660000e-96 361.0
25 TraesCS2D01G478900 chr4D 93.590 78 4 1 2454 2531 400236842 400236918 5.720000e-22 115.0
26 TraesCS2D01G478900 chr5B 83.264 484 43 21 2017 2463 35514885 35515367 6.520000e-111 411.0
27 TraesCS2D01G478900 chr5B 82.583 333 45 11 2021 2341 512932860 512933191 5.330000e-72 281.0
28 TraesCS2D01G478900 chr7A 82.268 485 49 16 2016 2463 20480424 20479940 3.950000e-103 385.0
29 TraesCS2D01G478900 chr7A 96.078 51 2 0 2464 2514 20479980 20479930 1.610000e-12 84.2
30 TraesCS2D01G478900 chr3B 80.619 485 54 20 2016 2463 747566963 747566482 3.120000e-89 339.0
31 TraesCS2D01G478900 chr5D 87.329 292 30 6 2016 2306 398644575 398644290 6.750000e-86 327.0
32 TraesCS2D01G478900 chr5D 81.982 111 14 3 1812 1922 365178279 365178383 3.470000e-14 89.8
33 TraesCS2D01G478900 chr5D 85.526 76 9 2 1813 1887 366751668 366751742 7.510000e-11 78.7
34 TraesCS2D01G478900 chr1D 87.330 221 18 2 2252 2463 31218632 31218413 6.990000e-61 244.0
35 TraesCS2D01G478900 chr1D 94.366 71 4 0 2461 2531 31218456 31218386 2.660000e-20 110.0
36 TraesCS2D01G478900 chr7B 94.203 69 3 1 2454 2522 712087525 712087458 1.240000e-18 104.0
37 TraesCS2D01G478900 chr6B 83.654 104 13 3 2371 2470 489537417 489537520 7.450000e-16 95.3
38 TraesCS2D01G478900 chr7D 87.654 81 6 2 2454 2531 20277642 20277721 9.640000e-15 91.6
39 TraesCS2D01G478900 chr6D 89.041 73 7 1 2459 2531 128912232 128912161 3.470000e-14 89.8
40 TraesCS2D01G478900 chr6A 88.732 71 8 0 2461 2531 79294735 79294805 1.250000e-13 87.9
41 TraesCS2D01G478900 chr6A 84.615 78 11 1 2454 2531 163204119 163204043 2.700000e-10 76.8
42 TraesCS2D01G478900 chr4A 90.476 63 6 0 1813 1875 642918108 642918170 1.610000e-12 84.2
43 TraesCS2D01G478900 chr4A 91.667 60 3 2 1721 1779 45711637 45711695 5.800000e-12 82.4
44 TraesCS2D01G478900 chr5A 84.091 88 10 3 2381 2464 485591546 485591459 5.800000e-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 TraesCS2D01G478900 chr2D 580002359 580004889 2530 True 4674.0 4674 100.0000 1 2531 1 chr2D.!!$R2 2530
1 TraesCS2D01G478900 chr2D 561935065 561937084 2019 True 332.0 512 80.5500 989 1562 2 chr2D.!!$R3 573
2 TraesCS2D01G478900 chr2D 559298219 559298767 548 False 272.5 424 88.7860 1981 2531 2 chr2D.!!$F1 550
3 TraesCS2D01G478900 chr2B 698302143 698303980 1837 True 626.5 1712 94.7185 1 1837 4 chr2B.!!$R3 1836
4 TraesCS2D01G478900 chr2B 698951337 698952236 899 True 317.0 484 96.0540 1 584 3 chr2B.!!$R4 583
5 TraesCS2D01G478900 chr2A 717877396 717879844 2448 True 519.2 1461 92.3462 1 1936 5 chr2A.!!$R3 1935

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
615 1395 0.162507 CAAGCGTGTCAGAAGAAGCG 59.837 55.0 0.0 0.0 0.0 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2031 4028 0.105709 GGAAGAGGAGGGAGGAGAGG 60.106 65.0 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
