Multiple sequence alignment - TraesCS4B01G315500

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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 TraesCS4B01G315500 chr4B 100.000 2347 0 0 1 2347 604887307 604889653 0.000000e+00 4335.0
1 TraesCS4B01G315500 chr4B 87.546 273 24 3 1974 2244 604904091 604904355 8.150000e-80 307.0
2 TraesCS4B01G315500 chr4B 92.558 215 13 3 68 282 604903885 604904096 2.930000e-79 305.0
3 TraesCS4B01G315500 chr4B 96.000 50 2 0 1926 1975 424024567 424024616 5.380000e-12 82.4
4 TraesCS4B01G315500 chr4B 95.918 49 2 0 1926 1974 591260122 591260170 1.930000e-11 80.5
5 TraesCS4B01G315500 chr3B 94.081 794 44 3 613 1404 724187671 724186879 0.000000e+00 1203.0
6 TraesCS4B01G315500 chr3B 90.962 343 26 5 273 612 724188111 724187771 7.640000e-125 457.0
7 TraesCS4B01G315500 chr3B 90.977 133 6 5 1478 1609 724186871 724186744 8.620000e-40 174.0
8 TraesCS4B01G315500 chr3B 85.926 135 15 3 1689 1822 724186551 724186420 8.740000e-30 141.0
9 TraesCS4B01G315500 chr3D 95.315 747 33 2 618 1362 547002071 547001325 0.000000e+00 1184.0
10 TraesCS4B01G315500 chr3D 92.391 276 17 3 357 629 547002739 547002465 7.860000e-105 390.0
11 TraesCS4B01G315500 chr3D 94.545 165 6 2 1478 1641 547001245 547001083 3.870000e-63 252.0
12 TraesCS4B01G315500 chr3D 93.458 107 6 1 2241 2347 19191228 19191123 8.680000e-35 158.0
13 TraesCS4B01G315500 chr3D 93.458 107 6 1 2241 2347 610418508 610418613 8.680000e-35 158.0
14 TraesCS4B01G315500 chr3D 94.937 79 2 2 1404 1480 172830746 172830824 3.170000e-24 122.0
15 TraesCS4B01G315500 chr3D 93.902 82 3 2 1404 1483 219572259 219572178 3.170000e-24 122.0
16 TraesCS4B01G315500 chr3A 93.478 736 40 4 618 1351 683549006 683548277 0.000000e+00 1086.0
17 TraesCS4B01G315500 chr3A 89.538 822 40 19 586 1401 24199793 24200574 0.000000e+00 1000.0
18 TraesCS4B01G315500 chr3A 93.377 604 36 4 751 1351 683681868 683681266 0.000000e+00 891.0
19 TraesCS4B01G315500 chr3A 93.296 358 19 5 273 628 683684049 683683695 7.430000e-145 523.0
20 TraesCS4B01G315500 chr3A 93.084 347 16 4 273 612 683549755 683549410 3.480000e-138 501.0
21 TraesCS4B01G315500 chr3A 93.030 330 21 2 273 601 24198790 24199118 4.540000e-132 481.0
22 TraesCS4B01G315500 chr3A 92.025 163 9 4 1478 1640 24200585 24200743 2.350000e-55 226.0
23 TraesCS4B01G315500 chr3A 89.051 137 11 2 1674 1810 683548029 683547897 1.440000e-37 167.0
24 TraesCS4B01G315500 chr3A 88.806 134 13 2 618 751 683683287 683683156 1.870000e-36 163.0
25 TraesCS4B01G315500 chr3A 85.034 147 18 2 1674 1820 683681020 683680878 1.880000e-31 147.0
26 TraesCS4B01G315500 chr3A 94.937 79 2 2 1404 1480 436662142 436662064 3.170000e-24 122.0
27 TraesCS4B01G315500 chr2A 91.149 757 37 7 653 1404 5291440 5290709 0.000000e+00 1000.0
28 TraesCS4B01G315500 chr2A 90.036 281 23 3 273 551 5292196 5291919 2.220000e-95 359.0
29 TraesCS4B01G315500 chr2A 93.082 159 10 1 1478 1636 5290701 5290544 5.040000e-57 231.0
30 TraesCS4B01G315500 chr2A 87.821 156 15 3 1821 1976 5290337 5290186 1.850000e-41 180.0
31 TraesCS4B01G315500 chr4D 95.652 276 11 1 1 276 478270624 478270898 2.140000e-120 442.0
32 TraesCS4B01G315500 chr4D 94.909 275 13 1 1974 2247 478270898 478271172 1.670000e-116 429.0
33 TraesCS4B01G315500 chr4D 92.364 275 19 2 1975 2247 478279284 478279558 7.860000e-105 390.0
34 TraesCS4B01G315500 chr4D 91.628 215 15 3 68 282 478279077 478279288 6.340000e-76 294.0
35 TraesCS4B01G315500 chr4A 90.106 283 24 4 1 282 684969897 684970176 4.770000e-97 364.0
36 TraesCS4B01G315500 chr4A 92.095 253 18 2 1997 2247 684970186 684970438 2.870000e-94 355.0
