Multiple sequence alignment - TraesCS6D01G145800

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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 TraesCS6D01G145800 chr6D 100.000 2616 0 0 1 2616 116346485 116343870 0.000000e+00 4831.0
1 TraesCS6D01G145800 chr6D 82.633 547 74 20 3 543 411541402 411541933 5.100000e-127 464.0
2 TraesCS6D01G145800 chr6A 89.528 1165 68 32 654 1775 144529295 144528142 0.000000e+00 1426.0
3 TraesCS6D01G145800 chr6A 89.610 693 44 16 1934 2616 144528055 144527381 0.000000e+00 856.0
4 TraesCS6D01G145800 chr6B 92.057 919 54 11 781 1682 206021353 206020437 0.000000e+00 1275.0
5 TraesCS6D01G145800 chr6B 86.555 357 35 12 1994 2342 427533855 427534206 5.280000e-102 381.0
6 TraesCS6D01G145800 chr6B 85.561 374 37 11 1997 2362 441122686 441122322 2.460000e-100 375.0
7 TraesCS6D01G145800 chr6B 76.129 465 65 33 143 590 676522861 676523296 4.410000e-48 202.0
8 TraesCS6D01G145800 chr6B 89.381 113 8 2 1833 1941 206019885 206019773 3.510000e-29 139.0
9 TraesCS6D01G145800 chrUn 91.107 596 46 6 1 591 24683354 24682761 0.000000e+00 800.0
10 TraesCS6D01G145800 chr7B 97.101 414 12 0 1081 1494 63934978 63935391 0.000000e+00 699.0
11 TraesCS6D01G145800 chr4A 96.867 415 13 0 1081 1495 48275451 48275865 0.000000e+00 695.0
12 TraesCS6D01G145800 chr4A 93.665 442 24 4 1062 1501 23611237 23610798 0.000000e+00 658.0
13 TraesCS6D01G145800 chr3B 96.394 416 15 0 1083 1498 479985968 479985553 0.000000e+00 686.0
14 TraesCS6D01G145800 chr3B 84.424 321 47 3 1 320 39568000 39568318 1.950000e-81 313.0
15 TraesCS6D01G145800 chr3D 96.154 416 16 0 1083 1498 368951439 368951024 0.000000e+00 680.0
16 TraesCS6D01G145800 chr3D 85.678 391 50 6 1 389 2178879 2179265 8.720000e-110 407.0
17 TraesCS6D01G145800 chr3D 88.210 229 19 7 224 450 495338997 495338775 1.540000e-67 267.0
18 TraesCS6D01G145800 chr4D 95.735 422 17 1 1077 1498 415583728 415583308 0.000000e+00 678.0
19 TraesCS6D01G145800 chr4D 91.860 86 4 3 508 591 461261289 461261373 1.640000e-22 117.0
20 TraesCS6D01G145800 chr1A 95.498 422 18 1 1081 1501 468599197 468598776 0.000000e+00 673.0
21 TraesCS6D01G145800 chr2A 87.167 600 56 16 1 589 725484262 725483673 0.000000e+00 662.0
22 TraesCS6D01G145800 chr4B 84.396 596 74 16 2 591 624609955 624609373 3.780000e-158 568.0
23 TraesCS6D01G145800 chr5A 84.642 586 69 19 1 581 540027687 540027118 4.890000e-157 564.0
24 TraesCS6D01G145800 chr3A 80.245 572 84 25 25 588 723171371 723170821 1.130000e-108 403.0
25 TraesCS6D01G145800 chr3A 79.826 575 89 23 22 589 723133231 723132677 6.790000e-106 394.0
26 TraesCS6D01G145800 chr2B 85.279 394 39 12 1994 2378 698341524 698341907 3.160000e-104 388.0
27 TraesCS6D01G145800 chr2B 86.636 217 28 1 2389 2605 698341971 698342186 3.360000e-59 239.0
28 TraesCS6D01G145800 chr1D 93.750 48 2 1 541 587 40007561 40007608 1.300000e-08 71.3


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 TraesCS6D01G145800 chr6D 116343870 116346485 2615 True 4831.0 4831 100.0000 1 2616 1 chr6D.!!$R1 2615
1 TraesCS6D01G145800 chr6D 411541402 411541933 531 False 464.0 464 82.6330 3 543 1 chr6D.!!$F1 540
2 TraesCS6D01G145800 chr6A 144527381 144529295 1914 True 1141.0 1426 89.5690 654 2616 2 chr6A.!!$R1 1962
3 TraesCS6D01G145800 chr6B 206019773 206021353 1580 True 707.0 1275 90.7190 781 1941 2 chr6B.!!$R2 1160
4 TraesCS6D01G145800 chrUn 24682761 24683354 593 True 800.0 800 91.1070 1 591 1 chrUn.!!$R1 590