203 204 3.988379 TCTTTTGAACTGGTGACATGC 57.012 42.857 0.00 0.00 41.51 4.06
270 511 7.739498 ATCTAATTTGTGACCTTAAACGTGT 57.261 32.000 0.00 0.00 0.00 4.49
271 512 8.836268 ATCTAATTTGTGACCTTAAACGTGTA 57.164 30.769 0.00 0.00 0.00 2.90
272 513 8.075593 TCTAATTTGTGACCTTAAACGTGTAC 57.924 34.615 0.00 0.00 0.00 2.90
273 514 6.930667 AATTTGTGACCTTAAACGTGTACT 57.069 33.333 0.00 0.00 0.00 2.73
274 515 5.721876 TTTGTGACCTTAAACGTGTACTG 57.278 39.130 0.00 0.00 0.00 2.74
275 516 4.389890 TGTGACCTTAAACGTGTACTGT 57.610 40.909 0.00 0.00 0.00 3.55
276 517 4.757594 TGTGACCTTAAACGTGTACTGTT 58.242 39.130 0.00 0.00 0.00 3.16
277 518 4.567558 TGTGACCTTAAACGTGTACTGTTG 59.432 41.667 5.08 0.00 0.00 3.33
278 519 4.567959 GTGACCTTAAACGTGTACTGTTGT 59.432 41.667 5.08 0.11 0.00 3.32
279 520 5.063817 GTGACCTTAAACGTGTACTGTTGTT 59.936 40.000 5.08 0.00 0.00 2.83
280 521 5.291614 TGACCTTAAACGTGTACTGTTGTTC 59.708 40.000 5.08 0.62 0.00 3.18
281 522 4.571984 ACCTTAAACGTGTACTGTTGTTCC 59.428 41.667 5.08 0.00 0.00 3.62
282 523 4.024641 CCTTAAACGTGTACTGTTGTTCCC 60.025 45.833 5.08 0.00 0.00 3.97
283 524 1.957668 AACGTGTACTGTTGTTCCCC 58.042 50.000 0.00 0.00 0.00 4.81
284 525 0.249573 ACGTGTACTGTTGTTCCCCG 60.250 55.000 0.00 0.00 0.00 5.73
285 526 1.562575 CGTGTACTGTTGTTCCCCGC 61.563 60.000 0.00 0.00 0.00 6.13
286 527 0.533308 GTGTACTGTTGTTCCCCGCA 60.533 55.000 0.00 0.00 0.00 5.69
287 528 0.180642 TGTACTGTTGTTCCCCGCAA 59.819 50.000 0.00 0.00 0.00 4.85
288 529 0.589708 GTACTGTTGTTCCCCGCAAC 59.410 55.000 0.00 0.00 44.50 4.17
292 533 3.742983 GTTGTTCCCCGCAACAAAA 57.257 47.368 2.00 0.00 45.57 2.44
293 534 2.011540 GTTGTTCCCCGCAACAAAAA 57.988 45.000 2.00 0.00 45.57 1.94
339 580 9.665719 TTTGCTATGAATGTTGTAGAGAATACA 57.334 29.630 0.00 0.00 0.00 2.29
465 1084 2.364324 GGGACATTCTCATGCATGCAAT 59.636 45.455 26.68 17.78 33.05 3.56
547 1327 5.733620 AAGCATTGATGTTGAGTGGAATT 57.266 34.783 0.00 0.00 0.00 2.17
581 1361 7.777910 CCTGAAACATAATCCCCATTTGTACTA 59.222 37.037 0.00 0.00 0.00 1.82
586 1366 9.574516 AACATAATCCCCATTTGTACTATTCTC 57.425 33.333 0.00 0.00 0.00 2.87
590 1370 5.437060 TCCCCATTTGTACTATTCTCTTGC 58.563 41.667 0.00 0.00 0.00 4.01
592 1372 5.297776 CCCCATTTGTACTATTCTCTTGCAG 59.702 44.000 0.00 0.00 0.00 4.41
593 1373 5.220931 CCCATTTGTACTATTCTCTTGCAGC 60.221 44.000 0.00 0.00 0.00 5.25
594 1374 5.355071 CCATTTGTACTATTCTCTTGCAGCA 59.645 40.000 0.00 0.00 0.00 4.41
595 1375 6.039047 CCATTTGTACTATTCTCTTGCAGCAT 59.961 38.462 0.00 0.00 0.00 3.79
597 1377 5.343307 TGTACTATTCTCTTGCAGCATCA 57.657 39.130 0.00 0.00 0.00 3.07
598 1378 5.733676 TGTACTATTCTCTTGCAGCATCAA 58.266 37.500 0.00 0.00 0.00 2.57