37 TraesCS4B01G315500 chr2D 95.327 107 5 0 2241 2347 328310543 328310649 1.120000e-38 171.0
38 TraesCS4B01G315500 chr2D 93.458 107 6 1 2241 2347 606669571 606669676 8.680000e-35 158.0
39 TraesCS4B01G315500 chr1D 94.393 107 5 1 2241 2347 307329920 307329815 1.870000e-36 163.0
40 TraesCS4B01G315500 chr1D 93.902 82 3 2 1404 1483 473933009 473932928 3.170000e-24 122.0
41 TraesCS4B01G315500 chr6A 93.458 107 6 1 2241 2347 46780206 46780311 8.680000e-35 158.0
42 TraesCS4B01G315500 chr1B 93.458 107 6 1 2241 2347 481075168 481075273 8.680000e-35 158.0
43 TraesCS4B01G315500 chr1B 92.857 84 4 2 1404 1485 426463896 426463813 1.140000e-23 121.0
44 TraesCS4B01G315500 chr1B 96.000 50 2 0 1929 1978 299716742 299716693 5.380000e-12 82.4
45 TraesCS4B01G315500 chr1B 96.000 50 2 0 1927 1976 480961736 480961687 5.380000e-12 82.4
46 TraesCS4B01G315500 chr1A 93.458 107 6 1 2241 2347 8304861 8304966 8.680000e-35 158.0
47 TraesCS4B01G315500 chr1A 93.458 107 6 1 2241 2347 27221125 27221020 8.680000e-35 158.0
48 TraesCS4B01G315500 chr5D 92.222 90 3 4 1404 1490 225253192 225253280 8.810000e-25 124.0
49 TraesCS4B01G315500 chrUn 92.771 83 4 2 1404 1484 37006441 37006359 4.100000e-23 119.0
50 TraesCS4B01G315500 chrUn 92.771 83 4 2 1404 1484 38258662 38258580 4.100000e-23 119.0
51 TraesCS4B01G315500 chrUn 92.771 83 4 2 1404 1484 196709568 196709650 4.100000e-23 119.0
52 TraesCS4B01G315500 chr7A 97.872 47 1 0 1929 1975 689369222 689369268 5.380000e-12 82.4
53 TraesCS4B01G315500 chr7A 95.745 47 2 0 1929 1975 251741191 251741237 2.500000e-10 76.8
54 TraesCS4B01G315500 chr6B 97.872 47 1 0 1929 1975 97593793 97593839 5.380000e-12 82.4
55 TraesCS4B01G315500 chr7D 92.308 52 4 0 1925 1976 562414945 562414996 9.000000e-10 75.0


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 TraesCS4B01G315500 chr4B 604887307 604889653 2346 False 4335.000000 4335 100.000000 1 2347 1 chr4B.!!$F3 2346
1 TraesCS4B01G315500 chr3B 724186420 724188111 1691 True 493.750000 1203 90.486500 273 1822 4 chr3B.!!$R1 1549
2 TraesCS4B01G315500 chr3D 547001083 547002739 1656 True 608.666667 1184 94.083667 357 1641 3 chr3D.!!$R3 1284
3 TraesCS4B01G315500 chr3A 683547897 683549755 1858 True 584.666667 1086 91.871000 273 1810 3 chr3A.!!$R2 1537
4 TraesCS4B01G315500 chr3A 24198790 24200743 1953 False 569.000000 1000 91.531000 273 1640 3 chr3A.!!$F1 1367
5 TraesCS4B01G315500 chr3A 683680878 683684049 3171 True 431.000000 891 90.128250 273 1820 4 chr3A.!!$R3 1547
6 TraesCS4B01G315500 chr2A 5290186 5292196 2010 True 442.500000 1000 90.522000 273 1976 4 chr2A.!!$R1 1703
7 TraesCS4B01G315500 chr4D 478270624 478271172 548 False 435.500000 442 95.280500 1 2247 2 chr4D.!!$F1 2246
8 TraesCS4B01G315500 chr4A 684969897 684970438 541 False 359.500000 364 91.100500 1 2247 2 chr4A.!!$F1 2246

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
212 214 1.418637 AGTTCGCCAGACCAGGTTTTA 59.581 47.619 0.0 0.0 0.0 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 4336 0.034767 TGCCCTCTCAAGCCATCAAG 60.035 55.0 0.0 0.0 0.0 3.02 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
133 135 7.871853 TGGCTTGACATTTCTAGAACTAAAAC 58.128 34.615 4.18 0.00 0.00 2.43
135 137 8.568794 GGCTTGACATTTCTAGAACTAAAACTT 58.431 33.333 4.18 0.00 0.00 2.66
173 175 6.670464 TGTGACCCTACAATGGATTTAGACTA 59.330 38.462 0.00 0.00 0.00 2.59
181 183 6.352516 ACAATGGATTTAGACTAGGCAAGAG 58.647 40.000 0.00 0.00 0.00 2.85
212 214 1.418637 AGTTCGCCAGACCAGGTTTTA 59.581 47.619 0.00 0.00 0.00 1.52