5 TraesCS6D01G145800 chr2A 725483673 725484262 589 True 662.0 662 87.1670 1 589 1 chr2A.!!$R1 588
6 TraesCS6D01G145800 chr4B 624609373 624609955 582 True 568.0 568 84.3960 2 591 1 chr4B.!!$R1 589
7 TraesCS6D01G145800 chr5A 540027118 540027687 569 True 564.0 564 84.6420 1 581 1 chr5A.!!$R1 580
8 TraesCS6D01G145800 chr3A 723170821 723171371 550 True 403.0 403 80.2450 25 588 1 chr3A.!!$R2 563
9 TraesCS6D01G145800 chr3A 723132677 723133231 554 True 394.0 394 79.8260 22 589 1 chr3A.!!$R1 567
10 TraesCS6D01G145800 chr2B 698341524 698342186 662 False 313.5 388 85.9575 1994 2605 2 chr2B.!!$F1 611

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
713 736 0.251564 TGTTTCATGGGACGGCCATT 60.252 50.0 11.0 0.0 35.15 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 2338 0.250901 ACAGGCTCTGCGGTTGATTT 60.251 50.0 0.0 0.0 34.37 2.17 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
88 89 2.171003 GTGGGGAGTGCTGCTATTTTT 58.829 47.619 0.00 0.00 0.00 1.94
149 152 7.226128 TCAGATCGAGAAAAATTCATGATCCAG 59.774 37.037 15.16 11.14 40.49 3.86
170 173 7.166167 TCCAGTGATAATCATTCATCTGATGG 58.834 38.462 17.06 2.23 36.03 3.51
236 240 2.232452 GAGGAAAGACTACTGCAGCTGA 59.768 50.000 20.43 1.36 0.00 4.26
307 311 2.119611 TGGAGCTGGGGAGTTCGA 59.880 61.111 0.00 0.00 0.00 3.71
356 361 2.698274 TCAAAACCCAGGCTTCCTTTTC 59.302 45.455 0.00 0.00 0.00 2.29
357 362 2.700371 CAAAACCCAGGCTTCCTTTTCT 59.300 45.455 0.00 0.00 0.00 2.52
358 363 2.294449 AACCCAGGCTTCCTTTTCTC 57.706 50.000 0.00 0.00 0.00 2.87
372 385 4.033587 TCCTTTTCTCTGTTTGTTTCGTCG 59.966 41.667 0.00 0.00 0.00 5.12
410 425 7.340487 ACTTGTAGTAGTTAATAACTAGCCGGT 59.660 37.037 12.70 5.68 44.16 5.28
435 450 6.071952 TGTCTGATGTATGCGATGCTTATCTA 60.072 38.462 0.00 0.00 0.00 1.98
459 480 0.402504 TTGTAATCCCAGGTGCGGTT 59.597 50.000 0.00 0.00 0.00 4.44
640 663 8.877864 TGAATGTAAATCCTATGAAACAGGTT 57.122 30.769 0.00 0.00 34.56 3.50
641 664 9.967451 TGAATGTAAATCCTATGAAACAGGTTA 57.033 29.630 0.00 0.00 34.56 2.85
651 674 9.832445 TCCTATGAAACAGGTTATACTTTGATC 57.168 33.333 0.00 0.00 34.56 2.92
652 675 9.057089 CCTATGAAACAGGTTATACTTTGATCC 57.943 37.037 0.00 0.00 0.00 3.36
668 691 4.614555 TGATCCGGAATTCGTTTGAATG 57.385 40.909 9.01 0.00 44.02 2.67
670 693 4.881273 TGATCCGGAATTCGTTTGAATGAT 59.119 37.500 9.01 0.00 44.02 2.45
674 697 6.110033 TCCGGAATTCGTTTGAATGATAGAA 58.890 36.000 0.00 0.00 44.02 2.10
689 712 8.664798 TGAATGATAGAACCATGAAAAGTTACG 58.335 33.333 0.00 0.00 0.00 3.18
691 714 6.469410 TGATAGAACCATGAAAAGTTACGGT 58.531 36.000 0.00 0.00 0.00 4.83
692 715 6.370442 TGATAGAACCATGAAAAGTTACGGTG 59.630 38.462 0.00 0.00 0.00 4.94
697 720 4.825085 ACCATGAAAAGTTACGGTGATGTT 59.175 37.500 0.00 0.00 0.00 2.71
698 721 5.300792 ACCATGAAAAGTTACGGTGATGTTT 59.699 36.000 0.00 0.00 0.00 2.83
699 722 5.856455 CCATGAAAAGTTACGGTGATGTTTC 59.144 40.000 0.00 0.00 0.00 2.78
700 723 6.434596 CATGAAAAGTTACGGTGATGTTTCA 58.565 36.000 12.84 12.84 37.75 2.69
713 736 0.251564 TGTTTCATGGGACGGCCATT 60.252 50.000 11.00 0.00 35.15 3.16
714 737 0.455815 GTTTCATGGGACGGCCATTC 59.544 55.000 11.00 0.00 35.15 2.67
727 750 0.543749 GCCATTCCTGCTACAGTCCT 59.456 55.000 0.00 0.00 0.00 3.85
728 751 1.745141 GCCATTCCTGCTACAGTCCTG 60.745 57.143 0.00 0.00 0.00 3.86
744 767 5.552870 AGTCCTGTACTGTGATTGAGTTT 57.447 39.130 0.00 0.00 36.93 2.66
749 772 2.664402 ACTGTGATTGAGTTTGCCCT 57.336 45.000 0.00 0.00 0.00 5.19
