Multiple sequence alignment - TraesCS5D01G080800

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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 TraesCS5D01G080800 chr5D 100.000 4796 0 0 874 5669 80709919 80705124 0.000000e+00 8857.0
1 TraesCS5D01G080800 chr5D 100.000 618 0 0 1 618 80710792 80710175 0.000000e+00 1142.0
2 TraesCS5D01G080800 chr5D 88.831 573 45 8 1 555 32757495 32756924 0.000000e+00 686.0
3 TraesCS5D01G080800 chr5D 86.417 427 35 6 150 555 62094267 62094691 4.030000e-121 446.0
4 TraesCS5D01G080800 chr5D 98.361 61 1 0 3400 3460 426293906 426293846 2.160000e-19 108.0
5 TraesCS5D01G080800 chr5B 94.968 4213 126 33 1494 5656 89638068 89633892 0.000000e+00 6527.0
6 TraesCS5D01G080800 chr5B 95.953 593 22 2 874 1465 89638653 89638062 0.000000e+00 961.0
7 TraesCS5D01G080800 chr5A 95.587 3286 99 20 1494 4764 77095232 77091978 0.000000e+00 5223.0
8 TraesCS5D01G080800 chr5A 90.316 919 49 12 4763 5655 77091946 77091042 0.000000e+00 1168.0
9 TraesCS5D01G080800 chr5A 96.147 597 17 3 874 1465 77095821 77095226 0.000000e+00 970.0
10 TraesCS5D01G080800 chr5A 90.789 76 4 3 3389 3462 557575312 557575238 1.300000e-16 99.0
11 TraesCS5D01G080800 chr5A 90.789 76 4 3 3389 3462 557864464 557864390 1.300000e-16 99.0
12 TraesCS5D01G080800 chr5A 87.879 66 5 3 3434 3497 132569262 132569326 2.190000e-09 75.0
13 TraesCS5D01G080800 chr6B 89.711 622 53 4 1 616 252242676 252243292 0.000000e+00 784.0
14 TraesCS5D01G080800 chr3A 91.103 562 42 3 1 555 521357442 521358002 0.000000e+00 754.0
15 TraesCS5D01G080800 chr3A 90.845 284 18 7 1 278 517808455 517808736 1.930000e-99 374.0
16 TraesCS5D01G080800 chr3A 90.184 163 16 0 390 552 517808921 517809083 4.450000e-51 213.0
17 TraesCS5D01G080800 chr1A 82.569 545 65 18 23 555 511252527 511252001 2.410000e-123 453.0
18 TraesCS5D01G080800 chr1A 81.125 551 76 20 23 564 81908072 81907541 3.160000e-112 416.0
19 TraesCS5D01G080800 chr4A 94.048 252 13 1 1 250 240359959 240360210 1.150000e-101 381.0
20 TraesCS5D01G080800 chr4A 88.963 299 27 2 321 618 240360500 240360793 1.160000e-96 364.0
21 TraesCS5D01G080800 chr4A 91.288 264 17 5 1 258 177597242 177597505 6.990000e-94 355.0
22 TraesCS5D01G080800 chr4A 84.375 224 30 4 333 555 177597792 177598011 1.240000e-51 215.0
23 TraesCS5D01G080800 chr3B 93.281 253 13 3 1 250 179383952 179383701 2.490000e-98 370.0
24 TraesCS5D01G080800 chr1D 82.216 388 30 18 3536 3893 490397462 490397084 1.190000e-76 298.0
25 TraesCS5D01G080800 chr1D 84.397 282 24 11 3524 3788 460552271 460551993 5.630000e-65 259.0
26 TraesCS5D01G080800 chr1D 82.171 258 26 11 2116 2360 490397796 490397546 2.680000e-48 204.0
27 TraesCS5D01G080800 chr1D 91.892 74 5 1 3389 3462 465522139 465522067 1.000000e-17 102.0
28 TraesCS5D01G080800 chr1D 91.892 74 2 3 3400 3473 458142840 458142909 3.610000e-17 100.0
29 TraesCS5D01G080800 chr7B 76.630 552 73 30 78 578 580669435 580668889 2.620000e-63 254.0
30 TraesCS5D01G080800 chr4B 96.875 64 1 1 3399 3462 33069920 33069982 7.770000e-19 106.0