246 248 2.946785 CCTCGACCAGAACCCTAGTAT 58.053 52.381 0.00 0.00 0.00 2.12
276 278 6.925610 TGTGTTCCTCTTCATTATATGCAC 57.074 37.500 0.00 0.00 0.00 4.57
277 279 6.653020 TGTGTTCCTCTTCATTATATGCACT 58.347 36.000 0.00 0.00 0.00 4.40
291 293 3.906649 CACTAGCTTGCGCTCGCG 61.907 66.667 9.73 6.98 45.15 5.87
316 318 4.926238 GGATATTCGCTCCTTGTGACATAG 59.074 45.833 0.00 0.00 34.56 2.23
406 413 3.138304 TCACCCTTCAGATTGTTGAACG 58.862 45.455 0.00 0.00 33.71 3.95
525 539 3.981212 ACATTAGGGCCTTGTTTAGCAT 58.019 40.909 13.45 0.00 0.00 3.79
558 574 2.104963 GGCCCTAAATCCCTACAGACTG 59.895 54.545 0.00 0.00 0.00 3.51
596 612 7.010160 TCCATTTTGATCTTAAGAACAGGGTT 58.990 34.615 14.24 0.00 0.00 4.11
620 1564 9.559958 GTTTGCCATCAATACATATATGCTAAC 57.440 33.333 12.79 5.31 31.33 2.34
672 1616 5.924356 TGAAAGGTTTGGGAGGAAATTTTC 58.076 37.500 0.24 0.24 0.00 2.29
1178 3415 4.156556 TGTTTGCTAATGGATGCAGAAGAC 59.843 41.667 0.00 0.00 40.46 3.01
1201 3438 2.019984 GGGATCTGATGGTTGTGAAGC 58.980 52.381 0.00 0.00 0.00 3.86
1213 3450 2.229675 TGTGAAGCTCATGATAGCCG 57.770 50.000 0.00 0.00 43.86 5.52
1370 3638 2.554806 ATGTCATTTCGTGCATGCTG 57.445 45.000 20.33 11.68 0.00 4.41
1397 3665 5.243954 TCGGTGCTATTGCTATGAGTCTATT 59.756 40.000 0.00 0.00 40.48 1.73
1401 3669 8.253810 GGTGCTATTGCTATGAGTCTATTCATA 58.746 37.037 0.00 0.00 36.75 2.15
1404 3672 9.868277 GCTATTGCTATGAGTCTATTCATAACT 57.132 33.333 0.00 0.00 39.02 2.24
1407 3675 9.926158 ATTGCTATGAGTCTATTCATAACTCTG 57.074 33.333 3.69 0.00 39.02 3.35
1409 3677 8.572185 TGCTATGAGTCTATTCATAACTCTGTC 58.428 37.037 3.69 0.00 39.02 3.51
1411 3679 9.891828 CTATGAGTCTATTCATAACTCTGTCAC 57.108 37.037 3.69 0.00 39.02 3.67
1412 3680 7.703058 TGAGTCTATTCATAACTCTGTCACA 57.297 36.000 3.69 0.00 40.07 3.58
1413 3681 8.298729 TGAGTCTATTCATAACTCTGTCACAT 57.701 34.615 3.69 0.00 40.07 3.21
1414 3682 9.408648 TGAGTCTATTCATAACTCTGTCACATA 57.591 33.333 3.69 0.00 40.07 2.29
1427 3695 9.871238 AACTCTGTCACATAATATAAGAACGTT 57.129 29.630 0.00 0.00 0.00 3.99
1428 3696 9.871238 ACTCTGTCACATAATATAAGAACGTTT 57.129 29.630 0.46 0.00 0.00 3.60
1443 3711 7.838771 AAGAACGTTTTTGACACTAGTTAGT 57.161 32.000 0.46 0.00 36.90 2.24
1467 3735 9.078753 AGTGTTAAAAACGTTCTTACATTTTGG 57.921 29.630 0.00 0.00 30.80 3.28
1468 3736 8.322428 GTGTTAAAAACGTTCTTACATTTTGGG 58.678 33.333 0.00 0.00 30.80 4.12
1469 3737 8.248945 TGTTAAAAACGTTCTTACATTTTGGGA 58.751 29.630 0.00 0.00 30.80 4.37
1470 3738 8.533965 GTTAAAAACGTTCTTACATTTTGGGAC 58.466 33.333 0.00 0.00 30.80 4.46
1471 3739 5.838531 AAACGTTCTTACATTTTGGGACA 57.161 34.783 0.00 0.00 0.00 4.02
1472 3740 5.432885 AACGTTCTTACATTTTGGGACAG 57.567 39.130 0.00 0.00 42.39 3.51
1473 3741 4.710324 ACGTTCTTACATTTTGGGACAGA 58.290 39.130 0.00 0.00 42.39 3.41
1474 3742 4.755123 ACGTTCTTACATTTTGGGACAGAG 59.245 41.667 0.00 0.00 42.39 3.35
1475 3743 4.154195 CGTTCTTACATTTTGGGACAGAGG 59.846 45.833 0.00 0.00 42.39 3.69
1476 3744 4.301072 TCTTACATTTTGGGACAGAGGG 57.699 45.455 0.00 0.00 42.39 4.30
1658 4070 5.576447 TTGAGAGAACAACCTTTTTCCAC 57.424 39.130 0.00 0.00 0.00 4.02
1659 4071 3.951680 TGAGAGAACAACCTTTTTCCACC 59.048 43.478 0.00 0.00 0.00 4.61
1660 4072 3.296854 AGAGAACAACCTTTTTCCACCC 58.703 45.455 0.00 0.00 0.00 4.61
1661 4073 2.028876 AGAACAACCTTTTTCCACCCG 58.971 47.619 0.00 0.00 0.00 5.28
1662 4074 0.462375 AACAACCTTTTTCCACCCGC 59.538 50.000 0.00 0.00 0.00 6.13
1663 4075 0.684805 ACAACCTTTTTCCACCCGCA 60.685 50.000 0.00 0.00 0.00 5.69
1664 4076 0.461961 CAACCTTTTTCCACCCGCAA 59.538 50.000 0.00 0.00 0.00 4.85
1665 4077 1.134670 CAACCTTTTTCCACCCGCAAA 60.135 47.619 0.00 0.00 0.00 3.68