758 781 2.818274 GTTTGCCCTCGTAGCCGG 60.818 66.667 0.00 0.00 33.95 6.13
774 807 3.399181 GGGTGGGCCATCGAGACA 61.399 66.667 10.70 0.00 36.17 3.41
777 810 2.182842 GTGGGCCATCGAGACATGC 61.183 63.158 10.70 0.00 0.00 4.06
819 852 1.003355 CCATTCGCCACCAGTCACT 60.003 57.895 0.00 0.00 0.00 3.41
874 907 1.002624 TCAATCGGCACCCTTCACC 60.003 57.895 0.00 0.00 0.00 4.02
876 909 4.778143 ATCGGCACCCTTCACCGC 62.778 66.667 0.00 0.00 46.49 5.68
880 913 2.663196 GCACCCTTCACCGCTACT 59.337 61.111 0.00 0.00 0.00 2.57
900 935 2.123251 ATCCGACGGCTCCCATCT 60.123 61.111 9.66 0.00 0.00 2.90
910 945 4.172232 TCCCATCTCCCTCCCCCG 62.172 72.222 0.00 0.00 0.00 5.73
1012 1048 0.314935 CCACACCGCAAAGCAATCTT 59.685 50.000 0.00 0.00 0.00 2.40
1014 1050 1.267806 CACACCGCAAAGCAATCTTCT 59.732 47.619 0.00 0.00 0.00 2.85
1016 1052 1.808945 CACCGCAAAGCAATCTTCTCT 59.191 47.619 0.00 0.00 0.00 3.10
1017 1053 2.227388 CACCGCAAAGCAATCTTCTCTT 59.773 45.455 0.00 0.00 0.00 2.85
1060 1099 1.228583 TCTCCGATCTCCCATCCCG 60.229 63.158 0.00 0.00 0.00 5.14
1462 1501 1.000396 GCCCAAGGACATCCAGCTT 60.000 57.895 0.00 0.00 38.89 3.74
1521 1562 2.491693 GCTTGCCATTGCTAGGTGTTTA 59.508 45.455 2.63 0.00 40.19 2.01
1522 1563 3.428045 GCTTGCCATTGCTAGGTGTTTAG 60.428 47.826 2.63 0.00 40.19 1.85
1546 1590 0.967662 TGTTCCCGTCGTGTTCCATA 59.032 50.000 0.00 0.00 0.00 2.74
1548 1592 2.199236 GTTCCCGTCGTGTTCCATATC 58.801 52.381 0.00 0.00 0.00 1.63
1561 1605 1.067060 TCCATATCTGCGTCGTTCCTG 59.933 52.381 0.00 0.00 0.00 3.86
1569 1613 1.608109 TGCGTCGTTCCTGTGTAACTA 59.392 47.619 0.00 0.00 38.04 2.24
1591 1635 0.040157 TTGTTGCTGTGCTTCGATGC 60.040 50.000 15.88 15.88 0.00 3.91
1592 1636 0.886043 TGTTGCTGTGCTTCGATGCT 60.886 50.000 22.11 0.00 0.00 3.79
1593 1637 0.239347 GTTGCTGTGCTTCGATGCTT 59.761 50.000 22.11 0.00 0.00 3.91
1608 1660 6.698008 TCGATGCTTTCAATGAAATATGGT 57.302 33.333 9.02 0.00 30.85 3.55
1615 1667 7.178274 TGCTTTCAATGAAATATGGTTACCAGT 59.822 33.333 10.74 0.00 31.72 4.00
1635 1688 6.846505 ACCAGTATGAGATAAATCCCTCTGAA 59.153 38.462 0.00 0.00 39.69 3.02
1636 1689 7.515514 ACCAGTATGAGATAAATCCCTCTGAAT 59.484 37.037 0.00 0.00 39.69 2.57
1637 1690 8.381636 CCAGTATGAGATAAATCCCTCTGAATT 58.618 37.037 0.00 0.00 39.69 2.17
1717 2221 3.616935 CAGGCGTTCTGAATGCATG 57.383 52.632 27.82 27.82 46.77 4.06
1721 2225 2.297033 AGGCGTTCTGAATGCATGTTTT 59.703 40.909 29.56 9.91 45.20 2.43
1732 2236 3.663995 TGCATGTTTTGAATGGACCTG 57.336 42.857 0.00 0.00 0.00 4.00
1751 2262 2.490115 CTGGTTAAAATTGCGGCTGGTA 59.510 45.455 0.00 0.00 0.00 3.25
1753 2264 3.511934 TGGTTAAAATTGCGGCTGGTATT 59.488 39.130 0.00 0.00 0.00 1.89
1766 2277 3.378427 GGCTGGTATTGGTGATTTCTGTC 59.622 47.826 0.00 0.00 0.00 3.51
1771 2282 5.221823 TGGTATTGGTGATTTCTGTCTGTGA 60.222 40.000 0.00 0.00 0.00 3.58
1775 2286 3.072915 TGGTGATTTCTGTCTGTGATGGT 59.927 43.478 0.00 0.00 0.00 3.55
1777 2288 4.631813 GGTGATTTCTGTCTGTGATGGTAC 59.368 45.833 0.00 0.00 0.00 3.34
1778 2289 4.631813 GTGATTTCTGTCTGTGATGGTACC 59.368 45.833 4.43 4.43 0.00 3.34
1779 2290 4.285775 TGATTTCTGTCTGTGATGGTACCA 59.714 41.667 18.99 18.99 0.00 3.25
1780 2291 4.908601 TTTCTGTCTGTGATGGTACCAT 57.091 40.909 27.70 27.70 39.69 3.55
1781 2292 4.908601 TTCTGTCTGTGATGGTACCATT 57.091 40.909 27.97 12.34 36.70 3.16
1782 2293 4.908601 TCTGTCTGTGATGGTACCATTT 57.091 40.909 27.97 8.46 36.70 2.32
1783 2294 5.241403 TCTGTCTGTGATGGTACCATTTT 57.759 39.130 27.97 7.62 36.70 1.82