599 1379 5.814188 TGTACTATTCTCTTGCAGCATCAAG 59.186 40.000 0.00 10.59 43.53 3.02
600 1380 3.626670 ACTATTCTCTTGCAGCATCAAGC 59.373 43.478 11.66 0.00 42.29 4.01
610 1390 3.963622 GCATCAAGCGTGTCAGAAG 57.036 52.632 0.00 0.00 0.00 2.85
611 1391 1.432514 GCATCAAGCGTGTCAGAAGA 58.567 50.000 0.00 0.00 0.00 2.87
612 1392 1.800586 GCATCAAGCGTGTCAGAAGAA 59.199 47.619 0.00 0.00 0.00 2.52
613 1393 2.159734 GCATCAAGCGTGTCAGAAGAAG 60.160 50.000 0.00 0.00 0.00 2.85
615 1395 0.162507 CAAGCGTGTCAGAAGAAGCG 59.837 55.000 0.00 0.00 0.00 4.68
617 1397 0.387878 AGCGTGTCAGAAGAAGCGAG 60.388 55.000 0.00 0.00 0.00 5.03
618 1398 1.950098 GCGTGTCAGAAGAAGCGAGC 61.950 60.000 0.00 0.00 0.00 5.03
619 1399 0.664466 CGTGTCAGAAGAAGCGAGCA 60.664 55.000 0.00 0.00 0.00 4.26
621 1401 1.658095 GTGTCAGAAGAAGCGAGCATC 59.342 52.381 0.00 0.00 0.00 3.91
633 1413 2.387309 GAGCATCGTGGACACATGG 58.613 57.895 0.00 0.00 34.31 3.66
634 1414 1.709147 GAGCATCGTGGACACATGGC 61.709 60.000 0.00 2.64 34.31 4.40
635 1415 2.764314 GCATCGTGGACACATGGCC 61.764 63.158 0.00 0.00 45.93 5.36
637 1417 2.601702 ATCGTGGACACATGGCCCA 61.602 57.895 0.00 0.00 44.80 5.36
638 1418 1.925285 ATCGTGGACACATGGCCCAT 61.925 55.000 0.00 0.00 44.80 4.00
639 1419 2.114670 CGTGGACACATGGCCCATC 61.115 63.158 0.00 0.00 44.80 3.51
640 1420 1.754234 GTGGACACATGGCCCATCC 60.754 63.158 0.00 0.00 44.80 3.51
641 1421 2.123726 GGACACATGGCCCATCCC 60.124 66.667 0.00 0.00 37.19 3.85
642 1422 2.123726 GACACATGGCCCATCCCC 60.124 66.667 0.00 0.00 0.00 4.81
693 1556 3.000476 CACGTACACGAATCAATTACCGG 60.000 47.826 9.04 0.00 43.02 5.28
717 1580 2.309764 AATCCAGAAATCACGCGCGC 62.310 55.000 32.58 23.91 0.00 6.86
875 1738 4.944048 AGAAATCAAACCCTCCAAAAACG 58.056 39.130 0.00 0.00 0.00 3.60
924 1787 5.471456 CCATTTTCCTCCCATTTATCTCGAG 59.529 44.000 5.93 5.93 0.00 4.04
925 1788 5.950544 TTTTCCTCCCATTTATCTCGAGA 57.049 39.130 19.19 19.19 0.00 4.04
926 1789 4.939052 TTCCTCCCATTTATCTCGAGAC 57.061 45.455 19.30 0.00 0.00 3.36
927 1790 2.885266 TCCTCCCATTTATCTCGAGACG 59.115 50.000 19.30 4.04 0.00 4.18
929 1792 1.340248 TCCCATTTATCTCGAGACGGC 59.660 52.381 19.30 0.00 0.00 5.68
935 1799 0.738975 TATCTCGAGACGGCCTTGTG 59.261 55.000 19.30 0.00 0.00 3.33
952 1816 6.352222 GGCCTTGTGCATATATACCATCTACT 60.352 42.308 0.00 0.00 43.89 2.57
972 1836 3.318006 TACACACAATCCCGGCCGG 62.318 63.158 37.99 37.99 0.00 6.13
1243 2121 1.815421 ATCGTCAAGCGCATCCACC 60.815 57.895 11.47 0.00 41.07 4.61
1289 2167 2.429058 CATCCAGATGGCCCTCCG 59.571 66.667 0.00 0.00 35.24 4.63
1313 2191 1.080705 GCGACCAGTTGTACTCGCT 60.081 57.895 15.27 0.00 36.46 4.93
1467 2345 4.719369 GTGGAGTCGCCGCTCGTT 62.719 66.667 0.00 0.00 44.03 3.85
1468 2346 3.057548 TGGAGTCGCCGCTCGTTA 61.058 61.111 3.21 0.00 40.66 3.18