31 TraesCS5D01G080800 chr6D 90.667 75 5 2 3389 3462 363593311 363593384 1.300000e-16 99.0
32 TraesCS5D01G080800 chr7D 93.478 46 1 1 3450 3495 600280490 600280533 3.670000e-07 67.6
33 TraesCS5D01G080800 chr7A 100.000 33 0 0 3464 3496 671145556 671145524 1.710000e-05 62.1


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 TraesCS5D01G080800 chr5D 80705124 80710792 5668 True 4999.500000 8857 100.000000 1 5669 2 chr5D.!!$R3 5668
1 TraesCS5D01G080800 chr5D 32756924 32757495 571 True 686.000000 686 88.831000 1 555 1 chr5D.!!$R1 554
2 TraesCS5D01G080800 chr5B 89633892 89638653 4761 True 3744.000000 6527 95.460500 874 5656 2 chr5B.!!$R1 4782
3 TraesCS5D01G080800 chr5A 77091042 77095821 4779 True 2453.666667 5223 94.016667 874 5655 3 chr5A.!!$R3 4781
4 TraesCS5D01G080800 chr6B 252242676 252243292 616 False 784.000000 784 89.711000 1 616 1 chr6B.!!$F1 615
5 TraesCS5D01G080800 chr3A 521357442 521358002 560 False 754.000000 754 91.103000 1 555 1 chr3A.!!$F1 554
6 TraesCS5D01G080800 chr3A 517808455 517809083 628 False 293.500000 374 90.514500 1 552 2 chr3A.!!$F2 551
7 TraesCS5D01G080800 chr1A 511252001 511252527 526 True 453.000000 453 82.569000 23 555 1 chr1A.!!$R2 532
8 TraesCS5D01G080800 chr1A 81907541 81908072 531 True 416.000000 416 81.125000 23 564 1 chr1A.!!$R1 541
9 TraesCS5D01G080800 chr4A 240359959 240360793 834 False 372.500000 381 91.505500 1 618 2 chr4A.!!$F2 617
10 TraesCS5D01G080800 chr4A 177597242 177598011 769 False 285.000000 355 87.831500 1 555 2 chr4A.!!$F1 554
11 TraesCS5D01G080800 chr1D 490397084 490397796 712 True 251.000000 298 82.193500 2116 3893 2 chr1D.!!$R3 1777
12 TraesCS5D01G080800 chr7B 580668889 580669435 546 True 254.000000 254 76.630000 78 578 1 chr7B.!!$R1 500

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
30 31 0.663153 GACAAGTGCCAGAACACACC 59.337 55.000 0.00 0.00 43.23 4.16 F
1463 1758 0.665369 GCAATGTGTGACAAGCTGGC 60.665 55.000 0.00 0.00 32.65 4.85 F
1467 1762 0.758734 TGTGTGACAAGCTGGCTACT 59.241 50.000 0.00 0.00 0.00 2.57 F
1469 1764 1.001406 GTGTGACAAGCTGGCTACTCT 59.999 52.381 0.00 0.00 0.00 3.24 F
1470 1765 1.273606 TGTGACAAGCTGGCTACTCTC 59.726 52.381 0.00 0.00 0.00 3.20 F
1471 1766 1.548269 GTGACAAGCTGGCTACTCTCT 59.452 52.381 0.00 0.00 0.00 3.10 F
1472 1767 2.028567 GTGACAAGCTGGCTACTCTCTT 60.029 50.000 0.00 0.00 0.00 2.85 F
1630 1929 2.105930 CTGAGTAGCGCTGCCTCC 59.894 66.667 26.45 16.31 0.00 4.30 F
3964 4310 0.597568 TGGAACATGAAAAGCCTGCG 59.402 50.000 0.00 0.00 0.00 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1479 1774 0.320247 GGCATCCTGATACCGAGCAG 60.320 60.000 0.00 0.00 38.90 4.24 R
2320 2632 0.958822 GAAACAAGTTCCGCCCATGT 59.041 50.000 0.00 0.00 0.00 3.21 R
3462 3774 6.264518 TCCATCCCAAAAAGTTTGTCTTAGAC 59.735 38.462 5.27 5.27 35.02 2.59 R
3501 3813 9.064706 AGTAGACATATGCTTAGTAATGTACGT 57.935 33.333 1.58 0.00 32.87 3.57 R
3502 3814 9.894783 AAGTAGACATATGCTTAGTAATGTACG 57.105 33.333 1.58 0.00 32.87 3.67 R
3697 4027 3.364664 GCCCAGCGTTTTGTAGTCTAAAC 60.365 47.826 0.00 0.00 36.48 2.01 R