1784 2295 5.630121 TCTGTCTGTGATGGTACCATTTTT 58.370 37.500 27.97 7.20 36.70 1.94
1785 2296 6.774673 TCTGTCTGTGATGGTACCATTTTTA 58.225 36.000 27.97 13.85 36.70 1.52
1786 2297 7.402054 TCTGTCTGTGATGGTACCATTTTTAT 58.598 34.615 27.97 5.93 36.70 1.40
1787 2298 7.888021 TCTGTCTGTGATGGTACCATTTTTATT 59.112 33.333 27.97 5.10 36.70 1.40
1788 2299 8.415950 TGTCTGTGATGGTACCATTTTTATTT 57.584 30.769 27.97 4.26 36.70 1.40
1789 2300 9.521841 TGTCTGTGATGGTACCATTTTTATTTA 57.478 29.630 27.97 9.48 36.70 1.40
1802 2313 8.875168 ACCATTTTTATTTAAGAATGTGGTGGA 58.125 29.630 10.77 0.00 36.56 4.02
1803 2314 9.889128 CCATTTTTATTTAAGAATGTGGTGGAT 57.111 29.630 10.77 0.00 36.56 3.41
1807 2318 8.770438 TTTATTTAAGAATGTGGTGGATTTGC 57.230 30.769 0.00 0.00 0.00 3.68
1808 2319 5.798125 TTTAAGAATGTGGTGGATTTGCA 57.202 34.783 0.00 0.00 0.00 4.08
1809 2320 5.999205 TTAAGAATGTGGTGGATTTGCAT 57.001 34.783 0.00 0.00 0.00 3.96
1810 2321 4.895668 AAGAATGTGGTGGATTTGCATT 57.104 36.364 0.00 0.00 33.14 3.56
1811 2322 5.999205 AAGAATGTGGTGGATTTGCATTA 57.001 34.783 0.00 0.00 30.96 1.90
1812 2323 5.999205 AGAATGTGGTGGATTTGCATTAA 57.001 34.783 0.00 0.00 30.96 1.40
1813 2324 6.357579 AGAATGTGGTGGATTTGCATTAAA 57.642 33.333 0.00 0.00 30.96 1.52
1814 2325 6.400568 AGAATGTGGTGGATTTGCATTAAAG 58.599 36.000 0.00 0.00 30.96 1.85
1815 2326 3.924144 TGTGGTGGATTTGCATTAAAGC 58.076 40.909 0.00 0.00 33.99 3.51
1816 2327 3.577848 TGTGGTGGATTTGCATTAAAGCT 59.422 39.130 4.10 0.00 35.10 3.74
1817 2328 4.040217 TGTGGTGGATTTGCATTAAAGCTT 59.960 37.500 4.10 0.00 35.10 3.74
1818 2329 4.389687 GTGGTGGATTTGCATTAAAGCTTG 59.610 41.667 0.00 0.00 35.10 4.01
1819 2330 4.040217 TGGTGGATTTGCATTAAAGCTTGT 59.960 37.500 0.00 0.00 35.10 3.16
1820 2331 4.389687 GGTGGATTTGCATTAAAGCTTGTG 59.610 41.667 0.00 0.70 35.10 3.33
1821 2332 5.229423 GTGGATTTGCATTAAAGCTTGTGA 58.771 37.500 0.00 0.00 35.10 3.58
1822 2333 5.119125 GTGGATTTGCATTAAAGCTTGTGAC 59.881 40.000 0.00 0.00 35.10 3.67
1827 2338 6.974932 TTGCATTAAAGCTTGTGACAAAAA 57.025 29.167 0.00 0.00 34.99 1.94
1850 2361 0.957395 CAACCGCAGAGCCTGTGAAT 60.957 55.000 14.87 3.12 43.78 2.57
1854 2365 1.703438 CGCAGAGCCTGTGAATGAGC 61.703 60.000 9.38 0.00 43.78 4.26
1879 2393 4.988708 AATTTATTTGCAGTTTGGCGTG 57.011 36.364 0.00 0.00 36.28 5.34
1880 2394 3.717400 TTTATTTGCAGTTTGGCGTGA 57.283 38.095 0.00 0.00 36.28 4.35
1884 2398 0.597118 TTGCAGTTTGGCGTGAATGC 60.597 50.000 0.00 0.99 36.28 3.56
1910 2425 4.391830 TGATTAAATCGTCTGACAACAGCC 59.608 41.667 8.73 0.00 43.17 4.85
1943 2458 9.860898 AAAATATTGTTAGCTTCAAACCTCATC 57.139 29.630 0.00 0.00 0.00 2.92
1958 2473 5.340891 ACCTCATCTCCTATAAGCCTACA 57.659 43.478 0.00 0.00 0.00 2.74
1979 2494 6.047511 ACAAAGAGAAGCATGATACTCACT 57.952 37.500 0.00 0.00 32.59 3.41
1987 2502 8.885494 AGAAGCATGATACTCACTATTCTTTC 57.115 34.615 0.00 0.00 0.00 2.62
1989 2504 5.694006 AGCATGATACTCACTATTCTTTCGC 59.306 40.000 0.00 0.00 0.00 4.70
1990 2505 5.463392 GCATGATACTCACTATTCTTTCGCA 59.537 40.000 0.00 0.00 0.00 5.10
1991 2506 6.346439 GCATGATACTCACTATTCTTTCGCAG 60.346 42.308 0.00 0.00 0.00 5.18
1992 2507 6.208988 TGATACTCACTATTCTTTCGCAGT 57.791 37.500 0.00 0.00 0.00 4.40
2049 2565 7.787725 AAGGGTAATTAGTTCTTAGATTGCG 57.212 36.000 0.00 0.00 0.00 4.85
2053 2569 6.018180 GGTAATTAGTTCTTAGATTGCGGTGG 60.018 42.308 0.00 0.00 0.00 4.61
2060 2580 2.851263 TAGATTGCGGTGGAAGTTGT 57.149 45.000 0.00 0.00 0.00 3.32