1666 4078 1.196012 ACCTTTTTCCACCCGCAAAA 58.804 45.000 0.00 0.00 0.00 2.44
1667 4079 1.555533 ACCTTTTTCCACCCGCAAAAA 59.444 42.857 0.00 0.00 32.05 1.94
1708 4120 4.203076 GGGACGTGCGGCTACGAT 62.203 66.667 24.23 12.86 46.46 3.73
1713 4125 1.354155 CGTGCGGCTACGATCACTA 59.646 57.895 16.28 0.00 46.46 2.74
1822 4234 1.072159 GGCCCAGCCTGTATAGCAG 59.928 63.158 0.00 0.00 46.69 4.24
1830 4242 3.191903 CTGTATAGCAGGAGCAGCG 57.808 57.895 0.00 0.00 45.49 5.18
1831 4243 0.319383 CTGTATAGCAGGAGCAGCGG 60.319 60.000 0.00 0.00 45.49 5.52
1832 4244 1.666234 GTATAGCAGGAGCAGCGGC 60.666 63.158 0.00 0.00 45.49 6.53
1833 4245 2.872388 TATAGCAGGAGCAGCGGCC 61.872 63.158 4.82 0.00 45.49 6.13
1854 4266 2.760650 CCAGCCCATATAGCGATCTGTA 59.239 50.000 0.00 0.00 34.64 2.74
1886 4298 2.687370 GCTTTTGCAAATCGACCCAAT 58.313 42.857 13.65 0.00 46.58 3.16
1887 4299 2.412770 GCTTTTGCAAATCGACCCAATG 59.587 45.455 13.65 0.00 46.58 2.82
1889 4301 0.246086 TTGCAAATCGACCCAATGGC 59.754 50.000 0.00 0.00 33.59 4.40
1907 4319 6.936335 CCAATGGCCAAAAATTCTTAAACTCT 59.064 34.615 10.96 0.00 0.00 3.24
1909 4321 9.487790 CAATGGCCAAAAATTCTTAAACTCTTA 57.512 29.630 10.96 0.00 0.00 2.10
1923 4335 8.147058 TCTTAAACTCTTAGATCTGATGATGGC 58.853 37.037 5.18 0.00 32.19 4.40
1924 4336 4.888326 ACTCTTAGATCTGATGATGGCC 57.112 45.455 5.18 0.00 32.19 5.36
1925 4337 4.491675 ACTCTTAGATCTGATGATGGCCT 58.508 43.478 5.18 0.00 32.19 5.19
1926 4338 4.906664 ACTCTTAGATCTGATGATGGCCTT 59.093 41.667 5.18 0.00 32.19 4.35
1927 4339 5.221682 ACTCTTAGATCTGATGATGGCCTTG 60.222 44.000 5.18 0.00 32.19 3.61
1928 4340 4.903649 TCTTAGATCTGATGATGGCCTTGA 59.096 41.667 5.18 0.00 32.19 3.02
1929 4341 5.546887 TCTTAGATCTGATGATGGCCTTGAT 59.453 40.000 5.18 0.00 32.19 2.57
1930 4342 4.022413 AGATCTGATGATGGCCTTGATG 57.978 45.455 3.32 0.00 32.19 3.07
1931 4343 2.651382 TCTGATGATGGCCTTGATGG 57.349 50.000 3.32 0.00 39.35 3.51
1945 4357 1.153005 GATGGCTTGAGAGGGCAGG 60.153 63.158 0.00 0.00 42.26 4.85
2005 4417 8.950210 CCTAGCCCATGTATATTTGTCTATTTG 58.050 37.037 0.00 0.00 0.00 2.32
2024 4436 1.539388 TGCCATGGTTAGTTTCTTGCG 59.461 47.619 14.67 0.00 0.00 4.85
2040 4452 1.904287 TGCGGTTTAGCATCCTTTGT 58.096 45.000 0.00 0.00 42.92 2.83
2171 4584 6.300354 ACGTTTAGTTCCTTGAATTGACAG 57.700 37.500 0.00 0.00 0.00 3.51
2217 4631 6.173427 AGGGTTAGTTTGTTGCAATTGAAT 57.827 33.333 10.34 0.00 0.00 2.57
2221 4635 6.478344 GGTTAGTTTGTTGCAATTGAATGTCA 59.522 34.615 10.34 0.00 0.00 3.58
2254 4668 3.668596 ACACTTAAGTTGTGTTCGCAC 57.331 42.857 5.07 0.00 45.11 5.34
2267 4681 4.764322 CGCACACGAACACGTTAC 57.236 55.556 0.00 0.00 43.93 2.50
2268 4682 1.199859 CGCACACGAACACGTTACC 59.800 57.895 0.00 0.00 43.93 2.85
2269 4683 1.199859 GCACACGAACACGTTACCG 59.800 57.895 0.00 0.00 38.21 4.02
2282 4696 1.643810 CGTTACCGTTTACCTTCGACG 59.356 52.381 0.00 0.00 36.61 5.12
2283 4697 1.386748 GTTACCGTTTACCTTCGACGC 59.613 52.381 0.00 0.00 35.60 5.19
2284 4698 0.109319 TACCGTTTACCTTCGACGCC 60.109 55.000 0.00 0.00 35.60 5.68
2285 4699 2.438954 CCGTTTACCTTCGACGCCG 61.439 63.158 0.00 0.00 35.60 6.46
2286 4700 2.438954 CGTTTACCTTCGACGCCGG 61.439 63.158 0.00 0.00 36.24 6.13
2287 4701 2.096442 GTTTACCTTCGACGCCGGG 61.096 63.158 2.18 0.00 36.24 5.73
2288 4702 3.299524 TTTACCTTCGACGCCGGGG 62.300 63.158 18.33 18.33 36.24 5.73
2289 4703 4.738998 TACCTTCGACGCCGGGGA 62.739 66.667 27.23 0.00 36.24 4.81
2291 4705 4.891727 CCTTCGACGCCGGGGATG 62.892 72.222 27.23 16.39 36.24 3.51
2292 4706 3.833645 CTTCGACGCCGGGGATGA 61.834 66.667 27.23 18.48 36.24 2.92
2293 4707 3.151710 TTCGACGCCGGGGATGAT 61.152 61.111 27.23 1.36 36.24 2.45