3964 4310 1.168714 GATTTCAGGGGTCAGTGTGC 58.831 55.000 0.00 0.00 0.00 4.57 R
4199 4553 5.237996 CCACCTGTATCAGCAAATCTACATG 59.762 44.000 0.00 0.00 0.00 3.21 R
5241 5652 0.768622 ACCCCGTGGAAAATGAGACA 59.231 50.000 0.00 0.00 34.81 3.41 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 0.663153 GACAAGTGCCAGAACACACC 59.337 55.000 0.00 0.00 43.23 4.16
75 81 7.840716 TGAAATCATACCCTGAATCCAAATCTT 59.159 33.333 0.00 0.00 37.44 2.40
319 586 1.741706 CTTGTTGATGCCGAGCTTGAT 59.258 47.619 1.22 0.00 0.00 2.57
324 601 3.426309 ATGCCGAGCTTGATGGGGG 62.426 63.158 1.22 0.00 0.00 5.40
527 816 1.063942 TCTTGCAGAGTAGGATCCCGA 60.064 52.381 8.55 0.00 0.00 5.14
543 832 1.587054 CGACGGAGGAAGCAGAAGT 59.413 57.895 0.00 0.00 0.00 3.01
578 868 1.708551 ACGAAGGAAAAGGGGATCCAA 59.291 47.619 15.23 0.00 38.23 3.53
585 875 2.558380 AAAGGGGATCCAAGCGAGGC 62.558 60.000 15.23 0.00 34.83 4.70
586 876 4.918201 GGGGATCCAAGCGAGGCG 62.918 72.222 15.23 0.00 0.00 5.52
587 877 3.849951 GGGATCCAAGCGAGGCGA 61.850 66.667 15.23 0.00 0.00 5.54
588 878 2.279784 GGATCCAAGCGAGGCGAG 60.280 66.667 6.95 0.00 0.00 5.03
589 879 2.786495 GGATCCAAGCGAGGCGAGA 61.786 63.158 6.95 0.00 0.00 4.04
1294 1588 8.097078 AGAGCTTATCTTAAATCATGCATCAC 57.903 34.615 0.00 0.00 32.99 3.06
1402 1696 7.553334 TCGAGGTAATTTACTTGTGCTCTTAT 58.447 34.615 6.52 0.00 0.00 1.73
1436 1730 2.149973 ATTGTGCTGAATTCCCTCCC 57.850 50.000 2.27 0.00 0.00 4.30
1438 1732 0.776810 TGTGCTGAATTCCCTCCCAA 59.223 50.000 2.27 0.00 0.00 4.12
1441 1736 1.272092 TGCTGAATTCCCTCCCAACTG 60.272 52.381 2.27 0.00 0.00 3.16
1458 1753 4.530388 CAACTGTAGCAATGTGTGACAAG 58.470 43.478 0.00 0.00 0.00 3.16
1459 1754 2.549754 ACTGTAGCAATGTGTGACAAGC 59.450 45.455 0.00 0.00 34.66 4.01
1460 1755 2.810274 CTGTAGCAATGTGTGACAAGCT 59.190 45.455 10.59 10.59 43.04 3.74
1461 1756 2.549329 TGTAGCAATGTGTGACAAGCTG 59.451 45.455 13.97 0.29 41.47 4.24
1462 1757 0.956633 AGCAATGTGTGACAAGCTGG 59.043 50.000 6.32 0.00 40.44 4.85
1463 1758 0.665369 GCAATGTGTGACAAGCTGGC 60.665 55.000 0.00 0.00 32.65 4.85
1464 1759 0.956633 CAATGTGTGACAAGCTGGCT 59.043 50.000 0.00 0.00 0.00 4.75
1465 1760 2.153645 CAATGTGTGACAAGCTGGCTA 58.846 47.619 0.00 0.00 0.00 3.93
1466 1761 1.813513 ATGTGTGACAAGCTGGCTAC 58.186 50.000 0.00 0.00 0.00 3.58
1467 1762 0.758734 TGTGTGACAAGCTGGCTACT 59.241 50.000 0.00 0.00 0.00 2.57
1468 1763 1.270305 TGTGTGACAAGCTGGCTACTC 60.270 52.381 0.00 0.00 0.00 2.59
1469 1764 1.001406 GTGTGACAAGCTGGCTACTCT 59.999 52.381 0.00 0.00 0.00 3.24
1470 1765 1.273606 TGTGACAAGCTGGCTACTCTC 59.726 52.381 0.00 0.00 0.00 3.20
1471 1766 1.548269 GTGACAAGCTGGCTACTCTCT 59.452 52.381 0.00 0.00 0.00 3.10
1472 1767 2.028567 GTGACAAGCTGGCTACTCTCTT 60.029 50.000 0.00 0.00 0.00 2.85
1473 1768 2.634940 TGACAAGCTGGCTACTCTCTTT 59.365 45.455 0.00 0.00 0.00 2.52
1474 1769 3.071602 TGACAAGCTGGCTACTCTCTTTT 59.928 43.478 0.00 0.00 0.00 2.27
1475 1770 4.283467 TGACAAGCTGGCTACTCTCTTTTA 59.717 41.667 0.00 0.00 0.00 1.52
1476 1771 5.221641 TGACAAGCTGGCTACTCTCTTTTAA 60.222 40.000 0.00 0.00 0.00 1.52