2099 2619 9.506018 TTCAGAATACATCTTCATCTTGTGAAA 57.494 29.630 0.00 0.00 45.74 2.69
2100 2620 9.506018 TCAGAATACATCTTCATCTTGTGAAAA 57.494 29.630 0.00 0.00 45.74 2.29
2151 2673 8.827832 TGAATCCAAGATTGAGGTTGAAATAT 57.172 30.769 0.00 0.00 0.00 1.28
2156 2678 6.183360 CCAAGATTGAGGTTGAAATATGGTCC 60.183 42.308 0.00 0.00 0.00 4.46
2161 2683 2.026262 AGGTTGAAATATGGTCCGCTGT 60.026 45.455 0.00 0.00 0.00 4.40
2163 2685 3.311596 GGTTGAAATATGGTCCGCTGTAC 59.688 47.826 0.00 0.00 0.00 2.90
2165 2687 5.353938 GTTGAAATATGGTCCGCTGTACTA 58.646 41.667 0.00 0.00 0.00 1.82
2186 2708 1.406539 CTTCTGGTTTGTGCTTGCTGT 59.593 47.619 0.00 0.00 0.00 4.40
2196 2718 3.481453 TGTGCTTGCTGTTTACCATGTA 58.519 40.909 0.00 0.00 0.00 2.29
2197 2719 3.885901 TGTGCTTGCTGTTTACCATGTAA 59.114 39.130 0.00 0.00 0.00 2.41
2198 2720 4.339530 TGTGCTTGCTGTTTACCATGTAAA 59.660 37.500 0.00 0.00 0.00 2.01
2201 2723 6.089417 GTGCTTGCTGTTTACCATGTAAATTC 59.911 38.462 3.05 0.00 0.00 2.17
2202 2724 6.155827 GCTTGCTGTTTACCATGTAAATTCA 58.844 36.000 3.05 0.00 0.00 2.57
2205 2727 8.531622 TTGCTGTTTACCATGTAAATTCATTG 57.468 30.769 3.05 0.00 0.00 2.82
2206 2728 7.890515 TGCTGTTTACCATGTAAATTCATTGA 58.109 30.769 3.05 0.00 0.00 2.57
2207 2729 8.530311 TGCTGTTTACCATGTAAATTCATTGAT 58.470 29.630 3.05 0.00 0.00 2.57
2208 2730 8.810427 GCTGTTTACCATGTAAATTCATTGATG 58.190 33.333 3.05 0.00 0.00 3.07
2212 2734 9.887629 TTTACCATGTAAATTCATTGATGCAAT 57.112 25.926 0.00 0.00 34.04 3.56
2274 2796 0.588252 CCAACTGCGGTTCTTGTGAG 59.412 55.000 8.28 0.00 32.73 3.51
2563 3150 4.202430 ACGAAAAGGACCCACTGATTACTT 60.202 41.667 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 2.257409 AATAGCAGCACTCCCCACCG 62.257 60.000 0.00 0.00 0.00 4.94
88 89 6.723298 TTTCTACATTTTCAAAGAGCCCAA 57.277 33.333 0.00 0.00 0.00 4.12
149 152 5.708697 TGCCCATCAGATGAATGATTATCAC 59.291 40.000 12.41 0.00 37.84 3.06
170 173 3.934579 GACCAATCAACAATCCATTTGCC 59.065 43.478 0.00 0.00 39.03 4.52
236 240 2.271800 CCGCTCGATTAGTTTTGCTCT 58.728 47.619 0.00 0.00 0.00 4.09
307 311 2.711542 CCAAATTAGCCTTCCAGTCGT 58.288 47.619 0.00 0.00 0.00 4.34
356 361 3.651562 AACACGACGAAACAAACAGAG 57.348 42.857 0.00 0.00 0.00 3.35
357 362 4.209703 GGATAACACGACGAAACAAACAGA 59.790 41.667 0.00 0.00 0.00 3.41
358 363 4.210537 AGGATAACACGACGAAACAAACAG 59.789 41.667 0.00 0.00 0.00 3.16
372 385 9.918630 TTAACTACTACAAGTTCAGGATAACAC 57.081 33.333 0.00 0.00 40.20 3.32
410 425 2.896745 AGCATCGCATACATCAGACA 57.103 45.000 0.00 0.00 0.00 3.41
435 450 2.171003 GCACCTGGGATTACAAAAGCT 58.829 47.619 0.00 0.00 0.00 3.74
459 480 5.204409 TCGAGCTAAAGGTTCAAACTACA 57.796 39.130 0.00 0.00 0.00 2.74
614 637 9.479549 AACCTGTTTCATAGGATTTACATTCAT 57.520 29.630 0.00 0.00 38.71 2.57
615 638 8.877864 AACCTGTTTCATAGGATTTACATTCA 57.122 30.769 0.00 0.00 38.71 2.57
625 648 9.832445 GATCAAAGTATAACCTGTTTCATAGGA 57.168 33.333 0.00 0.00 38.71 2.94
626 649 9.057089 GGATCAAAGTATAACCTGTTTCATAGG 57.943 37.037 0.00 0.00 41.22 2.57
627 650 8.765219 CGGATCAAAGTATAACCTGTTTCATAG 58.235 37.037 0.00 0.00 0.00 2.23
628 651 7.713507 CCGGATCAAAGTATAACCTGTTTCATA 59.286 37.037 0.00 0.00 0.00 2.15
629 652 6.542370 CCGGATCAAAGTATAACCTGTTTCAT 59.458 38.462 0.00 0.00 0.00 2.57
630 653 5.878116 CCGGATCAAAGTATAACCTGTTTCA 59.122 40.000 0.00 0.00 0.00 2.69
631 654 6.110707 TCCGGATCAAAGTATAACCTGTTTC 58.889 40.000 0.00 0.00 0.00 2.78
632 655 6.057321 TCCGGATCAAAGTATAACCTGTTT 57.943 37.500 0.00 0.00 0.00 2.83