1469 2347 2.180017 GGAGTCGCCGCTCGTTAA 59.820 61.111 3.21 0.00 39.67 2.01
1470 2348 1.872679 GGAGTCGCCGCTCGTTAAG 60.873 63.158 3.21 0.00 39.67 1.85
1488 2366 1.891616 GGAGGACTCCGAGTTCACC 59.108 63.158 9.60 8.50 40.36 4.02
1557 2534 6.546056 GCTTGATTAGAAGCGAATTGTTTC 57.454 37.500 0.00 0.00 39.10 2.78
1623 2600 5.481122 TCATGGAATTGTCATGTGGTGATTT 59.519 36.000 14.39 0.00 41.79 2.17
1801 2830 0.105964 TGGTCAGTTCGTTGGGTCAG 59.894 55.000 0.00 0.00 0.00 3.51
1807 2836 0.666374 GTTCGTTGGGTCAGGGTTTG 59.334 55.000 0.00 0.00 0.00 2.93
1808 2837 0.466555 TTCGTTGGGTCAGGGTTTGG 60.467 55.000 0.00 0.00 0.00 3.28
1816 2845 0.704664 GTCAGGGTTTGGGGGAGAAT 59.295 55.000 0.00 0.00 0.00 2.40
1869 2898 5.105756 GGAGAATGGTTTCGGAATTTGTCAT 60.106 40.000 0.00 0.00 36.93 3.06
1910 2939 1.153628 GACGGCGTTACCAGCTGAT 60.154 57.895 17.39 0.00 43.29 2.90
1911 2940 0.101759 GACGGCGTTACCAGCTGATA 59.898 55.000 17.39 0.00 43.29 2.15
1936 2969 3.935203 CACGAAATGCAGGTTCAGTAGAT 59.065 43.478 12.09 0.00 0.00 1.98
1937 2970 4.393062 CACGAAATGCAGGTTCAGTAGATT 59.607 41.667 12.09 0.00 0.00 2.40
1938 2971 5.003804 ACGAAATGCAGGTTCAGTAGATTT 58.996 37.500 12.09 0.00 0.00 2.17
1939 2972 5.122396 ACGAAATGCAGGTTCAGTAGATTTC 59.878 40.000 12.09 0.00 0.00 2.17
1940 2973 5.122239 CGAAATGCAGGTTCAGTAGATTTCA 59.878 40.000 12.09 0.00 30.96 2.69
1941 2974 6.348458 CGAAATGCAGGTTCAGTAGATTTCAA 60.348 38.462 12.09 0.00 30.96 2.69
1942 2975 5.886960 ATGCAGGTTCAGTAGATTTCAAC 57.113 39.130 0.00 0.00 0.00 3.18
1943 2976 3.745975 TGCAGGTTCAGTAGATTTCAACG 59.254 43.478 0.00 0.00 0.00 4.10
1944 2977 3.424962 GCAGGTTCAGTAGATTTCAACGC 60.425 47.826 0.00 0.00 0.00 4.84
1945 2978 2.993899 AGGTTCAGTAGATTTCAACGCG 59.006 45.455 3.53 3.53 0.00 6.01
1946 2979 2.093783 GGTTCAGTAGATTTCAACGCGG 59.906 50.000 12.47 0.00 0.00 6.46
1947 2980 2.991190 GTTCAGTAGATTTCAACGCGGA 59.009 45.455 12.47 0.00 0.00 5.54
1948 2981 2.876091 TCAGTAGATTTCAACGCGGAG 58.124 47.619 12.47 1.53 0.00 4.63
1949 2982 1.927174 CAGTAGATTTCAACGCGGAGG 59.073 52.381 12.47 0.00 0.00 4.30
1950 2983 1.822990 AGTAGATTTCAACGCGGAGGA 59.177 47.619 12.47 0.99 0.00 3.71
1951 2984 2.232941 AGTAGATTTCAACGCGGAGGAA 59.767 45.455 12.47 8.24 0.00 3.36
1952 2985 2.178912 AGATTTCAACGCGGAGGAAA 57.821 45.000 19.36 19.36 35.27 3.13
1965 2998 0.519077 GAGGAAAAACTGCTCCTGCG 59.481 55.000 0.00 0.00 42.34 5.18
1971 3004 0.247736 AAACTGCTCCTGCGACCTAG 59.752 55.000 0.00 0.00 43.34 3.02
1976 3009 2.442272 TCCTGCGACCTAGGCTCC 60.442 66.667 9.30 0.00 35.23 4.70
1977 3010 3.541713 CCTGCGACCTAGGCTCCC 61.542 72.222 9.30 0.00 0.00 4.30
1978 3011 2.443016 CTGCGACCTAGGCTCCCT 60.443 66.667 9.30 0.00 37.71 4.20
1979 3012 2.442272 TGCGACCTAGGCTCCCTC 60.442 66.667 9.30 0.00 34.61 4.30