1477 1772 5.241662 ACAAGCTGGCTACTCTCTTTTAAG 58.758 41.667 0.00 0.00 0.00 1.85
1478 1773 5.221742 ACAAGCTGGCTACTCTCTTTTAAGT 60.222 40.000 0.00 0.00 0.00 2.24
1479 1774 5.079689 AGCTGGCTACTCTCTTTTAAGTC 57.920 43.478 0.00 0.00 0.00 3.01
1480 1775 4.775253 AGCTGGCTACTCTCTTTTAAGTCT 59.225 41.667 0.00 0.00 0.00 3.24
1481 1776 4.867608 GCTGGCTACTCTCTTTTAAGTCTG 59.132 45.833 0.00 0.00 0.00 3.51
1482 1777 4.822026 TGGCTACTCTCTTTTAAGTCTGC 58.178 43.478 0.00 0.00 0.00 4.26
1483 1778 4.528596 TGGCTACTCTCTTTTAAGTCTGCT 59.471 41.667 0.00 0.00 0.00 4.24
1484 1779 5.106442 GGCTACTCTCTTTTAAGTCTGCTC 58.894 45.833 0.00 0.00 0.00 4.26
1485 1780 4.796312 GCTACTCTCTTTTAAGTCTGCTCG 59.204 45.833 0.00 0.00 0.00 5.03
1486 1781 4.181309 ACTCTCTTTTAAGTCTGCTCGG 57.819 45.455 0.00 0.00 0.00 4.63
1487 1782 3.574826 ACTCTCTTTTAAGTCTGCTCGGT 59.425 43.478 0.00 0.00 0.00 4.69
1488 1783 4.765856 ACTCTCTTTTAAGTCTGCTCGGTA 59.234 41.667 0.00 0.00 0.00 4.02
1489 1784 5.419471 ACTCTCTTTTAAGTCTGCTCGGTAT 59.581 40.000 0.00 0.00 0.00 2.73
1490 1785 5.892568 TCTCTTTTAAGTCTGCTCGGTATC 58.107 41.667 0.00 0.00 0.00 2.24
1491 1786 5.417894 TCTCTTTTAAGTCTGCTCGGTATCA 59.582 40.000 0.00 0.00 0.00 2.15
1492 1787 5.651530 TCTTTTAAGTCTGCTCGGTATCAG 58.348 41.667 0.00 0.00 0.00 2.90
1527 1822 6.882678 GTGGGAATGTGTAACTTACCTGTTAT 59.117 38.462 0.00 0.00 38.04 1.89
1529 1824 7.945664 TGGGAATGTGTAACTTACCTGTTATTT 59.054 33.333 0.00 0.00 38.04 1.40
1531 1826 9.620660 GGAATGTGTAACTTACCTGTTATTTTG 57.379 33.333 0.00 0.00 38.04 2.44
1553 1852 6.066054 TGTTGTGGTTGTGTACATTACATG 57.934 37.500 0.00 0.00 41.34 3.21
1630 1929 2.105930 CTGAGTAGCGCTGCCTCC 59.894 66.667 26.45 16.31 0.00 4.30
1674 1973 5.284861 TGGCAAGTGACACTCTTAACTTA 57.715 39.130 8.93 0.00 31.80 2.24
1745 2044 2.422127 AGTTGGTTGTTTTCGTGGTCTG 59.578 45.455 0.00 0.00 0.00 3.51
2005 2305 7.363880 CCTGTAGGAGCAGTGAATTAGACTTAA 60.364 40.741 0.00 0.00 37.39 1.85
2076 2376 4.511527 CACTTATCCAACTGCTCTCACAT 58.488 43.478 0.00 0.00 0.00 3.21
2319 2631 5.543714 TGTAACAAGATCGGTAGAAAAGCA 58.456 37.500 0.00 0.00 0.00 3.91
2320 2632 5.992829 TGTAACAAGATCGGTAGAAAAGCAA 59.007 36.000 0.00 0.00 0.00 3.91
2410 2722 4.035675 GGGAACAACTCTCAGAAAAGTGTG 59.964 45.833 0.00 0.00 0.00 3.82
2752 3064 5.612725 TGATTTCCCCCTTATGCATTTTC 57.387 39.130 3.54 0.00 0.00 2.29
3341 3653 5.876612 ATCAACTCATTCACTCAGCTTTC 57.123 39.130 0.00 0.00 0.00 2.62
3377 3689 7.831690 TGTATATTTTATGGGTCAACTCAGCAA 59.168 33.333 0.00 0.00 0.00 3.91
3500 3812 2.972713 TGGGATGGAGGTAATACTCAGC 59.027 50.000 0.00 0.00 39.27 4.26
3501 3813 2.972713 GGGATGGAGGTAATACTCAGCA 59.027 50.000 0.00 0.00 39.27 4.41
3502 3814 3.244249 GGGATGGAGGTAATACTCAGCAC 60.244 52.174 0.00 0.00 39.27 4.40
3503 3815 3.553096 GGATGGAGGTAATACTCAGCACG 60.553 52.174 0.00 0.00 39.27 5.34
3697 4027 4.440103 GCGATACATTCAGTAACTGTACCG 59.560 45.833 0.00 0.00 35.86 4.02
3964 4310 0.597568 TGGAACATGAAAAGCCTGCG 59.402 50.000 0.00 0.00 0.00 5.18