633 656 5.687166 TCCGGATCAAAGTATAACCTGTT 57.313 39.130 0.00 0.00 0.00 3.16
634 657 5.687166 TTCCGGATCAAAGTATAACCTGT 57.313 39.130 4.15 0.00 0.00 4.00
635 658 6.073765 CGAATTCCGGATCAAAGTATAACCTG 60.074 42.308 4.15 0.00 33.91 4.00
636 659 5.989777 CGAATTCCGGATCAAAGTATAACCT 59.010 40.000 4.15 0.00 33.91 3.50
637 660 5.756833 ACGAATTCCGGATCAAAGTATAACC 59.243 40.000 4.15 0.00 43.93 2.85
638 661 6.839820 ACGAATTCCGGATCAAAGTATAAC 57.160 37.500 4.15 0.00 43.93 1.89
639 662 7.549842 TCAAACGAATTCCGGATCAAAGTATAA 59.450 33.333 4.15 0.00 43.93 0.98
640 663 7.042950 TCAAACGAATTCCGGATCAAAGTATA 58.957 34.615 4.15 0.00 43.93 1.47
641 664 5.878116 TCAAACGAATTCCGGATCAAAGTAT 59.122 36.000 4.15 0.00 43.93 2.12
642 665 5.239351 TCAAACGAATTCCGGATCAAAGTA 58.761 37.500 4.15 0.00 43.93 2.24
643 666 4.069304 TCAAACGAATTCCGGATCAAAGT 58.931 39.130 4.15 0.00 43.93 2.66
644 667 4.678509 TCAAACGAATTCCGGATCAAAG 57.321 40.909 4.15 0.00 43.93 2.77
645 668 5.182190 TCATTCAAACGAATTCCGGATCAAA 59.818 36.000 4.15 0.00 43.93 2.69
646 669 4.697828 TCATTCAAACGAATTCCGGATCAA 59.302 37.500 4.15 0.00 43.93 2.57
647 670 4.257731 TCATTCAAACGAATTCCGGATCA 58.742 39.130 4.15 0.00 43.93 2.92
648 671 4.875544 TCATTCAAACGAATTCCGGATC 57.124 40.909 4.15 0.00 43.93 3.36
649 672 6.288294 TCTATCATTCAAACGAATTCCGGAT 58.712 36.000 4.15 0.00 43.93 4.18
650 673 5.666462 TCTATCATTCAAACGAATTCCGGA 58.334 37.500 0.00 0.00 43.93 5.14
651 674 5.984233 TCTATCATTCAAACGAATTCCGG 57.016 39.130 0.00 0.00 43.93 5.14
652 675 6.183360 TGGTTCTATCATTCAAACGAATTCCG 60.183 38.462 0.00 0.00 45.44 4.30
668 691 6.592607 TCACCGTAACTTTTCATGGTTCTATC 59.407 38.462 0.00 0.00 31.49 2.08
670 693 5.856156 TCACCGTAACTTTTCATGGTTCTA 58.144 37.500 0.00 0.00 31.49 2.10
674 697 4.394729 ACATCACCGTAACTTTTCATGGT 58.605 39.130 0.00 0.00 34.26 3.55
688 711 0.726827 CGTCCCATGAAACATCACCG 59.273 55.000 0.00 0.00 0.00 4.94
689 712 1.094785 CCGTCCCATGAAACATCACC 58.905 55.000 0.00 0.00 0.00 4.02
691 714 0.679640 GGCCGTCCCATGAAACATCA 60.680 55.000 0.00 0.00 0.00 3.07
692 715 0.679640 TGGCCGTCCCATGAAACATC 60.680 55.000 0.00 0.00 39.18 3.06
713 736 2.901338 AGTACAGGACTGTAGCAGGA 57.099 50.000 12.16 0.00 45.61 3.86
727 750 3.146066 GGGCAAACTCAATCACAGTACA 58.854 45.455 0.00 0.00 0.00 2.90
728 751 3.412386 AGGGCAAACTCAATCACAGTAC 58.588 45.455 0.00 0.00 0.00 2.73
758 781 1.524621 CATGTCTCGATGGCCCACC 60.525 63.158 0.00 0.00 0.00 4.61
762 785 1.890979 CCTGCATGTCTCGATGGCC 60.891 63.158 0.00 0.00 0.00 5.36
765 788 0.104487 AGCTCCTGCATGTCTCGATG 59.896 55.000 0.00 0.00 42.74 3.84
766 789 0.104487 CAGCTCCTGCATGTCTCGAT 59.896 55.000 0.00 0.00 42.74 3.59
790 823 0.960364 GGCGAATGGAAGACTGCCAA 60.960 55.000 6.17 0.00 42.03 4.52
819 852 4.585526 GATCGCGATCCGTGGGCA 62.586 66.667 33.80 0.00 37.97 5.36
840 873 3.428452 CGATTGAGTTTTGCATGCCTCAT 60.428 43.478 20.47 12.86 34.19 2.90
844 877 1.632422 CCGATTGAGTTTTGCATGCC 58.368 50.000 16.68 0.00 0.00 4.40
847 880 1.067635 GGTGCCGATTGAGTTTTGCAT 60.068 47.619 0.00 0.00 0.00 3.96
855 888 1.026718 GGTGAAGGGTGCCGATTGAG 61.027 60.000 0.00 0.00 0.00 3.02
874 907 2.331805 CCGTCGGATGGAGTAGCG 59.668 66.667 10.90 0.00 0.00 4.26
875 908 2.027751 GCCGTCGGATGGAGTAGC 59.972 66.667 20.37 0.01 0.00 3.58
876 909 1.655329 GAGCCGTCGGATGGAGTAG 59.345 63.158 20.37 0.00 0.00 2.57
880 913 4.770362 TGGGAGCCGTCGGATGGA 62.770 66.667 20.37 0.00 0.00 3.41
1012 1048 3.118555 TCGGGTGTTTTGAAGTGAAGAGA 60.119 43.478 0.00 0.00 0.00 3.10