1984 3017 2.522193 CCTAGGCTCCCTCGACCC 60.522 72.222 0.00 0.00 34.61 4.46
2040 4037 1.690985 CCCAAGTCCCCTCTCCTCC 60.691 68.421 0.00 0.00 0.00 4.30
2047 4044 2.018086 CCCCTCTCCTCCCTCCTCT 61.018 68.421 0.00 0.00 0.00 3.69
2159 4173 3.403558 GGGCCCTTCTCTTCGGCT 61.404 66.667 17.04 0.00 42.58 5.52
2161 4175 2.124942 GCCCTTCTCTTCGGCTGG 60.125 66.667 0.00 0.00 39.70 4.85
2255 4269 4.579384 CACGGCTGGTGGTGGGTT 62.579 66.667 0.00 0.00 43.16 4.11
2413 4456 2.124236 TGGCGTTTTTCGGTGGGT 60.124 55.556 0.00 0.00 40.26 4.51
2417 4460 2.482333 CGTTTTTCGGTGGGTGGCA 61.482 57.895 0.00 0.00 35.71 4.92
2418 4461 1.801309 CGTTTTTCGGTGGGTGGCAT 61.801 55.000 0.00 0.00 35.71 4.40
2419 4462 0.319469 GTTTTTCGGTGGGTGGCATG 60.319 55.000 0.00 0.00 0.00 4.06
2420 4463 1.467678 TTTTTCGGTGGGTGGCATGG 61.468 55.000 0.00 0.00 0.00 3.66
2421 4464 3.877344 TTTCGGTGGGTGGCATGGG 62.877 63.158 0.00 0.00 0.00 4.00
2423 4466 4.676951 CGGTGGGTGGCATGGGTT 62.677 66.667 0.00 0.00 0.00 4.11
2424 4467 2.996734 GGTGGGTGGCATGGGTTG 60.997 66.667 0.00 0.00 0.00 3.77
2425 4468 2.996734 GTGGGTGGCATGGGTTGG 60.997 66.667 0.00 0.00 0.00 3.77
2426 4469 4.313707 TGGGTGGCATGGGTTGGG 62.314 66.667 0.00 0.00 0.00 4.12
2431 4474 4.702274 GGCATGGGTTGGGGCACT 62.702 66.667 0.00 0.00 0.00 4.40
2432 4475 3.384532 GCATGGGTTGGGGCACTG 61.385 66.667 0.00 0.00 0.00 3.66
2433 4476 2.681064 CATGGGTTGGGGCACTGG 60.681 66.667 0.00 0.00 0.00 4.00
2434 4477 4.702274 ATGGGTTGGGGCACTGGC 62.702 66.667 0.00 0.00 40.13 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.653679 CGCTTCGACAGAAACAACACG 60.654 52.381 0.00 0.00 35.71 4.49
203 204 6.267817 CCACATATGCCAAACTGATTTACTG 58.732 40.000 1.58 0.00 0.00 2.74
264 505 1.807377 CGGGGAACAACAGTACACGTT 60.807 52.381 0.00 0.00 0.00 3.99
265 506 0.249573 CGGGGAACAACAGTACACGT 60.250 55.000 0.00 0.00 0.00 4.49
266 507 1.562575 GCGGGGAACAACAGTACACG 61.563 60.000 0.00 0.00 0.00 4.49
267 508 0.533308 TGCGGGGAACAACAGTACAC 60.533 55.000 0.00 0.00 0.00 2.90
268 509 0.180642 TTGCGGGGAACAACAGTACA 59.819 50.000 0.00 0.00 0.00 2.90
269 510 0.589708 GTTGCGGGGAACAACAGTAC 59.410 55.000 1.95 0.00 45.35 2.73
270 511 3.009612 GTTGCGGGGAACAACAGTA 57.990 52.632 1.95 0.00 45.35 2.74
271 512 3.836151 GTTGCGGGGAACAACAGT 58.164 55.556 1.95 0.00 45.35 3.55
274 515 2.011540 TTTTTGTTGCGGGGAACAAC 57.988 45.000 16.46 4.13 43.76 3.32
292 533 6.809689 GCAAAGTAACAACAGTACACCTTTTT 59.190 34.615 0.00 0.00 0.00 1.94
293 534 6.152154 AGCAAAGTAACAACAGTACACCTTTT 59.848 34.615 0.00 0.00 0.00 2.27
294 535 5.650703 AGCAAAGTAACAACAGTACACCTTT 59.349 36.000 0.00 0.00 0.00 3.11
297 538 6.425721 TCATAGCAAAGTAACAACAGTACACC 59.574 38.462 0.00 0.00 0.00 4.16