2294 4708 3.439513 TTCGACGCCGGGGATGATG 62.440 63.158 27.23 9.46 36.24 3.07
2296 4710 4.545706 GACGCCGGGGATGATGCA 62.546 66.667 27.23 0.00 0.00 3.96
2297 4711 4.856801 ACGCCGGGGATGATGCAC 62.857 66.667 27.23 0.00 0.00 4.57
2301 4715 4.854924 CGGGGATGATGCACCGCA 62.855 66.667 8.56 0.00 44.86 5.69
2302 4716 2.903855 GGGGATGATGCACCGCAG 60.904 66.667 3.56 0.00 43.65 5.18
2303 4717 3.589881 GGGATGATGCACCGCAGC 61.590 66.667 0.00 0.00 45.81 5.25
2304 4718 2.515523 GGATGATGCACCGCAGCT 60.516 61.111 5.76 0.00 45.80 4.24
2305 4719 2.541120 GGATGATGCACCGCAGCTC 61.541 63.158 5.76 1.23 45.80 4.09
2306 4720 1.816679 GATGATGCACCGCAGCTCA 60.817 57.895 5.76 0.39 45.80 4.26
2307 4721 2.044832 GATGATGCACCGCAGCTCAC 62.045 60.000 5.76 0.00 45.80 3.51
2308 4722 3.857854 GATGCACCGCAGCTCACG 61.858 66.667 0.00 0.00 43.65 4.35
2309 4723 4.687215 ATGCACCGCAGCTCACGT 62.687 61.111 5.06 0.00 43.65 4.49
2312 4726 4.700365 CACCGCAGCTCACGTCGA 62.700 66.667 0.00 0.00 0.00 4.20
2313 4727 3.973516 ACCGCAGCTCACGTCGAA 61.974 61.111 0.00 0.00 0.00 3.71
2314 4728 3.175240 CCGCAGCTCACGTCGAAG 61.175 66.667 0.00 0.00 0.00 3.79
2315 4729 3.175240 CGCAGCTCACGTCGAAGG 61.175 66.667 0.00 0.00 0.00 3.46
2316 4730 2.258591 GCAGCTCACGTCGAAGGA 59.741 61.111 0.00 0.00 0.00 3.36
2317 4731 1.803519 GCAGCTCACGTCGAAGGAG 60.804 63.158 0.00 7.74 0.00 3.69
2318 4732 1.876664 CAGCTCACGTCGAAGGAGA 59.123 57.895 16.63 7.92 0.00 3.71
2319 4733 0.455295 CAGCTCACGTCGAAGGAGAC 60.455 60.000 16.63 10.11 37.76 3.36
2320 4734 1.153997 GCTCACGTCGAAGGAGACC 60.154 63.158 16.63 0.00 37.85 3.85
2321 4735 1.507174 CTCACGTCGAAGGAGACCC 59.493 63.158 0.00 0.00 37.85 4.46
2322 4736 2.178521 CACGTCGAAGGAGACCCG 59.821 66.667 0.00 0.00 37.85 5.28
2323 4737 2.282040 ACGTCGAAGGAGACCCGT 60.282 61.111 0.00 0.00 37.85 5.28
2324 4738 2.331132 ACGTCGAAGGAGACCCGTC 61.331 63.158 0.00 0.00 37.85 4.79
2325 4739 2.883621 GTCGAAGGAGACCCGTCC 59.116 66.667 0.00 0.00 37.62 4.79
2326 4740 2.749044 TCGAAGGAGACCCGTCCG 60.749 66.667 0.00 0.00 42.05 4.79
2327 4741 3.823330 CGAAGGAGACCCGTCCGG 61.823 72.222 0.00 0.00 42.05 5.14
2328 4742 2.362120 GAAGGAGACCCGTCCGGA 60.362 66.667 0.00 0.00 42.05 5.14
2329 4743 1.980772 GAAGGAGACCCGTCCGGAA 60.981 63.158 5.23 0.00 42.05 4.30
2330 4744 1.946475 GAAGGAGACCCGTCCGGAAG 61.946 65.000 5.23 8.49 42.05 3.46
2331 4745 4.144703 GGAGACCCGTCCGGAAGC 62.145 72.222 5.23 0.00 37.50 3.86
2332 4746 4.493747 GAGACCCGTCCGGAAGCG 62.494 72.222 5.23 6.61 37.50 4.68
2339 4753 4.424566 GTCCGGAAGCGCGGTACA 62.425 66.667 12.91 0.00 0.00 2.90
2340 4754 4.424566 TCCGGAAGCGCGGTACAC 62.425 66.667 12.91 6.37 0.00 2.90
2341 4755 4.728102 CCGGAAGCGCGGTACACA 62.728 66.667 12.91 0.00 0.00 3.72
2342 4756 3.179265 CGGAAGCGCGGTACACAG 61.179 66.667 12.91 3.49 0.00 3.66
2343 4757 2.813908 GGAAGCGCGGTACACAGG 60.814 66.667 12.91 0.00 0.00 4.00
2344 4758 3.488090 GAAGCGCGGTACACAGGC 61.488 66.667 12.91 0.00 0.00 4.85
2345 4759 4.308458 AAGCGCGGTACACAGGCA 62.308 61.111 12.91 0.00 0.00 4.75
2346 4760 3.818121 AAGCGCGGTACACAGGCAA 62.818 57.895 12.91 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 135 1.531149 GTCACACACCCGAATCACAAG 59.469 52.381 0.00 0.00 0.00 3.16
135 137 0.250124 GGTCACACACCCGAATCACA 60.250 55.000 0.00 0.00 39.69 3.58
173 175 0.764369 TGGTCACCTCACTCTTGCCT 60.764 55.000 0.00 0.00 0.00 4.75
181 183 1.668151 GGCGAACTGGTCACCTCAC 60.668 63.158 0.00 0.00 0.00 3.51
291 293 2.866762 GTCACAAGGAGCGAATATCCAC 59.133 50.000 0.00 0.00 39.47 4.02
347 350 9.017669 GTCGTACATTGAGTTCTAATTCGTAAT 57.982 33.333 0.00 0.00 0.00 1.89