4062 4408 3.365868 GCGTGCAGGTTATTGTTGAATCA 60.366 43.478 8.40 0.00 0.00 2.57
4138 4492 6.182039 TCTTTCTTTGTCTGTTGTCACTTG 57.818 37.500 0.00 0.00 0.00 3.16
4228 4582 1.506025 TGCTGATACAGGTGGGCATA 58.494 50.000 0.00 0.00 31.21 3.14
4253 4607 4.883585 GGCATCAATATCACAAGTGAAGGA 59.116 41.667 7.02 3.46 43.58 3.36
4262 4616 2.035449 CACAAGTGAAGGACTCCGTGTA 59.965 50.000 0.00 0.00 35.04 2.90
4314 4668 4.020218 CCAAAGTTCTCCCATCTGTCAGTA 60.020 45.833 0.00 0.00 0.00 2.74
4341 4695 3.560251 CCGCTCCCCATACCCCTG 61.560 72.222 0.00 0.00 0.00 4.45
4366 4720 1.066587 CCGTCGATCTTCAGGAGCC 59.933 63.158 0.00 0.00 0.00 4.70
4434 4788 0.693049 AGCCAAAGGGTTCACTCGAT 59.307 50.000 0.00 0.00 36.17 3.59
4600 4954 1.413662 GGGAGGAGATGGAGGACATGA 60.414 57.143 0.00 0.00 40.72 3.07
4696 5051 1.082756 CGGTTTCTTCTGTGTGCGC 60.083 57.895 0.00 0.00 0.00 6.09
4700 5055 0.808060 TTTCTTCTGTGTGCGCGACA 60.808 50.000 12.10 9.00 0.00 4.35
4701 5056 0.599991 TTCTTCTGTGTGCGCGACAT 60.600 50.000 12.10 0.00 36.78 3.06
4710 5065 3.243267 TGTGTGCGCGACATATACATACT 60.243 43.478 12.10 0.00 36.78 2.12
4734 5093 3.341823 AGAGCTGCTGTAGGATGTTTTG 58.658 45.455 7.01 0.00 0.00 2.44
4735 5094 3.077359 GAGCTGCTGTAGGATGTTTTGT 58.923 45.455 7.01 0.00 0.00 2.83
4736 5095 2.816087 AGCTGCTGTAGGATGTTTTGTG 59.184 45.455 0.00 0.00 0.00 3.33
4775 5167 6.040247 TGTGATACGTGTGGAATATTCTCAC 58.960 40.000 21.03 21.03 0.00 3.51
4783 5175 5.049828 TGTGGAATATTCTCACGCATGTAG 58.950 41.667 21.72 0.00 33.74 2.74
4829 5227 4.193334 CGATCTGGCGTGCGAGGA 62.193 66.667 4.01 0.00 0.00 3.71
4991 5395 0.955428 GAGGTCAGTTGCCAATGCGA 60.955 55.000 0.00 0.00 41.78 5.10
5026 5430 1.078143 GCGGGGAGTTTGCAGAGAT 60.078 57.895 0.00 0.00 0.00 2.75
5030 5434 0.620556 GGGAGTTTGCAGAGATGGGA 59.379 55.000 0.00 0.00 0.00 4.37
5099 5509 1.577468 TTGGCGTATGAGTATTGCGG 58.423 50.000 0.00 0.00 0.00 5.69
5101 5512 1.137282 TGGCGTATGAGTATTGCGGAA 59.863 47.619 0.00 0.00 0.00 4.30
5140 5551 0.458370 GGAATTCAACATGGCACGGC 60.458 55.000 7.93 0.00 0.00 5.68
5160 5571 1.920574 CACGAGTTTCGCTCCTGTATG 59.079 52.381 0.00 0.00 45.12 2.39
5161 5572 1.816835 ACGAGTTTCGCTCCTGTATGA 59.183 47.619 0.00 0.00 45.12 2.15
5162 5573 2.427453 ACGAGTTTCGCTCCTGTATGAT 59.573 45.455 0.00 0.00 45.12 2.45
5163 5574 3.119101 ACGAGTTTCGCTCCTGTATGATT 60.119 43.478 0.00 0.00 45.12 2.57
5164 5575 4.097437 ACGAGTTTCGCTCCTGTATGATTA 59.903 41.667 0.00 0.00 45.12 1.75
5241 5652 3.018149 TGCCTTTGTTTTACTTCACCGT 58.982 40.909 0.00 0.00 0.00 4.83
5273 5684 4.495565 TCCACGGGGTTATAATATGGTCT 58.504 43.478 2.12 0.00 34.93 3.85
5284 5695 7.255139 GGTTATAATATGGTCTTTGACACTGGC 60.255 40.741 0.07 0.00 33.68 4.85
5530 5945 2.946329 GGAGCTCGAGAGTAATGAGTGA 59.054 50.000 18.75 0.00 32.32 3.41
5581 5996 4.816392 AGCATGTACGTACATCAGTTCAA 58.184 39.130 32.93 8.51 44.57 2.69
5583 5998 4.490319 GCATGTACGTACATCAGTTCAACG 60.490 45.833 32.93 20.89 44.57 4.10
5656 6079 3.991773 TGTTTCTCGTGTGCCATAGTAAC 59.008 43.478 0.00 0.00 0.00 2.50
5657 6080 2.554806 TCTCGTGTGCCATAGTAACG 57.445 50.000 0.00 0.00 35.64 3.18