339 580 4.625963 ACCCTTAGCTAGTTTCCAGAGAT 58.374 43.478 0.00 0.00 0.00 2.75
465 1084 5.950544 TTGCTAAGATTTAGACCTGCCTA 57.049 39.130 0.21 0.00 0.00 3.93
581 1361 1.400846 CGCTTGATGCTGCAAGAGAAT 59.599 47.619 18.96 0.00 46.31 2.40
584 1364 0.179197 CACGCTTGATGCTGCAAGAG 60.179 55.000 18.96 17.74 46.31 2.85
586 1366 0.453950 GACACGCTTGATGCTGCAAG 60.454 55.000 6.36 12.79 46.18 4.01
590 1370 1.128136 CTTCTGACACGCTTGATGCTG 59.872 52.381 0.00 0.00 40.11 4.41
592 1372 1.432514 TCTTCTGACACGCTTGATGC 58.567 50.000 0.00 0.00 38.57 3.91
593 1373 2.159734 GCTTCTTCTGACACGCTTGATG 60.160 50.000 0.00 0.00 0.00 3.07
594 1374 2.072298 GCTTCTTCTGACACGCTTGAT 58.928 47.619 0.00 0.00 0.00 2.57
595 1375 1.502231 GCTTCTTCTGACACGCTTGA 58.498 50.000 0.00 0.00 0.00 3.02
597 1377 0.032130 TCGCTTCTTCTGACACGCTT 59.968 50.000 0.00 0.00 0.00 4.68
598 1378 0.387878 CTCGCTTCTTCTGACACGCT 60.388 55.000 0.00 0.00 0.00 5.07
599 1379 1.950098 GCTCGCTTCTTCTGACACGC 61.950 60.000 0.00 0.00 0.00 5.34
600 1380 0.664466 TGCTCGCTTCTTCTGACACG 60.664 55.000 0.00 0.00 0.00 4.49
601 1381 1.658095 GATGCTCGCTTCTTCTGACAC 59.342 52.381 0.00 0.00 0.00 3.67
603 1383 0.919981 CGATGCTCGCTTCTTCTGAC 59.080 55.000 3.75 0.00 31.14 3.51
605 1385 0.644331 CACGATGCTCGCTTCTTCTG 59.356 55.000 5.63 0.00 45.12 3.02
607 1387 0.458543 TCCACGATGCTCGCTTCTTC 60.459 55.000 5.63 0.00 45.12 2.87
608 1388 0.737715 GTCCACGATGCTCGCTTCTT 60.738 55.000 5.63 0.00 45.12 2.52
609 1389 1.153745 GTCCACGATGCTCGCTTCT 60.154 57.895 5.63 0.00 45.12 2.85
610 1390 1.446099 TGTCCACGATGCTCGCTTC 60.446 57.895 5.63 0.00 45.12 3.86
611 1391 1.738099 GTGTCCACGATGCTCGCTT 60.738 57.895 5.63 0.00 45.12 4.68
612 1392 2.125912 GTGTCCACGATGCTCGCT 60.126 61.111 5.63 0.00 45.12 4.93
613 1393 1.811266 ATGTGTCCACGATGCTCGC 60.811 57.895 5.63 0.00 45.12 5.03
615 1395 1.709147 GCCATGTGTCCACGATGCTC 61.709 60.000 0.00 0.00 0.00 4.26
617 1397 2.764314 GGCCATGTGTCCACGATGC 61.764 63.158 0.00 0.00 0.00 3.91
618 1398 2.114670 GGGCCATGTGTCCACGATG 61.115 63.158 4.39 0.00 0.00 3.84
619 1399 1.925285 ATGGGCCATGTGTCCACGAT 61.925 55.000 20.49 0.00 32.90 3.73
621 1401 2.045045 ATGGGCCATGTGTCCACG 60.045 61.111 20.49 0.00 32.90 4.94
622 1402 1.754234 GGATGGGCCATGTGTCCAC 60.754 63.158 26.77 7.21 36.34 4.02
623 1403 2.682846 GGATGGGCCATGTGTCCA 59.317 61.111 26.77 9.54 36.34 4.02
624 1404 2.123726 GGGATGGGCCATGTGTCC 60.124 66.667 26.77 19.73 38.95 4.02
625 1405 2.123726 GGGGATGGGCCATGTGTC 60.124 66.667 26.77 10.41 38.95 3.67
629 1409 4.837797 TTGCGGGGATGGGCCATG 62.838 66.667 26.77 10.75 38.95 3.66
630 1410 3.615480 TTTTGCGGGGATGGGCCAT 62.615 57.895 21.39 21.39 38.95 4.40
631 1411 3.835382 TTTTTGCGGGGATGGGCCA 62.835 57.895 9.61 9.61 38.95 5.36
632 1412 3.000233 TTTTTGCGGGGATGGGCC 61.000 61.111 0.00 0.00 0.00 5.80