493 507 7.158697 ACAAGGCCCTAATGTTCAAAATAAAC 58.841 34.615 0.00 0.00 0.00 2.01
506 520 6.373005 AAAAATGCTAAACAAGGCCCTAAT 57.627 33.333 0.00 0.00 0.00 1.73
596 612 8.949177 CAGTTAGCATATATGTATTGATGGCAA 58.051 33.333 14.14 0.00 38.60 4.52
1178 3415 3.286329 TCACAACCATCAGATCCCATG 57.714 47.619 0.00 0.00 0.00 3.66
1201 3438 1.270518 CCCAGGTTCGGCTATCATGAG 60.271 57.143 0.09 0.00 0.00 2.90
1213 3450 0.819582 CATGTTGCCATCCCAGGTTC 59.180 55.000 0.00 0.00 0.00 3.62
1370 3638 3.257393 CTCATAGCAATAGCACCGATCC 58.743 50.000 0.00 0.00 45.49 3.36
1401 3669 9.871238 AACGTTCTTATATTATGTGACAGAGTT 57.129 29.630 0.00 0.00 0.00 3.01
1417 3685 9.538508 ACTAACTAGTGTCAAAAACGTTCTTAT 57.461 29.630 0.00 0.00 34.72 1.73
1418 3686 8.810427 CACTAACTAGTGTCAAAAACGTTCTTA 58.190 33.333 0.00 0.00 46.51 2.10
1419 3687 7.681903 CACTAACTAGTGTCAAAAACGTTCTT 58.318 34.615 0.00 0.00 46.51 2.52
1420 3688 7.230466 CACTAACTAGTGTCAAAAACGTTCT 57.770 36.000 0.00 0.00 46.51 3.01
1449 3717 5.591067 TCTGTCCCAAAATGTAAGAACGTTT 59.409 36.000 0.46 0.00 44.83 3.60
1450 3718 5.127491 TCTGTCCCAAAATGTAAGAACGTT 58.873 37.500 0.00 0.00 36.36 3.99
1451 3719 4.710324 TCTGTCCCAAAATGTAAGAACGT 58.290 39.130 0.00 0.00 0.00 3.99
1452 3720 4.154195 CCTCTGTCCCAAAATGTAAGAACG 59.846 45.833 0.00 0.00 0.00 3.95
1453 3721 4.459337 CCCTCTGTCCCAAAATGTAAGAAC 59.541 45.833 0.00 0.00 0.00 3.01
1454 3722 4.508405 CCCCTCTGTCCCAAAATGTAAGAA 60.508 45.833 0.00 0.00 0.00 2.52
1455 3723 3.010138 CCCCTCTGTCCCAAAATGTAAGA 59.990 47.826 0.00 0.00 0.00 2.10
1456 3724 3.245264 ACCCCTCTGTCCCAAAATGTAAG 60.245 47.826 0.00 0.00 0.00 2.34
1457 3725 2.719705 ACCCCTCTGTCCCAAAATGTAA 59.280 45.455 0.00 0.00 0.00 2.41
1458 3726 2.354328 ACCCCTCTGTCCCAAAATGTA 58.646 47.619 0.00 0.00 0.00 2.29
1459 3727 1.158007 ACCCCTCTGTCCCAAAATGT 58.842 50.000 0.00 0.00 0.00 2.71
1460 3728 3.449746 TTACCCCTCTGTCCCAAAATG 57.550 47.619 0.00 0.00 0.00 2.32
1461 3729 4.692523 ATTTACCCCTCTGTCCCAAAAT 57.307 40.909 0.00 0.00 0.00 1.82
1462 3730 4.479156 AATTTACCCCTCTGTCCCAAAA 57.521 40.909 0.00 0.00 0.00 2.44
1463 3731 5.313772 TCTTAATTTACCCCTCTGTCCCAAA 59.686 40.000 0.00 0.00 0.00 3.28
1464 3732 4.853276 TCTTAATTTACCCCTCTGTCCCAA 59.147 41.667 0.00 0.00 0.00 4.12
1465 3733 4.440808 TCTTAATTTACCCCTCTGTCCCA 58.559 43.478 0.00 0.00 0.00 4.37
1466 3734 4.141459 CCTCTTAATTTACCCCTCTGTCCC 60.141 50.000 0.00 0.00 0.00 4.46
1467 3735 4.686396 GCCTCTTAATTTACCCCTCTGTCC 60.686 50.000 0.00 0.00 0.00 4.02
1468 3736 4.164413 AGCCTCTTAATTTACCCCTCTGTC 59.836 45.833 0.00 0.00 0.00 3.51
1469 3737 4.112331 AGCCTCTTAATTTACCCCTCTGT 58.888 43.478 0.00 0.00 0.00 3.41
1470 3738 4.410555 AGAGCCTCTTAATTTACCCCTCTG 59.589 45.833 0.00 0.00 0.00 3.35
1471 3739 4.636536 AGAGCCTCTTAATTTACCCCTCT 58.363 43.478 0.00 0.00 0.00 3.69
1472 3740 4.656575 AGAGAGCCTCTTAATTTACCCCTC 59.343 45.833 0.00 0.00 37.60 4.30
1473 3741 4.636536 AGAGAGCCTCTTAATTTACCCCT 58.363 43.478 0.00 0.00 37.60 4.79
1474 3742 6.689663 ATAGAGAGCCTCTTAATTTACCCC 57.310 41.667 9.58 0.00 41.50 4.95
1475 3743 8.191534 TGTATAGAGAGCCTCTTAATTTACCC 57.808 38.462 9.58 0.00 41.50 3.69
1476 3744 9.646427 CATGTATAGAGAGCCTCTTAATTTACC 57.354 37.037 9.58 0.00 41.50 2.85
1636 3971 4.401202 GGTGGAAAAAGGTTGTTCTCTCAA 59.599 41.667 0.00 0.00 0.00 3.02
1668 4080 5.744666 TCGATCTCGTGGAAAAAGTTTTT 57.255 34.783 13.35 13.35 40.80 1.94
1669 4081 5.344207 CTCGATCTCGTGGAAAAAGTTTT 57.656 39.130 0.00 0.00 40.80 2.43
1670 4082 4.992381 CTCGATCTCGTGGAAAAAGTTT 57.008 40.909 0.00 0.00 40.80 2.66