5658 6081 2.086094 TCTCGTGTGCCATAGTAACGA 58.914 47.619 0.00 0.00 40.63 3.85
5659 6082 2.554806 TCGTGTGCCATAGTAACGAG 57.445 50.000 0.00 0.00 38.26 4.18
5660 6083 0.921347 CGTGTGCCATAGTAACGAGC 59.079 55.000 0.00 0.00 36.38 5.03
5661 6084 1.734377 CGTGTGCCATAGTAACGAGCA 60.734 52.381 0.00 0.00 36.38 4.26
5662 6085 2.343101 GTGTGCCATAGTAACGAGCAA 58.657 47.619 0.00 0.00 34.79 3.91
5663 6086 2.936498 GTGTGCCATAGTAACGAGCAAT 59.064 45.455 0.00 0.00 34.79 3.56
5664 6087 4.116961 GTGTGCCATAGTAACGAGCAATA 58.883 43.478 0.00 0.00 34.79 1.90
5665 6088 4.569162 GTGTGCCATAGTAACGAGCAATAA 59.431 41.667 0.00 0.00 34.79 1.40
5666 6089 4.808895 TGTGCCATAGTAACGAGCAATAAG 59.191 41.667 0.00 0.00 34.79 1.73
5667 6090 3.807622 TGCCATAGTAACGAGCAATAAGC 59.192 43.478 0.00 0.00 46.19 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 0.039618 AGCATGGTGTTGTTAGGGGG 59.960 55.000 0.00 0.00 0.00 5.40
43 46 3.824133 TCAGGGTATGATTTCAGCATGG 58.176 45.455 0.00 0.00 31.29 3.66
75 81 3.117474 TGATGTTAGGGGGTTGTGTTCAA 60.117 43.478 0.00 0.00 0.00 2.69
292 351 1.153353 CGGCATCAACAAGGTAACGT 58.847 50.000 0.00 0.00 46.39 3.99
324 601 2.272918 AAGCTCAGCGTCGTCTAGGC 62.273 60.000 0.00 0.00 39.33 3.93
527 816 0.533032 GCTACTTCTGCTTCCTCCGT 59.467 55.000 0.00 0.00 0.00 4.69
578 868 2.044848 TTCCTCTCTCGCCTCGCT 60.045 61.111 0.00 0.00 0.00 4.93
585 875 2.354203 CCAAGTTTCCCTTCCTCTCTCG 60.354 54.545 0.00 0.00 0.00 4.04
586 876 2.616765 GCCAAGTTTCCCTTCCTCTCTC 60.617 54.545 0.00 0.00 0.00 3.20
587 877 1.352687 GCCAAGTTTCCCTTCCTCTCT 59.647 52.381 0.00 0.00 0.00 3.10
588 878 1.352687 AGCCAAGTTTCCCTTCCTCTC 59.647 52.381 0.00 0.00 0.00 3.20
589 879 1.450360 AGCCAAGTTTCCCTTCCTCT 58.550 50.000 0.00 0.00 0.00 3.69
883 1173 4.873827 GCTGTAACGATTTTAGATGGTGGA 59.126 41.667 0.00 0.00 0.00 4.02
1294 1588 2.226912 GACTAAGACGATCCGATGGAGG 59.773 54.545 0.00 0.00 34.05 4.30
1402 1696 3.689161 AGCACAATAGCGCATACAGAAAA 59.311 39.130 11.47 0.00 40.15 2.29
1406 1700 2.204237 TCAGCACAATAGCGCATACAG 58.796 47.619 11.47 0.00 40.15 2.74
1436 1730 4.530388 CTTGTCACACATTGCTACAGTTG 58.470 43.478 0.00 0.00 0.00 3.16
1438 1732 2.549754 GCTTGTCACACATTGCTACAGT 59.450 45.455 0.00 0.00 0.00 3.55
1441 1736 2.095567 CCAGCTTGTCACACATTGCTAC 60.096 50.000 4.91 0.00 36.58 3.58
1458 1753 4.867608 CAGACTTAAAAGAGAGTAGCCAGC 59.132 45.833 0.00 0.00 0.00 4.85
1459 1754 4.867608 GCAGACTTAAAAGAGAGTAGCCAG 59.132 45.833 0.00 0.00 0.00 4.85
1460 1755 4.528596 AGCAGACTTAAAAGAGAGTAGCCA 59.471 41.667 0.00 0.00 31.27 4.75
1461 1756 5.079689 AGCAGACTTAAAAGAGAGTAGCC 57.920 43.478 0.00 0.00 31.27 3.93
1462 1757 4.796312 CGAGCAGACTTAAAAGAGAGTAGC 59.204 45.833 0.00 0.00 0.00 3.58
1463 1758 5.106078 ACCGAGCAGACTTAAAAGAGAGTAG 60.106 44.000 0.00 0.00 0.00 2.57
1464 1759 4.765856 ACCGAGCAGACTTAAAAGAGAGTA 59.234 41.667 0.00 0.00 0.00 2.59
1465 1760 3.574826 ACCGAGCAGACTTAAAAGAGAGT 59.425 43.478 0.00 0.00 0.00 3.24
1466 1761 4.181309 ACCGAGCAGACTTAAAAGAGAG 57.819 45.455 0.00 0.00 0.00 3.20
1467 1762 5.417894 TGATACCGAGCAGACTTAAAAGAGA 59.582 40.000 0.00 0.00 0.00 3.10