633 1413 1.948721 CTCTTTTTGCGGGGATGGGC 61.949 60.000 0.00 0.00 0.00 5.36
634 1414 1.322538 CCTCTTTTTGCGGGGATGGG 61.323 60.000 0.00 0.00 0.00 4.00
635 1415 0.323360 TCCTCTTTTTGCGGGGATGG 60.323 55.000 0.00 0.00 0.00 3.51
637 1417 2.532250 ATTCCTCTTTTTGCGGGGAT 57.468 45.000 0.00 0.00 0.00 3.85
638 1418 2.302587 AATTCCTCTTTTTGCGGGGA 57.697 45.000 0.00 0.00 0.00 4.81
639 1419 2.159435 CGTAATTCCTCTTTTTGCGGGG 60.159 50.000 0.00 0.00 0.00 5.73
640 1420 2.486592 ACGTAATTCCTCTTTTTGCGGG 59.513 45.455 0.00 0.00 33.61 6.13
641 1421 3.824414 ACGTAATTCCTCTTTTTGCGG 57.176 42.857 0.00 0.00 33.61 5.69
642 1422 5.263185 CCATACGTAATTCCTCTTTTTGCG 58.737 41.667 0.00 0.00 35.12 4.85
693 1556 3.163594 CGCGTGATTTCTGGATTCAAAC 58.836 45.455 0.00 0.00 0.00 2.93
717 1580 4.209288 CCGATTGGCTAGTGATTAAACTCG 59.791 45.833 0.00 0.00 0.00 4.18
848 1711 3.303938 TGGAGGGTTTGATTTCTTGCAA 58.696 40.909 0.00 0.00 0.00 4.08
875 1738 6.585322 GCAGGCATTGATTTCTTGCTATAATC 59.415 38.462 0.00 0.00 36.62 1.75
924 1787 3.000727 GGTATATATGCACAAGGCCGTC 58.999 50.000 0.00 0.00 43.89 4.79
925 1788 2.370519 TGGTATATATGCACAAGGCCGT 59.629 45.455 0.00 0.00 43.89 5.68
926 1789 3.052455 TGGTATATATGCACAAGGCCG 57.948 47.619 0.00 0.00 43.89 6.13
927 1790 4.848357 AGATGGTATATATGCACAAGGCC 58.152 43.478 0.00 0.00 43.89 5.19
929 1792 7.615403 ACAGTAGATGGTATATATGCACAAGG 58.385 38.462 3.10 0.00 0.00 3.61
935 1799 8.520351 TGTGTGTACAGTAGATGGTATATATGC 58.480 37.037 0.00 0.00 31.91 3.14
952 1816 1.003112 GGCCGGGATTGTGTGTACA 60.003 57.895 2.18 0.00 34.31 2.90
984 1848 2.336667 CCCATGGTTTTCGATGTTTGC 58.663 47.619 11.73 0.00 34.85 3.68
1107 1979 1.370172 GTAGTCGTAGCCGATGCCG 60.370 63.158 0.00 0.00 46.30 5.69
1243 2121 3.554342 CTCCGAGGCCATGAGGGG 61.554 72.222 5.01 0.00 37.04 4.79
1289 2167 1.372499 TACAACTGGTCGCAGTCGC 60.372 57.895 0.00 0.00 33.73 5.19
1302 2180 2.048503 ACGGCCAGCGAGTACAAC 60.049 61.111 2.24 0.00 0.00 3.32
1470 2348 0.898789 TGGTGAACTCGGAGTCCTCC 60.899 60.000 11.71 9.85 46.18 4.30
1488 2366 1.478510 AGCACGATGTAGACCTCCTTG 59.521 52.381 0.00 0.00 0.00 3.61
1505 2383 1.947456 ACGAGTGCACTATATCGAGCA 59.053 47.619 26.78 0.00 38.50 4.26
1557 2534 3.193263 CCAGATGAACGGATGAACTGAG 58.807 50.000 0.00 0.00 0.00 3.35
1590 2567 5.964958 TGACAATTCCATGAGAAAACTCC 57.035 39.130 0.00 0.00 38.21 3.85
1801 2830 2.453521 GTACAATTCTCCCCCAAACCC 58.546 52.381 0.00 0.00 0.00 4.11
1807 2836 2.027469 ACTGTTCGTACAATTCTCCCCC 60.027 50.000 0.00 0.00 32.92 5.40
1808 2837 3.329929 ACTGTTCGTACAATTCTCCCC 57.670 47.619 0.00 0.00 32.92 4.81
1869 2898 2.572340 TCTCCCCATCTGGATTTTCCA 58.428 47.619 0.00 0.00 45.98 3.53
1936 2969 2.018515 AGTTTTTCCTCCGCGTTGAAA 58.981 42.857 4.92 8.07 0.00 2.69