1680 4092 1.062685 CACGTCCCTCGATCTCGTG 59.937 63.158 14.37 14.37 43.77 4.35
1681 4093 2.762234 GCACGTCCCTCGATCTCGT 61.762 63.158 0.00 0.00 42.86 4.18
1688 4100 4.849329 GTAGCCGCACGTCCCTCG 62.849 72.222 0.00 0.00 46.00 4.63
1726 4138 2.036387 TGTCCAAGAGACCAACGAGAA 58.964 47.619 0.00 0.00 45.68 2.87
1727 4139 1.699730 TGTCCAAGAGACCAACGAGA 58.300 50.000 0.00 0.00 45.68 4.04
1728 4140 2.232452 AGATGTCCAAGAGACCAACGAG 59.768 50.000 0.00 0.00 45.68 4.18
1729 4141 2.248248 AGATGTCCAAGAGACCAACGA 58.752 47.619 0.00 0.00 45.68 3.85
1781 4193 3.445096 GCTGCTCCTGTAACAAAATGGAT 59.555 43.478 0.00 0.00 0.00 3.41
1813 4225 1.742146 CCGCTGCTCCTGCTATACA 59.258 57.895 0.00 0.00 40.48 2.29
1815 4227 2.737180 GCCGCTGCTCCTGCTATA 59.263 61.111 0.00 0.00 40.48 1.31
1831 4243 0.462759 GATCGCTATATGGGCTGGGC 60.463 60.000 0.00 0.00 0.00 5.36
1832 4244 1.134580 CAGATCGCTATATGGGCTGGG 60.135 57.143 0.00 0.00 0.00 4.45
1833 4245 1.552337 ACAGATCGCTATATGGGCTGG 59.448 52.381 0.00 0.00 0.00 4.85
1834 4246 3.445450 ACTACAGATCGCTATATGGGCTG 59.555 47.826 0.00 0.00 0.00 4.85
1835 4247 3.702792 ACTACAGATCGCTATATGGGCT 58.297 45.455 0.00 0.00 0.00 5.19
1836 4248 4.457834 AACTACAGATCGCTATATGGGC 57.542 45.455 0.00 0.00 0.00 5.36
1837 4249 6.761099 AGTAACTACAGATCGCTATATGGG 57.239 41.667 0.00 0.00 0.00 4.00
1838 4250 7.903946 CGTAAGTAACTACAGATCGCTATATGG 59.096 40.741 0.00 0.00 0.00 2.74
1839 4251 8.654215 TCGTAAGTAACTACAGATCGCTATATG 58.346 37.037 0.00 0.00 39.48 1.78
1840 4252 8.768957 TCGTAAGTAACTACAGATCGCTATAT 57.231 34.615 0.00 0.00 39.48 0.86
1854 4266 5.744666 TTTGCAAAAGCTCGTAAGTAACT 57.255 34.783 10.02 0.00 39.48 2.24
1881 4293 6.003326 AGTTTAAGAATTTTTGGCCATTGGG 58.997 36.000 6.09 0.00 37.18 4.12
1886 4298 8.472007 TCTAAGAGTTTAAGAATTTTTGGCCA 57.528 30.769 0.00 0.00 0.00 5.36
1887 4299 9.574458 GATCTAAGAGTTTAAGAATTTTTGGCC 57.426 33.333 0.00 0.00 0.00 5.36
1907 4319 5.514310 CCATCAAGGCCATCATCAGATCTAA 60.514 44.000 5.01 0.00 30.20 2.10
1909 4321 3.244946 CCATCAAGGCCATCATCAGATCT 60.245 47.826 5.01 0.00 30.20 2.75
1923 4335 0.750911 GCCCTCTCAAGCCATCAAGG 60.751 60.000 0.00 0.00 41.84 3.61
1924 4336 0.034767 TGCCCTCTCAAGCCATCAAG 60.035 55.000 0.00 0.00 0.00 3.02
1925 4337 0.034767 CTGCCCTCTCAAGCCATCAA 60.035 55.000 0.00 0.00 0.00 2.57
1926 4338 1.605992 CTGCCCTCTCAAGCCATCA 59.394 57.895 0.00 0.00 0.00 3.07
1927 4339 1.153005 CCTGCCCTCTCAAGCCATC 60.153 63.158 0.00 0.00 0.00 3.51
1928 4340 1.210204 TTCCTGCCCTCTCAAGCCAT 61.210 55.000 0.00 0.00 0.00 4.40
1929 4341 1.426251 TTTCCTGCCCTCTCAAGCCA 61.426 55.000 0.00 0.00 0.00 4.75
1930 4342 0.679321 CTTTCCTGCCCTCTCAAGCC 60.679 60.000 0.00 0.00 0.00 4.35
1931 4343 0.679321 CCTTTCCTGCCCTCTCAAGC 60.679 60.000 0.00 0.00 0.00 4.01
1945 4357 8.894768 AGATACATTATAACTGAGCACCTTTC 57.105 34.615 0.00 0.00 0.00 2.62
2005 4417 1.135402 CCGCAAGAAACTAACCATGGC 60.135 52.381 13.04 0.00 43.02 4.40
2024 4436 7.870445 TGTTAAAATCACAAAGGATGCTAAACC 59.130 33.333 0.00 0.00 0.00 3.27
2068 4480 5.942872 AGTGTAAATGATGCTAAACTGCAC 58.057 37.500 0.00 0.00 46.33 4.57
2110 4522 6.723282 GCAAACCATGTTAAATTGCAAGAAA 58.277 32.000 4.94 0.00 44.29 2.52
2217 4631 9.826574 ACTTAAGTGTTAAGAGTGTAAATGACA 57.173 29.630 7.48 0.00 44.19 3.58
2263 4677 1.386748 GCGTCGAAGGTAAACGGTAAC 59.613 52.381 0.00 0.00 36.92 2.50
2264 4678 1.668628 GGCGTCGAAGGTAAACGGTAA 60.669 52.381 0.00 0.00 36.92 2.85
2265 4679 0.109319 GGCGTCGAAGGTAAACGGTA 60.109 55.000 0.00 0.00 36.92 4.02
2266 4680 1.373371 GGCGTCGAAGGTAAACGGT 60.373 57.895 0.00 0.00 36.92 4.83
2267 4681 2.438954 CGGCGTCGAAGGTAAACGG 61.439 63.158 1.44 0.00 39.00 4.44