1468 1763 5.651530 TGATACCGAGCAGACTTAAAAGAG 58.348 41.667 0.00 0.00 0.00 2.85
1469 1764 5.394224 CCTGATACCGAGCAGACTTAAAAGA 60.394 44.000 0.00 0.00 41.90 2.52
1470 1765 4.806247 CCTGATACCGAGCAGACTTAAAAG 59.194 45.833 0.00 0.00 41.90 2.27
1471 1766 4.464951 TCCTGATACCGAGCAGACTTAAAA 59.535 41.667 0.00 0.00 41.90 1.52
1472 1767 4.021229 TCCTGATACCGAGCAGACTTAAA 58.979 43.478 0.00 0.00 41.90 1.52
1473 1768 3.628008 TCCTGATACCGAGCAGACTTAA 58.372 45.455 0.00 0.00 41.90 1.85
1474 1769 3.292492 TCCTGATACCGAGCAGACTTA 57.708 47.619 0.00 0.00 41.90 2.24
1475 1770 2.145397 TCCTGATACCGAGCAGACTT 57.855 50.000 0.00 0.00 41.90 3.01
1476 1771 1.959985 CATCCTGATACCGAGCAGACT 59.040 52.381 0.00 0.00 41.90 3.24
1477 1772 1.604185 GCATCCTGATACCGAGCAGAC 60.604 57.143 0.00 0.00 41.90 3.51
1478 1773 0.676184 GCATCCTGATACCGAGCAGA 59.324 55.000 0.00 0.00 41.90 4.26
1479 1774 0.320247 GGCATCCTGATACCGAGCAG 60.320 60.000 0.00 0.00 38.90 4.24
1480 1775 0.760567 AGGCATCCTGATACCGAGCA 60.761 55.000 0.00 0.00 29.57 4.26
1481 1776 0.394565 AAGGCATCCTGATACCGAGC 59.605 55.000 0.00 0.00 32.13 5.03
1482 1777 2.158900 ACAAAGGCATCCTGATACCGAG 60.159 50.000 0.00 0.00 32.13 4.63
1483 1778 1.837439 ACAAAGGCATCCTGATACCGA 59.163 47.619 0.00 0.00 32.13 4.69
1484 1779 1.942657 CACAAAGGCATCCTGATACCG 59.057 52.381 0.00 0.00 32.13 4.02
1485 1780 2.301346 CCACAAAGGCATCCTGATACC 58.699 52.381 0.00 0.00 32.13 2.73
1486 1781 2.092429 TCCCACAAAGGCATCCTGATAC 60.092 50.000 0.00 0.00 32.13 2.24
1487 1782 2.204463 TCCCACAAAGGCATCCTGATA 58.796 47.619 0.00 0.00 32.13 2.15
1488 1783 1.002069 TCCCACAAAGGCATCCTGAT 58.998 50.000 0.00 0.00 32.13 2.90
1489 1784 0.776810 TTCCCACAAAGGCATCCTGA 59.223 50.000 0.00 0.00 32.13 3.86
1490 1785 1.479323 CATTCCCACAAAGGCATCCTG 59.521 52.381 0.00 0.00 32.13 3.86
1491 1786 1.077663 ACATTCCCACAAAGGCATCCT 59.922 47.619 0.00 0.00 35.39 3.24
1492 1787 1.205417 CACATTCCCACAAAGGCATCC 59.795 52.381 0.00 0.00 35.39 3.51
1527 1822 6.920817 TGTAATGTACACAACCACAACAAAA 58.079 32.000 0.00 0.00 32.89 2.44
1529 1824 6.499172 CATGTAATGTACACAACCACAACAA 58.501 36.000 0.00 0.00 42.23 2.83
1553 1852 9.297037 AGACCCTGCAAATGGTATAATTATAAC 57.703 33.333 12.80 12.80 34.20 1.89
1630 1929 3.774066 TGTAGTGACATTGAGCTGATCG 58.226 45.455 0.00 0.00 0.00 3.69
1674 1973 1.812571 GCACGGACACAAATTCAGGAT 59.187 47.619 0.00 0.00 0.00 3.24
1745 2044 8.533153 GTTTCTCTTTAGCTCATGACGTATAAC 58.467 37.037 0.00 0.00 0.00 1.89
2005 2305 8.990693 ATAACCATATTATGAGGGTAAGAGGT 57.009 34.615 5.21 0.00 32.21 3.85
2176 2479 6.785488 TCGACAATATTAGCCTGCAATTAG 57.215 37.500 0.00 0.00 0.00 1.73
2319 2631 1.339929 GAAACAAGTTCCGCCCATGTT 59.660 47.619 0.00 0.00 35.86 2.71
2320 2632 0.958822 GAAACAAGTTCCGCCCATGT 59.041 50.000 0.00 0.00 0.00 3.21
2410 2722 7.051000 AGCATTCAACTAAGTCCTTATCTTCC 58.949 38.462 0.00 0.00 0.00 3.46
2752 3064 7.572523 TTATGGATTAATGCAAGACCTCAAG 57.427 36.000 14.00 0.00 0.00 3.02
3377 3689 9.134055 GAGTACTTTATAGTAGGAGGTGATGTT 57.866 37.037 0.00 0.00 37.53 2.71