1937 2970 1.332375 CAGTTTTTCCTCCGCGTTGAA 59.668 47.619 4.92 1.32 0.00 2.69
1938 2971 0.941542 CAGTTTTTCCTCCGCGTTGA 59.058 50.000 4.92 0.00 0.00 3.18
1939 2972 0.660300 GCAGTTTTTCCTCCGCGTTG 60.660 55.000 4.92 0.00 0.00 4.10
1940 2973 0.818040 AGCAGTTTTTCCTCCGCGTT 60.818 50.000 4.92 0.00 0.00 4.84
1941 2974 1.227853 AGCAGTTTTTCCTCCGCGT 60.228 52.632 4.92 0.00 0.00 6.01
1942 2975 1.497722 GAGCAGTTTTTCCTCCGCG 59.502 57.895 0.00 0.00 0.00 6.46
1943 2976 1.876664 GGAGCAGTTTTTCCTCCGC 59.123 57.895 0.00 0.00 36.17 5.54
1945 2978 0.884514 GCAGGAGCAGTTTTTCCTCC 59.115 55.000 0.00 0.00 41.86 4.30
1946 2979 0.519077 CGCAGGAGCAGTTTTTCCTC 59.481 55.000 0.00 0.00 41.86 3.71
1947 2980 0.108585 TCGCAGGAGCAGTTTTTCCT 59.891 50.000 0.00 0.00 44.59 3.36
1948 2981 0.238553 GTCGCAGGAGCAGTTTTTCC 59.761 55.000 0.00 0.00 42.27 3.13
1949 2982 0.238553 GGTCGCAGGAGCAGTTTTTC 59.761 55.000 0.00 0.00 42.27 2.29
1950 2983 0.179018 AGGTCGCAGGAGCAGTTTTT 60.179 50.000 0.00 0.00 43.12 1.94
1951 2984 0.685097 TAGGTCGCAGGAGCAGTTTT 59.315 50.000 0.00 0.00 43.12 2.43
1952 2985 0.247736 CTAGGTCGCAGGAGCAGTTT 59.752 55.000 0.00 0.00 43.12 2.66
1962 2995 2.442272 GAGGGAGCCTAGGTCGCA 60.442 66.667 21.78 0.00 43.69 5.10
1965 2998 1.829096 GGTCGAGGGAGCCTAGGTC 60.829 68.421 11.31 6.72 31.76 3.85
1976 3009 2.760385 GGAGAGGGTGGGTCGAGG 60.760 72.222 0.00 0.00 0.00 4.63
1977 3010 2.760385 GGGAGAGGGTGGGTCGAG 60.760 72.222 0.00 0.00 0.00 4.04
1978 3011 3.273654 AGGGAGAGGGTGGGTCGA 61.274 66.667 0.00 0.00 0.00 4.20
1979 3012 2.760385 GAGGGAGAGGGTGGGTCG 60.760 72.222 0.00 0.00 0.00 4.79
2029 3394 1.598856 AAGAGGAGGGAGGAGAGGGG 61.599 65.000 0.00 0.00 0.00 4.79
2031 4028 0.105709 GGAAGAGGAGGGAGGAGAGG 60.106 65.000 0.00 0.00 0.00 3.69
2033 4030 1.595058 GGGGAAGAGGAGGGAGGAGA 61.595 65.000 0.00 0.00 0.00 3.71
2239 4253 4.579384 CAACCCACCACCAGCCGT 62.579 66.667 0.00 0.00 0.00 5.68
2355 4389 4.481112 CCAAGCCGATGTTGCGCC 62.481 66.667 4.18 0.00 0.00 6.53
2391 4434 0.871722 CACCGAAAAACGCCAGATCA 59.128 50.000 0.00 0.00 41.07 2.92
2401 4444 1.467678 CCATGCCACCCACCGAAAAA 61.468 55.000 0.00 0.00 0.00 1.94
2417 4460 4.702274 GCCAGTGCCCCAACCCAT 62.702 66.667 0.00 0.00 0.00 4.00
2447 4490 4.335647 AACCCACAGCCGGAGCAG 62.336 66.667 5.05 0.00 43.56 4.24
2448 4491 4.641645 CAACCCACAGCCGGAGCA 62.642 66.667 5.05 0.00 43.56 4.26
2450 4493 4.722700 CCCAACCCACAGCCGGAG 62.723 72.222 5.05 0.00 0.00 4.63
2455 4498 4.603535 AGTGCCCCAACCCACAGC 62.604 66.667 0.00 0.00 34.48 4.40
2456 4499 2.598394 CAGTGCCCCAACCCACAG 60.598 66.667 0.00 0.00 34.48 3.66
2457 4500 4.217210 CCAGTGCCCCAACCCACA 62.217 66.667 0.00 0.00 34.48 4.17


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

AutoCloner maintained by Alex Coulton.