2268 4682 2.438954 CCGGCGTCGAAGGTAAACG 61.439 63.158 12.93 0.00 39.00 3.60
2269 4683 2.096442 CCCGGCGTCGAAGGTAAAC 61.096 63.158 12.93 0.00 39.00 2.01
2270 4684 2.262292 CCCGGCGTCGAAGGTAAA 59.738 61.111 12.93 0.00 39.00 2.01
2271 4685 3.762247 CCCCGGCGTCGAAGGTAA 61.762 66.667 12.93 0.00 39.00 2.85
2272 4686 4.738998 TCCCCGGCGTCGAAGGTA 62.739 66.667 12.93 0.00 39.00 3.08
2274 4688 4.891727 CATCCCCGGCGTCGAAGG 62.892 72.222 12.93 12.16 39.00 3.46
2275 4689 3.151958 ATCATCCCCGGCGTCGAAG 62.152 63.158 12.93 0.45 39.00 3.79
2276 4690 3.151710 ATCATCCCCGGCGTCGAA 61.152 61.111 12.93 0.00 39.00 3.71
2277 4691 3.911698 CATCATCCCCGGCGTCGA 61.912 66.667 12.93 0.00 39.00 4.20
2279 4693 4.545706 TGCATCATCCCCGGCGTC 62.546 66.667 6.01 0.00 0.00 5.19
2280 4694 4.856801 GTGCATCATCCCCGGCGT 62.857 66.667 6.01 0.00 0.00 5.68
2284 4698 4.854924 TGCGGTGCATCATCCCCG 62.855 66.667 6.80 6.80 43.22 5.73
2285 4699 2.903855 CTGCGGTGCATCATCCCC 60.904 66.667 0.00 0.00 38.13 4.81
2286 4700 3.589881 GCTGCGGTGCATCATCCC 61.590 66.667 0.00 0.00 38.13 3.85
2287 4701 2.515523 AGCTGCGGTGCATCATCC 60.516 61.111 0.00 0.00 38.13 3.51
2288 4702 1.816679 TGAGCTGCGGTGCATCATC 60.817 57.895 0.00 0.00 38.13 2.92
2289 4703 2.110967 GTGAGCTGCGGTGCATCAT 61.111 57.895 0.00 0.00 38.13 2.45
2290 4704 2.743538 GTGAGCTGCGGTGCATCA 60.744 61.111 0.00 0.00 38.13 3.07
2291 4705 3.857854 CGTGAGCTGCGGTGCATC 61.858 66.667 0.00 0.00 38.13 3.91
2292 4706 4.687215 ACGTGAGCTGCGGTGCAT 62.687 61.111 11.28 0.00 38.13 3.96
2295 4709 4.700365 TCGACGTGAGCTGCGGTG 62.700 66.667 11.28 4.12 0.00 4.94
2296 4710 3.898627 CTTCGACGTGAGCTGCGGT 62.899 63.158 11.28 0.00 0.00 5.68
2297 4711 3.175240 CTTCGACGTGAGCTGCGG 61.175 66.667 11.28 0.00 0.00 5.69
2298 4712 3.175240 CCTTCGACGTGAGCTGCG 61.175 66.667 0.00 0.00 0.00 5.18
2299 4713 1.803519 CTCCTTCGACGTGAGCTGC 60.804 63.158 0.00 0.00 0.00 5.25
2300 4714 0.455295 GTCTCCTTCGACGTGAGCTG 60.455 60.000 0.00 0.00 0.00 4.24
2301 4715 1.587933 GGTCTCCTTCGACGTGAGCT 61.588 60.000 0.00 0.00 34.75 4.09
2302 4716 1.153997 GGTCTCCTTCGACGTGAGC 60.154 63.158 0.00 0.00 34.75 4.26
2303 4717 1.507174 GGGTCTCCTTCGACGTGAG 59.493 63.158 0.00 0.00 34.75 3.51
2304 4718 2.330372 CGGGTCTCCTTCGACGTGA 61.330 63.158 0.00 0.00 34.75 4.35
2305 4719 2.178521 CGGGTCTCCTTCGACGTG 59.821 66.667 0.00 0.00 34.75 4.49
2306 4720 2.282040 ACGGGTCTCCTTCGACGT 60.282 61.111 0.00 0.00 34.75 4.34
2307 4721 2.484203 GACGGGTCTCCTTCGACG 59.516 66.667 0.00 0.00 34.75 5.12
2308 4722 2.883621 GGACGGGTCTCCTTCGAC 59.116 66.667 0.00 0.00 32.58 4.20
2309 4723 2.749044 CGGACGGGTCTCCTTCGA 60.749 66.667 0.00 0.00 32.58 3.71
2310 4724 3.823330 CCGGACGGGTCTCCTTCG 61.823 72.222 0.00 0.00 32.58 3.79
2311 4725 1.946475 CTTCCGGACGGGTCTCCTTC 61.946 65.000 1.83 0.00 37.00 3.46
2312 4726 1.982938 CTTCCGGACGGGTCTCCTT 60.983 63.158 1.83 0.00 37.00 3.36
2313 4727 2.362632 CTTCCGGACGGGTCTCCT 60.363 66.667 1.83 0.00 37.00 3.69
2314 4728 4.144703 GCTTCCGGACGGGTCTCC 62.145 72.222 1.83 0.00 37.00 3.71
2315 4729 4.493747 CGCTTCCGGACGGGTCTC 62.494 72.222 15.92 0.00 37.00 3.36
2325 4739 3.179265 CTGTGTACCGCGCTTCCG 61.179 66.667 5.56 0.00 37.57 4.30
2326 4740 2.813908 CCTGTGTACCGCGCTTCC 60.814 66.667 5.56 0.00 0.00 3.46
2327 4741 3.488090 GCCTGTGTACCGCGCTTC 61.488 66.667 5.56 0.00 0.00 3.86
2328 4742 3.818121 TTGCCTGTGTACCGCGCTT 62.818 57.895 5.56 0.00 0.00 4.68
2329 4743 4.308458 TTGCCTGTGTACCGCGCT 62.308 61.111 5.56 0.00 0.00 5.92


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

AutoCloner maintained by Alex Coulton.