3462 3774 6.264518 TCCATCCCAAAAAGTTTGTCTTAGAC 59.735 38.462 5.27 5.27 35.02 2.59
3500 3812 9.114965 GTAGACATATGCTTAGTAATGTACGTG 57.885 37.037 1.58 0.00 32.87 4.49
3501 3813 9.064706 AGTAGACATATGCTTAGTAATGTACGT 57.935 33.333 1.58 0.00 32.87 3.57
3502 3814 9.894783 AAGTAGACATATGCTTAGTAATGTACG 57.105 33.333 1.58 0.00 32.87 3.67
3697 4027 3.364664 GCCCAGCGTTTTGTAGTCTAAAC 60.365 47.826 0.00 0.00 36.48 2.01
3964 4310 1.168714 GATTTCAGGGGTCAGTGTGC 58.831 55.000 0.00 0.00 0.00 4.57
4193 4547 9.486497 CTGTATCAGCAAATCTACATGAAGTAT 57.514 33.333 0.00 0.00 30.93 2.12
4199 4553 5.237996 CCACCTGTATCAGCAAATCTACATG 59.762 44.000 0.00 0.00 0.00 3.21
4205 4559 1.678101 GCCCACCTGTATCAGCAAATC 59.322 52.381 0.00 0.00 0.00 2.17
4228 4582 4.508551 TCACTTGTGATATTGATGCCCT 57.491 40.909 0.00 0.00 0.00 5.19
4253 4607 3.762288 TTCATAAGCTGAGTACACGGAGT 59.238 43.478 3.00 0.00 36.56 3.85
4262 4616 3.540314 CTCTGCCTTCATAAGCTGAGT 57.460 47.619 9.82 0.00 45.05 3.41
4600 4954 1.548357 ATCTTGGACAGGTGCTCGCT 61.548 55.000 0.00 0.00 0.00 4.93
4710 5065 2.739943 ACATCCTACAGCAGCTCTACA 58.260 47.619 0.00 0.00 0.00 2.74
4734 5093 3.211045 TCACAAGAGTTTTAGCCCACAC 58.789 45.455 0.00 0.00 0.00 3.82
4735 5094 3.569194 TCACAAGAGTTTTAGCCCACA 57.431 42.857 0.00 0.00 0.00 4.17
4736 5095 4.092968 CGTATCACAAGAGTTTTAGCCCAC 59.907 45.833 0.00 0.00 0.00 4.61
4783 5175 3.983344 CAGTTCAATTGCAAAGCAGGTAC 59.017 43.478 1.71 0.00 40.61 3.34
4829 5227 3.181463 GGCATATGCATCACAAAACCCAT 60.181 43.478 28.07 0.00 44.36 4.00
4972 5376 0.955428 TCGCATTGGCAACTGACCTC 60.955 55.000 0.00 0.00 41.24 3.85
4977 5381 2.256174 CAGAAATCGCATTGGCAACTG 58.744 47.619 0.00 3.67 41.24 3.16
5014 5418 3.571401 CAGTTTTCCCATCTCTGCAAACT 59.429 43.478 0.00 0.00 35.36 2.66
5026 5430 2.378208 TCCATCCACATCAGTTTTCCCA 59.622 45.455 0.00 0.00 0.00 4.37
5030 5434 3.331889 AGGTCTCCATCCACATCAGTTTT 59.668 43.478 0.00 0.00 0.00 2.43
5099 5509 3.988379 TGCTCCACAACAGTCAAATTC 57.012 42.857 0.00 0.00 0.00 2.17
5101 5512 2.559668 CCATGCTCCACAACAGTCAAAT 59.440 45.455 0.00 0.00 0.00 2.32
5160 5571 6.385649 TTCACGGGCCAATTTAATCTAATC 57.614 37.500 4.39 0.00 0.00 1.75
5161 5572 6.406512 GGTTTCACGGGCCAATTTAATCTAAT 60.407 38.462 4.39 0.00 0.00 1.73
5162 5573 5.105675 GGTTTCACGGGCCAATTTAATCTAA 60.106 40.000 4.39 0.00 0.00 2.10
5163 5574 4.399934 GGTTTCACGGGCCAATTTAATCTA 59.600 41.667 4.39 0.00 0.00 1.98
5164 5575 3.194755 GGTTTCACGGGCCAATTTAATCT 59.805 43.478 4.39 0.00 0.00 2.40
5241 5652 0.768622 ACCCCGTGGAAAATGAGACA 59.231 50.000 0.00 0.00 34.81 3.41
5273 5684 3.930336 CAGATCTACTGCCAGTGTCAAA 58.070 45.455 7.83 0.00 39.86 2.69
5323 5734 4.707030 TCATTCACTCATTCATGCCAAC 57.293 40.909 0.00 0.00 0.00 3.77
5447 5862 5.561919 CGATGACTAGCTAATCCACTCACTC 60.562 48.000 0.00 0.00 0.00 3.51
5530 5945 4.634004 TGGCGATCGATTAAGAAAACATGT 59.366 37.500 21.57 0.00 0.00 3.21
5581 5996 2.185350 CGGCTCCATTCTCTGCGT 59.815 61.111 0.00 0.00 0.00 5.24
5583 5998 1.817099 CACCGGCTCCATTCTCTGC 60.817 63.158 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.