1014 1050 3.202906 CTCGGGTGTTTTGAAGTGAAGA 58.797 45.455 0.00 0.00 0.00 2.87
1016 1052 1.673920 GCTCGGGTGTTTTGAAGTGAA 59.326 47.619 0.00 0.00 0.00 3.18
1017 1053 1.305201 GCTCGGGTGTTTTGAAGTGA 58.695 50.000 0.00 0.00 0.00 3.41
1300 1339 1.590259 GAAGTCCTGCGCGATCTCC 60.590 63.158 12.10 0.00 0.00 3.71
1546 1590 0.885879 TACACAGGAACGACGCAGAT 59.114 50.000 0.00 0.00 0.00 2.90
1548 1592 0.782384 GTTACACAGGAACGACGCAG 59.218 55.000 0.00 0.00 0.00 5.18
1593 1637 9.913310 TCATACTGGTAACCATATTTCATTGAA 57.087 29.630 0.00 0.00 30.82 2.69
1608 1660 8.010697 TCAGAGGGATTTATCTCATACTGGTAA 58.989 37.037 0.00 0.00 31.37 2.85
1665 1721 2.551270 AGCCAGTAATTCAGAGGGTGA 58.449 47.619 0.00 0.00 0.00 4.02
1717 2221 7.519809 GCAATTTTAACCAGGTCCATTCAAAAC 60.520 37.037 0.00 0.00 0.00 2.43
1721 2225 4.321601 CGCAATTTTAACCAGGTCCATTCA 60.322 41.667 0.00 0.00 0.00 2.57
1732 2236 3.793797 ATACCAGCCGCAATTTTAACC 57.206 42.857 0.00 0.00 0.00 2.85
1751 2262 4.703575 CCATCACAGACAGAAATCACCAAT 59.296 41.667 0.00 0.00 0.00 3.16
1753 2264 3.072915 ACCATCACAGACAGAAATCACCA 59.927 43.478 0.00 0.00 0.00 4.17
1777 2288 9.889128 ATCCACCACATTCTTAAATAAAAATGG 57.111 29.630 4.71 0.00 34.23 3.16
1781 2292 9.213799 GCAAATCCACCACATTCTTAAATAAAA 57.786 29.630 0.00 0.00 0.00 1.52
1782 2293 8.370940 TGCAAATCCACCACATTCTTAAATAAA 58.629 29.630 0.00 0.00 0.00 1.40
1783 2294 7.901029 TGCAAATCCACCACATTCTTAAATAA 58.099 30.769 0.00 0.00 0.00 1.40
1784 2295 7.473735 TGCAAATCCACCACATTCTTAAATA 57.526 32.000 0.00 0.00 0.00 1.40
1785 2296 6.357579 TGCAAATCCACCACATTCTTAAAT 57.642 33.333 0.00 0.00 0.00 1.40
1786 2297 5.798125 TGCAAATCCACCACATTCTTAAA 57.202 34.783 0.00 0.00 0.00 1.52
1787 2298 5.999205 ATGCAAATCCACCACATTCTTAA 57.001 34.783 0.00 0.00 0.00 1.85
1788 2299 5.999205 AATGCAAATCCACCACATTCTTA 57.001 34.783 0.00 0.00 0.00 2.10
1789 2300 4.895668 AATGCAAATCCACCACATTCTT 57.104 36.364 0.00 0.00 0.00 2.52
1790 2301 5.999205 TTAATGCAAATCCACCACATTCT 57.001 34.783 0.00 0.00 33.31 2.40
1791 2302 5.063817 GCTTTAATGCAAATCCACCACATTC 59.936 40.000 8.38 0.00 33.31 2.67
1792 2303 4.937015 GCTTTAATGCAAATCCACCACATT 59.063 37.500 8.38 0.00 35.31 2.71
1793 2304 4.223477 AGCTTTAATGCAAATCCACCACAT 59.777 37.500 15.00 0.00 34.99 3.21
1794 2305 3.577848 AGCTTTAATGCAAATCCACCACA 59.422 39.130 15.00 0.00 34.99 4.17
1795 2306 4.192429 AGCTTTAATGCAAATCCACCAC 57.808 40.909 15.00 0.00 34.99 4.16
1796 2307 4.040217 ACAAGCTTTAATGCAAATCCACCA 59.960 37.500 15.00 0.00 34.99 4.17
1797 2308 4.389687 CACAAGCTTTAATGCAAATCCACC 59.610 41.667 15.00 0.00 34.99 4.61
1798 2309 5.119125 GTCACAAGCTTTAATGCAAATCCAC 59.881 40.000 15.00 1.98 34.99 4.02
1799 2310 5.221402 TGTCACAAGCTTTAATGCAAATCCA 60.221 36.000 15.00 2.75 34.99 3.41
1800 2311 5.229423 TGTCACAAGCTTTAATGCAAATCC 58.771 37.500 15.00 0.47 34.99 3.01
1801 2312 6.768029 TTGTCACAAGCTTTAATGCAAATC 57.232 33.333 15.00 2.43 34.99 2.17
1802 2313 7.551035 TTTTGTCACAAGCTTTAATGCAAAT 57.449 28.000 15.00 0.00 34.99 2.32
1803 2314 6.974932 TTTTGTCACAAGCTTTAATGCAAA 57.025 29.167 15.00 8.07 34.99 3.68
1804 2315 6.974932 TTTTTGTCACAAGCTTTAATGCAA 57.025 29.167 15.00 2.63 34.99 4.08
1827 2338 0.250901 ACAGGCTCTGCGGTTGATTT 60.251 50.000 0.00 0.00 34.37 2.17
1829 2340 1.376424 CACAGGCTCTGCGGTTGAT 60.376 57.895 0.00 0.00 34.37 2.57
1831 2342 0.957395 ATTCACAGGCTCTGCGGTTG 60.957 55.000 0.00 0.00 34.37 3.77
1836 2347 0.675837 TGCTCATTCACAGGCTCTGC 60.676 55.000 2.50 0.00 34.37 4.26
1850 2361 6.867816 CCAAACTGCAAATAAATTACTGCTCA 59.132 34.615 9.43 0.00 35.78 4.26
1854 2365 5.633182 ACGCCAAACTGCAAATAAATTACTG 59.367 36.000 0.00 0.00 0.00 2.74
1879 2393 6.183360 TGTCAGACGATTTAATCACAGCATTC 60.183 38.462 5.76 0.00 0.00 2.67
1880 2394 5.643348 TGTCAGACGATTTAATCACAGCATT 59.357 36.000 5.76 0.00 0.00 3.56
1884 2398 6.466308 TGTTGTCAGACGATTTAATCACAG 57.534 37.500 5.76 0.00 0.00 3.66
1910 2425 8.500837 TTGAAGCTAACAATATTTTTGTCACG 57.499 30.769 0.00 0.00 0.00 4.35
1942 2457 6.041069 GCTTCTCTTTGTAGGCTTATAGGAGA 59.959 42.308 0.00 0.00 0.00 3.71
1943 2458 6.183360 TGCTTCTCTTTGTAGGCTTATAGGAG 60.183 42.308 0.00 0.00 0.00 3.69
1979 2494 5.933187 TGTAGCAAAACTGCGAAAGAATA 57.067 34.783 0.00 0.00 40.27 1.75
1987 2502 6.689178 AAATACAATTGTAGCAAAACTGCG 57.311 33.333 22.03 0.00 40.27 5.18
1989 2504 9.248291 AGACAAAATACAATTGTAGCAAAACTG 57.752 29.630 22.03 13.87 40.90 3.16
1990 2505 9.816354 AAGACAAAATACAATTGTAGCAAAACT 57.184 25.926 22.03 14.18 40.90 2.66
2024 2540 7.282450 CCGCAATCTAAGAACTAATTACCCTTT 59.718 37.037 0.00 0.00 0.00 3.11
2033 2549 4.811969 TCCACCGCAATCTAAGAACTAA 57.188 40.909 0.00 0.00 0.00 2.24
2110 2630 8.324306 TCTTGGATTCATAGCCTAATATTCAGG 58.676 37.037 0.00 0.00 36.16 3.86
2125 2645 7.729124 ATTTCAACCTCAATCTTGGATTCAT 57.271 32.000 0.00 0.00 0.00 2.57
2151 2673 1.816835 CAGAAGTAGTACAGCGGACCA 59.183 52.381 2.52 0.00 0.00 4.02
2156 2678 3.428870 CACAAACCAGAAGTAGTACAGCG 59.571 47.826 2.52 0.00 0.00 5.18
2161 2683 3.813166 GCAAGCACAAACCAGAAGTAGTA 59.187 43.478 0.00 0.00 0.00 1.82
2163 2685 2.880890 AGCAAGCACAAACCAGAAGTAG 59.119 45.455 0.00 0.00 0.00 2.57
2165 2687 1.406539 CAGCAAGCACAAACCAGAAGT 59.593 47.619 0.00 0.00 0.00 3.01
2186 2708 9.887629 ATTGCATCAATGAATTTACATGGTAAA 57.112 25.926 0.00 4.25 32.39 2.01
2205 2727 9.917129 TGTTGATCCATATTCATAAATTGCATC 57.083 29.630 0.00 0.00 0.00 3.91
2207 2729 9.917129 GATGTTGATCCATATTCATAAATTGCA 57.083 29.630 0.00 0.00 0.00 4.08
2208 2730 9.917129 TGATGTTGATCCATATTCATAAATTGC 57.083 29.630 0.00 0.00 0.00 3.56
2212 2734 8.579006 GCCTTGATGTTGATCCATATTCATAAA 58.421 33.333 0.00 0.00 0.00 1.40
2227 2749 4.575645 ACAATTTTTGTGGCCTTGATGTTG 59.424 37.500 3.32 4.09 43.48 3.33
2274 2796 4.036262 TGCAAACACATTCCAACTACTCAC 59.964 41.667 0.00 0.00 0.00 3.51
2365 2952 9.859427 GTTTGATTGATCAGGTTTGATTGAATA 57.141 29.630 0.00 0.00 44.01 1.75
2366 2953 7.820872 GGTTTGATTGATCAGGTTTGATTGAAT 59.179 33.333 0.00 0.00 44.01 2.57
2369 2956 6.588756 CAGGTTTGATTGATCAGGTTTGATTG 59.411 38.462 0.00 0.00 44.01 2.67
2372 2959 5.384336 TCAGGTTTGATTGATCAGGTTTGA 58.616 37.500 0.00 0.00 38.19 2.69
2373 2960 5.710513 TCAGGTTTGATTGATCAGGTTTG 57.289 39.130 0.00 0.00 38.19 2.93
2374 2961 6.521151 GATCAGGTTTGATTGATCAGGTTT 57.479 37.500 9.03 0.00 45.68 3.27
2380 2967 6.097270 TGGGAAATGATCAGGTTTGATTGATC 59.903 38.462 0.09 7.36 44.01 2.92
2381 2968 5.959594 TGGGAAATGATCAGGTTTGATTGAT 59.040 36.000 0.09 0.00 44.01 2.57
2382 2969 5.331906 TGGGAAATGATCAGGTTTGATTGA 58.668 37.500 0.09 0.00 44.01 2.57
2383 2970 5.657474 CTGGGAAATGATCAGGTTTGATTG 58.343 41.667 0.09 0.00 44.01 2.67
2384 2971 4.161001 GCTGGGAAATGATCAGGTTTGATT 59.839 41.667 0.09 0.00 44.01 2.57
2385 2972 3.703052 GCTGGGAAATGATCAGGTTTGAT 59.297 43.478 0.09 0.00 46.61 2.57
2563 3150 6.286758 CAGCAAAGAAGATGATAGCCTCTAA 58.713 40.000 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.